key: cord- -iuo ukaz authors: engström, gustav; gars, johan; jaakkola, niko; lindahl, therese; spiro, daniel; van benthem, arthur a. title: what policies address both the coronavirus crisis and the climate crisis? date: - - journal: environ resour econ (dordr) doi: . /s - - -y sha: doc_id: cord_uid: iuo ukaz the coronavirus pandemic has led many countries to initiate unprecedented economic recovery packages. policymakers tackling the coronavirus crisis have also been encouraged to prioritize policies which help mitigate a second, looming crisis: climate change. we identify and analyze policies that combat both the coronavirus crisis and the climate crisis. we analyze both the long-run climate impacts from coronavirus-related economic recovery policies, and the impacts of long-run climate policies on economic recovery and public health post-recession. we base our analysis on data on emissions, employment and corona-related layoffs across sectors, and on previous research. we show that, among climate policies, labor-intensive green infrastructure projects, planting trees, and in particular pricing carbon coupled with reduced labor taxation boost economic recovery. among coronavirus policies, aiding services sectors (leisure services such as restaurants and culture, or professional services such as technology), education and the healthcare sector appear most promising, being labor intensive yet low-emission—if such sectoral aid is conditioned on being directed towards employment and on low-carbon supply chains. large-scale green infrastructure projects and green r&d investment, while good for the climate, are unlikely to generate enough employment to effectively alleviate the coronavirus crisis. electronic supplementary material: the online version of this article ( . /s - - -y) contains supplementary material, which is available to authorized users. as decision makers around the world scramble to respond to the coronavirus crisis and the deep and possibly prolonged recession that follows it, commentators have called for them to use the opportunity to also further our progress in mitigating climate change, which a majority of people believe to be as serious a crisis as the coronavirus (ipsos ) . by pursuing policies that can both alleviate the economic recession caused by the coronavirus and help reduce greenhouse gas emissions, the current crisis presents an opportunity to put the world on a new trajectory with a lower risk of future climate calamities. crisis management often requires exceptional policies, and may temporarily alter constraints on decision making. strategic vision at such a time can help decision makers take into account longer-term objectives, which might be difficult to meet under normal circumstances. as rahm emanuel famously said, "you never want a serious crisis to go to waste". yet, for climate policies to have a chance of implementation at this moment, they cannot be at odds with addressing the current crisis. in this paper, we seek to systematically identify where the intersection between 'coronavirus policies' and 'climate policies' lies. we are interested in which types of policies can help mitigate the impacts of the coronavirus crisis, and also make headway in setting societies on low-carbon pathways. we intentionally focus on long-term climate impacts. many coronavirus policies have temporary effects on carbon emissions (e.g., reduced traffic due to a lockdown), but we see such temporary effects as unimportant, given the long timescales involved in anthropogenic climate change (le quéré et al. ) . specifically, our contribution is the following. we first identify policies which alleviate the coronavirus crisis, as well as a set of channels through which relatively short-term policies can have impacts on climate change in the longer run. second, we present data on sector-specific economic activity and emissions. we then use these tools, together with previous research, to evaluate and score policies in terms of their usefulness in tackling the climate and coronavirus crises. policies ranked as 'good for climate' should be expected to yield substantial long-run emission reductions. policies ranked as 'good for coronavirus recession' should help alleviate the job losses due to the current recession and (in some cases) have public health benefits regarding current or future pandemics. we present a set of policies that can help reduce the economic fallout of the coronavirus crisis, and simultaneously aid societies in meeting climate change mitigation targets in the longer run. we hope this exercise can help policymakers think through their policy options if they want to chart a 'green recovery' while dealing with the coronavirus crisis. 'green stimulus' is of course not a new term. in the wake of the financial crisis of - , strand and toman ( ) evaluated potential stimulus policies in terms of their potential to improve long-term environmental outcomes. some of their recommendations are still valid. however, for the current crisis one has to evaluate policies that are specific to it, i.e., that are adapted to the health aspects of the coronavirus, and the unprecedented economic shock of a simultaneous sharp fall in both demand and supply. hence, our set of policies differ from strand and toman ( ) . we also consider some channels for long-run impacts that they did not touch upon. other, more recent, analyses (e.g., cat ) outline the climate effects of various policies, but ignore whether any of the policies (such as green r&d) are actually good at alleviating the coronavirus crisis. the paper by hepburn et al. ( ) has a similar objective to ours, but their analysis starts from previously used stimulus policies (since the financial crisis of [ ] [ ] and is based on surveys of expert opinions. we start from policies that seem especially appropriate in the current crisis, and evaluate them based on an analysis of the individual policies, combined with basic empirical observations about the carbon, labor and layoff intensity of different sectors and jobs. finally, helm ( ) discusses the broad effects macroeconomic policies intended to tackle the coronavirus may have on carbon emissions. we take a complementary perspective, looking at a large set of individual policies in more detail. we want to defuse two potential criticisms against the notion that crisis policies should be evaluated based also on their effect on environmental outcomes. the first relates to the tinbergen rule: that, to obtain an efficient outcome, one needs as many instruments as there are externalities. in particular, policymakers should use one set of instruments to deal with the health crisis, another to achieve macroeconomic stabilization, and a third to achieve long-term environmental objectives. in a first-best world this would of course be true. in practice there are constraintspractical and political-that make perfect fine-tuning difficult. given such constraints, we have to ensure that measures to address one goal do not undermine another. we illustrate with two examples from our analysis. first, implementing a carbon tax would, if done in isolation, likely worsen the current recession. but if the proceeds were used to lower labor taxes, the policy could instead alleviate the coronavirus crisis. second, economic stabilization will involve government investment, or subsidies to private investment, into capital assets. the question is then: which types of capital assets? the answer necessarily has to account for the effect the assets will have on the climate. the second criticism is that beneficial long-term effects on climate are unlikely to be achieved in the absence of long-term policies to price externalities (strand and toman ) . without pricing the externality directly, rebound effects can undo the beneficial effects of e.g. green stimulus policies. further, the general equilibrium effects of stimulus policies on emissions may be hard to assess. sectoral policies should consider the complementarity of targeted sectors with emissions-intensive sectors. a prominent example relates to sectors linked to air travel: e.g., hotels and restaurants have limited direct emissions, but high indirect emissions through tourism and business travel. stimulus payments aimed at such carbon-complementary sectors may backfire unless also accompanied by other measures, such as carbon pricing (dwyer et al. ) . uniform carbon pricing on all fuels would eliminate such concerns. our immediate answer is that we agree that long-term externality pricing is critical, and we include tax and subsidy reforms such as revenue-neutral carbon pricing in our set of policies. a further riposte, indeed to both of the above criticisms, is that long-term pricing policies are endogenous: policies today affect what is politically feasible tomorrow (acemoglu and robinson ). subsidies are not a substitute for carbon pricing (helm ) but may help pave the political route to their implementation. our goal is to evaluate policies in terms of their potential to mitigate the economic fallout of the coronavirus pandemic, and their long-term effect on climate change. to this end, we start by discussing what types of policies can help deal with the consequences of the pandemic. we then present channels via which relatively short-term policy interventions can have longer-run impacts on climate change and climate policy. these two classification exercises allow us to identify policies that have effects on both crises. we then present some data that will be useful in evaluating policies. when people are forced to stay at home they do not go to work and they consume less. the inability to work is a supply shock, while the reduction in consumption is a demand shock. the combination of the two implies bankruptcies and layoffs, aggravating income losses and lowering demand even further. the supply shock will disappear as an improving understanding of the coronavirus allows for more targeted public health measures, and eventual control of the pandemic. however, the economic effects on aggregate demand are likely to persist, so that the demand shock will outlive the supply shock. we mainly focus on policies implemented in the medium term, and thus centered around the economic recovery, rather than around pandemic control per se. economic stimulus policies-in particular, ensuring high demand by supporting incomes and employment-will be central for mitigating the economic fallout. it is well established empirically that wealthy capital owners tend to save a larger share of their income than people who are poorer and who rely on labor income (see e.g. bernheim and scholtz ; beverly ; browning and lusardi ; dynan et al. ; diamond and hausman ; gentry and hubbard ; quadrini ; alan et al. ; dupas and robinson ; gandelmann ) . hence to assess the potential of a policy to restart the economy, we will evaluate policies based on their potential to secure employment (which also benefits mental health) and labor income. some of the firms that now go bankrupt may not be able to quickly resume their old activities once the health crisis is over. it may take time for firms and labor to match, for investors and firms to match, and so on. helping businesses survive will reduce such frictions. for this reason, policies that reduce bankruptcies can also help the recovery. unfortunately, data on bankruptcies are not yet readily available. we conjecture (based, e.g., on andersen et al. , carvalho et al. , and our own analysis using preliminary data, see appendix a. ) that bankruptcies are highly correlated with layoffs. policies may have long-run implications on climate change through a variety of channels. we have identified four channels we see as particularly relevant for our purpose. . investment -direct effect of long-lived investments. to mitigate the unprecedented economic crisis, governments are planning to stimulate economies through massive investment programs, either implemented directly by governments, or by subsidizing private-sector investments. such investments have direct long-run impacts once sunk: some will be long-lived, and either substitute or complement fossil fuels (e.g., power generation or transportation infrastructure). once made, they will be used, and thus have long-run impacts on baseline emission pathways and on the cost of implementing future climate policies (shalizi and lecocq ; seto et al. ). . political -dynamic political economy effects. policy can be persistent: economic decisions taken by firms, in response to policies intended to be temporary, can affect political incentives, preventing a future reversal of a policy (coate and morris ) . this can happen as an indirect effect of sunk investments which changes the structure of vested interests (with respect to climate policies): a devaluation of fossil-related assets, or the introduction of new assets complementary to climate policies, will affect the power and incentives of interest groups to influence future policies (acemoglu and robinson ) . similar effects could result from the destruction of interest groups, e.g. due to bankruptcies in a sector that receives little stimulus money. the formation of special interest groups may also prove to be a self-fulfilling prophecy (grey ) , and short-term disruptions to interest group formation can have long-run effects. . technological -path dependence due to technological development. a further indirect effect may arise through changes in the direction of r&d (e.g. low carbon versus carbon intensive). when technological change is directional, temporary policies may determine in which direction an economy develops. such differences can persist: tem-porary growth in one type of technology may sustain itself, due to innovation incentives being geared towards a dominant technology, and due to complementarities in r&d (acemoglu et al. ; hart ; van der meijden and smulders ). . learning -forced experimentation and learning effects. consumers and producers may not perfectly optimize their choices, e.g. due to costs of finding out about the characteristics of various options, because of biases in decision making, institutional constraints, or because of habit formation favoring status quo behavior. temporary disruptions to choice sets may force them to look for new options, which may be preferred after the disruption has ended (seto et al. ; larcom et al. ; helm ) . policies that promote or subsidize experimentation can help a wider set of agents explore novel options, and thus promote permanent changes in behavior. we focus on two metrics for alleviating the coronavirus crisis: the number of layoffs in an industry and the labor intensity of the industry, expressed in employees per unit of value added. for judging the climate effects, we focus on the emissions intensity of an industry: climate goals suggest the long-run prospects of relatively clean industries should be prioritized. we use two empirical metrics: emissions per unit of value added, and per employee. we collect data on emissions, number of employees and value added by sector from eurostat. layoffs data are from national sources: swedish public employment service for sweden; the helsinki gse situation room for finland. we show results for labor and emissions intensity for the european union, germany, france, the united kingdom, sweden and finland. our results for layoffs are limited to the countries for which we could find reliable data on recent layoffs during the coronavirus recessions (sweden and finland). these roughly correlate with productivity and demand declines (see appendix figure a ). figure plots both layoffs and layoffs per thousand employees against co emissions per employee (note the logarithmic scale on the horizontal axis) for the sectors given in table . the most affected sectors in sweden, in terms of total layoffs, are i (hotels and restaurants), g (wholesale and retail trade), h (transport and storage), n (rental and real estate), and r (culture). some of these show large layoffs simply because of their size. when layoffs are normalized per , employees, the same sectors stand out except that sector e (water and sanitation) is badly affected while sector g (wholesale and retail trade) appears less affected. the picture for finland is broadly similar, except that there are more layoffs in sector c (manufacturing). we emphasize that this is a high-level categorization which masks detail-yet it serves as a useful benchmark for stimulus and other policy decisions. we specifically highlight three caveats. first, co intensity is measured in a narrow sense: direct emissions from the sector under consideration. since sectors are connected, a subsidy to one sector will affect other sectors as well, e.g. indirectly subsidizing sectors that produce complementary outputs. the full effect of a sector-specific subsidy should include any indirect emissions coming from the effects of the subsidy on related sectors, i.e., the total general-equilibrium effect. second, layoffs are a recent snapshot and may be temporary. figure is likely to change over the course of the coronavirus recession, and in the absence of uniform carbon pricing across all sectors, accounting for indirect emissions may be important. for example, hotels have a low emissions intensity as the emissions from associated travel are allocated to the transport sector, but clearly hotels facilitate (carbon-intensive) travel via tourism and business trips (dwyer et al. ) . greenhouse gas emissions from tourism are substantial, with estimates suggesting the sector accounts for more than % of global greenhouse gas emissions (lenzen et al. ; see appendix a. for a further discussion of this). a second example relates to the relationship between the emissions-intensive transport sector, and the seemingly low-emissions services sectors. an important fraction of transport demand results from activity in services sectors (alcántara and padilla ). in the construction sector, also, indirect emissions can make up a large share of total emissions (acquaye and duffy ). the indirect effects of policies on emissions, output and employment may be important to consider and could be tackled using input-output analysis (mäenpää and siikavirta ; markaki et al. ). this is a promising avenue for further research, both academically and for applied policymaking, but beyond the scope of the present paper. to overcome some of these concerns, fig. plots a measure of labor intensity (employees per million euros of value added) against a measure of emissions intensity (co emissions per million units of value added) for each of the sectors in the european union, germany, france, the united kingdom, sweden and finland. per amount of stimulus spent, industries with high labor intensity may also be relevant to target from a recession perspective, since each unit of spending can be expected to have a larger employment effect in those sectors. from the climate perspective, one would like to focus on sectors with low emission intensities. the results vary somewhat across countries, but paint a remarkably consistent picture. first, there is a slight negative relationship between labor intensity and emissions intensity, perhaps reflecting that sectors with low labor shares rely on more energy-intensive capital. industries that stand out as potential targets that score well on the coronavirus-climate interface are not necessarily the ones that have seen the most layoffs, although they overlap partially. for the european union as a whole, the set of high-labor, low-emissions sectors include i (hotels and restaurants), g (wholesale and retail trade), n (rental and real estate), q (health care and elder care), p (education), r (culture) and s (services). sectors i, g, n and r have also experienced a peak in recent layoffs. for each of the individual countries, almost the same set appear on the high-labor, low-emissions list. in appendix a. , we comment on these sectors individually, and end by commenting on some other industries. to structure our analysis we categorize policies along the following dimensions (table ) . first, we split them into policies that are primarily motivated by their effects stimulus spending refers to policies that require substantial amounts of government funds, with the aim to preserve employment, avoid bankruptcies, create new jobs, and help the hardest-hit consumers. the second category includes tax reform policies that are complementary or even somewhat orthogonal to stimulus, but that raise extra revenues that can be used as additional stimulus, and that have overall economic efficiency benefits. third, some policies do not require large financial injections from the government; e.g., mandates, standards, or bans. they may also span several categories. we group them under 'cross-cutting' policies. any categorization of policies is necessarily imperfect: there is no optimal choice of dimensions and policies will spill across categories or overlap with each other. policies vary in their breadth and budgetary requirements. the most important matter is that our list of policies is reasonably complete. we believe it is, with some caveats. we purposely omit some policies. we do not tackle coronavirus policies that have no long-run climate impacts, or that are not relevant beyond the immediate crisis. these include test-trace-isolate, travel restrictions, and vaccine development. similarly, some central policies to manage the pandemic have significant but short-lived effects on emissions-yet long-run climate impacts appear highly limited. these include distancing policies such as lockdowns, restricting access to public spaces, and the closing of restaurants and schools. we have evaluated the set of policies in tables and (the latter breaks down financial assistance to firms by industry). figure summarizes the conclusions from this analysis. we plot policies according to how good they are for the coronavirus crisis (vertical axis) and for the climate crisis (horizontal axis). policies marked green denote stimulus policies, policies marked red denote tax reform policies, and policies marked blue denote other cross cutting policies. below we proceed to comment on policies we have identified as particularly promising (located in the upper right corner). a detailed analysis of these-and other policies-can be found in the appendix (a. -a. ). there, after describing each policy and briefly analyzing it, we draw a conclusion as to how it scores in terms of alleviating the recession and its long-run climate impact. these scores take seven levels: very bad; bad; bad-to-neutral; neutral; neutral-to-good; good; very good (these results are also presented in tables and ). the precise scoring can be refined, but we present a conceptual framework for analyzing the joint set of policies meant to address the coronavirus recession and climate crises. small scale green infrastructure investment (good, good, a. ) aiding industries (see table and fig. we plot these policies in green, labelled by industry. there have been various policy proposals on how to support businesses and workers, in general, during the crisis. these include giving out loans or grants to small businesses, or providing firms with tax relief (becker et al. ; scarpetta et al. ) . these policies aim to support business owners, to support workers and allow them to maintain their relationship with the firm, or to prevent the overall collapse of businesses. the choice between different industries appears the most consequential decision that governments can make. how the stimulus funds are allocated across industries determines both the short-run employment effects and could have long-run climate implications. the question we therefore ask is: which sectors should be targeted for aid (bailouts, investments, loans, etc.) if the objective is for this to both alleviate the current crisis and be good for the climate? whether stimulus for particular industries has meaningful impacts on long-term climate goals depends on several factors. for example, preferentially saving firms in a given sector may not have a large direct impact on the sector in the long run. the reason is that the capital assets, many of them specific to the sector, will still exist; so will a large fraction of the sector-specific human capital. thus, even if a wave of bankruptcies were to destroy many businesses in some low-emissions sector, that sector may spontaneously recover once the crisis has passed. one potential long-run effect from extensive bankruptcies in a sector is that consumers and buyers may shift their habits away from that sector, implying a longrun decline in sector-specific demand. furthermore, persistent changes may result through the forced experimentation mechanism or long-lived government investments. bankruptcies among firms conducting r&d into renewables may lead to a slowing of technological change (which we address separately below). the political channel can also be at work. firms will likely vary in their ability to weather the current crisis along many dimensions. if there is systematic variation in survival probability between firms in competing subsectors, long-term effects may result from subsectors that see many firms go bankrupt being unable to represent their interests in the political process. for example, in the european electricity sector, the largest firms tend to focus on fossil-fuel technologies in their innovation. large firms also likely have better access to credit. thus, a wave of bankruptcies may mean policies in the recovery stage may favor large, fossil-oriented firms. such temporary disruption can have persistent effects, by strengthening the structure of vested interests in the sector, and thus the persistence of policy (brainard and verdier ; coate and morris ) . this presents another reason for supporting vulnerable 'green' industries. a word of caution is in place. aiding industries has at least two problems. first, it may not be politically feasible. second, it may not be very efficient in general compared to more direct measures at tackling unemployment. funds to aid firm survival will help firms' owners without necessarily boosting employment. the same holds for tackling climate change. this is since such assistance would work only indirectly to affect the goals (such as employment and lower emissions) and firms may not use the aid as intended. a valuable complement could be conditioning of aid at the firm or industry level, for those who receive it. this policy is orthogonal to other policies but could ensure that industry aid becomes more effective, by aligning the recipient's goals with those of the policy-maker. for instance, assistance could be made conditional on lowering emissions or on the funds being used for hiring or retaining labor. conditioning loans is common practice at the world bank and imf, and for many governments. there are several examples of such conditioning having already been used in the current crisis. for more details on contingent policies, see sect. . . . based on this analysis, previous research and data of employment and emissions, the sectors hotels and restaurants, health care and education would be good candidates but for different reasons (for a results of the other sectors see table ; for a fuller analysis of all sectors see also appendix a. ). restaurants are very labor intensive, have been hit hard by the lockdown and have low direct emissions. targeting this sector in the recovery phase could therefore be a good idea. hotels have also been severely affected, but subsidizing hotels likely aids the transport sector which is very emissions intensive. hence, a finer targeting may be needed here, for instance, only towards restaurants or more broadly to other service industries. we rank aiding this sector as good at alleviating the coronavirus crisis and neutral-to-good for the climate. the education sector has not been hit by the crisis. but having a high labor share and being essential in the structural transformation of the economy forced by the coronavirus crisis, this sector is key in dealing with that crisis. at the same time, it is low on emissions. stimulus may thus shift production and 'consumption' in a climate-friendly direction. we rank aiding this sector as good at alleviating the coronavirus crisis and good for the climate. health care also has high employment intensity. it of course has not seen any layoffs, being essential for dealing with the medical fallout of the current or future pandemics. it is also low on emissions, so the same motivation as for education applies here. we rank aiding this sector as good for alleviating the coronavirus crisis and good for the climate. economic stabilization can of course take the form of monetary stimulus. relatedly, it has been suggested the fiscal commitments could be funded as 'helicopter money'by printing money. we are not aware of research on the climate effects of such policies, so we do not include them in our ranking, summary and conclusions. see appendix a. for further details. these policies are also plotted in green. fiscal stimulus can be aimed at 'climate-oriented' infrastructure investment such as renewable-energy generation facilities, associated infrastructure, and energy-saving investments. governments have already announced very large investments in infrastructure as part of stimulus programs. on may th , the european commission presented a revamped long-term eu budget and a € . trillion recovery plan, with the explicit goal to provide the instruments to build a modern, clean and healthy economy, better known as the 'eu green deal' (new europe ). stimulus spending should be directed according to these plans if governments are serious about climate change mitigation. not doing so will undermine the climate targets: recovery from the coronavirus crisis will exhaust the appetite for public spending for many years. but from a coronavirus perspective, the immediate benefit of such investment stimulus is unclear. the stimulus would primarily operate through the construction sector. however, this sector has not seen severe layoffs due to the health crisis. there is thus a trade-off between optimizing strategic investments that move societies onto more sustainable pathways, and getting societies out of the immediate coronavirus recession as rapidly as possible. if there is potential for sufficiently skilled workers to move in from other sectors, there could be beneficial short-run effects on overall employment. the most direct long-term climate policy effect of green infrastructure investments is their emissions reduction throughout their long lifetimes. complementarities (for example due to network infrastructure investments) mean they can also spur further, private investment, and shift societies away from 'carbon lock-in' and towards a 'green lock-in' path. this lock-in can be reinforced by indirect channels. a shift towards green investment generates larger vested interests in favor of e.g. carbon pricing policies, given that renewable investments stand to gain from such policies. for example, in germany, the feed-in tariffs for renewables generated constituencies and advocacy groups which stabilized the policy regime and led to an expansion of the sector (jacobsson and lauber ; strunz et al. ) . further, any shift towards greener infrastructure and future pricing policies incentivizes green r&d investments, due to larger potential market size (acemoglu et al. ). the channels involved here are thus long-lived investment, changing political status quo and technological changes. an important point here is that the labor intensity of infrastructure projects depends on their scale: small-scale projects are more labor-intensive than large-scale projects (strand and toman ) . this could favor small-scale renewables such as residential solar and retrofit projects. our judgment of the effect on coronavirus crisis is therefore based on the scale of the projects. based on the above, we particularly want to highlight smallscale infrastructure projects such as retrofitting insulation and installing solar panels on houses. we rank this policy as good at alleviating the coronavirus crisis and good for the climate. for reasons similar to those in the case of large-scale infrastructure investment, we do not think that extensive green r&d investment, while good for climate, will be particularly well-suited to deal with the coronavirus crisis as the effects on employment in the short-to-medium run are essentially limited to those holding the right competence. investing in green r&d will just shift research labor from one area to another. fiscal stimulus to private r&d spending in the renewable energy sector, by way of grants or loans, can prevent bankruptcies and the breaking up of successful r&d teams. more details can be found in appendix a. . we rank both policies as neutral-to-good at alleviating the coronavirus crisis and good for the climate. another promising green stimulus option is planting trees. afforestation and reforestation activities are likely cost-effective both in terms of climate and in terms of the coronavirus crisis, as the trees will absorb co and as planting requires large numbers of manual and unskilled labor (strand and toman ) . we rank this policy as good at alleviating the coronavirus crisis and good for the climate (see more in appendix a. ). we plot these policies in red. while tax reforms obviously do not need to be climatemotivated, we have identified revenue-neutral 'green tax reform' (involving for example carbon taxes, an abolition of fossil fuel subsidies, tighter emission caps, and meat consumption taxes) as especially promising, because it would enable an even more aggressive stimulus package (see appendices a. -a. ). revenue-neutral policies not only have important long-run climate effects, but also have the potential to improve economic recovery. green taxes improve economic efficiency by internalizing the carbon externality. they would thus also help to internalize potential negative externalities from indirect emissions that could result from certain sectoral aid (e.g., aiding hotels and restaurants that are closely linked to travel). how the revenues are spent determines which industries and consumers are winners vs. losers (and thus whether the policy is on net favorable or unfavorable to preserve employment). there is a possibility of a double dividend if the revenues are used to offset preexisting distortionary taxes (goulder ; de mooij ) . the coronavirus recession may thus be a politically opportune moment for well-designed green tax reform that enables environmental and employment benefits at the same time. we rank carbon taxes, an abolition of fossil fuel subsidies and tighter emission caps as good at alleviating the coronavirus crisis and very good for the climate. we rank a meat consumption tax as good at alleviating the coronavirus crisis and good for the climate. as a benchmark for the neutrality of the green taxes, we assume that the proceeds are spent on reducing labor taxes. one reason for using this benchmark is that fiscal stimulus in the form of reduced labor taxes takes effect more quickly than monetary stimulus (kaplan and violante ) . this could be good for a rapid exit from the coronavirus crisis by stimulating labor demand. such tax cuts can also be tailored with distributional impacts in mind, and could thus be designed to help households most likely at risk of an immediate liquidity crisis. to use the proceeds for labor tax reductions is of course just one option out of many. a green tax reform would have an even more favorable impact on the climate if the revenues were spent on direct investments in renewable energy, clean tech r&d, and other low-carbon technologies. in this case, both the tax itself and the revenues provide immediate incentives to reduce emissions, while also benefiting from path-dependency effects of redirecting capital to build up a greener capital stock. this type of revenue recycling is less attractive from the perspective of mitigating the recession, as many green investments do not require much labor. we would therefore focus on policies that reduce labor taxes economy-wide. labor tax cuts are a form of fiscal stimulus which could be considered in isolation for tackling the coronavirus fallout. we are not aware of research that would shed light on the impact of labor tax reductions, in isolation, on climate outcomes. we rank this policy as good for the coronavirus crisis and neutral for climate. see appendix a. for further details. we plot the cross-cutting policies in blue. the pandemic has led many governments to impose different forms of regulations and restrictions on citizens and businesses, related for example to travel, sick leave, and way of doing business. there are also mandates that have been, or could be, imposed with the primary purpose to mitigate emissions and air pollution. these are relevant to analyze as they in turn may impact economic recovery, or adaptation potential for the current or future pandemics. we comment on the most promising of such policies here. neves and brand ( ) find that about % of short car trips could in theory be replaced by cycling or walking, reducing emissions from car travel by about %. city planning policies and infrastructure investments promote active modes of transportation by making car travel more expensive (e.g., congestion charging) and less convenient (winters et al. ) . we already see initiatives along these lines. milan plans to reallocate km of street space from cars to cycling and walking in the summer of , in response to the coronavirus crisis. given path dependencies of infrastructure investment and forced experimentation, initiatives like this can also foster persistent change. a shift towards active modes of transportation could also have long-run health effects in the form of lower rates of obesity, diabetes, and hypertension (pucher et al. ; rasmussen et al. ; grøntved et al. ). this reduces the share of people vulnerable to the coronavirus. we rank this policy as good at alleviating the coronavirus crisis and good for the climate. tighter air pollution regulation would reduce carbon emissions: this could involve switching from coal generation to gas generation, especially near population centers, and boosting less emission-intensive transport. such policies may involve long-lived investments (into renewables and gas-fired plants to replace coal) which will be long-lasting. they will also generate new interest groups (cyclists, drivers of electric vehicles) and perhaps reduce the power of coal generators. there is also some preliminary evidence that local air pollutants, such as nitrogen oxides (no x ) and atmospheric particulate matter with a diameter of less than . microm (pm . ) may increase mortality from the coronavirus (ogen ; wu et al. ). if these preliminary findings hold up, they point to long-term benefits if the virus becomes endemic, circulating in the population indefinitely. we rank this policy as good at alleviating the coronavirus crisis and good for the climate. there has been a broad debate about conditioning bailouts to firms in polluting sectors. if a bailout can be credibly conditioned on future changes in activity, and if, in the absence of bailouts, the industry is likely to resurrect after any bankruptcies, then conditional bailouts of emission-intensive sectors may be beneficial to the climate. consider airlines: a wave of bankruptcies will wipe out current shareholders, but the aircraft assets will be sold to new companies once the health crisis subsides, and these new firms will operate according to market incentives. a bailout will save the current firms, but it can set conditions on their future behavior, such as reducing the number of short-haul flights for which feasible low-emission alternatives exist. several airlines have already been given bailout loans with no conditions attached (laville ) . on the other hand, the bailout given to air france comes with the requirement that the company halve its carbon emissions from domestic routes, essentially forcing it to cut back services on routes (financial times ). we rank this policy as neutral-to-good at alleviating the coronavirus crisis and neutral-to-good for the climate. recapitalization is an alternative to conditional bailouts. rescuing firms by injections of equity using public funds are, effectively, partial nationalizations. as such, they give the state an ownership stake in the firm, and thus a voice in the management of the firm. many commentators warn against the state taking a role in commercial decisions, even in situations in which it does hold a stake. however, where a firm's commercial decisions involve important externalities, it may be justifiable to have the state exercise its owner's right to influence commercial decisions, so as to take account of the full social costs of these decisions. the recapitalization should be large enough to give a state a voice as a major shareholder. the channels involved here are thus through long-lived investment and political status quo. government may pay wages for private employees as a way to avoid the labor search costs associated with rehiring once the economy starts to recover (as proposed by sinn ). with regards to the long-term climate effects from this policy the results are less clear. if labor gets increasingly replaced by capital as a result of forced experimentation, where companies adopt new technologies or management practices that replace some of the previous jobs, this shift in the capital-labor share could potentially have a negative climate impact since capital is typically more fossil fuel intensive. the specific impacts may depend on industry; the analysis of sect. . . applies. we conclude that his policy is very good for addressing the coronavirus crisis and neutral-to-good in terms of climate. in this category we have also looked into tightening renewable portfolio standards, and encouraging working from home. we have ranked these policies as neutral for alleviating the coronavirus crisis and good for climate (the analysis is found in a. and a respectively). a cross-cutting policy that is not promising though is extending sick leave provisions (see appendix a. ). unless also financed by the government, such provisions may lead to bankruptcies and substitution away from labor. we rank this policy as neutral-to-bad for alleviating the coronavirus crisis and neutral-to-bad for climate. the severity and abruptness of the coronavirus crisis do not make the climate crisis any less pressing. our societies need to solve the former, immediate crisis without taking our eye off the latter, inexorable one. we have above identified a set of policies that would help in tackling both the coronavirus crisis and climate change. the most effective policies involve revenue-neutral tax reforms towards carbon pricing, which would be excellent climate policies and also help deal with the coronavirus crisis by allowing reductions to labor taxes. subsidizing temporary employment in less emissionsintensive industries (services sectors including leisure services like restaurants and culture; or professional services like technology, education, and healthcare) can help laid-off workers try out occupations that have potential even under tougher climate policies. here one needs to be aware of potential indirect emissions effects in sectors with complementary goods, but with proper carbon pricing, such effects could be internalized. labor-intensive investments into natural capital (tree planting) and into low-carbon physical capital can both support employment and incomes, while storing carbon or helping societies transition towards a low-carbon future. health and climate goals can also be achieved by promoting transport methods which not only reduce carbon emissions, but local pollutants too, improving cardiovascular health. all sectoral aid should be conditioned on being directed towards employment and on low-carbon supply chains. the crisis is ongoing, and the full outcomes in terms of health and unemployment are yet to be known. policies will be tried out, and their effects will be observed. thus, our results may require revision as more information becomes available. nevertheless, our approach provides a conceptual framework for how to jointly assess the medium-run effects of policies on the coronavirus crisis and the long-run effects on the climate crisis. both crises are severe and neither can be ignored. fortunately, modern societies should be capable enough to walk and chew gum at the same time. the environment and directed technical change economics versus politics: pitfalls of policy advice input-output analysis of irish construction sector greenhouse gas emissions the large and unequal impact of covid- on workers. voxeu do the rich save more? evidence from canada input-output subsystems and pollution: an application to the service sector and co emissions in spain the impacts of dietary change on greenhouse gas emissions, land use, water use, and health: a systematic review pandemic, shutdown and consumer spending: lessons from scandinavian policy responses to covid- do carbon taxes kill jobs? firm-level evidence from british columbia teams and bankruptcy. cepr discussion paper dp importance of food-demand management for climate mitigation is a residential relocation a good opportunity to change people's travel behavior? results from a theory-driven intervention study optimal dynamic carbon taxes in a climate-economy model with distortionary fiscal policy covid- is also a reallocation shock the global tree restoration potential available at https ://voxeu .org/artic le/corpo rate-debt-burde ns-threa ten-econo mic-recov ery-after -coron aviru s bernheim bd, scholz jk ( ) private saving and public policy how can the poor save? theory and evidence on saving in low-income households optimal environmental taxation in the presence of other taxes: general equilibrium analyses lobbying and adjustment in declining industries carbon emissions comparison of last mile delivery versus customer pickup household saving: micro theories and micro facts covid- and remote work: an early look at us data. mit initiative on the digital economy working paper series determinants of transport mode choice: a comparison of germany and the usa coronavirus profiteers' condemned as polluters gain bailout billions. the guardian the factors influencing car use in a cyclefriendly city: the case of cambridge tracking the covid- crisis with high-resolution transaction data a government roadmap for addressing the climate and post covid- economic crises global fossil fuel subsidies remain large: an update based on country-level estimates. imf working paper wp/ / policy persistence the environmental cost of global fuel subsidies oil costs less than zero after a sharp monday selloff handbook of environmental and resource economics, edward elgar demetriades po, mamuneas tp ( ) intertemporal output and employment effects of public infrastructure capital: evidence from oecd economies individual retirement and savings behavior vegetarian, vegan diets and multiple health outcomes: a systematic review with meta-analysis of observational studies why don't the poor save more? evidence from health savings experiments estimating the carbon footprint of australian tourism do the rich save more? moving to greener pastures? multinationals and the phh energy subsidies in the middle east and north africa assessing the growth of remote working and its consequences for effort, well-being and work-life balance commentary: what is the relationship between coronavirus and cardiovascular disease? the virus fight opens up a climate opportunity canada ties coronavirus help to climate goals environmental taxation and the double dividend hypothesis in cge modelling literature: a critical review helicopter money: the time is now do the rich save more in latin america? entrepreneurship and household saving tackling climate change through livestock: a global assessment of emissions and mitigation opportunities a tale of two tails: commuting and the fuel price response in driving anthropogenic land use change and infectious diseases: a review of the evidence environmental taxation and the 'double dividend': a reader's guide general equilibrium impacts of a federal clean energy standard corporate lobbying for environmental protection bicycling to work and primordial prevention of cardiovascular risk: a cohort study among swedish men and women grocery delivery or customer pickup-influences on energy consumption and co emissions in munich directed technological change and factor shares us fossil fuel giants set for a coronavirus bailout bonanza. the guardian energy-saving technical change the environmental impacts of the coronavirus zenghelis d ( ) will covid- fiscal recovery packages accelerate or retard progress on climate change? two thirds of citizens around the world agree climate change is as serious a crisis as coronavirus the politics and policy of energy system transformation-explaining the german diffusion of renewable energy technology a tale of two stimulus payments to fight the covid pandemic, policymakers must move fast and break taboos. voxeu the benefits of forced experimentation: striking evidence from the london underground network coronavirus: airlines seek € . bn in bailouts without environmental conditions attached. the guardian, nd april business case and technology analysis for g low latency applications the carbon footprint of global tourism temporary reduction in daily global co emissions during the covid- forced confinement effects of environmental regulation on foreign and domestic plant births: is there a home field advantage? france rules out coronavirus aid for tax-haven businesses the impact of clean energy investments on the greek economy: an input-output analysis the impact of a carbon tax on manufacturing: evidence from microdata covid- helicopter money: economics and politics fossil fuel consumption subsidies bounced back strongly greenhouse gases embodied in the international trade and final consumption of finland: an input-output analysis case fatality rate of cancer patients with coronavirus in a new york hospital system assessing the potential for carbon emissions savings from replacing short car trips with walking and cycling using a mixed gps-travel diary approach new europe ( ) eu recovery plan focuses on green deal initiatives canada passed a carbon tax that will give most canadians more money. the guardian assessing nitrogen dioxide (no ) levels as a contributing factor to the coronavirus (covid- ) fatality rate international monetary fund partridge j ( ) world's biggest fund manager vows to divest from thermal coal. the guardian new eu ets phase rules temporarily puncture waterbed understanding overlapping policies: internal carbon leakage and the punctured waterbed international comparison of health care carbon footprints economic optimization of a global strategy to address the pandemic threat walking and cycling to health: a comparative analysis of city, state, and international data entrepreneurship, saving, and social mobility can government purchases stimulate the economy? ten years after the financial crisis: what have we learned from the renaissance in fiscal research? associations between recreational and commuter cycling, changes in cycling, and type diabetes risk: a cohort study of danish men and women effects of an environmental tax on meat and dairy consumption in sweden supporting people and companies to deal with covid- : options for an immediate employment and social policy response. voxeu, th april carbon lock-in: types, causes, and policy implications carbon footprint of inbound tourism to iceland: a consumptionbased life-cycle assessment including direct and indirect emissions how best to fight the economic impact of the coronavirus pandemic. the guardian lawmakers roll out landmark bipartisan carbon bill. e&e news mitigation potential and global health impacts from emissions pricing of food commodities green stimulus, economic recovery, and long-term sustainable development the political economy of renewable energy policies in germany and the eu onlin e-inste ad-drivi ng-store van der meijden g, smulders s ( ) carbon lock-in: the role of expectations policies to promote active travel: evidence from reviews from the literature exposure to air pollution and covid- mortality in the united states: a nationwide cross-sectional study urban dietary changes and linked carbon footprint in china: a case study of beijing temporary incentives change daily routines: evidence from a field experiment on singapore's subways breaking the taboo: the political economy of covid-motivated helicopter drops. voxeu tax cuts for whom? heterogeneous effects of income tax changes on growth and employment publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations gustav engström · johan gars · niko jaakkola · therese lindahl , · daniel spiro · arthur a. van key: cord- -pm pfeeb authors: kunz, y.; horninger, w.; pinggera, g.-m. title: was sollte ein urologe zu sars-cov- wissen? risikoanalyse für urologische operationen und handlungsempfehlungen im klinischen alltag date: - - journal: urologe a doi: . /s - - -z sha: doc_id: cord_uid: pm pfeeb background: covid- poses a challenge to healthcare systems worldwide. due to the increasing number of cases, surgeons in urology have also been confronted with sars-cov‑ infections. thus, there is an urgent need for clinical guidance and recommendations. aim: our work aims to create a widespread assessment of a possible risk for infection with sars-cov‑ during surgical procedures. based on current data and current national and international guidelines, we try to assess the risk of infection when handling human tissue and the necessary hygienic measures that are needed. finally, recommendations for daily urologic work are derived and explained. materials and methods: the current literature in pubmed, biorxiv and medrxiv and data available from the who and robert-koch-institut on sars-cov‑ and surgical procedures in (potentially) infected patients are reviewed. the endpoint of our research was april . conclusion: based on our research, general and specific recommendations for clinical urologic praxis can be derived. although it remains unclear whether sars-cov‑ is transmitted via the aerosols produced, current ppe in operating rooms probably does not offer sufficient protection during surgical interventions during the sars-cov‑ pandemic. use of ffp‑ masks, safety goggles and full-body protective suits is crucial. to contain viral spread on surfaces and personnel, complex filter systems (hepa) should be used as well as closed suction devices during surgery. combined with consequent disinfection of surfaces and behavioral measures, a safe environment for healthcare workers in urology can be created. thus, according to current knowledge, we believe that emergency and urgent surgical procedures are not contraindicated, provided that appropriate precautionary safety measures are followed. mit beginn des . jahrhunderts sehen sich mediziner weltweit mit einer der größten gesundheitspolitischen herausforderung angesichts einer neuen pandemie konfrontiert und dies ungeachtet entstehender sozioökonomischen implikationen. mit datum . . hat die who diese viruserkrankung als covid- ("coronavirus disease ") klassifiziert. ausgelöst wird diese infektionskrankheit durch das virus sars-cov- ("severe acute respiratory syndrome coronavirus "), das zur familie der β-coronaviridiae bzw. der ordnung nidovirales gehört. aus humanpathogener sicht sind diese coronaviren als erreger von respiratorischen infekten bis hin zu schwerwiegenden pulmonalen erkrankungen von bedeutung. von den bekannten humanpathogenen stämmen bestehen in der medizinischen literatur erfahrungen mit vorangegangenen coronavirusinfektionen, wie jene als sars-infektion oder als mers ("middle east respiratory syndrome"). ungeachtet methodischer und länderspezifischer unterschiede sind in aktuellen datenerhebungen weltweit bereits über , mio. menschen bestätigt infiziert. leider sind auch über . todesfälle auf sars-cov- zurückzuführen [ ] . offensichtlich stellt diese pandemie eine herausforderung mit unabsehbaren folgen an unserer gesellschaft dar, wobei gesundheitssysteme weltweit, aber insbesondere das medizinische personal im fokus der öffentlichen wahrnehmung stehen [ , ] . das sars-cov- wird im wesentlichen via tröpfcheninfektion -und somit über aerosole -von symptomatischen covid- -patienten übertragen. daneben wird eine kontaktübertragung noch kontrovers diskutiert [ ] . neueste studien konnten darüber hinaus nachweisen, dass eine virustransmission selbst durch minimal symptomatische oder sogar asymptomatische personen erfolgen kann [ , ] . die besonderheit für covid- ist eine längere inkubationszeit (zwischen viruskontakt und symptomenbeginn) von - tagen mit maximal tagen. coronaviren, in winzigen aerosolen transportiert, stellen allerdings ein ernstzunehmendes risikodar, weshalbaufdieser weise von einer versteckten ansteckungsgefahr ausgegangen werden muss [ ] . laut studien können coronaviren bei raumtemperatur auf verschiedenen oberflächen bis zu tagen überdauern. dieses intervall ist länger als bisher angenommen und begründet z. t. das infektionspotenzial von sars-cov- [ , ] . gerade hinsichtlich der aktuellen sars-cov- -pandemie gilt es daher, entsprechende risikoabschätzungen und sop für urologische abläufe sowie für operationssäle zu erarbeiten. als Ärzte in der direkten patientenversorgung sind auch urologen einer infektionsgefahr mit covid- in ihrem täglichen arbeitsumfeld ausgesetzt. vermutlich können einige urologische eingriffe als elektiv betrachtet und ohne größeres risiko für einen gesundheitsschaden aufgeschoben werden; dennoch bestehen in der uroonkologie, in der traumachirurgie oder in der steinchirurgie ebenso dringliche und somit unaufschiebbare interventionsindikationen. während sicherheitsvorkehrungen auf intensivstationen und notaufnahmen bereits umfassend umgesetzt werden, liegt eine empfehlung seitens der europäischen urologenvereinigung (eau; [ ] ) online erst seit . april vor. generelle richtlinien bieten das robert-koch-institut, die weltgesundheitsorganisation sowie das cdc und ecdc. empfehlungen bezüglich endoskopischer eingriffe wurden bereits durch die gastroenterologische gesellschaft sages kommuniziert. um die unterschiedlichen empfehlungen zu bündeln und die hintergründe der empfehlungen zu beleuchten wurde eine umfassende literatursuche durchgeführt, mit dem ziel ein handlungsarmentarium und konkrete verhaltensvorschläge für urologen in dieser pandemie zu geben. es wurde eine literatursuche in pubmed, biorxiv und medrxiv sowie den datenbanken der who und des cdc über sars-cov- und chirurgisches prozedere bei infizierten patienten durchgeführt. zusätzlich wurden die empfehlun- background. covid- poses a challenge to healthcare systems worldwide. due to the increasing number of cases, surgeons in urology have also been confronted with sars-cov- infections. thus, there is an urgent need for clinical guidance and recommendations. aim. our work aims to create a widespread assessment of a possible risk for infection with sars-cov- during surgical procedures. based on current data and current national and international guidelines, we try to assess the risk of infection when handling human tissue and the necessary hygienic measures that are needed. finally, recommendations for daily urologic work are derived and explained. materials and methods. the current literature in pubmed, biorxiv and medrxiv and data available from the who and robert-koch-institut on sars-cov- and surgical procedures in (potentially) infected patients are reviewed. the endpoint of our research was april . conclusion. based on our research, general and specific recommendations for clinical urologic praxis can be derived. although it remains unclear whether sars-cov- is transmitted via the aerosols produced, current ppe in operating rooms probably does not offer sufficient protection during surgical interventions during the sars-cov- pandemic. use of ffp- masks, safety goggles and full-body protective suits is crucial. to contain viral spread on surfaces and personnel, complex filter systems (hepa) should be used as well as closed suction devices during surgery. combined with consequent disinfection of surfaces and behavioral measures, a safe environment for healthcare workers in urology can be created. thus, according to current knowledge, we believe that emergency and urgent surgical procedures are not contraindicated, provided that appropriate precautionary safety measures are followed. der urologe von krankheitsausbrüchen zeigen, dass , % der infektionen auf aufenthalte in innenräumen zurückzuführen war. hierbei waren überwiegend - patienten gleichzeitig betroffen, während nur ein krankheitsausbruch außerhalb im freien stattfand. [ ] . somit bleibt es systematisch zu untersuchen, welchen einfluss diese faktoren auf die gesundheit von krankenhausmitarbeitern und Ärzten mit sich bringen wird. manche autoren spekulieren eine beträchtlich erhöhte mortalität bei Ärzten, insbesondere bei direktem kontakt mit der versorgung von covid- -patienten. erfreulicherweise liegen bereits einige epidemiologische erkenntnisse über das coronavirus selbst vor. ursprünglich in wuhan isoliert, konnte sich das virus in alle erdteile ausbreiten. infektionszahlen steigen stetig und ein höhepunkt scheint derzeit noch nicht absehbar. nach neusten erkenntnissen der who liegt die altersverteilung unter covid- -patienten bei durchschnittlich jahren. insbesondere in deutschland und anderen vergleichbaren industrienationen wie usa oder italien sind männer gerade in der urologisch relevanten patientengruppe von - jahren überrepräsentiert [ ] . für die risikoabschätzung einer infektion im urologischen bereich muss zusätzlich die rate an asymptomatischen, aber potenziell virulenten patienten mitkalkuliert werden. die aktuelle durchseuchungsrate innerhalb der europäischen union wird mit ca. - % vermutet, teilweise jedoch mit bis zu , % als deutlich höher eingeschätzt (mittels einer igg/igm-antikörpertestung bestimmt; [ ] naturgemäß bedienen urologen ein breites feld an interventionstechniken und operationen. die wichtigsten teilbereiche sind die offene chirurgie, laparoskopische oder roboterassistierte chirurgie sowie die endourologie. in allen teilbereichen der urochirurgie aber auch in ambulanten bereichen besteht eine kontaktgefahr mit blut oder urin. die offene chirurgie beherbergt insbesondere bei abdominellen eingriffen mit eröffnung des darms ein risiko der tröpfcheninfektion durch intraoperativ generierte, virulente aerosolbildung. einerseits ist der darminhalt virusbelastet, anderseits könnten sogar organe selbst mit dem coronavirus sars-cov- infiziert sein. der nachweis einer nierenparenchyminfektion konnte in einer aktuellen studie erbracht werden. in elektronenmikroskopischen aufnahmen wurden virionen in nierenzellen festgestellt. nach invasion über den ace -rezeptor verursacht sars-cov- eine nekrose der tubuluszellen. eine darauf folgende lymphozyteninvasion kann zu einem akuten nierenversagen führen. hiervon ist durchschnittlich etwa ein viertel der patienten betroffen [ , ] . auch das endothel wird durch das coronavirus befallen, wodurch eine endotheliitis entsteht. insbesondere bei kardiovaskulären vorerkrankungen oder adipositas wird hierdurch die mortalität erhöht [ ] . diese pathomechanismen erklären daher auch, dass das erstsymptom einer organotropischen sars-cov- -spezifischen infektion oftmals eine mikrohämaturie mit einhergehender proteinurie sein kann. in der früherkennung einer drohenden niereninsuffizienz kommt deshalb einer urinanalyse eine wichtige rolle zu [ ] . im rahmen einer operativen intervention erfolgt üblicherweise eine elektrokaustische koagulation von gefäßen und gewebe. hierbei werden aerosole mit einer potenziellen viruslast generiert. hitzeentwicklungen in zusammenhang mit elektrokaustischer diathermie (monoals auch bipolar) lässt zellmembranen aufbrechen und führt zu rauchent-wicklung. dieser rauch besteht zu % aus wasser und % aus zellmaterial in der größe von , - , μm. in beschriebenem rauch finden sich auch viruspartikel und stellt somit einen potenziellen vektor bei covid-patienten dar [ ] . eine chirurgische maske bietet allerdings keine suffiziente schutzbarriere gegen aerosole. mit einer üblichen größe von < μm vermag eine n -maske (entspricht ffp- ) hingegen bis zu % der aerosole zu blockieren. in mehreren studien mit anderen viren, wie beispielsweise hepatitis b, hiv oder das papillomavirus, konnte nachgewiesen werden, dass der intraoperativ generierte rauch entsprechende viruspartikeln beinhaltet [ , ] . dennoch wird ein spezifisches infektionsrisiko für das involvierte personal nach wie vor kontrovers diskutiert [ ] . so konnte generell keine drastisch erhöhte infektionsrate bei chirurgen oder anderem op-personal, trotz vermeintlich jahrzehntelanger inadäquater sicherungsmaßnahmen zur expositionsprophylaxe, festgestellt werden. dennoch, absaugvorrichtungen und entsprechende masken (ffp- /ffp- ) erscheinen in diesem kontext sinnvoll und sollten eingefordert werden. das prostatagewebe scheint demgegenüber nicht von sars-cov- befallen zu werden, zumindest konnte eine chinesische gruppe in einer kleinen studie keine virus-rna im prostatasekret nachweisen [ ] . abgesehen von einem möglichen infektionsrisiko bei sars-cov- -positivem harn kann daher angenommen werden, dass eine sars-cov- -transmission streng genommen weder bei offener prostatachirurgie, noch bei endourolgischen eingriffen erhöht ist. viele spül-und ablaufsysteme in der endourologie basieren bereits auf geschlossenen pumpsystemen. wie auch in der europäischen leitlinie empfohlen, sollte somit ein direkter abfluss des urins ohne wesentliche kontaminationsmöglichkeit erfolgen. jedoch muss bei der evakuation von beispielsweise resektionsspänen sowie beim ein-und ausgehen mit dem gerät auf einen entsprechenden schutz geachtet werden. da basierend auf der oben angesprochenen studienlage eine sars-cov- -Übertragung mittels urin denkbar ist, muss bei covid- -patienten und unklaren verdachtsfällen zusätzlich zur gängigen schutzkleidung im operationssaal auf ffp- -masken und schutzbrillen zurückgegriffen werden. natürlich muss diese sicherung auch im ambulanten bereich anwendung finden. falls vorhanden, ist eine zystoskopische beurteilung an einem angeschlossenen monitor mehr als sinnvoll, da hier ein zusätzlicher abstand zum patienten geschaffen werden kann. die infektiosität bei generierten aerosolen stellt in allen bereichen der urochirurgie einen möglichen infektionsweg für das gesamte op-personal dar. während bei laparoskopischen eingriffen prinzipiell ein geschlossenes absaugsystem verwendung findet, scheint dies für die offene chirurgie nicht zuzutreffen. entsprechend den aktuellen studien gibt es derzeit keine eindeutigen daten, welche einen infektionsweg für sars-cov- über blut, stuhl oder urin dezidiert beschreiben. richtigerweise findet sich bei symptomatischen patienten eine sars-cov- -virämie [ , ] . darüber hinaus konnte eine sars-cov- -kontamination im harn nachgewiesen werden. so zeigten mehrere arbeitsgruppen eine kontamination des urins in , - , % bei rt-pcr bestätigten covid- -patienten [ ] [ ] [ ] . analog konnten in älteren studien sars-cov- -und mers-cov-viren im urin in , - % der fälle nachgewiesen werden. interessanterweise konnten die studienautoren z. t. nachweisen, dass die viren erheblich länger im urin persistieren und dies selbst dann noch, wenn bereits eine klinische clearance bei den untersuchten patienten stattfand [ ] [ ] [ ] . die kontamination mit viren im urin könnte vermutlich erst im verlauf der viruserkrankungen relevant werden, zumindest wurde in einer neuen arbeit bei allen patienten innerhalb der ersten woche nach symptombeginn keine virale rna im harn nachgewiesen [ ] . somit ist die datenlage bezüglich der viruslast im harn mit heutigem wissen nicht eindeutig belegbar, da ande-re studienautoren keinen virusnachweis im harn detektierten. Ähnliches gilt für den nachweis von sars-cov- im stuhl mit dem risikopotenzial eines fäkooralen Übertragungsweges. in rektalabstrichen konnte bei an covid- erkrankten patienten in , % erregerspezifische rna vermittels pcr nachgewiesen werden. auch hier waren die stuhlproben über mehrere tage nach bereits -fach wiederholten negativen oropharyngealen abstrichen anhaltend positiv, was zu einer entsprechenden who-warnung führte [ ] . in betrachtung der oben genannten aspekte sowie unter einhaltung der empfohlenen sicherheitsmaßnahmen ist die laparoskopie in zeiten der covid- -pandemie per se nicht kontraindiziert. sehr wohl sind hierbei besondere vorsichtsmaßnahmen zur sicherstellung der mitarbeitergesundheit im vorfeld zu treffen. durch verwendung geschlossener absaugsysteme kann ein nahezu aerosolfreies arbeitsumfeld geschaffen werden. niedrige arbeitsdrücke zur bildung des pneumoperitoneums können ebenfalls eine verbreitung des virus reduzieren. darüber hinaus ist ein sogfältiges absaugen des pneumoperitoneums zu operationsende noch vor trokarentfernung zu fordern. in der risikostratifizierung ist eine Übertragung von urin, blut oder gewebepartikeln, beispielsweise durch unkontrollierte dekompression in der laparoskopie, durch unerwartetes verspritzen von flüssigkeiten oder stichverletzungen, aufgrund der geschlossenen körperhöhle als weniger riskant einzustufen. in zeiten einer pandemie mit genereller ressourcenknappheit im gesundheitssystem muss auf die vorteile der laparoskopie als etablierte und sichere op-methode verwiesen werden; bekanntermaßen ist eine postoperative intensivmedizinische behandlung seltener, gleichzeitig profitieren patienten generell von einer geringeren komplikationsrate sowie durchschnittlich von einer reduzierten krankenhausaufenthaltsdauer [ , ] . daher sollte die möglichkeit zugunsten der laparoskopischer operation, wie bereits in den leitlinien der eau und dgu empfohlen, nicht durch die sorge einer coronavirusinfektion unberücksichtigt bleiben. chirurgische standard-op-masken bieten keinen ausreichenden schutz vor viren oder viruspartikeln in aerosolen [ ] . da aerosole nicht nur während der operation, sondern bereits zuvor im rahmen einer op-einleitung entstehen können, sollte laut aktuellen empfehlungen unbedingt auf ffp- -masken im falle eines zu behandelnden patienten mit verdacht auf oder einer bestätigten covid- -infektion zurückgegriffen werden. , zusätzliche schutzbrillen und Überschuhe verhindern eine virusübertragung entsprechend den erfahrungen auf intensivstationen in wuhan, china. anästhesiologische vorbereitung und intubation beherbergen das größte verteilungspotenzial für viren und sollten somit vorab in gesonderten räumen durchgeführt werden. damit wird eine viruslast im operationsbereich auf ein minimum reduziert [ ] . die durchführung einer lumbalanästhesie verursacht eine vergleichsweise geringere virusexposition und sollte somit nach möglichkeit und ausstattung erwogen werden. laut literatur kann hierdurch der häufigste risikofaktor für eine coronavirusinfektion im op deutlich reduziert werden [ ] . Ähnlich wie die für die chirurgie hpv-assoziierter krankheiten verwendeten absaugsysteme, sollte an eine solche technische umsetzung in der offenen chirurgie gedacht werden. hierdurch ist eine aerosolreduzierung durch direktes und nahes absaugen wie beispielsweise bei der verwendung von elektrokautern möglich. bezugnehmend auf die beschriebenen infektionen auf intensivstationen und die damit "iatrogene" transmission und ausbreitung des coronavirus müssen klimaanlagen und ventilatoren entsprechend kontrolliert und ausgestattet werden. hepa-filter ("high-efficiency particulate air") ha- https://www.rki.de/de/content/infaz/n/ neuartiges_coronavirus/hygiene.html. https://www.g-f-v.org/sites/default/ files/sars% stellungnahme% der% desinfektionsmittelkommission% von% dvv% und% gfv% _ -bsmodhhmsge _clean.pdf. ben nachweislich eine gute wirksamkeit gezeigt. hepa-filter sind in der lage, partikel bis zu einer größe von nm herauszufiltern, was im falle von sars-cov- mit einer größe von rund nm effektiv erscheint. hinzu kommen ausgeklügelte diffusion und impaktierung träger massen [ ] . coronaviren verbleiben nur für eine gewisse zeit schwebend in der luft. aufgrund von turbulenzen und luftbewegungen kommt es zu einer räumlichen verbreitung und schnellerem niederschlag dieser aerosoltröpfchen. durch die lange infektiosität von sars-cov- auf verschiedene oberflächen ist eine zeitnahe und korrekte reinigung des operationssaals einzufordern; selbstverständlich gilt dies auch für direkt und indirekt verwendete gegenstände. hier sollten zumindest begrenzt viruzide desinfektionsmittel zum einsatz kommen. zusätzlich sollte das gesamte op-personal einen wechsel der schuhe vor betreten der op-säle durchführen. die forderung einer maßvoll vertretbaren reduktion von personen ist nachvollziehbar. covid- -patienten zeigen ein erhöhtes koagulationsrisiko mit gefahr einer disseminierten intravaskulären koagulation (dic) und thrombose/ emboliebildung auf (z. b. bei d-dimer-anstieg um das -fache; [ , ] clinical features of patients infected with novel coronavirus in wuhan, china clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study covid- and italy: what next? lancet a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster transmission of -ncov infection from an asymptomatic contact in germany covid pandemic and gynaecological laparoscopic surgery: knowns and unknowns persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents survival of human coronaviruses e and oc in suspension and after drying onsurfaces: a possible source ofhospital-acquired infections risk of sars-cov- diffusion when performing minimally invasive surgery during the covid- pandemic a novel coronavirus from patients with pneumonia in china aerosol and surface distribution of severe acute respiratory syndrome coronavirus in hospital wards aerosol and surface stability of sars-cov- as compared with sars-cov- air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient indoor transmission of sars-cov- . medrxiv who ( ) coronavirus disease presymptomatic transmission of sars-cov- -singapore estimating the reproductive numberandtheoutbreaksizeofnovelcoronavirus disease (covid- ) using mathematical model in republic of korea the reproductive number of covid- is higher compared to sars coronavirus estimation of the reproductive number of novel coronavirus (covid- ) and the probable outbreak size on the diamond princess cruise ship: a data-driven analysis clinical characteristics of coronavirus disease in china novel coronavirus: where we are and what we know should covid- concern nephrologists? why and to what extent? the emerging impasse of angiotensin blockade human kidney is a target for novel severe acute respiratory syndrome coronavirus (sars-cov- ) infection. medrxiv endothelial cell infection and endotheliitis in covid- urinalysis, but not blood biochemistry, detects the early renal-impairment in patients with covid- human papillomavirus dna in leep plume dissemination of melanoma cells within electrocautery plume does exposure to laser plume place the surgeon at high risk for acquiringclinicalhumanpapillomavirusinfection? no sars-cov- in expressed prostatic secretion of patients with coronavirus disease : a descriptive multicentre study in china coronavirus disease : coronaviruses and blood safety persistence and clearance of viral rna in novel coronavirus disease rehabilitation patients coronavirus disease infection does not result in acute kidney injury: an analysis of hospitalized patients from wuhan, china novel coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples find the right sample: a study on the versatility of saliva and urine samples for the diagnosis of emerging viruses virological assessment of hospitalized patients with covid- the presence of sars-cov- rna in feces of covid- patients comparison of retropubic, laparoscopic and robotic radical prostatectomy: who is the winner? comparison of open versus laparoscopic versus hand-assisted laparoscopic nephroureterectomy: a systematic review and meta-analysis laparoscopicsurgery for hiv-infected patients: minimizing dangers for all concerned submicronand nanoparticulate matter removal by hepa-rated mediafiltersandpackedbedsofgranularmaterials hypothesis for potential pathogenesis of sars-cov- infection-a review of immunechangesinpatientswithviralpneumonia clinical observation and management of covid- patients prominent changes in blood coagulation of patients with sars-cov- infection european association of urology guidelines office rapid reaction group: an organisation-wide collaborative effort to adapt the european association of urology guidelines recommendationstothecoronavirusdisease era key: cord- -bmvazgj authors: trevisanuto, daniele; moschino, laura; doglioni, nicoletta; roehr, charles christoph; gervasi, maria teresa; baraldi, eugenio title: neonatal resuscitation where the mother has a suspected or confirmed novel coronavirus (sars-cov- ) infection: suggestion for a pragmatic action plan date: - - journal: neonatology doi: . / sha: doc_id: cord_uid: bmvazgj coronavirus disease (covid- ), caused by the novel sars-cov- virus, is rapidly spreading across the world. as the number of infections increases, those of infected pregnant women and children will rise as well. controversy exists whether covid- can be transmitted in utero and lead to disease in the newborn. as this chance cannot be ruled out, strict instructions for the management of mothers and newborn infants are mandatory. this perspective aims to be a practical support tool for the planning of delivery and neonatal resuscitation of infants born by mothers with suspected or confirmed covid- infection. the novel coronavirus-related infection has rapidly spread from wuhan (china) since december [ ] and was declared a pandemic on march , [ ] . initially defined as the -novel coronavirus ( -ncov) [ ] , on february , the pathogen has been officially named sars-cov- , and covid- (coronavirus disease ) its related disease [ ] . the main routes of transmission are via respiratory droplets or through direct contact ( - m) [ , ] . viral copies can be found in stools of positive patients, but the fecal-oral route transmission has not been confirmed [ , ] . in adults, the most frequent presentation at illness onset is characterized by fever, cough, myalgia, fatigue, and respiratory distress, but gastrointestinal symptoms may be present [ ] . of the entire population of confirmed co-vid- patients, children < years make up just . %, with about % of these being < year [ , ] , with rare deaths related to the disease in this population. urgent questions that need to be addressed promptly include whether pregnant women who have confirmed covid- infection are more likely to experience lifethreatening events, and whether sars-cov- could spread vertically and pose risks to the fetus and neonate [ , ] . perinatal transmission of the sars-associated coronavirus was excluded in a previous case series, where serial reverse transcriptase-polymerase chain reaction (rt-pcr) assays, viral cultures, and paired serologic titers were performed [ ] . based on current evidence based on relatively small studies, compared with sars and mers infections, sars-cov- appears to be less severe in pregnant women [ ] , and, similarly, not causing intrauterine transmission to the fetus [ , ] . this has been confirmed by two retrospective analyses of pregnant women with co-vid- , whose neonatal throat swabs tested negative [ , ] . among other samples collected in several retrospective studies (amniotic fluid, cord blood, placenta, breastmilk), none showed positive result for sars-cov- [ ] [ ] [ ] . as a consequence, sars-cov- seems to undergo transmission by droplets rather than intrauterine or transplacental transmission, but a word of caution is required due to the very limited available evidence [ , ] . neonatal cases appear to be milder and with better outcomes compared to adult ones [ , [ ] [ ] [ ] [ ] . although it is unlikely that neonates born from sars-cov- -infected mothers require an intensive care management related to the maternal infection [ , ] , coronaviruses may result in adverse outcomes for the fetus and infant (intrauterine growth restriction, preterm delivery, admission to the neonatal intensive care unit (nicu), spontaneous abortion and perinatal death) [ , , ] . international guidelines on resuscitation do not have the breadth to cover scenarios like the current covid- pandemic [ ] . in recent weeks, several recommendations on the care of pregnant women with suspected or confirmed covid- [ ] , management of delivery, admission and discharge of newborns to and from the nursery [ ] [ ] [ ] [ ] [ ] [ ] , and breastfeeding [ ] [ ] [ ] [ ] have been released. however, none of these has focused on the appropriate planning of neonatal resuscitation during delivery. some information on vertical transmission and infection control measures in neonatal units have been reported during the outbreak sars in southeast asia in [ , ] . this perspective aims to provide practical indications for the management of mothers and neonates before, during, and after delivery. in padua, we have implement-ed the described approach with positive feedback from healthcare professionals and parents, and with no newborns tested positive for sars-cov- . in padua, we have implemented an approach with positive feedback from healthcare professionals and parents, with no newborns testing positive for sars-cov- . where? from our experience, we suggest that regional plans aim at creating designated hub hospitals for pregnant covid- cases (fig. ) these can be organized for all the multidisciplinary needs. however, every hospital should be in the position to assist non-transferable pregnant women. a pre-triage area is mandatory, followed by separate paths for suspected and diagnosed cases, or non-covid- mothers. this approach requires two different delivery areas to be designated in all hospitals. at padua university hospital, triaging of patients is done in a tent mounted in front of the emergency department. in the obstetrical ward, we have identified one operating room (or) and labor/ delivery rooms (drs) exclusively dedicated to the care of women with suspected or confirmed covid- ; a dedicated path and a lift have also been dedicated to these patients. in the nicu, neonates with suspected infection are cared for in isolated areas (two single, negative-pressure rooms and one room equipped with six beds). examples of structural re-organization of a nicu have been previously described during an epidemic outbreak, but the model needs to be adapted to the local situation [ , ] . at least a dedicated dr and an or (possibly negativepressure rooms) should be arranged to manage mothers with suspected or confirmed covid- in every obstetric department. next to the dr, a room or area equipped with an infant warmer should be available. as an alternative, the infant warmer could be arranged in the dr, however > feet ( m) from the mother [ , , ] . preferably, screening of suspected or confirmed mothers should be done in a dedicated area before arrival to a labor and delivery unit. at padua university hospital, we have recently started to check all women admitted to the labor ward for sars-cov- infection because the lack of clinical symptoms does not rule out infection and transmission. how? team multidisciplinary management is mandatory, involving midwives, obstetricians, anesthesiologists, and neonatologists. simulation training, specific to managing suspected covid- cases, should be in place in every delivery suite. it is an important exercise during the acute phase, but ideally simulation training should be conducted on regular basis (for example, at least once a year) in all hospitals for preparing healthcare caregivers to provide care for patients infected with high-consequence pathogens [ ] . the contents of training include the centers for disease control and prevention (cdc) infection prevention and control procedures for healthcare providers, together with local requirements [ ] . a protocol focused on equipment and the correct use of personal protective equipment (ppe) including correct donning, doffing, and disposal of ppe should be provided [ ] . to minimize the need for ppe, the who recommends that respirators (i.e., n , ffp or equivalent standard) should be used for aerosol-generating procedures (e.g., tracheal intubation, noninvasive ventilation, tracheostomy, cardiopulmonary resuscitation, manual ventilation before intubation, bronchoscopy), while medical masks should be indicated for the other situations [ ] . however, the rational use for masks is still not codified and depends on country guidelines also at community level [ ] . the minimum number of health caregivers and minimum "contact time" between staff and patients for each specific scenario (i.e., vaginal delivery or cesarean section) should be planned. medical staff taking care of covid- -suspected or -positive women should wear protective clothing, n masks, goggles, and gloves before contact with the patients. at hospital admission, all women should wear a medical mask and should undergo a triage procedure that includes (i) history of tocc = travel, occupation, contact and clustering, (ii) clinical features e.g., fever, respiratory and/or gastrointestinal signs and symptoms, etc., and (iii) if possible, covid- rt-pcr test results. pregnant women with "influenza-like illness" (fever, cough, myalgia, sore throat, malaise) or history of contacts with persons suspected or confirmed covid- should be tested for sars-cov- infection at hospital admission. these patients and those with known covid- should wear a facemask and wait in a separate, well-ventilated waiting area at least feet from other people and should be isolated as soon as possible in an airborne infection isolation room, where possible. every dr should be arranged with all necessary equipment. a complete kit including the necessary ppe (mask with goggles/face-shield, gown, and gloves) for each team member should be available in dedicated envelopes in the delivery suite, as there is a potential need for aerosol-generating procedures (continuous positive airway pressure, intubation/extubation, deep suctioning, etc.) ( table ) . immediately, inform hospital infection office or authorities, as per local requirements. where? the laboring mother should be managed in an airborne infection isolation room until the delivery. preferably, the vaginal delivery would be assisted in the isolation room. in case of cesarean section, the woman with a face mask should be transferred to the or immediately before surgery, possibly through dedicated paths (i.e., possible dedicated corridors or passages, lifts, etc.) accompanied by staff wearing appropriate ppe [ ] . team a multidisciplinary approach including midwives, obstetricians, anesthesiologists, and neonatologists is recommended. covid- infection itself is not an indication for delivery, unless there is a need to improve maternal oxygenation. time and mode of delivery must be established on routine obstetrical indications. before the laboring woman's arrival in the dr or or, health caregivers should wear ppe (with n masks), because it is unknown if the neonate will need resuscitation maneuvers. the minimum number of providers should attend each procedure to reduce exposure and also to minimize the use of ppe, as materials would be in very short supply during an outbreak. for example, if neonatal resuscitation is expected, two team members should be considered. rescue personnel should be available for emergency and unattended situations in a room next to the delivery suit. also the "contact time" between staff and patients should be kept to a minimum. as person-to-person transmission of sars-cov- is thought to be due to respiratory droplets, skin-to-skin contact is not recommended, and maternal contacts should be avoided. vertical transmission from mother to fetus is currently uncertain, but available data suggest no evidence of this transmission mode [ , , ] . delayed cord clamping could still be performed as a standard of care, however by avoiding maternal skin contact [ ] . routine neonatal protocols will guide management of healthy newborns or of those in need of resuscitation. despite covid- infection alone not being an indication for changing established guidelines on neonatal resuscitation/stabilization [ ] , all aerosol-generating procedures (i.e., face-mask ventilation, tracheal intubation, non-invasive ventilation, continuous positive airway pressure) should be performed by using respirators, papr or n masks, eye protection, gloves, and gowns. disposable laryngoscopes should be preferred, and intubation by using a videolaryngoscope can be also considered in order to increase the distance between the provider and the neonate. despite limited evidence on their efficacy, viral filters on the expiratory limb of the ventilator circuit and closed suctioning systems could be also used, as reported in previous experiences [ , ] . the procedure should be performed by an expert provider. the multidisciplinary team must wear protective clothing, n masks, goggles, and gloves before contact with the patients and before mother's arrival in the delivery suite/operating theatre vaginal delivery assisted in the airborne isolation room or in the designated operating theatre if caesarean section consider general anesthesia for cs if mother with incipient respiratory insufficiency delayed cord clamping below the introitus or abdominal incision if no other contraindications skin-to-skin contact not recommended neonatal stabilization/resuscitation steps as usually indicated after delivery all ppe should be removed and put in plastic bags cleaning and disinfection of delivery room/operating theatre and equipment manage mother in an isolated room in the post-partum period care for the baby in an incubator possibly > feet ( m) from mother or in a different room or, if intensive care needed, put the infant in an incubator in an isolated room in the unit staff managing mother and baby should always wear ppe and be tested for sars-cov- (nasal and oropharyngeal swabs) every - weeks send maternal specimens for sars-cov- testing (placenta, amniotic fluid) test the baby for sars-cov- (nasal and oropharyngeal swabs) h after delivery consider expressed breast milk healthy neonates with two negative sars-cov- tests h apart should be discharged to their mother with contact and droplet precautions until mother has two negative sars-cov- monitor mother, baby, and family with a strict follow-up cols. for cesarean sections, general anesthesia should be considered in women developing severe respiratory insufficiency [ , ] . mask with goggles/face-shield, gown, and gloves must be worn by all the providers in the room where mother and baby are cared for. documentation is based on local maternal and neonatal charts. where? after birth, the dr or the or should be immediately cleaned and disinfected and made available for further patients. the procedure should be done according to local protocols. all the equipment (i.e., tubing, masks, laryngoscope) should be disposed or sterilized. the mother should be managed in an isolated room during the post-partum period. the baby can be cared for in the mother's room in a closed incubator at possibly > feet ( m) from the mother or in a closed incubator in a different room [ , , ] . benefits and risks of this decision will depend on logistical situations and medical decisions and will be discussed with parents. in the nicu, the baby should be cared for in an incubator in a single room. team at the end of the procedure, healthcare providers should remove the ppe that should be put in plastic bags and disposed of. staff managing the mother and the baby should wear ppe and should be tested for sars-cov- infection by nasal and oropharyngeal swabs every week for - weeks. as asymptomatic subjects are potentially contagious, in our nicu, nasal and oropharyngeal swabs are collected every week in all parents and medical staff. this "universal" approach has been adopted mainly for an epidemiological purpose and cannot be considered as standard of care. the mother should wear the face mask and should be managed based on routine local protocols. sick preterm and full-term infants should be admitted to the nicu and possibly managed by a limited number of healthcare providers exclusively dedicated to the care of these patients. at university hospital of padua, sick preterm and term infants born to mothers testing positive for sars-cov- are kept isolated in a dedicated area of the nicu ("quarantine zone"), where parents are not allowed, and physicians and nurses have to wear ppe according to cdc guidelines [ ] . in addition, nasal and oropharyngeal swabs are collected at h of life from those infants born from suspected or confirmed mothers whose swab result for sars-cov- is still pending. to reduce footfall within the unit and to relieve parental anxiety, video visits are strongly supported during hospital stay and after discharge [ ] . since it is not yet known whether sars-cov- can be transmitted through breast milk, only pasteurized human breast milk (donor or maternal) or formula milk is used for feeding preterm infants admitted to our nicu. considering that certain viruses (like cmv and hsv) can be transmitted through this route [ ] , we opted for a cautious approach. however, italian guidelines recommend using fresh expressed breast milk with no need to pasteurize it [ ] . healthy neonates with two negative nasal swabs h apart should be discharged to be with their mother. families need to receive clear information on specific precautions regarding contact and droplets, to be strictly followed until the mother has two negative sars-cov- tests. all test for sars-cov- in breastmilk were negative in mothers reported by chen et al. [ ] ; however, there is currently insufficient evidence regarding the safety of breastfeeding and the need for mother-baby separation. although many scientific institutions and societies support breastfeeding [ ] [ ] [ ] [ ] , caution may still be required. the optimal mode of infant feeding (breastfeeding, expressed breast milk given by the mother or healthcare giver, formula) should be considered by the mother in coordination with the healthcare team. a mask with goggles/face-shield, gown, and gloves must be worn by all the providers in the room where mother and baby are cared for. specimens for sars-cov- testing (placenta, amniotic fluid, umbilical cord blood) should be collected from suspected or confirmed mothers, analyzed, and stored neonatology doi: . / [ ] . mother, neonate, and family should be monitored with a strict follow-up. national and international perinatal registers for infants exposed to or suffering from covid- are currently being implemented. current recommendations on the management of suspected or confirmed covid- mothers and their infants are based on limited and incomplete data, requiring continuous and comprehensive updates. although evidence is still very limited, every effort should be done to ensure healthcare providers' safety that is of paramount importance to continue offering the best care possible to mother and child. our designated approach for the management of women with suspected or confirmed co-vid- and their infants before, during, and after delivery provides cues to reduce the chance of neonatal infection and therefore potential negative outcomes in the newborn. the authors have no potential conflicts of interest to disclose. none. prof. trevisanuto contributed to the study concept, study design, and writing of the manuscript and critically reviewed the manuscript. dr. moschino wrote the initial draft, revised the literature, and approved the final manuscript as submitted. dr. doglioni contributed to writing the draft, revised the literature, and approved the final manuscript as submitted. prof. roehr contributed to literature revision, provided relevant expertise, and critically reviewed the manuscript. dr. gervasi contributed to designing the study, collection of information, and critically reviewed the manuscript. prof. baraldi contributed to literature revision, provided relevant expertise, and critically reviewed the manuscript. all authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work. a novel coronavirus from patients with pneumonia in china who director-general's opening remarks at the media briefing on covid- situation report- naming the coronavirus disease (covid- ) and the virus that causes it. technical guidance center for disease control and prevention. interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease (covid- ) in healthcare settings. early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes covid- : gastrointestinal manifestations and potential fecaloral transmission sars-cov- infection in children: transmission dynamics and clinical characteristics characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention chinese pediatric novel coronavirus study team. sars-cov- infection in children the transmission and diagnosis of novel coronavirus infection disease (covid- ): a chinese perspective pregnancy and perinatal outcomes of women with severe acute respiratory syndrome infants born to mothers with severe acute respiratory syndrome. pediatrics coronavirus in pregnancy and delivery: rapid review ultrasound obstet gynecol an analysis of pregnant women with covid- , their newborn infants, and maternal-fetal transmission of sars-cov- : maternal coronavirus infections and pregnancy outcomes potential maternal and infant outcomes from (wuhan) coronavirus -ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections. viruses clinical characteristics and intrauterine vertical transmission potential of co-vid- infection in nine pregnant women: a retrospective review of medical records. lancet clinical analysis of neonates born to mothers with -ncov pneumonia neonatal early-onset infection with sars-cov- in neonates born to mothers with covid- in wuhan, china possible vertical transmission of sars-cov- from an infected mother to her newborn a case report of neonatal covid- infection in china neonati ricoverati con infezione sospetta o accertata da sars-cov- . sininforma european resuscitation council guidelines for resuscitation : section . resuscitation and support of transition of babies at birth. resuscitation coronavirus disease (covid- ) and pregnancy: what obstetricians need to know national clinical research center for child health and disorders and pediatric committee of medical association of chinese people's liberation army. a contingency plan for the management of the novel coronavirus outbreak in neonatal intensive care units chinese expert consensus on the perinatal and neonatal management for the prevention and control of the novel coronavirus infection medical association of chinese people's liberation army; editorial committee of chinese journal of contemporary pediatrics [emergency response plan for the neonatal intensive care unit during epidemic of prise en charge aux urgencies maternite d'une patiente enceinte suspectee ou infectee par le coronavirus coronavirus disease (co-vid- ) and neonate: what neonatologist need to know clinical management of severe acute respiratory infections (sari) when covid- disease is suspected. interim guidance. geneva: who british association of perinatal medicine resource page on covid- resource page on covid- covid- ): what parents should know center for disease control and prevention. pregnancy & breastfeeding. information about coronavirus disease infection control for sars in a tertiary neonatal centre infection control for sars in a tertiary paediatric centre in hong kong neonatal resuscitation and post-resuscitation care of infants born to mothers with suspected or confirmed sars-cov- infection simulation of a spontaneous vaginal delivery and neonatal resuscitation in a biocontainment unit. health secur world health organization. rational use of personal protective equipment for coronavirus disease (covid- ). interim guidance rational use of face masks in the co-vid- pandemic consensus statement: safe airway society principles of airway management and tracheal intubation specific to the covid- adult patient group information for healthcare professionals. version isuog interim guidance on novel coronavirus infection during pregnancy and puerperium: information for healthcare professionals ultrasound obstet gynecol short-term pasteurization of breast milk to prevent postnatal cytomegalovirus transmission in very preterm infants breastfeeding and coronavirus disease- . ad interim indications of the italian society of neonatology endorsed by the union of european neonatal & perinatal societies. matern child nutr covid- : indicazioni per gravida-partoriente, puerpera, neonato e allattamento key: cord- -ffh jl authors: guery, b; alfandari, s; leroy, o; georges, h; d’escrivan, t; kipnis, e; mouton, y; yazdanpanah, y title: syndrome respiratoire aigu sévère date: - - journal: médecine et maladies infectieuses doi: . /s - x( ) - sha: doc_id: cord_uid: ffh jl résumé le syndrome respiratoire aigu sévère (severe acute respiratory syndrome, sars) est apparu à l’automne dans la province de guangdong en chine. l’épidémie s’est rapidement propagée à travers le monde pour toucher, courant avril, plus de pays avec un total de cas à cette même date proche de cas. la symptomatologie associe des formes modérées se manifestant par une fièvre, une hypoxie, avec des formes de gravité majeure responsables de syndrome de détresse aigue nécessitant l’hospitalisation en unité de réanimation. des formes digestives ont aussi récemment été décrites. cette épidémie a suscité une réponse extrêmement rapide de la communauté internationale qui en quelques semaines a permis d’isoler l’agent responsable, un nouveau coronavirus, de proposer une prise en charge thérapeutique et des mesures spécifiques pour limiter la diffusion de l’épidémie. cette revue rassemble l’ensemble des données actuellement disponibles sur le sars, de l’histoire de l’épidémie aux propositions thérapeutiques disponibles en date d’avril . abstract in the fall of a report from guangdong province in china showed the occurrence of an outbreak of atypical pneumonia. this outbreak rapidly progressed from china to hong kong, singapore, toronto, and the usa, to more than countries worldwide and almost cases to date in april . the clinical features associate a fever with mild respiratory symptoms which can progress to a typical acute respiratory distress syndrome requiring intensive care unit admission. enteric forms with diarrhea were recently described in hong kong. the medical community responded very rapidly and united in front of this major health crisis. in a couple weeks, the agent, a new coronavirus was isolated, therapeutic guidelines were proposed and measures to limit the outbreak diffusion were started worldwide. we summarize here the history of the outbreak, the clinical, laboratory and radiological features of sars. april therapeutic guidelines are also reported. de novembre à février , dans la province de guangdong (sud de la chine), cas de pneumonies étaient signalés. cette pathologie hautement contagieuse, responsable d'une symptomatologie aspécifique qui la rapprochait des pneumonies dites à germes atypiques, était initialement attribuée à chlamydia pneumoniae. cet agent pathogène était écarté rapidement mais la responsabilité d'un nouveau coronavirus n'a été que récemment évoquée. fin février, une épidémie de pneumonie touchait hanoi et hong kong. la relation avec l'épidémie de guangdong n'a été officialisée que le mars. l'épidémie s'est étendue rapidement, justifiant, le mars , la publication d'une alerte mondiale par l'organisation mondiale de la santé (oms) [ ] . l'oms a proposé l'acronyme « sars » (pour severe acute respiratory syndrome) et des critères de définition des cas le mars [ ] . l'épidémie s'est propagée rapidement se propager dans le monde à partir de ce foyer initial chinois. À la date du avril , cas ont été déclarés au sein de pays, les sites les plus touchés étant la chine, hong kong, singapour, le canada et les États-unis. l'agent responsable du sars se devait de répondre au postulat de koch : • agent présent chez tous les individus présentant la pathologie ; • agent pouvant être cultivé ; • agent qui lorsque qu'il est introduit chez l'hôte, ou dans un modèle s'en rapprochant, induit le développement de la pathologie ; • possibilité de ré-isoler l'agent à partir d'un animal présentant la pathologie. les quelques semaines d'enquête aboutissant à l'identification et la caractérisation d'une nouvelle espèce de coronavirus ont été l'occasion d'une collaboration intense de plusieurs équipes de différents pays. la rapidité de l'obtention de résultats est exceptionnelle si l'on se souvient des années nécessaires avant l'identification du vih. plusieurs hypothèses ont été examinées par la communauté scientifique. c. pneumoniae, évoqué à guangdong a été rapidement éliminé. l'hypothèse suivante était celle d'une nouvelle grippe résultant de la recombinaison d'un virus humain à un virus aviaire. cette hypothèse était étayée par la survenue de cas, mortels, de grippe aviaire à hong kong le février. cela a conduit à préconiser dans la première partie de l'épidémie un traitement et des recommandations de prévention dirigées contre ce pathogène (essentiellement administration d'oseltamivir [ ] . deux éléments notables sont évoqués dans cette publication, tout d'abord le fait que seuls les patients atteints de sars ont des anticorps témoignant du fait que ce virus circule pour la première fois. d'autre part, ce coronavirus présente une particularité comparé aux autres coronavirus: c'est le seul coronavirus humain capable de se répliquer sur des cultures de cellules vero [ ] . À noter que cette faculté existe chez un coronavirus porcin entraînant des pathologies respiratoires mais, aucun lien de parenté entre ces deux virus n'a été mis en évidence. cela témoigne de la même manière du caractère émergent de ce virus. de l'ensemble de ces données, seul le coronavirus remplit les quatre conditions dictées par les postulats de koch. À ce jour, la responsabilité du coronavirus est admise par la communauté scientifique. les coronavirus sont des virus de taille modérée ( - nm), de forme arrondie contenant un arn monocaténaire ; la présence de projections membranaires à la surface du virus en forme de couronne est à l'origine de sa dénomination. il existe deux sérotypes connus de coronarovirus humain ; -e et oc . ce groupe de pathogène est responsable chez l'homme de pathologies respiratoires habituellement bénignes comme le rhume, le coronavirus est retrouvé avec une incidence de à / personnesannées [ ] . des pics saisonniers sont classiques en hiver et au printemps. le coronavirus a aussi été impliqué dans des symptomatologies respiratoires plus sévères dans un cadre nosocomial chez le nouveau né [ , ] , et chez l'adulte. une pneumonie à coronavirus a été rapportée au décours d'une greffe de moelle [ ] . ce virus est relativement résistant au milieu extérieur pouvant survivre jours en suspension et près de heures sur des surfaces sèches inertes suggérant une fois encore un autre mode potentiel de contamination. les données obtenues chez l'animal permettent de compléter le spectre clinique potentiel des coronavirus. le coronavirus bovin est associé à une symptomatologie digestive majeure à type de diarrhée [ ] . le coronavirus félin est associé à une forme parfois fatale de péritonite du chat [ ] . le virus de l'hépatite de la souris induit des formes d'hépatites fulminantes associées à des atteintes du système nerveux central (démyélinisation) [ ] . le coronavirus associé au sars donne, pour l'instant, une symptomatologie essentiellement respiratoire. des formes a prédominance digestives ont été récemment identifiées à hong kong. les données animales nous incitent dans ce contexte épidémique à ne pas négliger la possibilité de voir apparaître par analogie des formes hépatiques, neurologiques ou à type de péritonites. l'analyse des données de l'épidémie peut permettre en plus des renseignements déjà connus sur les coronavirus d'évaluer le mode de transmission de ce pathogène. le mode de transmission prédominant dans la phase initiale de l'épidémie semble être la voie respiratoire avec une transmission de type « gouttelettes ». cela est étayé par les charges virales élevées au niveau des sécrétions respiratoires montrées par drosten [ ] . même si l'aérosolisation semble prépondérante, on ne peut, à ce jour, éliminer une transmission aérienne (virus de petite taille avec une survie importante). cette hypothèse semble cependant peu probable si on compare l'épidémie de sars aux données connues sur la grippe, maladies hautement contagieuse. le virus influenza peut entraîner une maladie après inhalation de seulement trois virions. hors, quand influenza a est introduit dans une famille, à % des contacts vont présenter une infection (clinique ou séroconversion) [ ] . de même, une nouvelle souche d'influenza introduite sur un bateau induit une maladie chez % des membres d'équipage. enfin, un passager malade à bord d'un avion dont le système de ventilation reste défectueux pendant heures entraîne le développement d'une symptomatologie chez % des autres passagers dans les jours suivants [ , ] . dans le cas du sars, les premières analyses montrent que la contamination nécessite un contact prolongé et répété avec un malade présentant une symptomatologie pulmonaire. cela est étayé par les explorations préliminaires de poutanen et tsang, ainsi que celles de l'oms et du cdc [ , ] . tous les patients ont eu un contact avec un sujet atteint. pour certains cas, le lien démontré est cependant ténu : dans le travail de poutanen et al., le patient est contaminé lors de son passage dans l'hôtel a en même temps que le patient index de hong kong qui séjournait au même étage [ ] . mais, le patient était à un étage différent des patients et et du cas index, et n'a pas décrit de contact avec les trois autres cas. pour ce patient, l'hypothèse d'un contact prolongé et répété semble discutable. on pourrait envisager soit une contamination ailleurs qu'à l'hôtel, soit un patient source « super disséminateur », mais, si tel est le cas, on reste cependant étonné du peu de cas initiaux observés dans cet hôtel. enfin, l'existence de formes modérées voire asymptomatiques de la maladie permettrait d'expliquer ces dissensions, en effet, ne disposant pas de moyens diagnostiques fins en routine, seules les formes symptomatiques et sévères sont dépistées. une très grande proportion des cas initiaux de sars survenait chez du personnel soignant, facteur là encore en faveur d'un contact rapproché et prolongé. dans l'étude de lee, sur patients étudiés, étaient des cas secondaires et des cas tertiaires [ ] . les patients se répartissaient en soignants, étudiants et patients hospitalisés dans la même unité. les études animales ont montré une possibilité d'excrétion de coronavirus dans les fécès [ ] . peiris et al. ont montré la présente d'arn du coronavirus responsable du sars dans les selles des patients [ ] . À hong kong, personnes ont été contaminées au sein d'un même immeuble (cluster amoy garden) dont % résidant dans le même bloc. sur ces patients % ont présenté une diarrhée (contre à % dans les tableaux décrits habituellement). la contamination a ici été attribuée à un patient souffrant de diarrhée qui a en raison d'un système d'évacuation défectueux de l'immeuble associé à la mise en route de la ventilation mécanique des salles de bain permis la pénétration de gouttelettes contaminées sur les surfaces des appartements. ce rapport n'est actuellement pas totalement élucidé mais plaide en faveur d'une contamination orofécale, la modification de la symptomatologie (diarrhée à %) conforte cette hypothèse. tout cas possible présentant des signes de pneumopathie à la radiographie ou au scanner pulmonaire tout cas possible pour lesquels les quatre critères suivants sont remplis : • bon état clinique ; • absence d'atteinte à la radiographie ou au scanner pulmonaire lors du suivi ; • absence de lymphopénie ; • absence de contact avec un cas probable. la période d'incubation peut varier de à jours avec une moyenne à jours. la description symptomatique la plus relevante est actuellement issue du centre hong kong qui a rapporté les signes cliniques de patients hospitalisés pour sars [ ] . les principales caractéristiques sont résumées dans le tableau . on notera que dans la forme du cluster amoy garden précédemment décrite, la diarrhée est présente chez % des patients. on observe habituellement une leucopénie (< , l - ) et une lymphopénie ( , % dans la série de lee et al) [ ] . une thrombopénie ( mm - ) a été documentée chez , % des patients de cette série. un allongement du tca avec tp normal était observé dans , % des cas. les données biochimiques montraient une élévation des asat ( , %), des cpk ( , %), et des ldh ( %). la radiographie de thorax montrait des images aspécifiques [ ] : , % des patients présentaient une anomalie radiologique à type de condensation qui était focale et unilatérale dans , % des cas. en cas d'aggravation du patient les images s'aggravaient en à jours après l'admission. des images comparables avec un sdra ont ainsi été observées. dans le cas où la radiographie standard de thorax était peu contributive, un examen tomodensitométrique a été pratiqué. des aspects en verre dépoli essentiellement périphériques ont été retrouvés. l'aspect pouvait être dans certains cas comparable avec une bronchiolite oblitérante. les examens autopsiques ont permis de retrouver différents types de lésions : • un oedème alvéolaire avec des lésions focales hémorragiques et des formations de membranes hyalines [ , ] ; • une desquamation des pneumocytes [ ] qui pouvaient aussi être vacuolés et multinucléés [ ] ; • peu de cellules inflammatoires et une réaction fibroblastique. les septas interalvéolaires étaient épaissis, aucune nécrose n'a été remarquée [ ] ; • des lésions non spécifiques de sdra avec un infiltrat interstitiel et alvéolaire de cellules mononuclées évoquant une étiologie virale [ , ] . l'étude de hong kong sur sars a permis d'individualiser trois facteurs associés à un pronostic défavorable : • âge : odds ratio/décade : , ; ic % : , - , ; p = , ; • taux élevé de ldh : odds ratio/ u : , ; ic % : , - , ; p = , ; • taux élevé de neutrophiles à l'admission : odds ratio : , ; ic % : , - , ; p = , . sur l'ensemble des sars diagnostiqués selon la définition actuelle, le pourcentage de patients nécessitant la réanimation s'élève à %, la mortalité globale est proche de %. après élimination d'une pathologie respiratoire communautaire banale justifiant la prescription empirique d'une antibiothérapie, la prise en charge repose actuellement sur l'association ribavirine-corticoides. la ribavirine est un analogue nucléosidique qui induit une mutation létale de l'arn viral. il faut toutefois souligner qu'à ce jour, en l'absence d'indicateurs cliniques, il n'a pas été possible de clairement prouver l'efficacité de la ribavirine avec ou sans corticoides d'accompagnement. l'oms a proposé de mettre au point une approche multicentrique et coordonnée pour étudier l'efficacité du traitement par la ribavirine. tout cas possible ou probable doit être hospitalisé en isolement dans un service spécialisé en maladies infectieuses pour traitement et observation. l'hospitalisation est faite prioritairement dans les hôpitaux référents et en cas d'impossibilité vers le service d'infectiologie du chu le plus proche. les dernières recommandations de prise en charge émanent de toronto (greater toronto area sars working group) en date du avril : • ribavirine mg iv/ h pendant jours puis mg po/ h pendant jours ; • solumedrol mg iv/ h pendant jours puis prednisone mg po pendant jours. les doses de ribavirine sont inférieures aux doses initialement préconisées en raison des bons résultats obtenus à hong kong avec ces doses (meilleur rapport efficacité/toxicité). les doses initiales dérivaient des protocoles utilisés dans les fièvres hémorragiques [ ] . si la ribavirine doit être arrétée pour toxicité, les corticoïdes peuvent être poursuivis seuls. en cas d'aggravation, des bolus de solumedrol ( mg iv pendant jours) sont recommandés. • amélioration des modifications de la radiographie thoracique. • apyrexie pendant jours ; • sevrage de l'oxygène ; • amélioration de la radiologie de plus de % ; • un temps d'hospitalisation d'au moins semaines. • une fois le traitement terminé, le patient doit être surveillé pendant jours ce qui implique donc un temps d'hospitalisation minimum de jours ; • un patient peut être autorisé à sortir s'il est apyrétique depuis au moins jours. le sars est une pathologie émergente liée au coronavirus. la vitesse de réaction de la communauté internationale a permis dans un temps record d'identifier la pathologie, d'individualiser le pathogène responsable, de générer des publications permettant à la communauté médicale d'optimiser la prise en charge de cette pathologie. en mois une avancée majeure a été réalisée dans la connaissance de cette maladie. il demeure cependant un grand nombre de questions à résoudre : • y a-t-il des porteurs sains ? • À quel moment de la maladie l'excrétion virale et le au vu de la vitesse d'évolution des connaissances, elles seront probablement obsolètes à la date de sa parution. outbreak of severe acute respiratory syndrome-worldwide preliminary clinical description of severe acute respiratory syndrome identification of severe acute respiratory syndrome in canada coronavirus as a possible cause of severe acute respiratory syndrome identification of a novel coronavirus in patients with severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome propagation of the virus of porcine epidemic diarrhea in cell culture respiratory viral infections in the elderly nosocomial infections due to human coronaviruses in the newborn neonatal nosocomial respiratory infection with coronavirus: a prospective study in a neonatal intensive care unit coronavirus pneumonia following autologous bone marrow transplantation for breast cancer detection of bovine coronaviruses from adult cows with epizootic diarrhea and their antigenic and biological diversities pathogenesis of coronavirus-induced infections. review of pathological and immunological aspects mouse hepatitis virus how contagious are common respiratory tract infections? an outbreak of influenza aboard a commercial airliner outbreak of influenza in highly vaccinated crew of u.s. navy ship a cluster of cases of severe acute respiratory syndrome in hong kong a major outbreak of severe acute respiratory syndrome in hong kong fecal shedding of feline coronavirus in adult cats and kittens in an abyssinian cattery hemorrhagic fever viruses as biological weapons: medical and public health management key: cord- - x yubt authors: sawmya, shashata; saha, arpita; tasnim, sadia; anjum, naser; toufikuzzaman, md.; rafid, ali haisam muhammad; rahman, mohammad saifur; rahman, m. sohel title: analyzing hcov genome sequences: applying machine intelligence and beyond date: - - journal: biorxiv doi: . / . . . sha: doc_id: cord_uid: x yubt covid- pandemic, caused by the sars-cov- strain of coronavirus, has affected millions of people all over the world and taken thousands of lives. it is of utmost importance that the character of this deadly virus be studied and its nature be analysed. we present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. in a nutshell, we have prepared an analysis pipeline for hcov genome sequences leveraging the power of machine intelligence and uncovered what remained apparently shrouded by raw data. covid- was declared a global health pandemic on march , [ ] . it is the biggest public health concern of this century [ ] . it has already surpassed the previous two outbreaks due to the coronavirus, namely, severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov). the virus acting behind this epidemic is known as severe acute respiratory syndrome coronavirus or in short sars-cov- virus. it is a single stranded rna virus which is mainly , to , bases long in average [ ] . the novel coronavirus is spherical in shape and has spike protein protruding from its surface. these spikes assimilate into human cells, then undergo a structural change that allows the viral membrane to fuse with the cell membrane. the host cell is then attacked by the viral gene through intrusion and it copies itself within the host cell, producing multiple new viruses [ ] . as of mid-april, , about , of high-quality complete genome sequences were present in the gisaid initiative database [ ] collected from clinicians and researchers from around the world. to understand the viral evolution and its nature of spread among the different countries, we present an analysis pipeline of the genome sequence leveraging the power of machine intelligence. this paper makes the following key contributions. a. an alignment-free phylogenetic analysis is carried out with a goal to uncover the evolutionary history of sars-cov- . the resulting phylogenetic tree is able to highlight evolutionary relationships that can be explained by facts and figures and has further identified some mysterious relationships. b. several machine learning and deep learning models are used to identify the virulence of the strains (i.e., to classify a virus strain as either severe or mild). additionally, from the classification pipeline, important features are identified as sites of interest (sois) in the virus strains for further analysis. c. several cnn-rnn based models are used to predict mutations at specific sites of interest (sois) of the sars-cov- genome sequence followed by further analyses of the same on several south-asian countries. d. overall, we present an analysis pipeline that can be further utilized as well as extended and revised (a) to study where a newly discovered genome sequence lies in relation to its predecessors in different regions of the world; (b) to analyse its virulence with respect to the number of deaths its predecessors have caused in their respective countries and (c) to analyse the mutation at specific important sites of the viral genome. figure : the whole analysis pipeline consisted of three phases. in the first phase, the genome sequences are divided into subsets based on country and a phylogenetic tree is constructed considering only the "representative" sequences of each such subset using an alignment-free sequence comparison approach. in the second phase, we employed state of the art classification algorithms, leveraging both traditional and deep learning pipelines to learn to discriminate the viral strains of many countries as either mild or severe. we also identify the features that contributed the most as the discriminant factor in the classification pipeline. finally, we use the identified features from the previous stare to predict the mutation of the interesting sites in the viral strain using a deep learning model. figure presents our overall analysis pipeline. below we present the details of the pipeline. we have collected hcov genome sequences upto the date april, (cut-off date) from the gisaid initiative dataset [ ] . these are high quality complete viral genome sequences submitted by the scientists and scientific institutes of individual countries. we also have collected country wise death statistics (upto cut-off date) from the official site of who [ ] . the label was assigned based on a threshold of deaths which is the estimated median of the number of deaths in the data points. any genome sequence of a country having deaths below (above) the threshold were considered a mild (severe) strain, i.e., assigned a label ( ). a sample labelling is shown in the supplementary table . informatively, we have also considered some other metrics for labeling purposes albeit with unsatisfactory output (please see supplementary file for details) . we divided the whole dataset into training and testing subset in / ratio with a balanced number of data points per class for traditional machine learning pipeline and for deep learning classification routine, we created the subsets training/validation/testing in / / ratio. figure : the viral genome sequences were divided into subsets of sequences based on country. for each subset, each viral genome sequence is converted into a vector representation and pairwise euclidean distance was calculated among the vectors to create the distance matrix. as the matrix is very highdimensional, we used principal component analysis to find the principal component matrix from the distance matrix. representative sequences were identified through k-means clustering on the pca matrix, and a phylogenetic tree was constructed from the representative sequence of each country. we aim to identify and interpret the evolutionary relationships among the hcov genome sequences uploaded at gisaid from different regions around the globe ( figure ). to do that we have used an alignment-free genome sequence comparison method as proposed in [ ] as briefly described below. notably, we do not consider any alignmentbased method since it is not computationally feasible for us to align thousands of viral sequences for analysis and clustering purposes [ ] . at first the sequence set is divided into subsets of sequences based on the location. all sequences are converted into representative ℝ vector. pairwise distance among vectors derived from the fast vector method [ ] are computed using euclidean distance. due to the high dimensionality of the resulting distance matrix, we resort to principal component analysis (pca) technique [ ] to reduce the dimension of the matrix. subsequently, we use k-means clustering [ ] to identify the corresponding cluster centers. for the k-means clustering algorithm, we have used the implementation of [ ] and used the default parameters except for the number of clusters which were set to for determining the cluster center for each of the subsets. for each location-based cluster, the representative sequence (i.e., the "centroid" of the cluster) is then identified and used in the subsequent step of the pipeline. the evolutionary relationship among the representative sequences of different clusters (from section . ) has been estimated by constructing a phylogenetic tree. we have used the neighbor joining algorithm [ ] for phylogenetic tree construction since it is more reliable [ ] . we have used euclidean distance among the vectors, as described in the section . , to prepare the distance matrix. while we predominantly have used the alignment-free method of [ ] , in this stage, we have only representative sequences and hence we have also attempted a few other alignment-free and alignment-based methods to estimate the phylogenetic tree; however, these didn't produce satisfactory results (more details are in supplementary file). for traditional machine learning, we use a pipeline similar to [ ] (see figure in supplementary file). we extracted three types of features from the genomic sequence of novel sars-cov- . inspired by the recent works [ ] [ ] [ ] [ ] that focus only on sequences, we also extract only sequence-based features. these features are: position independent features, n-gapped dinucleotides and position specific features (see details in section of supplementary file). we use the gini value of the extremely randomized tree (extra tree) classifier [ ] to rank the features. subsequently, only the features with gini value greater than the mean of the gini values are selected for training a lightgbm classifier model [ ] (with default parameters) and performed -fold cross validation. lightgbm is a highly efficient and fast gradient boosting framework which uses tree-based algorithms. we use shap values and univariate feature selection to compare the importance of the features. shap (shapley additive explanations) is a game theoretic approach which is used to explain the output of a model [ ] . univariate feature selection works by selecting the best features based on univariate statistical tests [ ] . we use selectkbest univariate feature selection to get the top k highest scoring features according to anova f_classif feature scoring [ ] function. we leverage the power of different deep learning (dl) classification models, namely, vanilla cnn [ ] , alexnet [ ] and inceptionnet [ ] . we transform the raw viral genome sequences into two different representations, namely, k-mers spectral representation [ ] and one hot vectorization [ ] to feed those into the dl networks in a seamless manner. details of these representations are given in section . of the supplementary file. for k-mers spectral representation we experimented with different values of k (k = , , for vanila cnn and k = & only for the rest due to resource limitation). for one hot vectorization, we have trained inceptionnet for epochs for both -and -mers and trained alexnet for , and epochs for -, -and -mers respectively. we design a pipeline to predict mutation on specific sites (chosen in an earlier stage of the pipeline) in the sars-cov- genome (figure ). we follow a similar protocol followed by [ ] and adopt it to fit our setting as follows. we divide all the available countries and the states of the usa into different time-steps by the date of the first reported incidence of sars-cov- infected patients of that location. thus, every resulting time-step represents a date (tk for cluster k) and contains the clusters of genome sequences of the countries/states. then the time series samples are generated by concatenating sites from different time-step one-by-one that represent the evolutionary path of the sars-cov- viral strain. for example, t is the very first date when the virus is discovered in china. so, the time-step contains only one country, china. likewise, time-step t contains clusters for those countries where the virus is discovered on date t and so on. (check table in supplementary file for more details). we generate time series sequences by concatenating genome sites from t ,t ,....,tn (in our case, n = ) and then fed the samples to the model which consists of a convolutional one dimensional layer and a recurrent neural network layer [ ] . we experiment with both pure lstm and bidirectional lstm as our rnn layer (see section . of supplementary file). the model has a dense layer of neurons in the end which predicts the probability of the next base pair of the next time-step. so, in a nut-shell the model takes concatenated genome sequences from t ,t ,....,tn- as input and predicts the mutation for time tn. we further use our mutation prediction pipeline to identify and analyze possible parents of a mutated strain. for this particular analysis, we trained the models specifically for some south-asian countries, namely, bangladesh, india and pakistan. we only used the best performing model for this analysis and generated five time series samples. at the time of generating these samples, the country/location having the minimal euclidean distance was taken for each time-step. we have implemented our experiments mostly in python. we have used scikit-learn library [ ] for clustering and plotting the graphs. for deep learning models, scikit-learn, tensorflow and keras neural network libraries are used and for lightgbm classifier, python lightgbm framework has been used. the phylogenetic trees are constructed using the dendropy library of python [ ] keeping default parameters. we use the tree visualizer tools dendroscope [ ] and evolview [ ] for tree visualization and annotation. the experiments have been conducted in the following machines: a) clustering and phylogenetic analyses have been carried out in a machine with intel(r) core (tm) i - u cpu @ . ghz, ubuntu . os and gb ram. b) experiments involving the deep learning pipelines (i.e., both classification and mutation prediction) have been conducted in the work-stations of galileo cloud computing platform [ ] and the default gpu provided by the google colaboratory cloud computing platform [ ] . c) the lightgbm classifier model was trained in a machine with intel core i - u cpu @ . ghz x , windows os and gb ram. all the codes and data (except for the genome sequences) of our pipeline can be found at the following link: https://github.com/pythonloader/analyzing-hcov-genome-sequence. the genome sequence data have been extracted from and are publicly available at gisaid [ ] . we identify the representative sequence of each of the countries as present in the gisaid dataset (upto cut-off date). the estimated phylogenetic tree constructed from the representative sequences is shown in figure . in what follows, we will be referring to this tree as the sc (sars-cov- ) tree. the phylogenetic tree generated is expected to reveal the evolutionary relationship of the viral strains. however, with careful scrutiny we have some apparently unusual but interesting observations. for example, it is generally expected that the countries sharing (open) borders (e.g., countries in europe) should be either neighbours or at least in the same clade in the tree. however, surprisingly from the tree, we do not notice geographically adjacent countries in europe as neighbors; rather we see for example that china and italy are immediate neighbors. it is to be noted that these two countries are also the first countries to get hit by the first pandemic wave. in addition to that, although the usa and canada share the longest un-militarized international border in the world, representative strains do not appear to be sister branches as they should have been. also, we notice that the usa, uk, canada, turkey and russia are in the same clade which have a higher number of deaths than most of the other countries. all our classifiers are trained to learn whether a given strain is mild or severe. the classification accuracy of the lightgbm classifier (~ %) is superior to that of the deep learning classifiers (~ - %), which, while is somewhat surprising, is in line with the recent findings of [ ] . it should be noted that lightgbm had produced better results in significantly less time than deep learning models for this dataset. the results of the classifier models are shown in figure . quantitative results aside, we also have applied our classifiers on the sequences that have been deposited at gisaid after the cut-off date (i.e. april , ). since the cutoff date, the country wise death statistics [ ] has certainly changed significantly and this has pushed a few countries, particularly from asian regions and several states of the united states of america transition from mild to severe state (based on our predefined threshold). interesting, our classifiers have been able to predict the severity of the new strains submitted from these countries/states correctly. table in the supplementary file shows a snapshot of a few such countries/states with the relevant information. we preliminarily identify the top features of shap and selectkbest feature selection (with k= ). from these features, as sois, we have selected the features that are also biologically significant, i.e., cover different significant gene expression regions ( figure ). in particular, we have selected the position specific features pos_ _ , pos_ _ , pos_ _ and pos_ _ as the sois for the mutation prediction analyses down the pipeline. here, pos_x_y indicates the site from positions x to y of the virus strains. the reason for selecting these features as sois are outlined below. according to gene expression studies [ ] [ ], our sois, namely, pos_ _ and pos_ _ encode to two non-structural proteins, nsp and nsp , respectively. and, our other two sois, namely, pos_ _ and pos_ _ correspond to the spike protein of sars-cov- . nsp binds to viral rna, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing. it is an essential component of the replication/transcription complex [ ] . so, the mutation in this protein is expected to affect the replication process of the sars-cov- in host bodies. on the other hand, the spike protein sticks out from the envelope of the virion and plays a pivotal role in the receptor host selectivity and cellular attachment. according to wan et al. there exists strong scientific evidence that sars and sars-cov- spike proteins interact with angiotensin-converting enzyme (ace ) [ ] . the mutation on this protein is expected to have a significant impact on the human to human transmission [ ] . therefore, it is certainly interesting and useful to predict the mutation of such sois. cnn-lstm and cnn-bidirectional lstm performed in a similar manner for different sois of the genome registering . % and % accuracy, respectively, considering all sois together. for detailed results please check table and table of the supplementary material. for the model involving only bangladesh, we applied the cnn-bidirectional lstm model (as this is the best performer among the two) and achieved almost % accuracy. then we analyzed the ancestors in the time series test samples and noticed that some of the states of the usa are present in these samples. these states are california, massachusetts, texas, new jersey and maryland. for india and pakistan, we got similar results for some sites but for other sites, accuracy was not as high as bangladesh (check table of the supplementary file for details). our analyses reveal a very close (evolutionary) relationship between the genome sequences of china and italy. also, similarity was found among the virus strains of the usa, germany, qatar and poland. these countries have similar numbers of deaths and although not geographically directly adjacent (except for germany and poland) they have strong air connectivity among them. in fact, a number of interesting relationships can be inferred from the estimated phylogenetic tree as follows. chinese tourists [ ] . this relationship is clearly portrayed in the sc tree where the two strains appear to be immediate siblings. . poland's strain is in the same clade as that of germany, which can be explained by the fact that its strain (through poland's patient zero) came from germany [ ] . . taiwan is geographically very close to china. the virus was confirmed to have spread to taiwan on january , , through a -year-old woman who had been teaching in wuhan, china [ ] . the virus strains from these regions are also close together as can be seen from the sc tree, about branches apart. similar relationship can also be inferred from the tree between china and south korea: the strain of the virus in south korea is believed to be transmitted from china firstly through a -year old chinese woman and secondly by a -year old south korean national [ ] . interestingly, from the sc tree it can also be deduced that the south korean strain is very close to that of taiwan and also near to the strain from china. the incident of a taiwanese woman being deported from south korea after refusing to stay at a quarantine facility can be a probable explanation as to how the south korean strain might have found its path to taiwan [ ] . . on march , , the virus was confirmed to have reached portugal, when it was reported that a portuguese year-old man working in spain was tested positive for covid- after returning home [ ] . subsequently, within a span of days, more cases were reported all originating from spain [ ] [ ] . the fact that the first cases of covid- in portugal originated from spain is clearly captured in our sc tree. . the sc tree suggests that india's strain is closely related to that from china and also italy (around branches) and that it is also connected to that from saudi arabia. these relationships can be explained as follows. a . turkey's first identified case was a man who was travelling europe [ ] . turkey also announced a huge number of cases and subsequent deaths, which were originating from europe [ ] . in our inferred relationship, we can see that the turkish representative strain is quite close to several central and western european countries like russia, iceland and ireland which can be backed up by the two facts stated above. . it is visible from the sc tree that the strain of germany is very close to the strains of both poland and the usa. it might be the case that the community transmission occurred concurrently in both usa and poland from germany which hit the peak of pandemic before both usa and poland [ ] . . qatar has the second highest number of covid- patients in the middle-east [ ] . the first case of qatar was reported on february , to be a man working in iran [ ] . qatar introduced a travel ban to and from germany and the usa as precautionary measures in mid-march, quite a while later following the first occurrence. qatar has air-routes with germany and usa, with more than airlines operating in that route [ ] [ ] . though the first case has originated from iran, it might be the case that subsequent patients were found to be travelling from the aforementioned countries as a result of which the travel ban was introduced. our estimated sc tree places qatar very close to both the usa and germany. . while we can certainly explain many of the relationships identified by the estimated sc tree a above, there are some relationships which are not that apparent. one such example is the direct relationship between vietnam and greece. while apparently, there exists no direct relationship, when investigated further, we identified something interesting. patient zero of greece is believed to have been contaminated during her trip to the milan fashion week which took place during february - , [ ] . interestingly, the first covid- patient in hanoi [ ] left hanoi on february to visit family members living in london, england and three days later, she traveled from london to milan city. could she be in contact with patient zero of greece or any other who had been contaminated by the latter, before returning to london on february ? we can't be certain, but our inferred relationship between vietnam and greece certainly put a lot of legitimacy to that question. . finally, we are unable to find any apparent explanation analyzing the reported news sources for a few other strong relationships inferred by the tree (e.g., congo-iran, panama-malaysia, sweden-singapore, japan-australia, etc). this could be because of the inherent inaccuracies of the distance matrices as well as the limitations of the tree estimation algorithms: none of these algorithms are % accurate. from another angle, perhaps, the tree did identify these relationships correctly; but the relevant incidences were not accurately identified or not documented. in recent times, the number of deaths is increasing rapidly in india. we have been closely following the change in the virus strains of india before and after the cut-off date. a genome sequence (epi_isl_ ) was collected on april , (before our cutoff date) from a patient in ahmedabad, gujrat, india. it was predicted to be a severe strain (with low confidence) even though at that time we trained the classifier to consider the indian sequences as mild. according to our evolutionary relationship, india is very close to both italy and china. so, we calculated the distance between the representative sequence of both italy and china with this strain. we considered another strain (epi_isl_ ) which was collected from another patient from the same place in india on april , (after our cut-off date) and predicted the severity thereof. the classifiers declared this isolate to be severe with very high confidence (about %). we did the distance calculation like before. interestingly, it was identified that this isolate is closer to both italy and china's representative sequence than the previous less severe one. this strongly suggests that there were some mutations that turned the indian sequences from mild or less severe to severe or highly severe, respectively. also, the sequences from the us states of pennsylvania, maryland, indiana, illinois and florida that were collected on may , (about one month after our cut-off date) were analyzed and our classifiers could correctly capture the severity of the genome sequences (see table in the supplementary file). we conduct an analysis to predict possible parents of the (mutated) virus strains of the south asian region (bangladesh, india and pakistan). our mutation prediction pipeline suggests that the strains of some states of the usa, namely, california, massachusetts, texas, new jersey and maryland could be the parents/ancestors of these south asian strains. now, the total deaths in these states up to june , are , , , and respectively [ ] and the strains thereof are also classified to be severe by our classification pipeline. it thus seems quite likely that the sars-cov- situation in these south-asian countries will worsen in near future. bangladesh, india and pakistan are ranked th , th and nd in global health performance compared to the united states of america which is at the th position [ ] . in the majority of lower middle-income countries such as bangladesh, india and pakistan, available hospital beds are < bed per population and icu beds are < bed per , population [ ] . additionally, an uncontrolled epidemic is predicted to have , , deaths having a duration of nearly days in the majority of these countries [ ] . these predictions coupled with our findings call for stern actions (i.e., interventions) on part of these countries. bibliography: covid- ) outbreak situation genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding cryo-em structure of the -ncov spike in the prefusion conformation alignment-free sequence comparison: benefits, applications, and tools a novel fast vector method for genetic sequence comparison who coronavirus disease (covid- ) dashboard a deep learning approach to dna sequence classification dna sequence classification by convolutional neural network principal component analysis and factor analysis. (n.d.). principal component analysis springer series in statistics tempel: time-series mutation prediction of influenza a viruses via attention-based recurrent neural networks dendroscope : an interactive tool for rooted phy-logenetic trees and networks crisprpred(seq): a sequence-based method for sgrna on target activity prediction using traditional machine learning extra tree forests for sub-acute ischemic stroke lesion segmentation in mr sequences isgpt: an optimized model to identify sub-golgi protein types using svm and random forest based feature selection lightgbm: a highly efficient gradient boosting decision tree vietnam confirms th covid- patient -vnexpress international india confirms its first coronavirus case kerala defeats coronavirus; india's three covid- the weather channel, the weather channel india's first coronavirus death is confirmed in karnataka coronavirus: india 'super spreader' quarantines , people , indians quarantined after 'super spreader' ignores government advice responding to covid- -a once-in-a-century pandemic? data, disease and diplomacy: gisaid's innovative contribution to global health evolview, an online tool for visualizing, annotating and managing phylogenetic trees why neighbor-joining works coronavirus, primi due casi in italia: sono due turisti cinesi koronawirus w lubuskiem. godziny, dwa razy za wolno. daleko do laboratorium taiwan confirms st wuhan coronavirus case (update) austria's coronavirus cases are italian citizens greece confirms first coronavirus case, a woman back from milan as coronavirus takes hold, greece worries about migrant camps turkey remains firm, calm as first coronavirus case confirmed human mitochondrial genome compression using machine learning techniques google colaboratory the neighbor-joining method: a new method for reconstructing phylogenetic trees scikit, scikitlearn.org/stable/modules/generated/sklearn.cluster.kmeans.html dynamic interventions to control covid- pandemic: a multivariate prediction modelling study comparing worldwide countries imagenet classification with deep convolutional neural networks going deeper with convolutions europe's coronavirus numbers offer hope as us enters 'peak of terrible pandemic' algorithm as : a k-means clustering algorithm consistent individualized feature attribution for tree ensembles greece's 'patient zero' shares coronavirus experience (lead) taiwanese woman deported for refusing to stay at quarantine facility sağlık bakanı fahrettin koca: pozitif Çıkan yeni vakalarımız var -türkiye haberleri flights from qatar, www.qatar.to/united-states/qatar-to-united-states ministra confirma primeiro caso positivo de coronavírus em portugal scikit, scikitlearn.org/stable/modules/feature_selection.html#univariate-feature-selection nsp of coronaviruses: structures and functions of a large multi-domain protein receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus role of changes in sars-cov- spike protein in the interaction with the human ace receptor: an in silico analysis measuring overall health system performance for countries. global programme on evidence forhealth policy discussion paper no. qatar reports first case of coronavirus sklearn.feature_selection.f_classif ¶ dendropy: a python library for phylogenetic computing flights from qatar, www.qatar.to/germany/qatar-to-germany flights from qatar, www.qatar.to/united-states/qatar-to-united-states single-stranded rna genome of sars-cov sars-cov- (severe acute respiratory syndrome coronavirus ) sequences antigenic: an improved prediction model of protective antigens dpp-pseaac: a dna-binding protein prediction model using chou's general pseaac key: cord- -b xpq authors: mungmunpuntipantip, rujittika; wiwanitkit, viroj title: frequency of diarrhea in novel coronavirus infection date: journal: gastroenterol hepatol bed bench doi: nan sha: doc_id: cord_uid: b xpq nan . this disease started in china then it is imported to several countries. as a new disease, knowledge on its clinical feature is limited. in additional to respiratory manifestation, atypical clinical presentation of the new disease is possible. an important atypical clinical presentation is diarrhea. here, the authors performed a summative analysis on available data on cases of novel coronavirus infections ( - ) to calculate for frequency of diarrhea. of those cases, diarrhea is presented in cases. the frequency of diarrhea is . % ( % confidence interval = . % - . %). based on this observation, it can show that diarrhea is a possible atypical clinical presentation of novel coronavirus infection. in fact, diarrhea is usually a possible but forgotten clinical presentation in new emerging disease such as swine flu ( ) . practitioner should recognize the possibility that diarrhea might be the first clinical presentation of the patient with novel coronavirus infection. nevertheless, the exact pathophysiology of diarrhea in novel coronavirus infection is unknown. further study on this issue is recommende. emerging new coronavirus infection in wuhan, china: situation in early epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan analysis of clinical features of patients with novel coronavirus pneumonia wiwanitkit v diarrhoea as a presentation of bird flu infection: a summary on its correlation to outcome in thai cases key: cord- -ws xprt authors: ozoner, baris; gungor, abuzer; hasanov, teyyup; toktas, zafer orcun; kilic, turker title: neurosurgery practice during coronavirus disease (covid- ) pandemic date: - - journal: world neurosurg doi: . /j.wneu. . . sha: doc_id: cord_uid: ws xprt abstract coronavirus disease (covid- ), caused by severe acute respiratory syndrome coronavirus (sars-cov- ), is a highly contagious, life-threatening condition with unprecedented impacts for worldwide societies and healthcare systems. since the first detection in china, it has spread rapidly worldwide. the increased burden has substantially impacted the neurosurgery practice and intensive modifications were required in surgical scheduling, inpatient and outpatient clinics, management of emergency cases, and even academic activities. in some systems, non-overlapping teams were created to minimize transmission among healthcare workers. in case of a massive burden, neurosurgeons may be needed to reassign to the covid- wards, or teams from other regions may be needed to send to severely affected areas. in outpatient practice, if possible, appointments should be turned into telemedicine. all staff assigned in the non-covid treatment unit should be clothed in level personal protective equipment. if possible, postponement is recommended for operations that do not require urgent or emergent intervention. all patients indicated for surgery must receive a covid- screening, including nasopharyngeal swab, and thorax computed tomography. level protection measures would be appropriate during covid- negative patients' operations. operations of covid- positive patients, and emergency cases, where screening can not be obtained, should be performed following level protective measures. during surgery, the use of high-speed drills and electrocautery should be reduced to minimize aerosol production. screening is crucial in all patients since the surgical outcome is highly mortal in covid- patients. all educational and academic conferences can be turned into virtual webinars. coronavirus disease (covid- ) is an exceedingly infectious, life-threatening condition and its outbreak is now constituting unprecedented extraordinary threats and difficulties for worldwide societies and healthcare systems. [ ] [ ] [ ] since the first detection in china in late december , it has spread rapidly to countries around the globe and reached approximately . . confirmed cases with more than . deaths on april , . the increased burden of this pandemic disease has substantially impacted the entire health system, including the neurosurgery practice in most countries. [ ] [ ] [ ] in neurosurgery practice, intensive modifications were required in surgical scheduling, administration of inpatient and outpatient clinics, management of emergency cases, and even academic & educational activities. the major goal of this review is to compose a comprehensive guide using existing guides and recommendations for reorganizing daily practice and the academic routine of neurosurgery during the covid- pandemic. this study also aimed to refine the substantial information for neurosurgery practice about this pandemic disease. an outbreak of pneumonia of unknown origin showed up in wuhan city, the capital of hubei province in people's republic of china, in late december . , on january , china isolated a new coronavirus formerly called novel coronavirus ( -ncov) and presented virus genome data to the international society. later, coincidentally, on february , the coronavirus study group of the international committee on taxonomy of viruses gave a new name to the virus "severe acute respiratory syndrome coronavirus " (sars-cov- ) and the world health organization designed a name for epidemic disease "coronavirus disease " . virology sars-cov- , a positive-sense single-stranded rna virus, a member of the subgenus betacoronaviruses, is the seventh determined coronavirus that infects humans. , , the genetic sequence of the sars-cov- presents approximately % analogy to sars-cov. sars-cov- comprises four structural proteins: n (nucleocapsid), e (envelope), m (membrane), and s (spike) proteins ( figure ). the n protein supports the rna genome, and e, m, and s proteins compose the viral envelope. the s protein also is responsible for binding to the angiotensin-converting enzyme receptor on the human cell membrane. the median incubation period is approximately days and practically all cases experience symptoms in days after exposure to sars-cov- . transmission occurs mainly through direct contact with the infected material or via droplets spread by sneezing or coughing. sars-cov- primarily targets the respiratory system. the main clinical symptoms of covid- are fever, cough, myalgia or fatigue, expectoration, and dyspnea. , minor symptoms include headache or dizziness, diarrhea, and nausea & vomiting. , dyspnea may be observed in critical patients and may proceed to severe acute respiratory syndrome, sepsis, and multiple organ dysfunction syndrome. reduced total leukocyte and lymphocyte counts, increased c-reactive protein and lactate dehydrogenase are common results in the laboratory tests. , the typical appearance is bilateral, subpleural, ground-glass opacities with air bronchograms on thorax computed tomography (ct). the viral load is elevated throughout the upper respiratory tract mucosa, including the nasal cavity, and naso-oropharynx. the viral ribonucleic acid (rna) can be identified in the sputum, saliva, as well as in the serum. the blood-brain barrier works as a natural barrier against pathogenic microorganisms and reduces the risk of intracranial infection. some human coronaviruses can invade the central nervous system (cns) through hematogenous or neuronal retrograde dissemination, leading to encephalitis and exacerbation of existing neurologic diseases. the brainstem involvement of sars cov has been described in both clinic and experimental studies. [ ] [ ] [ ] given the high analogy between sars cov and sars cov- , it clarifies that the cns spread of sars cov- may be partly responsible for acute respiratory failure in covid disease. a recent study from wuhan city, china reported that some severe covid- patients developed neurologic manifestations, such as acute cerebrovascular diseases ( . %), and impaired consciousness ( . %). cerebrovascular accidents may occur due to a systemic highly prothrombotic state of covid- . furthermore, sars-cov- was isolated in cerebrospinal fluid (csf) by gene sequencing from a covid- patient in beijing ditan hospital, china on march . since results of encephalitis are highly mortal, early diagnosis is essential. severely affected and comatose patients with neurologic symptoms should undergo brain imaging and csf examination. magnetic resonance imaging (mri) would yield the definitive marks about the presence of infectious intracranial processes. the regional hyperintense abnormalities on t weighted(w), t -w, flair, and diffusion-weighted images are considered suspicious for viral encephalitis. in case of suspected cns infections, lumbar puncture is indicated. the obtained csf can be investigated to detect viral genetic material through a polymerase chain reaction (pcr) examination or using antibody testing. viral encephalitis may also be presented with neurologic deterioration related to massive cerebral edema. , in case of conservative management (corticosteroids, hyperventilation, hypertonics, hypothermia, and barbiturate coma) fails, decompressive craniectomy can be considered an option for the last chance therapy in selected cases. , faculty planning the regional disease burden surges during the pandemic and the disease also shows a significant transmission to healthcare professionals. in the algorithm proposed by the university of california san francisco (ucsf), surgical scheduling is organized according to the ''surge level'' that correlates with the rising viral transmission between local community. using this system, the green, yellow, red, and black levels represent the lowest, moderate, high and highest levels of the surge, respectively. in the green level (< covid- + inpatients, and no staffing shortages), all elective operations proceed as scheduled. in the yellow level ( - covid- + inpatients, or < % staffing shortages), the schedule is rearranged as yielding a % reduction in the capacity of all elective procedures and all outpatient procedures is designated to an off-site (covid- free) hospital. in the red level (> covid- + inpatients, or > % staffing shortages), a % reduction is done in elective scheduling. finally, at the black level, in which significant assistance required from outside institutions to resist the outbreak, only emergent surgical cases will be performed. ucsf recommends a system, based on the "paired coverage model", designed to minimize patient and provider viral exposure while providing continuous inpatient coverage for neurosurgical emergencies. in this model, each department is covered by nonoverlapping teams (rotating in d cycles: d on, d off), in which members will have contact only within the same team. this model is activated by a red level of surge and includes an assigned alternate pool of providers to replace who show covid- prodrome. in case of a massive increase in covid- cases, non-specialized physicians in respiratory or infectious diseases, including neurosurgeons, may need to be reassigned to the covid- wards to initiate supplementary emergency responses. remodeling the hospital system by identifying concentration centers for neurosurgical activities would be necessary for managing emergent and urgent cases. an instance of this circumstance is present in lombardy, northern italy. lombardy health system was rearranged as a ''spoke-and-hub system''. [ ] [ ] [ ] [ ] the local neurosurgical network was assembled in hub hospitals ( for cranial or spinal emergencies, and one for oncological emergencies ). all the other neurosurgery departments have converted the spokes. in this way, hub hospitals are available to manage neurosurgical emergencies, whereas spoke hospitals concentrate on covid- patients. [ ] [ ] [ ] [ ] in this system, a huge increase may be expected in the number of patients treated in hub hospitals. according to an early report from the university of insubria, italy, there was an increase of % and %, respectively, of hospitalized and surgically treated neurosurgical emergencies. healthcare professionals from other areas may need to be sent to regions that are heavily affected by pandemics. during the outbreak, more than , medical staff including teams from other regions of china have been dispatched to hubei province, of which teams are comprised of neurosurgeons. owing to the newly appointed teams, emergency operations could be performed even during worst times of the epidemic peak. robertson et al. suggested a ''task shifting and task sharing'' method that involves training, practice, and maintenance phases for increasing workforce capacity during the pandemic. according to this method, the most experienced neurosurgeons who are also from the most vulnerable age groups may practice on telemedicine encounters, guiding ethical decisions on appropriate neurosurgical interventions, or neurosurgery-specific cases. and, residents skilled in neurocritical care may receive intensive skills training in endotracheal intubation and mechanical ventilator management. , residents may serve remotely when possible to perform virtual visits, record notes, give orders, and call consults. according to the physicians' preference, patient follow-up and appointments should be turned into telemedicine, if possible. , besides, remote examinations are reported that they are often applicable. according to the harvard medical school experience, more than % of the outpatient visits have been able to be switched to telemedicine. also, in a validation study by neumarkt clinic, germany, remote neurological examination consisting of items performed via audio-visual telemedicine presented comparable results to bedside examination. on occasions, the assist of a person may be required for the patient to perform some parts of the examination, such as the laségue test for the spinal examination. the transmission of patients' radiological images to the outpatient team via a data transfer method before telemedicine appointment would be beneficial. actual visits should be preserved for selected patients, such as patients requiring wound control and stitch removal. also, the use of absorbable sutures in neurosurgical surgeries could be considered to decrease the contacts among clinicians and patients after discharge. besides, patients aged > years should be encouraged to shun visiting the out-patient clinic. the out-patient facilities and personnel should be separated in non-covid and covid treatment units during the pandemic. the work schedule should be organized with as minimal staff as possible using the proper protective equipment. physicians and staff assigned in out-patient facilities should be clothed in level personal protective equipment (ppe) during their practice. ppe according to handbook of covid- prevention and treatment is presented in table . accompanies for pediatric or non-ambulatory patients should be reduced to one person. and, ambulatory individuals should visit the outpatient clinics alone. the ''lockdown'' and the ''stay at home'' strategies during pandemic dramatically reduced the spinal and cranial traumas allowing the medical professionals to focus on covid- patients. , also a reduction in surgical treatments for degenerative pathologies is present. the drop of traumatic events can be explained by the reduced traffic and work activities. two potential reasons have been argued by dobran et al. for the demand decrease in surgical treatment for spinal degenerative pathologies: ( ) the prevalent fear in the community that regarding hospitals as a risky place for a possible infection; and ( ) the patients' overrating their impairments and pains that resulting in surgical overtreatment. a global study, which conducted on the impact of covid- on neurosurgeons and generated an acuity index for the triaging strategy for non-emergent operations, surveyed respondents from countries. % of respondents reported that all elective cases canceled and their clinics closed down. % of respondents reported that their operative density reduced more than %, and this rate was % in the most affected countries. if possible, medical care methods requiring less invasive interventions such as endovascular treatment in neurovascular conditions, and radiosurgery in certain neuro-oncological diseases may be considered. endotracheal intubation or high-speed drill use is not required during stereotactic radiosurgery, which reduces the risk of exposure to aerosols compared to open surgeries. the summary of measures during the covid- pandemic is presented in table . healthcare personnel including operation room staff are at high-level risk of exposure to the sars-cov- . up to % of the confirmed cases were healthcare staff in the initial cohort reports. later, according to the report of the chinese center for disease control and prevention, which included more than , cases, . % of the confirmed cases were medical staff, and . % of them were in critical or severe condition. minimal or no symptoms are observed during the incubation period (first - days) in the majority of the cases. still, these asymptomatic patients are able to spread the virus. so, all patients indicated for surgery must receive a covid- screening, including measuring body temperature, symptoms investigation, sars-cov- pcr and antibody test, nasopharyngeal swab, and thorax ct scan. different recommendations are present for covid negative patients for the protection of medical staff in the operating theatre. according to a surgical neuro-oncology team perspective, patients from low-risk areas who are verified covid- negative can be operated following level precautions. other perspectives from tongji medical college, wuhan, china and heinrich-heine university, düsseldorf, germany recommended that medical staff should take level protection measures due to the long incubation period. , for patients who are suspected or confirmed covid- positive, or patients from a high-risk area, the operations should be performed under level precautions. , in emergency cases, the results of sars-cov- tests may not be obtained before the surgery, therefore the surgery should be performed following strict measures (level protective measures) to reduce potential exposure. the route from the ward to the operation room, including the elevators, should be cleared during the transfer of a covid (+) patient. the transfer should be performed by the covid- ward nurses in full personal protective equipment (ppe ). the operation room of covid- (+) patients should be separated. an operation room with negative atmospheric pressure setting, and with independent access should be designated for all confirmed or suspected covid- (+) cases. , during the pandemic, the same operating room, and the same continuous flow anesthetic machine should be used for only covid- (+) patients. since the endotracheal intubation can generate aerosols, the intubation should be performed via the method with the maximum possibility of first-time success using a video-laryngoscope to avoid multiple attempts. during the operation of confirmed or suspected covid- patients, all operating room staff must wear level ppe under a surgical gown to prevent contamination. ppe is obligatory for all interventions involving close contacts, such as surgery, endotracheal intubation, intravenous cannulation, cardiac catheterization, and regional anesthesia. using powered air-purifying respirators (papr) by the surgical team is recommended. all personnel should be trained about wearing and removing ppe to prevent contamination. after extubation, it is recommended that the patient is worn a surgical mask as soon as possible. the viral exposure load of the operating room staff can be considered to be proportional to the duration of the surgery. during the pandemic period, the staff number in the operating theatre must be reduced to the absolute minimum. also, all neurosurgical procedures ought to be designed to reduce the operating theater time. if possible, only a single experienced neurosurgeon beyond her/his learning curve ought to carry out the procedure to reduce operation time and to prevent exposure of other physicians. powered instruments such as the high-speed drills, which are commonly used tools for cranial and spinal procedures, had been demonstrated to produce blood-containing aerosols with the identification of hemoglobin in the ambient air. and viruses, such as human immunodeficiency virus- , was showed to be survival in the aerosols produced by surgical power instruments. since the coronaviral rna can be determined in plasma or lymphocytes of confirmed or asymptomatic patients, so these aerosols produced during neurosurgical operations can be contagious. also, a recent study used the bayesian regression model (a statistical model uses probability to represent all uncertainty within the model) indicated that aerosol transmission of sars-cov- is plausible. so, attention should be paid to minimize aerosol generation in operations performed during the pandemic period. upholding the increase of using traditional hand drills and rongeurs would be beneficial. more meticulous irrigation and reduction of drill speed are some precautions that should be taken if cranial or spinal drilling is necessary. special caution should be taken during anterior skull base surgeries, to avoid breach frontal or ethmoidal sinuses. the use of electrocautery creates a gaseous by-product containing aerosol commonly referred to as ''surgical smoke''. viral transmission of human papillomavirus from patients to treating physicians through surgical smoke has been demonstrated. , due to potential transmission risk, using time of monopolar and bipolar electrocautery should be reduced and their power settings ought to be minimized to decrease aerosol dispersal during the pandemic period. endonasal procedures, using debriders and drills inside the nasal cavity, generate highly hazardous aerosols. otolaryngologists are among the worst affected medical professionals in wuhan city, china, and even n / (filtering face piece) ffp masks did not prevent transmission. , also, a patient with a mass lesion in the sellar region that underwent endonasal endoscopic surgery in neurosurgery department, tongji medical college, wuhan city, china was diagnosed with covid- after surgery, and disease was confirmed in healthcare professionals in the same clinic afterwards. according to an initial perspective from the society of british neurological surgeons, endonasal transsphenoidal endoscopic surgical approaches should be avoided during the pandemic period. alternatives routes to endoscopic surgery should be considered for patients whose surgery can not be postponed: ( ) craniotomy; and ( ) microscopic endonasal transsphenoidal surgery, with the submucosal approach and non-drill techniques used during the endonasal and sellar phase. another recent perspective from singapore suggests that endonasal procedures should be managed according to the covid- test results. they suggested wearing n / ffp mask, eye protection (goggles and full-face shield), and standard personal level equipment (gown and gloves) in patients whose test results are negative. and in patients with positive test results, they recommended doning an additional papr by the entire surgical and anesthesia team, including the circulating nurse and operating room attendant. they also recommended using rongeurs and chisels instead of power instruments during surgical exposure, and avoiding the use of nasal pledgets, whose removal may stimulate gagging or coughing in the postoperative phase. also, gowns, n / ffp masks, and face shelters are recommended to use during all outpatient nasal endoscopies. since the disease is asymptomatic in some patients, covid- screening is crucial in all patients before the operation. because, in addition to protecting healthcare professionals, high mortality risk is present in covid- patients who have undergone surgical intervention. university of brescia, italy was reported that the mortality rate of chronic subdural hematoma was % in covid- (+) patients. this rate was reported as . % in the control group treated before the pandemic. a meta-analysis including nearly covid- patients revealed that lower platelet count was associated with severe covid- . the thrombocytopenia can lead to re-bleeding that resulting in a poor outcome. also, in subclinical covid- patients, surgical intervention could impair the immune system, leading to the emergence of the covid- disease. , interstitial pneumonia progression after the surgical intervention may worsen the outcome. the conservative strategy should be preferred whenever operation could be postponed. this situation may be different for the baby and children population. the general observation is that newborns, infants, and children are relatively resistant to covid- . a case report from milan, italy presented that an -month-old infant with complex hydrocephalus underwent two consequent shunt revision interventions while his nasopharyngeal swab was positive for sars-cov- . the baby, who underwent two operations under general anesthesia without respiratory complications, showed a favorable neurological course. web-based conferencing systems have emerged and reached primacy. , all in-person conferences such as resident education lectures, multidisciplinary board meetings, and weekly morbidity & mortality conferences should be converted to video teleconferences with an individual person participating in the conference from one site. , , many elements of medical students' lectures may be converted into virtual webinars. involving of neurosurgery-willing students in department educational video teleconferences would intensify student learning and provide accessibility of the department to students. our country, turkey, is among the most-affected countries by the pandemic. in our country, the pandemic burden is being managed by in collaboration of state and private health institutions. a substantial or all part of the many hospitals were modified to covid- wards. when necessary, some of the operation rooms were used as intensive care units. during the pandemic period, most of the neurosurgeons attended in the front lines. the urgent and emergent surgeries were performed and the schedule for elective procedures was postponed. in india, one of the most affected countries in asia, a consensus was suggested for neuro-interventional teams to switch coverage model including days on work and days of self-isolation cycles. in this consensus statement, the categorization of the patients based on priority and postponing non-essential elective surgeries and outpatient visits are advocated. in an experience report from iran, one of the most-affected countries, it was reported that out-patient clinics were shut down, elective surgeries were canceled, and postponed, neurosurgery residents were reassigned in covid- wards. according to the iran university of medical sciences and health services experience, a significant decrease ( %) was noticed in elective and emergency neurological surgeries. an experience report from germany declared that spine cases fell . % below baseline ( ) levels. with the increasing burden of covid- pandemic worldwide, the need for various modifications in neurosurgery practice will proceed. during the pandemic period, strict measures are essential for both medical staff safety and patient care. in this paper, we outline substantial information and recommendations for the daily outpatient and inpatient practice, severe acute respiratory syndrome coronavirus (sars-cov- ) and coronavirus disease- (covid- ): the epidemic and the challenges covid- outbreak: an analysis of international health regulations annual report data from countries on pandemics: the impact of covid- on the practice of neurosurgery covid- and neurosurgical practice: an interim report neurosurgical activity during covid- pandemic : an expert opinion from china a novel coronavirus from patients with pneumonia in china a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster novel coronavirus ( -ncov ) situation report - the species and its viruses -a statement of the coronavirus study group. biorxiv (cold spring harb lab coronavirus disease (covid- ) situation report - a pneumonia outbreak associated with a new coronavirus of probable bat origin a new coronavirus associated with human respiratory disease in china analysis of therapeutic targets for sars-cov- and discovery of potential drugs by computational methods the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application covid- infection: origin, transmission, and characteristics of human coronaviruses the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak novel coronavirus patients' clinical characteristics, discharge rate and fatality rate of meta analysis radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study how do extracellular pathogens cross the blood-brain barrier? human coronaviruses: viral and cellular factors involved in neuroinvasiveness and neuropathogenesis severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ace lethal infection of k -hace mice infected with severe acute respiratory syndrome coronavirus detection of severe acute respiratory syndrome coronavirus in the brain: potential role of the chemokine mig in pathogenesis the neuroinvasive potential of sars-cov may be at least partially responsible for the respiratory failure of covid- patients neurologic manifestations of hospitalized patients with coronavirus disease characteristics of ischaemic stroke associated with covid- novel coronavirus and central nervous system diffusion-weighted mr imaging of viral encephalitis cranial imaging and lumbar puncture in patients with suspected central nervous system infection technological advances and changing indications for lumbar puncture in neurological disorders viral encephalitis: a clinician's guide decompressive craniectomy for encephalitis with brain herniation: case report and review of the literature neurosurgery and coronavirus (covid- ) epidemic: doing our part letter: the coronavirus disease global pandemic: a neurosurgical treatment algorithm neurosurgery during the covid- pandemic: update from lombardy, northern italy effects of covid- outbreak in northern italy neurosurgery in the storm of covid- : suggestions from the lombardy region, italy (ex malo bonum) hub and spoke' lombardy neurosurgery group. may we deliver neuro-oncology in difficult times (e.g. covid- )? coronavirus disease (covid- ) outbreak: single-center experience in neurosurgical and neuroradiologic emergency network tailoring response to covid- in chinese neurosurgery and beyond task shifting and task sharing for neurosurgeons amidst the covid- pandemic a neurosurgery resident's response to covid- : anything but routine early lessons in the management of covid- for the pediatric neurosurgical community from the leadership of the american society of pediatric neurosurgeons letter: adaptation under fire: two harvard neurosurgical services during the covid- pandemic telemedicine in general neurology: interrater reliability of clinical neurological examination via audio-visual telemedicine telemedicine in neurosurgery during the novel coronavirus (covid- ) pandemic letter: neurosurgical management of spinal pathology via telemedicine during the covid- pandemic: early experience and unique challenges letter : the use of absorbable sutures in neurosurgical procedures in the time of covid- handbook of covid- prevention and treatment letter to the editor by dobran mauro, paracino riccardo, and iacoangeli maurizio regarding "neurosurgery during the covid- pandemic: update from lombardy, northern italy our darkest hours (being neurosurgeons during the covid- war) the impact of covid- on neurosurgeons and the strategy for triaging non-emergent operations: a global neurosurgery study the management of emergency spinal surgery during the covid- pandemic in italy safety instructions for neurosurgeons during covid- pandemic based on recent knowledge and experience letter: covid- pandemic: safety precautions for stereotactic radiosurgery clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention clinical features of patients infected with novel coronavirus in wuhan transmission of -ncov infection from an asymptomatic contact in germany experiences of practicing surgical neuro-oncology during the covid- pandemic strategies for prevention and control of novel coronavirus infection among medical staf lessons learned: special precautions for performing emergency cerebrovascular procedures amid the covid- pandemic what we do when a covid- patient needs an operation: operating room preparation and guidance patients with coronavirus (covid- ) and surgery: guidelines and checklist proposal staff safety during emergency airway management for covid- in hong kong outbreak of a new coronavirus: what anaesthetists should know lessons from china when performing neurosurgical procedures during the coronavirus disease (covid- ) pandemic evaluation of contamination by blood aerosols produced during various healthcare procedures human immunodeficiency virus (hiv ) in the vapors of surgical power instruments coronavirus disease : coronaviruses and blood safety aerosol and surface stability of sars-cov- as compared with sars-cov- letter: rongeurs, neurosurgeons, and covid- : how do we protect health care personnel during neurosurgical operations in the midst of aerosol-generation from high-speed drills? letter : transmission of covid- during neurosurgical procedures -some thoughts surgical smoke -a review of the literature. is this just a lot of hot air? laryngeal papillomatosis with human papillomavirus dna contracted by a laser surgeon risk of acquiring human papillomavirus from the plume produced by the carbon dioxide laser in the treatment of warts covid- and the otolaryngologist -preliminary evidence-based review a covid- patient who underwent endonasal endoscopic pituitary adenoma resection : a case endonasal neurosurgery during the covid- pandemic: the singapore perspective letter: precautions for endoscopic transnasal skull base surgery during the covid- letter : covid- infection affects surgical outcome of chronic subdural hematoma thrombocytopenia is associated with severe coronavirus disease (covid- ) infections: a meta-analysis the perioperative immune response does major surgery induce immune suppression and increase the risk of postoperative infection? clinical characteristics of novel coronavirus disease (covid- ) in newborns, infants and children correspondence neurosurgery in an infant with covid- editorial. covid- and academic neurosurgery academic neurosurgery department response to covid- pandemic: the university ofmiami/jackson memorial hospital letter : maintaining neurosurgical resident education and safety during the covid- letter : covid- impact on the medical student path to neurosurgery neurosurgery and neurology practices during the novel covid- pandemic: a consensus statement from india the authors would like to thank to mrs. senay guner ozoner for her illustrative figure work. all authors certify that they have no affiliations with or involvement in any organization or entity withany financial or non-financial interest in the subject matter or materials discussed in this manuscript key: cord- -tvpo kxb authors: russell, r. g.; brian, d. a.; lenhard, a.; potgieter, l. n. d.; gillespie, d.; clapp, n. k. title: coronavirus-like particles andcampylobacter in marmosets with diarrhea and colitis date: journal: dig dis sci doi: . /bf sha: doc_id: cord_uid: tvpo kxb nan diarrhea and colitis were common clinical entities observed during a recent two-year interval in the marmoset colony located at oak ridge associated universities, oak ridge, tennessee. the diarrhea occurred in sporadic episodes of several weeks duration and affected up to % of all animals at any one time. the incidence of the colitis is unknown, but it appeared to be widespread. histologically, the colitis was similar to that described in cottontop tamarins (saguinus oedipus oedipus) at the new england primate center ( ) . there was infiltration of predominantly mononuclear cells into the interstitium, dilation of crypts with flattened epithelium, and accumulation of neutrophils and degenerated and necrotic epithelial cells in the lumen ( ) . the cause of either the diarrhea or the colitis is not known, nor is it known to what extent they are causally related. in this report we describe studies demonstrating both coronavirus-like particles and campylobacter in marmosets with diarrhea. coronavirus-like particles were found in % and campylobacter fetus subsp, jejuni in % of sampled animals with diarrhea. immunoblotting studies on serum from a small number of animals having diarrhea suggested the presence in the colony of antibodies to a coronavirus antigenically related to the bovine enteric coronavirus but not the porcine transmissible gastroenteritis virus. interestingly, all of the seven animals that died and exhibited histopathological lesions of colitis had coronavirus-like particles in their colon contents. marmosets and collection of fecal samples. a colony of approximately marmosets is housed at the marmoset research center, oak ridge associated universities, oak ridge, tennessee. these include the tamarins saguinus oedipus oedipus, saguinus fuscicollis spp., and the common marmoset caliithrix jacchus. animals are housed either singly in cages or as families in the breeding facility. stool samples were taken from animals during a two-year period over which episodes of diarrhea occurred. during one episode lasting two months, samples were taken~ of these being collected over a three-day period. all stool samples were obtained from adult marmosets - years of age either during signs of diarrhea or within one week of recovery. colon contents were collected at necropsy from eight marmosets that died spontaneously. the necropsy diagnosis of these animals is discussed in the results section. culturing for enteropathogenic bacteria. samples of feces were cultured at ~ c on macconkeys or heptone agar, or on selenite broth followed by subcultures, for salmonella and shigella, samples were also cultured at ~ c under microaerophilic s digestive diseases and sciences, vol , no. (december supplement) electron microscopy. stool samples were suspended in four volumes of distilled water, clarified at ~ g for min, and ml was pelleted at , g in a beckman sw- rotor for hr. the resulting pellet was suspended in . ml distilled water and ~ of this was mixed with txl of % phosphotungstic acid (ph . , adjusted to this ph by the addition of potassium hydroxide). the mixture was then sprayed from a glass nebulizer onto formvar-coated copper grids. electron microscopy was done on a phillips c electron microscope. growth and purification of virus, polyacrylamide gel electrophoresis, and immunoblotting. a plaquepurified stock of the bovine enteric coronavirus (bcv; mebus strain) was grown on the human rectal tumor cell line (hrt- ) ( ) using previously described methods ( ) . cells were grown on dulbecco's modified minimum essential medium (dmem) with % fetal bovine serum (sterile systems, inc.). cells were infected with a multiplicity of , and supernatant fluids were harvested at - hr postinfection, and clarified at , g for rain. a plaque-purified stock of the porcine transmissible gastroenteritis virus (tgev; purdue strain) was grown on the swine testicle cell line (st) ( ) using previously described methods ( ) . cells were grown on dmem with % adult bovine serum (sterile systems, inc.). cells were infected with a multiplicity of , and supernatant fluids were harvested at - hr postinfection, and clarified at , g for rain. each virus was separately pelleted in -ml tubes on a sorval rotor at , rpm, hr, at ~ c through a -rul cushion of % sucrose w/w in tmen- buffer [ mm tris acid maleate (ph ), . m nac , and mm edta], and the pellet was dissolved in sample treatment buffer [ . mm tris hydrochloride (ph . ), % sds, m urea] and diluted with sample treatment buffer until the concentration of viral protein was approximately ~g/~! as determined by coomassie blue staining of - xl aliquots on nitrocellulose ( ) . viral proteins were electrophoretically separated using the discontinuous buffer method of laemm!i ( ) . approximately . mg of viral protein was spread along a continuous well of a vertical slab ( . • x mm) electrophoresis apparatus (hoeffer scientific instruments) and electrophoresed through a -cm stacking gel of % polyacrylamide and an -cm separating gel of % polyacryl-amide. electrophoretic transfer of viral proteins from polyacrylamide gels to nitrocellulose sheets was done by the method of burnette ( ) . nitrocellulose sheets containing viral proteins were marked for alignment, cut into strips of mm width, and each strip was incubated with a : dilution of serum in -ml, siliconized, plastic, screw-capped centrifuge tubes. the procedure of burnette ( ) was used for radiodetection of bound immunoglobulins using i-labeled staphylococcus-a protein. labeled staphylor protein ( - ixci/txg) was purchased from icn. strips were then exposed to kodak x-omat r film for autoradiography. episodes of diarrhea involved approximately % of all animals over a two-year period. the largest episode occurred during a two-month period and involved over animals. many animals were treated with broad-spectrum antibiotics if diarrhea was accompanied by anorexia, or if diarrhea lasted longer than three days. because some animals were unresponsive to treatment and had no laboratory evidence of parasites or enteropathogenic bacteria, fecal samples were examined by electron microscopy for evidence of viruses. coronavirus-like particles were observed in feces from % of the samples examined by electron microscopy ( table ). the particles measured approximately - nm and had regularly spaced petal-shaped projections from the surface ( figure ). some also appeared to have an indentation of the surface and some were interpreted as having an empty nucleocapsid ( figure ). in three samples, a reovirus-like particle was found, but no other viruslike agents were observed. fecal specimens from marmosets with similar clinical signs were cultured bacteriologically. they were consistently negative for salmonella and shigella. campylobacter fetus subsp, jejuni was isolated from % of the stool samples (table ) . of marmosets examined for both viral and bacteriological agents, only one was found to have both coronavirus-like particles and campylobacter. the colon contents of eight animals that died were collected at necropsy and examined for the presence of coronavirus-like particles. of these, seven had mild to moderate enterocoiitis histologically (table ) . interestingly, all seven animals having colitis also had coronavirus-like particles in their colonic contents (table ) . ( ), and human rhabdomyosarcoma cells ( ) . in an initial attempt to identify the coronaviruslike agents as coronaviruses, serum from marmosets having diarrhea were reacted against viral proteins of the bovine enteric coronavirus and of the porcine transmissible gastroenteritis coronavirus, representatives of the two antigenic subgroups of the mammalian coronaviruses. coronaviral pro: teins were electrophoretically separated, electrophoresed to nitrocellulose paper, reacted with se, rum and subsequently with [ i]staph a protein. the results of serum from four marmosets are shown in figure . two of the five proteins of the bovine coronavirus but not of the proteins of the porcine transmissible gastroenteritis coronavirus appeared to bind antibodies in serum from six of ! animals examined. the results suggest that a coronavirus antigenica!ly related to the bovine coronavirus but not to the porcine transmissible gastroenteritis coronavirus exists in the marmoset colony. ~ whether these antibodies represent an immune response to the coronavirus-like agents observed in the feces of marmosets remains to be shown. we describe coronavirus-like particles and campylobacter in the feces of marmosets suffering diarrhea and colitis. to date no firm association can be drawn between either agent and the diarrhea or either agent and the colitis, but our results do allow us to design approaches to investigate possible causal relationships. the virus-like particles observed in fecal and colonic specimens were interpreted as probable coronavirus because of the ultrastructural morphology. these particles must be differentiated from fringed particles that are of nonviral origin ( ) . to confirm the existence of coronaviruses, two approaches should be taken: ( ) the coronavirus should be grown in tissue culture and further characterized at the molecular level. initial attempts have not yet been successful on primary marmoset cells and on cell lines of other animal species. inasmuch as replication of coronaviruses is enhanced on transformed cells ( ) , transformed marmoset cells should be tried. ( ) serum from a variety of colony animals should be used to attempt precipitation of viral particles by immune electron microscopy ( ) . evidence of immune clumping by antibody would support the notion that the observed coronavirus-like particles are infectious agents. further precipitation with known antiserum to other coronaviruses should be attempted for classification of these agents. initial attempts have been made to identify ,the presence of coronavirus antibodies in the marmoset colony. whereas no attempt has yet been made to react marmoset serum with the coronavirus-like particles observed in marmoset feces, marmoset serum was used to identify serological reactivity to the bovine enteric coronavirus and to the porcine tranmissible gastroenteritis coronavirus, each a representative of the two antigenic subfamilies of mammalian coronaviruses ( ) . reactivity in six marmosets was observed for the internal -kd phosphoprotein and the -kd glycoprotein of the bovine coronavirus but not to any identifiable protein of the porcine gastroenteritis coronavirus. since the -kd and -kd proteins are largely internal virion proteins ( ), they probably represent evolutionarily conserved proteins within this antigenic subgroup of coronaviruses. further investigation is necessary to establish the role of the coronavirus-like particles in both the diarrhea and the colitis observed in the marmosets. coronaviruses have been established as the cause of acute diarrhea in many animal species ( , ) . their presence in the stools of humans with nonbacterial gastroenteritis suggests they may be a cause of acute diarrhea in humans too ( ) ( ) ( ) ( ) ( ) . they have been found in the stools of nonhuman primates with diarrhea, but their role in this disease was not obvious since they were also found in the stools of nondiseased animals ( ) . the role of coronaviruses in chronic gastrointestinal disease in animals and man has been more difficult to establish. persistent shedding of coronaviruses from many animal species is documented, but no correlation with chronic intestinal disease has yet been made ( , ) . persistent shedding of coronavirus-like particles was observed over an eight-month period in a human individual with chronic intestinal maladsorption and suggests a possible role by coronaviruses in this disease ( ) . the role of campylobacter in marmoset diarrhea likewise needs further investigation. campylobacter has been described as the most common bacterial cause of acute enterocolitis in man ( , ) . histopathological findings in the large bowel for this disease are mild to moderate infiltration of mononuclear cells, neutrophils, and eosinophils in the lamina propria; cryptitis; and crypt abscesses ( ) ( ) ( ) . age groups affected are mainly teens and adults, although cases have been reported in infants and children. infection is usually not severe and is generally self-limiting ( , ) . campylobacter has been implicated in persistent and recurrent diarrhea of infants and adults ( , ) . campylobacter also has been implicated in acute and persistent diarrhea in nonhuman primates ( ) ( ) ( ) ( ) ( ) , but its high prevalence in apparently normal animals makes it difficult to establish its role in chronic disease ( , ) . experimental infection has not been successful in some studies ( ) , although oral infection of young nonhuman primates with a human isolate caused mild disease of short duration ( ) . histopathologic findings were absent in experimentally infected macaca mulatta ( ) . mild nonsuppurative enteritis was reported in erythrocelous patus monkeys with persistent diarrhea from which campylobacter was isolated ( ) . we thank john norman for excellent technical assistance. supported by a grant from the national foundation for ileitis and colitis, inc., by oak ridge associated universities corporation, by contract de-ac - digestive diseases and sciences, vol. , no. (december supplement) r between the department of energy, office of energy research, and oak ridge associated universities, and by national cancer institute, dhhs, grant n -cp- t . an analysis of the association of gastroenteric lesions with chronic wasting syndrome of marmosets histology of colitis: saguinus oedipus oedipus and other marmosets cultural and antigenic properties of newly estabfished cell strains derived from adenocarcinomas of the human colon and rectum bovine coronavirus structural proteins studies on transmissible gastroenteritis of swine. ii. selected characteristics of a cytopathogenic virus common to five isolates from transmissible gastroenteritis genome of porcine transmissible gastroenteritis virus electrophoretic transfer of proteins from sodium dodecyl snlfate-polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein a cleavage of structural proteins during the assembly of the head of bacteriophage t polypeptides and functions of antigens from human coronaviruses e and oc uses and abuses of diagnostic electron microscopy enhanced growth of a murine coronavirus in transformed mouse cells antigenic relationship of the feline infectious peritonitis virus to coronavirus of other species the biology and patfiogenesis of coronaviruses an enteric coronavirus infection of cats and its relationship to feline infectious peritonitis coronavirus particles in faeces from patients with gastroenteritis pleomorphic virus-like particles in human faeces coronaviruses in training center for intellectually retarded coronavirus-like particles in aboriginals and non-aboriginals in western australia occurrence of viruses in human stools in ahaggar (algeria) coronavirus-like particles in nonhuman primate feces corona-like virus particles in the feces of normal cats chronic enterocyte infection with coronavirus. one possible cause of the syndrome of tropical sprue? campylobacter enteritis--the first five years epidemiology of campylobaeter enteritis acute diarrhea: campylobacter colitis and the role of rectal biopsy campylobacter jejuni enterocolitis. a cfinicopathologic study campylobacter enteritis: a study of clinical features and rectal mucosal changes vibrionic enteritis in infants chronic diarrhea associated with campylobacter incidence of thermophilic campylobacter spp in newly imported simian primates with enteritis biphasic enteritis in imported cynomologus (macaca fascicularis) monkeys infected with shigella, salmonella, and campylobacter species campylobacterjejuni isolated from patas monkeys with diarrhea campytobacter enteritis in patas monkeys identification of campylobacter jejuni in macaca fascicularis imported from indonesia experimental infection of rhesus monkeys with a human strain of campylobacterjejuni campylobacter in monkeys key: cord- -kmj hj authors: babbar, s. title: battle with covid- under partial to zero lockdowns in india date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: kmj hj the cumulative records of covid- are rapidly increasing day by day in india. the key question prevailing in minds of all is when will it get over? there have been several attempts in literature to address this question using time series, machine learning, epidemiological and statistical models. however due to high level of uncertainty in the domain and lack of big historical data, the performance of these models suffer. in this work, we present an intuitive model that uses a combination of epidemiological model (seir) and mathematical curve fitting method to forecast spread of covid- in india in future. by using the combination model, we get characteristics benefits of these models under limited knowledge and historical data about the novel coronavirus. instead of fixing parameters of the standard seir model before simulation, we propose to learn them from the real data set consisting of progression of corona spread in india. the learning of model is carefully designed by understanding that available data set consist of records of cases under full, partial to zero lockdown phases in india. hence, we make two separate predictions by our propose model. one under the situation of full lockdown in india and, other with partial to zero restrictions in india. with continued strict lockdown after may , , our model predicted may , as the date of peak of coronavirus in india. however, in current scenario of partial to zero lockdown phase in india, the peak of coronavirus cases is predicted to be july , . these two predictions presented in this work provide awareness among citizens of india on importance of control measures such as full, partial and zero lockdown and the spread of corona disease infection rate. in addition to this, it is a beneficial study for the government of india to plan the things ahead. india reported the first confirmed case of the coronavirus infection on january , in the state of kerala. the affected had a travel history from wuhan, china. as of now, june , , confirmed cases stand at . lakhs with more than , deaths in the country. the top states with the highest number of cases include maharashtra, delhi, tamil nadu, gujarat, and uttar pradesh. to protect . billion population of india from getting infection, world's biggest lockdown in history was imposed in four phases by the government of india. the motive was to flatten the curve of the infection and slow the spread of this deadly virus. during full lockdown started from march , , india witnessed a surge in confirmed coronavirus cases due to tablighi jamaat religious congregation event held in delhi in mid march. the meeting was estimated to have been attended by more than , members including foreigners. it was an exceptional and undesirable event occurred under the toughest restrictions executed in india. with no doubt continued full lockdown after may, , might have resulted in controlled spread of disease in india. but at the same time, extending it for several more weeks was not a solution either. the four phases of serious lockdown in india has brought millions below the poverty line struggling for basic needs like food and shelter. the issue of migrant workers was one of the most crucial and highlighted issue in this pandemic where millions were rendered unemployed and stranded without money, and basic needs contributing to further growth of disease in india. it has been more than months to the prevailing situation of deadly coronavirus hounding india with rapid growth of cases. medical researchers all over the world are busy experimenting right vaccine for the virus, academic researchers are making predictions based on machine learning and time series models and astrologers are forecasting the end of disease based on planetary position and more. the key finding everyone is trying to uncover is: when this pandemic will get over?. it is a challenging task to be addressed for the reasons that there are several time variant factors that influence spread of coronavirus disease. this includes social distancing, population and density, public awareness, corona testing facility, lockdown and restrictions, medical facility, nature of virus and more. consider the factor of "social distancing" which is one way to reduce the speed of the spread of the infection through the population. social distancing not only helps in slowing the spread of infection, but also support by keeping the peak number of cases below the capacity of the medical system. consider figure from [ ] . where two curves of different shapes are shown. the curve on the left is a steep curve indicating exponential increase in the virus spread. with such infection rate, the local health care system gets overloaded beyond its capacity to treat people. whereas, the curve on the right is flatter showing a slower infection rate over longer period of time. under this situation, health care system is less stressed and the required medical attention can be given to the patients. the second curve is the output of maintaining adequate social distancing and lockdowns whereas, first curve is result of zero precautions. hence, following social distancing and lockdowns restrictions are the key to slow the spread of the virus. in this work, we show impact of full and partial to zero lockdowns in predicting likely end of coronavirus in india. from full lockdown we mean the phase starting from march , to may , . where the government of india imposed strict restrictions. whereas, partial to zero lockdown indicates the time period from may , to current date. where restrictions are lighten and india is moving from locking to unlocking stage. we used a combination of epidemiological model (seir) and mathematical curve fitting method to forecast spread of covid- in india in future. the key motivation to integrate two methods for the predictive task is to use benefits of seir model by making its key parameters learn using historical data of confirmed cases under full and partial to zero lockdowns in india. fundamentally, seir model works by fixing the parameters such as n (population of the country/state under study), β (expected amount of people an infected person infects), γ (the proportion of infected recovery), δ(the length of incubation period) and r o (computed as β n to identify lockdown scale of country/state under study) before simulation. however, we suggest that keeping these parameters fixed may affect the prediction capability of the model. consider the parameter r o . r o is a indicator of reproduction rate of disease. a r o < means that an outbreak is subsiding since each infected person is transmitting the virus to fewer than one other person. whereas, r > one means the virus is spreading exponentially. the scale at which virus is spreading cannot be same for every country/state. it depends upon several factors such as population and density, lockdown restrictions, rules and regulations, corona virus testing facility and more. hence, setting it fixed for predicting task is not a realistic solution. we propose to learn it from the data instead of keeping it fixed. on way to do is to use logistic function to learn r o . where function is learnt from the data. since this study is related to india so the data considered for the learning task is only meant for india. for robust learning of r o parameter the data set is carefully used so as the right values are learnt under full and partial to zero lockdowns phases in india. the learnt r o value is further used to evaluate parameter β. once the parameters are learned, seir model is simulated to produce two predictions under full and partial to zero lockdown states in india. more clearly, we show end of corona virus if the full lockdown was extended by government of india after may, , and, the prediction of date of peak of coronavirus under partial to zero lockdown in india. we also show similar predictions for capital of india, new delhi. our propose approach has resulted in a good performance giving mean absolute log error (male) of . and . on fitting india's and delhi's full lockdown data respectively. the rest of the paper is organized as follows. section reviews trendy models such as time series, machine learning and deep learning for predicting coronavirus spread in india. the summary of standard seir model, details on curve fitting model and our propose algorithms are presented in section . the data sets used in this work are detailed in section . results achieved by our proposed algorithms are summarized in section . finally, we conclude in section . the key contributions of this work is as follows: . we propose a novel algorithm that is integration of standard seir model and mathematical curve fitting to make predictions of coronavirus in india . predict and analyze confirmed infected cases of coronavirus in india under strict and partial to zero lockdowns. . to predict likely number of population to be affected in india and new delhi by the coronavrius. in work by t. hiteshi et. al. [ ] used various time series model such as, arima, single and double exponential methods and moving average to forecast future of corona virus cases in india. the data taken for study was from january , to may , . where, observations till april , were used for training the models and rest were used for the evaluation purpose. it was concluded that arima outperformed remaining time series models giving mean absolute percentage error of . . it was summarized in the paper that coronavirus cases with continue to grow in india for coming days. the study is not extended to show the prediction of arima in future beyond april , . the work is related to fitting arima on the available data and showcasing closeness of model performance with actual data. authors in [ ] used autoregressive time series models based on two-piece scale mixture normal distributions, called tp-smn-ar models to analyze the real world time series data of confirmed and recovered covid- cases. the data set comprising of confirmed and recovered corona cases from february, , t april, , were considered for experimentation purpose. model was trained on observations till april , and tested on remaining days. the performance of model was evaluated using mean absolute percentage error (mape). the reported mape were . % and . % for confirmed and recovery coronavirus cases respectively. low mape indicated better fitting of model to the existing data. however, future predictions on development of corona virus globally were not studied in the work. similar work has been proposed by [ ] where authors used arima model on johns hopkins epidemiological data to predict the corona epidemic trend of prevalence and incidence of covid- . arima( , , ) and arima( , , ) were discovered as best performing models to address prevalence and incidence of covid- on data set used till february, , . authors used to these models to forecast for next two days, i.e., february , and february , . the time series models arima and sarima have also been used in study [ ] on coronavirus data set for countries italy, spain and turkey. these authors also measured the performance of their model using mape. in addition to this, they extended their model to forecast new cases of coronavirus in the mentioned countries. it was revealed in their work . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . that likely decline of new cases in italy and spain is in july whereas; turkey will see the decline by september . machine learning models such as, linear regression, support vector regressor, deep neural network, recurrent neural network and long short-term memory have also been studied to predict coronavirus cases globally. in [ ] , authors used linear regression model to forecast growth of confirmed corona cases in india for weeks from march, , . where linear regression model was trained on data set of the disease before march , . the trained model was evaluated by root mean square log error metric, which resulted in . error. it was concluded in the work that india will see growth by - cases during the first two weeks of april, . authors in [ ] used support vector regressor, recurrent neural network and long short-term memory for predicting task. models were trained till observations dated april, , and, forecasted results were shown for next days. in work proposed by a. sina et.al. [ ] , machine learning and soft computing models were used to make extended prediction of days using corona virus data for countries usa, iran and germany. the predicted result revealed continuous progression of the outbreak in these countries. in another work by y. novanto [ ] long short-term memory model was used. the available global data set on coronavirus was divided in to sets namely, training ( february, , -march, , ) and test set (march, , to january, , ). where training set was used to learn long short-term memory model and its performance was tested on the test set. the root mean square error was reported to be . . authors did not use the trained model to forecast possible decline of coronavirus cases. authors in [ ] proposed machine learning and cloud computing based model to effectively to track the disease, predict growth of the epidemic and design strategies and policies to manage its spread. they fitted the available data on coronavirus using generalized inverse weibull distribution to develop a prediction framework that resulted in a statistically better performance than the baseline model ( by jianxi luo from singapore university of technology and design (sutd)) considered in the work. their model makes details country-wise predictions on growth and decline of coronavirus cases. in addition to this, they have deployed their model on a cloud computing platform for more accurate and real-time prediction of the growth behavior of the epidemic. the baseline model by jianxi luo used in their work proposed in [ ] was based on standard seir model. this work also presents countywise predictions on coronavirus cases. however, their published results on predictions do not match with current situation of coronavirus cases globally. for example, it was forecasted by their model that covid- may end in india by may, , but, it does not stand true. the key reason to the failure is that the uncertainty and changes are continuously evolving real-world scenarios affecting the affect the distribution of cases and hence to the curve parameters of any model. the models discussed in section are intuitive enough to predict the pattern of corona. however, they fail on revealing the likely date of maximum infected cases, the possible decline and importantly when will the pandemic ends. probable reason to their failure is poor training of model due to lack of historical data. in addition to this, every country is different in population, diversity, density, rules and regulations and geographic structure. data set of one country may not represent dynamics of some another country. it is not possible to have one standard training data set for a model to learn that suffice these constraints. with covid- occurring globally for the first time, these time series models fails to provide desired insights. by the end of covid- globally this time, each country will have enough historical data to learn and make future remedies to prevent further occurrence of this disease. in current situation, mathematical model namely seir is a good choice to analyze the spread and the control of corona infectious disease. the model categorizes each individual in the population into one of the following four groups: . susceptible (s) -people who have not yet been infected and could potentially catch the infection . exposed (e) -people who are exposed, but not yet infectious . infectious (i) -people who are currently infected (active cases) and could potentially infect others they come in contact with . recovered (r) -people who have recovered (or have died) from the disease and are thereby immune to further infections . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . these groups contain a certain number of people on each day. however, that number changes from day to day, as individuals move from one phase to another. for instance, individuals in compartment s will move to the compartment e, if they are exposed. similarly, exposed people will move to the recovered i group once they catch infection. from this stage people may move to recovery (r phase) or die from the disease. the total population n across the four groups (s+ e+ i+r) is assumed to remain the same at all times. where n is the total population of the country (or state/region) considered in the study. since, people move from one phase to other over time, the groups s,e,i,r are functioned of time t, represented by s(t): number of people susceptible on day t, e(t): number of people exposed on day t, i(t): number of people infected on day t and r(t): number of people recovered on day t as shown in figure . based on the chain between groups, goal is to find out how the number of people in each phase changes with time. seir model make three simple hypotheses on what drives the movement of people between these groups. first hypothesis controls the transmission from group s to e using parameter β. it defines expected amount of people an infected person infects per day. second hypothesis responsible for change from e to i is controlled by parameter δ. it represents the incubation period of the disease, which is the time between exposure to the virus and symptom onset. in case of coronavirus disease it is average of - days and can be up to days. lastly, the third hypothesis, controlled by parameter γ is responsible is defining proportion of infected recovery per day. in summary, seir model consist of system of nonlinear ordinary differential equations(ode's) in the time domain with three parameters namely, β, δ and γ. equation below represents the change in people susceptible to the disease and is moderated by the number of infected people and their contact with the infected. equation gives the people who have been exposed to the disease with time. it grows based on the contact rate and decreases based on the incubation period whereby people then become infected. the change in the infected people based on the exposed population and the incubation period is addressed by equation . it decreases based on the infectious period, so the higher γ is, the more quickly people die/recover and move on the final stage in equation . besides three fundamental parameters in seir model, there is one more important variable that is important to discuss, r o value. it is the total number of people an infected person infects. to calculate r o value, we use the formula = β γ . r is a indicator of reproduction rate of disease. a r o < means that an outbreak is subsiding since each infected person is transmitting the virus to fewer than one other person. whereas, r > one means the virus is spreading exponentially. r for corona virus is estimated by many gropus. the imperial college group has estimated r o to be somewhere between . and . . most modeling simulations that project future cases are using r in that range for predictive task. given r o and γ values from literature, β can be computed for corona virus disease and equations , , and are solved. one major limitation of standard seir model is the user sets the parameters that control this change often based on expert knowledge and, hence remains constant during modeling. this makes the model unrealistic to capture the real trend of development of the disease. consider the parameter r that controls the reproduction rate of . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . the disease. keeping this parameter constant while modeling seir may not be a good choice since it is influenced by several external factors. population density, divergent demographic regions, mitigation efforts, such as social distancing, school, business , malls closures, and wearing of face masks all contribute in driving the r o number down. in addition to this, the characteristics of corona virus itself majorly influences on the r o rate. in this work, we present a modified seir model wherein, we make the model learn seir specific parameters from the data instead of keeping them constant for the realistic performance. under our proposed model, we consider actual corona virus data related to india that details date wise confirmed, recovery and death cases. using this data, our proposed algorithm learns parameters over time t such as: r o , β(t), s(t),e(t), i(t), r(t). this brings change in standard equations of seir model represented by equations , , and as equations , , and respectively. the key intuition behind learning the parameters r o and thus β(t) as, r o = β γ from the data is to get the real change in reproductive rate over time. as discussed earlier, the key factors influencing reproductive rate are population, lockdown controls, rule and regulations. population of india is well known. what is unknown is how reproductive rate has grown since the first case india on january , . with increasing number of confirmed cases after january , , india imposed several lockdowns to control the effect of disease. the four lockdown phases were: march, , -april, , , april, , -may, , , may, , to may, , and may, , to mat, , . where first two lockdowns were very strict whereas, some relaxations were allowed in the last two lockdowns phases. the imposition of these strict and relaxing lockdowns has majorly contributed in forming the trend of confirmed corona infected cases in india. the main idea of this paper is to automatically learn the shift in r o value under zero, strict and relaxed lockdown phases in india and predict likely decline of covid- in india. as r o continuously changes when social distancing measures are loosened and tightened again. one choice that is adopted in this paper to capture r o is using the logistic function as discussed in [ ] . the function is defined as in equation . the summary of all those parameters that are learned and fixed in our proposed algorithm are defined in table r using equations , , , and we apply curve fitting using coronavirus data to generate a model. curve fitting is a process of constructing a mathematical function or a curve that best captures the series of data points given. ideally, a good model "best fit" by capturing the underlying trend governing the data for us to make predictions of how the given data series will behave in the future. the mathematical function used in this work to learn the function f(x) from the data was "least-square". where the idea is to choose the parameters of the function so as to minimize the fitting error, i.e., the distance between the data values y i and the y-values f(x i ) on the fitted curve. the "least-square" method uses root-mean-square error method to compute the difference between actual and fitted value as represented by equation . . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . we now detail our approach of curve fitting over seir model using coronavirus data in form of algorithm. for simplicity, whole process in divided into algorithms. the first algorithm which we call as "seir derivation" is responsible in computing derivatives of s, e, i and r over time. to compute r o using equation , we used algorithm called "r o derivation" . the third algorithm named "model derivation" describes model building by providing initial parameters and computation of β using "r o derivation" function. lastly, "curve fitting " algorithm fits the inputted coronavirus data using algorithms "seir derivation", "r o derivation" and "model derivation" . in this work, we used to real data set of india hosted on website [ ] . as stated earlier, the aim of this work to predict confirmed corona cases. so, we only considered data set containing date wise total confirmed, recovery, and deceased cases of individual states of india. the data set included observations from dates january, , to may, , making instances. where, january , marked the first case of corona in state kerala of india. as a first step to data preprocessing, we only kept features namely, date, total confirmed cases and state and deleted remaining features from the data set. the next step was to create two data sets from this main data set representing exclusive total confirmed cases of india and delhi respectively. this step was required since the aim was to develop predictive modeling for india and delhi separately on covid- confirmed cases. in this present . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . study, we considered india and delhi to showcase predictive results. however, our propose model is robust enough to be deployed on data set on other states for the predictive task. the above preprocessing steps resulted in two main data sets. one data set containing date wise cumulative confirmed cases in india starting from january , to may, , . second data set represents delhi from february , to may , with records. figures representes tend of daily-confirmed cases in india and delhi for and days respectively. for each data set, we performed two main predictive analyses considering strict and partial to zero lockdown. during the time period from march , to may, , , india was under strict lockdown phase. however, after may , , government of india reduced the strictness and eventually it became situation of zero lockdown. this gap between strict lockdown to almost zero lockdown has given rise to several fluctuations in corona confirmed cases. considering these fluctuations and to provide model the true behavior of confirmed cases under strict and zero lockdowns, we divided each data set in two parts. the period from till may, , in each data set was considered as strict lockdown whereas, remaining data from may, , was considered to be relaxing period. under strict predictive analysis, we made the model learn the trend of confirmed till may , and forecasted its performance for the next days. this analysis revealed the peak of confirmed corona cases conditioned on continued strict lockdown by the government. in case of relaxed lockdown, we made the model learn from the remaining time period left in the data set and discovered the peak of corona cases. in this section, we present experimental results on predicting peak of coronavirus cases in india and delhi under two main situations: (a) under strict lockdown and, (b) partial to zero lockdown. under strict lockdown phase, observations till may , were considered for all different data sets used in this work for model learning. and, predictions were made for next days using the learned model. the outcome of this experiment revealed situation of virus spread in india under continued strict lockdown beyond may , . besides extended predictions of days under strict lockdown situation, we also present the outcome of model fitting on strict lockdown data set using algorithms discussed in section . figures and represents fitting of learned model over actual new cases of coronavirus data set of india and delhi respectively. the curve fitting outcome on data set of india in figure shows similar trend of actual increase in new cases of coronavirus infection till may , . we notice, steep increase in cases from start of april . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . figure shows outcome on data set of delhi. the actual cases till may , in delhi were whereas, model predicted it be . the msle for this data set was computed to be . . we now present predictions on trend of new cases of coronavirus for continued strict lockdown beyond may , to discover its peak and decline. the fitting of real data set on our propose algorithm revealed that predicted peak in india was on may , and thereby was decline in new cases. in delhi peak predicted was may, , . figure and figure shows the peak and decline trend of new cases in india and delhi respectively. the % of corona virus effect was expected to vanish by early, july conditioned on continued strict lockdown. table summarizes values of parameters r ostart , r o end , k and x o learnt by the model on data sets of india, delhi and haryana. as per the results, peak of new cases were predicted on th day from start of spread of disease in india and th day in delhi. the above-presented results were to stand true if there was a situation of extended strict lockdown after may , in india. however, it is well known that relaxation in lockdown have been eased steadily after may , and, has reached to partial to zero lockdown stage in india. considering this, data available till today may not be a good choice for a model to learn since it is the combination corona cases occurred during of strict and zero lockdown phases in india. hence, to predict the situation of new cases of coronavirus in india, it was important to discard the records before may , . the key assumption made by the model to make new forecast for india was to consider relaxed lockdown. we made predictions for days by our proposed model with values of key parameters r ostart and r o end set manually instead of learning them from data. the results of prediction are shown in figure and figure for india and delhi respectively. as per the predictions by the model, the peak of coronavirus is expected to hit the nation on july , with over cases and thereby declining. the % cases are forecasted to vanish by september, . in delhi the disease will be at peak on july , . the model was fiited with r ostart of . , for india and . for delhi. . cc-by-nd . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted july , . . https://doi.org/ . / . . . doi: medrxiv preprint the study done in this work indicated that india is yet to achieve the peak in the spread of coronavirus disease. the predictive model proposed revealed that it is unlikely to get rid of covid- before end of october in india. it is ofcourse not good news, but has to be accepted to meet the basic survival. referring to the model development, it used combination of epidemiological model (seir) and mathematical curve fitting method to forecast the impact of the covid- in india. for conventional seir to begin simulation, the basic parameters such as, β, r o ,γ, δ, population are to be fixed. however, in reality these parameters may vary depending on several factors like country, states, lockdown strictness, rules and regulations and social distancing. keeping them fixed may affect the prediction accuracy of the model. while the factor population of can be easily be identified for the country, the other variable parameters are not easily retrievable. hence, approximating them through process of "curve fitting" proposed in this work is a good choice. to provide robust learning to the model, the historical data of coronavirus confirmed cases in india till may , was used. the key reason to choose the data till may , was because till this date india was under strict lockdown phase. extending the historical data beyond this time for the purpose of learning may have affected the curve parameters. the parameters β and r o were learnt through the method of "least-square" deployed on seir model. this fitting of historical data on seir model discovered the possible peak of corona, i.e., may , in india. however, situation in india was different after may , . people in india were given relaxation in movement, migration of labourers, change in diagnostic facilities and many such factors contributed in further progressive spread of the disease. to predict new peak of coronavirus under this situation is a challenging task since many variable factors influence the coronavirus infection rate from person to person. considering this, it was sensible to make the model relearn the situation of spread under partial to zero lockdown phase. this revised learning discovered new peak at july , to be the date of maximum confirmed cases to reach in india. similar predictions were also done for the capital of india, new delhi. the new predictions made for india under partial to zero lockdown are again under assumptions that things will move the way they are currently moving with no variations. however, the predictions for the future may change rapidly with time. where, different mobility patterns of indian people, social distancing, corona testing facility, ban on international travel and group activities will play a key role in increasing or decreasing the infection rate in india. another factor, which may influence the predictions and affect the distribution of infected cases in future is the virus mutation. however, a study like presented in this work will enable citizens of india, government and medical staff to plan their way forward. in addition to this, contribution of study provides insights on situation of virus spread under full, partial and zero lockdowns. it is the now the awareness of citizens of india to act and behave responsibly to bring life back to normal and mitigate affect of virus from the country. coronavirus (covid- ): arima based time-series analysis to forecast near future time series modelling to forecast the confirmed and recovered cases of covid- application of the arima model on the covid- epidemic dataset. data in brief forecasting of covid- cases and deaths using arima models seir and regression model based covid- outbreak predictions in india covid- epidemic analysis using covid- outbreak prediction with machine learning covid- growth prediction using multivariate long short term memory predicting the growth and trend of covid- pandemic using machine learning and cloud computing predictive monitoring of covid- . white paper covid- in india infectious disease modelling: fit your model to coronavirus data social distancing key to slowing covid- spread key: cord- -v kpmk b authors: hagemeijer, marne c.; rottier, peter j.m.; de haan, cornelis a.m. title: biogenesis and dynamics of the coronavirus replicative structures date: - - journal: viruses doi: . /v sha: doc_id: cord_uid: v kpmk b coronaviruses are positive-strand rna viruses that are important infectious agents of both animals and humans. a common feature among positive-strand rna viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in rna synthesis localize. double-stranded rna, presumably functioning as replicative intermediate during viral rna synthesis, has been detected at the double-membrane vesicle interior. recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. this review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral rna synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. positive-strand rna (+rna) viruses are the most abundant viruses in nature. many important pathogens belong to this category, including poliovirus (pv), hepatitis c virus (hcv) and the severe acute respiratory syndrome (sars)-coronavirus (cov). a distinctive common feature of +rna viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (rtcs) localize. the various membrane rearrangements observed in +rna virus-infected cells range in size from to nm, contain lipids that are derived from various cellular compartments and demonstrate an impressively diverse plethora of morphologies that include, among others, clusters of vesicles for the picorna-and togaviridae, spherule-like invaginations for the bromoviridae and nodaviridae, and vesicle packets and membranous webs for the flaviviridae (reviewed in [ ] [ ] [ ] ). these membrane rearrangements seem to be beneficial for (i) sequestering and concentrating all viral and cellular components necessary for viral rna synthesis and (ii) to provide a protective microenvironment against virus-elicited host defense mechanisms. also coronaviruses (covs), enveloped +rna viruses that belong to the family coronaviridae, extensively rearrange cellular membranes into organelle-like replicative structures during infection. these replicative structures consist of double membrane vesicles (dmvs) and convoluted membranes (cms). the viral replicase proteins involved in rna synthesis localize to both these structures, while double-stranded rna (dsrna), presumably functioning as replicative intermediate during viral rna synthesis, has been detected at the dmv interior [ , ] . recent studies have provided new insights into the assembly and functioning of the cov replicative structures. this review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the rtcs, and the location of viral rna synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. the coronaviridae are a family of evolutionary related, enveloped +rna viruses that together with the arteriviridae and the roniviridae, belong to the order of the nidovirales. historically, covs have been recognized as important infectious agents for domestic livestock, poultry and companion animals. in contrast to the animal viruses, human covs (hcovs) have been associated with relatively mild upper and lower respiratory tract infections, including ordinary common colds. however, in - the outbreak of a novel hcov in china, causing severe fatal atypical pneumonia in infected individuals, demonstrated that hcovs are also able to induce severe life-threatening disease in humans. this virus was called the sars-cov [ , ] and emerged in the human population from an animal reservoir, probably originating from bats, with palm civet cats acting as intermediate hosts [ , ] . among the +rna viruses, covs clearly distinguish themselves by carrying the most complex and largest genomes, which range in size from ~ to kb [ ] . despite the variation in size, the overall genome organization of the various covs is quite conserved. the genome contains all the genetic information necessary to direct both the synthesis of full-length genomic rna (replication) and the (discontinuous) production of subgenomic mrnas (transcription) [ ] . the linear +rna genome of covs is ' polyadenylated and has a ' cap structure, thereby mimicking cellular mrnas. the ' and ' ends of the genome contain untranslated regions (utrs) with cis-acting elements that are important for replication and transcription. two-thirds of the genome consists of two large open reading frames (orfs), orf a and orf b. the remaining ' one-third part encodes the structural proteins interspersed with sequences encoding some accessory proteins. a schematic picture of the prototype mouse hepatitis virus (mhv) genome is shown in figure a . the structural and the accessory proteins are expressed from a nested set of ' coterminal subgenomic (sg) mrnas that are generated via discontinuous transcription during subgenome-length minus-strand rna synthesis [ , ] . the rna-dependent rna polymerase (rdrp) copies the genomic positive-sense rna into a negative-sense template until it reaches a transcription-regulation sequence (trs). at this point, rna synthesis may either continue or the rdrp may relocate to the ' end of the genome and complete the negative-sense sgrna. these negative-sense sgrnas serve as templates for the synthesis of the corresponding positive-sense sgrnas. as a result, the positive-sense sgrnas form a nested set of mrnas, which extend for different lengths from a common ' terminus while also having a common ' end, which is known as the leader sequence. generally, only the ' first unique gene of each sgrna is translated (reviewed in [ ] ). minus-and plus-strand rna synthesis is already detected at to min post infection (p.i.) [ ] . minus-strand synthesis, of which the resulting rna species are mainly present as double-stranded intermediates because of their association with plus-strand rna molecules, peaks at to h p.i. after which the synthesis declines but does not stop [ ] . the plus-stranded rnas are produced in a -to -fold excess over their minus-strand counterparts [ , ] . the viral replicase is encoded by the two most ' orfs of the genomic rna, orf a and orf b. translation of orf a and orf b of the genomic rna generates two very large replicase polyproteins (pp), pp a and pp ab. the latter is synthesized via a − ribosomal frameshift mechanism mediated by a pseudoknot structural element at the end of orf a [ , ] . these replicase polyproteins are extensively processed by viral proteinases (reviewed in [ ] ), resulting in the generation of sixteen nonstructural proteins (nsps). a schematic representation of the cov replicase polyprotein is shown in figure b . the cov nsps form together with the nucleocapsid (n) protein, and presumably several host proteins, the membrane-associated rtcs. to generate the functional cov replication complexes, the replicase polyproteins pp a and pp ab have to be proteolytically processed to liberate the sixteen individual protein products. cleavage of pp a and pp ab is performed by two viral proteinases that reside in nsp and nsp : the papain-like proteases (plpro and plpro ) located in nsp and the chymotrypsin-like cysteine proteinase ( clpro), or main protease (mpro), present in nsp (reviewed in [ ] ). besides the mature nsps, also the intermediate and precursor polyproteins are likely to be functionally important. hence, the cleavage of these proteins may somehow be involved in the temporal regulation of plus and/or minus sense viral rna synthesis [ ] [ ] [ ] . schematic representation of the +rna genome of mhv-a . the coronavirus genome contains a ' cap structure and a ' poly(a) tail, together with untranslated regions (utrs). the first two-thirds of the genome consist of two large open-reading frames (orfs), orf a and orf b, which are translated into two large replicase polyproteins (pp a and pp ab). pp ab is synthesized via a − ribosomal frameshift mechanism at the end of orf a (rfs). the final one-third of the genome contains the canonical cov structural proteins-encoding genes (s, e, m and n), interspaced by several accessory genes ( a, he, , a); (b) a schematic representation of pp ab is shown. the coronavirus polyproteins are processed by viral proteinases residing in nsp (plpro and plpro ; grey arrowheads indicate cleavage sites) and nsp (mpro; black arrowheads indicate cleavage sites), thereby generating mature nsps. hydrophobic domains (tm , tm and tm ) in nsp , nsp and nsp are indicated, together with predicted and identified rna(-modifying) enzymes: the rna-dependent rna polymerase (rdrp; nsp ), the helicase (hel; nsp ), the exonuclease (exon; nsp ), the uridylate-specific endoribonuclease (n; nsp ), and the methyl transferase (mt; nsp ); (c). schematic representation of the topology of the coronavirus polyprotein. only the part of the polyprotein is shown that contains the hydrophobic domains (indicated by boxes) residing in nsp , nsp and nsp . nsp and nsp contain hydrophobic domains that do not span the lipid bilayer. mpro indicates the viral protease residing in nsp , in between nsp and nsp . the key enzyme involved in genome replication is the rna-dependent rna polymerase (rdrp), which is present in nsp [ ] . the nsp protein is able to utilize both homo-and heteropolymeric rnas as template but its rdrp activity is dependent on primers to copy the viral rna [ ] . these primers might be produced by a non-canonical rdrp activity that has been described for the nsp -encoded 'rna primase', as this protein is able to produce short oligonucleotides complementary to the rna genome [ ] . nsp has been shown to associate together with nsp into a hexadecameric complex, consisting of eight copies of each protein, thereby forming a channel that can harbor rna and may serve as a processivity factor for nsp [ ] . nsp also interacts with nsp in a : ratio [ ] and is able to synthesize much longer transcripts [ , ] . the cov nsp protein contains a superfamily helicase domain with an amino-terminal zincbinding domain that is important for the unwinding activity of duplex rna (and dna) in a '-to- ' direction [ ] [ ] [ ] . the resulting single-strands probably serve as templates for rna synthesis. the multifunctional nsp protein additionally possesses nucleotide triphosphatase activity [ , , ] and is likely to be involved in removal of one of the terminal phosphate groups at the ' end of the positivesense rnas, which is the first step in the formation of the ' cap structure. although the enzyme that subsequently adds the guanine to the terminal phosphates (guanylyl transferase) has not been identified yet, nsp has been shown to exert s-adenosyl-l-methionine (adomet)-dependent (guanine-n )methyltransferase (n -mtase) activity [ ] . finally, the cap- structure is formed by the adometdependent (nucleoside- 'o)-methyltransferase ( 'o-mtase) activity that is present in nsp [ ] , and for which the latter needs to form a complex with nsp [ , ] . covs possess the largest genomes among the +rna viruses [ ] . they encode a large number of additional rna-modifying enzymes, which are often not present in other rna viruses. these additional enzymatic activities are probably required to ensure proper rna synthesis and might account for their large size. in addition to the cap n -mtase activity, nsp has metal ion-dependent '-to- ' exoribonuclease (exon) activity [ ] and contains a nidoviral uridylate-specific endoribonuclease (nendou; nsp ) [ ] , both able to degrade rna and dsrna [ , ] . while the function of the nendou activity in the cov infection cycle is not known, it appears that the exon activity is required to ensure high replication fidelity of the extremely large cov genome [ , ] and that nsp may function as a proofreading enzyme [ ] . covs encode three nsps that contain hydrophobic stretches that are predicted to function as transmembrane domains: nsp , nsp and nsp . consistently, membrane association has been demonstrated for the nsp , nsp and nsp proteins of sars-cov [ ] [ ] [ ] and mhv [ ] [ ] [ ] [ ] . both nsp and nsp become n-glycosylated upon insertion into the membranes of the endoplasmic reticulum (er) [ ] [ ] [ ] . interestingly, transmembrane domain predictions based on the multiple alignment of cov replicase polyprotein sequences revealed an uneven number of hydrophobic domains for both nsp and nsp [ ] . this prediction is peculiar as it would separate the viral proteinases residing in nsp and nsp from their target sequences, implying that some of these hydrophobic domains might actually not span the membrane. in agreement herewith, and in contrast to the predictions, all three nsps were shown to have both their amino terminus and their carboxy terminus exposed in the cytoplasm. while all four hydrophobic domains of nsp span the lipid bilayer, this is the case for only two of the three hydrophobic domains in nsp and for six of the seven in nsp [ , ] . this experimentally established topology model ( figure c ) makes more sense, as it positions all of the proteinase cleavage sites on the same side of the membrane as the viral proteinases themselves. proteolytic processing of the replicase polyproteins probably starts during translation and prior to membrane insertion. interestingly, the cleavage between nsp and nsp appears to be a rapid event [ , , ] . this cleavage at the amino-terminus of the first hydrophobic/transmembrane domain of nsp probably facilitates the membrane insertion of nsp as it may enable the first hydrophobic domain to function as a signal peptide. the occurrence of conserved non-membrane spanning hydrophobic domains in nsp and nsp , which are likely to be peripherally associated with the membrane, suggests an important function for these domains, possibly in the biogenesis of the cov replicative structures. in this respect it is of interest to mention that the seventh hydrophobic domain of nsp contains putative palmitoylation sites (our own predictions and [ ] ). the addition of palmitic acid to this hydrophobic domain may stabilize its peripheral membrane association. in addition to the nsps mentioned above, other cov nsps are involved in rna binding (nsp and nsp ; [ , ] ) or in evasion of the antiviral response of the host (nsp and nsp ; [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ). the function of nsp is not yet known, although this protein was shown not to be essential for virus replication [ , ] . the reader is referred to several excellent reviews on this topic for more detailed insights [ , , ] . upon infection of host cells, covs induce a variety of membranous structures of which some have been associated with viral rna synthesis. the first detectable membrane rearrangements in cov-infected cells are to nm organelle-like structures that have been described for both mhv [ , ] and the sars-cov [ , ] and consist of spherical vesicles containing double lipid bilayers, termed dmvs ( figure ). in between the clusters of dmvs, reticular cms are characteristically present [ , , ] . later in infection large virion-containing vesicles (lvcvs) [ , , , ] , highly organized cubic membrane structures [ , ] and condensed tubular bodies [ , ] are formed. the latter two structures are likely a result of the overexpression of cov structural proteins during infection and do not seem to be involved in cov replication [ ] . electron tomography studies demonstrated that in sars-cov infected cells the dmvs and cms form an interconnected membranous network that is also continuous with the er [ ] . this latter observation is in agreement with previous reports describing dmvs in close proximity to the er or continuous with it [ , , ] . moreover, (partial) colocalization of replicase proteins together with the er resident protein disulfide isomerase (pdi) has been reported [ ] , while also the translocon subunit sec α was found to be redistributed to the replicative structures upon sars-cov infection [ ] . the combined data indicate that the er is the most likely membrane donor for the dmvs, despite the absence of most conventional er markers on these structures [ , , , ] . the cov replicative structures, i.e., dmvs and cms (figure ) , have been associated with viral rna synthesis, as the mhv and sars-cov nsps have been shown to localize to these structures [ , , , , , , , [ ] [ ] [ ] [ ] . in addition, antibodies recognizing dsrna, the presumed replicative intermediates, label the interior of the sars-cov-induced dmvs [ ] . newly synthesized viral rna, visualized by -bromouridine '-triphosphate (brutp) labeling, was observed in mhvinfected cells in close proximity to the replicative structures by immunoelectron microscopy [ , ] . remodeling of eukaryotic cellular membranes into the replicative structures is likely dependent on the combined effects of both viral and cellular proteins and probably also on the specific lipid composition of the membranes themselves. nevertheless, only few studies have been published addressing the involvement of cellular constituents in cov replication and the generation of the replicative structures. it is conceivable that covs hijack cellular pathways to meet the conditions that are required for their replication, consequently adopting intrinsic properties of the utilized pathways themselves. in agreement with the er being the most likely membrane donor of the dmvs, an intimate association between the early secretory pathway and cov replication has been demonstrated. rtc formation and replication in mhv-infected cells were inhibited when the secretory pathway was interfered with by blocking protein export at er exit sites by treatment with the kinase inhibitor h or by expression of a dominant active sar mutant [ ] . also treatment with brefeldin a (bfa), an inhibitor of er-to-golgi trafficking, or knockdown of its target gbf , inhibited mhv replication while reducing the number of dmvs [ ] . similar results were published for sars-cov infected cells treated with bfa and it was noticed that the inner and outer membranes of the dmvs were separated in bfa-treated cells [ ] , which may explain the observed inhibition of viral replication. by their main ultrastructural characteristic, the double lipid bilayer, cov dmvs very much resemble autophagosomes. this similarity prompted studies into the role of the autophagy machinery in cov replication. initial studies revealed a colocalization between the autophagosomal protein marker microtubule-associated protein light-chain (lc /atg ) with the replicative structures [ ] ; moreover, viral replication was impaired and dmvs were not detected in the absence of the essential autophagy protein atg [ ] . in other studies however, these colocalization data could not be reproduced [ ] , while the absence of atg did not affect cov replication [ , ] . yet, lc was found in association with the replicative structures by zhao and coworkers [ ] . furthermore, others showed that, while the endogenous lc protein was recruited to the replicative structures, this was not the case for a gfp-tagged form of lc [ , , ] that is often used as a marker for autophagosomes [ ] . in agreement herewith, cov replication was shown to be unaffected in autophagy-deficient cells lacking atg , although depletion of lc severely affected cov replication [ ] . unlike autophagosomes, which may also be induced by expression of cov nsp [ ] , cov replicative structures were shown to be decorated with the non-lipidated form of lc . similar findings were also reported for edemosomes [ , ] , er-derived vesicles that transport er chaperones to lysosomes. as the edemosome cargo proteins edem and os- were also detected in association with the cov replicative structures, it was proposed that covs hijack edemosomes for their replication [ , ] . in agreement herewith, the transmembrane sel l protein, which was recently shown to interact with lc and to have a critical function in edemosome biosynthesis, was also shown to colocalize with dsrna foci in cov-infected cells, while its depletion negatively affected cov replication [ ] . the cov nonstructural membrane proteins, nsp , and probably play an essential role in the membrane rearrangements required for the induction of the replicative structures and in the anchoring of the rtcs to these structures. these proteins were shown to be engaged in homo-and heterotypic interactions [ ] . interestingly, co-expression of nsp with the c-terminal one-third part of nsp (nsp c ) resulted in the relocalization of these proteins from the er into discrete foci mostly localizing to the perinuclear region of the cell [ ] . although nsp was not required for the observed relocalization, it was recruited to the perinuclear foci when co-expressed [ ] , in agreement with this protein interacting with nsp [ ] . ultrastructural analysis of cells co-expressing nsp and nsp c revealed that the membranes of the er exhibited more curvature, although these membranes did not resemble the dmvs observed in cov-infected cells [ ] , which may not be surprising as only the cterminal part of nsp was used in these co-expressions with nsp . similar membrane rearrangements were not observed when the nsp from mhv was co-expressed with nsp from sars-cov (or vice versa), while (deletion) mutagenesis studies indicated essential roles for the large luminal loops of nsp and nsp in the relocalization of these proteins [ ] . while co-immunoprecipitation and immunofluorescence assays indicate that nsp and nsp of mhv interact, this interaction could not be confirmed using the venus protein-fragment complementation assay [ ] . we hypothesize that the interactions between nsp and nsp mediate some kind of "zippering" of the lipid bilayers of the er, which ultimately leads to the formation of the dmvs. in this model nsp and nsp interact via their luminal loops in such a way that their interaction prevents reconstitution of a functional venus protein. several other studies also suggest an important role for nsp in the generation of the replicative structures. disruption of the nsp glycosylation sites present in the loop between the first and second hydrophobic region, leads to the formation of aberrant dmvs in which the inner and outer membranes are detached, while the number of cms is increased [ ] . in agreement herewith, although the fourth hydrophobic domain of nsp is dispensable, the other three transmembrane regions are required for cov replication [ ] . furthermore, co-expression of the counterparts of the cov nsp and nsp of the distantly-related equine arteritis virus (eav), resulted in the rearrangement of host cell membranes into dmvs, albeit with a morphology [ ] differing from that observed in eav-infected cells [ ] . mutations of cysteine residues present in the luminal loop of eav nsp (the eav counterpart of cov nsp ) resulted in altered morphologies of the dmvs, while the introduction of a n-glycosylation site in this loop also affected their morphology to some extent [ ] . like covs, other +rna viruses also somehow induce membrane rearrangements that are required for their replication and transcription. for several of these viruses similar membrane rearrangements can be induced by the (co-)expression of nsps (for reviews see [ ] [ ] [ ] ). these nsps are either integral transmembrane proteins, examples being the ns a proteins of dengue virus (denv) [ ] and kunjin virus [ ] and the ns b protein of hepatitis c virus (hcv) [ ] , or alternatively the proteins are only peripherally associated to the lipid bilayer, such as the a protein of brome mosaic virus (bmv) [ ] and the c protein of poliovirus (pv) [ ] . strikingly, however, also for the integral membrane proteins the occurrence of hydrophobic/amphipathic regions that do not span the lipid bilayer but are peripherally associated with membranes, which has also been demonstrated for cov nsp and nsp [ , , ] , appears to be a common feature [ , [ ] [ ] [ ] . another similarity among the nsps of different +rna viruses appears to be their ability to assemble into larger protein complexes. such interactions have been observed not only between nsp , nsp and nsp of covs, but also between the nsps of other +rna viruses, including the bmv a protein [ , ] and the flavivirus ns a and ns b proteins [ , ] . how are the nsps of covs able to induce the observed membrane rearrangements? we speculate that the similarities between the membrane-associated nsps of different +rna viruses relate to their common ability to remodel membranes. the induction of membrane curvature in lipid bilayers is critical when remodeling host cellular membranes. the membrane-associated viral proteins may act as multimeric scaffolds able to impose such curvature, for instance by acting as wedges by inserting their amphipatic helices partially into one side of the bilayer (reviewed in [ ] [ ] [ ] ). the viral proteins may function similar to host cellular proteins known to induce membrane bending via a scaffold mechanism, as exemplified by the copi and copii complexes, and/or via the insertion of amphipathic domains into the lipid bilayer, as has been proposed for the small gtpase sar (reviewed in [ , ] ). the last few decades have provided virologists with exciting new information regarding the functions and structures of individual nsps and the characterization and formation of the membranous structures induced by +rna viruses. these insights were obtained by classical biochemical, immunofluorescent and ultrastructural approaches. unfortunately, little information regarding the dynamics of the (viral) proteins present at the membranous replicative structures in living cells is known. such studies are important as classical approaches only provide static views of cellular processes and do not necessarily reflect the dynamics underlying virus replication in living cells. to date, only few studies on the dynamics of the replicative structures of plus-strand rna viruses and their associated proteins have been published [ ] [ ] [ ] [ ] [ ] [ ] [ ] . by using a gfp-tagged version of nsp , shown by immuno-electron microscopy (iem) to be recruited to the dmvs and cms, as a marker the dynamics of the cov replicative structures were studied using live cell imaging [ ] . these studies showed for the first time that the cov replicative structures are moving through the cell. however, it appeared that the cov replicative structures consist of two classes that demonstrate different mobilities: large structures lacking any displacement and smaller structures with relatively high saltatory mobility. the smaller replicative structures were hypothesized to correspond to individual dmvs, while the larger ones supposedly represent the dmv/cm assemblies that have been observed in ultrastructural studies of cov-infected cells [ , ] . in sars-cov-infected cells the dmvs are confined to a reticulovesicular network [ ] . we therefore speculate that the small structures have not yet been 'captured' into this network. however, correlative light-electron microscopy studies will be required to solve this issue. live cell imaging studies of hcv-and semliki forest virus (sfv)-infected cells also reveal the presence of replicative structures that could be discriminated on the basis of their size and mobility. hcv induces the formation of a so-called membranous web, in which dmvs can be observed [ ] . large hcv structures, probably representing membranous webs, exhibited limited movement, whereas smaller ones were mobile and could travel long distances throughout the cytoplasm [ ] . sfv-induced vacuoles are assembled at the plasma membrane after which they are transported to modified lysosomes [ , ] . sfv-infected cells also harbor large acidic immobile perinuclear vesicles and smaller acidic cytoplasmic vesicles that showed saltatory movements. in addition to these acidic vesicles, sfv-infected cells contain a class of non-acidic highly mobile vesicles that displayed multidirectional short-distance movements. moreover, fusion of the neutral mobile structures with the acidic mobile structures resulted in the formation of the large acidic structures [ ] . such events of fusion of smaller replicative structures into larger ones have not been observed (yet) for the cov and hcv replicative structures [ , ] . the calculated velocities of the saltatory movements of the smaller nsp -positive structures in cov-infected cells [ ] correspond to those measured for microtubule-mediated transport [ ] . the observed association of these structures with microtubules and the inhibition of trafficking in the presence of a microtubule network-disturbing drug confirmed the transport of the smaller structures on microtubular tracks [ ] . a role of the cytoskeleton in the movement of replicative structures has also been described for hcv, sfv, and pv [ , [ ] [ ] [ ] . disruption of a functional microtubular network inhibited the movement of the small hcv and nascent pv replicative structures [ , ] and the trafficking of sfv neutral vesicles to acidic organelles [ ] , concomitant with dispersal of these structures throughout the cytoplasm. strikingly, inhibition of microtubule-dependent trafficking did not or only modestly affect the replication of these viruses [ , , ] . disruption of the actin network also did not affect cov replication much, although the replicative structures again failed to accumulate in the perinuclear area [ ] . collectively, these results show that the cytoskeleton is required for the perinuclear accumulation of the replicative structure rather than for replication per se. additional studies are required to clarify the role of the perinuclear targeting of the cov replicative structures during infection. up till now, only few studies have addressed the dynamics of individual viral proteins when present at the replicative structures. recently, we analyzed the dynamic properties of three replication-associated proteins, i.e., the soluble nsp and n proteins and the integral membrane protein nsp , and demonstrated that these proteins display different diffusional mobilities when present at the replicative structures. nsp , when expressed in trans is recruited to the replicative structures [ ] . after recruitment, nsp was shown to be immobilized by using fluorescent recovery after photobleaching (frap) methodology. in other words, nsp already associated with the replicative structures was not exchanged by nsp present at other locations in the cell. similar results have been demonstrated for other +rna virus replication-associated proteins, although the published literature on this subject is limited. also in hcv-infected cells, ns a-positive structures showed a static internal architecture when (part of) the ns a fluorescent protein pool was bleached [ ] . when expressed individually, ns a is highly mobile [ ] , similar to nsp . apparently, in the context of a viral infection, when other viral proteins are present, mhv nsp and hcv ns a are immobilized at the replicative structures presumably due to protein-rna or protein-protein interactions. in agreement herewith, large-scale protein-protein interaction studies demonstrated that nsp of mhv and sars-cov is engaged in a multitude of interactions with itself, nsp , nsp , nsp , nsp , nsp , nsp , nsp and nsp [ , [ ] [ ] [ ] . these observations are remarkable in view of the dispensability of nsp during cov infection in vitro [ ] . yet, nsp has to be somehow important in vivo as its coding sequence is maintained during evolution. in addition to its structural role in the coronavirion, i.e., in packaging of the genomic rna into the rnp complex, the structural n protein is also important in coronavirus replication and has been detected in the perinuclear region of infected cells colocalizing with markers for the replicative structures [ , , , ] . the interaction of the n protein with nsp is presumably important for the initial recruitment of n to the replicative structures [ ] , while n-n protein interactions were sufficient for recruitment of (mutant) n proteins in the presence of wild type n proteins [ ] . in contrast to nsp , the n protein is not immobilized at the cov replicative structures but is associated with it rather dynamically [ ] . this may not be surprising, as the multifunctional n protein is both involved in viral replication [ ] [ ] [ ] and virion assembly [ ] . as the cov replicative structures and virion assembly sites appear to be spatially separated, the newly synthesized genomic viral rna needs to be transported from the replication sites to the assembly sites. the n protein presumably facilitates this transport, consistent with its dynamic behavior. when expressed in trans in infected cells, the nsp -gfp fusion protein was detected at the er and at the replicative structures [ , ] . by performing fluorescence loss in photobleaching (flip) experiments continuity was demonstrated between the membranes of the er and the replicative structures that harbor nsp [ ] , in agreement with the model that the dmvs and cms form an interconnected network that is continuous with the er [ ] . however, nsp displayed different diffusional mobilities at different subcellular locations [ ] . it was more mobile in the er than at the replicative structures. this reduced mobility may be (partly) due to its engagement in interactions with the other transmembrane-containing nsps as well as with itself [ ] . also the mobility of the hcv ns b protein, which is an integral transmembrane protein as well, depends on its intracellular location. when expressed in the absence of other viral proteins, this protein is present at the er and at so-called membrane-associated foci (mafs) that are induced upon expression of this protein [ ] . frap analysis showed that ns b present at the mafs had a reduced mobility compared to ns b at the er, which was suggested to result from ns b being engaged in different interactions when present on mafs or the er [ ] . currently, one of the most enigmatic issues regarding cov replication is the precise localization of the sites of active viral rna synthesis. although cov rna synthesis appears to be protected by membranes [ ] it is still unclear whether synthesis of nascent viral rna occurs at sites of dsrna accumulation, as pores connecting the interior of the coronavirus dmvs with the cytoplasm have not been detected [ ] , while the nsps localize to both dmvs and cms [ , , , , , , , [ ] [ ] [ ] [ ] . to identify sites of nascent viral rna synthesis, one has to define what actually constitutes the active viral replication complexes. although dsrna molecules function as intermediates of replication and transcription, their presence at certain sites per se does not imply (all) these structures to be actively involved in rna synthesis. likewise, the location of viral enzymes that are required for rna synthesis does not need to correlate with active rtcs. moreover, newly synthesized rnas are not necessarily located at their site of synthesis as they may diffuse or be transported away to other subcellular locations. in view of these considerations, sites active in rna synthesis are expected to contain at least three components: the rdrp, dsrna intermediates active in replication/transcription and nascent viral rna. newly synthesized viral rnas, visualized by -bromouridine '-triphosphate (brutp) labeling, were shown to colocalize with antibodies recognizing either nsp or the c-terminal part of pp a [ ] , and were observed in close proximity to the dmvs by immunoelectron microscopy in mhv-infected cells [ , ] . recently, a new method was used to detect and visualize newly synthesized coronaviral rna by incorporation of an alkyne-modified uridine analog, -ethynyl uridine (eu), onto which an azide-derivatized fluophore was coupled via a copper (i)-catalyzed cycloaddition reaction (click chemistry). with this method, it was shown that throughout mhv infection foci of nascent rnas could be detected, which colocalize with the rdrp-containing nsp , indicating that they correspond with sites of active coronaviral rna synthesis. the relationship between nascent rna and dsrna is, however, less clear. while early in infection nascent rnas colocalize at or adjacent to patches of dsrna dots, presumably corresponding to dmvs, this correlation is much less apparent at later times when the dsrna dots are spread throughout the cell. many dsrna dots are apparently not transcriptionally active as no eu labeling was associated with them, while many foci of eu labeling did not appear to colocalize with the dsrna dots [ ] . different models can be put forward to explain these observations. in one model, dmvs function as the sites of active rna synthesis. at the later times in infection, many dmvs are no longer active, while the ones that are active may contain only little dsrna, resulting in less apparent colocalization of dsrna and eu labeling. in another model, dmvs are non-functional end-stage products. they are not actively involved in rna synthesis, but rather harbor dsrnas that are not (longer) functioning as intermediates in rna synthesis. in this model, which is in agreement with the presumed absence of pores in these structures [ ] , the cms would be the only plausible alternative for the sites of active rna synthesis. in yet another model, dmvs may be the initial sites of active rna synthesis, particularly early in infection, while at later times the membranes become sealed, connections are lost and rna synthesis shifts to the cm assemblies. clearly, ultrastructural studies will be required, ideally (co)localizing nascent rnas as well as the rdrp, to definitely determine the precise localization of cov rna synthesis. for most other +rna viruses the identification of the sites of active rna synthesis appears less complicated. nascent rnas, as well as nsps, have been shown to label the spherules that are observed in bmv- [ ] , sfv- [ ] or flock house virus (fhv)- [ ] infected cells at the modified er, lysosomes and mitochondria, respectively, indicating that these structures correspond with the sites of active rna synthesis. nascent rnas were previously also shown to colocalize with dsrna in kunjin flavivirus-infected cells [ ] . electron tomography of the membrane rearrangements observed in flavirus-infected cells revealed that the inner content of the dmvs, which contains nsps and dsrna, is connected to the cytoplasm via a pore [ , ] , indicating that these dmvs are actually spherule-like invaginations (once) active in rna synthesis. cov replicative structures/rtcs are macromolecular assemblies, the components of which are engaged in a plethora of protein-protein, protein-rna, and protein-lipid interactions [ ] [ ] [ ] ] . currently, the exact composition of the replicative structures/rtcs is not known, let alone the full arsenal of interactions occurring within these structures. moreover, the replicative structures are likely to be subject to some form of maturation [ , , , ] , as their composition appears to change during the course of infection as determined by biochemical and immunofluorescence analyses. thus, it will be of interest to confirm, extend and refine the previously published protein-protein interactome studies that have been published for sars-cov [ ] [ ] [ ] , for example by investigating proteinprotein interactions of other covs using novel (large-scale) screening approaches. likewise, it will be of interest to get more insight into the involvement of host proteins in the formation of these structures, for example by screening for host proteins that interact with the cov nsps or by elucidating the protein content of purified replicative structures -preferably in time-using mass spectrometry. one of the difficulties associated with these studies is the complexity of discriminating whether host proteins are directly involved in the formation of the replicative structures themselves or in rna synthesis per se, as inhibition of either process will result in reduced rna synthesis, protein expression and dmv formation. therefore, assays are needed in which the formation of replicative structures can be studied independent of viral replication. such assays may be provided by co-expression of viral proteins [ , ] that induce the rearrangement of cellular membranes. recently, by using such a replication-independent assay, reticulons, which form a family of er membraneshaping proteins, were implicated in the formation of the bmv-induced, er-derived spherules that are associated with viral rna synthesis [ ] . reticulons are involved in the induction of er membrane curvature [ ] [ ] [ ] and seem to be required by bmv for determining the size of the spherules and for stabilizing the spherule necks [ ] . it will be of interest to study the putative role of these proteins in cov replication and in reshaping of the er membranes by cov nsps. other proteins playing a role in shaping and remodeling of the er are the atlastins and climp- [ , ] . also these proteins are putative candidates involved in cov-induced membrane remodeling and would deserve to be investigated. in addition to the role of virus and host proteins in formation of the replicative structures, lipids may also be important in this process. dynamic alteration of the lipid composition can induce curvature of membranes to some extent [ , , , ] , which is, however, unlikely to be sufficient to generate the organelle-like structures observed in +rna virus-infected cells. it is more likely that lipids, together with lipid-modifying enzymes, contribute to the formation of the replicative structures by providing a suitable microenvironment to which the viral (and cellular) membrane shaping proteins are recruited. even more, +rna viruses may specifically hijack lipid-modifying enzymes for their own advantage [ , ] . this is underscored by several studies, which show that inhibition of lipid synthesis by using either drugs or small interfering rnas dramatically affects the replication of +rna viruses [ , [ ] [ ] [ ] [ ] . it will be of interest to study how and to what extent cov infection affects the lipid homeostasis in infected cells, for example by analyzing the lipid repertoire of infected cells by lipidomics techniques. finally, as all processes occurring in living cells are inherently dynamic in nature, it is also desirable to get more insight into the biogenesis and functioning of the replicative structures using various live cell imaging approaches. for example, photoactivatable fluorescent proteins can be used to investigate the formation of the replicative structures in real-time by 'optical pulse-labeling' in living cells, while the behavior of individual nsps associated with the rtcs can be studied by selectively 'switching-on' (sub)populations of proteins [ , ] . furthermore, tagging of viral rna by genetic incorporation of specific rna sequences that bind fluorescently-tagged rna-binding proteins [ , ] , hybridization of fluorescent 'molecular beacons' to the viral rnas [ ] , or combining metabolic labeling of viral rnas with cu-independent click chemistry [ ] , will allow visualization and tracking of these ribonucleic acid species in living cells. concomitant live cell imaging of viral rna and the n proteins may be used to investigate the transport of nascent rna from the replication to the assembly sites. in addition, super resolution microscopy techniques, like photoactivated localization microscopy (palm), stimulated emission depletion microscsopy (sted) and stochastic optical reconstruction microscopy (storm) [ ] [ ] [ ] can all be applied to investigate the cov rtcs and the membranous replicative structures at the ultrastructural level using fluorescently-tagged proteins, while eu-labeling of viral rna in combination with correlative light-electron microscopy may provide the resolution to indisputably pinpoint the exact location of viral rna synthesis [ ] . organelle-like membrane compartmentalization of positive-strand rna virus replication factories cytoplasmic viral replication complexes modification of intracellular membrane structures for virus replication sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum identification of a novel coronavirus in patients with severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome isolation and characterization of viruses related to the sars coronavirus from animals in southern china bats are natural reservoirs of sars-like coronaviruses evolving the largest rna virus genome a contemporary view of coronavirus transcription coronaviruses use discontinuous extension for synthesis of subgenome-length negative strands sequence motifs involved in the regulation of discontinuous coronavirus subgenomic rna synthesis coronavirus minus-strand rna synthesis and effect of cycloheximide on coronavirus rna synthesis the rna structures engaged in replication and transcription of the a strain of mouse hepatitis virus the primary structure and expression of the second open reading frame of the polymerase gene of the coronavirus mhv-a ; a highly conserved polymerase is expressed by an efficient ribosomal frameshifting mechanism characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an rna pseudoknot virus-encoded proteinases and proteolytic processing in the nidovirales processing of open reading frame a replicase proteins nsp to nsp in murine hepatitis virus strain a replication functional and genetic analysis of coronavirus replicase-transcriptase proteins the rna polymerase activity of sars-coronavirus nsp is primer dependent non-canonical rna-dependent rna polymerase in sars coronavirus insights into sars-cov transcription and replication from the structure of the nsp -nsp hexadecamer nonstructural proteins and of feline coronavirus form a : heterotrimer that exhibits primer-independent rna polymerase activity the sars-coronavirus nsp +nsp complex is a unique multimeric rna polymerase capable of both de novo initiation and primer extension a complex zinc finger controls the enzymatic activities of nidovirus helicases the human coronavirus e superfamily helicase has rna and dna duplex-unwinding activities with '-to- ' polarity the severe acute respiratory syndrome (sars) coronavirus ntpase/helicase belongs to a distinct class of ' to ' viral helicases multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase human coronavirus e nonstructural protein : characterization of duplex-unwinding, nucleoside triphosphatase, and rna '-triphosphatase activities functional screen reveals sars coronavirus nonstructural protein nsp as a novel cap n methyltransferase coronavirus nonstructural protein is a cap- binding enzyme possessing (nucleoside- 'o)-methyltransferase activity in vitro reconstitution of sars-coronavirus mrna cap methylation molecular mapping of the rna cap '-o-methyltransferase activation interface between severe acute respiratory syndrome coronavirus nsp and nsp discovery of an rna virus '→ ' exoribonuclease that is critically involved in coronavirus rna synthesis major genetic marker of nidoviruses encodes a replicative endoribonuclease rna recognition and cleavage by the sars coronavirus endoribonuclease infidelity of sars-cov nsp -exonuclease mutant virus replication is revealed by complete genome sequencing an rna proofreading machine regulates replication fidelity and diversity rna '-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp /nsp exoribonuclease complex identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity topology and membrane anchoring of the coronavirus replication complex: not all hydrophobic domains of nsp and nsp are membrane spanning localization and membrane topology of coronavirus nonstructural protein : involvement of the early secretory pathway in replication membrane topology of murine coronavirus replicase nonstructural protein detection of nonstructural protein in murine coronavirus-infected cells and analysis of the transmembrane topology by using bioinformatics and molecular approaches identification of mouse hepatitis virus papain-like proteinase activity rna replication of mouse hepatitis virus takes place at double-membrane vesicles the nsp replicase protein of sars-coronavirus, structure and functional insights dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp coronavirus non-structural protein is a major pathogenicity factor: implications for the rational design of coronavirus vaccines plp of mouse hepatitis virus a (mhv-a ) targets tbk to negatively regulate cellular type i interferon signaling pathway severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp and rational design of an attenuated strain severe acute respiratory syndrome coronavirus nsp suppresses host gene expression, including that of type i interferon, in infected cells the adp-ribose- "-monophosphatase domains of sars-coronavirus and human coronavirus e mediate resistance to antiviral interferon responses severe acute respiratory syndrome coronavirus nsp protein suppresses host gene expression by promoting host mrna degradation a two-pronged strategy to suppress host protein synthesis by sars coronavirus nsp protein murine coronavirus nonstructural protein p arrests cell cycle in g /g phase murine coronaviruses encoding nsp at different genomic loci have altered replication, protein expression, and localization the nsp replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication coronaviruses post-sars: update on replication and pathogenesis the coronavirus replicase: insights into a sophisticated enzyme machinery qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex an electron microscope study of the development of a mouse hepatitis virus in tissue culture cells proliferative growth of sars coronavirus in vero e cells integrity of the early secretory pathway promotes, but is not required for, severe acute respiratory syndrome coronavirus rna synthesis and virus-induced remodeling of endoplasmic reticulum membranes mouse hepatitis coronavirus rna replication depends on gbf -mediated arf activation identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins coronaviruses hijack the lc -i-positive edemosomes, er-derived vesicles exporting short-lived erad regulators, for replication colocalization and membrane association of murine hepatitis virus gene products and de novo-synthesized viral rna in infected cells localization of mouse hepatitis virus nonstructural proteins and rna synthesis indicates a role for late endosomes in viral replication coronavirus replication complex formation utilizes components of cellular autophagy coronavirus nsp proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate autophagy-independent lc function in vesicular traffic the intracellular sites of early replication and budding of sars-coronavirus vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker segregation and rapid turnover of edem by an autophagy-like mechanism modulates standard erad and folding activities the endoplasmic reticulum crossroads for newly synthesized polypeptide chains role of the sel l:lc -i complex as an erad tuning receptor in the mammalian er mobility and interactions of the coronavirus nonstructural protein murine hepatitis virus nonstructural protein regulates virus-induced membrane modifications and replication complex function genetic analysis of murine hepatitis virus nsp in virus replication non-structural proteins and interact to modify host cell membranes during the formation of the arterivirus replication complex open reading frame a-encoded subunits of the arterivirus replicase induce endoplasmic reticulum-derived double-membrane vesicles which carry the viral replication complex formation of the arterivirus replication/transcription complex: a key role for nonstructural protein in the remodeling of intracellular membranes the non-structural protein a of dengue virus is an integral membrane protein inducing membrane alterations in a k-regulated manner regulated cleavages at the west nile virus ns a- k-ns b junctions play a major role in rearranging cytoplasmic membranes and golgi trafficking of the ns a protein expression of hepatitis c virus proteins induces distinct membrane alterations including a candidate viral replication complex identification of sequences in brome mosaic virus replicase protein a that mediate association with endoplasmic reticulum membranes amino terminal regions of poliovirus c protein mediate membrane binding topology of the membrane-associated hepatitis c virus protein ns b flock house virus rna polymerase is a transmembrane protein with amino-terminal sequences sufficient for mitochondrial localization and membrane insertion subcellular localization and membrane topology of the dengue virus type non-structural protein b interactions between the structural domains of the rna replication proteins of plant-infecting rna viruses analysis of the interaction of viral rna replication proteins by using the yeast two-hybrid assay bartenschlager, r. ns b self-interaction through conserved c-terminal elements is required for the establishment of functional hepatitis c virus replication complexes subcellular localization and some biochemical properties of the flavivirus kunjin nonstructural proteins ns a and ns a membrane curvature and mechanisms of dynamic cell membrane remodelling mechanisms shaping the membranes of cellular organelles how proteins produce cellular membrane curvature mobility analysis of an ns a-gfp fusion protein in cells actively replicating hepatitis c virus subgenomic rna mobility of the hepatitis c virus ns b protein on the endoplasmic reticulum membrane and membrane-associated foci visualizing the dynamic behavior of poliovirus plus-strand rna in living host cells biogenesis of the semliki forest virus rna replication complex phosphatidylinositol -kinase-, actin-, and microtubule-dependent transport of semliki forest virus replication complexes from the plasma membrane to modified lysosomes a dynamic view of hepatitis c virus replication complexes intracellular location and translocation of silent and active poliovirus replication complexes dynamics of coronavirus replication-transcription complexes cytoplasmic dynein-associated structures move bidirectionally in vivo cytoskeletal requirements for hepatitis c virus (hcv) rna synthesis in the hcv replicon cell culture system visualizing coronavirus rna synthesis in time by using click chemistry the sars-coronavirus plnc domain of nsp as a replication/transcription scaffolding protein genome-wide analysis of protein-protein interactions and involvement of viral proteins in sars-cov replication analysis of intraviral protein-protein interactions of the sars coronavirus orfeome four proteins processed from the replicase gene polyprotein of mouse hepatitis virus colocalize in the cell periphery and adjacent to sites of virion assembly the putative helicase of the coronavirus mouse hepatitis virus is processed from the replicase gene polyprotein and localizes in complexes that are active in viral rna synthesis an interaction between the nucleocapsid protein and a component of the replicase-transcriptase complex is crucial for the infectivity of coronavirus genomic rna the coronavirus nucleocapsid protein is dynamically associated with the replication-transcription complexes the nucleoprotein is required for efficient coronavirus genome replication in vitro replication of mouse hepatitis virus strain a selective replication of coronavirus genomes that express nucleocapsid protein molecular interactions in the assembly of coronaviruses sars-coronavirus replication/transcription complexes are membrane-protected and need a host factor for activity in vitro a positive-strand rna virus replication complex parallels form and function of retrovirus capsids three-dimensional analysis of a viral rna replication complex reveals a virus-induced mini-organelle nascent flavivirus rna colocalizedin situwith double-stranded rna in stable replication complexes the endoplasmic reticulum provides the membrane platform for biogenesis of the flavivirus replication complex composition and three-dimensional architecture of the dengue virus replication and assembly sites rna-rna and rna-protein interactions in coronavirus replication and transcription membrane-shaping host reticulon proteins play crucial roles in viral rna replication compartment formation and function a class of dynamin-like gtpases involved in the generation of the tubular er network membrane proteins of the endoplasmic reticulum induce high-curvature tubules a class of membrane proteins shaping the tubular endoplasmic reticulum subdomain-specific localization of climp- (p ) in the endoplasmic reticulum is mediated by its luminal α-helical segment mechanisms of membrane deformation mechanisms determining the morphology of the peripheral er viral reorganization of the secretory pathway generates distinct organelles for rna replication recruitment and activation of a lipid kinase by hepatitis c virus ns a is essential for integrity of the membranous replication compartment phospholipid biosynthesis and poliovirus genome replication, two coupled phenomena dengue virus nonstructural protein redistributes fatty acid synthase to sites of viral replication and increases cellular fatty acid synthesis synthesis of semliki forest virus rna requires continuous lipid synthesis dengue virus infection perturbs lipid homeostasis in infected mosquito cells photobleaching and photoactivation: following protein dynamics in living cells development and use of fluorescent protein markers in living cells single mrna molecules demonstrate probabilistic movement in living mammalian cells lambdan-gfp: an rna reporter system for live-cell imaging molecular beacons: probes that fluoresce upon hybridization copper-free click chemistry for dynamic in vivo imaging imaging intracellular fluorescent proteins at nanometer resolution sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (storm) breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy correlative light-electron microscopy (clem) combining live-cell imaging and immunolabeling of ultrathin cryosections we would like to thank oliver wicht and christine burkhard from the virology division, faculty of veterinary medicine, utrecht university for stimulating discussion and fulvio reggiori the authors declare no conflict of interest. key: cord- -n i authors: ioannidis, john p. a. title: coronavirus disease : the harms of exaggerated information and non‐evidence‐based measures date: - - journal: eur j clin invest doi: . /eci. sha: doc_id: cord_uid: n i the evolving coronavirus disease (covid- ) epidemic is certainly cause for concern. proper communication and optimal decision-making is an ongoing challenge, as data evolve. the challenge is compounded, however, by exaggerated information. this can lead to inappropriate actions. it is important to differentiate promptly the true epidemic from an epidemic of false claims and potentially harmful actions. the evolving coronavirus disease (covid- ) pandemic is certainly cause for concern. proper communication and optimal decision-making are an ongoing challenge, as data evolve. the challenge is compounded, however, by exaggerated information. this can lead to inappropriate actions. it is important to differentiate promptly the true epidemic from an epidemic of false claims and potentially harmful actions. based on altmetric scores, the most discussed and most visible scientific paper across all + million papers published in the last years across all science is a preprint claiming that the new coronavirus' spike protein bears "uncanny similarity" with hiv- proteins. the altmetric score of this work has reached an astronomical level of points as of march . the paper was rapidly criticized as highly flawed, and the authors withdrew it within days. regardless, major harm was already done. the preprint fuelled conspiracy theories of scientists manufacturing dangerous viruses and offered ammunition to vaccine deniers. refutation will probably not stop dispersion of weird inferences. the first report documenting transmission by an asymptomatic individual was published in the new england journal of medicine on january . however, the specific patient did have symptoms, but researchers had not asked. understanding the chances of transmission during the asymptomatic phase has major implications for what protective measures might work. lancet published on february an account from two chinese nurses of their front-line experience fighting coronavirus. the authors soon retracted the paper admitting it was not a first-hand account. these examples show how sensationalism affects even top scientific venues. moreover, peer review may malfunction when there is little evidence and strong opinions. opinionbased peer review may even solidify a literature of spurious statements. as outlined below, for the main features of the epidemic and the response to it, circulating estimates are often exaggerated, even when they come from otherwise excellent scientists. an early speculation that %- % of the global population will be infected went viral. early estimates of the basic reproduction number (how many people get infected by each infected person) have varied widely, from . to . . these estimates translate into manyfold difference in the proportion of the population eventually infected and dramatically different expectations on what containment measures (or even any future vaccine) can achieve. the fact that containment measures do seem to work, means that the basic reproduction number is probably in the lower bound of the . - . range, and can decrease below with proper measures. the originator of the " %- % of the population" estimate tweeted on march a revised estimate of " %- % of adults," but this is probably still substantially exaggerated. even after the %- % quote was revised downward, it still remained quoted in viral interviews. early reported cfr figures also seem exaggerated. the most widely quoted cfr has been . %, reported by who dividing the number of deaths by documented cases in early march. this ignores undetected infections and the strong age dependence of cfr. the most complete data come from diamond princess passengers, with cfr = % observed in an elderly cohort; thus, cfr may be much lower than % in the general population, probably higher than seasonal flu (cfr = . %), but not much so. observed crude cfr in south korea and in germany, countries is about . %. some deaths of infected, seriously ill people will occur later, and these deaths have not been counted yet. however, even in these countries many infections probably remain undiagnosed. therefore, cfr (or, more properly called, infection fatality rate, counting as cases all infected individuals) may be even lower rather than higher than these crude estimates. at face value, the epidemic curve of new cases outside china since late february is compatible with exponential community spread. however, reading this curve is very difficult. part of the growth of documented cases could reflect rapid increases in numbers of coronavirus tests performed. the number of tests done depends on how many test-kits are available and how many patients seek testing. even if bottlenecks in test availability are eventually removed, the epidemic curve may still reflect primarily population sensitization and willingness for testing rather than true epidemic growth. china data are more compatible with close contact rather than wide community spread being the main mode of transmission. under alarming circumstances, extreme measures of unknown effectiveness are adopted. china initially responded sluggishly, but subsequently locked down entire cities. school closures, cancellation of social events, air travel curtailment and restrictions, entry control measures and border closure are applied by various countries. italy adopted country-level lockdown on march , and many countries have been following suite. evidence is lacking for the most aggressive measures. a systematic review on measures to prevent the spread of respiratory viruses found insufficient evidence for entry port screening and social distancing in reducing epidemic spreading. plain hygienic measures have the strongest evidence. , frequent hand washing and staying at home and avoiding contacts when sick are probably very useful. their routine endorsement may save many lives. most lives saved may actually be due to reduced transmission of influenza rather than coronavirus. most evidence on protective measures comes from nonrandomized studies prone to bias. a systematic review of personal protective measures in reducing pandemic influenza risk found only two randomized trials, one on hand sanitizer and another on facemasks and hand hygiene in household members of people infected with influenza. given the uncertainties, one may opt for abundant caution and implement the most severe containment measures. by this perspective, no opportunity should be missed to gain any benefit, even in the absence of evidence or even with mostly negative evidence. this reasoning ignores possible harms. impulsive actions can indeed cause major harm. one clear example is the panic shopping which depleted supplies of face masks, escalation of prices and a shortage for medical personnel. masks, gloves and gowns are clearly needed for medical personnel, and their lack poses healthcare workers' lives at risk. conversely, they are meaningless for the uninfected general population. however, a prominent virologist's comment that people should stock surgical masks and wear them around the clock to avoid touching their nose went viral. policymakers feel pressure from opponents who lambast inaction. also, adoption of measures in one institution, jurisdiction or country creates pressure for taking similar measures elsewhere under fear of being accused of negligence. moreover, many countries pass legislation that allocates major resources and funding to the coronavirus response. this is justified, but the exact allocation priorities can become irrational. for example, undoubtedly research on coronavirus vaccines and potential treatments must be accelerated. however, if only part of resources mobilized to implement extreme measures for covid- had been invested towards enhancing influenza vaccination uptake, tens of thousands of influenza deaths might have been averted. only %- % of the population in china is vaccinated against influenza. even in the united states, despite improvements over time, most adults remain unvaccinated every year. as another example, enhanced detection of infections and lower hospitalization thresholds may increase demands for hospital beds. for patients without severe symptoms, hospitalizations offer no benefit and may only infect health workers causing shortage of much-needed personnel. even for severe cases, effectiveness of intensive supportive care is unknown. excess admissions may strain health care systems and increase mortality from other serious diseases where hospital care is clearly effective. an argument in favour of lockdowns is that postponing the epidemic wave ("flattening the curve") gains time to develop vaccines and reduces strain on the health system. however, vaccines take many months (or years) to develop and test properly. maintaining lockdowns for many months may have even worse consequences than an epidemic wave that runs an acute course. focusing on protecting susceptible individuals may be preferable to maintaining countrywide lockdowns longterm. the potential consequences on the global economy are already tangible. february - was the worst week for global markets since , and the worse may lie ahead. moreover, some political decisions may be confounded with alternative motives. lockdowns weaponized by suppressive regimes can create a precedent for easy adoption in the future. closure of borders may serve policies focused on limiting immigration. regardless, even in the strongest economies, disruption of social life, travel, work and school education may have major adverse consequences. the eventual cost of such disruption is notoriously difficult to project. a quote of $ . trillion is totally speculative. much depends on the duration of the anomaly. the global economy and society is already getting a major blow from an epidemic that otherwise (as of march ) accounts for . % of all million annual global deaths from all causes and that kills almost exclusively people with relatively low life expectancy. leading figures insist that the current situation is a once-ina-century pandemic. a corollary might be that any reaction to it, no matter how extreme, is justified. this year's coronavirus outbreak is clearly unprecedented in amount of attention received. media have capitalized on curiosity, uncertainty and horror. a google search with "coronavirus" yielded results on march and results on march . conversely, "influenza" attracted -to -fold less attention although this season it has caused so far more deaths globally than coronavirus. different coronaviruses actually infect millions of people every year, and they are common especially in the elderly and in hospitalized patients with respiratory illness in the winter. a serological analysis of cov e and oc in adult populations under surveillance for acute respiratory illness during the winters of - (healthy young adults, healthy elderly adults, high-risk adults with underlying cardiopulmonary disease and a hospitalized group) showed annual infection rates ranging from . % to % in prospective cohorts, and prevalence of . %- . % in the hospitalized cohort. case fatality of % has been described in outbreaks among nursing home elderly. leaving the well-known and highly lethal sars and mers coronaviruses aside, other coronaviruses probably have infected millions of people and have killed thousands. however, it is only this year that every single case and every single death gets red alert broadcasting in the news. some fear an analogy to the influenza pandemic that killed - million people. retrospective data from that • a highly flawed nonpeer-reviewed preprint claiming similarity with hiv- drew tremendous attention, and it was withdrawn, but conspiracy theories about the new virus became entrenched • even major peer-reviewed journals have already published wrong, sensationalist items • early estimates of the projected proportion of global population that will be infected seem markedly exaggerated • early estimates of case (infection) fatality rate may be markedly exaggerated • the proportion of undetected infections is unknown but probably varies across countries and may be very large overall • reported epidemic curves are largely affected by the change in availability of test kits and the willingness to test for the virus over time • of the multiple measures adopted, a few have strong evidence, and many may have obvious harms • panic shopping of masks and protective gear and excess hospital admissions may be highly detrimental to health systems without offering any concomitant benefit • extreme measures such as lockdowns may have major impact on social life and the economy (and those also lives lost), and estimates of this impact are entirely speculative • comparisons with and extrapolations from the influenza pandemic are precarious, if not outright misleading and harmful pandemic suggest that early adoption of social distancing measures was associated with lower peak death rates. however, these data are sparse, retrospective and pathogenspecific. moreover, total deaths were eventually little affected by early social distancing: people just died several weeks later. importantly, this year we are dealing with thousands, not tens of millions deaths. the box summarizes the problems with inaccurate and exaggerated information in the case of covid- . even if covid- is not a -recap in infection-related deaths, some coronavirus may match the pandemic in future seasons. thus, we should learn and be better prepared. questions about transmission, duration of immunity, effectiveness of different containment and mitigation methods, the role of children in viral spread, and assessment of the effectiveness of vaccines and drugs are essential to settle timely. this research agenda requires carefully collected, unbiased data to avoid unfounded inferences. larger-scale diagnostic testing should help get more unbiased estimates of cases, basic reproduction number and infection fatality rate. the research agenda also deserves proper experimental studies. besides candidate vaccines and drugs, randomized trials should evaluate also the real-world effectiveness of simple measures (eg face masks in different settings), least disruptive social distancing measures and healthcare management policies for documented cases. if covid- is indeed the pandemic of the century, we need the most accurate evidence to handle it. open data sharing of scientific information is a minimum requirement. this should include data on the number and demographics of tested individuals per day in each country and the demographics and background diseases of patients requiring hospital care and intensive care and those who die. proper prevalence studies and trials are also indispensable. if covid- is not as grave as it is depicted, high evidence standards are equally relevant. exaggeration and overreaction may seriously damage the reputation of science, public health, media and policymakers. it may foster disbelief that will jeopardize the prospects of an appropriately strong response if and when a more major pandemic strikes in the future. characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention uncanny similarity of unique inserts in the -ncov spike protein to hiv- gp and gag study claiming new coronavirus can be transmitted by people without symptoms was flawed how many people might one person with coronavirus infect? an updated estimation of the risk of transmission of the novel coronavirus ( -ncov) coronavirus may infect up to % of world's population, expert warns experts: rapid testing helps explain few german virus deaths early containment strategies and core measures for prevention and control of novel coronavirus pneumonia in china physical interventions to interrupt or reduce the spread of respiratory viruses effectiveness of personal protective measures in reducing pandemic influenza transmission: a systematic review and meta-analysis coronavirus could cost the global economy $ . trillion. here's how responding to covid- -a once-in-a-century pandemic? global mortality associated with seasonal influenza epidemics: new burden estimates and predictors from the glamor project clinical impact of human coronaviruses e and oc infection in diverse adult populations an outbreak of human coronavirus oc infection and serological cross-reactivity with sars coronavirus transmissibility of pandemic influenza public health interventions and epidemic intensity during the influenza pandemic key: cord- -qz yxuph authors: fuertes, víctor; monclús, enrique; agulló, alberto title: current impact of covid- pandemic on spanish plastic surgery departments: a multi-center report date: - - journal: eur j plast surg doi: . /s - - - sha: doc_id: cord_uid: qz yxuph background: after its initial description in china, covid- is hitting nations across the world, with spain as the third country in number of deaths, after the usa and italy. similarly to what is happening in other countries, an important reduction in available operating rooms is affecting our departments. in this study, we aim to know how covid- pandemic is affecting the delivery of plastic surgery services in spain. methods: a questionnaire addressing some of our concerns about how the coronavirus crisis might severelyimpact our specialty has been sent to the heads of the divisions of plastic surgery of several hospitals across spain. results: a total of plastic surgery departments from different hospitals across the country agreed to participate in the survey. most plastic surgery teams will need to maintain – % of their staff in order to be able to offer emergency and undelayable oncological procedures. the total amount of procedures currently being performed ranged from to % of the figures before the coronavirus outbreak, except for one department, with elective surgery mainly affected. microsurgical cases have been massively discontinued during this crisis. conclusions: plastic surgery delivery in the spanish health system is being severely impacted as a collateral damage from this pandemic. most of the elective surgery is currently stopped. our departments seem to be vulnerable regarding their capacity to keep offering emergency care. level of evidence: not ratable (multi-center survey) after its initial description and spreading in the province of wuhan, china, covid- is hitting nations across the world, with the center of the crisis now located in europe and the usa. the situation has already been declared a public health emergency of international concern by the world health organization (who). to date, spain is the third country in the world, after the usa and italy, with regard to the number of deaths caused by covid- virus (who). a cumulative figure of , positive cases and , deaths have been reported by april , (ministry of health, spain). our center is a third level hospital with an estimated capacity of hundred beds. our department attends to a regional population of approximately a million and a half patients and includes a burn unit and a pediatric clinic. similarly to what is happening in the north of italy [ ] , and according to our hospital guidelines, we have adopted several new measures. most of our outpatient clinics have been postponed. all elective, non-urgent, and non-cancer procedures have been stopped in an effort to anticipate the need of relocating nurses and anesthesiologists to tackle covid- situations. consequently, we have reduced the number of attending surgeons and residents working on a daily basis to the minimum required. the goal is to keep the department functioning, while avoiding infections between the team members. emergency surgeries during the on-call shifts will continue. we should not underestimate how these necessary measures, and the associated reduction in effective or time, will affect not only plastic and reconstructive surgery (prs) departments but other medical and surgical specialties as well. in this study, we aim to discover how covid- pandemic is affecting the delivery of prs services in spain. a questionnaire addressing some of our main concerns as to how the coronavirus crisis might severely impact the delivery of prs has been sent to the heads of the divisions of prs in several hospitals across spain. only departments in third-level hospitals with over beds were considered. in an effort to achieve a realistic picture as to how this pandemic is affecting departments in the entire country, we have contacted hospitals from all the regions, including those less affected by the outbreak. the survey was sent to the selected departments on march , . the questions (q) included in this multi-center survey are presented in table . the hospital name from which each set of data is coming from has been kept confidential. when responding to questions regarding data submission before the crisis started, an average figure of january and february inputs is recommended. for answers about the present data, the first weeks of april (during the peak of the pandemic) will be considered. the questionnaire was sent to prs departments from different hospitals across the country. a total of departments ( %) agreed to participate in the survey and answered by email. those departments include hospitals from a wide range of locations, where the outbreak has been evolving differently. thus, we believe a representative sample has been obtained. all the detailed information with the complete answers from each department is included in table . each question row is identified as q and a number/letter representing their order in the questionnaire. highlights are summarized in the following paragraphs. eight people out of ( . %) of the staff members from the units consulted in our study have been tested positive for coronavirus. when asking about the percentage of the team members that a department would need to be working in order to maintain their on-call system running as usual, the most common answers were between and % of the entire team. two of the institutions consulted, stated that they might be able to continue their on-call activity while maintaining active only % and % of their respective teams. in two of the centers we have contacted, the staff has been properly trained on the medical management of covid- patients. one of those departments specified that the training consisted of a -h duration course. according to the hospital guidelines, members of that group have joined internal medicine teams to assist them on covid- monographic wards. in table questionnaire. ppe, personal protective equipment q a b please specify your team members, including consultants and residents. how many colleagues have been tested positive for covid- /are isolated due to have been in contact with a positive patient amongst the surgical team, including residents? q what is the percentage of your team members that you estimate you will need to keep the emergency calls and the most basic surgical procedures (oncological cases excluding those that you can delay at least weeks) running? *please consider as the limit for maintaining your current emergency call flow either the need to transform in-hospital duties to on-call duties or the increase in the on-call days per month in double or more per consultant. q a b did any of the team members receive any specific education on covid- patient medical management? did any of them have already been re-located and currently providing medical care to coronavirus patients? please specify the number of residents and consultants and if these positions have been randomly assigned or are voluntary. what was the total amount of surgical procedures, excluding those done under local anesthetic, performed by week in your department? how many cases are you currently operating? please differentiate elective and urgent surgeries as well as inpatient and day-care cases q similarly, reduction in the number of oncological surgical procedures q a b are you actually seeing patients in your clinics other than immediate surgical follow-ups and oncological new cases? what was the total amount of patients seen in your clinics per week before the onset of coronavirus and today? q are your elective micro cases (such as dieps) still taking place? in case that your department includes pediatric population, are you still operating elective cases such as cleft lip and palate, congenital hand anomalies or microtia? q have you implemented a specific protocol in your burn unit? (in case you have it at your facility). please explain the four main changes q does your team have access to ppe*-ffp (n ) masks/goggles/face screens-when performing surgeries close to the patient airways or other types or surgeries in positive patients? q did you ever experience any restrictions in the surgical ward of your hospital regarding supply of normal surgical gowns, masks and gloves? a drastic reduction in surgical capacity has occurred. nonurgent or activity has notably dropped in all but one of the hospitals answering our survey. the total amount of procedures currently being performed ranged from to % of the figures before the coronavirus outbreak (fig. a, b) ; except for one hospital, that was declared to maintain the same surgical activity ( %). the decrease in the total amount of daycare procedures (as compared to in-hospital surgeries) is highly variable between the centers analyzed in this article. only two departments provided accurate data regarding the number of urgent procedures before and after the crisis. in one of them, urgent cases have been reduced by %. at the second one, urgent surgeries are now % of what they used to be before the outbreak of coronavirus. the vast majority of respondents indicated that the available operating time is now mainly occupied in treating cancer cases. consequently, they do not expect a decrease in the amount of non-delayable oncological procedures during the crisis. nonetheless, consistent data about this question has not been obtained and solid conclusions are not possible. nine departments have sent their total number of consults before and after this crisis. prs clinics have diminished their in-person activity by %. elective microsurgical cases have been uniformly discontinued during this crisis. one department has delayed not only microsurgical breast reconstruction but also implantbased cases. five of the prs divisions included in the study declared to have a burn unit. in four of these units, substantial changes have been implemented. some of the more prevalent measures include screening protocols for coronavirus among patients and workers, increasing hygiene measures, reducing the number of visitors per patient, directing burn patients who tested positive to other units and trying to apply day-care/ delay surgeries whenever this is possible. one unit does not have a specific protocol. all the departments have access to adequate personal protective equipment (ppe) when performing surgeries in positive patients. five out of the institutions checked have experienced restrictions in accessing basic surgical gowns, masks, and gloves. another center clarified that reusable gowns are becoming scarce, and thus, fabric ones are being worn. in an effort to save as much units as possible, most of our hospitals are monitoring the number of surgical masks received per person. incidence of covid- among plastic surgeons is expected to be considerably lower as compared to positive cases in colleagues from other specialties acting in the first line of defense against the pandemic (emergency wards, internal medicine, or intensive care units). nevertheless, testing asymptomatic members of our teams is not common yet. prs teams in the spanish public health system tend to be small when compared to other surgical specialties. we found an average size of consultants/ residents per team in the departments participating in this study, with the biggest one counting up to consultants. consequently, even short reductions in our groups could easily cause unsustainable increases in the number of shifts per consultant. this might pose a challenge against the delivery of emergency surgeries and cancer care to our community if this pandemic lasts for a prolonged period long time according to our analysis, reductions of about - % in the total number of consultants per team may lead to this situation. some centers (such as the one stating that keeping only % of its staff would be enough) are maybe more resistant to this situation as they do not have a burn unit, nor they attend to trauma patients. most of the plastic surgeons working at the institutions included in this study have not been relocated to frontline departments directly attending to pandemic cases. on the other hand, hospitals have generally provided education on updated surgical protocols for the current scenario. overall, non-urgent surgical activity in our departments represents about one-third ( %) of the total number of cases that we used to have before the onset of coronavirus. only one of the institutions we have contacted maintains its usual activity. this is probably related to the geographical location of this center, in a region where the pandemic is considerably milder compared to other places. analyzing how the approach to day-care surgery is different amid the departments may lead to interesting conclusions. while some departments have stopped most of their day-care procedures and operate only more severe, inpatient cases; others try to do as many cases as they can in a day-care approach, minimizing admissions. these two alternative options are most likely related to the availability of beds and the severity of the outbreak in each hospital. it has been difficult to obtain data from urgent cases only. it will be interesting to know if urgent cases have actually been reduced. nhs hospitals in england have also been told to suspend all non-urgent elective surgery for at least months from april as a measure to deal with the covid- pandemic [ ] . as previously stated, the reduction in surgical activity seems to have mainly impacted elective reconstructive surgery. departments are currently using all their resources to perform cancer-related surgeries that cannot be delayed. however, further analysis needs to be conducted in order to confirm that access to oncological surgeries is not being significantly affected. if the current situation keeps worsening, the delay in diagnosis and management of cancer patients could be catastrophic. our hospital guidance for the pandemic, similar to those used in other institutions, has established three possible levels of alert. they will be applied depending on the severity of this continuously evolving crisis. we are currently in the phase scenario. in the last step (phase ), ventilators might become hardly available, and life-saving surgeries are the only procedures performed [ ] . some general surgery departments in china [ ] adopted guidelines recommending multidisciplinary approaches and encouraging them to use non-surgical anti-tumor therapies as the first choice for the management of gastrointestinal malignancies. by doing so, even oncological surgeries were reduced to those that are unavoidable. some of these surgeries can include the absence of therapeutic alternatives to surgery for tumor control, intestinal obstructions not amenable to stenting, or gastrointestinal bleeds not controlled by embolization. a uniform and steep decrease in prs clinics have taken place in all the hospitals in this article. as a general rule, only oncological new consults (mainly melanomas and other cutaneous malignancies) and immediate follow-ups are being received in our hospitals. all the other cases are usually delayed or managed with telemedicine. microsurgery has become a secondary option. it is only performed when other surgical approaches are not feasible, such as for trauma patient's coverage and head and neck cancer reconstructions. according to the paper by andrea et al. [ ] , solid organ transplants have been reduced to only the most urgent cases during the covid- outbreak in the epidemic area of the north of italy. similarly, elective micro cases such as immediate or delayed dieps have been temporarily suspended in spain. unfortunately, this population of patients consumes longer or times, occupies more resources at the reanimation units, and stays longer periods of time in our facilities. additionally, patients with an active or former cancer have shown a significantly higher risk of severe events if infected by covid- . a paper by liang et al. [ ] , from the hospital of guangzhou, demonstrated a rr of . ( % ci . - . ) for severe events in oncological patients with wuhan pneumonia. according to the experience of two similar teams in china [ , ] , several institutions across the world [ ] (including ours) have applied a protocol to optimize burn units. this will ultimately help to reduce the exposure of such a sensitive group of chronically ill patients and their health care providers. some of the embraced measures encompass: -interviewing all the patients about any symptoms suggesting a possible case of coronavirus and checking their temperature before nursing them either at the ward or in our clinics. similar measures have been applied in the other spanish units consulted for this article. these measures have been taken as a strategy to attempt to keep our burn units free of covid- . by doing so, health care will remain available for burn patients during the pandemic. however, if the burden of the pandemic becomes overwhelming, burn units will always be amenable to be transformed into polytrauma/surgical/ covid- intensive care units [ ] . access to ppe seems to be guaranteed country-wide if performing surgeries in positive patients; but generalized testing of patients before surgery and other important measures, still need to be implemented. an article by wang et al. [ ] , from shanghai ninth people's hospital, highlighted the measures that allow them to perform over surgical procedures without any health care professional or patient resulting infected: -telehealth clinics -triage workflow: infra-red fever measure and thorough symptoms/travel history survey to all patients attended in the hospital; chest ct scan and pcr test for patients being admitted. suspicious patients were sent to quarantine for weeks. confirmed positive cases were sent to centralized institutions for surgery -environmental control measures: maximizing hygiene measures, using rapid sequence induction for general anesthesia patients and disinfecting all the ors with uv lights for at least min -staff protection measures: ppe for surgeries on negative patients included ffp (n ) masks, disposable waterproof protective suits, and goggles/facial screens. isolation screens were added when performing emergency cases and during long procedures our hospital has divided the facilities into two separate parts: a covid- area (corresponding to a general hospital) and a covid- -free one (at the trauma center). both buildings admit surgical and non-surgical patients of all specialties, depending solely on their condition as positive/negative for coronavirus. similarly, we have divided the surgical ward of the hospital in two parts, covid- positive and covid- negative, with different patient's entry and exit circuits. some institutions have temporarily experienced a lack of basic surgical protection equipment. limitations of the present study may include its descriptive nature and the fact that participating in the questionnaire was voluntary. prs services delivered in the spanish health system are being severely impacted as a consequence of the pandemic. in an effort to continue operating new cancer cases in these under-resourced circumstances, most of elective surgery is currently ceased. an increase in the waiting list (in days per week of the crisis) is expected to happen. not only surgical cases are not being performed but also the new consults are being canceled, and will eventually compound. we anticipate the need of a follow-up report about this issue once the burden of coronavirus disease has receded. our departments seem to be very vulnerable regarding their capacity to keep offering emergency care. losing a small number of staff members will represent a big proportion of the team, potentially compromising the normal function of the units. authors' contributions all authors contributed to the study conception and design. material preparation, data collection, and analysis were performed by fuertes vand monclús e. the first draft of the manuscript was written by fuertes v and all authors commented on previous versions of the manuscript. fuertes v, monclús e, and agulló a read and approved the final manuscript. data availability the data that support the findings of this study are available from the corresponding author, upon reasonable request, but will not identify the specific departments from which they were generated. conflict of interest víctor fuertes, enrique monclús and alberto agulló declare that they have no conflict of interest. ethical approval the local ethics committee has confirmed that no ethical approval is required for studies that involve questionnarie surveys. consent to participate participants in the survey consented for publication of the results. consent for publication upon submission, all authors consent to the publication of the manuscript in the european journal of plastic surgery. covid- pandemic: perspectives on an unfolding crisis covid- : all non-urgent elective surgery is suspended for at least three months in england covid- : pandemic surgery guidance treatment strategy for gastrointestinal tumor under the outbreak of novel coronavirus pneumonia in china coronavirus disease and transplantation: a view from the inside cancer patients in sars-cov- infection: a nationwide analysis in china recommendations for the regulation of medical practices of burn treatment during the outbreak of the coronavirus disease management strategies for the burn ward during covid- pandemic burn center function during the covid- pandemic: an international multi-center report of strategy and experience our experiences on plastic and reconstructive surgery procedures during covid- pandemic from shanghai ninth people's hospital publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations key: cord- -o zpu authors: anser, muhammad khalid; yousaf, zahid; khan, muhammad azhar; sheikh, abdullah zafar; nassani, abdelmohsen a.; abro, muhammad moinuddin qazi; zaman, khalid title: communicable diseases (including covid- )—induced global depression: caused by inadequate healthcare expenditures, population density, and mass panic date: - - journal: front public health doi: . /fpubh. . sha: doc_id: cord_uid: o zpu coronavirus (covid- ) is spreading at an enormous rate and has caused deaths beyond expectations due to a variety of reasons. these include: (i) inadequate healthcare spending causing, for instance, a shortage of protective equipment, testing swabs, masks, surgical gloves, gowns, etc.; (ii) a high population density that causes close physical contact among community members who reside in compact places, hence they are more likely to be exposed to communicable diseases, including coronavirus; and (iii) mass panic due to the fear of experiencing the loss of loved ones, lockdown, and shortage of food. in a given scenario, the study focused on the following key variables: communicable diseases, healthcare expenditures, population density, poverty, economic growth, and covid- dummy variable in a panel of selected countries from through . the results show that the impact of communicable diseases on economic growth is positive because the infected countries get a reap of economic benefits from other countries in the form of healthcare technologies, knowledge transfers, cash transfers, international loans, aid, etc., to get rid of the diseases. however, the case is different with covid- as it has seized the whole world together in a much shorter period of time and no other countries are able to help others in terms of funding loans, healthcare facilities, or technology transfers. thus, the impact of covid- in the given study is negatively impacting countries' economic growth that converts into a global depression. the high incidence of poverty and social closeness increases more vulnerable conditions that spread coronavirus across countries. the momentous increase in healthcare expenditures put a burden on countries' national healthcare bills that stretch the depression phase-out of the boundary. the forecasting relationship suggested the negative impact of the coronavirus pandemic on the global economy would last the next years. unified global healthcare policies, physical distancing, smart lockdowns, and meeting food challenges are largely required to combat the coronavirus pandemic and escape from global depression. is spreading at an enormous rate and has caused deaths beyond expectations due to a variety of reasons. these include: (i) inadequate healthcare spending causing, for instance, a shortage of protective equipment, testing swabs, masks, surgical gloves, gowns, etc.; (ii) a high population density that causes close physical contact among community members who reside in compact places, hence they are more likely to be exposed to communicable diseases, including coronavirus; and (iii) mass panic due to the fear of experiencing the loss of loved ones, lockdown, and shortage of food. in a given scenario, the study focused on the following key variables: communicable diseases, healthcare expenditures, population density, poverty, economic growth, and covid- dummy variable in a panel of selected countries from through . the results show that the impact of communicable diseases on economic growth is positive because the infected countries get a reap of economic benefits from other countries in the form of healthcare technologies, knowledge transfers, cash transfers, international loans, aid, etc., to get rid of the diseases. however, the case is different with covid- as it has seized the whole world together in a much shorter period of time and no other countries are able to help others in terms of funding loans, healthcare facilities, or technology transfers. thus, the impact of covid- in the given study is negatively impacting countries' economic growth that converts into a global depression. the high incidence of poverty and social closeness increases more vulnerable conditions that spread coronavirus across countries. the momentous increase in healthcare expenditures put a burden on countries' national healthcare bills that stretch the depression phase-out of the boundary. the forecasting relationship suggested the negative impact of the coronavirus pandemic on the global economy would last the next years. communicable diseases are not novel for the world; governments have learned from different infectious diseases in the past, such as human immunodeficiency virus (hiv), tuberculosis (tb), ebola, and spanish influenza a century before. the history of communicable diseases dates back much further, however we have only reported on the past years. the influenza pandemic is considered to be one of the most deadly epidemics in recent history, which affected about one-third of the world's population, with a death toll of at least million people globally. the list of communicable diseases is long, as more than infectious diseases across the globe have been reported to date. the united states was largely affected by hemagglutinin type and neuraminidase type (h n ) virus, where the death toll exceeded , people ( ) ( ) ( ) . four decades later, the world was again hit by another communicable disease in with a new mutant influenza a, which is caused by an hemagglutinin type and neuraminidase type (h n ) virus that spread from east asia, also called "asian flu." asian influenza -a is different from hini virus, as it is comprised of two different genes, i.e., hemagglutinin genes (h ), and neuraminidase (n ) genes. the virus was reported in singapore first in february , and hit the us in the summer of the same year; the world death toll from this virus was . million people, out of which the death toll around , in the us, making it the worst hit affected country [( - ), etc.]. the pandemic did not end as its mutation, caused by influenza -a ( pandemic), caused by a hemagglutinin type and neuraminidase type (h n ) virus. this virus was comprised of h hemagglutinin and contained the n neuraminidase from asian influenza . it was reported in the us in september , and largely affected the older population; the median age was years and above. the worldwide death toll exceeded million and about % of the death toll was reported in the us alone. this virus continued to move worldwide as a seasonal flu that led to severe illness [( - ), etc.]. this virus did not end, as in the spring of , a new mutant influenza -a caused by h n virus was detected in the us and quickly spread around the world. an estimated range of , - , people globally died from this pandemic virus infection in the first year. it is a seasonal virus that causes serious illness and increases hospitalizations and mortalities [( , ), etc.]. on may , , a(h n )pdm pandemic was detected in two imported cases in thailand, which increased up to cases by the end of the month, and by july the virus had been transmitted and detected in all thai provinces, which increased the death toll up to . the pandemic waves followed two irregular interval periods, which started from may , maxing out in july and falling in december, while the second wave began in early january , maxing out in february and ending in april. in between the year time period, around , registered influenza cases were reported in the country, , of which were confirmed virus patients with a(h n )pdm infections, and the death toll reached ( ) . the ebola outbreak that was experienced in west africa in march , affected a number of affiliated bordering countries. more than , cases were registered and more than , deaths were reported with this virus. however, with unified healthcare policies and strengthening response capacities, the affected countries limited the transmission of the deadly disease in a given course of time [( , ) , etc.]. unified healthcare policies are desirable to improve countries' economic growth ( , ) . in late december , wuhan city in china detected a novel coronavirus (covid- ) that threatened human lives; to date ( th april, ) covid- has affected , , people across countries. the death toll exceeds , people, while the recovered cases are , across the globe ( ) . the who has declared an alert about this global pandemic, which represents a large family of viruses and causes serve respiratory problems like sars, mers, etc. the covid- virus is a mutant strain of the coronavirus family, known as sars-cov- . figure shows the total death tolls reported in the five most affected countries by covid- for easy reference. since the emergence of coronavirus, a great amount of scholarly writing has been done on the given issue. for instance, lai et al. ( ) collected a cross-sectional data of , healthcare workers working in different chinese hospitals and analyzed their mental health states after handling coronavirus patients. the results suggested that, as healthcare workers are directly exposed to the coronavirus, there is a high need for physiological support and interventions to take care of frontline workers to reduce the symptoms of distress, insomnia, depression, anxiety, etc. phelan et al. ( ) argued that coronavirus was spreading all over the world from china, thus there was a need to handle this outbreak with global healthcare governance and strategies, including surveillance, testing, treatments, cooperation, technology transfers, and healthcare information. wang et al. ( ) discussed the early transmission channel of coronavirus in wuhan city in china by considering a single center case study of patients infected with novel coronavirus ( -ncov). the statistics show that the rate of patients administered to the intensive care unit (icu) were % of the total, while the death toll was . %. the hospital associated human-to-human transmission rate was suspected to be %. the study concludes that the risk of transmission of coronavirus could not be analyzed as it was becoming increasingly dangerous as the weeks progressed. livingston and bucher ( ) concluded that the coronavirus pandemic spread with an enormous rate despite aggressive control efforts. the study argued that the case-fatality ratio is higher in the elderly population, with a median age of more than and equal to years. italy is highly infected with coronavirus, which is an issue that needs to be taken seriously and controlled with effective interventions and surveillance. torales et al. ( ) reviewed the coronavirus associated studies and confirmed the psychological illnesses that were reported in the healthcare workers, suspected patients, and the general public. the results derived that the coronavirus outbreak is leading to additional health problems, including fear of death, anxiety, depression, insomnia, anger, etc. the need for efficient psychotherapy in suspected patients and counseling to the general masses would have a positive impact on reducing the risk of transmission of this disease. table shows the recent pieces of literature on the interlinkages between the coronavirus pandemic and economic activities all across the globe. the study is important in the given circumstances, where coronavirus fear and depression have appeared around the world, creating chaos among community members as they seek remedial actions to get rid of the pandemic ( ) . a few policy actions have been derived by the international community to prevent the epidemic, including maintaining physical/social distancing among community members, increasing healthcare expenditures, and reducing poverty and hunger. this study has included all these factors and has examined their impact on the country's economic growth, which considers a proxy for economic suffering leads to a depression. the epidemic proportionally affected developed and developing countries, therefore, the current studies included both developed and developing countries in a panel of selected countries during - . the outbreak of coronavirus creates many healthcare issues, including inadequate healthcare equipment, patents' facilitation centers, quarantine issues, fear, depression, and many other sanitation issues that cause the situation to worsen. the global depression phase becomes lengthier if these critical issues are unresolved. this study intended to explore the answers to the following critical questions: do communicable diseases, including covid- , exert a greater magnitude of stress in terms of negatively affecting countries economic growth which then converts into global depression? the second question is whether high population density and poverty incidence may increase the length of the coronavirus pandemic around the globe? and finally, how may we reduce human suffering and death tolls from the coronavirus plague across countries? knowing the answers to these questions will aid in helping the world with the coronavirus outbreak and stabilize the world from depression. in a given context, the study prepared a set of research objectives to analyze global depression through some policy instruments, including healthcare expenditures, population density, and poverty incidence in a panel of countries. the research objectives are: (i) to examine the impact of communicable diseases, including (covid- ), on a country's economic growth. and % in the us and eu, respectively, is likely due to coronavirus. economic growth is expected to further decrease growth by . and . % in the us and the eu, respectively. hasanat et al. malaysia e-business online business is affected by the coronavirus pandemic due to lockdown, low sales and purchase, less buying intensions, supply chain issues, fear, etc. odhiambo et al. kenya agriculture services, and the manufacturing sector due to the coronavirus outbreak, the agriculture sector decreased the share of . % in total gdp, subsequently, tourism, construction, infrastructure development, and manufacturing dropped their share at around . , . , . , and . %, respectively. it is predicted that in the mild scenario, economic growth will drop in the range of between and %, depending upon the country's profile, while in the given sample of countries, the median drop in gdp is expected to be − . % in . the service sector is also affected due to breakdowns in the supply chain process, which tends to decrease economic growth in the crisis period as expected between . and % per month. huang et al. china smes business due to the coronavirus pandemic, the smes sector has been badly affected and is highly dependent upon government support in terms of tax rebates, reduction in tax duties, provision of subsidies, flexible repayment of loan schedules, low interest rates, liquidity support, etc. wolf ( ) worldwide economic growth macroeconomic policies would largely support country's economic growth during the crisis period associated with coronavirus bandyopadhyay ( ) global evidences general discussion on economy the closure of educational institutions, travel restrictions, hospitality industry, financial, and related markets has caused economic declines across the globe. rodela et al. developing countries the coronavirus outbreak increases the high out-of-pocket healthcare expenditures that increases poverty incidences across countries. nseobot et al. nigeria trade due to the coronavirus outbreak, a unit decrease in oil price put a stress on the economic growth by . units. the death toll from coronavirus has not exceeded . % globally, whereas the death rate increase by air pollution was about . % in worldwide. due to lockdown, many polluting industries were temporarily shut down, which decreased n o emissions and carbon emissions by and %, respectively. (ii) to investigate the role of healthcare expenditures in reducing the coronavirus outbreak (iii) to observe the changes in poverty rates and population density due to the coronavirus pandemic on economic growth across countries (iv) to determine the inter-temporal relationship between the coronavirus pandemic and economic growth over a time horizon. these objectives have been set and analyzed by using sophisticated econometric techniques in order to reach some conclusive findings. the study used the following key factors that affect a country's economic growth and which turn into economic losses during the outbreak of communicable diseases, including covid- . economic growth (denoted by eg) is used as a proxy variable for analyzing economic losses due to an emerging epidemic, which served as a response variable. the data of gdp per capita in constant us$ is used in the given analysis. the explanatory variables are as follows: poverty incidence (denoted by pi) is used to get an insight into the "mass panic" among the country's residents during the coronavirus pandemic, as poor populations are directly exposed to communicable diseases caused by a lack of knowledge, low/no direct income, persistent unemployment, and inadequate healthcare facilities. this restlessness then creates more panic during the emergence of the epidemic that negatively affects the country's economic growth. the headcount ratio in percentage form is used for this reason. covid- (denoted by covid-dum) is used to assess the magnitude and the intensity of coronavirus that largely increases due to high social contact between the population members, as this virus easily spreads through close contact in the community, like, handshaking, sneezing, coughing, touching, etc., hence it is highly possible to get infected with the virus when people per square km of the land area are living in compact places. thus, the covid-dum is formed and assigned values of and . the covid-dum value represents the likely occurrence of coronavirus when the population density is in triple digits (i.e., people per square km of land area) and represents otherwise. the covid-dum data is extracted from the data set of population density (denoted by pd), which is further included in the regression estimates to get more insight into social distancing. the data of deaths caused by communicable diseases (denoted by cd) as a percentage of total deaths and per capita healthcare expenditures (denoted by he) as in us$ is added to the study to minimize the probability of omission bias problems in the given model. further, both the variables have important policy implications on the country's economic growth that can be used to assess global depression caused by insufficient healthcare expenditures, which links to the increasing cause of deaths by communicable diseases including . table a in the appendix shows the list of sample countries used in the study, which covered a period of - . the data is taken from world bank ( ) and povcal net database. the strong viability of regressors and regressand in the given context need an empirical model that would facilitate answering the causes of global depression associated with high communicable diseases including covid- . the study utilized a traditional solow growth model that considers a starting point for any growth-specific modeling, i.e., where y shows economic output, l shows labor stock, k shows capital investment, t shows technology, i and t show crosssections and time period, and ε shows error term. equation ( ) shows the conventional style solow growth model that comprises labor, capital, technology, and their resulting impacts on economic output. further, the moderation effect of technology with labor and capital stock shows the labor-augmented technology and capital-augmented technology that would increase many times to the output through a multiplier effect. equation ( ) is modified and extended by the given set of parameters in order to get fresh insight into the real-time issue faced by the world regarding the coronavirus pandemic, i.e., where eg shows economic growth, comd shows communicable diseases, he shows healthcare expenditures, pd shows population density, pi shows poverty incidence, covid-dum shows covid dummy, i and t show countries and time period from to . equation ( ) shows that it is likely that communicable diseases, including covid- , will increase economic suffering in the form of decreasing a country's economic output that will have a negative impact on the globalized world, which causes global depression. the other factors, including healthcare expenditures, population density, and poverty incidence, would likely place more pressure on economic output because of insufficient healthcare resources, highly-dense populations, and poverty and hunger. these factors are crucial and need a fair assessment in order to devise strong policies to reduce economic suffering caused by the coronavirus and other factors to lessen global depression through economic opportunities. figure shows the research framework of the study. figure shows the different causes of global depression that are interconnected with poverty incidence, communicable diseases, population density, and healthcare resources. the blend of efficient healthcare, economic, social, and environmental policies are largely desirable to escape from this pandemic with the adoption of curative and preventative policies across the globe. the stated objectives need to be checked by sophisticated econometric techniques to get fresh evidence about global depression due to the outbreak of coronavirus. the study employed a differenced panel gmm estimator. this technique is utilized on longitudinal data sets where the cross-section identifiers are greater than the time period that is used in this study, i.e., cross-sections consist of selected countries while data is used from to . the second reason is that the differenced gmm estimator controls for possible endogeneity issues and serial correlation issues from the model. third, it includes the dynamic nature of the regressand in the list of regressors, where the regressand is included with the regressors to analyze the initial convergence in the growth model. fourth, the list of regressors can be further utilized as instrumental variables added by their first lagged, hence it can control for possible endogenous issues and autocorrelation issues in the model, and finally, the validity of using regressors as an instrumental variable by their first lagged is a real challenge to check whether the given instruments are reliable or not. for this purpose, the j-statistic and instrumental ranks are used to determine its validity. these features give clear distinctions from the rest of the instrumented techniques, for instance, simple ols, two-stage least squares, three-stage least squares, and simple gmm estimates with fixed and random effect. further, the study benefits from using the innovation accounting matrix that consists of two basic inter-temporal techniques, i.e., impulse response function (irf) and variance decomposition analysis (vda). the technique is based upon both the var specifications and determined by the shocks pertaining to the regressand by their set of regressors over a time horizon. thus, it specified the nature and magnitude of the explanatory factors to the outcome variable in forecasting apparatus. the statistics clearly show that the panel consists of all the representatives of the countries across the globe where highincome to low-income countries have been included in the given model to give equal rank to all of them without any special attention. this uniqueness gives reliable estimates and provides evidence for both sides of the coin. the maximum count of deaths caused by communicable diseases is about . % of total deaths, with a mean value of . %. poverty incidence shows the maximum value of . % with a mean value of . %. the data of covid- dummy is extracted from the population density data, as population density shows that the selected panel of countries has a high to low dense population data; the highest value is . people per square km of land area while the lowest value is . . thus, on the basis of ranking the population density data, the covid-dum is assigned a value to those countries where the population density is more than and equal to three digits, i.e., , while is assigned otherwise. the mean value of covid-dum shows . , which depicts that on average % of the countries in the selected panel have a population density that is more than or equal to three digits, while % of countries have a population compactness that is limited to two digits. table shows the differenced panel gmm estimates and found that communicable diseases other than coronavirus increase the country's economic growth in the form of receiving aid and other technology transfers from the rest of the world. this aid has controlled or reduced the intensity of some infectious diseases, like ebola, hepatitis, flu, tuberculosis, measles, rabies, zika, etc. however, the novel coronavirus has largely affected the whole world and the world's biggest economies, including the united states and other european countries that [ the results of this study further show that healthcare expenditures enormously increase in a given scenario that after obtaining the parameter estimates of the studied coefficients, there is a greater need for exploring the forecasted (inter-temporal) relationship between the stated variables for the next years. for this purpose, the study used innovation accounting matrix, which is based upon two innovative functions, impulse response function (irf) and variance decomposition analysis (vda). the irf estimates assist to identify the direction of the stated variables that could be seen by various economic and healthcare shocks over a time horizon. on the other side, the vda estimates showed the magnitude of the candidate variables on the response variable over time. thus, both innovation estimates help to determine future preventive strategies to minimize the covid- pandemic across countries. table shows the irf estimates for easy reference. the estimates show that communicable diseases and healthcare expenditures will likely increase countries' economic growth over a time horizon, whereas population density and covid- will mainly increase economic suffering in the form of decreasing economic output for the next years. the poor income group experience decreased economic growth up to however, after it countries' economic growth begins to increase due to increased income inequality across countries. the rest of the effects can be seen in figure for easy reference. table shows the vda estimates and suggests that population density will exert a greater magnitude on countries' economic growth with a standard error shock of %, followed by healthcare expenditures, covid- , and communicable diseases, while poverty incidence will have the least effect on countries' economic growth over a time horizon. the complete description can be visualized in figure . the world has been relentlessly affected by the outbreak of this deadly coronavirus, even though it is still only developing. in this study, a number of important factors have been identified, which might help researchers and policy makers to understand the emerging global depression. this study has selected a panel of developed and developing countries in order to examine the vulnerabilities caused by coronavirus across all the segments of society. the overall results come to the following policy conclusions: (i) communicable diseases, including covid- , largely increase economic suffering through the increased demand for healthcare infrastructure, exacerbated by poverty incidence and social compactness. thus, the need for healthcare technology transfers from developed to developing countries, fund allocation for poor nations to reduce global inequality which would help them out from poverty, hunger, and diseases, and smart cities planning with them about symptomatic treatment and immunity boosters to get an increased chance of early recovery from this infectious disease. (viii) population mixing is the main transmission route of spreading coronavirus from one person to another, thus there is a high need to raise awareness among community members to avoid massive gatherings. the government should have to take some initiatives for providing homebased jobs and given them enough salary to convince the massive population to stay at their homes. (ix) extreme physical distancing options, including school closures, business closures, and travel restrictions, may result in a few early achievements as they raise awareness in the community about how to avoid this infectious disease, however, if these strategies are delayed, these activities should be substituted by other options, like online teaching, work at home, meetings conducted online, risk management, online training programs, and other social programs that a person can be engaged with and learn new things to resettle his/her self quickly in a new mode. (x) the lower-income strata group will largely suffer from this pandemic due to low awareness, inadequate healthcare resources, unemployment, illiteracy, the absence of social safety net programs, a lack of voice, etc., and all these vulnerabilities will largely victimize poor people more than non-poor. thus, there is a greater need to support poorer countries through cash transfer programs. the provision of basic food material, basic healthcare services, sanitation facilities, and proper counseling and guidance would minimize the risk of spreading infectious disease. it is a reality in a given context that social/physical distancing and smart lockdowns exert a positive health effect, but these measures have potentially caused more economic suffering that will lead to a global depression. the disruption of the supply chain, fear of business losses, supply-demand production gap, and the global healthcare crisis will make this episode more painful. the need for joint global efforts, unified economic and healthcare policies, and subsidized economic sectors may decrease the intensity of the global depression and progress toward the eradication of the coronavirus. the basic limitation of the current study is inadequate data availability for covid- ; hence, the study selected given countries on the basis of the country's economic growth per capita. the impact of covid- on case per million and death per million is also important, which can be further explored in future studies. data is freely available at the world development indicators, published by the world bank. https://databank.worldbank.org/ source/world-development-indicators. mka: conceptualization, methodology, and supervision. zy: software and formal analysis. mk: resources. an: formal analysis, writing-reviewing, and editing. mmqa: visualization. kz: data curation and validation. all authors: contributed to the article and approved the submitted version. pandemic influenza: public health preparedness for the next global health emergency britain and the - influenza pandemic: a dark epilogue the origin and virulence of the "spanish" influenza virus an update on swine-origin influenza virus a/h n : a review avian influenza a (h n ) the next influenza pandemic: lessons from hong kong avian-to-human transmission of the pb gene of influenza a viruses in the and pandemics impact of influenza vaccination on seasonal mortality in the us elderly population h n influenza detection of molecular markers of drug resistance in pandemic influenza a (h n ) viruses by pyrosequencing lessons learned from influenza a (h n ) pdm pandemic response in thailand ebola viral disease outbreak-west africa the spread of the ebola virus disease and its implications in the west african sub-region health care expenditure and economic growth in saarc countries ( - ): a panel causality analysis modeling determinants of health expenditures in malaysia: evidence from time series analysis covid- coronavirus pandemic factors associated with mental health outcomes among health care workers exposed to coronavirus disease the novel coronavirus originating in wuhan, china: challenges for global health governance clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan coronavirus disease (covid- ) in italy the outbreak of covid- coronavirus and its impact on global mental health becker friedman institute for economics working paper the impact of coronavirus (covid- ) on e-business in malaysia modeling kenyan economic impact of corona virus in kenya using discrete-time markov chains economic effects of coronavirus outbreak (covid- ) on the world economy saving china from the coronavirus and economic meltdown: experiences and lessons covid- coronavirus and macroeconomic policy coronavirus disease (covid- ): we shall overcome economic impacts of coronavirus disease (covid- ) in developing countries covid- : a situation analysis of nigeria's economy the dramatic impact of coronavirus outbreak on air quality: has it saved as much as it has killed so far? does communicable diseases (including covid- ) may increase global poverty risk? a cloud on the horizon world development indicator europe: how do the outbreak patterns compare? the new york times us overtakes china as country with most covid- cases available online at what happens when it hits the poor ones? ( ) as coronavirus spreads to poorer countries, here's how the world can help covid- ): situation report, . world health organization ( ) duty to plan: health care, crisis standards of care, and novel coronavirus sars-cov- . nam perspectives. discussion paper prudent public health intervention strategies to control the coronavirus disease transmission in india: a mathematical modelbased approach covid- : how doctors and healthcare systems are tackling coronavirus worldwide an unprecedented global crisis! the global, regional, national, political, economic and commercial impact of the coronavirus pandemic available online at coronavirus: how some countries are keeping -or not keeping -people indoors. the straits times coronavirus: trump extends us social distancing guidelines -as it happened coronavirus crisis could double number of people suffering acute hunger -un. the guardian world hunger is still not going down after three years and obesity is still growing -un report. world health organization the economic impact of coronavirus could worsen food security for the world's hungry people disproportionately hurt the poor-and that's bad for everyone as coronavirus deepens inequality, inequality worsens its spread. the new york times researchers supporting project number (rsp- / ), king saud university, riyadh, saudi arabia. the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright © anser, yousaf, khan, sheikh, nassani, abro and zaman. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord- -clxzp ph authors: weber, olaf; schmidt, axel title: coronavirus infections in veterinary medicine date: journal: coronaviruses with special emphasis on first insights concerning sars doi: . / - - - _ sha: doc_id: cord_uid: clxzp ph nan tion is high frequency rna recombination [ ] . this strategy might be important for the crossing of species barriers for many important animal coronaviruses as well as the "sars-cov". the members of the nidovirales order, however, especially differ with respect to their envelopes and nucleocapsids [ ] . the biology of coronaviruses has been described in detail in other chapters. therefore, this chapter focuses on clinical and economical aspects of coronavirus infections in companion (pets), live-stock (farm) and laboratory animals. based on phylogenetic analysis and antigenic cross reactivity, three groups can be distinguished in the coronaviridae family. some important viruses that are discussed below belong to group i and include the canine enteric coronavirus (cecov), the transmissible gastroenteritis virus (tgev) of swine, the porcine epidemic diarrhoea virus (pedv), the porcine respiratory coronavirus (prcov) and the feline coronaviruses (fcovs). most coronaviruses are enzootic and/or endemic in the respective host species. the vast majority of infections occur with inapparent clinical signs. the virus usually infects and replicates in epithelia and outbreaks of gastrointestinal and/or respiratory diseases are often seasonal. clinical signs are in general more severe in younger animals. immunocompromised animals and infected adults also serve as a major virus reservoir. genomic recombination appears to be a very common event in vitro and in vivo [ ] in coronaviruses also relevant in animal health. therefore, interactions of different coronaviruses can lead to new types and novel clinical entities [ , ] . porcine coronaviruses include i) tgev; ii) prcov which is a mutant of tgev; iii) pedv i and ii; and iv) haemagglutinating encephalomyelitis virus (hev). the latter belongs to the coronavirus group ii. tgev and pedv are highly infectious and highly contagious enteric viruses of swine. pedv and tgev infections are considered difficult to distinguish clinically and also histopathologically [ ] [ ] [ ] but can be distinguished by using modern, up-to-date techniques such as pcr and/or specific sequencing [ ] . tge is an economically important disease that might result in high mortality and was first described in the s. while older animals generally recover by time, piglets under the age of three weeks usually die from the infection. the tgev genome consists of a single-stranded, positive-sense . -kb rna. the viral membrane contains three transmembrane proteins: the s protein ( kda), m protein ( to kda), and minor e protein ( -kda). the s surface protein initiates the infection by binding to the cell surface. it also mediates the subsequent fusion between the viral and cellular membranes. the s protein binds to aminopeptidase n and to sialic acid. aminopeptidase n binding is required for tgev to initiate the infection of cells [ ] . recognition of sialic acids appears to be important for both, the haemagglutinating activity and the enteropathogenicity of tgev [ ] . the enteric tropism of tgev presumably also requires the binding to a co-receptor that maps around amino acid of the s protein as well as other additional co-factors [ , ] . the importance of sialic acid binding for entropathogenicity is supported by the fact that the non-enteropathogenic prcov lacks sialic acid binding activity. this can be explained by a large deletion in the s gene that results in a truncated spike protein [ , ] . prcov causes a mostly mild and moderate epizootic respiratory disease and might have worked like a vaccine against tge in a number of swine populations. tgev is transmitted either directly or indirectly through contact with feces of infected pigs or via vector animals such as dogs and cats. like other coronaviruses, tgev is fragile and highly sensitive to disinfectants as further detailed in the chapter by wolff et al. epidemic peaks mostly occur during the cold season. after an incubation period of one to three days, symptoms of tgev-associated disease emerge that include watery diarrhea, typical foul smelling yellowish-green feces that often contains flecks of undigested milk, vomiting, and loss of appetite. while the mortality rate is high in suckling piglets -up to % in piglets under two weeks of ageclinical symptoms in older piglets and adults are often mild and these animals will survive if especially their hydration status is adequate and ensured. the mortality rate is generally lower in these animals and will largely depend on additional factors such as secondary bacterial infections, cardiovascular decompensation, chilling and dampness. outbreaks usually only last a couple of weeks with occurrence of specific neutralizing antibodies in mucosa, blood and milk. further, lactating sows are highly susceptible. clinical signs may include vomiting, severe diarrhea, malnutrition, and cease of lactation. in large herds the disease can persist for some time, often contributing to post-weaning diarrhea. the clinical symptoms of endemic/enzootic tge are usually less severe in the older pigs, making a clinical differentiation between tge and other infectious enteric diseases, like that caused by rotaviruses and/or clostridia, impossible. upon histopathological examination, villous atrophy is frequently found in both rotaviral and enzootic tge infections. mixed infections are possible and underscore the importance of a strict disease management and/or prevention regimen. tge represents a reportable disease also in eu member states. there is no specific treatment available yet, however, electrolytes, nursing and enhanced management of the piglets may reduce mortality and lethality. in smaller herds cross-suckling of affected piglets onto recovered sows would offer a biological treatment. it is critical to almost impossible to assess general hygiene measures in prevalently infected herds. modified live vaccines are available and immunization of pregnant swine is a common vaccination strategy. cecov is associated with moderate to severe enteritis in young puppies. the genome contains the open reading frames (orfs) a and b, encoding polyproteins leading to the viral replicase formation. downstream of orf b are orfs encoding the coronavirus structural proteins s (orf ), e (orf ), m (orf ) and the nucleocapsid (n) protein [ ] . the e protein has a function for virus assembly [ ] , the m protein is a type iii glycoprotein [ ] . orf encodes the spike (s) protein, a glycoprotein ranging from , to , amino acids (aa) in length [ ] . this large protein has three structural domains. the large external domain at the n-terminus is furthermore organized into two sub-domains s and s with the s sub-domain including the n-terminal half of the molecule and forming the globular portion of the spikes. s contains sequences responsible for binding specific cellular receptors. s sequences are extremely variable, and mutations in the s region have been associated with problems of altered antigenicity and pathogenicity/virulence. in contrast, s sequences are genetically much more conserved and contain two heptad repeat motifs that suggest a coiledcoil structure [ ] . sequence analyses of cecov detected in fecal samples that were collected from dogs with diarrhea showed mutations accumulating over the m gene [ ] . a genetic drift to fcov type ii was also observed in the sequence of cecov detected in the faeces of puppies infected naturally during the late stages of long-term viral shedding. infection by mixed populations of genetically different cecov and recombination in vivo might, therefore, be common events [ ] . the clinical signs of these coronavirus infections vary. they commonly include vomiting, diarrhea and "unspecific" symptoms such as depression, anorexia, and fever. puppies most obviously die from severe dehydration. the majority of dogs that are not severely affected recover without any treatment. animals with severe symptoms of dehydration need supportive care stabilizing the hydration status. antibiotic/antibacterial treatment may be indicated in order to prevent exacerbations of bacterial superinfections. although vaccination may be indicated in kennels, sanitation is also the economically most effective way to control these coronavirus infections and, therefore, should be maintained by keeping the kennels free of feces and cleaning the environment by an appropriate desinfection regimen. fcov is commonly associated with mild enteric infections but is also associated with feline infectious peritonitis (fip). fip is a routinely fatal disease in both wild and domestic felidae. fcov can be distinguished into two serotypes: i and ii, on the basis of a virus neutralization assay in vitro using both type-specific feline sera and monoclonal antibodies directed against the s protein [ ] [ ] [ ] . the prevalence of these two serotypes is uncertain; type ii fcovs may account for up to thirty percent of the fip cases in cats in japan [ ] . the s protein of the type ii fcov shares immunodominant neutralization epitopes with the s protein of canine coronavirus [ ] . the s proteins of type ii fcov strains show great amino acid sequence identity to those of cecov (approximately %) and tgev (approximately %) but not to several type i strains (approximately %) [ , ] . in the first phase of the infection the symptoms are extremely unspecific. a mild upper respiratory disease, as evidenced by watery eyes and sneezing, might be diagnosed. a high percentage of primarily infected cats clear the virus; some of them, however, become long-term virus carriers. only a small percentage of exposed cats -higher, up to twenty percent in kennels -develop fip, months or years after primary infection. it is still unclear whether an endogenous reactivation could also be responsible for this pathomechanism. the clinical signs of fip usually gradually increase in severity over a period of several months, starting with rather unspecific signs such as inappetence, depression, rough fur, weight loss and fever. the forms of the lethal fip may be effusive (wet) and/or non-effusive (dry and/or proliferative). combinations of both clinical manifestations are rather common. the most characteristic clinical sign of wet fip is ascites. other symptoms may be rather unspecific like swollen lymph nodes, ocular symptoms with conjunctivitis and/or corneal ulcers. as the name suggests, fluid accumulation is minimal in the dry form of fip. instead, other, rather unspecific symptoms dominate. the dry form progresses slowly, often making clinical diagnosis difficult. weight loss, depression, anemia, and fever, are frequently observed symptoms. signs of severe kidney and/or liver failure, pancreatic, neurological or ocular disorders are observed in various combinations. a characteristic granulomatous inflammation is mostly observed by biopsy or in pathological examinations if performed. a cure does not exist yet. the therapy should provide supportive care and to alleviate the self-destroying inflammatory response of the disease. short-term remissions in a small percentage of patients have been described. a combination of corticosteroids, cytostatic drugs and antibiotics may be helpful in some cases despite the often fatal overall prognosis pro vitam. virulence of fcov strains appears to correlate to their ability to infect macrophages [ ] . the clinical symptoms are induced by immune complex reactions. antibodies are not only not protective, they might even accelerate the onset and the course of the disease in form of an antibody-enhanced infection (aei) such as observed in dengue fever in humans [ ] . the pathogenesis of the lesions, however, is not yet fully understood in its complexity. on the one hand there is evidence that immune complexes and subsequent activation of complement factors play an important role in the pathogenesis of fip [ ] . on the other hand, abnormal cytokine or chemokine secretion patterns -i.e. in infected immunocompetent cellscould also play a pathogenic role in the development of typical fip lesions like in granulomas [ ] . bovine coronavirus (bcov) is an important cause of neonatal calf diarrhea [ ] but may also infect the respiratory tract and has been recognized as the causing agent especially for winter dysentery in adult cattle. enteric and respiratory virus strains are antigenically related [ ] but differ genetically [ ] . amino acid alterations in the s subunit of the s protein (e.g. residues , , , , , , and ) of respiratory isolates conferred significant changes to the structure of the protein compared with the bcov strains that cause winter dysentery and calf diarrhea. bcov was first reported in [ ] [ ] [ ] . the zoonotic potential of bcov remains to be determined although a case of transmission to humans has been reported [ ] . bcov possesses a single-stranded, enveloped, nonsegmented rna genome of positive polarity [ ] . the mature virion con-tains five major structural proteins -the nucleocapsid (n) protein, the transmembrane (m) protein, the haemagglutinin/esterase (he) glycoprotein, the spike (s) protein, and a small membrane (e) protein [ , ] . he fulfills receptor binding and detachment functions. the s glycoprotein also recognizes the -o-acetylated sialic acid, apparently with a higher affinity than he [ , ] . the s protein is proposed to be responsible for the primary attachment of bcov to other cell surface receptors [ ] . variations in the s glycoprotein are most likely responsible for host specificity and tissue tropism [ ] . bcov is distributed worldwide and antibodies can be detected in the vast majority of cattle [ , ] . bcov infects calves/cattle by both the oral and/or respiratory route. although the virus can be detected in healthy animals, the most common source of enteric infection is diarrhoeic faeces from other infected animals. the virus infection of the enteritic tract starts in the small intestine and spreads after an initial replication throughout the gastrointestinal (gi) tract. since the virus replicates in the surface distal villi of the epithelial cells of the gi tract, these cells will eventually be destroyed, leading to fusions of adjacent villi in the small intestine and to atrophy of the colonic ridges [ ] . the severity of clinical signs varies with the age and especially the immunological status. usually, a yellowish diarrhea is observed that lasts for about three to seven days. it is difficult to distinguish between rota-and coronavirus-associated infection based on clinical signs solely. if diarrhea is severe, calves become pyrexic and dehydrated. infections with respiratory bcov often appear after stress such as shipment and/or environmental disturbances. infected animals will develop clinical signs of respiratory distress including wheezing and nasal discharge three to four days after infection. bacterial superinfections often complicate the clinical status. respiratory disease was induced experimentally after oral inoculation in colostrum-deprived calves [ ] . as for other coronaviruses, seasonal changes in temperature, environmental factors but also the immune status play an important role in the transmission of the virus and the clinical outcome of the infection. different virus isolates have been reported to have differences in tissue tropism [ ] . these authors report that about % of the infections in calves involve the respiratory tract in parallel and the enteric tract, whereas each % only involve either the respiratory or the gi tract. as for other coronaviruses, diagnosis/diagnostics requires detection of specific nucleic acids. virus isolation may be difficult and mostly not practicable in all day diagnostics. alternatively, nasal swabs might be used for detection of bcov antigen by immunofluorescence tests or other appropriate immunological methods. interestingly, a fragment amplified from "sars-cov" (bni fragment) showed % homology with bcov and mouse hepatitis virus (mhv) at the amino acid level [ ] . infectious bronchitis virus (ibv) is a major cause of disease in domestic fowl and causes an acute, highly contagious disease of the respiration and sometimes also urogenital tract [ ] . the ibv genome consists of approximately kb [ ] and codes for the spike (s) glycoprotein, the membrane (m) glycoprotein, and the nucleocapsid (n) phosphoprotein [ ] . ibv is distributed worldwide, and different variants have been isolated [ ] [ ] [ ] [ ] [ ] [ ] . ibv strains within a geographic region might be unique and distinct, examples are europe, the usa, and australia, i.e. for avian ibv [ ] . the different antigenic types make the use and possible efficacy of a single vaccine extremely questionable. the natural hosts for ibv are chicken and pheasants. ibv infections represent an important economic threat for the poultry industry. infected animals of all ages show signs of an acute, highly contagious respiratory disease. it is characterized by coughing, sneezing, and a nasal discharge. the major production loss results from the reduction in egg production and inferior egg quality. in younger birds there may be a high death rate, weight losses, or problems in weight development. some virus strains may also induce primary infectious kidney lesions. the lethality in these animals may be up to %. as for other coronavirus infections, only a virological examination, mainly based on serological techniques, can lead to the appropriate diagnosis. other important respiratory diseases include newcastle disease (nd) and infectious laryngotracheitis (ilt). according to regulations of many eu member states, nd is a disease that requires immediate reporting and action by veterinary authorities. ilt is also a reportable animal disease. there is no specific treatment for infectious bronchitis. antibiotic treatment might help to prevent or reduce secondary, i.e. bacterial superinfections. strict hygienic management and/or isolation of the flock may help to interrupt the disease cycle. different live virus vaccines have been developed and are currently in use; however, the use of live vaccines complicates especially serological diagnostics. sequencing of the s glycoprotein gene is the method recommended by the oie (office international des epizooties) to discriminate between different ibv strains. turkey coronavirus (tcov) causes acute and highly contagious enteritis of significant economical importance in turkeys [ ] . the clinical signs usually appear at seven to days of age in turkeys under six weeks of age and consist of diarrhea, litter eating, decreased feed efficiency and decreased weight development. morbidity is high, although mortality might be low. tcov is difficult to eradicate. tcov-induced enteritis has been described to be minnesota's most costly turkey disease from to [ ] . tcov treatments of the disease are often unsuccessful and there are currently no effective vaccines and/or other medications to prevent this disease. the local immune system of the mucosa of the gastrointestinal tract plays a major role in the protection against an infection and modulates clinical signs as well. recent studies indicate that neutralizing, intestinal secretory mucosal iga antibodies to tcov are elicited in turkeys following infection with tcov and that local mucosal antibodies may provide protective immunity for infected turkeys to recover from tcov infection [ ] . as for other coronaviruses, mechanical vectors play an important role in the transmission of the virus: it was demonstrated recently that house flies can transmit tcov [ ] . tcov from intestinal contents of diarrheal poults could be propagated in a human adenocarcinoma line and one-day-old turkey poults inoculated orally with tissue culture-adapted tcov isolates developed mild to severe diarrhea [ ] . however, the passaging of tcov could not be reproduced by other investigators so far [ , ] . this viral enteritis is different from haemorrhagic enteritis (he), another economically important disease of turkeys that is caused by a type ii adenovirus (reviewed by sharma [ ] ). in contrast to bluecomb disease, turkeys younger than four weeks of age are clinically "resistant" to he. in addition to the enteritis, a pathological frequent finding is hepatosplenomegalia. bursectomy and/or splenectomy abrogate clinical he [ ] . mhv belongs to the coronaviridae family and represents one of the most important pathogens of the laboratory mouse. mhv is serologically related to other coronaviruses of rats, pigs, cattle, and also humans. it is a very well-studied virus, because of its adverse influence on several research approaches and consecutively also results. about different mhv strains have been reported so far. some strains are polytropic; they infect a variety of tissues and cause symptoms in various organs. other strains are more specifically organotropic, e.g. enterotropic, and cause villus attenuation, syncytia formation and mucosal necrosis of the terminal small intestine and the colon. mhv is very contagious; transmission occurs by aerosol, faeces and many other contacts/transmission routes. there are usually no clinical symptoms in infected adult mice. clinical signs such as weakness, diarrhea, wasting and weight loss are observed in young mice. the mortality rate varies but might be high. since laboratory animals almost always come from controlled breeding providers/animal environment (e.g. spf = specifically pathogen free), serology is a highly reliable method to detect the target infection. considering the costs of modern biomedical research, infection with mhv is an economically important disease in small laboratory animals. the effects of the mhv infection on immunocompromised mice include enhanced phagocytic activities of macrophages, rejection of xenograft tumors [ ] , abnormal tumor growth patterns [ ] , altered response to chemical carcinogens [ ] , and impaired liver regeneration. pharmcokinetics of test compounds might also be altered due to a change of enzyme activities. in immunocompetent mice, effects observed include immunoestimulation and, later on, immunodepression [ , ] . macrophage function is altered in infected mice [ ] , and effects on other immune competent cells are frequently found in infected mice as well. often the best solution for infected facilities is to eliminate the entire affected stock with a consecutive appropriate desinfection regimen. host range mutants of mhv strains were isolated from mixed cultures containing progressively increasing concentrations of non-permissive syrian baby hamster kidney (bhk) cells. the mutant virus was polytrophic, replicating efficiently in normally non-permissive bhk cells, syrian and chinese hamster (ddt- and cho) cells, human adenocarcinoma (hrt), primate kidney (vero) and in murine cl- cell lines [ ] . the coronaviridae now comprises two genera, coronavirus and torovirus: report of the coronaviridae study group nidovirales: a new order comprising coronaviridae and arteriviridae a comparative sequence analysis to revise the current taxonomy of the family coronaviridae high-frequency rna recombination of murine coronaviruses molecular evolution of corona-and toroviruses recombination and coronavirus defective interfering rnas human coronavirus e enters susceptible cells via the endocytic pathway fields virology. lippincott-raven the size and morphology of transmissible gastroenteritis and vomiting and wasting disease viruses of pigs a new coronavirus-like particle associated with diarrhea in swine experimental infection of pigs with a new porcine enteric coronavirus, cv differentiation between porcine epidemic diarrhea virus and transmissible gastroenteritis virus in formalinfixed paraffin-embedded tissues by multiplex rt-nested pcr and comparison with in situ hybridization aminopeptidase n is a major receptor for the entero-pathogenic coronavirus tgev point mutations in the s protein connect the sialic acid binding activity with the enteropathogenicity of transmissible gastroenteritis coronavirus targeted recombination demonstrates that the spike gene of transmissible gastroenteritis coronavirus is a determinant of its enteric tropism and virulence two amino acid changes at the n-terminus of transmissible gastroenteritis coronavirus spike protein result in the loss of enteric tropism porcine respiratory coronavirus differs from transmissible gastroenteritis virus by a few genomic deletions coronavirus immunogens virus taxonomy, classification and nomenclature of viruses characterization of the coronavirus mouse hepatitis virus strain a small membrane protein the coronavirus membrane protein coronaviridae: the viruses and their replication variation of the sequence in the gene encoding for transmembrane protein m of canine coronavirus (ccv) m gene evolution of canine coronavirus in naturally infected dogs feline coronavirus type ii strains - and - originate from a double recombination between feline coronavirus type i and canine coronavirus characterization of monoclonal antibodies against feline infectious peritonitis virus type ii and antigenic relationship between feline, porcine, and canine coronaviruses the prevalence of types i and ii feline coronavirus infections in cats molecular cloning and sequence determination of the peplomer protein gene of feline infectious peritonitis virus type i nucleotide sequence and expression of the spike (s) gene of canine coronavirus and comparison with the s proteins of feline and porcine coronaviruses intrinsic resistance of feline macrophages to coronavirus infection correlates with in vivo virulence virologic and immunologic aspects of feline infectious peritonitis virus infection antibody, immune complexes, and complement activity fluctuations in kittens with experimentally induced feline infectious peritonitis bovine coronavirus comparison of the s genes and the biological properties of respiratory and enteropathogenic bovine coronavirus molecular analysis of the s subunit of the spike glycoprotein of respiratory and enteric bovine coronavirus isolates neonatal calf diarrhea: results of a field trial using a reo-like virus vaccine neonatal calf diarrhea: propagation, attenuation and characteristics of a coronavirus-like agent reactivity of antibodies in human serum with antigens of an enteropathogenic bovine coronavirus the genome organization of the nidovirales: similarities and differences between arteri-, toro-, and coronaviruses nucleotide and predicted amino acid sequences of all genes encoded by the ' genomic portion ( . kb) of respiratory bovine coronaviruses and comparisons among respiratory and enteric coronaviruses the molecular biology of coronaviruses the s protein of bovine coronavirus is a haemagglutinin recognizing -o-acetylated sialic acid as a receptor determinant recognition of n-acetly- -o-acetylneuraminic acid by bovine coronavirus and haemagglutinating encephalomyelitis virus coronavirus spike proteins in viral entry and pathogenesis antigens of bovine coronavirus strain ly and their diagnostic properties detection by radioimmunoassay and enzyme-linked immunosorbent assay of coronavirus antibodies in bovine serum and lacteal secretions experimental infection with a virulent pneumoenteric isolate of bovine coronavirus infectious bovine rhinotracheitis, parainfluenza- and respiratory coronavirus clinical detection of polymerase gene of sars-associated coronavirus infectious bronchitis completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus the structure and replication of coronaviruses the classification of new serotypes of infectious bronchitis virus isolated from poultry flocks in britain occurrence and significance of infectious bronchitis virus variant strains in egg and broiler protection in the netherlands identification of recent infectious bronchitis virus isolated that are serologically different from current vaccine strains isolation, pathogenicity, and h protection efficacy of infectious bronchitis viruses isolated in taiwan genetic grouping for the isolates of avian infectious bronchitis viruses in taiwan isolation and identification of infectious bronchitis virus from chickens in sichuan avian infectious bronchitis virus coronaviral enteritis of turkeys (bluecomb disease) coronaviral enteritis pf turkeys (bluecomb disease) specific mucosal iga immunity in turkey poults infected with turkey coronavirus mechanical transmission of turkey coronavirus by domestic houseflies (musca domestica linnaeaus) isolation and trypsin-enhanced propagation of turkey enteric (bluecomb) coronaviruses in a continuous human rectal adenocarcinoma cell line antigenic characterization of a turkey coronavirus identified in poultry enteritis-and mortality syndromeaffected turkeys the in vitro propagation of stunting syndrome agent haemorrhagic enteritis of turkeys role of splenectomy in prevention of haemorrhagic enteritis and death from hemorrhagic enteritis virus in turkeys influence of the mouse hepatitis virus (mhv) infection on the growth of human tumors in the athymic mouse influence of mouse hepatitis virus on the growth of human melanoma in the peritoneal cavity of the athymic mouse research complications and state of knowledge of rodent coronaviruses the role of circulating interferon in the modifications of the immune responsiveness to mouse hepatitis virus (mhv- ) natural patogens of laboratory mice, rats and rabbits and their effects on research peritoneal and macrophage alterations caused by naturally occurring mouse hepatitis virus virus-receptor interactions and interspecies transfer of a mouse hepatitis virus key: cord- - br faov authors: xu, shuang-fei; lu, yi-han; zhang, tao; xiong, hai-yan; wang, wei-bing title: cross-sectional seroepidemiologic study of coronavirus disease (covid- ) among close contacts, children, and migrant workers in shanghai date: - - journal: int j environ res public health doi: . /ijerph sha: doc_id: cord_uid: br faov ( ) background: along with an increasing risk caused by migrant workers returning to the urban areas for the resumption of work and production and growing epidemiological evidence of possible transmission during the incubation period, a study of coronavirus disease (covid- ) is warranted among key populations to determine the serum antibody against the sars-cov- and the carrying status of sars-cov- to identify potential asymptomatic infection and to explore the risk factors. ( ) method: this is a cross-sectional seroepidemiologic study. three categories of targeted populations (close contacts, migrant workers who return to urban areas for work, and school children) will be included in this study as they are important for case identification in communities. a multi-stage sampling method will be employed to acquire an adequate sample size. assessments that include questionnaires and blood, nasopharyngeal specimens, and feces collection will be performed via home-visit survey. ( ) ethics and dissemination: the study was approved by the institute review board of school of public health, fudan university (irb# - - ). before data collection, written informed consent will be obtained from all participants. the manuscripts from this work will be submitted for publication in quality peer-reviewed journals and presented at national or international conferences. since the first known case of pneumonia infected with the novel coronavirus was reported in the city of wuhan in late december of , coronavirus disease (covid- ), caused by sars-cov- and announced by the world health organization on february , unexpectedly and quickly spread in china and many other countries with rapid geographical expansion and a sudden increase in the number of cases [ , ] . on january , covid- was added into china's "law on prevention and control of infectious diseases" as a class b notifiable disease and necessitated prevention and control measures as a class a because of its emergences [ ] . on january, the chinese government began to limit population movement in and out of wuhan. in the following week, provinces in mainland china successively launched response level i of the major public health emergency to respond to the covid- epidemic, including the lockdown of whole cities, cancelation of celebration activities of spring festival (chinese new year), and deferral of attendance at school and work. to our knowledge, the common clinical features of covid- are non-specific, such as fever, dry cough, and bilateral and peripheral ground-glass and consolidative pulmonary opacities on chest computed tomography (ct) scans, in addition to other symptoms including dyspnea, headache, muscle soreness, and fatigue [ , ] . according to the released data from the chinese center for disease control and prevention, the overall case-fatality rate (cfr) was . %, though the cfr was much higher among the critical ( %) and the elderly cases ( - %). of the total cumulative confirmed cases on february , , the majority ( %) were classified as non-pneumonia and mild pneumonia, and no death has been documented among those with mild or severe symptoms [ ] . at the end of february , a total of , confirmed covid- cases were recorded in mainland china, of whom , had been discharged and had died [ ] . thus far, the majority of published studies focused on hospitals and confirmed/suspected cases rather than on the population at risk in communities. along with the resumption of work and production activities and the adjustment of the emergency response level, an increasing number of migrant workers across the whole country are gradually returning to urban areas, which adds an extra burden on disease prevention and management. meanwhile, several studies provided epidemiological evidence of possible transmission of sars-cov- from pre-symptomatic and asymptomatic cases (asymptomatic people with sars-cov- detected in respiratory specimens or immunoglobulin m (igm) detected in serum) [ , ] . thus, a cross-sectional seroepidemiologic study of covid- among key populations is warranted to determine the potential risk of sars-cov- infection in different scenarios. the study introduces no significant risk to participants, with no medication or intervention involved. the study was approved by the institute review board of school of public health, fudan university (irb# - - ). before data collection, the purpose and procedures of the study will be explained to all the eligible participants. written informed consent will be obtained from all participants and from the parents of minors. participants can withdraw from the study at any point without any adverse consequences. all data are anonymous and will be managed confidentially. to determine the serum antibody level against the sars-cov- and the carrying status of sars-cov- among key susceptible populations to identify potential asymptomatic infection and to explore the risk factors. three categories of study participants will be recruited in the study as they are important for case finding in communities. participants must meet the following inclusion criteria: close contacts: the definition of "close contacts" is based on prevention and control of novel coronavirus pneumonia ( th edition), which refers to people who had unprotected close contact (within meter) with a confirmed or suspect case within two days before illness onset, or with an asymptomatic infected person within two days before sampling [ ] . in china, the tracing and management of close contacts is implemented by the local center for disease control and prevention (cdc), and all identified close contacts are recorded in health administration departments. • volunteer to participate in the survey and provide written informed consent. domestic migrant workers returning to urban areas for work: • aged years and above; • unconfirmed covid- cases; • volunteer to participate in the survey and provide signed informed consent. school children: • aged above years; • attending primary school, middle school, or high school (non-vocational high school); • unconfirmed covid- cases; • volunteer to participate in the survey and provide signed informed consent themselves and/or through their parent(s). • history of any neurologic disorders; • language disorders. this is a cross-sectional study design. the sample size is calculated according to the following formula: where nsrs is the sample size under simple random sample assumption; zα/ is the statistic corresponding to level of confidence, assumed to be . (when α = . ); d is precision, assumed to be %*p [ ] ; k is the missing rate, assumed to be % [ ] ; n is the minimum required sample size; p is the expected seroprevalence of antibodies against sars-cov- among the target populations. however, these parameters for the above three categories of study participants remain unclear. although the spread of sars-cov- is much faster than that of the sars-cov in , these two coronaviruses share a similar transmission mode, such as airborne transmission and close person-to-person contact, via respiratory droplets from sneezing or coughing, and fomites. thus, we consider referring to the transmission data of sars epidemic. in , after the sars epidemic, the seroprevalence of antibodies against sars-cov tested by enzyme-linked immunosorbent assay (elisa) among close contacts, general population and school children were . - . %, . - . % and - . %, respectively [ ] [ ] [ ] [ ] [ ] . similarly, we assume the expected seroprevalence of sars-cov- among close contacts, migrant workers, and school children to be %, %, and %, respectively. if the research designers in different regions obtain more specific local data, they can adjust the calculations. finally, in our design, the expected sample sizes for close contacts, migrant workers, and school children are , , and , respectively. multi-stage sampling methods will be employed to acquire adequate sample size. primary sampling units (psus) are sampled with a probability proportional to size (pps), that is, the number of subunits within each psu. given the different population sizes of the three categories of study participants and the different sampling strategies, the selected psus for each target population may not be identical. for close contacts, the specific sample size will be determined by the cumulative number of contacts in the city. it is best to include all contacts of the confirmed covid- cases, to maximize the statistical power of the study. otherwise, one-stage design with cluster sampling is chosen. here, "size" in pps refers to the number of close contacts in each district, which is now replaced by the size of confirmed covid- cases because there are no open data about close contacts in shanghai. the four districts, from the total , selected as psus with pps sampling were pudong district, xuhui district, yangpu district, and songjiang district ( table ) . all eligible close contacts in the selected districts will be enrolled. for migrant workers returning to the city for work, a two-stage design with pps and successive sampling is chosen. at the first stage, pps ("size" here refers to the floating population count in each district) sampling is employed to select four psus. considering the distribution of floating population in each district released by the shanghai statistics bureau in , pudong district, putuo district, baoshan district, and qingpu district were selected (table ) . at the second stage, a fixed number of individuals will be enrolled using successive sampling. for migrant workers, to our knowledge, migrants returning to shanghai are required to actively register with the village/neighborhood committees since january, . thus, all eligible migrant workers in each psu will be recruited one-by-one from the registers until the expected sample size is reached. for school children, a three-stage design with pps, simple random sampling (srs), and cluster sampling is chosen. at the first stage, pps ("size" here refers to the number of schools in each district at the second stage) sampling is employed to select psus. taking shanghai for example again, based on the data from shanghai education bureau [ ], pudong district, jing'an district, minhang district, and songjiang district were selected (table ) . at the second stage, schools in each district will be stratified as primary school, middle school, and high school, and srs will be used to select ~ schools from each stratum. at the third stage, or classes in each grade will be chosen at random, and all eligible students should be enrolled (the specific number of classes can be adjusted by the admission size). the sample size for school children is "deff" (the design effect in cluster sampling, assumed to be . ), which multiplies the expected value (n = ). sociodemographic characteristics: name, telephone (mobile) number, date of birth, sex, e-mail address, current address, ethnicity, job, educational level, parent employment status, educational level (only for children) and preferred mode of contact (telephone, email, or express delivery); . underlying conditions: pregnancy, obesity, cancer, diabetes, hypertension, heart disease, asthma requiring medication, chronic lung disease (non-asthma), chronic liver disease, chronic hematological disorder, chronic kidney disease, chronic neurological impairment/disease, and other underlying conditions. in addition, respiratory-pathogen-related vaccinations will be reviewed. clinical symptoms within the last days: body temperature, fever, chill, dry cough, sore throat, runny nose, shortness of breath, nausea, vomiting, diarrhea, and other symptoms. general exposure information: possible contact with confirmed/suspected cases, visits to medical facilities, and travel history (including destination, transfer, and duration) within the last days. appropriate personal protective equipment should be worn when specimens are being collected. specimens of close contacts will be collected by the designated local cdcs and medical facilities. specimens of migrant workers and school children will be collected by qualified technicians. all specimen containers should be labeled with the full name of the person being sampled, time and date of collection, and one other unique identifier such as the national medical insurance number. blood specimen: a ml whole-blood sample will be collected with a vacutainer with no anticoagulant. once the blood is drawn, the vacutainer should be inverted or times and placed at room temperature. when the blood specimen is sent to the laboratory, the vacutainer will be centrifuged for min at - rpm at room temperature. serum will be extracted by pipette and stored in a sterile spiral plastic tube. in addition, another ml whole-blood sample will be collected with a vacutainer containing edta anticoagulant. once the blood is drawn, the vacutainer should be inverted at least times and placed at room temperature for min. then the vacutainer will be centrifuged for min at - rpm at room temperature. plasma and blood cells will be separately collected into sterile spiral plastic tubes. • nasopharyngeal (np) swab: two np swabs will be collected for each eligible participant. the swab will be directly put in the nose parallel to the base of the np passage. the swab should move without resistance until reaching the nasopharynx, located about one-half to two-thirds the distance from the nostril to an ear lobe. if resistance occurs, the swab will be removed, and an attempt will be made to take the sample entering through the same or the other nostril. once the swab reaches nasopharynx, the swab will be rotated • , or left in place for s to saturate the swab tip; and then the swab will be removed slowly. then the swab head will be inserted into the tube containing . ml of virus preservation buffer (virus transport medium (containing hank's balanced salt solution, polymyxin b, vancomycin, bovine serum albumin, cryoprotectant, biobuffer, etc.), shanghai comagal microbial technology co. ltd.) and swab shaft will be evenly broken at the scored line to fit in tube and replace cap tightly. feces or anal swab: - ml of stool that has not been mixed with urine will be collected in a clean, dry, leak-proof container. if it is not convenient to collect fecal samples, an anal swab can be collected. the disinfectant cotton swab will be gently inserted into the anus to a depth of - cm, then it will be gently rotated pulled out, and immediately put into a ml screw-capped sampling tube containing - ml virus preservation buffer. then, the swab shaft will be evenly broken at the scored line to fit in tube and the cap will be replaced tightly. blood specimens, np swabs, and anal swabs should be taken at the home visit. feces could be collected the next day. all specimens will be shipped to the laboratory in a sealed biohazard bag within h after collection at • c on ice packs. if transportation will be delayed more than h, specimens should be reserved at − • c and shipped on dry ice. it is important to avoid repeated freezing and thawing of specimens. laboratory examinations • serological testing: the serum specimen will be available for qualitative detection of sars-cov- -specific total antibodies (including igm, igg, iga, and other antibody types) with novel coronavirus ( -ncov) antibody test kit (chemiluminescence immunoassay method) (registered number: ), developed by xiamen innodx biotech co., ltd. (xiamen, china) and which is the world's first approved total antibody detection reagent with the double-antigen sandwich method for sars-cov- . it can rapidly and simply detect specific antibodies within min. • etiological testing: a real-time fluorescence-based reverse transcriptase-polymerase chain reaction (rt-pcr) assay will be applied to the np specimen and feces to detect sars-cov- . the primers and probes (targeting open reading frame ab (orf ab) and nucleocapsid protein (n) in the novel coronavirus genome) used for sars-cov- detection by rt-pcr is from the novel coronavirus pneumonia: laboratory testing guideline, released by national health commission of the prc. in addition, np specimens will be further examined for a total of respiratory pathogens (table ) via gene chips (micro-fluid chip for respiratory pathogens, product number: ). in this cross-sectional survey, participants with serological evidence (sars-cov- -specific igm and igg detectable in serum) or etiological evidence (real-time fluorescent rt-pcr indicating positive for sars-cov- nucleic acid) will be diagnosed as confirmed cases. the study design is presented in figure . investigators will communicate with the selected participants or guardians in advance to assure their intention of participating this program. the refusers will be replaced by resampling without replacement in each psu. investigators will visit the eligible participants at the appointed time; obtain written informed consent; complete the questionnaire survey; and collect blood specimens, np swabs, and annal swabs. feces specimens are limited to diarrheal participants and will be self-collected with sterile containers. investigators will take them in the next day. during the investigation, investigators will inform the participants of laboratory results via their preferred mode of contact, such as telephone, email, or express delivery. the identified asymptomatic cases in the survey will immediately report to local cdcs and transfer to medical facilities. the primary benefit of the investigation is to prevent the further spread of the virus. on completion of the investigation, data will be imported into the data analysis software (spss version . and sas version . ) for data cleaning and statistical analysis. the prevalences of sars-cov- -specific antibodies in serum and those of sars-cov- , and other respiratory pathogens in np specimens will be presented with their % confidence intervals (cis). participants' characteristics will be described as means ± sds for normally distributed variables, as medians, and interquartile ranges (iqrs) for non-normally distributed variables, and as frequencies and proportions for categorical variables. bivariate and multivariable analyses will be performed to identify potential factors associated with infection of sars-cov- and other respiratory pathogens among study participants. differences between groups will be compared with independent-samples t tests or mann-whitney u tests (for continuous variables), χ tests or fisher's exact tests (for categorical variables), and analysis of variance or kruskal-wallis where applicable. appropriate statistical models (logistic regression models and generalized linear mixed models) will be performed to estimate the odds ratios (ors) of factors associated with sars-cov- infection. adjusted odds ratios (aors) will be obtained using a multivariable model, including the following covariates: age, gender, occupation, education. further analysis will be determined upon more discussion. a p-value < . will be considered statistically significant. on completion of the investigation, data will be imported into the data analysis software (spss version . and sas version . ) for data cleaning and statistical analysis. the prevalences of sars-cov- -specific antibodies in serum and those of sars-cov- , and other respiratory pathogens in np specimens will be presented with their % confidence intervals (cis). participants' characteristics will be described as means ± sds for normally distributed variables, as medians, and interquartile ranges (iqrs) for non-normally distributed variables, and as frequencies and proportions for categorical variables. bivariate and multivariable analyses will be performed to identify potential factors associated with infection of sars-cov- and other respiratory pathogens among study participants. differences between groups will be compared with independent-samples t tests or mann-whitney u tests (for continuous variables), χ tests or fisher's exact tests (for categorical variables), and analysis of variance or kruskal-wallis where applicable. appropriate statistical models (logistic regression models and generalized linear mixed models) will be performed to estimate the odds ratios (ors) of factors associated with sars-cov- infection. adjusted odds ratios novel coronavirus ( -ncov): situation report, . ; world health organization early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia national health commission of the people 's republic of china. announcement by the national health commission relationship to duration of infection updated understanding of the outbreak of novel coronavirus ( -ncov) in wuhan the novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of novel coronavirus diseases (covid- )-china, . china cdc wkly national health commission of the people's republic of china. the latest status of -novel-coronavirus ( -ncov) pneumonia at o' clock clinical characteristics of asymptomatic infections with covid- screened among close contacts in nanjing a familial cluster of infection associated with the novel coronavirus indicating possible person-to-person transmission during the incubation period national health commission of the people' s republic of china. protocol on prevention and control of novel coronavirus pneumonia sars-cov antibody prevalence in all hong kong patient contacts seroprevalence of igg antibodies to sars-coronavirus in asymptomatic or subclinical population groups severe acute respiratory syndrome among children epidemiological research on sars coronavirus antibody in serum among healthy population of qingyuan city seroepidemiological study on severe respiratory syndrome among different population in taiyuan the authors declare no conflict of interest. key: cord- -n gz pi authors: samudrala, pavan kumar; kumar, pramod; choudhary, kamlesh; thakur, nagender; wadekar, gaurav suresh; dayaramani, richa; agrawal, mukta; alexander, amit title: virology, pathogenesis, diagnosis and in-line treatment of covid- date: - - journal: eur j pharmacol doi: . /j.ejphar. . sha: doc_id: cord_uid: n gz pi sars-cov- , a newly emerged pathogen in december , marked as one of the highly pathogenic coronavirus, and altogether this is the third coronavirus attack that crossed the species barrier. as of (st) july , it is spreading around countries, areas or territories, and a total of , , and , confirmed cases and death reports, respectively. the sars-cov- virus entered into the target cells by binding with the hace receptors. spike glycoprotein promotes the entry of the virus into host target cells. literature reported a significant mutation in receptor binding sites and membrane proteins of the previous sars-cov to turned as sars-cov- virus, responsible for most dreadful pandemic covid- . these modifications may be the probable reason for the extreme transmission and pathogenicity of the virus. a hasty spread of covid- throughout the world is highly threatening, but still, scientists do not have a proper therapeutic measure to fight with it. scientists are endeavoring across the world to find effective therapy to combat covid . several drugs such as remdesivir, hydroxychloroquine, chloroquine, ribavirin, ritonavir, lopinavir, favipiravir, interferons, bevacizumab, azithromycin, etc. are currently under clinical trials. vaccine development from various pharmaceutical companies and research institutes is under progress, and more than ten vaccine candidates are in the various phases of clinical trials. this review work highlighted the origin, emergence, structural features, pathogenesis, and clinical features of covid- . we have also discussed the in-line treatment strategies, preventive measures, and vaccines to combat the emergence of covid- . the coronavirus (cov) as believed to be originated from bats, was known for years, confirmed by many works of literature. these are positive-sense single-strand rna viruses with around similar species from the family of coronaviridae. this family of coronaviridae is further categorized as α, β, λ, and δ based on its distinct genetic features. however, among these, only alpha (α) and beta (β) coronavirus genera are pathogenic to mammalian and humans (chen et africa is listed as a minimally affected region ( , cases and , deaths) till date (who, a) . during this outbreak of covid- , the world is frightened with an unpredictable and hasty impact of the infection, and the data is changing day by day. coronaviruses are crown shape peplomers, positive-sense ssrna (single strand rna) virus, which was reported in the pleomorphic form with - nm size . it is a nonsegmented and rna virus ranging from to kb. coronavirus comes under the order- nidovirus, family-coronaviridae, subfamily-coronavineae which were further divided into α, β, ϒ and δ genus. among these, α and β genus of coronavirus mainly affect the human population. the α genus contains hcov- e (human coronavirus) and nl , while the β genus consists of hku , e, oc , mers-cov, sars-cov and latest outbreak sars- cov- . coronavirus has been mainly reported with single-strand rna, nucleocapsid protein, envelop protein, membrane protein, spike glycoprotein (s), etc., as shown in figure (lei et al., ) . spike (s) glycoprotein is responsible for the characteristic feature of the coronavirus because it forms the crown-like structure on the outer surface of the virus. the s-protein divides into two subunits, namely, s and s . the s subunit further classified into three domains, particularly a, b, and c (angeletti et al.) . generally, domain a of the subunit s present on cov-oc and cov-hku is binding with the host receptors (hulswit et al., ) . interestingly, the structure of the s protein in both sars-cov and novel sars-cov- viruses is almost similar to a few differences. recent literature reveals that rbd of the s subunit of the " s " protein is responsible for binding with ace (angiotensin-converting enzyme) receptors (letko et al., ) . this rbd in coronaviruses is highly variable. based on studies, six rbd amino acids that remain present on the s subunit are very critical for binding to the receptors. interestingly, different structural and functional studies stated that five of these six residual proteins are distinct in sars-cov- compared to sars-cov. accordingly, the coordinates based on the covid- (l , f , q , s , n , and y ) compared to those found in sars-cov (y , l , n , d , t , and y ) differ in only five distinct residues except y (andersen et al., ). these differences may be the probable reason for the high affinity of sars-cov- with the receptors and therefore are optimal for receptor binding a polybasic cleavage site (rrar) is present at the union site of s and s subunit of spike protein. in addition, proline residue is also introduced prior to this cleavage site, and the sequence in sars-cov- becomes prra (unique protein sequencing in sars-cov- ). insertion of the cleavage site has been seen but also the conversion of low pathogenicity virus into highly pathogenic forms is well observed (alexander and brown, ; ito et al., ) . however, the function of the predicated o-linked glycans is still not clear, but based on the literature, they may create a mucin-like domain that helps in immunoevasion ( are assembled into the nucleocapsid and viral envelope at the er or ergic, followed by release of virus by exocytosis or by fusing with the plasma membrane. although the pathogenesis behind covid- is not well understood, the pathogenesis of mers-cov and sars-cov still can be the best source of information regarding covid- (li et al., b) . recent literature suggests that the modified residues of rbd of s subunit, presence of rrar and partially opened state of 's' trimer may be a reason for high pathogenicity and transmission capacity of covid- . these rbd of s subunit on spike proteins binds to the hace receptor which are mainly present in the lungs, particularly type- pneumocytes. this the clinical symptoms of covid- infection can be seen after to days of incubation which mainly differs from age and immune system of the person. males are more susceptible to sars-cov- as compare to females. people with the age of more than are more sensitive to sars-cov- (li et al., a; the, ). the most common clinical features of sars-cov- infection are fever (more than % cases), cough (more than % cases), fatigue (more than % cases), sputum production (more than % cases), and shortness of breath (more than % cases). however, less common features include headache, muscle weakness, breathlessness, sore throat, and pleuritic pain ( - %). apart from this nausea, vomiting, chest tightness is the rare features pro-inflammatory cytokines are secreted by alveolar macrophages results in the recruitment of neutrophil and monocyte or macrophage along with activation of t-cells of epithelial cells, which further starts inflammation and tissue injury (ritchie and singanayagam, ). in medical term, ard is called "diffuse alveolar damage," or epithelial-cell hyperplasia. the diagnostic parameter for ard is hypoxia, which mainly decides based on the ratio between the blood pressure of oxygen and the percentage of oxygen supply, formulated as pao /fio mmhg. in severe cases, pao /fio found to be ≤ mmhg while in moderate cases, found to be ≤ . this ratio falls from to in mild cases of ard due to sars-cov- . other parameters that can distinguish ard are bilateral opacities followed by the collapse of lungs, which can be diagnosed through ct scan or ultrasound, where lung infiltration found to be > % (lai et al., a) . it is a reliable technique to isolate the affected population from the large population. it is also essential for initial screening for auxiliary diagnosis. a thermal camera was first introduced at hospital entrances and in the emergency department to recognize any persons with incremental body temperature. the scanning distance required for such cameras is meters. however, numerous potential pre-analytical and analytical risks are associated with rt- pcr. such risks are false (-) identification, sample preparation, specificity, sensitivity, stability issues, and also, it is a time-consuming process. although calibration of the instruments is also a matter of great concern, as it may provide false or misleading results, therefore it is highly recommended to calibrate the rt-pcr regularly to avoid any misleading readings. besides, the diagnostic kit should also be pre-validated in terms of the accuracy and reliability of the data (lippi et al., ) . during the outbreak, remdesivir was tested on three covid- infected patients in the u.s., which showed improvement of symptoms with no significant side effects, and also fda has given permission about patients to use this product. as far as safety is a major concern, gilead sciences announced phase iii clinical trial of remdesivir to prove its safety and efficacy in covid- infection (keown, . . ). after a preliminary investigation, gilead announced the results of the initial phase simple trial. the drug significantly reduced the mortality rate upon days of treatment and showed improvement in % of cases (gilead, ) . based on these results, the fda issued emergency use authorizations for the use of remdesivir against covid- ; however, full approval is still not provided anywhere in the world (fda, ). the fda already approves the drug chloroquine for treating malaria, arthritis and lupus hydroxychloroquine and azithromycin. they reviewed the data of patients, they treated with hydroxychloroquine on the first day at a dose of mg twice a day, followed by mg twice daily. azithromycin was given at a dose of mg per day. they observed prolongation of qt interval from day of therapy. very importantly, severely prolonged qt interval was observed in a subset of nine patients with more than mg against the baseline average of ± mg (mean ± sd). qt interval prolongation is a known marker for the high risk of sudden cardiac death (chorin et al., ) in the latest news, on th march , reported that favipiravir marketed as avigan found effective against covid- . xinmin zhang from the ministry of science and technology, china, said that favipiravir gives positive results in a clinical trial on patients in shenzhen and wuhan city. the drug was developed by toyama chemicals and prescribed for influenza infection. in february , it got approval for the experimental treatment of novel coronavirus infection. in the wuhan trial, the treatment with favipiravir improved the symptoms of infection and reduced the duration of fever. according to the guardian report, some patients with early covid- symptoms showed recovery; however, the patients with severe or advanced symptoms do not show a similar response (bryner, ) . bevacizumab, a recombinant humanized monoclonal antibody against vegf, was first approved by usfda on th february for the first-line treatment for metastatic colorectal cancer (cowling and leung, ) . subsequently, the fda approved this product along with chemotherapy to treat many cancers like lung cancer, renal cancer, cervical cancer, ovarian cancer, etc. (zhang and zhou, ). in addition, recent studies suggest that higher levels of blood vegf in covid- patients compared with normal and also pulmonary edema, dyspnea, acute respiratory distress and acute lung injury are the most detrimental symptoms of covid- . numerous studies reported that vegf was a critical factor in pulmonary edema, acute respiratory distress and acute lung injury (schoeman and fielding, ). based on this evidences, qilu hospital of shandong university has also initiated clinical trials on this product for treating the covid- (clinical trials.gov). protease inhibitors are approved by usfda to treat hiv, and also, these drugs previously immunodeficiency virus) (pronker et al., ) . usually, successful development of a vaccine takes around ten years. in this pandemic crisis of covid- , the world is sorely needed a potential vaccine to combat this threatful situation. as per the available data, around ten vaccines are presently under clinical trial against sars-cov- from which the scientists from oxford university and astrazeneca expected to have the data of phase iii trial by this summer (as shown in table ). however, many experts around the globe suspect the credibility of this work as it takes a minimum of months to develop the first vaccine even after tremendous efforts. while some presume that a huge dose of vaccines (around hundreds of million) will be ready to launch by the end of this year (iserson, ) . ppes are being used by health care professionals to protect from the infection of sar-cov- to avoid secondary transmission in hospitals. ppe should cover the whole body to prevent the chances of infection through the patient. health care professionals should also wear respirator masks such as n (filters > % of airborne particles), ffp (filters > % of airborne particles), and ffp (filters > % of airborne particles) to avoid infection. adequate training of ppes handling should be given to health care workers to avoid careless handling. also, proper care should be taken for the disposal of used ppes (kraemer et al., ) . many health advisory bodies have compelled the use of masks across the world as a preventive measure to avoid the spread of covid- . mask control the virus spread through the droplets of an infected person by acting as a shield/barrier to prevent the exposure of the critical body parts responsible for the spreading of the covid- . however, in the absence of a mask, it is advisable to cover the face with bending elbow over the face or to cover with a handkerchief/tissue paper while sneezing or coughing (adhikari et al., ; who, b). cleaning of hands from time to time with alcohol-based sanitizers is advisable to protect individuals against coronavirus disease. washing hands with soap and water before and after meals must be practiced as a preventive measure. as suggested, the content of alcohol should be more than % in hand sanitizes, and therefore children should be kept away from alcohol-based sanitizers (who, b). although, there is a great need to produce sufficient evidence by successful clinical studies to assure the safety and efficacy of these drug substances. the development of a vaccine for the prevention and cure of covid- and a promising diagnostic tool is also essential. hopefully, the constant scientific efforts and thorough understanding of sars-cov- pathogenesis and life cycle will soon find out the solution for this. gaurav suresh wadekar: writing-original draft epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (covid- ) during the early outbreak period: a scoping review correlation of chest ct and rt-pcr testing in coronavirus disease permeation enhancers: specialized components of mucoadhesives history of highly pathogenic avian influenza. revue scientifique et technique membrane binding proteins of coronaviruses the proximal origin of sars-cov- how will country-based mitigation measures influence the course of the covid- epidemic? the role of the nsp and nsp in its pathogenesis global aspects of viral glycosylation covid- : towards controlling of a pandemic activation of the sars coronavirus spike protein via sequential proteolytic cleavage at two distinct sites identification of new respiratory viruses in the new millennium. viruses coronavirus infections reported by promed flu drug used in japan shows promise in treating covid- human immunopathogenesis of severe acute respiratory syndrome (sars) zhejiang da xue xue bao. yi xue ban = journal of zhejiang university emerging coronaviruses: genome structure, replication, and pathogenesis the qt interval in patients with covid- treated with hydroxychloroquine and azithromycin. nature medicine role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings epidemiological research priorities for public health control of the ongoing global novel coronavirus ( -ncov) outbreak. euro surveillance : bulletin europeen sur les maladies transmissibles origin and evolution of pathogenic coronaviruses ct imaging and differential diagnosis of covid- . canadian association of radiologists journal = journal l'association canadienne des radiologistes screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture roche coronavirus test receives emergency use authorisation from fda coronaviruses: an overview of their replication and pathogenesis breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial observational study of hydroxychloroquine in hospitalized patients with covid- . the new england journal of medicine first known person-to- person transmission of severe acute respiratory syndrome coronavirus (sars-cov- ) in the usa gilead announces results from phase trial of investigational antiviral remdesivir in patients with severe covid- clinical characteristics of coronavirus disease coronavirus disease (covid- ): what we know? covid- : what is next for public health? azithromycin-induced torsade de pointes clinical features of patients infected with novel coronavirus in wuhan use of chest ct in combination with negative rt-pcr assay for the novel coronavirus but high clinical suspicion human coronaviruses oc and hku bind to -<em>o</em>-acetylated sialic acids via a conserved receptor-binding site in spike protein domain a angiotensin-converting enzyme protects from severe acute lung failure sars-cov- (covid- ) vaccine development and production: an cambridge quarterly of healthcare ethics : cq : the international journal of healthcare ethics committees generation of a highly pathogenic avian influenza a virus from an avirulent field isolate by passaging in chickens a paper raises some safety concerns for gilead's covid- treatment azithromycin as a cause of qt-interval prolongation and torsade de pointes in the absence of other known precipitating factors sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum the effect of human mobility and control measures on the covid- epidemic in china a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus (sars-cov- ): facts and myths severe acute respiratory syndrome coronavirus (sars-cov- ) and coronavirus disease- (covid- ): the epidemic and the challenges effective strategies to prevent coronavirus disease- (covid- ) outbreak in hospital. the journal of hospital infection nsp of coronaviruses: structures and functions of a large multi-domain protein functional assessment of cell entry and receptor usage for sars-cov- and other lineage b betacoronaviruses structure of sars coronavirus spike receptor-binding domain complexed with receptor molecular immune pathogenesis and diagnosis of covid- development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis potential preanalytical and analytical vulnerabilities in the laboratory diagnosis of coronavirus disease (covid- ) receptor usage and cell entry of porcine epidemic diarrhea coronavirus hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses sars-cov, mers-cov, and -ncov covid- vaccines: knowing the unknown neurological manifestations of hospitalized patients with china: a retrospective case series study coronavirus (covid- ): managing stress and anxiety trypsin treatment unlocks barrier for zoonotic bat coronavirus infection clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected structures of mers-cov spike glycoprotein in complex with sialoside attachment receptors coronavirus infections-more than just the common cold findings of lung ultrasonography of novel corona virus pneumonia during the - epidemic coronaviruses post-sars: update on replication and pathogenesis risk in vaccine research and development quantified immunosuppression for hyperinflammation in covid- : a double-edged sword? the lancet roche's cobas sars-cov- test to detect novel coronavirus receives fda emergency use authorization and is available in markets accepting the ce mark the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak coronavirus envelope protein: current knowledge structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry a review of coronavirus disease- (covid- ) regulatory updates and analytical methodologies for nitrosamine impurities detection in sartans, ranitidine, nizatidine and metformin along with sample preparation techniques animal models and novel therapeutic interventions for middle east respiratory syndrome coronavirus infections. frontiers in microbiology chloroquine and its analogs: a new promise of an old drug for effective and safe cancer therapies genetic recombination, and pathogenesis of coronaviruses. trends in microbiology the covid- vaccine development landscape covid- : fighting panic with information of chloroquine and covid- function, and antigenicity of the sars-cov- spike glycoprotein function, and antigenicity of the sars-cov- spike glycoprotein receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus xiao, g., a. remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro unique epidemiological and clinical features of the emerging novel coronavirus pneumonia (covid- ) implicate special control measures who, a. coronavirus disease (covid- ): situation report - coronavirus disease (covid- ) advice for the public, advice for public. world health organization cryo-em structure of the -ncov spike in the prefusion conformation overview of the novel coronavirus ( - ncov): the pathogen of severe specific contagious pneumonia (sscp) pathological findings of covid- associated with acute respiratory distress syndrome. the lancet. respiratory medicine the deadly coronaviruses: the sars pandemic and the novel coronavirus epidemic in china the deadly coronaviruses: the sars pandemic and the novel coronavirus epidemic in china clinical characteristics of death cases with covid- bevacizumab with dose-dense paclitaxel/carboplatin as first-line chemotherapy for advanced ovarian cancer a pneumonia outbreak associated with a new coronavirus of probable bat origin covid- ): a perspective from china ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.☐the authors declare the following financial interests/personal relationships which may be considered as potential competing interests:none key: cord- - almssg authors: crespo, roland mojica; morales crespo, mairim melissa title: pandemia covid- , la nueva emergencia sanitaria de preocupación internacional: una revisión date: - - journal: semergen doi: . /j.semerg. . . sha: doc_id: cord_uid: almssg resumen a finales de diciembre del , se reportaron una serie de casos de neumonía atípica, en ese momento, de origen desconocido en wuhan, china. días más tarde se identificó al agente etiológico como un nuevo coronavirus. a este nuevo coronavirus, se le llamó sars-cov- y a la enfermedad que produce se le denominó covid- . el origen de este nuevo virus se presume zoonótico siendo los murciélagos su probable vector. debido al acelerado número de contagios y muertes que se produjeron primero en china y posteriormente alrededor del mundo, la infección de este virus pasó rápidamente de ser un brote aislado en una región china, a convertirse en una emergencia sanitaria de preocupación internacional y posteriormente, en una pandemia. el propósito de esta revisión es estudiar la información más relevante y actual del patógeno, así como la epidemiología, patología, características clínicas, transmisión, prevención y tratamiento de la enfermedad. abstract in late december , some cases of atypical pneumonia, at that time of unknown origin, were reported in wuhan, china. days later, the etiologic agent was identified as a new coronavirus. this new coronavirus was called sars-cov- and the disease it produces was named covid- . the origin of this new virus is presumed zoonotic, with bats being its probable vector. due to the rapid number of infections and deaths that occurred first in china and later around the world, the infection of this virus quickly went from being an isolated outbreak in a chinese region to becoming a health emergency of international concern and later, a pandemic. the purpose of this review is to study the most relevant and current information on the pathogen, as well as epidemiology, pathology, clinical features, transmission, prevention, and treatment of the disease. j o u r n a l p r e -p r o o f radiológicas incompatibles con las de una neumonía causada por las bacterias y virus más comunes - . el surgimiento de estos casos levantó sospechas, sobre todo posterior a que varios de los pacientes que presentaban este cuadro clínico, referían tener de antecedente trabajar como distribuidores o vendedores en el mercado de mariscos y vida animal silvestre de huanan. debido al surgimiento de este brote, la autoridad sanitaria en china alertó a la organización mundial de la salud (oms) el día de diciembre del , sobre la aparición de casos de neumonía atípica de origen desconocido con la sospecha de una posible zoonosis , . a pacientes originalmente identificados que padecían de esta neumonía, se les tomaron múltiples muestras del tracto respiratorio, sangre y heces. las cuales fueron analizadas a través de la reacción en cadena de la polimerasa en tiempo real (rt-pcr, del inglés "real time pcr") en la cual se identificó un nuevo coronavirus que fue aislado en el fluido resultante del lavado broncoalveolar, de las muestras del tracto respiratorio inferior de pacientes. en ese momento, a este nuevo coronavirus se le llamó -ncov (del inglés: -novel coronavirus) y fue identificado por las autoridades sanitarias chinas como el agente causal de estos casos de neumonía atípica , , . los coronavirus son un grupo amplio de virus envueltos de material genético tipo arn, los cuales deben su nombre a la apariencia de una corona, que es observada en su superficie a través de la microscopía electrónica , . existen diferentes tipos de coronavirus los cuales pueden llegar a causar múltiples afecciones respiratorias, gastrointestinales o incluso la muerte. entre los síntomas respiratorios, pueden causar desde un resfriado común hasta una neumonía, aunque en la mayoría de los casos, los síntomas suelen ser menores y mitigables con facilidad , . no obstante, a lo largo de la historia se han documentado cepas que pueden causar afecciones y enfermedades severas , . tal es el caso del sars-cov (del inglés: severe acute respiratory syndrome coronavirus) identificado por primera vez en las infecciones por el nuevo coronavirus comenzaron a tomar progresivamente protagonismo a nivel internacional cuando el día de enero del , la oms reportaba el primer caso de infección fuera de china, ocurrido en tailandia . a partir de este punto, y previniendo que el virus se propagara a escala internacional, la oms ofreció su asesoramiento y guía para el manejo de esta nueva infección . no obstante, y a pesar de estos esfuerzos durante el mes de enero, el número de infectados aumentó rápidamente y se reportaron las primeras muertes . hacia final de mes, el día de enero la oms declaró la enfermedad causada por el nuevo coronavirus como una emergencia de salud pública de preocupación internacional, ya que para aquel momento se habían reportado casos en todas las regiones de la oms en solo un mes , . a poco más de un mes del inicio del brote, la oms anunció que la enfermedad causada por el nuevo coronavirus aislado en wuhan, china sería llamada "covid- " que responde a la forma corta del nombre "coronavirus disease ". mientras que el agente causal fue denominado sars-cov- por el comité internacional de taxonomía de virus . a partir de este punto, la línea cronológica de eventos ,así como la de infectados, se tornó muy precipitada(figura. ). conforme el paso de los días, el sars-cov- se fue propagando en todas las regiones del mundo y progresivamente el número de infectados y muertos se aceleró bruscamente por los meses subsiguientes. hasta el punto de que la oms caracterizó esta enfermedad como pandemia el día de marzo los coronavirus son un grupo grande de virus los cuales están envueltos de arn en sentido positivo no segmentado, que pertenecen a la familia coronaviridae del orden de los nidovirales. a su vez, los coronavirus son clasificados en géneros: alfa, beta, gamma y delta , . de estos géneros, se sabe que el género alfa y beta infectan a los seres humanos ocasionando generalmente afecciones y síntomas tanto respiratorios como gastrointestinales, aunque raramente también pueden ocasionar alteraciones hepáticas y neurológicas , , , , . page of j o u r n a l p r e -p r o o f en cuanto a su morfología y estructura, son reportados por la literatura microbiológica como virus de forma aproximadamente esférica de una capacidad moderada al pleomorfismo. en cuanto sus dimensiones, se reporta que el diámetro de este tipo de virus varía de entre - nanómetros , . mediante el estudio de la superficie de estos virus a través de microscopía electrónica, se ha descubierto la existencia de estructuras sobre la superficie del virión, las cuales están dispuestas de manera de proyecciones largas, separadas las unas de las otras. estas estructuras están constituidas por complejos triméricos de la glicoproteína viral s (spike) , , . adicionalmente se han identificado sobre la superficie del virión, otro tipo de proyecciones las cuales, en contraste con las anteriores, son cortas y están formadas por complejos diméricos de las proteínas hemaglutina-esterasa (he). en lo referente a la envoltura viral, se sabe que está reforzada por la proteína más abundante de la superficie del virión, la cual es llamada glicoproteína de membrana (m), y que además se encuentra ensimismada en la membrana por dominios transmembranales - . además de los componentes ya mencionados de la estructura del virus, existe la proteína de envoltura (e), esta se encuentra en menor proporción que las demás, ya que es de menor tamaño y tiene como característica principal ser altamente hidrofóbica hasta este momento, se plantea que el origen de este coronavirus es debido a una zoonosis , , . es sabido que los coronavirus entre sus diferentes géneros están presentes y circulan entre un amplio espectro de seres vivos, entre ellos los mamíferos y consecuentemente los seres humanos. según se ha observado, la mayor variedad de coronavirus está presente en los murciélagos, por lo que se lo que ocasiona el comienzo de su patogenicidad , . el motivo por el que se piensa que la transmisión sintomática es la que mayor número de contagios ocasiona, es debido a que estudios han demostrado que durante los primeros días de la infección, esta se encuentra mayormente localizada en las vías respiratorias superiores (nariz y garganta), lo que genera que las gotitas de flügge, portadoras del virus, sean más fáciles de expeler . el periodo de incubación del sars-cov- es de días, pudiendo incluso llegar a extenderse hasta por días según se asevera en distintas fuentes , , . a este periodo de tiempo también se le conoce como periodo presintomático. la transmisión presintomática ocurre cuando un persona ya infectada, es capaz de contagiar a otras personas aun cuando esta no haya presentado hasta ese momento síntomas de la infección , - . en cuanto a la transmisión asintomática, se le refiere a la ocurrida cuando una persona sana es contagiada por alguien que analíticamente resulta positivo al virus pero que en ningún momento del curso de la infección manifiesta síntomas . hasta este momento, se cuenta con información muy limitada en cuanto a este tipo de transmisión. sin embargo, la literatura médica actual ha demostrado la contagiosidad de esta infección a partir de individuos asintomáticos y la proporción de enfermos que este tipo de transmisión aporta a la pandemia aún está sujeta a estudio - . cabe además destacar el tipo de transmisión intrahospitalaria que se ha reportado en todo el mundo. donde personal médico y personal asociado a la atención sanitaria, se ha contagiado por el estrecho e inevitable contacto con los pacientes infectados y su espacio vital, pese a las medidas de prevención y el uso de equipo sanitario desechable de protección individual a base de batas, guantes, mascarillas y gafas , - . ante una pandemia de las características de covid- , es importante conocer el índice de contagio, es decir, la capacidad de transmisión que tiene un patógeno. para tal efecto, se utiliza internacionalmente el número reproductor básico (r ) el cual es un parámetro teórico que proporciona información sobre la velocidad con la que una enfermedad infecciosa puede propagarse en una población determinada; y que además es utilizado para medir la dinámica promedio de casos secundarios que se producen a partir de un caso inicial , la propia tormenta de citocinas que genera el slc causa daño en el sistema microvascular lo cual activa el sistema de coagulación e inhibición de la fibrinólisis. esta alteración del sistema microvascular conduce a la aparición de la coagulación intravascular diseminada (cid) la cual es señalada como una de las principales causantes de falla orgánica en pacientes graves y que analíticamente es observada a través del aumento progresivo del dímero d y fibrinógeno . según los primeros informes epidemiológicos generados en china, la edad media de los pacientes que contrajeron la infección se ubicó entre los - años, con una ligera predominancia entre individuos del género masculino. casos en individuos menores a los años se observaron, pero estos fueron reportados como casos aislados. entre las comorbilidades o condiciones médicas coexistentes más prevalentes entre estos pacientes, se reportó: hipertensión, diabetes, enfermedades cardiovasculares, consumo de tabaco, enfisema pulmonar y obesidad , , . a partir de estas comorbilidades, se determinó que los pacientes de mayor riesgo para presentar un cuadro clínico severo, son aquellos que padezcan alguna de las condiciones médicas anteriores, así como adultos mayores de años, personas inmunocomprometidas, mujeres embarazadas y asmáticos , , , . en españa mediante la red nacional de vigilancia epidemiológica (rnve), se ha comprobado que los primeros informes sobre las características demográficas, clínicas y epidemiológicas, originados en los países asiáticos, no difieren mucho de lo que se ha observado en el país durante la pandemia, por lo que en muchos aspectos los datos son superponibles(tabla. a) . los síntomas producidos por covid- son inespecíficos. no obstante, el espectro clínico puede ir desde un cuadro clínico asintomático hasta una neumonía severa que produzca insuficiencia respiratoria a causa del síndrome de distrés respiratorio del adulto (sdra). la presencia del sdra, está asociado al slc y a la cid; mismos que han sido descritos por la literatura médica actual como las principales causas del daño multiorgánico que presentan estos pacientes y que consecuentemente originan la alta mortalidad de covid- en pacientes de alto riesgo , , , . la neumonía es la manifestación clínica más severa que comúnmente se ha presentado durante el transcurso de la enfermedad en pacientes graves. esta es caracterizada principalmente por presentar fiebre, tos, disnea e infiltrados en las imágenes de tórax. sin embargo, así como sucede con otras infecciones respiratorias virales, no existen síntomas que sean específicos para poder diferenciar una neumonía ocasionada por otros virus, a la ocasionada por sars-cov- , , , . entre los principales síntomas inespecíficos de covid- que han sido reportados en china, europa y en muchas otras partes del mundo son: fiebre, tos seca, astenia, mialgias, artralgias, escalofríos, cefalea, odinofagia y disnea (presente en casos graves). siendo menos frecuente la presentación de anosmia, ageusia, diarrea, vómitos, congestión nasal y hemoptisis , , , , , . en cuanto a la presentación de los síntomas de covid- en españa, los datos son nuevamente equiparables con los reportados en la literatura médica e informes de la oms. concretamente la rnve en su informe n° del día de mayo enumera los principales síntomas presentados por el conjunto de la población española, hasta la fecha y a base de una muestra de , casos, de la siguiente manera: entre estos hallazgos, es comúnmente observar la leucopenia y linfopenia, siendo esta última característica de covid- . ya que el slc propicia la detección de il- , hiperferritinemia y la depleción linfocitaria. se ha reportado elevación de la enzima lactato deshidrogenasa (ldh) y creatinquinasa (ck) en respuesta al estado de sepsis que desarrollan los casos severos de la enfermedad. la mitad de los pacientes llegan a padecer algún grado de función hepática anormal manifestada con la elevación de las enzimas aspartato aminotransferasa (ast) y alanina aminotransferasa (alt). puede coexistir además la elevación en suero de la proteína c reactiva, pero sin elevación de la procalcitonina. y hasta un tercio de los pacientes, sobre todo los que se encuentran en estado crítico, pueden presentar elevación del dímero d, en respuesta de la activación de la coagulación y sus mediadores procoagulantes, los cuales causan fenómenos trombóticos observados los hallazgos imagenológicos han demostrado una alta eficiencia cuando estos hallazgos son adecuadamente integrados con la clínica del paciente. no obstante, hay que tener en cuenta que las manifestaciones radiológicas son diversas y que estas progresan rápidamente , . entre los estudios de imagen que se han sido utilizados, destacan las radiografías de tórax (rx-tx), así como las tomografías computarizadas de tórax con ventana pulmón (tc-tx). como es sabido, las rx-tx tienen una sensibilidad menor a las tc-tx. sin embargo, las primeras logran ser útiles en los casos donde un tomógrafo no se encuentra disponible, como sucede en sistemas sanitarios en países menos desarrollados. en general, el hallazgo imagenológico principal tanto en las rx-tx y tc-tx es el de una neumonía atípica u organizada(figura. a). en las rx-tx se suelen observar opacidades asimétricas irregulares como en vidrio esmerilado, datos de consolidación, con distribuciones bilaterales, periféricas y de los campos pulmonares inferiores. la afección pulmonar tiende a progresar en el trascurso de la infección por lo que estos hallazgos pueden variar según el momento de evolución en el que el cuadro clínico se encuentre; aunque según la literatura médica, hasta un % de los casos no presentan ni presentaran estos hallazgos radiológicos en ningún momento de la enfermedad(figura. b) , . en cuanto a lo referente a las tc-tx, los hallazgos predominantes son las opacidades en vidrio esmerilado y las consolidaciones distribuidas irregularmente, como si fueran parches, principalmente en la zona medial y externa de los campos pulmonares. entre los hallazgos tomográficos menos comunes, se han reportado: derrame pleural, cavitaciones, adenopatías y neumotórax , , . según un estudio, las anormalidades tomográficas alcanzan su punto máximo en la mayoría de los pacientes hacia el día de la infección, cuando además de los hallazgos ya mencionados, se puede observar un patrón reticular con una importante distorsión anatómica y en fases tardías, bronquiectasias por tracción(figura. c) . como se menciona en los informes de la oms y la experiencia adquirida desde el inicio del brote hasta este momento, aproximadamente el % de los pacientes enfermos de covid- cursarán con un cuadro clínico medio a moderado sin neumonía o con una neumonía leve no complicable. mientras que aproximadamente el % restante cursará con un cuadro severo de la enfermedad y un . % del total de los enfermos morirá , , , . por esta situación, los pacientes pueden ser clasificados en grupos clínicos en función de la severidad de su estado(tabla. b). esta clasificación ayuda a establecer quiénes son los pacientes que mayor soporte médico requieren, y contribuye a que la atención médica sea priorizada a quienes más la necesiten sin que se saturen los servicios médicos existentes , . la sospecha de encontrarnos ante un caso de covid- debe ser primordialmente basada en la historia clínica del paciente y en la evolución de su cuadro clínico. un paciente que presente los síntomas asociados de covid- o que refiera datos de alguna enfermedad de vías respiratorias sin que se haya identificado una causa concreta, debe ser estudiado como caso sospechoso. más aún si al interrogatorio, el paciente refiere haber tenido contacto cercano con un caso confirmado o sospechoso de covid- en los últimos días o si manifiesta residir o haber viajado en los últimos días a cualquier lugar del mundo dónde se conozca que existe la transmisión comunitaria del virus . como se ha evidenciado en la literatura revisada, la tc-tx ha demostrado ser una herramienta muy útil de apoyo para establecer el diagnóstico. estudios han puesto a prueba la capacidad de utilizar la tc-tx a la par de la rt-pcr y se ha reportado que la tc-tx tiene una sensibilidad diagnóstica de %, con un valor predictivo positivo de % y negativo de %. en un estudio comparativo similar, con una muestra menor, se obtuvieron resultados parecidos donde la tc-tx tuvo una sensibilidad del % . para el diagnóstico definitivo de covid- , es indispensable la realización de una rt-pcr. este es el método diagnóstico que ha sido ampliamente utilizado j o u r n a l p r e -p r o o f en el caso de las pruebas rápidas por determinación de anticuerpos, estas surgen desde la idea de que el sistema inmunitario desarrolla inmunoglobulinas (ig) frente al virus, dependiendo de la fase de la infección en la que el individuo se encuentre. siendo la igm la inmunoglobulina de fase aguda, mientras que la igg es la de fase crónica, de memoria o de recuperación . aunque hasta la fecha no existe consenso entre la comunidad médica sobre el tiempo en el que los títulos de igm e igg aumentan para ser detectables, se ha postulado que la igm comienza a elevarse entre - días posterior al momento del contagio (siendo su pico detectable entre - días) mientras que la igg se vuelve detectable a partir del día al , . las pruebas rápidas adquieren su mayor utilidad cuando son empleadas para detectar oportunamente la infección por sars-cov- , sobre todo cuando la rt-pcr no se encuentra disponible o no se puede realizar de forma masiva. sin embargo, es imprescindible que estas sean valoradas junto con la situación epidemiológica y clínica del paciente (tabla. a). hasta este momento, no se dispone de un tratamiento específico contra el covid- , ni de una vacuna capaz de prevenir la infección por sars-cov- . motivo por el cual, las medidas masivas de salud pública, optadas por gran parte de la comunidad internacional, han sido y han demostrado ser las únicas formas efectivas para la contención de la propagación de la enfermedad y su mitigación. tales medidas masivas de salud pública se han basado principalmente en el distanciamiento social y la cuarentena . entre las recomendaciones generales de la oms para la prevención de la enfermedad(tabla. b), es importante hacer énfasis en de estas medidas; el lavado de manos y el uso de mascarilla. el lavado de manos se tiene que realizar bajo una técnica adecuada según la técnica de la oms, donde las manos se tienen que frotar durante - segundos y de - segundos si las manos se notan sucias. además, es importante que estas sean lavadas con agua y con jabón, o con una solución a base de alcohol %. ya que, se demostró que el sars-cov- puede estar presente en superficies inanimadas hasta por días, y que una solución de alcohol al - % disminuye su infectividad en las superficies después de su exposición de al menos minuto , . por lo que es importante también lavar las manos frecuentemente, sobre todo después de que estas hayan estado en contacto con alguna superficie. en el caso específico del personal de salud, el lavado de manos además se tiene que realizar después de estar en contacto con el paciente o con su medio, ya sea directa o indirectamente, así como después de realizar cualquier procedimiento médico . el uso de mascarillas por parte de la población general ha sido un tema ampliamente discutido como medida efectiva de prevención, ya que hasta la fecha no existe evidencia científica concluyente que demuestre que el uso de mascarillas en el ámbito comunitario reduzca el contagio de sars-cov- o alguna otra infección respiratoria aguda viral . ante esto, la oms ha recomendado el uso de mascarillas solo a la población infectada y no recomienda su uso generalizado. entre otras cosas, porque optar únicamente por esta medida no es suficiente para evitar el contagio. ya que esta medida por sí sola no confiere el adecuado nivel de protección. por lo tanto, otras medidas deberían también ser adoptadas . el uso de mascarillas quirúrgicas entre el personal sanitario que atiende pacientes con covid- , no es efectivo debido a que las partículas virales son capaces de penetrar a través del material del que están hechas. por lo que la oms recomienda el uso de respiradores de alta eficiencia, los cuales cuentan con un filtro de partículas de entre a micras de diámetro. entre los ejemplos más conocidos de respiradores de alta eficiencia a nivel mundial, se encuentran los ffp y ffp que poseen una eficiencia de % y . % respectivamente, los cuales están avalados por la unión europea y por tanto son los utilizados en los países europeos. en contra parte existen los respiradores n , n y n con una eficiencia de %, % y  otros agentes: interferón-α/β utilizados junto con otros de los fármacos anteriores.  otras terapias coadyuvantes: anticuerpos monoclonales contra citocinas proinflamatorias como il- (tocilizumab) y terapia de inmunoglobulinas con inmunoglobulinas extraídas del plasma de pacientes recuperados de la infección. tratamientos bajo investigación para su uso estándar en covid- : favipiravir: con experiencia clínica limitada en covid- . sin embargo, con resultados alentadores en otros coronavirus. remdesivir: utilizado por primera vez en la pandemia de ébola . medicamento que hasta la fecha tiene mayor expectativa de ser utilizado como de uso estándar. protocolos de ensayos aleatorizados, doble ciego controlado con placebo se han realizado sobre este medicamento y uno de ellos demostró un ligero acortamiento en el tiempo de estancia intrahospitalaria de los pacientes que fueron tratados oportunamente con este medicamento, aunque no se pudo asociar en este estudio ningún otro beneficio clínico . a raíz de una serie de ensayos aleatorizados realizados por la farmacéutica gilead y el national institute of allergy and infectious diseases (niaid), el día de mayo la fda (u.s. food and drug administration) emitió una autorización de uso urgente de este medicamento en presentaciones graves de la enfermedad. aunque se aclara que esta autorización es temporal y que el medicamento tendrá que transitar por el procedimiento normal para la aprobación de medicamentos de la fda . desde el comienzo del brote y su progresión pandémica, la expectativa mundial está concentrada en el desarrollo de una vacuna. sin embargo, el desarrollo de vacunas no es un proceso corto, ya que se tiene que contar con una base teórica fuerte, tecnología necesaria y su prueba en animales pequeños y en humanos; para lo cual se necesita contar con ciertas regulaciones actualmente el mundo se encuentra luchando arduamente en contra de la que quizás es la pandemia más severa a la que se haya enfrentado la humanidad. esta lucha se encuentra liderada por la oms en apoyo de los gobiernos del mundo y respaldada por miles de científicos y médicos quienes invaluablemente han ofrecido sus conocimientos y experiencia para el control de la pandemia y para evitar más muertes. las medidas de distanciamiento social y la cuarentena han sido claves para mitigar la pandemia debido a que hasta la fecha no se dispone de un tratamiento médico eficaz o de alguna vacuna. la contribución de la población aislándose, ha representado un importante sacrificio pero que conforme pasan las semanas, ha demostrado un impacto significativo en el desarrollo positivo de la pandemia. es importante que el médico de familia conozca las generalidades de la clinical features of patients infected with novel coronavirus in wuhan, china. the lancet brotes epidémicos: neumonía de causa desconocida -china. publicado: enero brotes epidémicos: actualización. nuevo coronavirus china a novel coronavirus from patients with pneumonia in china the molecular biology of coronaviruses coronavirus infections-more than just the common cold clinical characteristics of coronavirus disease in china the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- covid- ) -events as they happen. who.int. publicado: inicialmente el diciembre , actualizable día a día world health organization. situation report - . publicado: enero declaración sobre la segunda reunión del comité de emergencias del reglamento sanitario internacional ( ) acerca del brote del nuevo coronavirus ( -ncov). publicado: enero world health organization. interim guidance. global surveillance for human infection with coronavirus disease (covid- ). publicado: febrero coronavirus disease (covid- ): what we know? coronavirus envelope protein: current knowledge human coronavirus: host-pathogen interaction emerging coronaviruses: genome structure, replication, and pathogenesis association of the infectious bronchitis virus c protein with the virion envelope serological evidence of bat sars-related coronavirus infection in humans human-animal interactions and bat coronavirus spillover potential among rural residents in southern china world health organization. situation report - . publicado: febrero a pneumonia outbreak associated with a new coronavirus of probable bat origin from sars to mers, thrusting coronaviruses into the spotlight sars and mers: recent insights into emerging coronaviruses a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster importation and human-to-human transmission of a novel coronavirus in vietnam world health organization. situation report - . publicado: abril las gotitas de flügge publicado: febrero surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient virological assessment of hospitalized patients with covid- the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application a familial cluster of infection associated with the novel coronavirus indicating possible person-to-person transmission during the incubation period potential presymptomatic transmission of sars-cov- presymptomatic transmission of sars-cov- -singapore asymptomatic and presymptomatic sars-cov- infections in residents of a long-term care skilled nursing facility asymptomatic cases in a family cluster with sars-cov- infection. the lancet infectious diseases clinical characteristics of asymptomatic infections with covid- screened among close contacts in nanjing, china preventing intra-hospital infection and transmission of coronavirus disease in health-care workers the lancet. covid- : protecting health-care workers covid- and the risk to health care workers: a case report supporting the health care workforce during the covid- unraveling r : considerations for public health applications early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia un mundo, una salud: la epidemia por el nuevo coronavirus covid- preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a datadriven analysis in the early phase of the outbreak centro de coordinación de alertas y emergencias sanitarias. informaciÓn cientÍfica-tÉcnica enfermedad por coronavirus covid- en españa. evolución pandemia, declaración agregada. publicado: diariamente receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus are patients with hypertension and diabetes mellitus at increased risk for covid- infection ema advises continued use of medicines for hypertension, heart or kidney disease during covid- pandemic. publicado: marzo another decade, another coronavirus informe sobre la situación de covid- en españa. informe covid- nº frequency and distribution of chest radiographic findings in covid- positive patients time course of lung changes on chest ct during recovery from novel coronavirus (covid- ) pneumonia cross-country comparison of case fatality rates of covid- /sars-cov- . osong public health res perspect characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention the role of ct in case ascertainment and management of covid- pneumonia in the uk: insights from high-incidence regions. the lancet respiratory medicine detection of sars-cov- in different types of clinical specimens viral dynamics in mild and severe cases of covid the lancet infectious diseases. : temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study. the lancet infectious diseases profiling early humoral response to diagnose novel coronavirus disease (covid- ) antibody responses to sars-cov- in patients of novel coronavirus disease quarantine alone or in combination with other public health measures to control covid- : a rapid review persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents world health organization. technical documentation. water, sanitation, hygiene and waste management for covid- . publicado: marzo revisión rápida del uso de cubrebocas quirúrgicos en ámbito comunitario e infecciones respiratorias agudas advice on the use of masks in the context of covid- . publicado: abril world health organization. interim guidance. infection prevention and control during health care when novel coronavirus (ncov) infection is suspected. publicado: marzo world health organization. who guidelines. infection prevention and control of epidemic-and pandemic prone acute respiratory infections in health care pharmacologic treatments for coronavirus disease remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial. the lancet fda news release. coronavirus (covid- ) update: fda issues emergency use authorization for potential covid developing covid- vaccines at pandemic speed the covid- vaccine development landscape world health organization. draft landscape of covid- candidate vaccines. publicado: mayo key: cord- -kn q nb authors: flinders, matthew title: democracy and the politics of coronavirus: trust, blame and understanding date: - - journal: parliam aff doi: . /pa/gsaa sha: doc_id: cord_uid: kn q nb this article explores the relationship between crises and democracy through a focus on the unfolding coronavirus pandemic. its central argument is that to interpret the current pandemic purely in terms of its epidemiology and public health implications risks overlooking its potentially more significant socio-political consequences. this is because the challenges posed by the coronavirus crisis have themselves become overlaid or layered-upon a pre-existing set of concerns regarding the performance, efficiency and capacity of democratic political structures. the aim of this article is to try and understand and warn against what might be termed a rather odd form of cross-contamination whereby the cynicism, negativity and frustration concerning politicians, political processes and political institutions that existed before the coronavirus outbreak is allowed to direct, define and automatically devalue how democratic structures are subsequently judged in terms of how they responded to the challenge. as such, this article focuses on the link between the coronavirus crisis and the democratic crisis; or, more precisely, the risk that the coronavirus crisis may mutate into and fuel a broader crisis of democracy. keeping democracy healthy during a pandemic has already proved problematic in many countries where politicians have seized upon the crisis in order to claim emergency powers and strengthen their position (hungary, israel, etc.) . at the same time, the victorious claims of countries such as china and singapore have raised potentially far-reaching questions about whether authoritarian regimes handle pandemics more effectively than democratic ones (see, e.g. kleinfeld, ) . the fact that this is happening in a global context that already contained an 'autocratization alert' (see v-dem, ) , concerns about 'democratic backsliding' (see idea, ) and an increase in populist pressures simply underlines this article's emphasis on the need to understand the link-or more specifically the interplay-between the 'new' covid-focused crisis and the pre-existing democratic crisis (on the latter see keane, ) . although this article is primarily focussed upon the uk the themes, issues and challenges that it highlights have a far broader international and global relevance. the link between the coronavirus and the crisis of democracy is explored and developed through a focus on three inter-related themes: trust, blame and understanding. the first section focusses on public trust in politics before the pandemic emerged and how the outbreak appears to have affected public attitudes. the interesting element of this discussion is the contrast it offers with the public's trust in scientists and experts and the implications this has in terms of culpability, credit and censure. this brings the discussion to a second focus on the issue of blame in the second section. the simple argument is that if previous pandemics offer insights into the post-crisis politics of coronavirus it is likely that a series of intense and multi-dimensional blame games will rapidly emerge. the main focus of this section is upon the early emergence of potential blame-limitation strategies within the british government's approach. this focus on scapegoats, sacrificial lambs and self-preservation strategies flows into a third and final focus on tolerance and understanding. the aim being to acknowledge the realities of decision-making and governing under pressure in times of crisis and through this develop an argument concerning balance, empathy and proportionate scrutiny. the manner in which a large number of legislative select committees have already announced their intention to launch pandemic-linked inquiries, not to mention demands for wider national and international in-depth reviews, underlines the contemporary relevance of this argument. taken together, a focus on these three topics (trust, blame and understanding) provides a buckle or link through which the relationship(s) between the coronavirus crisis and crisis of democracy can be understood. the aim of this section is to make three relatively straightforward arguments about levels of public trust in elected politicians. the first is that the coronavirus crisis emerged at a time of fundamental concern about the global state of democracy; the second is that the limited data that is currently available suggests the existence of a common crisis-linked 'rallying around the flag' effect; and (third) that this uplift in public confidence and trust may well prove to be short-lived. as a first-step to substantiating these arguments, table provides a precis of the core findings of a number of authoritative and evidence-based reviews on the taken together, the core conclusions suggest that the anxieties that have surrounded democracy for at least half a century have in recent years grown in scale, complexity and intensity. this is linked to the emergence of a clear populist signal, the growth of anti-political sentiment and-critically-the emergence of a clear 'trust gap' between the governors and the governed. within this democratically dubious context the uk held a particularly prominent position due to a combination of generalised and long-standing concerns regarding the nature and limits of a majoritarian power-hoarding democracy plus more specific and related concerns regarding the country's relationship with the european union. the hansard society's th audit of political engagement ( ) provides a powerful evidence base for these arguments and its headline findings can be summarised as: • opinions of the system of governing are at their lowest point in the -year audit series-worse now than in the aftermath of the mps expenses scandal; • people are pessimistic about the country's problems and their possible solution, with sizable numbers willing to entertain radical political changes; and • core indicators of political engagement remain stable but, beneath the surface, the strongest feelings of powerlessness and disengagement are intensifying. it would at this point be possible to drill-down into each of these points through the provision of evidence-based insights such as: % of those surveyed said the system of governing needs 'quite a lot' or 'a great deal' of improvement; asked whether the problem is with the political system or the people running it was the th consecutive year of decline in global freedom drift towards 'division and dysfunction' global phenomenon in which freely elected leaders distance themselves from political norms the largest response group ( %) replied 'both'; % of those surveyed believed the main parties and politicians did not care about people like them; % thought political parties were too internally divided to serve the best interests of the country; % thought britain's system of government is rigged to advantage the rich and the powerful; the number who 'strongly disagree' that political involvement can change the way the uk is run ( %) had hit a -year low; as had the % who felt they had no influence at all over national decision-making. if this was not bad enough, then the survey also detected hints of what might be interpreted as an illiberal swing away from the core tenets of liberal democracy. when it came to the public's levels of confidence and trust in different professions, for example, the 'military/armed forces' ( %) and 'judges/courts' ( %) scored far higher than mps ( %) or members of the government ( %). added to this was the fact that only % of the public had confidence in mps' handling of brexit (with the government faring only slightly better on %). of particular concern was that over half ( %) of those surveyed agreed with the statement that 'britain needs a strong leader willing to break the rules', and % thought that many of the country's problems could be dealt with more effectively if the government did not have to worry so much about votes in parliament. the ipsos mori veracity index-published just days before the general election-found that public trust in politicians had fallen to just %, a % fall from . professors were, by contrast, highly ranked at % but government ministers lowly ranked at % which represented a level of distrust far greater than that even suggested by the hansard society's audit of political engagement but which did resonate with the broader data and evidence on the global state of democracy (see table , above). the gap, or more precisely chasm, between public trust in scientists/experts/professors, on the one hand, compared with politicians on the other, is striking and forms a central element of arguments offered later in this article. it is, however, worth noting at this early point that the edelman trust barometer's 'trust and the coronavirus' report of april that surveyed , people across ten countries found that: % of respondents agreed that 'we need to hear more from the scientists and less from politicians'; % were concerned about the politicisation of the crisis ('certain people are making the situation seem worse than it is for political gain'); and that scientists were trusted to tell the truth by % of those surveyed, compared to % who trusted their prime minister or president. the aim of emphasising these statistics on (dis)trust is simply to underline that the health of democracy was not in good shape when the pandemic emerged and that populists had for some time been fuelling and funnelling public frustration in an attempt to gain power and legitimate the construction of 'strong leader' illiberal democracies (i.e. what the institute for democracy and electoral assistance refer to as 'democratic backsliding'). the obvious risk, and one that has already come into fruition in some countries, is that the pandemic will be used by populists to further dilute or remove democratic safeguards (what daniel levitsky and daniel zilatt refer to in their hopefully not prophetic book how democracies die as the 'soft handrails' that checks-and-balances provide) as part of the 'autocratization' process that the varieties of democracy project has warned against. the issue of public trust therefore provides the first strand in the link between the coronavirus crisis and crisis of democracy. but what is interesting in this regard is that the immediate impact of the pandemic appears to have been a sharp increase in the popularity of incumbent national leaders (see jennings, ) . two elements stand out within this general trend: the first is that the 'boris bounce' was exceptional, rising to % by mid-march (up % from his ratings just before the december general election); the second is that the 'trump jump' fell fairly flat when compared with the spike in public support enjoyed by most leaders. although approval ratings are very different to precise trust-based assessments, they do point to the existence of a social phenomenon that political science has identified for some time and that is certainly related to questions of trust-'the rallying around the flag effect'. this concept was first coined by john mueller in and relates to the observation that groups tend to unify in times of crisis and at the national level, this is commonly exhibited through support for national leaders. the march 'boris bounce' is essentially the uk's equivalent of a 'rallying around the union jack effect' but it is dissecting and understanding this change in social attitudes that more light can be spread on the emergent politics of coronavirus and in this regard three issues deserve brief comment. the first two issues concern the two main and inter-related variables that are generally offered by scholars to explain this effect. the first of these emphasises the social-psychological dimensions of a crisis and particularly the power of patriotism (for a discussion, see baker and oneal, ) . in times of crisis, national leaders are, the theory suggests, viewed as almost the embodiment of national unity fighting the crisis for the public good, which is especially significant when the leader is both head of state and head of government as in the usa. the second theory, that has been explored in the work of hetherington and nelson ( ) amongst others, believes that the rallying effect occurs due to more institutional reasons and particularly due to the opposition's general reluctance to openly attack the government during a clear crisis. a reduction in 'attack politics' by opposition parties leads to less conflict being reported in the media and so, this approach suggests, the public assumes the government must be performing better than normal. the public may not trust their political leaders but they might view them as competent in terms of governing capacity which leads to a third and final point about rallying around flags-it usually does not take long for 'fleeing the flag' to occur. this is a critical point. although most analyses of 'rallying around the flag' effects are concerned with wars, invasions or terrorist attacks with a clear enemy, rather than public health pandemics in which the enemy is a new strain of virus, the overall conclusion is that the 'rally effect' is usually short-lived. the public is fickle and it may be just one or two months before public opinion returns to pre-crisis levels. in the uk, there are already suggestions that the public's support for the government's approach and levels of trust in key ministers was by early april already waning (see opinium, ) . this fall in public support may well reflect the existence of major concerns about unpreparedness and indecision within the government which was underlined in the sudden shift from a focus on 'herd immunity' and basic precautions (notably handwashing) to a policy of legally enforced social distancing and 'lockdown'. from personal protective equipment to the repatriation of citizens, through to the availability of ventilators and questions concerning the police's use of 'lockdown' powers, not to mention mix-ups, muddles and misunderstandings concerning virus-testing and care home policy, a range of issues have combined to produce accusations that the government's response has been little short of 'a disaster' (see jenkins, ) . this raises at least two issues that emerge out of this section's focus on trust and serve to refocus attention back on the link between the specific 'covid crisis' and broader 'crisis of democracy'. the first revolves around the issue of blame and warns against the political system going 'mad' in the sense of falling victim to 'multiple-accountabilities disorder' (koppell, ) and the scapegoating, scalp-hunting and sacrificial practices that usually come with it. the second (flip-side) issue underlines the need for public understanding in the sense of not only appreciating the realities of crisis management situations but also about the manner in which coronavirus is itself being politicised by different actors. the first of these themes is the focus of the next section. amongst the contemporary chaos, there are three predictions that can be made with relative certainty. the first is that around a year from now there is going to be a baby boom which will reflect what those couples that have enjoyed spending time together have been up to. the second is that the baby boom is likely to be matched by a similarly spectacular increase in divorces (reflecting those couples that did not enjoy spending so much time together). the final confident prediction is that in just a matter of weeks or months the 'covid crisis' will lead to an outbreak of divisive and disruptive political blame games as politicians, policymakers, advisers and experts all seek to avoid carrying the can for those decisions or opinions that inevitably turned-out to be wrong. it is in the context of this core prediction that this sub-section makes three arguments: (i) the analysis of previous pandemics exposes the existence of a powerful socio-political 'negativity bias'; (ii) politicians will try and manage this situation through a mixture of blame-games and self-preservation strategies; and (iii) it is already possible to identify a dominant strategy in the uk context that for the sake of brevity can be labelled 'hugging the experts'. when it comes to considering the link between public trust and blame even the most cursory review of the existing scholarship on how governments have attempted to cope with pandemics in the past reveals a body of work that is primarily framed around the notion of 'policy failure'. this is a critical point. no matter what steps a government might take or how quickly measures are put in place the fact that by its very existence a pandemic brings with it crisis and chaos intermixed with death and suffering ensures that any governmental response will be seen in generally critical terms. the title of greg behrman's book the invisible people: how the u.s. has slept through the global aids pandemic, the greatest humanitarian catastrophe of our time reflects this point. although it could actually be seen as fairly successful in terms of protecting life, the political reaction to the severe acute respiratory syndrome pandemic at the beginning of the millennium is generally critiqued in terms of either over-reaction or under-reaction (see, e.g. freedman, ; hooker and harr aliis, ). add to this, the manner in which 'what went wrong?' seems to be the dominant lens through which responses to both swine flu and ebola are judged and the link between pandemic control and blame attribution becomes clear (see kamradt-scott, ) . but what is also interesting about this seam of scholarship on pandemic crisis management is the manner in which it is infused with discourses not only of political blame and counter-blame, but also with discussions of self-blame, notions of shame and an awareness of the cultural apportionment of blame to specific countries or communities that is generally not discussed within the fields of public administration, executive studies or mainstream public policy (see, e.g. abeysinghe and white, ; nerlich and koteyko, ) . a link is, however, provided in the work of cáceres and otte in their work on blame apportioning and the emergence of zoonoses (i.e. diseases that can be transmitted from animals to humans) during the last years when they note: [b]lame games take place between infected and non-infected regions, as well as between developed and developing nations. apportioning of blame, more commonly known as finger pointing, is an inherent feature of human beings. this blaming process can be either active or passive depending on the issue(s) and given context(s). evidently, blaming is used to shift responsibilities onto others, it singles out a culprit, finds a scapegoat and pinpoints a target, regrettably however, apportioning blame comes at a cost to those that are blamed. expanding our epidemiological understandings into the realms of blamers and blamed permits a more realistic, emphatic and conscientious look into the unintended consequences of individual and institutional actions, and the extent to which other countries or regions are detrimentally affected by misguided pre-conceptions. (cáceres and otte, , pp. - ) this focus on the 'cost' of blame and 'unintended consequences' brings us to a second argument and the suggestion that the politics of the coronavirus pandemic (in the uk and beyond) is already beginning to revolve around the issue of blame (blame-shifters, blame-shiftees, blame-boomerangs, etc.). in this regard, political science offers a rich seam of scholarship on blame avoidance behaviour that arguably dates back to at least machiavelli but has more recently been developed in the work of scholars including r. kent weaver ( ) and christopher hood ( ) . synthesised and simplified down to its core elements, this body of work reveals how politicians are primarily motivated by avoiding blame for failure rather than trying to claim credit for success for the simple reason that the public possess a strong 'negativity bias'. praise will be as fickle as it is short-lived, whereas vitriol will be as strong as it will long-lived. the implication being that politicians will use all sorts of tricks and tactics-agenda-shaping, scapegoating, buck-passing, deflection and secrecy as part of a deeper 'teflon immorality' (see smilansky, ) -in order to keep themselves blame free. the relevance of this literature to the link between the coronavirus crisis and the broader crisis of democracy is the manner in which it connects the focus on public trust (discussed above) with the performative and substantive content of governmental policy responses. in this regard, the work of christopher hood on 'the risk game and the blame game' (see table , above) is particularly valuable for at least three reasons: first, it highlights the range of blame-avoidance strategies that politicians can utilise (notably presentational strategies, policy positions and the delegation of responsibility to arm's-length agencies); secondly, it contextualises the use of these strategies through an emphasis on public attitudes; and thirdly, it highlights that blame-shifting can backfire if those to whom responsibility is directed push back (hence the emphasis on blame-reversion, boomerangs and lightning-rods). the key question then becomes how this framework contributes to our understanding of the unfolding politics of coronavirus? working across a very wide and fluid empirical landscape and using a fairly broad analytical brush, the main answer to this question can be summarised as follows. first and foremost (and as the previous section emphasised), public attitudes to politicians, political processes and political institutions were in fairly poor health in most advanced liberal democracies as the pandemic emerged. high levels of political frustration, apathy and anger were identified within large sections of the public and this had led to the emergence of a potentially democratically dangerous level of anti-political sentiment. in contextual terms and with table in mind, public attitudes were arguably leaning more towards the 'vindictive' than the 'sympathetic' vis-à-vis hood's schema and this matters because the literature on pandemics and disease control clearly shows that whether the public is willing to follow government advice is highly dependent on preexisting levels of political trust, hence its common focus on 'crying wolf', metacommunication patterns, 'epidemic intelligence' and 'vaccine hesitation' (see nerlich and koteyko, ; mesch and schwirian, ) . the lack of pre-existing public trust may well have significant implications in terms of preventing what has been variously labelled 'crisis fatigue' or 'lockdown fatigue' (flinders, ) amongst the public and a reluctance to abide by social isolation advice. the fact that in the uk these risks exist in the context of well-documented 'brexit fatigue' underlines the manner in which the coronavirus crisis cannot be studied in isolation and should more accurately be conceived as being layered-upon or interwoven with a complex patchwork of challenges. a second way in which hood's framework helps focus attention on the pandemic-democracy link, in general, and blame, in particular, is through the identification of specific blame-avoidance strategies. in the uk, there has arguably been a very clear strategy at play which has revolved around the adoption of a technocratic, science-based and evidence-led approach that has ensured that no government statement has been made without the explicit caveat about 'following the advice of the experts'. this 'hugging the experts' is possibly even a future blameavoidance tactic in preparation that represents an amalgam of presentational, policy and delegatory elements. the sight of boris johnson or other senior ministers flanked at the daily press conferences by the chief medical officer and chief scientific advisor is without doubt a strategic performative act of blame-sharing and blame-displacement. this is by no means unique to the uk. in some countries, a new public service bargain seems to have emerged whereby the politicians depart the stage to an almost total extent and let the experts become the public face of the crisis. take, for example, anthony fauci, the director of the national institute of allergy and infectious diseases in the usa, fernando simó n, the head of health emergency centre in spain, christian drosten, the head of virology at charité hospital in germany, jérô me salomon, head of the national health authority in france and prof. chris whitty and sir patrick vallance in the uk (the chief medical adviser and government chief scientific adviser, respectively). as jon henley ( ) has illustrated, its 'the experts' that are now the household names. not only does this raise issues about the political selection of expert advice (discussed below) but it also raises questions about the political protections afforded to scientists who become drawn into major debates and may become blame-shiftees or sacrificial lambs when the scrutiny industry kicks-in. and 'kick-in' it will. a third way in which the literature on blame games is relevant to the current coronavirus crisis is due to the manner in which it underlines the aggressive and adversarial nature of public accountability. this is encapsulated in the notion of the 'negativity bias' and simply reflects that manner in which political decisions are generally taken in a low-trust, high-blame environment. put slightly differently, public accountability is generally of the 'gotcha!' variety (which is a particularly problematic paradigm when placed within the contours of hilliard et al. ( ) scholarship on 'the perils of accountability after crisis'). the aim is very rarely to undertake a reasoned, balanced or proportionate review of what happened in order to learn lessons but primarily to apportion blame and demand some form of sacrificial responsibility. this is particularly true in power-hoarding majoritarian democracies like the uk and especially due to the focussing impact of the convention individual ministerial responsibility to parliament. any attempt by ministers to deflect blame therefore risks bouncingback on them in the form of a 'blame boomerang' if the expert, scientist or publicly trusted professor refuses to be scapegoated. the fact that the dark clouds of intense public and parliamentary scrutiny are already visible and hanging over the coronavirus is symptomatic of the potentially pathological politics of accountability that this section is attempting to underline. the world health organisation declared the outbreak to be a pandemic on the march and by the end of the second week of april , parliamentary committees had public administration and constitutional affairs has announced its intention to call ministers to account on the topic but it has not launched a formal inquiry (yet). already announced inquiries (some multiple inquiries) into various elements of the government's response (see table , below). the number or range of select committee inquiries-or, for that matter, any forms of public accountability process-is not the issue. the point being made relates to the nature and ambitions of those scrutiny processes and whether they themselves become part of the problem with democracy, due to a focus on scalphunting and shallow adversarialism that is devoid from any appreciation of the realities of crisis management, or part of the solution, in terms of promoting a balanced assessment of what went wrong, why and how similar patterns might be avoided in the future. in essence, this is the argument relating to understanding that forms the focus of the next and final section but before engaging with this argument it is necessary to conclude this section with a very brief discussion of three final blame-related insights. the first is that it is likely that the coronavirus crisis will serve to redefine the scholarship on blame-shifting just as it is likely to alter the contours of the debate concerning democracy. the complexity and intricacies of crisis responses will somehow have to be accommodated within models that have generally been constructed around and within the notion of national systems. and yet we can already see the emergence of global blame games wherein specific and primarily american politicians and organisations are attempting to blame china for the crisis (see henderson et al., ) ; while china seeks to pass the buck back to the usa in what has become a 'war of words' amidst covid- (see the straits times, ). donald trump is widely interpreted as trying to scapegoat the world health organisation by withdrawing american funding. european blame games are also beginning as, for example, italy blames the european union for being too slow to help member states (see boffey, ) . within the uk cracks and pressure-points are already beginning to appear as tensions grow between departments, ministers, officials, agencies and advisers as the prospect of public scrutiny become ever more immediate. this brings us to a second issue and the 'blame attraction' or 'buck stops here' qualities (see table , above) that come with being a minister. despite the cross-governmental nature of the challenge, in strict constitutional terms, it is the secretary of state for health and the prime minister who are likely to emerge as the 'lightning rods' when it comes to the allocation of blame and as key targets when it comes to demands for a 'sacrificial lamb' to carry-the-can. and yet even here the curiosities of coronavirus may well defeat conventional understandings. on the one hand, the emergence of the health secretary from virus enforced self-isolation on the nd april to announce that mistakes had been made and that a u-turn on testing policy was needed that would see capacity increased to , tests a day by the end of april was a clear attempt to bolster public confidence by taking very clear personal responsibility for the target; on the other hand, the announcement that the prime minister had been taken to hospital and then moved into intensive care potentially insulates him from some element of blame, and may well fuel a second 'rallying around the flag' effect for the government as the media and opposition parties soften their stance. although there is evidence to support this claim, it might be more accurate to identify the existence of a post-hospitalisation surge in support for the prime minister rather than the government. boris johnson was discharged from hospital on the april and a yougov approval rating poll conducted at the time found a staggering leap in the proportion of the public who thought he was doing 'very well' as prime minister ( %, up from % in mid-march), with % suggesting he was doing 'fairly well' (up from %). boris's teflon-coated qualities and blame-avoidance behaviour have been discussed throughout his political career and he has been known to adopt cunning exit strategies in the past when faced with tricky situations. nevertheless, the notion of 'medical distancing' as a blame avoidance strategy would be extreme even for this most unconventional politician and boris appears to be more popular than ever, possibly to the despair of his opponents. that said, the core argument of this section remains true: the coronavirus crisis is likely to spark a veritable tsunami of complex and aggressive blame games. this creates a strong risk that the structures of democratic governance will themselves fall victim to the painful politico-administrative malady that is generally labelled going 'mad' (i.e. koppell's ( ) 'multiple accountabilities disorder'). this occurs when politicians and their officials are expected to account through so many different accountability channels and to so many scrutiny bodieswhich themselves often demand very different forms of information and are blame-orientated rather than understanding-focussed-that they are distracted from focussing on their core tasks. put slightly differently, mad occurs when senior staffs are expected to spend too much time 'accounting-up' instead of focussing on 'delivering-down' which, in turn, increases the chances that mistakes and errors will be made which would, in turn, simply increase the scrutiny placed upon them. the potential pathologies of highly politicised accountability, as matthew flinders ( ) has demonstrated, means that too much accountability can be as problematic as too little. this leads the discussion to a possibly unexpected focus on understanding as the final strand that connects the coronavirus crisis to the crisis of democracy. democratic politics, as bernard crick sought to explain in his defence of politics ( ), is a rather rough and ready affair. it grates and it grinds, it is frequently cumbersome and generally clunky, it can be inefficient and its basis on the art of compromise can make it difficult to understand for those that are not intricately connected with those processes. it is messy. and yet those characteristics are from crick's perspective not failings but elements of the very beauty of politics; they reflect the simple manner in which politics is charged with somehow generating broadly acceptable decisions and choices in an environment that is increasingly defined by complexity and incompatibility. it would, of course, be possible to make politics smoother and more efficient, to impose clarity and clearer control mechanisms through a uniformity of style and structure. but the cost of such measures would in all likelihood be a decline in the sensitivity of that system to the rights and views of the individuals and communities within it. this matters because at the heart of any understanding of the link between the coronavirus and the crisis of democracy, there has to be a fundamental understanding of the existence of inevitable trade-offs and dilemmas. the existence of these dilemmas is generally far more apparent in times of crisis due to the emphasis that is generally placed on the responsive capacity of the state rather than on the democratic sensitivity of the system. tough decisions will have to be taken quickly, on the basis of imperfect information and without the possibility of extensive consultation and compromise in what might be seen as a capacity/democracy trade-off. understanding the rationale, logic and implications of this shift are critical not just in terms of how it flows through to influence public trust, or how it structures subsequent blame-games but also due to the manner in which it shapes the ideational space-the simple realm of ideas-about how assessments regarding the future of democracy should be made. in order to understand this focus on understanding and demonstrate its centrality to this article's central focus on the nexus between the current covid- crisis and broader debates concerning the crisis of democracy, this section adopts a multi-levelled approach. this takes us from a micro-level understanding of politicians as individuals operating in a crisis context; through to a mid-range governmental focus on understanding and gauging 'policy success' as well as 'policy failure'; to a final macro-political focus on the grand narratives and regime battles that coronavirus appears to have unleashed. taken together, what this three-level focus on understanding provides is a fresh and timely analysis of how two very different crises have come to be inter-woven with the risk that one (i.e. covid) will be politicised and utilised in order to inflame the second (i.e. democracy). defending democracy-or more specifically promoting an understanding of its inner beauty, inescapable inadequacies and the inevitable trade-offs that come with any choice of organising society-has therefore been the underlying ambition of this article. this is a point that brings us to begin by reflecting on the scale of the challenge; not in relation to defending democracy but more specifically in relation to the challenges posed by coronavirus. this is a new virus, it can be highly aggressive and it is easily transmitted. with this in mind, it is possible to move across the three levels from the individual, to the system, to the basic notion of democracy. any defence of democratic politics must to some extent seek to defend politicians. although frequently demonised, derided and dismissed as self-serving and self-interested characters, the simple fact is that politicians are at the -end-of-theday humans, as the manner in which several leading politicians have succumbed to coronavirus reflects. notwithstanding clear concerns about patterns of political recruitment and the degree to which the political class reflect the diversity to be found within society, this does not alter the basic point that promotes some understanding of the practical and day-to-day pressures under which politicians generally operate. put slightly differently, 'governing under pressure' is incredibly demanding and an evidence-based debate about the mental health and well-being of politicians was already emerging before the coronavirus crisis emerged (for a review, see flinders et al., ) . these pressures increase as individuals assume the responsibilities of ministerial office and are particularly pronounced in times of crisis, especially when the source of the crisis is new and therefore no clear knowledge of 'what works' is available. crisis situations by their very nature demand that someone ultimately has to assume control and make decisions under extreme pressure, on the basis of imperfect information and in the full knowledge that they are dealing with matters of 'life and death' for which they will at some point be held to account. in a democracy, it is elected politicians to whom these decisions and situations fall. the public demands clarity ('when will lock-down end?', 'when will a vaccine be found?', 'what is going to happen next?') when politicians are themselves charged with grappling with uncertainty and cannot produce simple answers to complex questions. this may explain their strategy of 'hugging the experts' but as expert opinion itself divides and becomes more contested then so the ability of politicians to look to science for answers, at least in the short-term begins to wane. the micro-level argument is therefore simply one that promotes some understanding of the professional challenges and personal pressures that those who have at least dared to step into the arena and assume the burdens of office are attempting to manage. it would at this point be possible to explore the contemporary relevance of theodore roosevelt's 'it's not the critic who counts' speech of april but such temptations must be resisted in order to move to a second mid-level focus on understanding institutional change. the simple argument here is that although, as the second section (above) suggested, the response of democratic governments around the world is likely to be seen through interpretations of 'policy failure'-and some mistakes and failures will undoubtedly have occurred-it is also important to understand the scale of what has actually been achieved. in the uk, the whitehall machine and wider-state structures have demonstrated an ambition and agility that although not perfect cannot be denied. the scale of the achievements is worthy of reflection, irrespective of whether it relates to building new hospitals, launching new policies, negotiating new powers, liaising with other governments, co-ordinating a vast network of organisations and suppliers, calming and informing the public, reshaping the economy or building new financial safety nets. interestingly, it is possible to identify a strong 'negativity bias' within academe as well as within society more broadly. to enter the fields of public administration and public policy is generally a fairly depressing experience due to the almost obsessional focus of these fields on failures, catastrophes and disasters. the publication in april manifesto 'towards positive public administration' by scott douglas, paul t'hart and a large group of leading scholars was an explicit attempt to rebalance the analytical scales and promote an understanding of structural successes, policy achievements and democratic innovations. the mid-level argument is therefore one that seeks to promote some understanding of the structural and institutional accomplishments that have been achieved in the content of a truly exceptional and potentially transformative crisis. democratic politics has not been able to 'make all sad hearts glad' as crick admitted it never could in his defence over half a century ago and to some extent the covid-crisis has shown this, but at the same time its achievements in response to the public health pandemic should not be too easily dismissed. this argument matters because it underpins a far broader macro-political dispute about the global state of democracy and how the coronavirus is already reshaping the debate about regime legitimacy and state capacity. the danger of the 'credit-claiming' behaviour of china in containing the crisis through technologically powered surveillance is that it may engender an 'authoritarian appeal' or 'strong leader' effect that was to some extent already evident in many countries through the drift towards populism (see table , above). 'the new coronavirus pandemic is not only wreaking destruction on public health and the global economy but disrupting democracy and governance worldwide' frances brown et al. ( ) have argued 'it has hit at a time when democracy was already under threat in many places, and it risks exacerbating democratic backsliding and authoritarian consolidation'. the geopolitical consequences of this can already be seen in the 'power grab' behaviour of some national leaders and also in the attempts by international actors to defend democracy. the existence of what dan kelemen ( ) has labelled an 'authoritarian equilibrium' within the european union has raised particular concerns. the decision of the secretary general of the council of europe to publish an open letter to the hungarian prime minister, viktor orbán, on the march regarding the use of covid-emergency measures, plus the decision to launch a new eu action plan on human rights and democracy the very next day that is explicitly designed 'to defend human rights and democracy all over the world by using all our resources faster and more effectively', captures the sense that a new phase in the long-running tension between authoritarian and democratic regimes may well have started. understanding the dynamic and dialectical relationship between concerns regarding the crisis of democracy and the unfolding coronavirus pandemic is necessary in order to prevent a form of socio-political cross-contamination, whereby the cynicism, negativity and frustration concerning politicians, political processes and political institutions that existed before the coronavirus outbreak is allowed to direct, define and automatically devalue how democratic structures are subsequently judged in terms of how they responded to the challenge. without appreciating (i) the fragility and significance of public trust, (ii) the potentially pathological impacts of blame-games or (iii) understanding the achievements of individuals and institutions working together to address a collective threat, there is a very real risk that the coronavirus crisis will fuel a broader crisis of democracy. the avian influenza pandemic how to win the blame game patriotism or opinion leadership? the nature and origins of the "rally 'round the flag" effect italy critics eu for being slow to help over coronavirus epidemic how will the coronavirus reshape democracy and global governance blame apportioning and the emergence of zoonoses over the last years daring to be a daniel: the pathology of politicized accountability in a monitory democracy coronavirus and the politics of crisis fatigue governing under pressure? the mental wellbeing of politicians sars and regime legitimacy in china the politics of blame: bargaining before an audience coronavirus: meet the scientists who are the new household names, the guardian anatomy of a rally effect: george w. bush and the war on terrorism the perils of accountability after crisis: ambiguity, policy legacies, and value trade-offs' the blame game sars and security: health in the addressing the ills, reviving the promise the british government's response to the coronavirus has been a disaster coronavirus: why boris johnson and other world leaders have become more popular during outbreak what went wrong? the world health organization from swine flu to ebola the new despotism the european union's authoritarian equilibrium do authoritarian or democratic countries handle pandemics the best pathologies of accountability social and political determinants of vaccine hesitancy presidential popularity from truman to johnson crying wolf? biosecurity and metacommunication in the context of the swine flu pandemic opinium ( ) opinium 'public opinion on coronavirus - st april towards positive public administration: a manifesto teflon immorality" and the perversity of life us military may have brought coronavirus to wuhan, says china in war of words with us democracy report : autocratization surges -resistance grows the politics of blame avoidance boris johnson approval rating tracker none. none. none. key: cord- -udhajlx authors: tang, lei; zhang, xiaoyong; wang, yvquan; zeng, xianchun title: severe covid- pneumonia: assessing inflammation burden with volume-rendered chest ct date: - - journal: radiol cardiothorac imaging doi: . /ryct. sha: doc_id: cord_uid: udhajlx nan technique (pulmo d software, vb ; siemens healthineers, forchheim, germany) highlighted the distribution of pulmonary opacities, which was useful to determine the extension of the disease (fig , movie [supplement] ). her nasopharyngeal swab was positive for covid- with real-time fluorescence polymerase chain reaction test. the patient was diagnosed with severe covid- pneumonia. when treated with oxygen inhalation, moxifloxacin, lopinavir/ritonavir, umifenovir, interferon, and thymosin, her body temperature returned to normal and the symptoms slightly improved. ct reexamination on the th day of hospitalization indicated increased lesions and mild absorption on the th day. this copy is for personal use only. to order printed copies, contact reprints@rsna.org severe covid- pneumonia: assessing inflammation burden with volume-rendered chest ct early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a novel coronavirus from patients with pneumonia in china ct imaging of the novel coronavirus ( -ncov) pneumonia references . world health organization. novel coronavirus ( -ncov) situation reports disclosures of conflicts of interest: l.t. disclosed no relevant relationships. x. zhang disclosed no relevant relationships. y.w. disclosed no relevant relationships. x. zeng disclosed no relevant relationships. key: cord- -di n wyd authors: venturini, elisabetta; palmas, giordano; montagnani, carlotta; chiappini, elena; citera, francesco; astorino, valeria; trapani, sandra; galli, luisa title: severe neutropenia in infants with severe acute respiratory syndrome caused by the novel coronavirus infection date: - - journal: j pediatr doi: . /j.jpeds. . . sha: doc_id: cord_uid: di n wyd nan to the editor: infection with severe acute respiratory syndrome caused by the novel coronavirus (sars-cov- ) and resulting coronavirus disease (covid- ) is a global pandemic. pediatric cases have some peculiarities, such as milder clinical manifestations and different laboratory abnormalities. a systematic review on laboratory data identified articles, with a total of pediatric patients. [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] lymphopenia was found in only % of children, whereas lymphopenia often is described in adult patients. , neutropenia was recorded in % of cases, but it was never less than . Â /l in this population. we describe a -day-old and a -day-old infant with mild covid- and severe neutropenia who were cared for at our tertiary care referral pediatric hospital. they both came to medical attention with low-grade fever and mild respiratory symptoms with a history of contact with an infected person or persons. at admission, leukocyte and neutrophil counts were normal, nasopharyngeal swab tested positive for covid- , and co-infection with influenza-like viruses was excluded. on the fifth day and days after the beginning of symptoms, the -day-old girl and the -day-old girl developed severe neutropenia, with a nadir of . Â /l neutrophils and . Â /l neutrophils, respectively (figure) . no other alterations on routine examinations were recorded and the neutrophil values improved without clinical complications. the presence of isolated severe neutropenia has not been described in children with covid- . this finding is noteworthy, because postinfectious transient neutropenia has been associated with many other viral infections in infancy, which might share pathogenic mechanisms. , moreover, the evidence of neutropenia in neonates and infants could be another manifestation of the age-related different immunologic response to sars-cov- infection. complete blood counts might be indicated - days after illness onset to detect neutropenia. we hope to alert providers to evaluate children, especially the youngest, with evidence of new symptoms during the second week after onset of illness to exclude severe neutropenia and possible secondary infection. world health organization. novel coronavirus (covid- ) situation epidemiological characteristics of pediatric patients with coronavirus disease in china laboratory abnormalities in children with novel coronavirus disease clinical and biochemical indexes from -ncov infected patients linked to viral loads and lung injury a familial cluster of pneumonia associated with the novel coronavirus indicating personto-person transmission: a study of a family cluster a case series of children with novel coronavirus infection: clinical and epidemiological features analysis of ct features of children with novel coronavirus infection a well infant with coronavirus disease (covid- ) with high viral load clinical analysis of cases of novel coronavirus infection in children from six provinces (autonomous region) of northern china novel coronavirus infection in a three-month-old baby china's first neonatal coronavirus pneumonia twin girls infected with sars-cov- a case of children with novel coronavirus infection chinese pediatric novel coronavirus study team. sars-cov- infection in children china medical treatment expert group for covid- . clinical characteristics of coronavirus disease in china infectious etiologies of transient neutropenia in previously healthy children. pediatr transient and chronic neutropenias detected in children with different viral and bacterial infections key: cord- - tl mtb authors: xia, jianhua; tong, jianping; liu, mengyun; shen, ye; guo, dongyu title: evaluation of coronavirus in tears and conjunctival secretions of patients with sars‐cov‐ infection date: - - journal: j med virol doi: . /jmv. sha: doc_id: cord_uid: tl mtb objective: this study aimed to assess the presence of novel coronavirus in tears and conjunctival secretions of sars–cov‐ ‐infected patients. methods: a prospective interventional case series study was performed, and confirmed novel coronavirus pneumonia (ncp) patients were selected at the first affiliated hospital of zhejiang university from january to february . at an interval of to days, tear and conjunctival secretions were collected twice with disposable sampling swabs for reverse‐transcription polymerase chain reaction (rt‐pcr) assay. results: twenty‐one common‐type and nine severe‐type ncp patients were enrolled. two samples of tear and conjunctival secretions were obtained from the only one patient with conjunctivitis yielded positive rt‐pcr results. fifty‐eight samples from other patents were all negative. conclusion: we speculate that sars‐cov‐ may be detected in the tears and conjunctival secretions in ncp patients with conjunctivitis. in december , cases of unexplained pneumonia were clustered in wuhan, hubei province, china. most of the infected people were confirmed to be related to the south china seafood market. on january , the chinese center for disease control and prevention isolated and confirmed this pathogen as a novel type of coronavirus through a throat swab. this coronavirus was then named -ncov by the world health organization (who). the origin of the virus remains unknown, and the virus-host is suspected to be a species of bat. on january , the who confirmed that the virus was spread via human-to-human transmission and family-aggregated infections and is less contagious to healthcare professionals, unlike severe acute respiratory syndrome coronavirus (sars-cov) and the middle east respiratory syndrome-related coronavirus. on january , the who characterized the outbreak as a public health emergency of international concern. at the close of day (on february at : : ), the cumulative number of infected people worldwide was , and the cumulative number of infected people in china was . the virus had spread to other countries globally, with deaths worldwide. at present, the mortality rate in china is about . %, and the number of infected and dead people continues to increase. on february , the who officially named infection due to the virus as coronavirus disease (covid- ) study group of the international committee on taxonomy of viruses named -ncov severe acute respiratory syndrome-related coronavirus , or sars-cov- . at present, covid- poses a huge threat to china and the world. covid- is highly infectious and transmitted mainly through respiratory droplets and contact with infected persons. the possibility of feco-oral and aerosol transmission remains to be further studied. in , some researchers found that the tears of sars patients tested positive for viral nucleic acid, some patients only showed positive results with tear samples, and the chromosome of sars-cov- was % similar to that of sars-cov. a previous study reported the case of a clinician who was infected while working with only his eyes unprotected. lu et al reported that the disease can be transmitted through the mucous membranes, including the conjunctiva. there have been many case reports in which many ophthalmologists were found to be infected through routine diagnosis and treatment. considering that the virus is present in the body fluids of patients, tear fluid is a type of body fluid, and sars-cov- is similar to sars-cov, it is speculated that there may be a risk of tear and conjunctival transmission. therefore, this is a focus of the current research to understand whether covid- is transmitted via other routes and reduce further spread of the epidemic. in the present study, the tear and conjunctival secretions of a prospective interventional case series study was designed. we rt-pcr protocol: . the collected specimen was shaken for seconds. we pipetted to ml of the specimen and stored it in an eppendorf tube. . the tube was then centrifuged at r/min for minutes and µl of the supernatant was pipetted and added to the prepared deep well plate. then, we added µl of proteinase k and µl of settling agent to extract the nucleic acid. the extraction was completed after about minutes. then, the nucleic acid was stored in a new eppendorf tube. altogether, patients with common-type and patients with severe-type were included, with an average age of . ± . years and a male/female ratio of / . by the time of first collection of tear and conjunctival secretions, the mean time of onset was . ± . days. the average body temperature of the patients was . °c ± . °c at the time of sampling. details of the characteristics of the study participants are provided in table . two conjunctival swab samples from the only one common-type patients with conjunctivitis (patient no. ) yielded positive rt-pcr results and his sputum samples were also positive. fifty-eight conjunctival swab samples from common-type patients and severe-type patients were all negative. currently, it is difficult to screen for ncp. some patients have no obvious fever or respiratory manifestations, or even obvious symptoms in the early stages of the disease. during clinical diagnosis and treatment, particularly at the outpatient clinic, it is difficult to quickly screen patients with early-stage disease or carriers of the virus. according to recent reports, a large number of ophthalmologists involved in the diagnosis and treatment of the disease on a daily basis accidentally acquired ncp. thus, many doctors suspect that it is related to contact with tears or conjunctival secretions of patients. in the study of this small sample, we used conjunctival test paper to obtain tears and con- we speculate that sars-cov- may be detected in the tears and conjunctival secretions in ncp patients with conjunctivitis. further high-volume studies are warranted to evaluate this issue. outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle origin and evolution of the novel coronavirus novel coronavirus ( -ncov) situation report- emergency committee regarding the outbreak of novel coronavirus ( -ncov). geneva, switzerland: world health organization novel coronavirus ( -ncov) situation report- christening of new coronavirus and its disease name create confusion office of state administration of traditional chinese medicine. notice on the issuance of a programme for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (trial the severe acute respiratory syndrome coronavirus in tears genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan peking university hospital wang guangfa disclosed treatment status on weibo and suspected infection without wearing goggles. beijing news -ncov transmission through the ocular surface must not be ignored office of state administration of traditional chinese medicine. notice on the issuance of a programme for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (trial clinical features of patients infected with novel coronavirus in wuhan potential maternal and infant outcomes from (wuhan) coronavirus -ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections infection control guidelines for optometrists detection of novel coronavirus ( -ncov) by real-time rt-pcr epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study a meta-analysis to evaluate the effectiveness of real-time pcr for diagnosing novel coronavirus infections tears and conjunctival scrapings for coronavirus in patients with sars evaluation of coronavirus in tears and conjunctival secretions of patients with sars-cov- infection the authors declare that there are no conflict of interests. jhx took part in sample collection. jt and ml took part in data collection and interpretation. ys and dg designed the study, analysis and interpretation of the data, and wrote the manuscript. http://orcid.org/ - - - key: cord- - znmkvy authors: montecino-latorre, diego; goldstein, tracey; gilardi, kirsten; wolking, david; van wormer, elizabeth; kazwala, rudovick; ssebide, benard; nziza, julius; sijali, zikankuba; cranfield, michael; mazet, jonna a. k. title: reproduction of east-african bats may guide risk mitigation for coronavirus spillover date: - - journal: nan doi: . /s - - - sha: doc_id: cord_uid: znmkvy background: bats provide important ecosystem services; however, current evidence supports that they host several zoonotic viruses, including species of the coronaviridae family. if bats in close interaction with humans host and shed coronaviruses with zoonotic potential, such as the severe acute respiratory syndrome virus, spillover may occur. therefore, strategies aiming to mitigate potential spillover and disease emergence, while supporting the conservation of bats and their important ecological roles are needed. past research suggests that coronavirus shedding in bats varies seasonally following their reproductive cycle; however, shedding dynamics have been assessed in only a few species, which does not allow for generalization of findings across bat taxa and geographic regions. methods: to assess the generalizability of coronavirus shedding seasonality, we sampled hundreds of bats belonging to several species with different life history traits across east africa at different times of the year. we assessed, via bayesian modeling, the hypothesis that chiropterans, across species and spatial domains, experience seasonal trends in coronavirus shedding as a function of the reproductive cycle. results: we found that, beyond spatial, taxonomic, and life history differences, coronavirus shedding is more expected when pups are becoming independent from the dam and that juvenile bats are prone to shed these viruses. conclusions: these findings could guide policy aimed at the prevention of spillover in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding. in these periods, contact with bats should be avoided (for example, by impeding or forbidding people access to caves). our proposed strategy provides an alternative to culling – an ethically questionable practice that may result in higher pathogen levels – and supports the conservation of bats and the delivery of their key ecosystem services. the order chiroptera is the second largest order of mammals with more than identified species [ ] . the members of this order, bats, provide important ecosystem services (reviewed in [ , ] ). for example, insectivorous bats can reduce arthropod herbivory [ ] [ ] [ ] , increase agricultural yields [ ] , reduce the need for insecticides [ ] , and prevent large financial losses in agriculture [ ] [ ] [ ] . plant-visiting chiropterans provide pollination and seeddispersing services (reviewed in [ ] ), certain nectivorous bats are pollinators of economically important plants [ ] , and frugivorous bats can be important for reforestation [ ] . finally, cave-roosting bats produce guano, the main energy source in many cave ecosystems [ , ] , and the mining of this product is an income source in poor communities [ ] . however, current evidence supports that bats are a natural host of several disease-causing viruses across the globe, including zoonotic viruses, such as rabies virus (rhabdoviridae, genus lyssavirus); hendra and nipah viruses (paramyxoviridae, genus henipavirus); and marburg and ebolaviruses (filoviridae, genus marburgvirus and ebolavirus, respectively; [ , ] ). bats are also hosts of several viruses of the coronaviridae family [ ] [ ] [ ] [ ] . molecular evidence suggests that the severe acute respiratory syndrome betacoronavirus (sars-cov beta-cov) and the middle-east respiratory syndrome betacov (mers-cov) originated from bats [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . both viruses emerged in humans during the past two decades, specifically in china ( ) and saudi arabia ( ). the sars-cov pandemic included cases in countries with a~ % case fatality [ ] , while mers-cov has affected people in countries with a case fatality of % [ ] . incidental cases of mers-cov are still detected mainly in saudi arabia [ ] , and it is thought that camels are important for human infection [ ] [ ] [ ] . today it is known that: i) a high genetic diversity of coronaviruses (covs) is present in more than bat species, including viruses related to sars and mers cov [ ] ; ii) covs are prone to move and adapt to new host species [ ] ; iii) plausibly, all mammalian-adapted covs may have originated in bats [ , , ] , including a recently emerged highly fatal alphacoronavirus in piglets [ ] and the e human cov [ , , ] ; and iv) covs found in bats can use human receptors for cell entry [ , , , ] . these lines of evidence suggest that future spillover of coronaviruses humans is feasible. because covs are found in bat species that have adapted to be in close contact with humans, such as the straw-colored fruit bat (eidolon helvum) and the brazilian free-tailed bat (tadarida brasiliensis [ , ] ), high contact "bat-human" interfaces currently exist around the world. if the bats in these interfaces shed covs with the ability to infect humans, then opportunities for spillover through direct exposure to feces [ ] or the contamination of food are created, as these viruses can remain infectious in the environment for days [ ] . therefore, strategies aiming to mitigate human exposure to covs, and thus, the risk of spillover and disease emergence are needed, while supporting the conservation of bats and their important ecological roles. longitudinal sampling with specific species has shown that the proportion of bats shedding covs varies seasonally [ ] [ ] [ ] [ ] and that fecal cov-rna loads can also be heterogeneous over time [ , ] . if exposure through contact with bat feces is a main pathway for zoonotic cov spillover to humans but shedding of these pathogens is not uniform over time, then mitigation strategies aiming to prevent bat cov-shed exposure could be targeted temporally, directed especially at highrisk seasons. such a strategy could guide policy in limitedresource settings where sampling bats for cov testing is not feasible and it could support an ethically acceptable management to mitigate spillover risk. however, the few species and locations tested to date do not allow for identification of a potential seasonal shedding pattern to responsibly suggest temporal spillover risk management across species and geography. therefore, assessment of the cov dynamics in a broader range of bat species that show different life history traits, as well as in diverse geographic and ecological circumstances, could be extremely useful. to this end, we evaluated the dynamics of cov shedding in different bat species sampled in several locations in east africa at different times of the year. this geographical region has been identified as a hotspot of pathogen emergence [ ] , where cov host switching events seem to be higher compared to other areas [ ] , but, to our knowledge, no study on cov dynamics in bats has been conducted. specifically, we hypothesized that bat species exhibit seasonal trends in cov shedding that are associated with the reproductive season. we assessed this hypothesis by fitting bayesian statistical multivariable models to evaluate whether cov shedding in bats is positively associated with the time period when pups are becoming independent from the dam. beyond the inclusion of several species sampled in different countries at different times, we explicitly identified the reproductive events for each species at the time of sampling and also included other traits, such as the aggregation of individuals at the roost, that may be involved in cov dynamics. samples (rectal swabs and fresh feces) were collected from bats captured in uganda, rwanda, and tanzania ( fig. ) , between september and april with permission from local authorities and under the institutional animal care and use committee at the university of california, davis (protocol number: ). bats were captured in unique locations between latitudes − . and − . (fig. ). these locations were selected because they represented potentially high-risk interfaces for contact between bats and humans, such as areas of land-use change, human-dwellings, ecotourism sites, markets, and places with potential for occupational exposure [ ] . locations in close proximity (euclidean distance < km) in which sampling was conducted within the same week were considered a single sampling event. the remaining sampling events that occurred in the same location or spatially close to others but conducted in different weeks were considered independent sampling events. as result, we collected samples from unique sampling events. all captures were conducted using mist nets set in the early morning or at dawn. individuals were released after sample collection. samples were handled as previously described [ , ] . each sample was immediately transferred to vials containing viral transport media and nuclisens® lysis buffer (biomérieux, inc., marcy-i'Étoile, france), which were maintained in liquid nitrogen until storage in a - c freezer in each country. rna was extracted from all samples, and cdna was prepared as previously described [ , ] . two broadly reactive consensus pcr assays targeting non-overlapping fragments of the orf ab were used to detect both known and novel covs [ , ] . amplified products of the expected size were cloned and sequenced as described in [ ] . sequences were analyzed and edited using geneious prime . . [ ] . a sample was considered positive when at least one pcr assay yielded a sequence that matched coronaviruses in genbank. coronavirus sequences were classified as belonging to a specific taxa following previously described methodologies [ ] . bats were categorized as adults and juveniles based on size, and morphological and behavioral characteristics were observed at sample collection. the sex of the bats was also recorded. identification of some bat species can be challenging in the field. for this reason, field-identified species were confirmed by dna barcoding using the cytochrome b or cytochrome oxidase subunit mitochondrial genes [ ] . obtained sequences were compared against sequences in the genbank and barcode of life databases [ , ] . when possible or necessary, sequences from both genes were used for species identification. a threshold of % nucleotide identity was used to confirm the species; sequences with - % nucleotide identity were assigned a "conferre" (cf.) species status, and sequences below % nucleotide identity were either classified to the genus level or as unidentified. sequences with > % nucleotide identity to more than one species for either gene, were classified to the genus level unless they clearly clustered with sequences from other animals in the same geographic area. if barcoding results for all of the first ten bats tested per species were in agreement with the field identification, we assumed that the field identification for the remaining bats of that species in each country was correct. otherwise, all of the remaining samples were barcoded to ensure correct speciation. we recorded when sampled females were pregnant based on abdominal palpation, had attached pups (indicating recent parturition), and were lactating, as well as when juveniles were captured. therefore, we were able to track pregnancy, lactation, and recent birth pulses. moreover, we accessed the data in the pantheria [ ] and amniote [ ] databases, and we thoroughly reviewed the literature on the biology of the bats species we sampled for latitudes similar to our sampling locations. with the gathering of these information sources we established the timing of the birth pulses, lactation periods, and the weaning of pups for each species. for the details justifying the dates inferred for these three life history events for each species and the corresponding bibliographical references see additional file . once the timing of these events was confirmed or inferred, we were able to establish seasons that occur at least once during the year across all observed bat species: i) when juveniles are being weaned and female-pup contact decreases ("recent weaning" [rw]) and ii) the rest of the year (hereafter "n-rw" for "not recent weaning"). we chose to evaluate risk of cov shedding for the first period because past longitudinal studies with microchiropterans in germany and china found higher cov-rna loads approximately month after parturition [ , ] . similarly, peaks were found months after the formation of a maternity colony of myotis macropus [ ] , which would match a post weaning period for that species. here, we defined the end of the rw period as month after the last pups were weaned. we assumed that month would provide a reasonable time window for the colony to "clear" the cov susceptibility status of this period and acquire the susceptibility corresponding to the season(s) when weaning does not occur (n-rw period), if differences actually exist. finally, once we determined these two seasons, we categorized each bat sample into one of them depending on the week of the year in which they were taken. because some species had more than one litter per year, there could be more than one rw period during the year. it is worth noting that we were able to define these periods for those species in our dataset that have synchronized reproduction, whose biology was properly described, and whose taxonomy is generally accepted. when we could not assign a reproductive period to specific bats, this season was imputed (see methods: statistical analysis). we characterized specific traits of each bat species studied based on previous scientific literature on pathogen dynamics in bats [ , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] : colony size (small, medium, or large if a typical colony contains one to dozens, hundreds to thousands, or thousands to millions of individuals, respectively); roost type ("closed" if the species has been reported to use caves, mines, roofs, or other confined spaces; or "open" if the bats have been typically reported roosting in the foliage of trees); the aggregation of bats in clusters while roosting (no, yes); and the number of litters per year of the species at equatorial latitudes. references are provided in additional file . we also considered data from pantheria and amniote [ , ] . we could not include other species traits, such as the mating strategy (harem or another) and the segregation of females in maternity colonies, because available studies were incomplete or contradictory. we did not include factors, such as multi-species occupancy of the roost, because we did not observe all of the roosts. further, we did not assess postpartum estrus, as within the study area, it is only known to occur in some molossid bats [ ] , of which we only sampled a small number. to statistically estimate the association between the rw and cov detection we used a bayesian inference to model the detection of covs as a bernoulli process of the form: where cov i , the detection of cov in rectal swabs ( if detected, otherwise) from the i th bat (sample), is assumed to follow a bernoulli process parameterized by p i , the probability of cov detection on the i th bat. this parameter was related to a set of candidate covariates as: with s j~n ormal ( , σ s ) and sp k~n ormal ( , σ sp ). here x and y are binary covariates representing the rw season and juvenile age category. we specifically included these two terms to separate the potential association of the season with cov detection from the seasonal presence of juveniles. because it was not feasible to allocate all species in the rw or n-rw seasons based on previous research, we assumed that these unknown reproductive seasons were "missing at random" and they were imputed as a function of the latitude at sampling, the day of the year of the sampling event, the number of litters per year of the corresponding species (one litter per year versus more than one litter per year), and the historical precipitation of the month at the sampling event location. the description of the imputation model is provided in additional file . the terms s j and sp k represent the sampling eventand the species-specific intercepts, respectively, because we assumed that bats sampled in the same event and bats belonging to the same species were not independent with respect to cov detection. no sampling event involved the same bat colony in successive rw and n-rw seasons, therefore, we assumed that cov detection was not temporally correlated within sampling locations. we constructed the model by adding other covariates one-at-a-time to this working model: the c ...l categorical variables; and they remained in the model if they were judged to confound the relationship between cov detection and the reproductive seasons or between age and cov detection (i.e., their inclusion caused meaningful changes in the posterior probability distributions [ppds] of the specific reproductive season or age coefficients). finally, c ...l categorical variables could be retained as well if they were marginally associated with cov detection (the corresponding coefficient ppd did not include zero). to assess the goodness-of-fit of the models, we evaluated the congruence between cov detection in the data and in the posterior predictive distributions yielded by the models by: i) ages and seasons, ii) age, iii) per season, iv) per age and season, and v) per sampling event. all models were constructed using "stan" v. . . [ ] which was run from "r" v. . . [ ] through the package "rstan" v. . . [ ] . weakly informative priors were assigned for all coefficients: normal( , . ) for the estimates of α , β's, γ, and ρ's. the σ s and σ sp had a prior half-cauchy ( , ) following previous suggestions [ , ] . the ppds were estimated by sampling in parallel from mcmc chains for iterations following iteration warm-up for a total of saved samples for each parameter ppd. convergence was assessed by the gelman-rubin statistic [ ] and graphically using trace plots. the code to fit the models is available at https://github.com/ dmontecino/east-african-bats-and-cov-shedding. we sampled individuals, all of them aged and successfully identified to belonging to species. nycteris thebaica, pipistrellus hesperidus, and rhinolophus clivosus were assigned the "conferre" status. hipposiderids were assigned only to the genus level because barcoding did not provide certainty on species identification in line with previously recognized taxonomic difficulties [ ] [ ] [ ] ; however, the biology of the candidate hipposiderid species is similar ( fig. ; [ , ] ), and we were able to used them for estimation purposes. we excluded scotophilus viridis (n = ) from the analysis because their reproductive traits are unknown, and this species also has taxonomic difficulties for species identification [ ] . therefore, these six individuals were removed, and bats were included in the study. we were able to infer the reproductive season for all bats except for lissonycteris angolensis, rhinolophus cf. clivosus, and pipistrellus cf. hesperidus (n = , adults and juveniles) that had limited available knowledge on biology and reproductive season. these reproductive seasons were imputed as explained above. this imputation process did not substantively affect the proportion of bats in each reproductive period or the crude cov detection per age (additional file : figure s . ). moreover, we had partial data for neoromicia nana and triaenops persicus lactation period and we assigned one that is likely longer than it would be in reality based on the other species. even under this overextended period, none of these bats (n. nana and t. persicus) could have being sampled during the rw season, so this knowledge gap did not risk a misclassification (fig. ) . in the end, and bats were allocated in the n-rw and rw periods, respectively. the distribution of bats across the reproductive periods per age and sampling event was heterogeneous as expected due to the opportunistically nature of sampling. indeed, and adult bats were in the n-rw and rw periods, respectively, while and juvenile bats were sampled in these seasons, respectively. in total, . % bats were positive for covs (n = ). within the subset of adult bats, . % were positive (n = ) while . % of the juvenile bats were positive (n = ). the detection of cov shedding was variable across seasons and bat species, as well as across sampling events ( , , . , and . % for the minimum, maximum, median, and mean detection, respectively). the covs found per species are shown in additional file : table s . a summary of the roosting and reproductive traits of the bat species sampled is provided in table . all bats except n. nana (n = ) and e. helvum (n = ) roosted in "closed" structures, such as caves, abandoned mines, and roofs. within the group of bats using "open" structures, e. helvum was the only species with cov positive individuals. therefore, we did not use this covariate to assess a potential association with cov shedding. the models showed adequate sampling. the markov chain monte carlo chains converged graphically, whilst all gelman-rubin statistics were < . . the selected model had a number of effective samples for each coefficient of at least . the data were properly fitted, as well (additional file : figure s . ), although some predictions lacked precision. the ppds of the fixed coefficients are shown in additional file : figure s . . the selected model to assess periodic differences in cov shedding included season and age, species-specific intercepts, and sampling event-specific intercepts. beyond the species-specific terms, we included a binary categorical covariate equal to for e. helvum and t. persicus and otherwise. we incorporated this term because cov detection in these species was remarkably higher than the other species. as expected, this fixed effect was correlated with the corresponding species-specific intercepts (the remaining correlations were all low); however, we decided to keep it to assess if the main findings hold even when accounting for the bat species with highest detection. the corresponding means, standard deviations, and % hpdi are shown in table . the coefficients' ppds from the selected model indicate an association between age and cov shedding, with juveniles presenting . - . times higher odds to shed compared to adult bats ( % hpdi). the coefficients' ppds also point to an association between the reproductive season and cov shedding as well, with an estimated odds . - . times higher to shed during the period when pups are being compared to other seasons ( % hpdi). the proportions of cov shedders estimated by reversing the % hpdi of the logits were: . - . , . - . , . - . , and . - . for juveniles during the "n-rw" and "rw" periods, and adults during the "n-rw" and "rw" periods, respectively ( % hpdi). these values refer to bats not belonging to the species e. helvum or t. persicus. finally, the predicted cov detections, based on the posterior predictive distributions, were . - . , . - . , . - . , and . - . , for these same groups ( % hpdi; fig. , left) . in practical terms, these last values imply that juveniles during the "rw" period are, on average, . times more likely to be detected shedding covs compared to juveniles in the "n-rw" period. adults during the "rw" period are, on average, . times more likely to be detected shedding covs compared to adults in the "n-rw" period. in both seasons, juveniles are, on average, more likely to shed covs, than adults. the selected model suggests a higher odds of cov detection in e. helvum and t. persicus compared to other species. the species-specific intercept terms, once the e. helvum -t. persicus effect is included, suggest no further differences in terms of cov (fig. , right) ; however, the estimates are not precise. the sampling event-specific random intercepts suggest that a few specific locations could show differential cov shedding but that most of them do not explain further variation (additional file ). if coronavirus shedding by bats follows temporal patterns that are generalizable across species and locations, then mitigation strategies targeting the prevention of human exposure and potential spillover could be directed toward high-risk periods, through mechanisms that can also support bat-human coexistence and the provision of bat ecosystem services. previous research has focused on viral identification in specific locations and in few species [ ] [ ] [ ] [ ] , resulting in a limited representation of viral dynamics in association with few ecological settings, biological traits, and reproductive strategies. additionally, few studies of coronavirus shedding patterns have employed statistical models and, in consequence, the potential complex web of factors and causal relationships that may determine this process has not been fully explored. here, we aimed to address these issues by statistically modeling coronavirus rna detection in several bat species, captured at different times and locations in east africa and involving different ecological contexts and life histories. using data from several hundreds of bats, we found that, beyond spatial, taxonomic, and life history differences; i) the odds of coronavirus shedding is higher during the period when pups are being weaned (up to a month after the lactation period is over), and ii) juvenile bats have higher odds to shed these viruses. moreover, the ratios of predicted detections per bat category (age and reproductive season) suggest that juvenile bats during the recent weaning period have relatively higher shedding compared to bats out of this period no matter their age. caution must be taken with these ratios because we used a logit link and our data had high proportion of cov shedding in specific groups. however, our results are consistent, and they are in agreement with previous research conducted in a restricted number of species and locations. similar seasonality of coronavirus shedding has been observed in germany, australia, thailand, china, and ghana (west africa). in the specific species involved in these previous studies, higher coronavirus shedding and viral loads were detected weeks after the birth pulse [ ] [ ] [ ] [ ] [ ] [ ] ] . further, and consistent with our results, detection of higher levels of coronavirus in juveniles has been reported in micro-as well megabats from africa, asia, europe, and north and south america [ , , , [ ] [ ] [ ] [ ] . it has been proposed that the increased detection of coronaviruses after the birth pulse is attributable to the waning of passively-received maternal antibodies in juveniles [ ] . this idea has been frequently cited; however, we are not aware of any longitudinal age-specific sd standard deviation and %, hpdi = % high posterior density interval coronavirus seroprevalence study in bats. such studies are important to understand the drivers of pathogen persistence and spillover risk, and in consequence, to ethically manage and prevent bat pathogen exposure. nevertheless, this kind of research is difficult to conduct due to logistical challenges, our questionable ability to obtain statisticallyrepresentative samples across age groups, cross-reactivity of serological assays, and the difficulties to differentiate serodynamics derived from closed-population processes from those caused by migratory movements. although extrapolations for antibody dynamics across viruses and species are not simple [ ] , bat serodynamics for hendra virus are congruent with the increased detection of coronaviruses after the birth pulse. pups passively receive maternal hendra virus antibodies which decline after the first month of age up to months of age [ ] [ ] [ ] [ ] . this decline would lead to a period in which young bats tend to be more susceptible to infection, become infected, and then shed virus. consistently, coronavirus shedding peaked weeks after the birth pulse in a german and a chinese species [ , ] and immunologically naïve bats shed higher coronavirus loads [ ] . over time, as young bats clear hendra virus infection, they become seropositive again [ ] [ ] [ ] [ ] . concordantly, capture-mark-recapture studies support the clearance of coronaviruses in infected bats [ , ] , which would become seropositive. however, young bats may not reach adult seroprevalence levels until they are older than a year, as occurs with hendra virus [ , , ] . therefore, the population of juvenile bats would remain comparatively more susceptible to viral infection and shedding beyond the period immediately after weaning. age-specific henipavirus seroprevalence in african e. helvum is in agreement with the serodynamics described for hendra virus [ ] . additionally, coronavirus transmission may be favored by high colony density created by the birth pulse, as previously proposed [ , ] , and then the seasonal influx of susceptible juveniles could accelerate viral spread across the entire colony, including adult bats. indeed, adult myotis macropus in an australian colony showed a peak of coronavirus detection after the birth pulse [ ] . the peak of coronavirus detection for two hipposideros species and nycteris cf. gambiensis sampled in ghana occurred during the months that encompassed the birth pulse and nursing after accounting for the age of the sampled individuals [ ] . higher coronavirus infection has also been reported in lactating females [ , ] , which overlap with the period of pup weaning and decay of maternally-derived immunity; however, the opposite has also been found [ , , ] . in practical terms, public health managers could anticipate high risk periods for coronavirus shedding to target interventions. assuming that higher spillover risk is a function of higher viral shedding [ ] and that all coronaviruses with zoonotic potential behave ecologically similarly to coronaviruses detected in this study, managers could target the prevention of human-bat direct (consumption) or indirect (bat droppings) contact specifically during the high-risk season: around and just after weaning, the timing of observable juveniles or individuals smaller than adults. for the species and interfaces defined herein, those management periods have now been determined (fig. ) . for others, direct observation of bats at high-risk transmission interfaces could be used to identify time periods when non-adult sized bats are present. however, observation of dependent pups is not always easy [ ] . of course, for specific species, birth pulses and lactation seasons could also be used to more precisely establish high risk periods similar to the methods we used here, including a combination of direct observation, reports from previous literature, and consultation with knowledgeable bat biologists. our proposed risk-driven strategy i) is evidence-based, as it builds upon coronavirus shedding patterns observed across several chiropteran species present around the world; ii) does not require the advanced laboratory capacity often lacking in resource-restricted settings where intense bat-human interfaces usually occur; iii) is a good alternative to the ideal but expensive and resourceintensive longitudinal surveys; and iv) it may prevent the exposure to viruses belonging to other taxa whose observed bat shedding dynamics resemble our findings for coronaviruses (e.g. paramyxoviruses [ ] ), the lower coronavirus detections in african emballonurids (c. afra and t. mauritianus) and the higher detections in e. helvum, african hipposiderids (hipposideros sp. and t. persicus), and r. cf. clivosus that we found are consistent with previous reports [ , , , ] and should be considered by managers when providing risk-based spillover prevention strategies. moreover, sars-like coronaviruses in africa have been found in hipposiderid, rhinolophid, and molossid bats [ , , ] , and mers-related coronaviruses have been found in vespertillionid bats [ , , ] . therefore, it seems reasonable to prioritize the identification of birth pulses and lactation seasons, and thus determine high-risk periods of coronavirus shedding, for these bat families. interestingly, e. helvum roost in tight clusters that can contain hundreds of individuals [ ] , similar to t. persicus. on the other hand, emballonurids, showing the lowest crude detection levels across families (represented by coleura afra and taphozous mauritanus here) tend not to cluster while roosting [ , ] . we did find an association between coronavirus shedding and whether the species typically aggregate in clusters while roosting when the variable "e. helvum -t. persicus" was not considered, but we chose a different model not including this term because we did not directly assess bat roosts and our categorization may oversimplify the continuum from mostly solitary roosting (e.g., neromocia nana) to common tight aggregations of bats (e.g., mops condylurus). using this categorization could be misleading, as some species differentially cluster while roosting depending on temperature, colony size, colony type (e.g., maternity colony versus not a maternity colony), and season [ ] . future studies should consider the roosting habits of bats, as this trait could further support riskbased management to prevent or reduce human exposure. the risk-driven strategy we propose provides a contactreduction alternative that is ethically favorable compared to often-employed measures, such as culling or other reactive measures, that ensue when the public becomes aware of a health threat without a suggested practical option to reduce their risk for exposure. in addition to ethical concerns and being logistically difficult and expensive, culling has failed to reduce disease in wild populations and can result in even higher pathogen levels. for example, "badger culling can make no meaningful contribution to cattle tuberculosis control in britain" [ ] . a culling program to reduce echinococcus multilocularis prevalence in red foxes (vulpes vulpes) resulted in an increase of infection [ ] . this strategy has also failed to control rabies in canids around the globe [ ] . similar results have been observed in bats. culling failed to reduce rabies seroprevalence in desmodus rotundus in perú and could have increased the levels of exposure to the virus [ , ] . in argentina, the extermination of bats changed the direction of spread of rabies in livestock but did not prevent its advancement [ ] . in uganda, miners exterminated a colony of rousettus aegyptiacus bats after an outbreak of marburg virus in that involved miners in close contact with these bats. five years later, a new outbreak occurred in miners from the same mine. the second time, marburg virus rna was detected in a higher proportion in the r. aegyptiacus that recolonized the mine ( . %, n = ; [ ] ) compared to rna detection before culling in this cave ( . %, n = ; [ ] ) and other caves in uganda ( . %, n = ; [ ] ) and gabon ( . %, n = ; [ ] ) where culling has never been reported. culling can also cause demographic changes, leading to a higher proportion of juvenile individuals. this change may occur because of a disproportionate cull of older individuals; the potential increase in survival of pups at lower population densities, followed by higher recruitment of juvenile females into reproductive age [ ] ; the hypothetical increase of young dispersers immigrating from neighboring colonies into culled, less dense, and better resourced colonies [ , ] ; or by causing compensatory reproduction [ ] . this last possibility may have not been studied in bats but seems unlikely due to their high conception rates and usual litter size of one. examples of younger populations after culling have been reported in the red deer (cervus elaphus), racoon (procyon lotor), american mink (mustela vison), and australian brushtail possums (trichosurus vulpecula), among others [ ] [ ] [ ] [ ] . as our results and past research consistently show higher viral shedding and detection in young individuals, activities leading to a younger bat population are not advisable for viral spillover management. similar results are expected when fruit bats are culled based on being categorized as "agricultural pests"; therefore, this kind of management may create higher risk of viral exposure to the human population. virological, ecological, and epidemiological research on bats over the last years has helped to identify chiropterans as hosts of zoonotic viruses and to document that human-driven environmental change, human behavior, and human-to-human transmission are the key drivers for the creation of bat-human interfaces, spillover, and epidemics of emergent viruses, respectively [ ] [ ] [ ] . in the context of the current biodiversity and bat conservation crisis [ , ] , we must not omit these facts when attempting to effectively, and responsibly frame and communicate disease risks associated with bats. realistic, data-based risk communication is of paramount importance to avoid framing bats as a threat to humans and to support bat conservation given their important ecological roles [ , ] . with this background, it seems a proper time for the scientific community studying "bat-associated" viruses to move the conversation from bat spillover risk assessments to the planning of pro-biodiversity and subsequently pro-ecosystem strategies aiming to mitigate spillover risk. science is valued not only for the diagnosis of problems but because it finds solutions to them. here, we have attempted to aid the progress of scientific and management dialogue by proposing, not only a management strategy to limit potential coronavirus spillover, but one that is context-and logistically-grounded and pro-conservation, promoting the delivery of the key ecosystem services provided by bats. data from hundreds of bats collected in east-africa show that coronavirus shedding is expected to be more frequent when pups are becoming independent from the dam, independently of the age of the bats, their species, their location, and their life histories; however, the odds of shedding do differ by species. these results can guide temporal-based mitigation strategies to prevent bat-associated coronavirus exposure using non-lethal methods in limited-resource settings, where longitudinal surveillance is not feasible, by identifying high-risk periods for coronavirus shedding when contact with bats should be avoided. supplementary information accompanies this paper at https://doi.org/ . /s - - - . additional file : summary of the inferred start date of the birth pulse, the end of the lactation period, and the start date of the mating period per microchiropteran species. additional file : bibliographic references for the traits of the bat species included in the study. additional file : imputation of the reproductive season to those bats whose biology is insufficiently known. model methods, results, and literature cited. table s . summary of the coefficients' posterior probability distributions of the selected model for the imputation of the reproductive seasons of bats missing this data. figure s carlo iteration. right: the distribution of the crude coronavirus detection per reproductive season across the , markov chain monte carlo sampling iterations after imputing the periods when un-inferred. the black boxplots show the distribution of the coronavirus detection per period, while the light and dark colored boxes above and below show the interquartile detection in non-adults and adult bats, respectively, per period. additional file : table s . summary of the alpha-and betacoronaviruses (alphacov and betacov, respectively) found in the microbats tested. additional file : results of the model to assess the association between cov shedding and the "recent weaning" season in eidolon helvum and microbats. figure s authors' contributions dml = designed the project; collected, analyzed, and interpreted data; and drafted, edited, and prepared the final manuscript and figures. tg = guided laboratory analysis and generated data, especially barcoding and sample testing, and supported manuscript writing. kg, dw, evw, rk = organized data collection and supported manuscript writing. bs, jn, zs, mc = data collection and supported manuscript writing. the predict consortium = provided support in the design and implementation of surveillance and interpretation of data. jkm = designed and supervised the project, including sampling design and data collection; supported data analysis and interpretation; and drafted, edited, and prepared the final manuscript. all authors read and approved the final manuscript. this study was supported by the generous support of the american people through the united states agency for international development (cooperative agreement numbers ghn-a-oo- - - and aid-oaa-a − - ). the contents of this paper are the responsibility of the authors and do not necessarily reflect the views of the us agency for international development or the us government. mammal diversity database. . www.mammaldiversity.org increasing awareness of ecosystem services provided by bats ecosystem services provided by bats bats limit arthropods and herbivory in a tropical forest bats limit insects in a neotropical agroforestry system top-down control of herbivory by birds and bats in the canopy of temperate broad-leaved oaks (quercus robur) bats and birds increase crop yield in tropical agroforestry landscapes brazilian free-tailed bats as insect pest regulators in transgenic and conventional cotton crops economic value of the pest control service provided by brazilian free-tailed bats in south-central texas conservation. economic importance of bats in agriculture economic value of bat predation services--a review and new estimates from macadamia orchards ecological and economic importance of bats the role of frugivorous bats in tropical forest succession coprophagy in a caveadapted salamander; the importance of bat guano examined through nutritional and stable isotope analyses ecosystems of the world subterranean ecosystems investigating the role of bats in emerging zoonoses: balancing ecology, conservation and public health interest. rome: fao bats as viral reservoirs bats: important reservoir hosts of emerging viruses molecular diversity of coronaviruses in bats evolutionary insights into the ecology of coronaviruses ecology, evolution and classification of bat coronaviruses in the aftermath of sars global patterns in coronavirus diversity bats are natural reservoirs of sars-like coronaviruses further evidence for bats as the evolutionary source of middle east respiratory syndrome coronavirus isolation and characterization of a bat sars-like coronavirus that uses the ace receptor intraspecies diversity of sars-like coronaviruses in rhinolophus sinicus and its implications for the origin of sars coronaviruses in humans bat origin of human coronaviruses close relative of human middle east respiratory syndrome coronavirus in bat rooting the phylogenetic tree of mers-coronavirus by characterization of a conspecific virus from an african bat severe acute respiratory syndrome coronavirus-like virus in chinese horseshoe bats middle east respiratory syndrome coronavirus in bats, saudi arabia summary of probable sars cases with onset of illness from middle east respiratory syndrome coronavirus middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation detection of the middle east respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient evidence for camel-to-human transmission of mers coronavirus dbatvir: the database of bat-associated viruses coronavirus diversity, phylogeny and interspecies jumping discovery of a novel swine enteric alphacoronavirus (seacov) in southern china evidence for an ancestral association of human coronavirus e with bats distant relatives of severe acute respiratory syndrome coronavirus and close relatives of human coronavirus e in bats isolation and characterization of a novel bat coronavirus closely related to the direct progenitor of sars coronavirus discovery of novel bat coronaviruses in south china that use the same receptor as mers coronavirus surveillance of bat coronaviruses in kenya identifies relatives of human coronaviruses nl and e and their recombination history detection of alphacoronavirus in velvety free-tailed bats (molossus molossus) and brazilian free-tailed bats (tadarida brasiliensis) from urban area of southern brazil human coronaviruses: insights into environmental resistance and its influence on the development of new antiseptic strategies ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related rhinolophus bat coronavirus in china reveal bats as a reservoir for acute, self-limiting infection that allows recombination events longitudinal study of age-specific pattern of coronavirus infection in lyle's flying fox (pteropus lylei) in thailand persistent or long-term coronavirus infection in australian bats epidemiology and ecology of virus and host: bats and coronaviruses in ghana, west africa, doctor of philosophy dissertation amplification of emerging viruses in a bat colony longitudinal surveillance of sars-like coronaviruses in bats by quantitative real-time pcr global trends in emerging infectious diseases the human/animal interface: emergence and resurgence of zoonotic infectious diseases a strategy to estimate unknown viral diversity in mammals bat coronaviruses and experimental infection of bats, the philippines identification of a severe acute respiratory syndrome coronavirus-like virus in a leaf-nosed bat in nigeria geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit i and cytochrome b gene sequences the barcode of life data system pantheria: a species-level database of life history, ecology, and geography of extant and recently extinct mammals an amniote life-history database to perform comparative analyses with birds, mammals, and reptiles network analysis of host-virus communities in bats and rodents reveals determinants of cross-species transmission diseases and causes of death in european bats: dynamics in disease susceptibility and infection rates evidence of henipavirus infection in west african fruit bats seasonal pulses of marburg virus circulation in juvenile rousettus aegyptiacus bats coincide with periods of increased risk of human infection coordinated change at the colony level in fruit bat fur microbiomes through time a comparative analysis of viral richness and viral sharing in cave-roosting bats cryptic connections illuminate pathogen transmission within community networks host social organization and mating system shape parasite transmission opportunities in three european bat species mammals of africa volume iv-hedgehogs, shrews and bats a probabilistic programming language r: a language and environment for statistical computing. r foundation for statistical computing rstan: the r interface to stan prior distributions for variance parameters in hierarchical models (comment on article by browne and draper) on the half-cauchy prior for a global scale parameter inference from iterative simulation using multiple sequences mammal species of the world: a taxonomic and geographic reference morphologically uniform bats hipposideros aff. ruber (hipposideridae) exhibit high mitochondrial genetic diversity in southeastern senegal variation of mitochondrial dna in the hipposideros caffer complex (chiroptera: hipposideridae) and its taxonomic implications mammals of africa volume iv: bats and shrews hipposideros cafer sundevall's roundleaf bat elucidating the species limits and range boundaries of the african yellow house bats, genus scotophilus. senior thesis australian bat coronaviruses, philosophical doctor thesis detection and prevalence patterns of group i coronaviruses in bats, northern germany identification of sars-like coronaviruses in horseshoe bats (rhinolophus hipposideros) in slovenia alphacoronaviruses in new world bats: prevalence, persistence, phylogeny, and potential for interaction with humans human betacoronavirus c emc/ -related viruses in bats, ghana and europe support for viral persistence in bats from age-specific serology and models of maternal immunity reproduction and nutritional stress are risk factors for hendra virus infection in little red flying foxes (pteropus scapulatus) duration of maternal antibodies against canine distemper virus and hendra virus in pteropid bats henipavirus neutralising antibodies in an isolated island population of african fruit bats evidence of endemic hendra virus infection in flying-foxes (pteropus conspicillatus)-implications for disease risk management persistent infections support maintenance of a coronavirus in a population of australian bats (myotis macropus) how does africa's most hunted bat vary across the continent? population traits of the straw-coloured fruit bat (eidolon helvum) and its interactions with humans leptospira and paramyxovirus infection dynamics in a bat maternity enlightens pathogen maintenance in wildlife detection of novel sars-like and other coronaviruses in bats from kenya independent scientific group on cattle tb. bovine tb: the scientific evidence. london: defra publications echinococcus multilocularis management by fox culling: an inappropriate paradigm evidence-based control of canine rabies: a critical review of population density reduction ecological and anthropogenic drivers of rabies exposure in vampire bats: implications for transmission and control resolving the roles of immunity, pathogenesis, and immigration for rabies persistence in vampire bats control of bovine rabies through vampire bat control marburgvirus resurgence in kitaka mine bat population after extermination attempts isolation of genetically diverse marburg viruses from egyptian fruit bats is marburg virus enzootic in gabon? impact of human disturbance, density, and environmental conditions on the survival probabilities of pipistrelle bat (pipistrellus pipistrellus) bats and emerging zoonoses: henipaviruses and sars compensatory reproduction in feral horses consequences of harvesting on age structure, sex ratio and population dynamics of red deer cervus elaphus in central norway effects of culling on mesopredator population dynamics demography of three populations of american mink mustela vison in europe effects of intensive trapping on breeding and age structure of brushtail possums, trichosurus vulpecula the consequences of human actions on risks for infectious diseases: a review factors in the emergence of infectious diseases human ecology in pathogenic landscapes: two hypotheses on how land use change drives viral emergence accelerated modern human-induced species losses: entering the sixth mass extinction bats in the anthropocene the role of one health in wildlife conservation: a challenge and opportunity the role of protected areas in supporting human health: a call to broaden the assessment of conservation outcomes publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations we appreciate the support of the american people through the united states agency for international development (usaid) emerging pandemic threats predict project (cooperative agreement number ghn-a-oo- - - ). we thank the governments of rwanda, tanzania, and uganda for permission to conduct this study, and the country predict teams that led and conducted the field activities. we are mostly grateful of all the technicians involved in the processing, testing, and barcoding of the samples, especially ruth maganga (sokoine university of agriculture) and brett smith (one health institute, university of california -davis). finally, we appreciate the help of dr. evan eskew for supporting with stan coding and dr. wes johnson for guidance with bayesian inference. key: cord- -joiajgs authors: shah, vibhuti kumar; firmal, priyanka; alam, aftab; ganguly, dipyaman; chattopadhyay, samit title: overview of immune response during sars-cov- infection: lessons from the past date: - - journal: front immunol doi: . /fimmu. . sha: doc_id: cord_uid: joiajgs after the flu pandemic, the world is again facing a similar situation. however, the advancement in medical science has made it possible to identify that the novel infectious agent is from the coronavirus family. rapid genome sequencing by various groups helped in identifying the structure and function of the virus, its immunogenicity in diverse populations, and potential preventive measures. coronavirus attacks the respiratory system, causing pneumonia and lymphopenia in infected individuals. viral components like spike and nucleocapsid proteins trigger an immune response in the host to eliminate the virus. these viral antigens can be either recognized by the b cells or presented by mhc complexes to the t cells, resulting in antibody production, increased cytokine secretion, and cytolytic activity in the acute phase of infection. genetic polymorphism in mhc enables it to present some of the t cell epitopes very well over the other mhc alleles. the association of mhc alleles and its downregulated expression has been correlated with disease severity against influenza and coronaviruses. studies have reported that infected individuals can, after recovery, induce strong protective responses by generating a memory t-cell pool against sars-cov and mers-cov. these memory t cells were not persistent in the long term and, upon reactivation, caused local damage due to cross-reactivity. so far, the reports suggest that sars-cov- , which is highly contagious, shows related symptoms in three different stages and develops an exhaustive t-cell pool at higher loads of viral infection. as there are no specific treatments available for this novel coronavirus, numerous small molecular drugs that are being used for the treatment of diseases like sars, mers, hiv, ebola, malaria, and tuberculosis are being given to covid- patients, and clinical trials for many such drugs have already begun. a classical immunotherapy of convalescent plasma transfusion from recovered patients has also been initiated for the neutralization of viremia in terminally ill covid- patients. due to the limitations of plasma transfusion, researchers are now focusing on developing neutralizing antibodies against virus particles along with immuno-modulation of cytokines like il- , type i interferons (ifns), and tnf-α that could help in combating the infection. this review highlights the similarities of the coronaviruses that caused sars and mers to the novel sars-cov- in relation to their pathogenicity and immunogenicity and also focuses on various treatment strategies that could be employed for curing covid- . the whole world is currently confronting a crisis situation that first appeared in late december as merely a few cases of pneumonia in wuhan, china. the patients were exhibiting common symptoms like fever, dry cough, sore throat, breathlessness, and fatigue. sample swabs from the oral cavity and anal region were collected along with the blood and bronchoalveolar lavage fluid (balf) from all seven of the patients, irrespective of their age and gender, which were then sent to the wuhan institute of virology for further examination. as the outbreak initiated at the seafood market with the onset of winter, similar to that of the previous severe acute respiratory syndrome (sars) infection, the scientists first screened the samples using pan-cov qpcr primers. surprisingly, five samples were reported positive for coronavirus. thorough investigation employing next-generation sequencing and phylogenetic analysis led to the identification of the causative agent of this respiratory disease, a novel coronavirus ( -ncov) ( ) . as more cases started to appear around the world, on february , , the world health organization assigned a name, corona virus disease or covid- , to the disease and declared it a pandemic on march , . the virus was renamed from -ncov to sars-cov- by the international committee on taxonomy of viruses on the basis of its genetic similarity to a previously known coronavirus, severe acute respiratory syndrome coronavirus (sars-cov) ( ) . transmission of sars-cov- occurs when a healthy individual inhales or comes into contact with respiratory droplets from an infected person. the average incubation period before patients exhibit disease symptoms ranges from to days ( ) . before the spread of covid- , sars emerged as an epidemic in , followed by middle east respiratory syndrome (mers) in , both caused by a novel coronavirus of zoonotic origin and assigned to the genus betacoronavirus ( ) . the worldwide outbreak of sars-cov- has put life on hold, having a major impact on the world's economy, and has claimed ∼ , lives globally as of june , ( , ) . unlike previous episodes of coronavirus spread, where it took months to identify the cause of infection and perform genome sequencing ( ) , advancement in science and technology made it possible to identify the causative organism swiftly. within a few weeks of the outbreak, different laboratories across the world had sequenced the whole viral genome and had also provided structural and functional insights into the essential proteins required by the virus for its survival. these immediate scientific inputs helped with developing diagnostic kits and defining treatment strategies for effective prognosis and prevention ( ) ( ) ( ) . in this review, we are emphasizing the immunological aspect of sars-cov- pathogenesis by taking into consideration the previous experimental and clinical knowledge obtained from the coronaviruses that were responsible for causing sars and mers. this approach will assist in utilizing immunotherapies, repurposing the previously approved antiviral drugs, and developing therapeutic vaccines specific to novel coronavirus more effectively. initial genome sequencing and phylogenetic analysis of novel coronavirus sars-cov- has shown that it is genetically similar to previously known coronavirus sars-cov and hence is placed under the family coronaviridae. coronavirus contains positivesense single-stranded rna (+ve ssrna) as its genetic material, which can be about kb in length and is mostly protected by an outer fatty layer of an envelope that also helps the virus to evade host immune response and assists its entry inside the host cell ( , ) . the subfamily coronavirinae is further subdivided into four genera, namely alpha-, beta-, gamma-, and delta-coronavirus (α-cov, β-cov, γ-cov, and δ-cov). viruses having the potential to infect humans are placed under the genus α-cov and β-cov (sars-cov & mers-cov), whereas viruses of γ-cov and δ-cov genera are mostly known to infect avians and pigs ( ) . the novel coronavirus, sars-cov- falls under the genus β-cov, as it shares % sequence identity with sars-cov-like coronaviruses (derived from bat) but is only % identical to sars-cov and % identical to mers-cov ( ) . thus, it can be deduced by its genome identity that the immediate host of this virus could be a bat, which then transmitted it to some unknown intermediate host that acted as a source for the transmission of the virus to humans. like those of sars-cov and mers-cov, the sars-cov- genome comprises of open reading frames (orfs) in number. at the ′ end of the viral genome, overlapping orfs a and b are present that encode the rna polymerase and other nonstructural proteins of the virus and occupy approximately twothirds of the genome. genes encoding structural proteins such as spike (s), membrane (m), envelope (e), and nucleocapsid (n), are present in the remaining one-third of its genome spanning from the ′ to the ′ terminal, along with several genes encoding non-structural proteins (nsps) and accessory proteins scattered in between, as shown in figure . despite being in the same serogroup, there is a slight difference in the nucleotide number, sequence, gene order, and expression method among previously known coronaviruses and the novel sars-cov- ( , , ) . recent reports highlight that a few amino acid substitutions have occurred in the novel coronavirus genes encoding the s protein, nsp , nsp , and receptor-binding domain (rbd). these mutations in the nsp & nsp are also believed to impart the enhanced infection abilities of the novel coronavirus ( , ) . rna viruses are prone to acquiring genetic mutations that eventually help them to escape the host immune system and develop drug resistance. researchers have also found minor mutations in sars-cov- genotype in different covid- patients ( ) . one such hotspot of mutation in the sars-cov- genome is the rna-dependent rna polymerase gene. on analyzing sequences across the globe, eight repetitive novel point mutations were observed. viral genetic sequences accessed from europe exhibited five mutation hotspots, whereas the remaining three point mutations were solely present in the sequences from north america. these unique mutations suggest that the viral strains are continuously evolving across the globe figure | schematic representation of the coronavirus structure and genomic comparison of coronaviruses. (a) representation of coronavirus showing different components of the particle, which is - nm in diameter. the single-stranded rna (ssrna) genome, covered with the envelope and membrane proteins, gains access into the host cell and hijacks the replication machinery. (b) the ssrna of sars-cov- is about kb and has similarities with the genomes of sars-cov and mers-cov. translation of this ssrna results in the formation of two polyproteins, namely pp a and pp ab, that are further sliced to generate numerous non-structural proteins (nsps). the remaining orfs encode for various structural and accessory proteins that help in assembly of the viral particle and evading immune response. and that the strains from europe, north america, and asia might have co-existed the whole time ( ) . another similar report analyzed , global viral genomic sequences and found unique mutation sites on sars-cov- genome that encodes nsps and s protein, suggesting that the virus is trying to adapt to its new host ( ) . as numerous drugs are currently being designed to target the proteins that are essential for the survival of the virus, rapid genetic mutation occurring in these proteins might not prove to be a potential candidate for drug design. therefore, the invariable region of the virus could be a better target to avoid drug failures. interestingly, sars-cov- , similar to sars-cov, exploits the angiotensin-converting enzyme (ace ) receptor to gain access inside human cells, whereas mers-cov binds specifically to dipeptidyl peptidase (dpp ) receptor ( , ) . binding of the virus particle to the specific receptor on the host cell plays a key role in governing its pathogenicity. functional evaluation was carried out to reveal the potential receptors for different betacoronaviruses (β-cov) including sars-cov- , and it was found out that the entry of the virus particle was enhanced in human cells expressing ace receptor instead of dpp or aminopeptidase n (apn) in the case of the novel coronavirus ( ) . recent structural insights provided by cryo-em studies of s protein in prefusion conformation highlighted that the binding efficiency of ace and s protein of sars-cov- is - times greater than for the previously known sars-cov ( , ) . the latest reports suggest that the trimeric s protein of sars-cov- is sliced by transmembrane protease serine (tmprss ), similar to sars-cov ( , ) . hence, profound knowledge of the potential receptors to which the virus particle can bind and its associated proteases will help us in designing specific antiviral drugs and neutralizing antibodies and will lead us to foresee whether particular coronaviruses of zoonotic origin could be able to adapt and infect humans. all coronaviruses initiate entry inside the target cell by engaging the host receptor with the s glycoprotein present on their surface so as to gain entry inside the target cell. the region of s protein containing the rbd is present on the s subunit. in a few coronaviruses, rbd is present at the n-terminus region of s , whereas in sars-cov, it is situated at the c-terminus region ( , ) . the fusogenic activity of virus-cell membrane is governed by two tandem domains, heptad repeats (hr , ) that are present on the s region of s protein ( , ) . initially, it was believed that sars-cov enters the target cell merely by virtue of cell membrane integration of virus particle and host cell membrane ( ) . later, it was discovered that an essential proteolytic cleavage event takes place in the s protein at the s position of sars-cov that results in membrane fusion and facilitates virus entry inside the cell ( ) . once the coronavirus is inside the host cell via membrane fusion, it releases its +ve ssrna genome into the cytoplasmic compartment, where the translation of orf- a and orf- b begins resulting in the formation of two large polyproteins (pp a and pp ab). three functional proteases then cleave the polyproteins into non-structural proteins (nsp - ), which eventually create the viral rna polymerase and other accessory proteins for virus assembly ( ) ( ) ( ) . an uninterrupted replication-transcription event results in the formation of various nested sets of subgenomic (sg) mrnas that eventually translate into numerous structural and accessory proteins ( ) . the e glycoproteins after synthesis are incorporated into the rough endoplasmic reticulum or golgi membrane. the +ve ssrna combines with capsid protein to form the nucleocapsid, followed by budding of assembled virus particles in the er-golgi intermediate compartment (ergic) ( ) . lastly, the virus particle-loaded vesicles are fused with the cell membrane for effective shedding of the virus ( ). these new virions are now accessible to infect the neighboring healthy cells and are also released into the surrounding environment via respiratory droplets that are highly contagious and hence potentially spread the disease to healthy individuals. the path followed by sars-cov- to reach the lungs is via the naso-oral cavity. once the virus is inhaled, it enters the epithelial cells of the nasal cavity by engagement of ace receptor with the viral rbd and initiates its replication ( , , ) . this initial asymptomatic phase lasts for about - days, during which the virus multiplies in the upper respiratory tract, where no major hindrance is caused by the innate immune cells. within - days of initial encounter, the common symptoms of covid- start to appear, which are similar to those of sars and mers, i.e., fever, dry cough, pharyngitis, shortness of breath, joint pain, and tiredness. numerous problems arise during this phase of the disease, including nosocomial and fomite transmission of infection, which enhances the chances of community spread ( ) . soon, the virus begins to move toward the lower respiratory tract via airways, and this triggers a strong innate immune response. patients at this stage start exhibiting enhanced pro-inflammatory response that leads to viral sepsis accompanied by other complications, including pulmonary edema, acute respiratory distress syndrome (ards), different organ failures, and death in the worst scenarios ( ) . the infected individuals rarely show the intestinal symptoms like diarrhea that were evident in other coronavirus infections. patients are recommended to be quarantined to prevent community spread of this pandemic virus ( ) . the severity of covid- has been found to be greater in aged individuals and in people with a health history, such as those immune-compromised by hiv infection or by chemotherapy for cancer. diabetic and asthma patients, along with individuals with hypertension, obesity, or heart, kidney, or liver disorders, are also at higher risk if they acquire the disease ( ) . autopsy reports of individuals who died due to sars show multi-organ dysfunction, with the highest viral titers in the lungs and immune cells in circulation, thus damaging the pulmonary and immune system ( , ) . as opposed to adults, only a very small population of children has been infected with sars-cov- . in one study, the symptoms displayed by children above years were found to be milder as compared to those of younger children, who showed severe symptoms but with rare deaths and better prognosis ( ) . the study speculated two major possibilities related to covid- severity in children among different age groups. one of these rests on the finding that ace activity is higher in children aged - years; after this age, it starts to decline until adolescence. this could be one of the reasons why lung fibrosis is observed mainly in younger children. secondly, differential cd + and cd + t cell populations have been seen in children as compared to adults ( , ) . a large number of clinical and epidemiological criteria were defined to assess probable pediatric cases of covid- ( ) . a preliminary report from a cross-sectional study of children admitted to us and canadian pediatric intensive care units (picus) during march -april , , revealed that the children were admitted in the usa whereas no covid- cases were reported in canadian picus. the study revealed that there are fewer covid- cases in children as compared to adults and that there is a median picu time of days ( ). a recent preprint from paris reports that children (age . - . ) were admitted experiencing symptoms similar to kawasaki disease (kd) along with gastrointestinal issues and elevated inflammatory markers. further investigation suggested that they were also sars-cov- -positive, speculating that this could be the reason for kd shock syndrome ( ) . similar cases have been observed in new york, where four otherwise healthy sars-cov- -positive children started displaying symptoms similar to kd and toxic shock syndrome, thereby needing intensive care ( ) . therefore, medical practitioners should be prepared to tackle such sudden post-infection complications to avoid the associated risks. once the virus gains access inside the target cell, the host immune system recognizes the whole virus or its surface epitopes, eliciting the innate or adaptive immune response (figure ). pathogen recognition receptors (prrs) present on immune cells, mainly toll-like receptors , , and , are the first to identify the virus, which leads to enhanced interferon (ifn) production. the function of host innate immune cells is impaired during sars-cov and mers-cov infection by their non-structural proteins, which affects the overall cytokine production ( ) ( ) ( ) . humoral response against sars-cov- has been found to be similar to that against other coronavirus infections, involving the characteristic igg and igm production. at the onset of sars-cov infection, b cells elicit an early response against the n protein, while antibodies against s protein could be detected after - days from the appearance of initial symptoms ( , ) . although n protein is smaller than s protein, it is highly immunogenic, and the absence of glycosylation sites on it results in n-specific neutralizing antibody production at an early stage of acute infection ( ) . sars-cov-specific iga, igg, and igm antibodies were detected after the onset of symptoms at different time points in infected patients. a persistent level of igg was detected for a longer period, whereas igm levels started to decline after months ( , ) . in an observational case study of sars-cov- patients, anti-s-rbd igg was detected in all of the subjects, whereas anti-n igg and anti-s-rbd igm were detected in patients and anti-n igm in patients ( ) . an elisa-based time kinetics study to detect the covid- specific humoral immune response showed that the patients produced igm and igg antibodies that did not cross-react with other human coronaviruses except sars-cov. igm and iga antibodies were detected days after the onset of initial symptoms, whereas igg was detected after days ( ) . another kinetic study of viral shedding and antibody detection was published in a preprint and reported the presence of higher igg and igm antibody titers in severe patients. they also observed that weak responders for igg antibody had higher viral clearance than strong responders. this observation suggests that robust antibody response leads to disease severity while feeble response is associated with the elimination of virus ( ) . a case study on pediatric patients reports that out of children showed a protective humoral response, with neutralizing igg and igm antibodies targeting the n and s-rbd proteins of sars-cov- ( ) . these studies propose that igm-based elisa can be used for early diagnosis of patients along with qpcr techniques to improve the sensitivity and specificity of the technique. in addition to neutralizing antibodies, which are defensive and useful, there are numerous non-neutralizing antibodies in the system that aid the infection of immune cells and apcs. previously existing sars-cov antibodies may promote the viral infection in fcr-expressing cells ( ) . this ace -independent pathway of viral entry does not result in viral replication; rather, viral shedding by macrophages enhances inflammation and tissue injury by myeloid cell activation. this mechanism of viral entry through non-neutralizing antibody that results in aberrant activation of immune cells is called ade (antibody-dependent enhancement) ( , ) . ade has been observed in a number of viral infections, including sars and mers. in the case of sars, anti-s antibodies were observed to be involved in ade to gain entry into fcr-expressing cells ( ) , while in mers, a neutralizing mab (mersmab ) targeting rbd aided in mers pseudo-virus entry via the dpp pathway ( ) . although there is no clear evidence regarding ade in sars-cov- infection, it is still necessary to consider all of the odds in the pursuit of developing vaccines and treatment regimens involving antibodies ( ) . during viral infection, t cells also recognize the viral antigens presented by mhc class i [mhc; human leukocyte antigen (hla) in humans], which in turn promotes the cytokine release and cytotoxic activity of cd + t cells ( ) . but in some other cases, mhc class ii is also found to present sars-cov peptides to cd + t cells. due to the genetic polymorphism of hla, some haplotypes, like hla-b * , hla-b * , hla-drb * ( ) , and hla-cw * ( ) , are found to be more susceptible to coronavirus infection, whereas the hla-drb * , hla-a * , and hla-cw * haplotypes are protected from sars-cov infection ( ) . similarly, hla-drb * and hla-dqb * were found to be vulnerable to mers-cov infection ( ) . additionally, mhc expression is also found to be reduced during the infection due to epigenetic modifications of downstream molecules ( , ) . so far, hla association is not very wellidentified for sars-cov- infection, and this could be crucial for the prevention and treatment of covid- . however, in a recent report, blood plasma from covid- patients was able to block the expression of hla-dr on cd + monocytes, which was restored effectively on inhibiting il- , suggesting that decreased hla-dr expression in sars-cov- patients is due to the buildup of hyper-inflammatory conditions ( ) . decrease in mhc expression is also evident in cancer cells, which is a mechanism by which they evade the immune response by epigenetically modifying calnexin promoter. but infection with influenza virus in these cancer cells results in enhanced mhc-i presentation due to the increased expression of chromatin remodeling proteins, which stabilizes p expression and hence augments the immune surveillance of cancer cells ( ) . therefore, molecules that can upregulate chromatin regulators and increase the mhc-i expression could potentially be used for covid- . most of the t-cell epitopes presented by mhc complex are derived from structural proteins such as the s and n proteins of the coronavirus in both humans and animal models, while the nsps have regulatory effects on the signaling cascade ( , ) . t cells can be stimulated by epitopes, most of which are observed to be located on orf and the s protein in sars patients ( ) . in a large cohort study during sars-cov infection, s protein was the only immuno-dominant epitope for cd + t-cell activation ( ) , whereas, in mers, cd + response was against the s and n proteins along with some of the m/e epitopes ( ) . these t-cell epitopes have been tested in animal models by assessing the lung pathology and t-cell response upon infection in balb/c and c bl/ mice ( , ). the sequence of sars-cov- being more similar to sars-cov than to mers-cov, with no mutation in epitopes, provides a prospective subunit vaccine for stimulating a strong t-cell response in covid patients ( ) . in a recent study, samples from convalescing covid- patients were analyzed to check the development of adaptive immune response during infection. the results highlighted that helper t cells were eliciting a robust immune response against s, m, and n protein. the effect of adaptive immune response on humoral immunity was also compared, where a strong cd + t-cell response against sars-cov- eventually resulted in an increase in anti-s-rbdspecific igg and iga antibody titer. along with cd + t cells, immunogenic epitopes on s, m, and n proteins were also able to activate cd + t cells. however, such t-cell response was not specific to recovered patients only but was also present in - % of the individuals who were not exposed to sars-cov- . further analysis showed that they had pre-existing cross-reactive cd + t cells, which might have been generated in response to some previous coronavirus infection. hence, these t-cells could impart protective immunity in such individuals against sars-cov- to some extent ( ) . these epitopes could be a promising factor in developing immunotherapy by small molecules that can increase the presentation of viral epitopes. a rapid and coordinated immune response during viral infection leads to enhanced secretion of various cytokines, which acts as a defense mechanism against the virus. numerous reports suggest that individuals affected with sars-cov or mers-cov have dysregulated cytokine production from both innate and adaptive immune cells. in the case of sars, infected hematopoietic cell, monocyte-macrophages, and other immune cells trigger enhanced secretion of pro-inflammatory cytokines like tnf-α, il- , and ifn-α/-γ, with reduced anti-inflammatory cytokines ( ) ( ) ( ) . similarly, mers-cov infection leads to delayed but increased production of ifn-α and pro-inflammatory cytokines like il- , il- , and il- β ( ) ( ) ( ) . such elevated levels of cytokines were associated with multi-organ dysfunctional syndrome (mods) and ards due to the accumulation of numerous immune cells like macrophages, neutrophils, and dendritic cells in the lungs causing alveolar damage and edema ( , , ) . similarly, in covid- patients, secretion of cytokines and chemokines, which attract the immune cells to the lungs, was increased, hence causing ards, which is fatal to critically ill individuals ( , ) . signature cytokines in severely ill covid- patients were consistent with those in sars and mers, i.e., enhanced expression of il- , tnf-α, macrophage inflammatory protein -α (mip- α), mcp , gm-csf, il- , and ip- along with elevated chemokines (ip- , ccl /mcp , cxcl , cxcl ) were also detected in sars-cov- infection ( ) ( ) ( ) ( ) . in children, the increased inflammatory markers include il- , il- , and c-reactive protein along with procalcitonin in serum ( ) . in a case study, a -year-old child with cytokine storm was treated with anakinra (il- receptor antagonist) in order to stabilize the respiratory illness and other clinical symptoms ( ) . transcriptomic analysis of pbmc and balf showed that a number of immune regulators were upregulated, particularly cxcl , with respect to balf. this study also reported that several apoptotic genes and p signaling molecules were upregulated, suggesting a possible reason for lymphopenia in these patients ( ) . therapeutic measures to control such cytokines involve neutralizing antibodies or small molecular drugs that can stop the signaling cascade for cytokine production. the most potent antiviral machinery acquired by immune cells is the secretion of interferons that act as secondary messengers stimulating the neighboring cells. most innate immune cells are efficient in producing ifns that are involved in obstructing cell proliferation, apoptosis, and immunomodulation ( , ) . as an escape mechanism, sars-cov or mers-cov uses several ways to overcome the host immune response, one of which is by severe leukopenia and lymphopenia ( ) ( ) ( ) . after gaining entry to the cell, these viruses encode different proteins that interact with downstream signaling molecules of tlrs and the jak-stat pathway. mers-cov encoded matrix protein, accessory proteins from orf a, b, and , which directly inhibits the ifn promoter and nuclear localization of irf ( ) . plpro, encoded by sars-cov and mers-cov, prevents the dissociation of nf-κb from iκbα, whereas nonstructural proteins of sars-cov, i.e., plpro and orf b, inhibit irf phosphorylation and hence its translocation to the nucleus ( , , ). these viral accessory proteins also inhibit the jak-stat pathway, resulting in inhibition of genes by isre promoters ( ) ( ) ( ) (figure ) . a new investigation revealed that sars-cov- infection leads to an overall decrease in the transcription of antiviral genes because of the lower production of type i and iii interferons with sufficient isg expression, along with elevated chemokine secretion. results obtained from in-vivo and ex-vivo covid- experiments were in tune with the in-vitro findings. therefore, a decrease in the innate antiviral response, along with hyper-inflammation, could be one of the causes of covid- severity ( ) . in addition to reduction in t cells, sars-cov- infection also enhances the exhaustion of effector t cells, decreasing the immune response against the virus ( , ) . exhaustion and loss in function of effector t cells is the result of increased expression of inhibitory receptors like pd- , tim- , and tigit on its surface as a result of cytokines like il- , il- , and tnf-α or by decreasing the regulatory t-cell population ( , ) . following viral/antigen clearance, most of the effector t cell undergoes apoptosis in the contraction phase. subsequently, a pool of memory t cells are generated that are programmed to fight against re-infection. cd + memory t cells, upon restimulation, trigger b cells and other immune cells by cytokine production, while cytotoxic memory t cells help in destroying the infected cells during subsequent infection ( , ). case studies in recovered sars patients showed that both cd + and cd + memory t cells were efficient in eliciting immune response from months to years without the presence of any antigens ( ) . in a case study of recovered sars-cov patients, the patients showed very low frequencies of memory b cells, while memory t cells elicited a response against the s protein in % of recovered individuals ( ) . considering the memory t-cell subset, n-specific helper t cells had more of central memory markers (cd ra − , ccr + , cd l − ) while the cd + t cell population had the effector memory (cd ra + , ccr − , cd l − ) phenotype in a steady-state manner ( ) . the study suggests that an effective vaccine or t cell epitopes could be used to target a particular population for rapid viral clearance. in recent reports, covid- subjects have shown reduced regulatory t cell populations and memory t cells, which may aggravate the inflammatory response leading to cytokine storm and hence enhance the tissue damage and organ failure ( ) . in a mouse model, the use of cd + memory t cells as a vaccine by the intranasal, but not the subcutaneous, route imparted a protective response against the human coronavirus. the infused cd + memory t cell, upon re-stimulation, produces ifn-γ and recruits cd + t cells for rapid clearance in response to sars-s peptide ( ) . recently, a human ace- -expressing mouse model has been developed by crispr/cas technology that recapitulates the human symptoms upon infection with sars-cov- through the intra-nasal route. this tool will be beneficial for evaluating the efficacy of vaccines for covid- and also to study its transmission and pathogenesis ( ) . just like sars and mers, there are no specific clinically approved drugs available for covid- as of june , ( ) . currently, the treatment regime focuses mainly on providing intensive care in order to alleviate the symptoms and discomfort associated with covid- . conservative fluid therapy accompanied by broad-spectrum antibiotics are also given to the patients as a protective measure to avoid opportunistic bacterial infections. however, ventilator support for respiration is provided to the patient under extreme conditions ( ) . numerous fda-approved antiviral drugs, vaccines, and immunotherapies that are already being used to treat other diseases have also been considered as a possible approach for treating covid- ( table ) . but this approach may reduce the availability of these drugs and vaccines for the intended diseases and for the patients with the greatest need. the molecular, structural, and functional relationships of lopinavir viral protease involved in immature, noninfectious hiv virus particle, and inhibits plpro or clpro in sars-cov- . favilavir viral rna polymerase purine analog blocking viral rna synthesis. remdesivir ( ) ribavirin guanosine nucleoside binds to nucleoside binding pocket of the enzyme. ( , , ) galidesivir adenosine analog, effective against ebola, zika, and other rna viruses. chloroquine/hydroxychloroquine heme polymerase and ace increases endosomal ph and terminal glycosylation of ace , inhibiting sars-cov- entry. ( , ) nitazoxanide glutathione-s-transferase alters ph and inhibits viral maturation. reported against tb, helminthic, and protozoan infection. umifenovir/arbidol n/a interacts with aromatic residues of viral glycoproteins. is being trialed for prophylactic action against covid- . sars-cov- with sars-cov might define the use of existing anti-viral drugs against covid- ( , ) , considering the total time it takes to perform clinical trials and get fda approval for the use of novel drugs and vaccines. the increasing knowledge of the genetic, immunological, and molecular mechanisms behind its enhanced pathogenicity might help in developing specific treatment approaches for covid- in the future. considering the studies on the molecular mechanism of coronavirus infection ( ) , several antiviral drugs could be repurposed for the treatment of covid- . remdesivir is a nucleotide analog that acts as an antiviral agent for a wide variety of viruses and has been tested widely against previous epidemics of coronavirus infections in both in-vitro and in-vivo models ( , ( ) ( ) ( ) . this adenosine analog gets incorporated into the newly synthesized viral rna, which inhibits the addition of further nucleotides by viral rnadependent rna polymerase and hence terminates the ongoing transcription. administration of intravenous remdesivir was found to be effective in treating the first known patient of covid- in the usa ( ) . a randomized double-blinded clinical trial on , adult hospitalized covid- patients was sponsored by the national institute of allergy and infectious diseases, usa, to further test the potency of intravenously administered remdesivir. the preliminary outcomes of the trial reported that remdesivir treatment decreased the median recovery time in the treatment group ( days) as compared to the placebo group ( days). the mortality rate was also less in the treatment group ( . %) in contrast to the placebo group ( . %) ( ) . numerous clinical studies, similar to this, are required so as to validate the proposed drugs for covid- . favipiravir, ribavirin, and galidesivir are also potential nucleoside analogs that might be useful against novel coronavirus infection ( ) . the combinatorial therapy approach of using remdesivir along with chloroquine, a well-known anti-malarial drug, has also been tested in vitro so as to study its effectiveness against sars-cov- ( , ) . it has been reported that chloroquine immuno-modulates the host microenvironment and also interferes with the replication of the virus and its interaction with the receptor ( , ) . in a randomized clinical trial (nct ) involving asymptomatic individuals across the us and canada who had come into close contact with potential covid- patients, the individuals were given either hydroxychloroquine or placebo as a prophylactic measure. the results revealed that hydroxychloroquine treatment had the same effect as did the placebo group. the usage of hydroxychloroquine resulted in minor side effects ( . %) as compared to the placebo treatment ( . %). however, no cardiovascular disorder or treatment-related major complications were observed ( ) . based on the putative function of hydroxychloroquine on the endosomal acidification, whereby it is presumed to hinder viral uncapping, it can be observed that it has a great potential for prophylaxis, not to prevent infection but to reduce effective viral load in patients and thus lead to milder disease. numerous clinical trials to further explore the usage of hydroxychloroquine in different combinations are in the pipeline and will finally provide a better understanding of the efficacy of this drug for covid- . a few anti-hiv drugs, such as lopinavir/ritonavir in combination with interferon beta (ifn-β), have been tested in vivo for treating coronavirus infections (sars-cov, mers-cov) and have also been used in the case of covid- ( , , ) . various complementary therapies could also be employed as a preventive measure against viral infections. many essential proteases, such as chymotrypsin ( c-like protease) and plpro, which are required by coronavirus for completing the replication process, can also be targeted using drugs. cinanserin, flavonoids, and some small molecules are known to inhibit clpro, whereas diarylheptanoids are used to inhibit plpro ( ) ( ) ( ) . in a recent study, potential anti-hcov drugs were identified through a systems biology-based approach, such as melatonin, mercaptopurine, sirolimus, dactiomycin, and toremifene, which are to be tested further for their potency ( ) . in the absence of any dependable vaccine or drugs with tested efficacy and when the pandemic onslaught is ongoing, a worthy therapeutic approach is passive immunization using purified antibodies. the source of such antibodies could be the sera of convalescing individuals, mabs, or genetically modified antibodies from an animal host, which can efficiently neutralize the virus. this is an age-old practice, with pioneering work having been done by the nobel laureate, emil behring, who applied this approach for diphtheria, and has been used whenever there are sudden outbreaks of viral diseases like sars, mers, h n , h n , ebola, and many others ( , , ) . as opposed to active vaccination, plasma therapy is the only means to provide immediate immunity for viral clearance, as in the case of sars-cov- . as in other epidemic diseases, convalescent sera are currently being employed for covid- in a number of countries ( , ) . although a randomized controlled trial is yet to be reported, limited studies in patients have been documented with no remission of severe respiratory afflictions on receiving neutralizing antibodies from convalesced donors with antibody titers of : , along with drugs and oxygen support ( ) . a report from hong kong suggested that this therapy had poor outcome in sars patients, with a number of limitations in their study ( ) . as with transfusion of any blood products, precautionary screening of infectious agent is warranted in plasma transfusion. recently, the fda in the usa has approved trials of convalescent plasma therapy in covid- under specific guidelines; plasma donation is advised weeks after a patient becomes virus-negative on pcr. the major challenge in this therapy is obtaining donors with similar blood antigens with a high antibody titer of sars-cov- ( ) . another potential adverse effect of this approach is ade of infection, which is common in so many other viruses. but, to date, the incidence of ade has not been reported in the case of sars-cov- . another major point of contention is the selection of patients for this therapeutic approach. in most clinical trials, patients with severe diseases are being recruited, while the presumed mechanism of action of convalescent plasma, based on its content of virus-neutralizing antibodies, rather points to plausible favorable outcomes in earlier phases of the disease because in the later, more severe phases, the hyperimmune response, rather than the viral load, becomes the more critical pathology. finally, there are no available data on the heterogeneity of response to convalescent plasma transfusion, which may further illustrate the importance of careful evidencebased patient selection, as heterogeneity of response may result from both virus and host-intrinsic factors which are, to date, not revealed. researchers around the world are working hard to develop a potential vaccine candidate so as to stop the deadly pandemic caused by sars-cov- . however, vaccine development is not an easy task, as a number of successful clinical trials are required before approval for patients. different approaches are being utilized for designing a specific vaccine targeting either the structural proteins or viral replication process, which eventually results in the inhibition of viral growth and its further transmission. the common strategies involve the use of live attenuated vaccine (lav), inactivated virus, subunit vaccines, monoclonal antibody vaccine, virus vectors, protein vaccines, and dna/rna-based vaccines ( ) ( ) ( ) ( ) . there are numerous subunit vaccines targeting all or a part of s protein that have already been tested for sars and mers in animal models ( ) and could be potential candidates for testing against sars-cov- . a recent pilot study with a purified inactivated sars-cov- virus vaccine displayed very promising outcomes in different animal models. the neutralizing antibodies generated after vaccination were able to effectively target different strains of sars-cov- without developing any ade of infection ( ) . various randomized controlled trials (nct , nct ) are also underway to evaluate the effectiveness of the bcg vaccine against sars-cov- for healthcare professionals. an adenovirus vector-based vaccine candidate, chadox (presently azd ), developed by oxford university (licensed to astrazeneca) for use against sars-cov- has been reported to activate both the humoral and cell-mediated immune response when tested in rhesus monkey ( ) . the phase i clinical trial to confirm its potency is also in progress (nct ). another group has followed a similar approach by using a recombinant adenovirus type (ad -ncov) vectorbased vaccine for covid- . the full report from the phase i clinical trial (nct ) of ad -ncov shows that it is very effective in generating both humoral and rapid t-cell response post immunization. the group is now ready for the next clinical trial phase to further strengthen the effectiveness of the ad -ncov vaccine ( ) . it should be noted that there are potential risks associated with the usage of live attenuated viruses, for example, complications resulting in lung damage by infiltrating eosinophils, as seen in in vivo models ( , ) . however, eosinophil immunopathology due to sars-cov vaccine could be reduced by using tlr agonist as an adjuvant ( ) . viral neutralizing antibodies specifically targeting various regions of s, i.e., s -rbd, s -ntd, or the s region, and blocking the interaction of virus with the receptor are well-known for sars and mers ( ) . these neutralizing antibodies could prove to be the best and potential candidate for cross-neutralization of sars-cov- . despite being structurally related, some of the sars-cov neutralizing monoclonal antibodies failed to interact with the s-protein of sars-cov- , which could be attributable to the substantial differences in their rbd ( ) . a recent study reported the presence of high titres of neutralizing anti-s-rbd igg antibodies, but no antibodies were detected against the n protein in recovered covid- patients, suggesting that anti-s igg persists longer than does anti-n igg. along with the humoral immune response, they also observed an s protein-specific t cell-population producing ifn-γ, which further contributes to conferring protective immunity against sars-cov- infection ( ). recently, a monoclonal antibody ( d ) has been identified from sars-spike hybridomas that targets the conserved s-rbd region (residue - ) and therefore can very effectively neutralize sars-cov- along with sars-cov ( ). on similar lines, a group has isolated a single-domain antibody from a phage display library targeting the s-rbd region of sars-cov- . the fully humanized singledomain antibody was able to neutralize the virus by interacting with a cryptic epitope in s protein ( ) . these mab and singledomain antibodies could be used to treat as well as to design quick diagnostic kits for covid- . the new technology of the microneedle array (mna) has been employed for delivering sars-cov- s subunit vaccine, which could be really helpful in the treatment of the emerging covid- outbreak ( ) . the transfer of s subunit by mna elicited a strong virus specific-antibody response in sars-cov- ( ) . a novel encapsulated mrna vaccine candidate developed by modernatx, inc. that encodes full length s protein of sars-cov- , is also under clinical trial (nct ). there is an urgent need to develop more such specific vaccines that could neutralize the novel coronavirus effectively ( ) . the host innate immune system encounters upcoming infections, and this results in elevated production of various cytokines and type i interferons (ifns). in the case of prolonged infection, hyperactivation of the immune system may also result in the development of a pro-inflammatory microenvironment, leading to adverse outcomes and even death. the induction of numerous lymphokines, such as il- , il- β, tnf-α, and ccl , that are pro-inflammatory in nature has also been observed in the case of covid- ( ) ( ) ( ) . a previous study in a mers animal model showed that treatment with recombinant type- ifn (rifn) decreased the viral rna level in lungs with a decrease in ifn-stimulating gene expression. early treatment with rifn resulted in a dampening of cytokine and chemokine release that lowered the migration of neutrophils and other cells in lung ( ) . an allogenic mesenchymal stem cell-based (remestemcel-l) therapy developed by mesoblast, which has been previously used for inflammatory conditions and graft vs. host disease in children and adults, is now being assessed for covid- ( ) ( ) ( ) . in this therapy, bone marrow-derived mscs from the donor are grown in vitro and are then transfused to the recipient patients. upon infusion, these cells exhibit antiinflammatory activity by reducing pro-inflammatory cytokine production via the recruitment of anti-inflammatory cells in the affected tissue ( ) . currently, a randomized placebo-controlled trial (nct ) with patients is ongoing for treating ards caused by covid- . treatment with rifn, inhibitors of the pro-inflammatory pathway, cytokine inhibitors such as tocilizumab, lenzilumab, and many others are still to be used in combination with other drugs for treating covid- . so far, there is not much evidence from clinical trials of such inhibitors with which to predict the outcome of these anticytokine therapies. considering the current situation of more than million people being infected, with ∼ , deaths as of june , , there is an urgent need to control the sars-cov- pandemic. the fatality rate of sars-cov- in lower than those of other coronaviruses that caused catastrophes in the past, but the higher infectivity rate makes it worse. raising awareness of this contagious virus is one of the many ways by which its spread can be prevented. the governing authorities concerned in every country have approved guidelines and taken necessary action to quarantine infected people and break the chain of community spread. antibodies, vaccines, and drugs developed for previously emerged coronaviruses could potentially be used for treating sars-cov- . the combination of various neutralizing antibodies against s protein could enhance the effectiveness of viral clearance. among various antivirals and other small molecules that are fda approved, chloroquine/hydroxychloroquine has shown better positive outcome in covid- patients. in clinical trials, some of the combinational antiviral drugs like lopinavir + ritonavir and blockers like angiotensin receptor blocker that were thought to be effective, have failed in curing the disease ( , ) . cytokine storm being one of the symptoms of infected individuals, anticytokine therapy for tnf and il- should be attempted to determine the efficacy of these antibodies in the treatment of sars-cov- infection. clinical trial chictr with tocilizumab, a monoclonal humanized antibody against il- receptor, has shown some efficacy, but this still needs to be tested in a larger cohort. with the increasing number of deaths, there is an immense need to accelerate the development of rapid and sensitive diagnostic kits and to commence clinical trials of the readily available and safe drugs to reduce the rising infections and covid- -related deaths so as to bring life back on track. vs and pf contributed equally in writing the review. conception of idea was done by sc, vs, and pf. manuscript writing and editing was done by all the authors. we are thankful to csir-indian institute of chemical biology, jadavpur, kolkata and national centre for cell science (nccs), pune for providing infrastructure facilities. we would also like to acknowledge department of biotechnology-systems medicine cluster (dbt-symec) grant and j c bose fellowship-serb (science and engineering research board) to sc, for the financial support. a pneumonia outbreak associated with a new coronavirus of probable bat origin genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient sars and mers : recent insights into emerging coronaviruses estimates of the severity of coronavirus disease : a model-based analysis united nation, department of economic and social affairs ( ) the genome sequence of the sars-associated coronavirus a new coronavirus associated with human respiratory disease in china crystal structure of sars-cov- main protease provides a basis for design of improved α-ketoamide inhibitors structural basis for the recognition of the sars-cov- by full-length human ace a novel coronavirus from patients with pneumonia in china coronavirus envelope protein: current knowledge human coronaviruses: a review of virus-host interactions origin and evolution of pathogenic coronaviruses from sars to mers, thrusting coronaviruses into the spotlight genome composition and divergence of the novel coronavirus ( -ncov) originating in china covid- : the role of the nsp and nsp in its pathogenesis origin and evolution of the novel coronavirus emerging sars-cov- mutation hot spots include a novel rna-dependent-rna polymerase variant emergence of genomic diversity and recurrent mutations in sars-cov- angiotensinconverting enzyme is a functional receptor for the sars coronavirus wenhui dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc functional assessment of cell entry and receptor usage for sars-cov- and other lineage b betacoronaviruses cryo-em structure of the sars coronavirus spike glycoprotein in complex with its host cell receptor ace cryo-em structure of the -ncov spike in the prefusion conformation host cell proteases: critical determinants of coronavirus tropism and pathogenesis sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor localization of neutralizing epitopes and receptor-binding site in murine coronavirus spike protein viral shedding patterns of coronavirus in patients with probable severe acute respiratory syndrome current advancements and potential strategies in the development of mers-cov vaccines fusion mechanism of -ncov and fusion inhibitors targeting hr domain in spike protein characterization of severe acute respiratory syndrome-associated coronavirus (sars-cov) spike glycoprotein-mediated viral entry activation of the sars coronavirus spike protein via sequential proteolytic cleavage at two distinct sites characterization of the expression, intracellular localization, and replication complex association of the putative mouse hepatitis virus rna-dependent rna polymerase coronavirus transcription: a perspective host factors in coronavirus replication identification of novel subgenomic rnas and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus the c-terminal domain of the mers coronavirus m protein contains a trans-golgi network localization signal structure, function, and antigenicity of the sars-cov- spike glycoprotein sars-cov- entry factors are highly expressed in nasal epithelial cells together with innate immune genes available online at infection control: severe acute respiratory syndrome coronavirus (sars-cov- ). ( ) immune responses in covid- and potential vaccines: lessons learned from sars and mers epidemic people who are at higher risk for severe illness | coronavirus | covid- severe acute respiratory syndrome-associated coronavirus in lung tissue multiple organ infection and the pathogenesis of sars sars-cov- infection in children vulnerability of children with covid- infection and ace profiles in lungs possible causes for decreased susceptibility of children to coronavirus diagnosis and treatment recommendations for pediatric respiratory infection caused by the novel coronavirus characteristics and outcomes of children with coronavirus disease (covid- ) infection admitted to us and canadian pediatric intensive care units outbreak of kawasaki disease in children during covid- pandemic: a prospective observational features of covid- post-infectious cytokine release syndrome in children presenting to the emergency department links between innate and adaptive immunity via type i interferon interferon and cytokine responses to sarscoronavirus infection sars-cov regulates immune function-related gene expression in human monocytic cells profiles of antibody responses against severe acute respiratory syndrome coronavirus recombinant proteins and their potential use as diagnostic markers early detection of antibodies against various structural proteins of the sarsassociated coronavirus in sars patients serological assays for emerging coronaviruses : challenges and pitfalls profile of specific antibodies to the sars-associated coronavirus t cell responses to whole sars coronavirus in humans temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study profiling early humoral response to diagnose novel coronavirus disease (covid- ) viral kinetics and antibody responses in patients with covid- protective humoral immunity in sars-cov- infected pediatric patients the potential danger of suboptimal antibody responses in covid- medical countermeasures analysis of -ncov and vaccine risks for antibody-dependent enhancement (ade) antibody-dependent enhancement of sars coronavirus infection and its role in the pathogenesis of sars molecular mechanism for antibody-dependent enhancement of coronavirus entry avoiding pitfalls in the pursuit of a covid- vaccine novel immunodominant peptide presentation strategy: a featured hla-a * -restricted cytotoxic t-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory syndrome coronavirus nucleocapsid protein association of human leukocyte antigen class ii alleles with severe acute respiratory syndrome in the vietnamese population epidemiological and genetic correlates of severe acute respiratory syndrome coronavirus infection in the hospital with the highest nosocomial infection rate in taiwan in humanleukocyte antigen class i cw and class ii dr genotypes are associated with resistance to severe acute respiratory syndrome (sars) infection association of human leukocyte antigen class ii alleles with severe middle east respiratory syndrome-coronavirus infection cell host response to infection with novel human coronavirus emc predicts potential antivirals and important differences with sars coronavirus mers-cov and h n influenza virus antagonize antigen presentation by altering the epigenetic landscape complex immune dysregulation in covid- patients with severe respiratory failure smar favors immunosurveillance of cancer cells by modulating calnexin and mhc i expression t cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice priming with sars cov s dna and boosting with sars cov s epitopes specific for cd + and cd + t cells promote cellular immune responses recovery from the middle east respiratory syndrome is associated with antibody and t cell responses sars coronavirus nucleocapsid immunodominant t-cell epitope cluster is common to both exogenous recombinant and endogenous dna-encoded immunogens preliminary identification of potential vaccine targets for the covid- coronavirus (sars-cov- ) based on sars-cov immunological studies targets of t cell responses to sars-cov- coronavirus in humans with covid- disease and unexposed individuals human immunopathogenesis of severe acute respiratory syndrome (sars) plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel middle east respiratory syndrome coronavirus: implications for pathogenesis and treatment active replication of middle east respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis ifn-i response timing relative to virus replication determines mers coronavirus infection outcomes clinicopathologic, immunohistochemical, and ultrastructural findings of a fatal case of middle east respiratory syndrome coronavirus infection in the united arab emirates elucidating the molecular physiopathology of acute respiratory distress syndrome in severe acute respiratory syndrome patients reduction and functional exhaustion of t cells in patients with coronavirus disease (covid- ) pathological findings of covid- associated with acute respiratory distress syndrome covid- : consider cytokine storm syndromes and immunosuppression pathogenic t cells and inflammatory monocytes incite inflammatory storm in severe covid- patients anti-inflammation treatment of severe coronavirus disease (covid- ): from the perspective of clinical immunologists from china the cytokine storm in covid- : an overview of the involvement of the chemokine/chemokine-receptor system novel paediatric presentation of covid- with ards and cytokine storm syndrome without respiratory symptoms transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in covid- patients the interferon in tlr signaling: more than just antiviral haematological manifestations in patients with severe acute respiratory syndrome:retrospective analysis significant changes of peripheral t lymphocyte subsets in patients with severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia the structural and accessory proteins m, orf a, orf b, and orf of middle east respiratory syndrome coronavirus (mers-cov) are potent interferon antagonists severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of regulation of irf- -dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus molecular determinants for subcellular localization of the severe acute respiratory syndrome coronavirus open reading frame b protein severe acute respiratory syndrome coronavirus open reading frame (orf) b, orf , and nucleocapsid proteins function as interferon antagonists pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses imbalanced host response to sars-cov- drives development of covid- elevated exhaustion levels and reduced functional diversity of t cells in peripheral blood may predict severe progression in covid- patients dysregulation of immune response in patients with covid- in wuhan, china lees jr, farber dl. generation, persistence and plasticity of cd t-cell memories characterization of sars-cov-specific memory t cells from recovered individuals years after infection lack of peripheral memory b cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study longlived memory t lymphocyte responses against sars coronavirus nucleocapsid protein in sars-recovered patients airway memory cd + t cells mediate protective immunity against emerging respiratory coronaviruses a mouse model of sars-cov- infection and pathogenesis coronaviruses-drug discovery and therapeutic options a rapid advice guideline for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (standard version) potent cross-reactive neutralization of sars coronavirus isolates by human monoclonal antibodies potent neutralization of mers-cov by human neutralizing monoclonal antibodies to the viral spike glycoprotein the cytokine release syndrome (crs) of severe covid- and interleukin- receptor (il- r) antagonist tocilizumab may be the key to reduce the mortality preventing covid- -induced pneumonia with anticytokine therapy fda approves emergency ind use of humanigen's lenzilumab for compassionate use in covid- patients altasciences completes phase i study on gimsilumab for ards in covid- type interferons as a potential treatment against covid- covid- and emerging viral infections: the case for interferon lambda learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by -ncov research and development on therapeutic agents and vaccines for covid- and related human coronavirus diseases small molecule inhibitors of the sars-cov nsp endoribonuclease an orally bioavailable broad-spectrum antiviral inhibits sars-cov- in human airway epithelial cell cultures and multiple coronaviruses in mice baricitinib as potential treatment for -ncov acute respiratory disease comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov a trial of lopinavirritonavir in adults hospitalized with severe covid- old weapon for new enemy: drug repurposing for treatment of newly emerging viral diseases remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro ribavirin and interferon alfa- a for severe middle east respiratory syndrome coronavirus infection: a retrospective cohort study protection against filovirus diseases by a novel broad-spectrum nucleoside analogue bcx new insights on the antiviral effects of chloroquine against coronavirus: what to expect for covid- ? mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology the efficacy of lopinavir plus ritonavir and arbidol against novel coronavirus infection molecular mechanisms of severe acute respiratory syndrome (sars) receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus gs- and its parent nucleoside analog inhibit filo-, pneumo-, and paramyxoviruses. sci rep prophylactic and therapeutic remdesivir (gs- ) treatment in the rhesus macaque model of mers-cov infection gs- ) protects african green monkeys from nipah virus challenge first case of novel coronavirus in the united states remdesivir for the treatment of covid- -preliminary report new nucleoside analogues for the treatment of hemorrhagic fever virus infections chloroquine analogs as antimalarial candidates with potent in vitro and in vivo activity chloroquine is a potent inhibitor of sars coronavirus infection and spread effects of chloroquine on viral infections: an old drug against today's diseases? a randomized trial of hydroxychloroquine as postexposure prophylaxis for covid- treatment of middle east respiratory syndrome with a combination of lopinavir-ritonavir and interferon-β b (miracle trial): study protocol for a randomized controlled trial cinanserin is an inhibitor of the c-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro inhibition of sars-cov cl protease by flavonoids diarylheptanoids from alnus japonica inhibit papain-like protease of severe acute respiratory syndrome coronavirus network-based drug repurposing for novel coronavirus -ncov/sars-cov- feasibility of using convalescent plasma immunotherapy for mers-cov infection, saudi arabia treatment with convalescent plasma for influenza a (h n ) infection the convalescent sera option for containing covid- breadth of concomitant immune responses prior to patient recovery: a case report of non-severe covid- effectiveness of convalescent plasma therapy in severe covid- patients use of convalescent plasma therapy in sars patients in hong kong available online at sars vaccines: where are we? neutralizing antibody against severe acute respiratory syndrome (sars)-coronavirus spike is highly effective for the protection of mice in the murine sars model sars corona virus peptides recognized by antibodies in the sera of convalescent cases severe acute respiratory syndrome (sars) coronavirus: application of monoclonal antibodies and development of an effective vaccine subunit vaccines against emerging pathogenic human coronaviruses development of an inactivated vaccine candidate for sars-cov- chadox ncov- vaccination prevents sars-cov- pneumonia in rhesus macaques safety, tolerability, and immunogenicity of a recombinant adenovirus type- vectored covid- vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial a double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge immunization with sars coronavirus vaccines leads to pulmonary immunopathology on challenge with the sars virus effects of toll-like receptor stimulation on eosinophilic infiltration in lungs of balb/c mice immunized with uv-inactivated severe acute respiratory syndrome-related coronavirus vaccine neutralizing antibodies against sars-cov- and other human coronaviruses potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody detection of sars-cov- -specific humoral and cellular immunity in covid- convalescent individuals a human monoclonal antibody blocking sars-cov- infection identification of human single-domain antibodies against sars-cov- microneedle array delivered recombinant coronavirus vaccines: immunogenicity and rapid translational development sars-cov- vaccines: status report induction of pro-inflammatory cytokines (il- and il- ) and lung inflammation by coronavirus- (covi- or sars-cov- ): anti-inflammatory strategies mast cells contribute to coronavirus-induced inflammation: new anti-inflammatory strategy clinical features of patients infected with novel coronavirus in wuhan a phase , single-arm, prospective study of remestemcel-l, ex vivo culture-expanded adult human mesenchymal stromal cells for the treatment of pediatric patients who failed to respond to steroid treatment for acute graft-versus-host disease remestemcel-l: human mesenchymal stem cells as an emerging therapy for crohn's disease transplantation of ace -mesenchymal stem cells improves the outcome of patients with covid- pneumonia mesoblast to evaluate anti-inflammatory cell therapy remestemcel-l for treatment of covid- lung disease are patients with hypertension and diabetes mellitus at increased risk for covid- infection? key: cord- -oh lnxwt authors: kock, florian; nørfelt, astrid; josiassen, alexander; assaf, a. george; tsionas, mike title: understanding the covid- tourist psyche: the evolutionary tourism paradigm date: - - journal: ann tour res doi: . /j.annals. . sha: doc_id: cord_uid: oh lnxwt studies across the social sciences are making increasing use of an evolutionary perspective. yet, despite its potential, the application of evolutionary psychology in tourism research is scant. evolutionary psychology is arguably one of the most useful approaches to understanding the effects of the coronavirus pandemic on the tourist's psyche. this research highlights, explains, and empirically demonstrates the vast untapped potential of this perspective for post-covid- tourism research. the authors develop an evolutionary tourism paradigm, which is based on biological epistemology and theory to address questions in post-covid- tourism research. this paradigm is brought to life through a developed ocean and islands model, and its utility for future research endeavors on the coronavirus pandemic is empirically demonstrated in two studies. the impact of the coronavirus pandemic on tourism and hospitality is unprecedented. in response, a large amount of descriptive research is being conducted on the immediate and short-term effects of the pandemic. often, such research is simply confirming what is already known: that the pandemic is wrecking the tourism industry all over the globe. in many cases, such research is of limited use because it is merely mechanically reciting the numbers of a suffering industry. specifically, these endeavors are prone to be a snap-shot in time only, lacking in theoretical reasoning on what is happening, why it is happening, and how the pandemic may change tourism in the long run. what is largely missing in the literature is theory-based research that sets out to investigate how tourism could be fundamentally different in a post-covid- era. while the pandemic will reshuffle taken-for-granted determinants of tourism as we know it, a crucial shift is likely to occur in tourists' psyche: the pandemic will eventually fade and travel barriers will be lifted, yet, some tourists' psyches will likely settle on a new equilibrium. while the full impact on the tourist psyche cannot reliably be predicted at this point in time, its eventual implications for tourism may be of seismic proportions. understanding the altered make-up of tourists' psyches will be a crucial success factor for both tourism researchers and businesses during and after the covid- era. this research provides a novel theoretical frame that allows to formalize such changes, and is thus, in contrast to most existing research on the pandemic, not describing the status-quo but rather forward-looking. we thereby answer calls for covid- tourism research that goes beyond "the obvious and purely descriptive," and instead investigates "deeper underlying relationships" (zenker & kock, , p. ) . the current pandemic can constitute a paradigm shift in research on tourists' behavior and decisionmaking. what was previously taken for granted may not hold anymore in the covid- era, urging researchers to critically reassess the underlying assumptions of the conventionally used theories, frameworks, and models. we postulate that the investigation of tourists' covid- psyche and the paradigm shift in tourists' behavior demands new theory-based mindsets to be leveraged in tourism research. we suggest that the evolutionary psychology literature, which has recently been endorsed as a valuable and creative theoretical lens for future tourism research (crouch, ; kock, josiassen & assaf, ) , is well-positioned to facilitate the paradigm shift that is necessary to understand many of the emerging and future challenges facing tourism research. this is because the pandemic unsheathes and amplifies many deep-rooted human anxieties of contagious diseases, physical harm, and social isolation. all these factors are important research subjects, and evolutionary psychology explicitly studies these deep-rooted threats and offers a plethora of explanations of how they can impact human thinking, feeling, and behavior. thus, if we want to understand, and not only describe, why tourists react to the pandemic and how it shapes their psyche, evolutionary psychology is a powerful lens through which to do so. researchers in the humanities, social sciences, and natural sciences are increasingly employing evolutionary theory, and evolutionary psychology in particular, to examine the foundations of human behavior. in recent years, these burgeoning efforts have yielded novel hypotheses and enabled researchers to tackle phenomena in business research areas such as marketing (saad, ) , tourism , and leadership (bastardoz & van vugt, ) . the key notion of evolutionary psychology is that modern human beings have inherited psychological mechanisms that predispose them to act in ways that increased reproductive fitness in ancestral times. that means, evolutionary psychologists seek to explain human behavior through the adaptive function that the behavior might have served, or potentially still serves (griskevicius & kenrick, ) . despite mounting interest in and popularity of evolutionary psychology, knowledge of its unique epistemology and theoretical underpinnings is often limited in the social sciences, leaving interested researchers with no guidelines on how to apply it to their field of study. in response to this, we develop the evolutionary tourism paradigm, which makes use of the logic, epistemology, and theory of evolutionary psychology to leverage tourism research, particularly addressing those questions arising from the coronavirus pandemic. this paradigm rests on three features: evolutionary epistemology, fundamental evolutionary motives, and behavioral ecology. we bring the evolutionary tourism paradigm and its three features to life through the ocean and islands model that visualizes the epistemological and theoretical commitments of evolutionary psychology that sharply distinguish it from all other disciplinary streams used in tourism research. the ocean and islands model is a visualization intended to guide interested researchers through the use of evolutionary psychology in their own research endeavors. this guide is necessary for at least two reasons. first, researchers in the tourism domain typically do not receive any training in the theory of biology, specifically in the branches of evolution and ecology. second, while principles of evolutionary theory seem intuitive at first sight, leveraging their potential requires mastery and a holistic understanding thereof. these two reasons suggest that a more rigorous training in key principles of evolutionary psychology can increase its usability in tourism research, consequently helping to advance the discipline. in the following section, we develop the evolutionary tourism paradigm, and make it actionable via the ocean and islands model. we then turn to an empirical application of the model to generate both a broad and deep understanding of how the coronavirus pandemic changes tourists' psyche. specifically, drawing on research from evolutionary psychology on the behavioral immune system, we demonstrate across two studies how this pandemic impacts important tourism phenomena, such as tourist xenophobia (kock, josiassen & assaf, a) . applications of evolutionary psychology have to be grounded in a solid understanding of its epistemological and theoretical principles. the evolutionary tourism paradigm is meant to facilitate the comprehension of what it means to take an evolutionary approach in the tourism discipline. outlining the paradigm, we first explicate the three constituting features on which biology-based examinations in tourism shall rest, and then explain the connections between them. as for the first feature, we provide a theory-based discussion of the epistemology of evolutionary psychology, which is fundamentally different from how tourism research has traditionally explained the world. the paradigm's second feature provides the theoretical backbone for the epistemology: the model of fundamental motives that underlie many behaviors. the third feature constitutes the behavioral ecology according to which socio-ecological factors in the environment activate certain motives. the central epistemological approach of evolutionary psychology (i.e., the manner in which knowledge is generated and answers are developed) is to explain human behavior by revealing its adaptive function ("which function did/does the behavior serve?") and fundamental motive ("how does this function increase reproductive fitness?"). grounded in the influential works of ernst mayr ( ) and nobel prize-winning ethologist niko tinbergen ( ) , the evolutionary epistemology distinguishes between proximate motives (i.e., immediately obvious) and ultimate motives that cause behavior. accordingly, this research stream, which also contributed considerably to the philosophy of research (beatty, ) , is labeled causation. a proximate motive of a behavior is a corresponding immediate stimulus, such as when the sight of a snake causes someone to frighten and flee. in contrast, an ultimate motive of a behavior is the evolutionary explanation that human beings fear snakes and flee because it increased the probability of survival in ancestral times. while both types of explanation are correct, only ultimate explanations identify the adaptive function that the respective behavior has served for our ancestors, and might still serve. thus, researchers examining proximate motives are interested in showing how something works, while researchers examining ultimate motives are interested in investigating why something exists. to this day, the overwhelming majority of studies in tourism research has focused on proximate motives to explain behavior, thereby neglecting ultimate motives . the second feature of the paradigm is the existence of fundamental, or ultimate, motives. while the epistemology of evolutionary psychology postulates to explain behavior through its underlying ultimate function, the fundamental motives framework is the theoretical substrate for this epistemology. in order to survive and procreate, our ancestors had to surmount various evolutionary challenges. evolutionary psychology maintains that these evolutionary challenges have predisposed our ancestors to develop fundamental motivational systems that helped to solve each of these challenges. thus, evolutionary psychology postulates that humans have not only inherited physiological characteristics, but also psychological mechanisms that manifest in various motives such as self-protection, disease avoidance, affiliation, status, mate acquisition, mate retention and kin care (griskevicius & kenrick, ) . as an illustration of using the paradigm, we focus here on research to be conducted on the coronavirus pandemic, and thus focus on disease avoidance as the most relevant fundamental motive. yet, it is important to note that each motive provides a myriad of unique ultimate explanations to many human behaviors and can serve as the starting point for an evolutionary based investigation in tourism research. for example, as a rare application, kim and seo ( ) found a link between the activation of the mating motive and a preference for risky travel activities in men, arguing that risk-taking serves the adaptive function of increasing mating success. in addition, motives beyond those mentioned by griskevicius and kenrick ( ) exist and are likely to play important roles in tourists' behavior (see kock et al., for an overview of the motives and their relevance for tourism research). for example, in a recent study, nørfelt, kock and josiassen ( ) suggest that the fundamental motive of exploration is a focal evolutionary driver of contemporary tourism activity. based on existing evolutionary theory, the authors argue that the inclination to explore, the fascination with foreignness and the experience of curiosity have played important roles in our ancestral past where survival was ensured by venturing into new territories and accessing new resources such as food, shelter, water or mating partners. understanding tourism as a contemporary remnant of such an evolutionary motive is profoundly different from existing sociological accounts that explain tourism through social developments (e.g. , blackshaw, ) , or psychological accounts that explain the existence of tourism through the mere j o u r n a l p r e -p r o o f fact that it is pleasant. importantly, those explanations are also correct but they exist on a more proximate level. these examples illustrate that researchers who are familiar with evolutionary psychology can creatively spot motives that different tourism activities could be rooted in. importantly, such an understanding does not only answer why something exists but allows for novel conceptual reasoning of causality, contingency and interconnectedness. scholars have argued for the relevancy of a macro-environmental perspective when studying behavior (oishi, ) . the third feature of the paradigm is therefore behavioral ecology. behavioral ecology connects with the fundamental motives through the observation that each of the deeply ingrained motives is activated by different socio-ecological factors that draw an individual's attention to opportunities or threats mapped onto specific evolutionary challenges (kenrick, griskevicius, neuberg & schaller, ; uskul & oishi, ) . important socio-ecological factors include pathogen threats, population density, resource scarcity, unpredictability, or sex ratio (sng, neuberg, varnum & kenrick, ) . behavioral ecology examines the adoption of different behaviors depending on such socio-ecological factors. this adoption process and resulting behavior is labeled phenotypic plasticity, according to which animals and humans with the same gene pool can adapt their behavior, physiology or morphology in response to different ecological conditions (sng et al., ) . the relevance of behavioral ecology for understanding the current pandemic rests on its notion (along with comprehensive empirical documentation) that pathogen threat and unpredictability are crucial socio-ecological factors that trigger different motives and thus result in phenotypic plasticities (sng et al., ) . in order to bring the three features to life (i.e., turning them into an actionable research paradigm), we develop the ocean and islands model that illustrates how evolution-infused research can be conducted. the model has four components: plasticities, proximate motives, ultimate motives, and the ecology. while the motives and ecology are the constituting features of the model, the epistemology is what keeps the model floating ( figure ) . a unique characteristic of the model is that it has no predetermined starting point, but implies that an evolutionary research endeavor can start with each of the four components. yet, in order to be theoretically sound and empirically executable, researchers have to identify all components and associative links between them in their own research endeavor. for reasons of simplicity, we start our first illustration with phenotypic plasticity. the phenotypic plasticity is the behavior (or other attitudinal phenomenon) that the attentive researcher can observe; similar to the palms of an island which one can easily spot when overlooking the ocean (see kock, assaf & tsionas, for a comprehensive discussion of the 'observe' strategy). following the evolutionary epistemology, the researcher then inquires what gave cause to this observed phenotypic plasticity, or to maintain the metaphor of the island: if one spots a palm on the ocean, one would conclude that this palm stands on an island. implicit in the label 'phenotypic plasticity', a behavior does not exist for its own right (i.e., sui generis), but serves an adaptive function that the researcher needs to formalize. before applying the model, we first illustrate it on the phenomenon of sex tourism as the observed behavior. following the ocean and islands model, a traditional research approach would explain the observed behavior with what is directly observable. accordingly, the researcher would conclude that sex tourism exists because people seek sexual pleasure. this is the proximate motive, and thus re adily observable at the water surface (i.e., one can easily spot the palms, but also the island if look ing carefully). the evolutionary paradigm now asks for the adapative function and fundamental motive that gave cause to the observed proximate motive and the phenotypic plasticity. in our example, the fundamental motive that motivates sex tourism is mating, with the adaptive function of increasing reproductive fitness. similar to the island underwater, the fundamental motive is what gives cause to the observable features, yet, it is not directly observable. in turn, the identification of this ultimate motive enables the researcher to theorize which ecological factor might give rise to the behavior of j o u r n a l p r e -p r o o f sex tourism. like a person who focuses on the island to understand it, and not the ocean which is surrounding it, most researchers do not take into account the ecology in which the behavior takes place. however, the researcher who is well-versed in evolutionary psychology would suggest that the socio-ecological factor of sex ratio may give rise to sex tourism through the activation of the mating motive. indeed, it is only this network of arguments that yields this hypothesis because the mating motive alone could not explain why people seek a mating partner abroad and not at home. however, in some cases, the ultimate motive is not as easily detectable. considering the burgeoning tourism phenomenon of sharing travel experiences on social media (i.e., the plasticity), proximate explanations would suggest that such behavior is a consequence of the digitalization (a sociotechnological explanation), merely a pleasant activity (a cognitive psychological explanation), or a means to share experiences with peers at home (a socio-psychological explanation). while these explanations are certainly correct, they are proximate and neglect the adaptive functions of this behavior. evolutionary psychology would explain this behavior as a means to address fundamental motives such as to conspicuously elevate one's status among peers, affiliate with others or even attracting a mating partner (indeed, research in progress of one of the authors indicates that travelers who are single post significantly more on social media). such insights can be the starting point of intriguing examinations that would not be possible without evolutionary reasoning. once all four components of the ocean and islands model are formalized, the researcher may proceed to empirical testing. in addition to being an easy to understand guide to evolutionary psychological research endeavors, the ocean and islands model explicitly allows for two important additional considerations. first, it accommodates the possible existence of more than one island in the ocean. that is, one ecological factor can cause various islands and palms. as we will see now, the ecological factor of pathogen threat can give rise to various phenotypic plasticities, symbolized by palms. second, the metaphor implies that the ocean is an amalgam of various elements (not just h o), and similarly, the ecology is based on various factors that the researcher can consider. prior literature has noted the importance of tourists' tendency to avoid disease. specifically, studies investigate the (perceived) health risks associated with travel and how they influence tourism j o u r n a l p r e -p r o o f outcomes (jonas, mansfeld, paz & potasman, ; lepp & gibson, ; reisinger & mavondo, ) . such studies are complemented by a smaller research stream that examines how tourists assess their vulnerability to disease and how they limit infection risk (chien, sharifpour, ritchie & watson, ; wang, liu-lastres, ritchie & mills, ) . a third stream investigates the effects of epidemics and pandemics on tourism, both in the form of economic analyses (kuo, chen, tseng, ju & huang, ; yang, zhang & chen, ) and analyses of tourist behavior. fenichel, kuminoff, and chowell ( ) found that tourists performed self-protective behaviors (such as voluntarily missing flights) during the swine flu epidemic. cahyanto, wiblishauser, pennington-gray and schroeder ( ) also empirically linked antecedents, such as perceived susceptibility to ebola, to travel avoidance. while these findings indicate the importance of disease avoidance for understanding behavior, they remain on a proximate level. the covid- pandemic is, however, likely to awaken deep-rooted, evolved mechanisms, which warrants analysis spanning both the proximate and ultimate level and the interplay between ecology, psychology, and behavior. as an exception to the general state of the literature, kock et al. ( a) briefly illustrated a link between disease avoidance, xenophobia, preference for travel-vaccination, and intention to try local food. we now go further in demonstrating how the evolutionary tourism paradigm can be used to provide an ultimate-level perspective on tourists' reactions to the covid- pandemic. in doing so, we also answer calls for tourism research on the link between the pandemic and outcomes such as ethnocentrism, xenophobia, and crowding perceptions (zenker & kock, ) . applying the ocean and islands model, we formalize the covid- outbreak as an ecological determinant, more specifically, as a pathogen threat that has significantly changed the global ecology. this conceptualization builds on literature that has identified pathogen threat as an important ecological dimension (oishi, ; sng et al., ) . according to the concept of phenotypic plasticity, a change in the ecology along the pathogen dimension would likely lead to changes in tourist behaviors. while a link between a disease outbreak and tourism behaviors has been noted in prior tourism literature (cahyanto et al., ) , the ocean and islands model allows us to go one step further in conducting a process study (oishi, ) . that is, we explain why the ecology is linked to different behaviors through a psychological mediator: in this case, the fundamental motive of disease avoidance. we outline the theory behind this further in the following section. dying from a contageous disease constituted a major threat for our ancestors. consequently, a disease avoidance motive evolved (griskevicius & kenrick, ) . disease avoidance is based on the idea of a behavioral immune system, which is complementary to the physiological immune system, and aims to preemptively prevent individuals from contracting diseases (griskevicius & kenrick, ; schaller & park, ) . the disease avoidance motive is triggered by cues that could signal a pathogen threat (tybur & lieberman, ) , such as coughing, sneezing, dirtiness, foul smells, deformity or all kinds of pathogen-transmitting objects (e.g., feces, blood, rotten food). the activation of this motive is signaled to the individual through the experience of the emotion disgust, and it is functional in the way that it predisposes people to engage in a wide variety of diseaseavoidance behaviors (griskevicius & kenrick, ) . the behavioral immune system has consequences for cognition, affect, and behaviors , and has been used to explain a wide range of phenomena at both the individual-and group-level. for example, the behavioral immune system has been linked to an increased prejudice toward people with physical disabilities, overweight people, and the elderly because atypical morphology and movement is (falsely) interpreted as the presence of pathogens (schaller & neuberg, ) . however, the behavioral immune system is not only occupied with the appearance of others, but is also linked to an increased concern for one's own physical appearance due to the potential of being stigmatized by others (ackerman, tybur & mortensen, ) . furthermore, the behavioral immune system has j o u r n a l p r e -p r o o f implications for personality traits and values. indeed, regions historically characterized by a high degree of pathogen threat tend to score lower on extraversion, sociosexuality and openness to experience . similarly, pathogen threat has been linked to increased conformity, political conservatism, strong family ties and religiosity (beall, hofer & schaller, ; fincher & thornhill, ; murray & schaller, ) . like other evolutionarily shaped adaptations, the behavioral immune system is not perfect in its ability to detect and respond to threats as it is prone to overgeneralizing and false positive errors. error management theory explains this phenomenon by noting that the direction of a bias depends on the relative costs of false positive to false negative errors (haselton, nettle & murray, ) . in the case of the behavioral immune system, the cost of contracting an infectious disease has usually been much higher than the cost of avoiding something or someone that pose s no threat, meaning that a tendency toward false positive errors would be adaptive (haselton et al., ) . this bias is particularly strong when the benefits of avoiding disease clearly outweigh the costs, such as when a person is, or feels, particularly vulnerable to disease (faulkner, schaller, park & duncan, ; schaller & park, ) . unsurprisingly, this may be the case during regional or global disease outbreaks (kim, sherman & updegraff, ) . based on the above considerations, we argue that it is highly relevant to study the effects of tourists' behavioral immune system in relation to the covid- pandemic. in line with previous literature (duncan, schaller & park, ; kim et al., ) , we specifically examine the construct of perceived covid- infectability as a proxy for the activation of the behavioral immune system. in doing so, we link a dimension of the ecology (the pathogen threat posed by covid- ) to different behaviors (phenotypic plasticities or 'palms') through a psychological mechanism. we test perceived covid- infectability in two complementary studies including outcomes derived from evolutionary psychology such as crowding perceptions, xenophobia and ethnocentrism (study ) and more traditional tourism constructs and psychological antecedents (study ). previous evolutionary-based research has noted that perceptions of and attitudes toward crowding vary depending on which fundamental motive is activated. for example, the affiliation motive has been linked to a preference for crowded retail spaces as a way of getting closer to others (thomas & saenger, ) , while the activation of the behavioral immune system increases people's perceptions of crowding and the feeling of negative affect toward such environments (wang & ackerman, ) . the latter finding has been explained as an adaptive way of avoiding disease as the risk of contracting a disease is higher in crowded environments (wang & ackerman, ) . indeed, depictions of a crowded space have even been used as part of measuring disgust sensitivity (curtis, de barra & aunger, ) . prior literature has investigated tourists' perceptions of crowding and demonstrated how crowding perceptions impact tourist experiences (lee & graefe, ; li, zhang, nian & zhang, ) . however, due to the absence of evolutionary research in tourism, disease avoidance has yet to be investigated as an important determinant of tourists' crowding perceptions. we examine the association between these constructs in study . in today's globalized world, xenophobia is maladaptive and detrimental, however, in ancestral environments, avoiding contact with out-group members served several functions (schaller & neuberg, ) . specifically, xenophobia serves the function of disease avoidance: out-group members could have carried diseases the in-group had not built immunity against (faulkner et al., ) . many studies have empirically found links between the behavioral immune system and xenophobia, documenting that negative attitudes toward outgroups are predicted by perceived vulnerability to disease and disease risk perceptions (faulkner et al., ; kim et al., ; prati & pietrantoni, ) . unsurprisingly, such effects are then particularly relevant during major disease outbreaks: during the ebola outbreak, the higher american respondents' perceived j o u r n a l p r e -p r o o f vulnerability to the disease was, the more xenophobic their responses were (kim et al. , ) , and a link between ebola risk perceptions and prejudice toward african immigrants was found amongst an italian sample (prati & pietrantoni, ) . while some tourism scholars have hinted at xenophobic responses in the wake of the covid- pandemic, they provide rather proximate explanations for the tendency, such as biased media coverage (wen, aston, liu & ying, ) . in contrast, kock et al. ( a, p. ) , explain the role of xenophobia through the fundamental motive of disease avoidance. tourist xenophobia is defined as "a tourist's perceptual discomfort and anxiety associated with strangers encountered at foreign destinations" and the researchers demonstrate its association with outcomes such as preference for travel vaccination, willingness to travel to foreign destinations, and intention to book travel insurance. we develop their line of thinking further in study by examining the relationship between perceived covid- infectability and tourist xenophobia. following a similar logic as with xenophobia, pathogen threat has also been linked to increased ingroup favorability. that is, when a pathogen threat is present it becomes more attractive to interact with in-group members, as it poses less health risks and in-group members may provide support in cases where an individual has contracted a disease (navarrete & fessler, ) . in support of this theory, scholars have found a link between perceived vulnerability to disease and ethnocentrism (navarrete & fessler, ) . ethnocentrism has even been found to be particularly strong during the first trimester of pregnancy, where the mother and fetus are particularly vulnerable to pathogens (navarrete, fessler & eng, ) . at a regional scale, researchers have also found a correlation between collectivism (of which ethnocentrism is said to be a specific manifestation) and the prevalence of pathogens (fincher, thornhill, murray & schaller, ) . while ethnocentrism has received little attention in a tourism context, it has important implications for tourism behaviors. indeed, kock, josiassen, assaf, karpen, and farrelly ( b, pp. - ) found a link between tourism ethnocentrism (defined as "an individual's prescriptive beliefs and felt moral obligation to support the domestic tourism economy") and willingness to engage in domestic tourism and support for tourism development. however, the potential association between pathogen threat and tourism ethnocentrism has yet to be examined. the objective of study is to examine whether the covid- pandemic is associated with important tourism phenomena that we identified through an evolutionary lens. based on the evolutionary tourism paradigm and, more specifically, the theory on disease avoidance (ultimate motive) presented above, this study tests whether a higher pathogen threat (ecology) relates to tourists' crowding perceptions and increased levels of xenophobia and ethnocentrism (phenotypic plasticities). the nomological networks tested in study and are complementary, and visualized and theoretically connected in figure . while the studies are theoretically connected, the data collection was divided in two to limit potential problems of respondent fatigue. to test the relationships, we recruited american participants through the crowdsourcing platform mturk. we chose u.s. respondents because the u.s. is a very important tourism outbound market: it is the second-biggest spender ( usd billion) after china ( usd billion) on international tourism, and growing faster than china (unwto, ). mturk data has been reported to be of good quality by prior studies (goodman & paolacci, ; kees, berry, burton & sheehan, ; ramsey, thompson, mckenzie & rosenbaum, ) . however, like any data collection method, collecting data from mturk has certain limitations, such as participant non-naivety, issues of self-selection, and issues with participants not paying attention or engaging in biasing response be haviors (hauser, paolacci & chandler, ) . to mitigate the risk of the latter, we used an instructional manipulation check ('please select 'agree' as answer here') (paas, dolnicar & karlsson, ) . the use of such check questions can effectively detect and alleviate biasing response behavior. we obtained the data in the first week of may . in alignment with previous literature (boley, jordan, kline & knollenberg, ; kock et al., a) , we aimed to reach people who, at least hypothetically, consider or engage in travelling. such a stratification is useful because not every potential respondent is willing or able to travel . this may be due to psychological reasons (e.g., psychological impairment, inertia or agoraphobia), physical impairment (e.g., a disease or a disability), private responsibilities (e.g., looking after a family member) or financial constraints. importantly, this stratification is not theoretically linked to this study but merely helps to filter out individuals who are barred from travel. to this end, we put three restrictions on the types of participants to recruit: ) they had to be or older, ) they had to have a household income of above $ , usd per year, and ) they had to have travelled distances of over miles in the past two years. while this stratification cannot ensure that all participants have required means and abilities to travel, it filters out those who are barred from travel per se, while retaining those who can travel on a smaller budget. we collected completed questionnaires. another respondents were removed from the sample because they failed the instructional manipulation check (i.e., . %). see table we adopted the ethnocentrism and xenophobia measures and adapted the remaining measures. adaptation was necessary because the original scales where either designed for a different context (and not the coronavirus pandemic) or consisted of more facets than what we intended to capture. the adaptation of scales was executed in two steps. first, two authors rephrased and deleted items while ensuring face and content validity vis-a-vis the definition and conceptual frame of the respective construct. employing this judgemental criterion is crucial because adapted scales may potentially alter the theoretical meaning of the measure; a problem that is not detectable by statistical criteria only (wieland, kock & josiassen, ) . second, we assessed the statistical parameters of each item and its respective scale through both exploratory and confirmatory factor analyses, verifying that the adapted scale is both reliable and valid (table ) . drawing on existing measures also required the adoption of the -point ordinal answer format of the original scales. while no single optimal survey format exists, ordinal scales can be prone to different types of response bias and impair both the data analysis and construct validity. thus, alternative answer formats (dolnicar, ) should be considered when a new scale is developed or substantially amended. we captured the perception of a pathogen threat related to the coronavirus pandemic by adapting the perceived infectability measure from ackerman et al. ( ) , which is a subscale of the perceived vulnerability to disease measure (duncan et al., ) . this measure has been confirmed in various seminal disease-related studies as a proxy for a perceived pathogen threat, and thus activation of the behavioral immune system. we adopted the measures of tourist xenophobia (kock et al. a ) and tourism ethnocentrism (kock et al., b) . in a pre-study, we had also included tourism xenophilia (nørfelt et al., ) but decided to drop it due to the high shared covariance with xenophobia. we also dropped the variable support for tourism development because it had been tested together with tourism ethnocentrism before (kock et al., b) . we adapted the crowding perceptions measure of wang and ackerman ( ) by showing respondents a picture of a crowded touristic situation for five seconds. respondents were instructed to pay attention and memorize the picture. after the five seconds, they were asked to remember how many people were in the scene, followed by two questions measured on -point ordinal scales: j o u r n a l p r e -p r o o f 'how likely are the people on the picture to bump into or brush against each other?' (very unlikely/very likely) and 'how crowded do you think the scene is?' (empty/ very crowded). further, we measured respondents' feelings toward crowdedness with the third question: 'how would you feel in this scene?' (very uncomfortable/very comfortable) (wang & ackerman, ) . as a control, we asked respondents how much they visualized themselves in the scene. lastly, we recorded respondents' age, gender, education and perceived own health. while we tested an indoor setting in this study (restaurant), future research on understanding crowdedness perceptions in the context of the pandemic is advised to examine potential differences between indoor and outdoor crowds. all measures met the key assumptions of multivariate normality (see table a in the supplementary data). discriminant validity between all measures was established through both the fornell-larcker criterion and the heterotrait-monotrait ratio criterion. assessing the correlations between each pair of constructs further corroborated the discriminant validity. for example , for tourist xenophobia and tourism ethnocentrism, the pairwise correlation was . . . everyone should support the american economy by spending their holiday in the us. . . it comes down to all americans to spend their holiday in the us and support the country. . . americans should spend their holiday in the us because this secures jobs in the american tourism industry. . . how likely are the people on the picture to bump into or brush against each other? . j o u r n a l p r e -p r o o f . how crowded do you think the scene is? . . how would you feel in this scene? we estimated a structural model through a covariance-based structural equation modelling approach in amos . the model fit was good ( /df = . ; cfi = . ; nnfi = . ; rmsea = . ; srmr = . ), indicating that the data fit the model well. the results (table ) provide strong support for our evolutionary approach, demonstrating the benefits of working within the evolutionary tourism paradigm to explain more distant and less obvious tourism phenomena. specifically, perceived vulnerability to covid- relates positively to crowding perceptions (. , p < . ), xenophobia (. , p < . ) and ethnocentrism (. , p < . ). further, vulnerability relates negatively to respondents' anticipated comfort with being in the crowded situation (-. , p < . ). we found no significant results with the demographic correlates or perceived own health. study study empirically demonstrated that the pathogen threat induced by the covid- pandemic has considerable associations with important phenomena in tourism that would not have been investigated without an evolutionary lens. to complement these insights, in study , we set out to empirically examine how a pathogen threat (ecology), as related to disease avoidance (ultimate motive), is associated with tourists' travel-related predispositions (phenotypic plasticities) as well as investigate the psychological roots of the pathogen threat. for this investigation, we draw on theory of disease avoidance from evolutionary psychology (e.g., tybur, lieberman & griskevicius, ) and its prior application in tourism (e.g., kock et al., a) as well as other disease-related tourism literature (cahyanto et al., ) . the nomological network is shown in figure . for study , we obtained the data in the second half of april . we followed a similar data collection approach as in study , thus we recruited american participants through the j o u r n a l p r e -p r o o f crowdsourcing platform mturk. we also included the same instructional manipulation check as in study . we collected completed questionnaires and another respondents were excluded due to failing the instructional manipulation check. the sample characteristics are provided in table . in order to identify those tourists who might be particularly prone to a pathogen threat, we captured respondents' disgust propensity. disgust propensity is a frequently used concept in evolutionary psychology that can explain individual differences in reactions toward disgust-eliciting cues such as pathogens, sexually-, or morally-offensive behavior (e.g., tybur et al., ) . we adapted the disgust propensity scale from tybur et al. ( ) . further, we measured tourists' covid- self-efficacy by adapting the scale from cahyanto et al. ( ) . this measure captures tourists' perceived selfefficacy in taking cognitive and behavioral actions that mitigate the probability of contracting covid- . we used the same two-step adaptation procedure as in study . in the same questionnaire, we also included the variable prevention focus but dropped it in the analysis due to its high covariance with the other two antecedents. in addition, we included the same perceived infectability measure as well as the same demographic variables as in study . we further included a set of travel-related predispositions that evolutionary psychology and tourism research hint may be behavioral consequences of the coronavirus threat: destination loyalty, intention to book travel insurance, group travel preference, vaccination intent, intention to engage with locals, and domestic travel intent. we would expect all these travel-related intentions to decrease, directly or psychologically, travel-related risks and should therefore relate positively to a perceived coronavirus threat. as such, they serve as adaptive phenotypic plasticities in an ecology that poses pathogen threats. for reasons of parsimony, we refer the reader to kock et al. ( a) and kock et al. ( b) for detailed discussions on these variables, their risk-mitigating functions and relation to xenophobia and ethnocentrism. we decided to exclude from the analysis travel vaccination, domestic travel intent and intent to engage with locals for external validity reasons. as for vaccination intent, due the course of the dynamic development of the pandemic, we could not ensure that participants would actually view the vaccination as a travel vaccination (and not a covid- vaccination which was not existent when data was collected). as for domestic travel, we could not ensure that participants would actually consider a foreign travel an alternative because travel restrictions were in place when data was collected. similarly, we could not ensure that respondents would consider the locals to be foreign. this research employs behavioral intention measures because actual travel behavior could not be meaningfully measured during the pandemic. this constitutes an inevitable limitation but we do not expect severe impairments of the validity of our results because the intentions we capture are not subject to social desirability. table presents the items used in the final model, and, for the multi-item measures, also the respective psychometric parameters. correlations between all constructs are included in the supplementary data (table c) . all items met the assumptions of multivariate normality ( table b in the supplementary data). the estimated model fits the data reasonably well: ( /df = . ; cfi = . ; nnfi = . ; rmsea = . ; srmr = . ). the results document that a perceived pathogen threat relates to tourists' travel-related predispositions (table ) . specifically, perceived infectability of the pandemic relates positively to group travel (. , p < . ), intention to book travel insurance (. , p < . ), and destination loyalty (. , p < . ). further, we find that disgust propensity relates positively to perceived infectability (. , p < . ), while covid- self-efficacy relates negatively to perceived infectability (-. , p < . ), thereby confirming our conceptualization. the coronavirus pandemic has revived people's existential anxieties by reminding them of their physical and economic vulnerability. it is during these times that our deeply-rooted evolutionary protection mechanisms are activated. these mechanisms, and the behavioral immune system in particular, have been shaped over thousands of years in our ancestral past. once activated, they are likely to override culturally learned and socially constructed paradigms in our contemporary lives. the current pandemic is a testament to this, and understanding its consequences for tourism research without considering an evolutionary lens results in an incomplete picture at best. evolutionary psychology bears significant potential to enhance our understanding of the impact of the coronavirus pandemic on tourists' psyche, as well as on various other tourism phenomena. the present paper conceptually develops and empirically documents the considerable untapped potential of evolutionary psychology for understanding the tourists' psyche in the covid- era. this j o u r n a l p r e -p r o o f is achieved by drawing researchers' attention to the principles of evolutionary psychology , which we tailor into a tourism research paradigm, visualized through the proposed ocean and islands model. by doing so, we hope to spur an infusion of biological epistemology and theorization into tourism research, encouraging researchers to begin exploring the evolutionary roots of tourist behavior. almost every behavior includes an evolutionary explanation, and by analyzing this explanation, we can better understand the effects of the coronavirus pandemic on the tourists' psyche, as well as tackle other modern-day problems in tourism. a key strength of evolutionary psychology and our paradigm is that it allows researchers to conceptually and empirically connect seemingly standalone phenomena to generate new knowledge. instead of examining only proximate motives that provide narrow explanations in one constraint area, evolutionary psychology can highlight parallels between seemingly unrelated phenomena by tracing them back to fundamental motives. this perspective allows for tracing various behaviors back to a common ultimate motive, such as the motive of disease avoidance. our research demonstrates this conceptual strength; in two consecutive studies, we document that taking an evolutionary perspective yields novel insights and creative explanations that would not have been generated without it. specifically, we found that the psychological concepts of ethnocentrism, xenophobia and crowdedness perceptions relate to perceived covid- infectability (study ). importantly, only the evolutionary reasoning paved the way to test these relationships because each of these phenomena provides a different way to cognitively or conatively adapt to and counter the pathogen threat. for example, xenophobia is a direct evolutionary means to minimize the risk of contagion. in addition, the behavioral phenomena of group travel preference, travel insurance and destination loyalty (study ) provide the tourist with a feeling of security that lowers travel-related risk perceptions. understanding that these, at first sight unrelated, phenomena relate to each other contributes to a deeper understanding of the relationship between the pandemic and tourists' psyche. based on these results, we urge future research to build on our endeavors to unveil more phenotypic plasticities (i.e., 'spotting more islands and palms in the ocean') . the fundamental motive of affiliation could, for example, be used to investigate how the social isolation of the covid- pandemic affects tourists' psyche. another strength of evolutionary psychology is its meta-level: evolutionary psychology is not a single theory but a rich interdisciplinary network of countless theories (i.e., it is a meta-theory). evolutionary psychology is therefore not a narrow field of research, but a way of thinking about and making sense of observed psychological phenomena. this constituent factor reshapes how evidence is reasoned in evolutionary psychology because it requires researchers to always ensure the logical alignment of the different types of explanation in both theory and results and across all examined phenomena. by paying attention to this logical alignment, an evolutionary perspective counteracts the emergence of isolated research areas, and thus helps to prevent the academic insulation of tourism research, and more broadly, the social sciences. a further strength of evolutionary psychology is that its theoretical foundations rest on complementary evidence from various disciplines, such as biology, psychology, genetics, and anthropology (saad, ) . this multi-disciplinary ethos also yields unique epistemological frameworks for developing new explanations for human behavior, as well as promoting methodological pluralism, because many hypotheses are best tested through the use of experimental study designs. this focus on experimental testing can also help to address recent calls for more experimental designs (viglia & dolnicar, ) . further, the fundamental motives are universal and thus applicable across cultures. however, it is important to emphasize that almost all behaviors include both an evolutionary and cultural explanation, thus we suggest a nature and nurture approach rather than a dogmatic nature vs. nurture approach. importantly, while an evolutionary approach is powerful in identifying new phenomena and tackling these phenomena through new approaches, it is not a justification for the observed behavior. although evolutionary psychology offers an explanation for why people may become more xenophobic, it does not imply that xenophobia or other social problems are inevitable and should be accepted. insight from evolutionary psychology may even be used to limit such tendencies (griskevicius, cantú & van vugt, ) . as an example, cues of invulnerability to disease (schaller, park & faulkner, ) may be used to situationally lower perceived covid- infectability and tourist xenophobia in places where interaction between residents and tourists is frequent. there is a long-standing divide with "soft" or social sciences on one side and "hard" or natural sciences (such as evolution and ecology) on the other side. while scholars in both domains study behavior, their epistemologies and theories are only rarely applied across disciplinary borders. the current pandemic highlights that new research perspectives may be needed to more holistically understand the complex effects and intertwined consequences for applied fields such as tourism. this pandemic urges us to consider that the time is right to join forces by building bridges between the social and natural sciences. this research provides conceptual and empirical evidence of the usefulness of the evolutionary tourism paradigm to inform research specifically on this pandemic and, more broadly, on tourism. infectious disease and imperfections of self-image the nature of followership: evolutionary analysis and review. the leadership quarterly infections and elections: did an ebola outbreak influence the us federal elections (and if so, how)? the proximate/ultimate distinction in the multiple careers of ernst mayr the antecedents of modern leisure social return and intent to travel the dynamics of travel avoidance: the case of ebola in the us travelers' health risk perceptions and protective behavior: a psychological approach disgust as an adaptive system for disease avoidance behaviour asking good survey questions perceived vulnerability to disease: development and validation of a -item self-report instrument evolved disease-avoidance mechanisms and contemporary xenophobic attitudes skip the trip: air travelers' behavioral responses to pandemic influenza parasite-stress promotes in-group assortative sociality: the cases of strong family ties and heightened religiosity pathogen prevalence predicts human cross-cultural variability in individualism/collectivism crowdsourcing consumer research the evolutionary bases for sustainable behavior: implications for marketing, policy, and social entrepreneurship fundamental motives: how evolutionary needsinfluence consumer behavior the evolution of cognitive bias the handbook of evolutionary psychology common concerns with mturk as a participant pool: evidence and solutions determinants of health risk perception among low-risk-taking tourists traveling to developing countries renovating the pyramid of needs: contemporary extensions built upon ancient foundations an analysis of data quality: professional panels, student subject pools, and amazon's mechanical turk an evolutionary perspective on risk taking in tourism fear of ebola: the influence of collectivism on xenophobic threat responses on the origin of tourist behavior the xenophobic tourist tourism ethnocentrism and its effects on tourist and resident behavior developing courageous research ideas assessing impacts of sars and avian flu on international tourism demand to asia crowding at an arts festival: extending crowding models to the frontcountry tourist roles, perceived risk and international tourism tourists' perceptions of crowding, attractiveness, and satisfaction: a second-order structural model threat (s) and conformity deconstructed: perceived threat of infectious disease and its implications for conformist attitudes and behavior disease avoidance and ethnocentrism: the effects of disease vulnerability and disgust sensitivity on intergroup attitudes elevated ethnocentrism in the first trimester of pregnancy tourism xenophilia: examining attraction to foreignness cause and effect in biology socioecological psychology instructional manipulation checks: a longitudinal analysis with implications for mturk knowledge, risk perceptions, and xenophobic attitudes: evidence from italy during the ebola outbreak psychological research in the internet age: the quality of web-based data travel anxiety and intentions to travel internationally: implications of travel risk perception on the method of evolutionary psychology and its applicability to consumer research pathogens, personality, and culture: disease prevalence predicts worldwide variability in sociosexuality, extraversion, and openness to experience danger, disease, and the nature of prejudice(s) advances in experimental social psychology the behavioral immune system (and why it matters) prehistoric dangers and contemporary prejudices the behavioral ecology of cultural psychological variation feeling excluded? join the crowd: how social exclusion affects approach behavior toward consumer-dense retail environments on aims and methods of ethology human pathogen avoidance adaptations microbes, mating, and morality: individual differences in three functional domains of disgust international tourism highlights editorial overview: what is socio-ecological psychology a review of experiments in tourism and hospitality the infectiousness of crowds: crowding experiences are amplified by pathogen threats travellers' self-protections against health risks: an application of the full protection motivation theory effects of misleading media coverage on public health crisis: a case of the novel coronavirus outbreak in china scale purification: state -of-the-art review and guidelines coronavirus pandemic and tourism: dynamic stochastic general equilibrium modeling of infectious disease outbreak the coronavirus pandemic-a critical discussion of a tourism research agenda key: cord- -ykcd d authors: cheung, carmen ka man; law, man fai; lui, grace chung yan; wong, sunny hei; wong, raymond siu ming title: coronavirus disease (covid- ): a haematologist's perspective date: - - journal: acta haematol doi: . / sha: doc_id: cord_uid: ykcd d coronavirus disease (covid- ) is affecting millions of patients worldwide. it is caused by the severe acute respiratory syndrome coronavirus (sars-cov- ), which belongs to the family coronaviridae, with % genomic similarities to sars-cov. lymphopenia was commonly seen in infected patients and has a correlation to disease severity. thrombocytopenia, coagulation abnormalities, and disseminated intravascular coagulation were observed in covid- patients, especially those with critical illness and non-survivors. this pandemic has caused disruption in communities and hospital services, as well as straining blood product supply, affecting chemotherapy treatment and haematopoietic stem cell transplantation schedule. in this article, we review the haematological manifestations of the disease and its implication on the management of patients with haematological disorders. coronavirus disease is caused by the severe acute respiratory syndrome coronavirus (sars-cov- ), a positive-strand rna virus belonging to the family coronaviridae with about % genomic similarities with sars-cov [ ] [ ] [ ] . the virus is highly contagious, with over million confirmed cases causing more than , deaths worldwide, reported to the who by the end of april [ ] [ ] [ ] [ ] [ ] . viral infection is well known to be associated with abnormal haematological parameters. autopsy of patients who died of covid- showed markedly shrunken spleen with reduced lymphocyte, macrophage proliferation, and phagocytosis [ ] . lymphocytes were also depleted in lymph nodes, and all haematopoietic cell lineages were reduced in the bone marrow. the battle against covid- is likely to be a marathon and the pandemic has a major impact on health care systems in many countries [ ] . the virus will continue to pose a risk to people without immunity to it. in this article, we review the haematological manifestations of covid- and its implications on the management of patients with haematological disorders. lymphopenia is a common finding in viral infection. in a multicentre study including , patients from sites in china, lymphopenia was present in . % of patients on admission [ ] . many other studies in china reported rates of lymphopenia ranging from % to % (table ) [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . in a large us series that included , patients, lymphopenia was present in around % ( , ) of patients on initial laboratory tests [ ] . lymphopenia was observed on admission in . and % of cov-id- patients reported in singapore and korea, respectively [ , ] . lymphopenia has been consistently found to correlate with the severity of covid- infection and might have a predictive value in the clinical setting. zhou et al. [ ] evaluated risk factors for mortality in a retrospective cohort study involving patients and showed that baseline lymphocyte count was significantly higher in survivors than non-survivors ( . × /l versus . × /l, p < . ). in survivors, lymphocyte count was lowest on day after onset of illness and improved during hospitalization, whereas severe lymphopenia was observed until death in non-survivors. in another retrospective analysis of cases, zhang et al. [ ] demonstrated that the level of lowest lymphocyte count correlated with disease severity and a composite endpoint including intensive care unit (icu) admission, mechanical ventilation, or death. among patients with lymphocyte counts < . × /l, . % were classified as severe cases and all of them reached the composite endpoint, while in patients with lymphocyte counts > . × /l, only . % were severe cases and . % reached the composite end point. in a retrospective cohort including patients, lymphopenia during the disease course was also reported to be associated with the development of acute respiratory distress syndrome (ards) [ ] . a significantly higher number of patients requiring treatment in icu had low lymphocyte counts on presentation [ , , ] . fan et al. [ ] also found that on serial monitoring, the median nadir absolute lymphocyte count in the icu group was . × /l compared to . × /l in the non-icu group. wang et al. [ ] analysed dynamic changes in the haematological parameters of patients from day to day after onset of disease and showed that non-survivors developed more severe lymphopenia over time. lymphopenia was frequently encountered in patients requiring icu care, ranging from % to % in various case series [ ] [ ] [ ] . however, there was no significant difference in median lymphocyte counts between survivors and non-survivors in a retrospective observational study involving critically ill patients in wuhan [ ] . depletion of t cells and nk cells was seen in patients suffering from covid- [ , [ ] [ ] [ ] . lymphopenia on presentation correlated with a high viral load, as reflected by the low cycle threshold value in respiratory samples [ ] . liu et al. [ ] analysed the correlation between dynamic changes in the nasopharyngeal viral load and the lymphocyte count. it was found that the higher the rna load in the nasopharynx, the lower the cd + and cd + t lymphocyte count and these changes were closely related to the severity of covid- . jiang et al. [ ] evaluated lymphocyte subsets in patients, which revealed that cd +, cd +, and cd + t cells and nk cells were significantly decreased in covid- patients with a more severe decrease in cd + t cells compared with cd + t cells. in addition, severe covid- patients showed significant decreases in lymphocyte subset counts compared to mild to moderate patients, especially in cd +, cd +, and cd + t cells [ ] . another study analysed lymphocyte subsets of patients at presentation and found that both cd + and cd + t cells were below normal levels in patients with covid- infection, but the decline in cd + cells was more pronounced in severe cases [ ] . the percentage of naïve helper t cells (cd +, cd +, cd ra+) increased and memory helper t cells (cd +, cd +, cd ro+) decreased in severe cases when compared with non-severe cases [ ] . wan et al. [ ] analysed lymphocyte subsets in patients on the first day of hospital admission and - days before discharge. although there was a greater reduction of cd + and cd + t cells in the severe group, both cd + and cd + t cells improved before discharge, suggesting that the cellular immunity had been restored. liu et al. [ ] reported that the decrease of t cells, especially cd + t cells, in the severe patient group reached its lowest within the first week during the course of the disease, and then t cell numbers gradually increased during the second week with recovery to a level comparable to that of the mild patient group in the third week. all the severe patients survived the disease in the study [ ] . another study which compared lymphocyte subsets before and after treatment showed that post-treatment decrease of cd + t cells and b cells and increase of cd +/cd + ratio were independent predictors of poor treatment efficacy [ ] . lower cd t lymphocyte counts may predict a longer persistence of sars-cov- rna in stool, where viral clearance may be further delayed by corticosteroid [ ] . hence, lymphocyte subset may serve as a biomarker for disease evolution, and its monitoring may help to predict disease outcome. sars-cov- could trigger necrosis or apoptosis of lymphocytes resulting in lymphopenia. the virus induced nkg a expression and possibly correlated with functional exhaustion of nk and cd + t cells at an early stage, resulting in disease progression [ ] . a dysregulated/exuberant innate response also contributed to sars-cov-mediated pathology [ ] . cytokine storm with elevation of interleukin (il)- r, il- , il- β, il- , il- , granulocyte colony-stimulating factor (g-csf), tumour necrosis factor-α (tnf-α), ip , mcp , and mip α was seen in covid- patients and may also lead to lymphopenia [ ] . compared to lymphopenia, thrombocytopenia is less commonly seen in patients suffering from covid- . the reported rates of thrombocytopenia varied from less than % to about . % (table ) [ , , , , , , , , , ] . platelet count has been evaluated as a biomarker to predict the severity of covid- in multiple studies, but the results were confounded by heterogeneity regarding definitions of thrombocytopenia and endpoints used. two meta-analyses showed that a lower platelet count is associated with an increased risk of severe disease and mortality in patients with covid- and may serve as a marker for progression of illness [ , ] . in the multicentre study by guan et al. [ ] , thrombocytopenia (platelet count < × /l) on admission was more commonly seen in severe ( . %) than nonsevere ( . %) patients [ , ] . zhou et al. [ ] reported that % of non-survivors had platelet counts less than × /l on admission compared to only % in survivors (p < . ). in contrast, no difference in platelet count on admission was observed between patients requiring icu care compared with those that did not in other studies [ , ] . a study that monitored the sequential changes in platelet count in the first weeks after admission found that there was a gradual drop in platelet counts with a lower nadir among non-survivors compared to survivors ( vs. [ - ], p < . ) [ ] . dynamic changes of platelets were also reported to be closely related to mortality [ ] . an increment in platelets was associated with decrease in mortality, suggesting the role of monitoring platelets in predicting prognosis during hospitalization [ ] . a case series including hospitalized covid- patients evaluated the prognostic value of dynamic changes in platelet count and found that a higher platelet-to-lym-phocyte ratio (plr) at peak platelet count was associated with longer hospital stay and the change in plr was more prominent in severe patients, which may be caused by cytokine storm provoking inflammation resulting in the stimulation and release of platelet [ ] . yang et al. [ ] analysed the predictive role of plr and showed that a higher plr was seen in severe patients ( . ± . ) compared to non-severe patients ( . ± . ; p < . ). elevated plr showed a trend of association with disease progression (hazard ratio [hr] . , % ci . - . by multivariate cox regression), but the statistical significance was lost after adjustment of gender and age, limiting its clinical utility [ ] . experience from previous sars patients, caused by sars-cov- , suggested that coronavirus could cause thrombocytopenia by direct viral infection of bone marrow haematopoietic stem cells via cd or cd a, formation of auto-antibodies and immune complexes, disseminated intravascular coagulopathy (dic), and consumption of platelet in lung epithelium [ , ] . higher soluble vascular cell adhesion molecule- (svcam- ) level was found in sars patients, which enhanced vascular sequestration resulting in thrombocytopenia [ ] . several mechanisms by which covid- causes thrombocytopenia have been proposed, including (a) reduction in platelet production due to direct infection of bone marrow cells by the virus, destruction of bone marrow progenitor cells by cytokine storm, and indirect effect of lung injury; (b) increased platelet destruction by autoantibodies and immune complex; and (c) platelet aggregation in the lungs, resulting in microthrombi and platelet consumption [ ] . cytokine storm of severe disease may lead to secondary haemophagocytic lymphohistiocytosis, which can also result in thrombocytopenia [ ] . thrombocytopenia-associated bleeding is uncommon in covid- . platelet transfusion is recommended in patients with active bleeding and a platelet count less than × /l. for patients at high risk but without active bleeding, platelet transfusion may be considered if the platelet count is less than - × /l [ ] . anaemia is not a major problem in patients suffering from covid- [ , , , , , , , ] . in a cohort of patients with covid- , only . % of them required blood transfusion, while the transfusion requirement was higher in those admitted to icu [ ] . been reported, including blood loss during continuous renal replacement therapy and gastrointestinal bleeding with or without anticoagulant use [ ] . autoimmune haemolytic anaemia was also reported in patients with covid- within a timeframe compatible with the development of cytokine storm [ ] . sars-cov- can enter epithelial cells of the gastrointestinal tract via the angiotensin-converting enzyme (ace ) receptor [ ] . endoscopy revealed oesophageal bleeding caused by erosions and ulcers with detection of sars-cov- in a patient with severe infection [ ] . sars-cov- was demonstrated in gastric, duodenal, and rectal epithelial cells by rna detection and intracellular staining of viral nucleocapsid protein [ ] . the direct viral invasion into the gastrointestinal tract may result in mucosal damage resulting in bleeding and subsequent need of blood transfusion. ribavirin has been used as treatment for covid- [ , ] . haemolytic anaemia is one of the major side effects of ribavirin, but most patients did not require transfusion according to previous sars experience [ ] . a randomized controlled trial on the safety and efficacy of its use in covid- patients is ongoing [ ] . adequate haemoglobin level is important to ensure sufficient tissue oxygenation. phlebotomy by small-volume blood tubes may help to reduce iatrogenic blood loss [ ] . iron replacement should be given to patients with pre-existing iron deficiency anaemia. use of erythropoiesis-stimulating agents in critically ill patients should be cautious if thromboembolic event is a concern [ ] . decision on allogeneic red cell transfusion should be individualized. a single-unit policy should be followed whenever possible [ ] . diverse coagulation abnormalities in covid- infection have been described [ , , , , , , , ] . a study in chongqing showed that the majority of the patients had normal coagulation indexes, probably explained by the fact that % of the included patients had mild disease [ ] . dic is characterized by activation of coagulation and generation and deposition of fibrin, leading to microvascular thrombi deposition in various organs and subsequently multiple organ dysfunction, which predicts mortality in septic patients [ ] . tang et al. [ ] studied coagulation parameters in patients suffering from covid- and found that . % of non-survivors devel-oped overt dic compared to only . % among survivors. patients who died had significantly higher d-dimer, fibrin degradation product levels, and longer pt on admission [ ] . the study by guan et al. [ ] showed that . % patients who reached the primary composite endpoint (icu admission, mechanical ventilation, or death) had elevated d-dimer level (≥ . mg/l) on admission compared to . % not reaching the primary endpoint. wu et al. [ ] showed that significant prolongation of pt (median . s) and higher d-dimer level ( . μg/ml) at presentation were observed in patients with ards compared to those without (median pt . vs. . s, median d-dimer level . vs. . μg/ml, p < . for both comparisons). elevated d-dimer level has been shown to be associated with higher mortality rates in various studies [ , , , ] . in a retrospective study including patients in wuhan, patients with d-dimer levels ≥ μg/ ml on admission had higher mortality compared to those with d-dimer level < μg/ml (hr . , % ci . - . ) [ ] . a d-dimer cut-off value of ≥ μg/ml on admission could predict in-patient mortality with a sensitivity of . % and a specificity of . % [ ] . prolongation of pt and markedly elevated d-dimer on admission were associated with poor prognosis and were more commonly seen in patients requiring icu care [ , ] . in addition to coagulation parameters on presentation, dynamic change in coagulation profile could predict disease severity and progression. tang et al. [ ] reported dynamic changes in coagulation parameters from day to day after admission. non-survivors demonstrated significant increase in d-dimer and fibrin degradation product as well as prolongation of pt by day - , while fibrinogen and antithrombin activity were significantly lower when compared with survivors [ ] . other studies also showed similar findings of a gradual increase in d-dimer levels among non-survivors [ , ] . pooled results in a metaanalysis including studies revealed that pt and d-dimer levels were significantly higher in patients with severe covid- [ ] . dynamic change in fibrinogen concentration has also been shown to correlate with an increased risk of death [ ] . covid- patients with acute respiratory failure presented with severe hypercoagulability due to hyperfibrinogenaemia resulting in increased fibrin formation and polymerization that may predispose to thrombosis [ ] . the systemic inflammatory response triggered by viral infection results in an imbalance in homeostatic procoagulant and anticoagulant. cytokine storm, endothelial dysfunction, von willebrand factor elevation, tolllike receptor activation, and tissue-factor pathway activa- doi: . / tion may contribute to hypercoagulability [ ] . overactivation of nadph oxidase- (nox ), resulting in increased reactive oxidant species, is implicated in arterial vasoconstriction, clotting, and platelet activation [ ] . tang et al. [ ] provided data in a retrospective study on patients and showed that anticoagulant with unfractionated heparin ( , - , u/day) or low-molecular-weight heparin (lmwh, enoxaparin - mg/ day) reduced mortality in patients with sepsis-induced coagulopathy score (a scoring system including platelet count, pt, and major organ failure assessment) of ≥ (from . % to . %, p = . ) [ , ] . a % reduction in mortality was also seen in patients with d-dimer level -fold the upper limit of normal who received anticoagulant [ ] . interestingly, no improvement in mortality was seen in anticoagulation therapy for patients with severe pneumonia caused by pathogens other than sars-cov- even with high d-dimer level [ ] . a brief report showed that % of patients with severe covid- requiring icu care developed venous thromboembolism (vte) [ ] , which may explain the promising results of anticoagulation. in a cohort of patients admitted to the icu who received at least standard doses of thromboprophylaxis, the cumulative incidence of vte and arterial thrombosis was % [ ] . coagulopathy, defined as spontaneous prolongation of pt > s or aptt > s, was an independent predictor of thrombotic complications (adjusted hr . , % ci . - . ). in another multicentre prospective cohort of patients with ards admitted to icu, ( . %) of them developed pulmonary embolisms and ( %) developed deep vein thrombosis despite prophylactic or therapeutic anticoagulation [ ] . since diagnostic tests were only performed based on clinical suspicion, the actual incidence of thrombosis could have been underestimated. llitjos et al. [ ] conducted a retrospective study on patients admitted to icu with systematic screening of vte using complete duplex ultrasound performed on days - of icu admission, followed by a second scan on day if the first one was negative. the incidence of vte was % in the group of patients who received anticoagulation [ ] . autopsy of consecutive covid- deaths revealed deep vein thrombosis in patients ( %) in whom vte was not suspected before death. pulmonary embolism was the direct cause of death in patients [ ] . histologic analysis of pulmonary vessels in patients who died from covid- showed widespread thrombosis with microangiopathy and a much higher prevalence of alveolar capillary microthrombi when compared with those who died from influenza-associated respiratory failure [ ] . in addition to vte, arterial thromboses such as acute myocardial infarction have been reported [ ] . large vessel stroke can be a presenting feature in young patients [ ] . in a retrospective study of hospitalized patients from wuhan, . % of the severe patients suffered from acute cerebrovascular disease [ ] . hypercoagulability was also demonstrated in icu patients with respiratory failure by thromboelastography [ ] . all these findings suggested a pro-coagulant tendency in covid- patients, especially if critically ill. middeldorp et al. [ ] administered thromboprophylaxis to all patients admitted for covid- . patients admitted to the general ward received nadroparin , iu once daily or , iu for patients with a body weight of ≥ kg. from april onwards, the dose of anticoagulation in icu patients was doubled. symptomatic vte was detected in out of ( %) icu patients and out of ( . %) ward patients (sub-distribution hazard ratios . ; % ci . - ) [ ] . lodigiani et al. [ ] studied venous and arterial thromboembolic complications in hospitalized patients. thromboprophylaxis was used in all icu patients and % of those on the general ward. eight events occurred in icu patients ( . %; % ci . - . %), while events occurred in patients on the general ward ( . %; % ci . - . %), corresponding to cumulative rates of . and . %, respectively. importantly, events in the general ward occurred in patients with cancer, highlighting that additional risk factors might further increase the risks of vte [ ] . racial difference on thrombotic risk should also be taken into consideration [ ] . the international society on thrombosis and haemostasis (isth) suggested all patients (including non-critically ill) who require hospital admission for covid- infection should receive a prophylactic dose of lmwh unless contraindicated (table ) [ ] . lmwh was the preferred drug of choice due to a high instability of international normalized ratio for vitamin k antagonists and drug-drug interaction between direct oral anticoagulants and anti-viral agents [ ] . the american society of hematology (ash) recommended all hospitalized patients with covid- should receive pharmacological thromboprophylaxis. if it is contraindicated or unavailable, mechanical prophylaxis should be implemented [ ] . however, the recommendations of pharmacological thromboprophylaxis on non-critically ill patients are still controversial [ , ] . we recommend physicians stay vigilant to thrombotic complication. decision on thromboprophylaxis should also be based on clinical judgement and other risk factors, such as prolonged immobilization, active malignancy, obesity, previous history of vte, and ethnicity. the efficacy, safety, and optimal dosage of anticoagulation in non-critically ill covid- patients need to be confirmed by prospective studies. a more recent consensus statement recommended vte risk assessment for non-critically ill patients, and only to consider pharmacological thromboprophylaxis in patients with a moderate to high risk of vte [ ] . a significant reduction of blood donations has been reported after the outbreak [ ] . possible reasons include lockdown, stay-at-home order, anxiety for volunteer donors to attend blood donation centres, and additional deferral policy on travel history. the number of eligible donors may further decrease if the outbreak continues to evolve. establishment of a crisis system to reduce usage (e.g., deferring elective surgery), coordination of blood products delivery to areas with a shortage, use of social media to promote blood donation, etc. might help to overcome the crisis of paucity in blood supply [ ] . if the supply of blood product is limited, there may be a need to adopt a more restrictive blood transfusion approach. transfusion alternatives such as use of iron supplement in iron deficiency anaemia and erythropoiesisstimulating agents should be encouraged. currently there is no reported case of transmission of the coronavirus from donor to recipient through blood product transfusion or cellular therapies, but given that sars-cov- rna was detected in the serum of covid- patients [ ] , the actual risk of transfusion transmission of sars-cov- remains unknown [ ] . there is no additional screening test for blood donors recommended by the american association of blood banks (aabb) at the moment [ ] . use of riboflavin and ultraviolet light-based photochemical treatment to plasma and platelet products may be effective in reducing the theoretical risk of transfusion-transmitted sars-cov- [ ] . the covid- pandemic poses a big challenge for the medical community, with a great impact on management of patients with haematological conditions. in a cohort study of hospitalized subjects with haematological cancers at two centres in wuhan, they have a similar rate of covid- compared with normal health care providers but have more severe disease and a higher case fatality rate [ , ] . non-hospitalized patients with haematological cancers may also have a higher chance of developing symptomatic covid- . in a study using a questionnaire to evaluate subjects with chronic myeloid leukaemia in hubei, prevalence of covid- in chronic myeloid leukaemia patients was -fold higher than the . % reported in normal [ , ] . chemotherapy and transplant schedules have been affected during the outbreak when hospitals are overwhelmed by confirmed covid- cases. the huge demand in isolation facilities compromises the care of patients who have received myelosuppressive therapy complicated with profound neutropenia requiring isolation rooms and prolonged hospitalization. treatment may also be deferred due to lockdown, quarantine order, disrupted medical health care service, shortage of isolation bed and blood product, and phobia towards attending hospital. delay in treatment may have a negative impact on the clinical conditions and outcomes of patients, especially those with more aggressive diseases. their need for timely treatment should not be neglected. in general, less essential service should be postponed [ ] in order to reduce the number of patients requiring hospital care so as to minimise risk of nosocomial covid- infection, to conserve personal protective equipment for high-risk clinical activities, and to maintain the capacity of the health care system. monitor d-dimers, pt, platelet count, and fibrinogen can help to stratify patients who may need admission and close monitoring prophylactic dose lmwh should be given to all patients (including non-critically ill) who require hospital admission unless contraindicated (active bleeding and platelet count < × /l) transfuse and aim platelet count above × /l; fibrinogen above . g/l; pt < . lmwh, low-molecular-weight heparin; pt, prothrombin time. cheung/law/lui/wong/wong acta haematol doi: . / table . suggested strategies in the management of haematological malignancies under covid- pandemic [ , [ ] [ ] [ ] disease management recommendation aml induction and consolidation -all patients should be tested for covid- prior to initiation of intensive chemotherapy -delay treatment if possible for patients positive for covid- -standard induction therapy should be offered to eligible patients -intermediate-dose cytarabine ( . g/m ) or decreasing the number of consolidation cycles can be considered in patients who achieve complete remission salvage therapy -intensive re-inductions should be performed according to the algorithms of the individual centre -for patients without proliferative disease or significant transfusion dependence, therapy may be temporarily postponed hsct -consider cryopreservation of donor cells prior to the start of conditioning apl -standard regime including atra and ato should be given -prophylactic dexamethasone should be considered for patients at high risk of differentiation syndrome all induction and consolidation -all patients should be tested for covid- prior to initiation of intensive chemotherapy -delay treatment if possible for patients positive for covid- ; intrathecal chemotherapy may be given if cns symptoms are present -philadelphia chromosome negative -proceed with standard curative induction therapy -dose reduction may be considered for patients at high risk for complications -philadelphia chromosome positive -consider tki with minimal steroid exposure as initial treatment salvage therapy -treatment that can be administered at outpatient setting such as inotuzumab or blinatumomab should be considered for b-all hsct -allogeneic hsct should be considered for patient who achieved cr despite the pandemic aggressive lymphoma -standard regime such as r-chop for diffuse large b-cell lymphoma and da-epoch-r for double-hit and primary mediastinal b-cell lymphomas should be offered -dose reduction or limiting treatment cycle can be considered for elderly or early stage disease -consider subcutaneous rituximab to reduce patient's time spent in clinical area -for relapse/refractory disease, admission for asct may be delayed if another cycle of outpatient chemotherapy can be administered indolent lymphoma -treatment deferral with close monitoring is recommended for asymptomatic patients -when treatment is indicated, consider rituximab monotherapy rather than chemoimmunotherapy -treatment options that minimize clinic or chemotherapy unit visits are preferred hl initial therapy -strategies to reduce the risk of bleomycin pneumonitis should be prioritized especially during the pandemic -standard treatment such as abvd, aavd, and radiotherapy should be given general recommendation -patients should be tested for covid- before hospital admission, starting a new treatment, cell apheresis, or asct in countries with high spread of sars-cov- -treatment re-schedule and de-intensification can be considered for responding patients -patients receiving bisphosphonates should reduce frequency of drug infusion to every months or temporarily withheld transplant eligible -bortezomib, lenalidomide, or daratumumab-based triplet therapy for - cycles should be offered -for patients with standard risk disease, delay asct by additional induction cycles and/or lenalidomide maintenance -patients with high-risk disease may proceed with asct after exclusion of covid- infection transplant ineligible -dexamethasone should be reduced to mg weekly -all-oral drug combinations, e.g., lenalidomide with dexamethasone, are preferred -addition of bortezomib or daratumumab can be considered for patients with high-risk disease relapsed/refractory -watchful waiting may be considered for biochemical relapses -orally administered agents (such as ixazomib, lenalidomide, pomalidomide, and panobinostat) should be considered -modify treatment regime to minimize clinic/hospital visit, such as once weekly instead of twice weekly bortezomib/ carfilzomib and monthly daratumumab infusions are recommended confirmed covid- -if anti-myeloma treatment has been started, therapy might be continued for asymptomatic covid- infection, although pausing of treatment is also an option; steroids and drugs inducing lymphopenia should be de-intensified -for symptomatic infection, treatment should be interrupted and steroids should be tapered to zero until full recovery from covid- aavd, brentuximab vedotin, adriamycin, vinblastine, dacarbazine; abvd, adriamycin, bleomycin, vinblastine, dacarbazine; all, acute lymphoblastic leukaemia; aml, acute myeloid leukaemia; apl, acute promyelocytic leukaemia; asct, autologous stem cell transplantation; atra, all-trans-retinoic acid; ato, arsenic trioxide; bcr, b-cell receptor; cll, chronic lymphocytic leukaemia; cml, chronic myeloid leukaemia; cns, central nervous system; cr, complete remission; da-epoch-r, dose-adjusted etoposide, prednisolone, vincristine, cyclophosphamide, doxorubicin-rituximab; hl, hodgkin lymphoma; hsct, haematopoietic stem cell transplantation; mm, multiple myeloma; nhl, non-hodgkin lymphoma; pd- , programmed cell death protein ; r-chop, rituximabcyclophosphamide, doxorubicin, vincristine, prednisolone; tfr, treatment-free remission; tki, tyrosine kinase inhibitor. life-saving chemotherapy for conditions such as acute leukaemia or aggressive lymphoma should not be delayed. watchful waiting approach may be considered for patients with indolent diseases if the risk of severe co-vid- infection outweighs treatment benefit, while single-agent monoclonal antibody instead of combination chemoimmunotherapy can be considered in patients who require treatment. oral formulation is preferred to intravenous injection to minimize hospital visit. prioritization and triage of anti-cancer therapy should be based on disease-and patient-specific considerations through communication with specialists and patients [ ] . recommendations on induction, consolidation, and salvage therapies on haematological malignancy during the pandemic by the ash, european hematology association (eha), and international myeloma society are summarized in table [ , [ ] [ ] [ ] . primary prophylaxis using g-csf in patients receiving intensive chemotherapy reduces the risk of febrile neutropenia and the risk of hospitalization and thus should be considered [ , ] . effective non-immunosuppressive treatments, such as intravenous immunoglobulin and thrombopoietin receptor agonists, may be considered in lieu of high-dose steroid for patients with immune thrombocytopenia purpura and severe thrombocytopenia. if patients are stable on low doses of immunosuppressive drugs, no modification of drug regimen is needed. infection prevention measures such as hand hygiene in ambulatory chemotherapy centres or clinics should be implemented. screening procedures, including questionnaire on respiratory symptoms, travel and contact history, and measuring of body temperature, should be performed for patients and hospital visitors [ ] . patients may benefit from increased surveillance of sars-cov- infection and protective isolation [ ] [ ] [ ] . psychosocial support should be provided where possible, when measures of social distancing might have affected the well-being of patients with haematological malignancies. great obstacles on allogeneic haematopoietic stem cell transplantation have been encountered during the co-vid- outbreak. closure of international borders, travel restriction, and shutdown of air travel has affected international donor travel and the shipping of cellular products. cryopreserved stem cell transplantation during the pandemic can be considered if alternative cellular products or donors are not available and does not appear to have a negative impact on the long-term outcome [ , ] . appropriate measures such as home quarantine and screening of donors for covid- prior to donation should be implemented in areas with a high frequency of sars-cov- infection [ ] . all transplant recipients should also be tested negative for sars-cov- irrespective of respiratory symptoms before initiating conditioning chemotherapy [ ] . treatment cycles may be increased to achieve a deeper remission before proceeding to allogeneic haematopoietic stem cell transplantation. the european society for blood and marrow transplantation (ebmt) proposed suggestions on haematopoietic stem cell transplantation during the covid- pandemic, which is shown in table [ ] . in summary, the covid- disease has had notable haematological manifestations. lymphopenia, thrombocytopenia, and coagulation abnormalities on presentation and during the disease courses have been associated with poor outcomes, and serial monitoring is recommended. physicians should stay vigilant against vte and for transplant candidate ---for confirmed covid- patients with high-risk malignancy, hsct should be deferred for a minimum of days until the patient is asymptomatic and has two negative virus pcr swabs taken at least h apart in patients infected with covid- with low-risk malignancy, a -month hsct deferral is recommended for patients who had close contact with a person diagnosed with covid- , any transplant procedures (pbsc mobilization, bm harvest, conditioning) shall not be performed within at least days from the last contact for donor ---donors should have been asymptomatic for at least days before donation and a negative test for covid- is recommended in case of diagnosis of covid- , donor should be excluded from donation. stem cell collection should be deferred for at least days after recovery. if the recipient's need for transplant is urgent and the donor is completely well and there are no suitable alternative donors, an earlier collection may be considered if local public health requirements permit, subject to careful risk assessment in case of close contact with a person diagnosed with sars-cov- , the donor shall be excluded from donation for at least days; if the patient's need for transplant is urgent, the donor is completely well, a test is negative for sars-cov- , and there are no suitable alternative donors, earlier collection may be considered subject to careful risk assessment bm, bone marrow; hsct, haematopoietic stem cell transplantation; pbsc, peripheral blood stem cell; pcr, polymerase chain reaction. consider pharmacological thromboprophylaxis in highrisk patients. changes in clinical practice are unavoidable in the current pandemic. treatment decision should be tailored on an individual basis to minimize risk of infection without jeopardizing the disease outcome. coronavirus infections and immune responses a new coronavirus associated with human respiratory disease in china. nature a pneumonia outbreak associated with a new coronavirus of probable bat origin who health emergency dashboard coronavirus (covid- ): world health organization (who) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study estimation of the reproductive number of novel coronavirus (covid- ) and the probable outbreak size on the diamond princess cruise ship: a data-driven analysis preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a data-driven analysis in the early phase of the outbreak chinese clinical guidance for covid- pneumonia diagnosis and treatment the untold toll -the pandemic's effects on patients without covid- china medical treatment expert group for covid- . clinical characteristics of coronavirus disease in china epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan. china: jama initial clinical features of suspected coronavirus disease in two emergency departments outside of hubei clinical characteristics of patients infected with sars-cov- in wuhan clinical characteristics and imaging manifestations of the novel coronavirus disease (covid- ): a multi-center study in wenzhou city clinical features and treatment of co-vid- patients in northeast chongqing early clinical and ct manifestations of coronavirus disease (cov-id- ) pneumonia clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province clinical features of covid- in elderly patients: a comparison with young and middle-aged patients clinical characteristics of medical workers ct features of coronavirus disease (covid- ) pneumonia in patients in wuhan, china clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by sars-cov- chest ct findings in patients with coronavirus disease and its relationship with clinical features novel coronavirus ( -ncov) pneumonia. radiology clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series clinical characteristics of cases of corona virus disease (covid- ) in changsha differences between covid- and suspected then confirmed sars-cov- -negative pneumonia: a retrospective study from a single center clinical features of patients infected with novel coronavirus in wuhan and the northwell covid- research consortium. presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the hematologic parameters in patients with covid- infection korea national committee for clinical management of covid- . clinical course and outcomes of patients with severe acute respiratory syndrome coronavirus infection: a preliminary report of the first patients from the korean cohort study on covid- clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study. lancet analysis of clinical characteristics and laboratory findings of cases of novel coronavirus pneumonia in wuhan, china: a retrospective analysis risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease pneumonia in wuhan, china characteristics and outcomes of critically ill patients with covid- in washington state covid- in critically ill patients in the seattle region -case series clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study dysregulation of immune response in patients with covid- in wuhan, china clinical and immunological features of severe and moderate coronavirus disease lymphocyte subset (cd +, cd +) counts reflect the severity of infection and predict the clinical outcomes in patients with covid- clinical and biochemical indexes from -ncov infected patients linked to viral loads and lung injury correlation between relative nasopharyngeal virus rna load and lymphocyte count disease severity in patients with covid- t cell subset counts in peripheral blood can be used as discriminatory biomarkers for diagnosis and severity prediction of covid- relationships among lymphocyte subsets, cytokines, and the pulmonary inflammation index in coronavirus (covid- ) infected patients longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of sars-cov- infected patients characteristics of peripheral lymphocyte subset alteration in covid- pneumonia persistence and clearance of viral rna in novel coronavirus disease rehabilitation patients functional exhaustion of antiviral lymphocytes in covid- patients t cellmediated immune response to respiratory coronaviruses covid- : immunopathology and its implications for therapy hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease (covid- ): a meta-analysis thrombocytopenia is associated with severe coronavirus disease (covid- ) infections: a metaanalysis diagnosis and treatment of adults with community-acquired pneumonia. an official clinical practice guideline of the american thoracic society and infectious diseases society of america thrombocytopenia and its association with mortality in patients with covid- hematological features of persons with covid- . leukemia association between platelet parameters and mortality in coronavirus disease : retrospective cohort study platelet-to-lymphocyte ratio is associated with prognosis in patients with coronavirus disease- the diagnostic and predictive role of nlr, d-nlr and plr in covid- patients. int immunopharmacol the effect of sars coronavirus on blood system: its clinical findings and the pathophysiologic hypothesis. zhongguo shi yan xue ye xue za zhi thrombocytopenia in patients with severe acute respiratory syndrome (review) role of vascular cell adhesion molecules and leukocyte apoptosis in the lymphopenia and thrombocytopenia of patients with severe acute respiratory syndrome (sars). microbes infect mechanism of thrombocytopenia in covid- patients. ann hematol hlh across speciality collaboration, uk. covid- : consider cytokine storm syndromes and immunosuppression the scientific standardization committee on dic of the international society on thrombosis haemostasis. guidance for diagnosis and treatment of dic from harmonization of the recommendations from three guidelines covid- ): a haematologist's perspective blood and blood product use during covid- infection autoimmune haemolytic anaemia associated with covid- infection evidence for gastrointestinal infection of sars-cov- gastrointestinal symptoms of cases with sars-cov- infection novel coronavirus treatment with ribavirin: groundwork for an evaluation concerning covid- potential therapeutic agents against covid- : what we know so far haematological manifestations in patients with severe acute respiratory syndrome: retrospective analysis comparative effectiveness and safety of ribavirin plus interferon-alpha, lopinavir/ritonavir plus interferon-alpha, and ribavirin plus lopinavir/ritonavir plus interferon-alpha in patients with mild to moderate novel coronavirus disease : study protocol a cohort study assessing the impact of small volume blood tubes on diagnostic test quality and iatrogenic blood loss in a cohort of adult haematology patients safety and efficacy of erythropoiesis-stimulating agents in critically ill patients admitted to the intensive care unit: a systematic review and meta-analysis patient blood management during the covid- pandemic: a narrative review prominent changes in blood coagulation of patients with sars-cov- infection abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia international society on thrombosis and haemostasis score for overt disseminated intravascular coagulation predicts organ dysfunction and fatality in sepsis patients d-dimer levels on admission to predict in-hospital mortality in patients with covid- changes in blood coagulation in patients with severe coronavirus disease (covid- ): a meta-analysis covid- -related severe hypercoagulability in patients admitted to intensive care unit for acute respiratory failure coagulation disorders in coronavirus infected patients: covid- , sars-cov- , mers-cov and lessons from the past hypercoagulation and antithrombotic treatment in coronavirus : a new challenge anticoagulant treatment is associated with decreased mortality in severe coronavirus disease patients with coagulopathy scientific and standardization committee on dic, and the scientific and standardization committee on perioperative and critical care of the international society on thrombosis and haemostasis. diagnosis and management of sepsis-induced coagulopathy and disseminated intravascular coagulation difference of coagulation features between severe pneumonia induced by sars-cov and non-sars-cov prevalence of venous thromboembolism in patients with severe novel coronavirus pneumonia incidence of thrombotic complications in critically ill icu patients with covid- high risk of thrombosis in patients with severe sars-cov- infection: a multicenter prospective cohort study. intensive care med high incidence of venous thromboembolic events in anticoagulated severe covid- patients autopsy findings and venous thromboembolism in patients with covid- pulmonary vascular endothelialitis, thrombosis, and angiogenesis in covid- virus disease (covid- ) presenting as acute st elevation myocardial infarction large-vessel stroke as a presenting feature of covid- in the young neurologic manifestations of hospitalized patients with coronavirus disease hypercoagulability of covid- patients in intensive care unit: a report of thromboelastography findings and other parameters of hemostasis incidence of venous thromboembolism in hospitalized patients with covid- humanitas covid- task force. venous and arterial thromboembolic complications in covid- patients admitted to an academic hospital in more on covid- coagulopathy in caucasian patients isth interim guidance on recognition and management of coagulopathy in covid- . j thromb haemost switch from oral anticoagulants to parenteral heparin in sars-cov- hospitalized patients ash) recommendations on coronavirus disease and covid- re: isth interim guidance to recognition and management of coagulopathy in covid- isth interim guidance on recognition and management of coagulopathy in cov-id- : a comment prevention treatment of vte associated with covid- infection consensus statement group. prevention and treatment of venous thromboembolism associated with coronavirus disease infection: a consensus statement before guidelines prepare to adapt: blood supply and transfusion support during the first weeks of the novel coronavirus (covid- ) pandemic affecting washington state coronavirus disease (covid- ) and decrease in blood donation: experience of iranian blood transfusion organization (ibto) coronavirus disease : coronaviruses and blood safety american association of blood bank (aabb)'s coronavirus resources inactivation of severe acute respiratory syndrome coronavirus in plasma and platelet products using a riboflavin and ultraviolet light-based photochemical treatment covid- in persons with haematological cancers perspective: sars-cov- , cov-id- and haematologists hubei anti-cancer association. covid- in persons with chronic myeloid leukaemia health impact of hospital restrictions on seriously ill hospitalized patients: lessons from the toronto sars outbreak cancer, covid- and the precautionary principle: prioritizing treatment during a global pandemic management of patients with multiple myeloma in the era of covid- pandemic: a consensus paper from the european myeloma network (emn). leukemia international myeloma society recommendations for the management of myeloma patients during the covid- pandemic eha) covid- hematology hub granulocyte colony-stimulating factor in combination with intensive chemotherapy in the treatment of acute myeloid leukemia barron r. the impact of primary prophylaxis with granulocyte colony-stimulating factors on febrile neutropenia during chemotherapy: a systematic review and meta-analysis of randomized controlled trials. support care cancer managing oncology services during a major coronavirus outbreak: lessons from the saudi arabia experience cryopreservation of allogeneic pbsc from related and unrelated donors is associated with delayed platelet engraftment but has no impact on survival long-term follow-up of leukaemia patients after related cryopreserved allogeneic bone marrow transplantation coronavirus and haematopoietic stem cell transplantation. worldwide network for blood & marrow transplantation. wbmt coronavirus disease covid- : european society for blood and marrow transplantation (ebmt) recommendations update the authors have no relevant conflict of interest to disclose. carmen k.m. cheung: acquisition, analysis, and interpretation of data/references; drafting and approving the manuscript. man fai law: acquisition, analysis, and interpretation of data/references; drafting and approving the manuscript. grace c.y. lui: analysis, interpretation of data/references; revising critically and approving the manuscript. sunny hei wong: analysis, interpretation of data/references; revising critically and approving the manuscript. raymond s.m. wong: analysis, interpretation of data/references; drafting, revising critically, and approving the manuscript. key: cord- -e ey eo authors: patel, urvish; malik, preeti; mehta, deep; shah, dhaivat; kelkar, raveena; pinto, candida; suprun, maria; dhamoon, mandip; hennig, nils; sacks, henry title: early epidemiological indicators, outcomes, and interventions of covid- pandemic: a systematic review date: - - journal: journal of global health doi: . /jogh. . sha: doc_id: cord_uid: e ey eo background: coronavirus disease- (covid- ), a pandemic that brought the whole world to a standstill, has led to financial and health care burden. we aimed to evaluate epidemiological characteristics, needs of resources, outcomes, and global burden of the disease. methods: systematic review was performed searching pubmed from december , , to march , , for full-text observational studies that described epidemiological characteristics, following moose protocol. global data were collected from the jhu-corona virus resource center, who-covid- situation reports, kff.org, and worldometers.info until march , . the prevalence percentages were calculated. the global data were plotted in excel to calculate case fatality rate (cfr), predicted cfr, covid- specific mortality rate, and doubling time for cases and deaths. cfr was predicted using pearson correlation, regression models, and coefficient of determination. results: from studies of patients, . % of patients died, . % recovered, . % were admitted to icu and . % required ventilation. covid- was more prevalent in patients with hypertension ( . %), smoking ( . %), diabetes mellitus ( %), and cardiovascular diseases ( . %). common complications were pneumonia ( %), cardiac complications ( . %), acute respiratory distress syndrome ( . %), secondary infection ( . %), and septic shock ( . %). though cfr and covid- specific death rates are dynamic, they were consistently high for italy, spain, and iran. polynomial growth models were best fit for all countries for predicting cfr. though many interventions have been implemented, stern measures like nationwide lockdown and school closure occurred after very high infection rates (> cases per population) prevailed. given the trend of government measures and decline of new cases in china and south korea, most countries will reach the peak between april - , if interventions are followed. conclusions: a collective approach undertaken by a responsible government, wise strategy implementation and a receptive population may help contain the spread of covid- outbreak. close monitoring of predictive models of such indicators in the highly affected countries would help to evaluate the potential fatality if the second wave of pandemic occurs. the future studies should be focused on identifying accurate indicators to mitigate the effect of underestimation or overestimation of covid- burden. viewpoints research theme : there are confirmed cases worldwide with ( . %) deaths and ( . %) recovered cases [ ] . new york is the current epicenter of covid- ( cases and deaths) of united states of america (usa) ( cases, ( . %) deaths and ( . %) recovered patients) while italy ( deaths) and spain ( deaths) being worst affected countries [ , ] . globally, the epidemiological scenario of covid- is changing on a daily basis. the origin of severe acute respiratory syndrome coronavirus (sars-cov- ) virus was linked to a seafood market in wuhan from the handling and close contact with animals [ ] . in usa, the first case was reported on january , , with a recent travel history to wuhan [ ] . according to emerging literature, covid- symptoms can range from mild respiratory illness causing fever, dry cough, dyspnea, myalgia and fatigue to more severe manifestation of pneumonia, cardiac complications requiring intensive care unit (icu) admission and mechanical ventilation [ ] . the median incubation period is around days (range: - days), requiring prolonged monitoring in extreme cases [ , ] . real-time reverse transcriptase polymerase chain reaction (rt-pcr) of nasopharyngeal and/or oropharyngeal swabs are usually used to confirm the diagnosis [ , ] . preliminary demographic data of the infected patients suggests that most patients have mild disease, with older adults (≥ years) appearing to be more susceptible to severe illness requiring hospitalization [ , ] . covid- shows evidence of human to human transmission via respiratory droplets and from contact with contaminated surfaces or objects, with estimated median basic reproduction number (r ) of . (range: . - . ) [ ] , making the spread of the disease tough to contain. while recently published observational studies have provided insights on the epidemiology of this pandemic, their sample sizes are too limited for any definitive conclusions. hence, we sought to conduct a systematic review and analysis of all available studies comparing outcomes. primary aim of the study is to evaluate the epidemiological characteristics, needs of resources, and patients' outcomes. secondary aim is to evaluate the global burden and interventions. we evaluated epidemiological characteristics, risk factors, laboratory and imaging findings, complications and treatment utilized. we also calculated the mortality, recovery, and needs of resources like icu beds and mechanical ventilators. in order to evaluate the primary outcome, we performed a systematic review of these observational studies according to moose guidelines [ , ] . we searched the pubmed database for original observational studies that described any details on epidemiological characteristics on patients with covid- . the database was searched from december , , to march , . the search was conducted using the following keyword/mesh terms: ((covid- [title/abstract]) or coronavirus [title/abstract]) or sars-cov- [title/abstract] or -ncov [title/abstract]. all studies that compared outcomes of interest in covid- patients were included. any literature other than observational studies was excluded. non-english literature, non-full text, and animal studies were excluded. abstracts were reviewed, and articles were retrieved accordingly. two independent reviewers performed the search and literature screening (up, pm), with disputes resolved by consensus following discussion with a third author (cp). for the ease of understanding, we used a flow diagram to describe literature search and study selection process in figure s in the online supplementary document. a prespecified data collection excel sheet was used to collect the data relating to study characteristics and outcomes of interest by two authors (pm and cp), and discrepancies were solved by a discussion with a third author (up). the following study characteristics were extracted: publication year, country of origin, sample size, age, sex, direct exposure to infection, travel history, signs and symptoms, risk factors and comorbidities, laboratory and radiology findings, treatment utilized, and complications. data on the following outcomes were extracted: mortality, recovery, need for icu beds and mechanical ventilators. viewpoints research theme : covid- pandemic all analysis was done in excel (microsoft inc, seattle wa, usa) and sas . (sas institute, cary, nc, usa). the frequencies and percentages of epidemiological characteristics and outcomes were calculated. we evaluated the global burden of covid- including case fatality rates (cfr), strength of association between deaths and cases to predict cfr, case doubling time, covid- specific mortality rates, and control measures by governments to prevent spread among usa, china, italy, iran, spain, germany, india, and south korea. for this purpose, data were taken from the johns hopkins university corona-virus resource center [ ] , kff.org [ ] , world health organization-covid- situation reports [ ] , and worldometers.info [ ] up until march , . we evaluated changes in cases and deaths, cfr, created a predictive modeling for cfr, covid- specific mortality rate, and doubling time for cases and deaths. cfr was defined as the number of cases divided by the number of the diagnosed patients with covid- , and covid- specific mortality rate was defined by deaths due to covid- infections divided by total population of the country in , counted per population [ ] pearson correlation coefficient (r) was obtained to establish the strength of association between deaths and cases for individual countries. to predict cfr, we modelled the epidemic curves with simple linear regression, exponential growth, and polynomial growth models and used a coefficient of determination (r ) for model selection. the time of reporting the first death was used as the starting point for that country for all three models. we utilized government websites, national media, and other standard open sources to evaluate the governments' interventions during covid- pandemic, infection rate [(diagnosed cases/country' s population in ) per population] [ ] at the time of interventions like nationwide school closure and lockdown, and effects of such measures to predict the dates of peak number of cases in each country. our search resulted in studies, out of which non-human studies and other than observational studies, non-full text and articles with non-english language information were excluded. full-text studies were screened and studies with insufficient clinical information or outcomes-related information were excluded. full-text articles were assessed for eligibility. the final analysis included fulltext observational studies, presented in table , including a total of patients. [ ] china jan , -feb , young, mar [ ] singapore jan , -feb , - chang, feb [ ] china jan , -jan , wang, feb [ ] china jan , -jan , ng, mar [ ] singapore jan , -feb , - spiteri, mar [ ] europe jan , -feb , - covid- national incident room surveillance team, mar [ ] australia mar xu, feb [ ] china jan , -jan , . - bajema, feb [ ] usa jan , --ki, feb [ ] south korea jan , --chen, jan [ ] china jan , -jan , zhang, feb [ ] china jan , -feb , --yang, feb [ ] china figure s in the online supplementary document. several models, including a simple linear regression, exponential and polynomial (quadratic) growth models, were used to determine the type of association between cumulative deaths and cumulative cases to predict cfr ( table ) . the polynomial growth model had the best fit (higher r ) and indicates that for all countries the death rate increases with the number of cases, and this increase is steeper than a linear relationship. interestingly, while for the usa, italy, iran, spain, and india this association is always positive, for china, south korea, and germany the initial slope is negative but then is reversed as the number of cases continues to increase (figure ). figure s a in the online supplementary document). the daily covid- specific death rate is highest in spain (daily . deaths per population) and italy (daily . deaths per population) followed by usa (daily . deaths per population) ( figure s b in the online supplementary document). the county-specific timeline of doubling time for cases and deaths is shown in table and the increment in cases and deaths are plotted in (figure in the online supplementary document). march barred entry of foreign nationals who had been to european countries within last days [ ] march nationwide schools closed [ ] , lockdown in new york [ ] march a us$ trillion coronavirus stimulus bill was passed and signed by the president [ ] march more than half of us states underwent lockdown [ ] china: january response to public health emergency launched by hubei [ ] january the central government of china imposed a lockdown in wuhan and other cities in hubei province; public transport suspended. the wuhan airport, railway stations and metro were closed, not allowing residents to leave the city without permission [ ] ; public health emergency response announced by mainland province of zhejiang [ ] january mainland china has initiated public health emergency response [ ] ; quarantined whole hubei province [ ] ; curfew laws implemented in huanggang,wenzhou and other mainland cities [ ] south korea: an unlicensed covid- test authorized by the korea centers for disease control and prevention (cdc) [ ] ; travel denied to foreign nationals from hubei province into south korea [ ] february all kindergartens, elementary schools, middle schools, and high schools were announced to delay the semester start [ ] february entire country opened drive-through testing [ ] italy: january state of emergency declared, flights to and from china suspended [ ] february the council of ministers announced a new decree-law to quarantining more than people from different municipalities in northern italy [ ] march nationwide schools and universities closed [ ] march prime minister imposed nationwide quarantine lockdown [ ] march all commercial activities except pharmacies and supermarkets ordered to shut down [ ] ; € billion allocated by the government [ ] april drive-through testing began [ ] iran: all concerts and other cultural events cancelled for one week by ministry of islamic culture and guidance [ ] ; closure of educational institutions in several cities and provinces announced by the ministry of health and medical education [ ] march checkpoints placed between cities to limit travel [ ] march fatima masumeh shrine, jamkaran mosque in qom city, and imam reza shrine in mashhad closed [ ] viewpoints research theme : germany: new health security measures enacted to regulate air and sea travel that required passengers from china, south korea, japan, italy and iran to report their health status before entry [ ] ; federal police stepped up checks within km of the border [ ] march bavaria declared a state of emergency for days and measures to limit public movement and additional funds for medicine supplies were introduced [ ] ; all flights from iran and china stopped by german ministry of transport [ ] ; travelling in coaches, attending religious meetings, visiting playgrounds or engaging in tourism prohibited [ ] finance minister announced us$ billion stimulus package [ ] infection rate at the beginning of the major intervention (nationwide closure of school or major table mentions the predicted dates of the peak number of cases based on strict interventions. in china and south korea, it took - days and - days respectively in order to achieve the peak of the pandemic before the new number of cases began to decline. we have used a - days post-interventional model to calculate the peak of the pandemic keeping in mind the effect of china' s model of interventions. covid- has significantly impacted the entire world both socially and economically. the rapid human-to-human transmission has posed a great public health threat. across studies included in this review, we found confirmed cases of covid- with the majority of the published studies from china. % of the cases had a history of direct exposure or being exposed to the seafood market in wuhan, % were china residents and % had a travel history to china. initially the virus was limited to only wuhan and despite travel restriction, the virus continued to spread across the world at a rapid rate from china, likely due to asymptomatic transmission in the initial stages of the outbreak with a median incubation period of only days [ , ] , before travel restrictions. the covid- cases are increasing exponentially but underestimated due to mild symptoms in a portion of cases, long incubation periods, and shortage of testing kits. in concurrence with other studies [ , ] , we found that clinical characteristics of covid- are similar to those of sars and influenza virus. fever ( %), cough ( %) and myalgia or fatigue ( %) were the most prominent symptoms. % of patients reported dyspnea and sputum production/expectoration. major comorbidities were hypertension, smoking, diabetes mellitus, and cardiovascular disease. patients with these comorbidities are at high risk for complications including pneumonia, ards and cardiovascular complications. we found that patients had increased inflammatory markers including elevated crp in %, lymphopenia in % and elevated esr in % which is similar to other respiratory infections (sars, influenza). few studies [ , ] , have reported abnormal liver function in covid- patients, and we found % of patients had elevated alt and ast. additionally, increased ldh ( %), d-dimer( %) may indicate the severity of the disease [ ] . some studies have also reported elevated neutrophil count and cytokine storm induced by virus leading to coagulation activation and sustained inflammatory response [ ] associated with higher mortality [ ] . there is no proven therapy available as of now for covid- [ ] . large scale clinical trials for these drugs are under way. % patients received oxygen and antibiotics ( %), antivirals ( %) and steroids ( %) as supportive therapies. the prognosis of patients after receiving these treatments is not yet clear. in people with compromised immune systems such as older age, hiv, malignancy, diabetes, chronic pulmonary disease if treated promptly with antibiotics, convalescent plasma to increase the immune support might reduce the risk of complications and mortality [ ] . in our analysis, % of the patients required icu admission, % needed mechanical ventilation, % died and % recovered and were discharged from the hospital. these findings are consistent with guan et al. and wang et al that present similar rates [ , ] . currently in the usa, covid- is in the acceleration phase surpassing china and italy, and a national emergency was declared by the president, but the viewpoints research theme : duration and severity may vary depending on the virus characteristics and public health response [ ] . if confirmed cases continue to grow with this trend, soon the covid- pandemic will cause shortages of ventilators. as per institute for health metrics and evaluation (ihme) projections, on a peak day in the usa, there would be a shortage of icu beds by and a need of ventilators [ ] . the growing number of cases will place a burden on the current capacity of hospitals and hence it is essential to develop and implement strategies to mitigate the gap by increasing capacity and fair allocation of available resources. as of march , cfr in italy was . % and . % in china. according to onder et al. [ ] , cfr stratification by age, shows similar rates for - years ( %- . %) but higher in > years( %- . %). this difference might be due to high cfr reported in people > years in italy and no data from china for the same age group [ ] . other reasons might be demographics differences between two countries (≥ years population: italy- . % vs china- . %), overwhelming health care system, and shortage of icu beds and ventilators, which might lead to prioritizing treatment to younger and otherwise healthy patients over older patient [ ] . in our analysis cfr in italy increased from . % on february to . % on march , possibly due to the implementation of a strict policy of testing only suspected cases with severe symptoms [ ] . though widespread and drive-through testing is becoming more available in usa, cumulative tests conducted per million population lags behind compared to germany, italy, south korea, and spain. our data driven polynomial growth model predicts more deaths in future with an increase in cases in usa [ ] , italy, iran, spain, and india. as per our model predictions, doubling time of cases in the usa, germany and india is decreasing suggesting that they are inching towards the peak. different countries undertook interventions at different points in the timeline of spread of virus. the infection rates in the usa, italy, iran, spain, and germany were higher when they undertook substantial measures compared to china, south korea, and india, suggesting a delayed response and failure to undertake timely measures. the aforementioned timelines for peaks look optimistic because multiple other factors may influence the trajectory of spread, ie, population density, economy, demographics, health care, religious beliefs, and legislation. for instance, despite the growing number of cases, iran continued to keep its shrines open to pilgrims for a long time, but recently closed them, and no stringent curfew laws were imposed. also, many states in usa have still not implemented strict quarantine measures. such practices can seriously impede the efforts at containing the spread and skew the projection in many ways. restrictions have neither been homogeneously imposed nor simultaneously adopted throughout the country, making it difficult to predict the exact model of the spread. also, covid- testing capacity of the nations are limited and the true number of the infected people might have been higher than the estimated numbers at the time of our analysis. hence, an early phase covid- specific death rate would be a better estimate than cfr to compare the severity of the disease. many factors contribute to the accurate estimation of cfr such as testing capacity, care seeking and lack of understanding of the proportion of asymptomatic and pre symptomatic cases [ , ] . limited knowledge of these factors in the early covid- phase might have contributed to overestimation of cfr in our study. the use of serological testing for presence of igm or igg antibodies against sars-cov- will provide a better estimate of cumulative prevalence of covid infection [ ] . as recommended by who, measuring the seroprevalence of antibodies to covid- is crucial and will contribute to determine accurate cfr and help plan adequate public health response [ ] . the research on covid- is rapidly evolving and new publications are becoming available daily. the majority of the epidemiologic data are coming from single center with limited sample sizes. to overcome this limitation and provide a global view of the covid- pandemic, we have analyzed data on over patients from peer-reviewed studies. as a result, we provided more generalizable estimates of laboratory findings, clinical symptoms and complications of covid- patients. we have included data from several countries/regions; however, one limitation is that the majority of cohorts are from china, and as more data from other countries become available, additional meta-analyses would be essential. this is the first study rigorously tracking the timing of government interventions across multiple countries; however, as mentioned earlier, the adherence to those interventions could vary from one country to another, making the projections of the potential effectiveness challenging. we have not evaluated the duration of strict interventions in all these countries. the population prevalence data are based on the symptomatic patients with confirmed rt-pcr testing. since some patients can be infected and present mild or no symptoms, or have not undergone rt-pcr testing, serological antibody testing in the future may allow a viewpoints research theme : covid- pandemic more accurate understanding of the disease prevalence and death rates. despite all the limitations, this is the first study in our knowledge, highlighting and explaining epidemiological indicators, testing capacity, interventions, and expected burden of the covid at early phase. we have reviewed the burden of this pandemic and steps taken by the governments of different countries. though the governments can continue strict lockdowns, it is not a long-term solution. good hand hygiene, widespread testing, detection and isolation of new cases, rigorous contact tracing in low-prevalence settings, early vaccine development and its quick distribution, strengthening the overburdened health care system, and protecting frontline health care workers may help to gradually relax the strict lockdowns and cope with covid- pandemic. this would only be possible by a collective approach undertaken by responsible governments, wise strategy implementation, and receptive populations. the future studies should be focused on identifying accurate indicators to mitigate the effect of underestimation or overestimation of covid- burden. close monitoring of such indicators in highly affected countries is very crucial to evaluate the potential fatality if the second wave of pandemic occurs. who director-general' s opening remarks at the media briefing on covid- - coronavirus covid- global cases by the center for systems science and engineering (csse) at johns hopkins university. (jhu). first case of novel coronavirus in the united states clinical characteristics of coronavirus disease in china incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application interim guidelines for collecting, handling, and testing clinical specimens from persons for coronavirus disease detection of novel coronavirus ( -ncov) by real-time rt-pcr clinical characteristics of coronavirus disease in china the novel coronavirus pneumonia emergency response epidemiology team. the epidemiological characteristics of an outbreak of novel coronavirus diseases (covid- ) -china estimation of the reproductive number of novel coronavirus (covid- ) and the probable outbreak size on the diamond princess cruise ship: a data-driven analysis covid- ) situation reports countries in the world by population the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application clinical features of patients infected with novel coronavirus in wuhan a comparative study on the clinical features of covid- pneumonia to other pneumonias epidemiologic features and clinical course of patients infected with sars-cov- in singapore epidemiologic and clinical characteristics of novel coronavirus infections involving patients outside wuhan, china clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china evaluation of the effectiveness of surveillance and containment measures for the first patients with covid- in singapore first cases of coronavirus disease (covid- ) in the who european region clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series persons evaluated for novel coronavirus -united states epidemiologic characteristics of early cases with novel coronavirus ( -ncov) disease in korea. epidemiol health epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of patients infected with sars-cov- in wuhan clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical features of cases with coronavirus disease in wuhan, china clinical characteristics of refractory covid- pneumonia in wuhan, china characteristics and outcomes of critically ill patients with covid- in washington state risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study statement from the press secretary regarding the president' s coronavirus task force trump declares coronavirus a public health emergency and restricts travel from china trump signs emergency coronavirus package, injecting $ . billion into efforts to fight the outbreak trump administration announces measures to speed coronavirus testing here' s what trump' s coronavirus emergency declaration does new york launches drive-thru testing site for covid- see which states and cities have told residents to stay at home dhs notice of arrival restrictions on china, iran and certain countries of europe map: coronavirus and school closures. house passes $ trillion coronavirus stimulus bill, which includes direct payments to americans and business loans notice of the people ' s government of hubei province on strengthening the prevention and control of pneumonia infected by new coronavirus china coronavirus: lockdown measures rise across hubei province zhejiang: newly diagnosed cases of new coronavirus infection and pneumonia were launched, and the first-level response to major public health emergencies was initiated all provinces in mainland china have initiated first-level response to public health emergencies xiangyang railway station is closed, and the last prefecture-level city "hubei" in hubei province ningbo have implemented the most restrictive order south korea learned its successful covid- strategy from a previous coronavirus outbreak: mers korea bars foreigners traveling from hubei province s ministry of education opening on march south korea pioneers coronavirus drive-through testing station italy suspends all china flights as coronavirus cases confirmed in rome ten lombard municipalities: thousand people forced to stay at home. quarantine at the milanese hospital in baggio. italy orders closure of all schools and universities due to coronavirus italy extends emergency measures nationwide merkel warns virus could infect two-thirds of germany coronavirus emergency, the government' s plan rises to billion. gualtieri to the eu: 'stimulus is needed'. we will make a day long holiday' to contain coronavirus, as sixth victim dies coronavirus: iran limits travel and urges banknote avoidance. shiite hardliners in iran storm shrines that were closed to stop coronavirus spread germany enacts new health security measures against coronavirus infections these rules apply in bavaria. germany halts flights from iran and china over coronavirus: bild. deutschland im shutdown-modus -die alternativlos-kanzlerin kehrt zurück. bayern impose curfew! contact bans on more than two people, hairdressers too -the federal and state governments have agreed on this spain prohibits all direct flights from italy until the community of madrid decrees the mandatory closure of bars, restaurants and clubs until spain to impose nationwide lockdown -el mundo marlaska suspends free movement and reestablishes border controls predictions and role of interventions for covid- outbreak in india coronavirus: all international arrivals to india to share travel history at airports. icmr to test for community transmission of covid- coronavirus: icmr recommends hydroxychloroquine for high-risk population. coronavirus: india enters 'total lockdown' after spike in cases global airlines have completely stopped flying scheduled flights due to travel bans, airspace closures, and low demand for travel fm nirmala sitharaman announces rs . lakh crore relief package for poor. to understand the global pandemic, we need global testing -the our world in data covid- testing dataset early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a comparative study on the clinical features of covid- pneumonia to other pneumonias remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial treatment of critically ill patients with covid- with convalescent plasma covid- ) -united states icu-days, ventilator days and deaths by us state in the next months case-fatality rate and characteristics of patients dying in relation to covid- in italy. jama. . online ahead of print italian doctors on coronavirus frontline face tough calls on whom to save the many estimates of the covid- case fatality rate evidence supporting transmission of severe acute respiratory syndrome coronavirus while presymptomatic or asymptomatic seroprevalence of immunoglobulin m and g antibodies against sars-cov- in china population-based age-stratified seroepidemiological investigation protocol for coronavirus (covid- ) infection key: cord- -gkzebyda authors: hoz, samer s.; al-sharshahi, zahraa f.; dolachee, ali a.; matti, wamedh e. title: letter to the editor: “beyond containment: tracking the impact of coronavirus disease (covid- ) on neurosurgery services in iraq” date: - - journal: world neurosurg doi: . /j.wneu. . . sha: doc_id: cord_uid: gkzebyda nan letter to the editor: "beyond containment: tracking the impact of coronavirus disease (covid- ) on neurosurgery services in iraq" letter: t he coronavirus disease (covid- ) pandemic is one of the greatest threats to humankind. the contagion is rising at an alarming pace and is testing the limits of the health care systems worldwide. despite stringent containment measures to stem the spread of the virus, the situation has deteriorated rapidly; the virus has now swept across the globe, with a total of , fatalities and . million confirmed cases worldwide. in iraq, a nation that has been through cycles of ongoing violence for decades, the situation is rather peculiar. the crippled state of the health care system, the socioeconomic disparities, the lack of social security, and health insurance systems, along with the volatile political context and the absence of a stable political leadership all create a precarious and high-risk environment for a full-fledged covid- outbreak. ironically, in the first few months of the pandemic, the virus seemed to be sparing our fragile communities, with just deaths and confirmed cases as of march , . however, around mid-may, and coinciding with the end of ramadhan (eid al-fitr holidays), the number of confirmed cases increased -fold, from fewer than cases on may to , on june . , since then, the country has witnessed enormous daily jumps in the number of cases that quickly overwhelmed our already-strained health care system. currently, there are , confirmed cases and deaths; the population in iraq is million (data as of the world health organization situation report on august , ). hospitals across the nation have been hit hard, particularly after the drop in oil prices and the resultant cuts in government funding. while all efforts are being made to adhere to best practice guidelines, deviations are inevitable, given the country's exceptional circumstances. [ ] [ ] [ ] in this letter, we track the impact of the pandemic on neurosurgery services at the nation's largest tertiary neurosurgery center, focus on our efforts to survive the pandemic, and on potential steps to mitigate the risk of an impending catastrophe. the neurosurgery teaching hospital (nth) in baghdad, iraq, provides neurosurgical care for . million people-approximately % of the population in baghdad, with a total capacity of beds, neurosurgical intensive care unit (nicu) beds, and operating rooms. the hospital hosts neurosurgeons and residents. as part of the response plan that we have introduced over the past few months, the hospital capacity has been expanded with the addition of nicu beds. a new covid- unit, comprising beds, was also set up in the hospital. however, these measures are far from adequate and the hospital remains a full-house at all times, with at least patients per hospital room, challenging the proper implementation of social distancing guidelines. the admission rate decreased to % of that before the covid- era. two admission pathways have been established; emergency and urgent. time-dependent cases are directly admitted to the hospital. cases requiring less immediate care are only admitted if the condition is deemed to be "urgent." this decision is the responsibility of a newly assembled local hospital committee, composed of senior neurosurgeons. all admitted patients are screened for fever and exposure status. symptomatic patients undergo polymerase chain reaction swap testing. full personal protective equipment is only provided to workers in the nicu and those employed at the covid- facility. for the majority of the hospital personnel, only basic surgical masks are available. remarkably, in the absence of a structured ambulance network in the country, almost all trauma and other emergency cases are brought on by relatives, who seldom comply with the reception staff orders for personal protection. all this, along with the extreme shortage of terminal cleaning supplies in the hospital, dispels any efforts to curb the rate of cross-contamination in the hospital. in patients who are found to be positive for covid- , efforts are usually made to postpone surgery if the condition permits. reducing intraoperative exposure risk is also attempted by a range of steps, including avoiding bone drilling during craniotomy; limiting the use of microscopes, endoscopes, and surgical chairs; reducing the number of theater personnel on duty; and ensuring that only senior neurosurgeons who are beyond their learning curve handle the operation. the room is then sterilized, ventilated, and isolated for the ensuing e hours. patients are discharged early and followed up through regular, scheduled phone calls. in general, postoperative stays are now shortened to days for patients requiring a craniotomy (previously was e days) and day for spine cases (previously was e days). on january , , the nth declared a delay in all elective and semielective cases until further notice to curb the spread of the virus. from january to july , a total of operations were performed, as compared with operations over this same period in , a net decrease of . %. elective spinal and peripheral nerve surgeries were mostly affected, with a total decrease of . % (from to operations). the number of elective cranial operations went from to , a total decrease of . %. trauma and other emergency operations were reduced to a lesser extent, from to , a decrease of . %. this reduction in trauma cases may be attributed to the nationwide curfew that has been imposed by the government and the reduction in referral rates from the other governates. world neurosurgery : - , november www.journals.elsevier.com/world-neurosurgery the outpatient department since january , , hospital outpatient department visits have been limited to cases referred from regional hospitals and primary care centers, resulting in a total % reduction in the monthly inperson visits department visits, as compared to the pre-covid- era. however, the number of referred patients surged again in july, coinciding with the nationwide closure of private health clinics. certain presentations, primarily lower back pain and headache, showed the most remarkable decline; % (p < . ). to date, % of hospital staff, or of , have tested positive for the virus. as for patients, a total of acute trauma cases have been confirmed to be positive by immediate postoperative polymerase chain reaction. such situations are hazardous and require urgent legislative change that determines the covid- status of all admitted patients to be positive unless proven otherwise. nevertheless, given the existing constraints of national and institutional capital, additional measures, including greater-level strategic planning, are urgently required. in addition, national public education plans for the de-stigmatization of the disease are needed, since many reports of transmission to hospital personnel have been traced back to patients who have denied their symptoms or exposure status. here, at the nth in baghdad, the conditions are indicative of the country-wide situation. given the regional, system, and resource limitations, our response has been far from ideal, which necessitates sharing this experience with the world to draw the attention of international societies and initiate collaborative plans of countries with a similar set of circumstances, which may provide a gateway from the crisis with the least-possible loss. iraq to whom correspondence should be addressed coronavirus disease (covid- ): situation report e coronavirus disease (covid- ): situation report e coronavirus disease (covid- ): situation report e coronavirus disease (covid- ): situation report e covid- : recommendations for management of elective surgical procedures elective medical services, and treatment recommendations coronavirus disease (covid- ) and neurosurgery: literature and neurosurgical societies recommendations update conflict of interest statement: the authors declare that the article content was composed in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.https://doi.org/ . /j.wneu. . . . key: cord- -mettlmhz authors: ortiz-prado, esteban; simbaña-rivera, katherine; gómez-barreno, lenin; rubio-neira, mario; guaman, linda p.; kyriakidis, nikolaos c; muslin, claire; jaramillo, ana maría gómez; barba-ostria, carlos; cevallos-robalino, doménica; sanches-sanmiguel, hugo; unigarro, luis; zalakeviciute, rasa; gadian, naomi; lópez-cortés, andrés title: clinical, molecular and epidemiological characterization of the sars-cov virus and the coronavirus disease (covid- ), a comprehensive literature review date: - - journal: diagn microbiol infect dis doi: . /j.diagmicrobio. . sha: doc_id: cord_uid: mettlmhz abstract coronaviruses are an extensive family of viruses that can cause disease in both animals and humans. the current classification of coronaviruses recognizes species in subgenera that belong to the family coronaviridae. from those, at least seven coronaviruses are known to cause respiratory infections in humans. four of these viruses can cause common cold-like symptoms. those that infect animals can evolve and become infectious to humans. three recent examples of these viral jumps include sars cov, mers-cov and sars cov- virus. they are responsible for causing severe acute respiratory syndrome (sars), middle east respiratory syndrome (mers) and the most recently discovered coronavirus disease during (covid- ). covid- , a respiratory disease caused by the sars-cov- virus, was declared a pandemic by the world health organization (who) on march . the rapid spread of the disease has taken the scientific and medical community by surprise. latest figures from th may show more than million people had been infected with the virus, causing more than , deaths in over countries worldwide. the large amount of information received daily relating to covid- is so abundant and dynamic that medical staff, health authorities, academics and the media are not able to keep up with this new pandemic. in order to offer a clear insight of the extensive literature available, we have conducted a comprehensive literature review of the sars cov- virus and the coronavirus diseases (covid- ). the viral membrane contains the spike (s) glycoprotein that forms the peplomers on the virion surface, giving the virus its 'corona'or crown-like morphology in the electron microscope. the membrane (m) glycoprotein and the envelope (e) protein provide the ring structure. within the virion interior lies a helical nucleocapsid comprised of the nucleocapsid (n) protein complexed with a single positive-strand rna genome of about kb in length [ ] . the first genome of sars-cov- named wuhan-hu- (ncbi reference sequence nc_ ) was isolated and sequenced in china in january [ , ] . the sars-cov- genome has similarities to other viruses: approximately % similarity to the bat coronavirus batcov rath ; an estimated % similarity with sars-cov [ ] , and an estimated % identity with mers-cov [ , ] . sars-cov- has a positive-sense single-stranded rna genome. it is approximately , bases in length and comprises of a ′ terminal cap structure and a ′ poly a tail. according to wu et al. [ ] , this novel coronavirus (ivdc-hb- / strain) has open reading frames (orfs) encoding proteins. the ' terminus of the genome contains the orf ab and orf a genes. orf ab is the largest gene and encodes the pp ab protein that contains non-structural proteins named nsps (nsp -nsp and nsp -nsp ). orf a encodes the pp a protein and also has nsps (nsp -nsp ) [ ] . the ' terminus of the genome contains four structural proteins: spike (s) glycoprotein; envelope (e) protein; membrane (m) glycoprotein and nucleocapsid (n) phosphoprotein. it also contains accessory proteins ( a, b, p , a, b, b, b and orf ) [ ] (figure b ). the global scientific community from countries have united to study this novel coronavirus by sequencing and submitting , sars-cov- genomes to the global initiative on sharing all influenza data (gisaid) (https://www.gisaid.org/) between december and april [ , ] . sars-cov- has accumulated mutations in its rna genome as the outbreak progresses. as an intracellular obligate microorganism, the coronavirus exploits the host cell machinery for its own replication and spread. since virus-host interactions form the basis of diseases, knowledge about their interplay is of great importance, particularly when identifying key targets for antivirals. j o u r n a l p r e -p r o o f ace is a type i membrane protein that participates in the maturation of angiotensin, a peptide hormone that controls vasoconstriction and blood pressure [ ] . in the respiratory tract, ace is widely expressed on the epithelial cells of alveoli, trachea, bronchi, bronchial serous glands [ ] , and alveolar monocytes and macrophages [ ] . xu et al. reported the [ ] rna-seq profiling data of organs with para-carcinoma normal tissues from the cancer genome atlas (tcga; https://www.cancer.gov/tcga) and organs with normal tissue from fantom cage (https://fantom.gsc.riken.jp/). these were used to validate the expression of the human cell receptor ace in the virus and may indicate the potential infection routes of sars-cov- [ ] . interestingly, the ace receptor is expressed more in oral cavity than lung. this potentially could indicate that susceptibility and infectivity of sars-cov- is greater from oral mucosa surfaces [ ] . following the binding of the rbd in the s subunit to the receptor ace , sars-cov- s protein is cleaved by the cell surface-associated transmembrane protease serine tmprss , which activates s domain for membrane fusion between the viral and cell membrane [ ] . a functional polybasic (furin) cleavage site was found at the s -s boundary through the insertion of nucleotides [ , , ] . the s , t and s residues of o-linked glycans flank the cleavage site and are unique in sars-cov- [ ] . in addition to the s glycoprotein -ace receptor complex, wang following the release and uncoating of viral rna to the cytoplasm, coronavirus replication starts with the translation of orf a and orf b into polyproteins pp a and pp ab via a frameshifting mechanism (figure ) [ ] . subsequently, polyproteins pp a and pp ab are processed by internal viral proteases, including the main protease m pro , a potential drug target whose crystal structure was recently determined for sars-cov- [ ] . polyprotein cleavage yields mature replicase proteins, which assemble into a replicationtranscription complex that engages in negative-strand rna synthesis. both full-length and multiple subgenomic negative-strand rnas are produced. the former serves as template for new full-length genomic rnas and the latter template the synthesis of the subgenomic mrnas required to express the structural and accessory protein genes residing in the ′proximal quarter of the genome [ ] . coronavirus rna replication occurs on a virusinduced reticulovesicular network of modified endoplasmic reticulum (er) membranes [ ] . the assembly of virions is quickly ensued with the accumulation of new genomic rna and structural components. the n protein complexes with genome rna, forming helical structures. then, the transmembrane m protein, localized to the intracellular membranes of the er -golgi intermediate compartment (ergic) , interacts with the other viral structural proteins (s, e and n proteins) to allow the budding of virions [ , ] . following assembly and budding, virions are transported in vesicles and eventually released by exocytosis. normal immune responses against the majority of viruses involve a rapid containment phase mediated by innate immunity components and -if necessary-a delayed, yet more sophisticated adaptive immunity phase that should be able to eradicate the pathogen andhopefully-generate long-lasting immunological memory. the former includes antiviral type i interferons (ifns), macrophage and neutrophil activation that leads to proinflammatory cytokine production and nk cells on the other hand, anti-viral adaptive immune responses involve a virus-tailored coordinated attack by antigen specific cd + cytotoxic t cells (ctls), the th subset of cd + t helper cells that orchestrates the j o u r n a l p r e -p r o o f immune response against viruses and other intracellular pathogens, specific antibody producing plasma cells, and finally the production of memory t and b cell subsets. immune responses following sars-cov- infection can be a double-edged sword. a rapid and robust type i ifn orchestrated response can lead to virus clearance and -given that antiviral lymphocytes are activated and expanded-immune memory. conversely, a late activation of innate immunity, possibly owing to is usually associated with severe pathology that can lead to pneumonia, ards, septic shock, multi-organ failure and, eventually, death. in this line, a delayed type i ifn response and inefficient sars-cov- clearance by alveolar macrophages can promote excessive viral replication that can lead to severe pathology accompanied by increased viral shedding and, thus, viral transmissibility. accordingly, in patients whose immune system is weakened or otherwise dysregulated, such as older men with comorbidities, severe covid- is clearly more likely to occur [ ] [ ] [ ] . a recent study has demonstrated that the average duration of sars-cov- viral shedding was days after covid- onset, raising a debate as to the optimal time of patient isolation [ ] . however, in terms of transmission viral shedding seems to be more relevant in the early phases of the infection as it can precede covid- symptoms by - days whilst up to % of infections are associated with viral shedding by asymptomatic cases [ ] [ ] [ ] therefore, individuals that mount efficient containment-phase immune responses accompanied by decreased inflammatory responses will not experience infection-or immune response-mediated overt manifestations, but may be important silent spreaders of sars-cov- . type i ifns are mainly produced by plasmacytoid dendritic cells (pdcs) and have a plethora of antiviral effects such as blocking cell entry and trafficking of viral particles, inducing rnase and dnase expression to degrade virus genetic material, enhancing presentation of viral antigens by mhc-i, inhibiting protein synthesis, inducing apoptosis of j o u r n a l p r e -p r o o f infected cells and activating anti-viral subsets such as macrophages and cytotoxic nk cells and t lymphocytes [ ] . pathogen recognition receptors like cytosolic rig-i and mda- [ , ] or endosomal toll like receptors (tlrs) and that recognize viral rna [ ] are responsible for the activation of signaling cascades that activate the transcription factors nf-kb, interferon regulatory factor (irf) and irf that translocate to the nucleus and induce proinflammatory cytokines and type i interferon (ifn) production. in turn, type i ifns activate the downstream jak-stat signal pathway resulting in expression of ifnstimulated genes (isgs) [ , ] . our experience from sars-cov and mers-cov infection has shown that delayed type i ifn production and excessive recruitment and activation of infiltrating proinflammatory cells (neutrophils and monocytes-macrophages) are possible mediators of lung dysfunction and bad prognostic factors for the outcome of the infection. delayed type i ifn production allows for highly efficient viral replication that, in turn, results in recruitment of hyperinflammatory neutrophils and monocytes. therefore, the pathogen recognition receptors (prrs) of these proinflammatory cells recognize high numbers of their ligands and subsequently secrete excessive amounts of proinflammatory cytokines that lead to septic shock, lung pathology, pneumonia or acute respiratory distress syndrome. it has been shown that in severe cases both sars-cov and mers-cov fruitfully employ an immune evasion mechanism whereby early type i ifn responses to viral infection are dampened [ ] . this can be achieved by blocking signaling both upstream, as well as downstream of type i ifn expression. sars-cov can inhibit irf nuclear translocation, whereas mers-cov can impede histone modification [ ] . additionally, both viruses can inhibit ifn signaling by decreasing stat phosphorylation [ ] . due to the many sequence similarities of sars-cov- with sars-cov and mers-cov it would be enticing to speculate that similar mechanisms are also present, however further studies are needed to shed light to this hypothesis. hyperactivated neutrophils and monocytes-macrophages are the usual source of the cytokine storm. in this aspect, absolute neutrophil counts and neutrophil to lymphocyte j o u r n a l p r e -p r o o f ratio (nlr) were strongly associated with disease severity in a large cohort of covid- patients and were proposed as markers of adverse disease prognosis [ ] . interestingly, the increased amounts of proinflammatory cytokines in serum associated with pulmonary inflammation and extensive lung damage described both in sars [ ] and mers diseases [ ] were also reported in the early study of patients with covid- in wuhan [ ] . evidence shows that the leading cause of covid- mortality is respiratory failure caused by acute respiratory distress syndrome (ards). there is an association with a cytokine storm mediated by high-levels of proinflammatory cytokines including il- , il- , il- , g-csf, ip- , mcp- , mip- a and tnf-α. ards was associated with increased fatality and subsequent studies confirmed il- and c-reactive protein are significantly upregulated in patients that died compared to convalescent patients [ ] moreover, a recent study of patients in wuhan identified that severe cases showed significantly higher cytokines and chemokines such as tumor necrosis factor-α (tnf-α), il- , il- , il- and il- expressed [ ] . in accordance with these findings, therapeutic strategies are being tested. a phase randomized controlled trial of il- blockade (anakinra) in sepsis has shown significant survival benefit in patients with hyperinflammation, without apparent increased adverse events [ ] . currently, a multicenter, randomized controlled trial of tocilizumab (il- receptor blockade, licensed for cytokine release syndrome), is being trialed in patients with covid- pneumonia presenting with high levels of il- in china (chictr ) [ ] . moreover, several clinical trials are exploring if the well-established antiviral [ ] and anti-inflammatory effects of hydroxychloroquine will be effective in treating patients with covid- as has previously been suggested for sars-cov infection [ ] . this has also been demonstrated in vitro for sars-cov- [ ] . in contrast, janus kinase (jak) inhibition has been proposed as a potential treatment in order to reduce both inflammation and cellular viral entry in covid- [ ] . thus, it comes as no surprise that in a recent correspondence, lancet authors have identified the following potential therapeutic options for cytokine storm syndrome including ards the use of corticosteroids, selective cytokine blockade (eg, anakinra or tocilizumab) and jak inhibition [ ] . j o u r n a l p r e -p r o o f virus presentation to the different t cell subsets stands on the crossroads between innate and adaptive immune responses. studies on sars-cov and mers-cov [ ] presentation have identified several susceptibility and protection conferring hla alleles. the dearth of similar data regarding sars-cov- antigen presentation to t cells and possible virus evasion mechanisms of this process suggests it is a virgin investigation field to be explored. apart from the sustained inflammation and cytokine storm, lymphopenia has been implicated as a major risk factor for ards and mortality in the context of covid- [ ] . similar findings were described for sars-cov infected patients who had considerable decreases of cd + t and cd + t cells [ ] . however, in convalescent patients specific tcell memory responses to sars-cov were still found six years post infection [ ] . showed no reactivity with viral antigens. however, the small number of sera used (n= ) implies that further investigation is needed to corroborate these results [ ] . nonetheless, since we are currently in early stages of sars-cov- pandemic more studies need to be carried out to shed light on antibody persistence (both igm and igg) and protective effects. recently, macaques re-challenged with sars-cov- after a primary infection did not show signs of re-infection, suggesting that protective immunity and memory responses were fruitfully mounted. this finding can also impact vaccine production strategies [ ] . importantly, covid- convalescent sera was shown to hold promise as a passive immune therapy alternative to facilitate disease containment [ ] . to the best of our knowledge, at j o u r n a l p r e -p r o o f least one pharmaceutical company, takeda, is preparing to purify antibody preparations from covid- convalescent sera against sars-cov- [ ] . a recently published case report of a patient with mild-to-moderate covid- revealed the presence of an increased activated cd + t cells and cd + t cells, antibody-secreting cells (ascs), follicular helper t cells (tfh cells), and anti-sars-cov- igm and igg antibodies, suggesting that both cellular and humoral responses are important in containing the virus and inhibiting severe pathology [ ] . antibody dependent enhancement (ade) is a mechanism whereby non-protective antibodies produced during an infection with an agent either mediate increased uptake of this agent into target cells or cross-recognize a different pathogen and facilitate its entrance to target cells [ ] . evidence emerging over the past two decades suggests that antibodies against different coronavirus can cross-react to some extent and mediate ade [ ] . ade in the context of sars-cov was thought to be mediated by antibodies produced against e-cov [ ] and was contemplated as contributing to high mortality rates in china [ ] . the described mechanism suggests that low affinity or low title anti-spike protein antibodies rather than neutralizing the virus result in fc receptor mediated infection of immune cells, further aggravating the dysregulation of anti-sars-cov immune responses [ ] . indeed, in vitro as well as in vivo experimental models have shown that ade hinders the ability to manage inflammation in the lung and elsewhere. this may lead to ards and other hyperinflammation-induced clinical manifestations also observed in several of the documented cases of severe covid- [ , ] . while the molecular and immunological host response to sars-cov- infection has not yet been fully elucidated to confirm ade is occurring, anti-sars-cov- antibodies have been shown to partially cross-react with sars-cov, suggesting enhancement is a possibility. with this in mind, ade in populations previously exposed to other coronavirus can partially explain the geographic discrepancies observed in covid- pathogenesis and severity. finally, ade can have several implications in vaccine development as low-affinity or low-titer antibody producing vaccines can increment susceptibility rather than confer protection against the pathogen as has previously been described for a dengue vaccine [ ] [ ] [ ] . j o u r n a l p r e -p r o o f detection methods based on nucleic amplification are often used in the case of sars-cov, mers-cov and other viruses, because have high sensitivity and specificity, particularly in the acute phase of infection [ ] . case identification and surveillance of covid- spread although rt-qpcr assay is considered the gold-standard method to detect viruses such as sars-cov and mers-cov [ , ] , currently available rt-qpcr assays targeting sars-cov- have important considerations. firstly, due to the genome similarity of j o u r n a l p r e -p r o o f sars-cov- to sars-cov ( % of nucleotide identity [ ] ), some of the primer-probe sets described by different groups and listed in the who coronavirus disease (covid- ) technical guidance [ ] , have cross-reaction with sars-cov and other bat-associated sars-related viruses, therefore, it is important to run confirmatory tests. loop-mediated isothermal amplification (lamp) is a one-step isothermal amplification reaction that couples amplification of a target sequence with four to six primers, to ensure high sensitivity and specificity, under isothermal conditions ( - °c), using a polymerase with high strand displacement activity [ ] . in the case of an rna sample, lamp, is preceded by the reverse transcription of the sample rna. rt-lamp has been used before for the detection of various pathogens [ ] . including sars-cov- and other respiratory viruses [ , ] . recently, it received emergency use authorization (eua) from the u.s. j o u r n a l p r e -p r o o f serological tests also, called immunoassays, are rapid and simple alternatives for screening of individuals that have been exposed to sars-cov- based on the qualitative or quantitative detection of sars-cov- antigens and/or anti-sars-cov- antibodies. there are several types of serological tests available, including elisa (enzyme-linked immunosorbent assay), iift (indirect immunofluorescence test), lateral flow immunoassays and neutralization tests. immunoassays assays are very useful because they allow to study the immune response(s) to sars-cov- in a qualitative and quantitative manner. in addition, help to determine the precise rate of the infection [ , ] , and to determine more precisely the fatality rate of the infection [ ] . several sars-cov- targeted serological tests are commercially available or in development [ ] . a recently developed kit, reported a sensitivity of . % and specificity of . % [ ] using sars-cov- igg-igm combined antibody rapid (within minutes) test [ ] . despite their simple and fast readout and their potential for being used outside laboratory environments (bedside, small clinics, airports, train stations, etc.), serological tests have a critical disadvantage; given the fact that antibodies specifically targeting the virus would normally appear after days or longer [ ] after the illness onset [ ] , tests based on this principle have a lag period of approximately to days post-infection. during this lag period, infected and non-infected individuals will both result in a negative output. in addition, it is important to highlight that because serological tests depend on the ability to produce antibodies, intrinsic immunological differences and/or responses between individuals, can significantly affect the outcome of these tests. recently, some commercially available immunoassays received ce mark for professional use [ , ] , and therefore are registered as in vitro diagnostic devices. currently, there are a plethora of antibody tests for covid- with variable performance (sensitivity varying from to %, specificity from to %, reviewed in (foundation for innovative new diagnostics) [ ] . different manufacturers of serological assays declare that their assays have no cross reactivity to other human coronaviruses and other respiratory viruses. however, despite the data provided by manufacturers, recent studies highlighted that several of the commercially available tests have sensitivity and/or specificity issues that should be considered for using and analyzing results of many of these tests [ ] [ ] [ ] [ ] [ ] . j o u r n a l p r e -p r o o f as mentioned before, immunoassays -particularly tests detecting anti-sars-cov- igm and/or igg-indicate that the person has been exposed to the virus. in the case of other viral infections, having antibodies targeting a pathogen has often been considered an indication of having immunity against that pathogen [ ] . based on this idea, some governments have suggested using serological tests, to determine who has developed immunity against sars-cov- and provide positive individuals a "risk-free certificate" or "immunity passports", which would enable them to travel or to return to work, assuming that they are protected against re-infection [ ]. however, based on the limited knowledge of how immunity to this virus works [ ] , there is not enough evidence to declare a person immune, or to confirm that people who have anti-sars-cov- antibodies are protected from a re-infection. even though covid- can be diagnosed using qpcr as the gold standard, inadequate access to reagents and equipment has slowed disease detection even in developed countries such as the us. several low cost and rapid tests using different approaches have been described. unlocking) technique for the detection of covid- and the detectr (developed by mammoth biosciences) prototype rapid detection diagnosis kit using crispr to detect the sars-cov- in human samples have been described [ ] . the use of rna aptamers, have recently emerged as a powerful background-free technology for live-cell rna imaging due to their fluorogenic properties upon ligand binding, a technology that could be of use to diagnose sars-cov- infection [ ] . finally the use of next generation sequence (explify®) might be used to detect and identify bacterial, viral, fungal, and parasitic pathogens by their unique genome sequences [ ] . in covid- symptomatic infection, the clinical presentation can range from mild to ventilation assistance [ ] . the spectrum of symptoms of covid infection are characteristic of a mild disease in most of the cases, however, it is important to point that the progression could lead to a severe respiratory distress. asymptomatic infection (while incubation occurs) was described both in the first cases in wuhan and in other cohorts. a group of isolated patients were screened for sars-cov- , where % ( cases) were positive for the test, and half of these cases had no symptoms. on the other hand, there are reports of cases without overt symptoms in which there were ground glass images in the chest tomography in up to % of patients [ ] . of the asymptomatic cases studied in wuhan city, the . % of people exposed developed specific symptoms in . days, and the remaining . % were symptomatic in the following . days (ci, . to . days). the median estimated incubation period was . days ( % ci, . to . days) [ ] . some patients with initially mild symptoms had symptom progression over the course of one week [ ] . the descriptive studies available so far have concluded that the majority of cases are mild infections (more than % of cases); with up to % of patients being sever j o u r n a l p r e -p r o o f in most cohorts, and less than % have been considered as critical cases with high vital risk [ ] . in a study describing patients with covid- pneumonia in wuhan, the most common clinical characteristics at the onset of the disease were described. this is consistent with other international cohorts (table ) [ ] . it is important to note that fever is not always present and up to % of patients could had a low grade temperature between . to degrees celsius or normal temperature [ ] . if these patients required hospitalization, % developed a fever during the course of the illness. rarer accompanying symptoms included headache without warning signs, odynophagia and rhinorrhea. gastrointestinal symptoms such as nausea and watery diarrhea were relatively rare [ ] . dyspnea develops after a median of to days from the onset of symptoms. it is important to notice that, if dyspnea is an important clinical finding, not all the patients with this j o u r n a l p r e -p r o o f symptom will develop severe respiratory distress or require oxygen supplementation [ ] . according to world health organization (who) guidelines, covid- infection can present as pneumonia without signs of severity, and could be managed in the outpatient setting. this is applicable to those patients who do not need supplemental oxygen [ ] . as previously mentioned, the most serious manifestation of covid infection is pneumonia, characterized by cough, dyspnea, and infiltrates on chest images; the latter is indistinguishable from other viral lung infections. acute respiratory distress syndrome (ards) is a major complication of covid pneumonia in patients with severe disease. this develops in % after a median of eight days. mechanical ventilation is implemented in . % of cases [ ] . in different case reports, the need for supplemental oxygen via the nasal cannula was required in approximately % of hospitalized patients. % required non-invasive mechanical ventilation, and less than % required invasive mechanical ventilation with or without extracorporeal membrane oxygenation (ecmo) [ ] . it is important to mention that the proportion of severe cases is highly dependent on the study population and may be related to the epidemiological behavior of the infection in each country. additionally, the number of people tested will influence the denominator. in italy, the average age of people infected with covid- is between and years, and % of those hospitalized require admission to the intensive care unit (icu) [ ]. the who recommendations had established that severe covid- disease could be defined by the following parameters in table [ ] . [ ] . among the established risk factors for the development of ards is age greater than years, diabetes mellitus and hypertension, in at least % of patients [ ] . it should be clarified that, although advanced age is identified as a risk factor for a severe infection, those of any age may suffer from severe illness from covid- . the descriptions made so far of the patients from china have determined that almost % of the patients were between the ages of and years (cohort of , cases) [ ] . in other population settings, such as in the united states, more than % of confirmed the clinical characteristics of symptomatic cases and their severity has been described. in addition to the symptoms reported by the patients, the findings on physical examination may be absent during mild coivd- infection. those with moderate to severe covid- infection have various signs during pulmonary auscultation, however the most common findings include: wet rales; global decrease in respiratory sounds and increased thrill [ ] . early recognition is essential to classify cases as potential cases and initiate one of the most important measures to contain the pandemic, isolation. . anyone who has resided or been traveling in areas where widespread community transmission has been reported. . any patient who has had potential exposure through attending events or has spent time in specific settings where cases of covid- have been reported. the scenarios described respond to the context of a high suspicion of covid- infection. the world health authorities (cdc, who) continually update these contexts. there have been multiple case definitions and clarifications regarding when to perform a covid- test: • they have pointed out the importance of fever, cough and dyspnea as sentinel symptoms, since these should form part of the clinical judgment that guides doctors. this allows to expand the group of suspicious patients. • in cases of severe respiratory distress of undetermined etiology and that do not meet the previously indicated criteria, a screening for covid- would be indicated. • in areas of limited resources, the suggestion is to prioritize cases that require hospital care, and in this way guide the epidemiological fence to order isolation and protect the most vulnerable people (chronically ill and over years of age), as well as test those with the greatest possibility of exposure (travelers and health personnel). currently, there is no laboratory data profile that is framed in covid infection. from a cohort of patients confirmed with covid , these findings were classified as mild, moderate and severe disease [ ] . high levels of d-dimer and more severe lymphopenia have been associated with mortality due to a prothrombotic state that determines multi-organ failure. in general, leukopenia and / or leukocytosis can be found in the interpretation of blood biometry, however, the most widely described finding is lymphopenia [ ] . it should be considered that in the context of viral pneumonia biomarkers such as procalcitonin and pcr are not useful, as often these biomarkers are in the normal range for patients with covid- . among other findings, descriptive studies have reported considerable elevations of lactate dehydrogenase and ferritin as well as alteration in aminotransferases; although elevation ranges for these parameters have not been established [ ] . about the imaging findings, covid viral pneumonia has similar features on imaging to other viral infections. although computed tomography (ct) is the test of choice, it is not useful for a definitive diagnosis due to the wide variety of images that can be found in patients with covid infection. this statement is derived from a large cohort of more than wuhan patients, where rt-pcr confirmation of covid and chest ct images of these patients were correspondingly analyzed. ct images were determined to have a sensitivity of %; however, the specificity was only % [ ] . in general, the majority of descriptive studies concur that the finding of ground glass opacifications is most common. it is typically basal and bilateral, and rarely associated with underlying consolidation. a multicenter chinese study that retrospectively reviewed the ct scans of patients found that % had typical ground-glass images and up to % had this finding along with consolidations. these findings were more frequent in the most j o u r n a l p r e -p r o o f severe and older age groups of patients [ ] . pleural effusion ( %), and lymphadenopathy ( . %) [ ] . the emergence and outbreak of sars-cov- , the causative agent of covid- , has rapidly become a global concern that highlights the need for fast, sensitive, and specific tools to monitor the spread of this infectious agent. diagnostic protocols to detect sars-cov- using real-time quantitative polymerase chain reaction (rt-qpcr) were listed on the world health organization (who) website as guidance, however, various institutions and governments have chosen to establish their own protocols that might not be publicly available or listed by who. there are important challenges associated with close surveillance of the current sars-cov- outbreak. firstly, the rapid increase of cases has overwhelmed diagnostic testing capacity in many countries, highlighting the need for a high-throughput, scalable pipelines for sample processing [ , ] . secondly, given that sars-cov- is closely related to other coronaviruses [ ] , some of the currently available nucleic acid detection assays can result in false positives [ ] . thirdly, critical concern for molecular detection is the low sensitivity reported for rt-qpcr assays [ ] and serological tests [ ] , particularly in the early stages of infection. additionally, most of the available rt-qpcr assays require sample processing and equipment only available in diagnostic and/or research laboratories. it is important to mention that coinfection is a possibility, as some reports from italy and in spain, less than % of cases in a cohort correspond to plwh, which have had a satisfactory evolution and less than half required an intensive care unit [ ] . in the us, of the , hospitalized patients in the new york area, only patients had hiv, while in san francisco, data was published on , people who had diagnosed with sars-cov- infection, of which less than % had hiv and none of them developed severe covid- [ ] . despite the existence of in vitro studies on the efficacy of the use of lopinavir / ritonavir, it is currently known that its effect in cases of moderate and severe covid- is null, and therefore at the moment no recommendation can be given nor how treatment, much less as prophylaxis [ ] . this clarification is important given that there is a belief that plwhs could be protected if they take antiretroviral therapy. therefore, current recommendations for plwhs are to maintain antiretroviral therapy with the goal of controlling hiv as well as following the same standards of care as the general population to avoid acquiring a sars-cov- infection [ ] . regarding sars-ncov infection in pregnant women, there is currently limited evidence about the effect of the virus on the mother or fetus. however, due to the physiological changes typical of pregnancy, especially on the immune system (immunosuppression) and the cardiopulmonary system, pregnant women are thought to be more susceptible to developing severe symptoms when they acquire the viral respiratory disease. in , when influenza a h n infection occurred, only % of the infected population were pregnant, yet they accounted for % of infection-related deaths [ ] . pregnancy ( %) [ ] . in another study of pregnant patients infected with mers-cov, presented adverse results ( %), neonates were admitted to the neonatal intensive care unit ( %) and three of them died ( %) [ ] . however, it is important to note the small sample size which could increase the risk of bias and low power of the study. with information obtained so far from the wuhan sars-cov- outbreak, the infection appears to be less severe for pregnant women, compared to previous sars-cov and mers-cov outbreaks [ ] . however, it is important to take into account that the data from covid- infection should be monitored with a doppler ultrasound every two weeks, due to the risk of developing intrauterine growth restriction [ , ] . the time of termination of the pregnancy, as well as the method, also depend on several factors, including gestational age, maternal condition in relation to sars-cov- infection, presence of maternal comorbidities, and fetal condition. decisions must be made collaboratively during multidisciplinary team discussions, with individualized management plans established for each patient [ ] . a diagnosis of covid- alone is not an indication for the termination of pregnancy, rather it should be made in combination with consideration of morbidity and mortality of both the fetus and mother. after delivery, the use of corticosteroids is recommended for antenatal fetal lung maturation, with betamethasone or dexamethasone [ ] ; taking special care in critically nursing patients, as this may worsen their condition, and may delay delivery, which is necessary for the management of these patients [ , ] . the symptoms children present with are similar to adults, as is the incubation period ranging from to days (mean of . ). a cough is the most frequent presenting symptom ( %) followed by fever ( %). there is a higher occurrence of gastrointestinal symptoms including diarrhea ( %), nausea, vomiting ( %) and abdominal pain. these gastrointestinal symptoms are usually more variable in children than adults and are sometimes the only clinical manifestation in associations with fevers. [ , ] . the clinical progression and disease severity in pediatric patients is markedly different from that of adults. over % of affected children are asymptomatic or have mild to moderate disease [ ] . the majority of serious cases in children are related to those with significant comorbidities such as heart disease, immunosuppression, etc. to date of this review, only a few cases of children without underlying comorbidities have died as a result of covid have been reported. this difference of severity of illness between adults and j o u r n a l p r e -p r o o f children has not been clarified, however, several theories have been postulated. these include that children express more ace receptors in their lungs which confer some protection to severe injuries such as those caused by rsv and which would decrease dramatically with age [ , ] . immunological factors may also influence outcomes, as in childhood we are most exposed to frequent challenges including recent seasonal viruses such as rsv in the winter months. most likely, it is multifactorial and depends on factors from both the host and the virus itself [ ] . abnormal radiological (ct) findings are found in asymptomatic children and consist of bilateral lung lesions ( %). elevated crp (creactive protein), procalcitonin pct ( %), and liver enzymes are present in most affected children, unlike adults in whom pct is not a reliable marker. virus elimination via the stool even after the negativity in the nasopharyngeal mucosa and the disappearance of symptoms makes them a potential source of contagion through the fecal-oral route [ ] . patients with cancer are generally more susceptible to infections than healthy people, because they have a state of systemic immunosuppression that is exacerbated during chemotherapy or radiotherapy [ ] . in china, according to national surveillance data, coronavirus infection occurs in . % of patients with malignant tumors. this is a much higher proportion than the general incidence of . % [ ] . p< . ) even after adjusting for age [ ] . further research, completed in a tertiary hospital in wuhuan -china similarly found that % of patients with cancer and sars-cov- infection died, most of them over years of age [ ] . due to these findings, it has been proposed by many international entities that during the pandemic, for prevention, an individualized plan based on the patient's specific conditions is required, with the aim to minimize the number of visits to health institutions.  for early-stage patients with need of post-surgical adjuvant chemotherapy, especially those whose clinical, pathologic, and molecular biologic staging suggest a better prognosis, the start time of adjuvant chemotherapy may be delayed up to days after surgery without affecting the overall effect of treatment [ ] .  for patients with advanced cancer, the main approach should be to minimize hospitalization in covid- positive installations. replacing the existing intravenous treatment regimen with oral chemotherapy during this special period may be considered, to ensure that treatment is not interrupted for a long time during the pandemic [ ] . however, if there is a suspicion of covid- infection in this population group, the same updated diagnostic guidelines and the corresponding management should be followed depending on their severity of illness. moreover, an individualized follow-up plan should be outlined due to higher likelihood of complications in this group of population [ ] . it should be noted that patients attending out-patient appointments for cancer have higher levels of anxiety, depression and other mental health problems than the general population. studies have shown that approximately % of malignant tumor survivors have a moderate to severe fear of tumor recurrence [ ] . for this reason, psychologist surveillance of outpatients in quarantine or during hospitalization should be considered. reported complications derived from covid- describe a severe disease that requires management in an intensive care unit (icu) in approximately % of proven infections. j o u r n a l p r e -p r o o f appear to be most susceptible to the life-threatening complications. the risk of patient-topatient transmission in the icu is currently unknown, therefore adherence to infection control precautions is paramount [ , ] . progressive deterioration of respiratory function is undoubtedly the most common and lifethreatening complication of the infection. the prevalence of hypoxic respiratory failure in covid- patients is %, and it can progress to acute respiratory distress syndrome (ards), with the need of mechanical ventilation support at . days on average. one study found that between and % of hospitalized patients require admission to the icu due to respiratory deterioration [ ] . as respiratory complications are the most common cause of severe deterioration, early identification of them will undoubtedly help in timely support. support provided should be adapted to take into account risk factors such as advanced age, neutrophilia and organic dysfunction for the development of ards. the diagnostic support of pulmonary tomography is undoubtedly a valid tool; images in patients with different clinical types of covid- have characteristic manifestations, but it can become an operational problem due to the difficulty in performing imaging on critically ill patients. on the contrary, lung ultrasound at the bed-side could provide an alternative to radiographs and tomography during the diagnosis of covid- [ , ] . since more than % of hospitalized patients will require supplemental oxygen, it is recommended that oxygen should be started when pulse oximetry values fall below %. an upper-limit of % saturation should be established, since higher values have been shown to be harmful [ , ] . hemodynamic deterioration has a variability of presentation, this depends on the study population and the definition [ ] , the presence of shock in the intensive care unit may be present between to % [ , ] . cardiomyopathy related to viral infection is one of j o u r n a l p r e -p r o o f the main causes of hemodynamic detriment, occurring in up to % of patients with covid- [ ] . hemodynamic failure is one of the main causes of death in these patients, with percentages of up to %, inconclusive risk factors are associated to date such as diabetes, hypertension, lymphopenia, and elevation of d-dimer [ ] . acute kidney injury (aki) is present in up to % of critically ill patients, podocytes and proximal tubule cells are potential host cells for sars-cov- , caused by the virus induced cytopathic effect. the diagnosis is based on markers of early kidney injury and urinary output [ ] . initial management of shock is based on fluid resuscitation, based on the application of dynamic parameters to predict response to fluids, such as variation in stroke volume (svv), variation in pulse pressure volume (ppv) and change in stroke volume with passive leg elevation or fluid challenge above static parameters [ ] . variables such as skin temperature, capillary refill time and/or serum lactate measurement are currently valid tools to assess shock. the volume of liquids used in resuscitation should be restricted and administered in relation to dynamic assessment. a liberal water resuscitation strategy is not recommended, rather a balance of crystalloids over colloids as resuscitation liquids should be encouraged and avoiding the use of hydroxyethyl starches, albumin, dextrans or gelatins [ , ] . indirect evidence suggests that the target mean arterial pressure (tam) for patients with septic shock is mmhg using vasoactive support [ ] . the recommendation of norepinephrine use as the first agent is maintained. if norepinephrine is unavailable, vasopressin or epinephrine could be used, avoiding the use of dopamine as the initial vasopressor due to the potential development of arrhythmias [ , ] . in patients with covid- and shock with evidence of cardiac dysfunction and persistent hypoperfusion despite fluid resuscitation and norepinephrine use, dobutamine as inotropic is recommended. given the development of refractory septic shock, the suggestion of the use of hydrocortisone in continuous infusion is maintained, as indirect evidence, this in favor of reducing the length of stay in the icu and the resolution time of the shock [ ] . according to the investigative mission of the who in china, the case-fatality rate ranged other reports from china have coincided with this clinical risk profile, for example, a study that included confirmed cases, patients who had ards had as main underlying diseases: diabetes and high blood pressure. of these cases, patients died [ ] . according to who, the recovery time is estimated to be two weeks for patients with mild infections and three to six weeks for those with serious illnesses. on the other hand, cdc established that people who had symptoms in the mild to moderate spectrum and maintained home isolation have a resolution of days after the fever decrease, and there was a substantial improvement in respiratory symptoms, even without use of medications. isolation may be limited to days from resolution of symptoms, however, it must be adapted to the population circumstances of the epidemic [ ] . the evolution of the epidemiological curve in covid- outbreak makes consider containment strategies in china primarily, and other countries based on nonpharmaceutical interventions (npis). according to the who, the most effective measure is hands washing [ ] . combination as public health measures reduced contact rates in the population and therefore reduce virus transmission (table ) [ ] . table non -pharmacological measures. increasing the level of hand cleanliness to % in places with a high concentration of people, like all airports in the world would have a reduction of % in the impact of a potential disease spreading [ ] . the epidemiological evolution of the covid- pandemic through phases has required the application of specific measures according to the time or phase in which the virus is found in each country. the evolution in the non-pharmacological measures has been as variable as the pharmacological ones, in such a way, since january to march, it was ensured that the use of face masks was limited only to people who had contact with epidemiological foci, not to healthy people [ ] . this concept was also reinforced by cdc, in order to optimize the use of masks for health workforce. definitely the course of the pandemic was changing rapidly, which also demanded the change from containment measures to mitigation. the recommendations in the current context remain regarding the use of a facial mask in the community, but its optimization is important for health professionals. the use of the mask is not a substitute for handwashing and social distancing measures, as these ones together allow avoiding viral particles in aerosols or drops, as a low cost and accessible measure for general population [ , ] . there is still non-specific information for the recommendation of masks, in general, having in several studies claims that surgical or cotton cloth masks do not prevent the spread of the sars-cov- virus [ ] . the evidence about the transmission of the virus in the asymptomatic period also changed the containment measures, suggesting the community use of masks. it is from this that the recommendations for the rational use of masks arise since in some j o u r n a l p r e -p r o o f countries the massive use of n masks was reported, masks indicated for the use of medical personnel [ ] . regarding to this non pharmaceutical recommendations, the studies suggest to priories the resources on vulnerable population, in endemic areas, older people, adult with comorbidities and health workforce. studies are still needed on the duration of the protective effect of the masks and above all the possibility of their reuse for resource optimization. meanwhile the most important recommendation continues to be its use in addition to hand hygiene and social distancing [ ] . therapeutic j o u r n a l p r e -p r o o f this effect is reinforced by azithromycin. there were the best results in terms of viral load reduction, even though is mentioned some limitations in the study like small sample size, a short long-term outcome follow-up, and dropout of six patients from the study [ ] . concerning to mortality rates, a study was conducted in new york with patients ( . - . ). thus, it concludes that the use of hcq is not associated with either a decreased or increased clinical impairment, intubation or death [ ] results reinforced by other study in hospitalized patients with covid- diagnosis in new york city, whom received treatment with hydroxychloroquine, azithromycin, or both drugs was not associated with significantly reduction in mortality [ ] . relating to safety of this drug, in a study carried out in patients in which the theoretical complications of the use of hcq and its combination with macrolides (azithromycin) were assessed by serial electrocardiograms, the following results were obtained. in % of patients ( ) received chloroquine, % ( ) received hcq, and % ( ) [ ] . supportive therapies in immune regulation, together with the use of antivirals, are important to take into account, especially in those patients in a serious and critical state, in which they could improve the clinical response and perhaps avoid residual lung injuries. the convalescent plasma is extracted from recovered individuals from an infection, being an antibody transfer medium to provide passive immunity (neutralizing antibodies and globulin). the goal is to provide a rapid immune response until the patient can develop their own active immune response in the hope that there will be clinical improvement [ ] . improvement in most individuals, as well as viral suppression days after treatment [ ] . in the same country, at the shenzhen hospital, cases of patients with severe covid- were reported who met criteria for acute respiratory distress syndrome (ards), who were administered convalescent plasma (titration greater than : and neutralizing antibodies greater than ). it was found that clinical recovery occurred approximately days after the transfusion ( patients) and of the patients were discharged days after admission. it is important to mention that this group of patients also received antivirals, methylprednisolone and all the necessary support measures in intensive care [ ] . other drugs like ivermectin, nitazoxanide, and others have been studied in the context of covid- treatment, but the results are inconsistent. all of the clinical trials evidence, supporting or against the use of mentioned drugs are detailed in (supplementary table ). this review summarized some drug repurposing agents previously known to has efficacy against other virus like sars-cov, mers-cov, influenza. actually, exist some new drugs with high potential action on targets for covid- therapeutics. it is important to notice that there is no specific treatment for the coronavirus approach. in context of the scientific evidence exposed and the particular clinical features of each patient, the reader will be able to make the best clinical and therapeutic decisions. when it comes to vaccine design and manufacturing, the main objectives are to ensure its safety, its efficacy in activating specific adaptive immune responses and the production ofideally-long term memory. thus, eliciting protective immune responses including neutralization antibodies and/or ctl generation is of paramount importance. huge challenges need to be tackled in order to minimize the long and cumbersome process of vaccine generation. among them, candidate antigen targets need to be identified, immunization routes and delivery systems investigated, animal models set, adjuvants optimized, scalability and production facility considered, target population selected, and vaccine safety and long-term efficiency evaluated. currently there are no approved vaccines against any human coronavirus, suggesting that their generation is quite novel. several candidate vaccines against sars-cov had shown promise reaching phase i or phase ii clinical trials [ , ] , but the rapid containment of sars-cov expansion rendered them redundant, did not allow for a test population for phase iii trials and, therefore, put their further assessment to a halt. ctl memory could last up to years after infection [ ] . these data suggest that vaccine strategies employing viral structural proteins that can elicit effective, long-term memory t cell responses could yield fruitful results. on the other hand, the s spike protein region containing the ace receptor binding domain (rdb) is the obvious option when neutralizing antibody responses are considered [ ] [ ] [ ] . indeed, a candidate sars vaccine antigen consisting of the rbd of sars-cov spike protein was created and found it could elicit robust neutralizing antibody responses and long-term protection in vaccinated animals [ ] . the fact that covid- convalescent sera shows potential as a therapeutic approach [ ] aligns with the theory that efficient b cell responses are mounted and lead to production of protective antibodies. two different groups, using an immunoinformatic approach mapped several ctl and b cell epitopes on different proteins of the virus [ , ] . moreover, various ctl epitopes were found to be binding mhc class i peptide-binding grooves via multiple contacts, illustrating their probable capacity to elicit immune responses [ , ] . consequently, these identified b and t cell epitopes could be potential targets for therapeutic vaccines. however, important safety considerations should be taken into account before releasing a new vaccine in the market. previous studies on macaque models have shown that a vaccineinduced anti-spike protein antibody at the acute stage of sars-cov infection can provoke severe acute lung injury [ ] . similar observations of sars-cov vaccine-induced pulmonary injury have also been described in multiple several murine and monkey animal models [ ] . an additional factor that needs to be checked in phase ii and iii trials is that the vaccine does not cause ade of the pathogen, as has previously been described. such concerns have risen in the context of a dengue vaccine [ ] . the pharmaceutical companies that are currently on a race to produce a vaccine for covid- along with the vaccine developing strategies they are using are summarized in table and figure . as can be easily deduced from table hospitalization and admission to already heavily charged icus due to these pathologies that could prove critical for weaker health systems that would struggle to carry the burden of combined outbreaks. moreover, vaccinating health care workers is crucial for reducing the risk of absence due to disease, thereby strengthening the healthcare workforce and minimizing the risk to infect covid- hospitalized patients with additional pneumoniacausing pathogens. lastly, covid- patients vaccinated for influenza and streptococcus pneumoniae allow their immune system to focus on one pathogen and, therefore, give it a better fighting chance against sars-cov- infection [ ] . high risk groups prioritized for vaccination for these two pathogens include pregnant women, persons with immunocompromised immune systems (either due to congenital or acquired immunodeficiencies), children, adults ≥ years and health care professionals. j o u r n a l p r e -p r o o f heat or chemical treatment inactivation. f) attenuated live pathogen vaccine strategies consist in administering a live pathogen that due to cell culture passaging has lost its virulence. they usually elicit robust and long-term memory immune responses without the need to administer an adjuvant. g) in dna vaccines the dna codifying a highly immunogenic antigen is administered and captured by professional antigen presenting cells (apcs) leading to antigen production and presentation by these cells. h) moderna's vaccine candidate already in phase i clinical trials uses an mrna vaccine approach whereby the genetic information codifying for the s protein of sars-cov- is delivered in lnps to enhance absorption by apcs. once uptaken by apcs the mrna induces the expression of s antigen that is subsequently mounted on and presented by mhc molecules to elicit adaptive immune response. numerous studies confirm that climate has an impact on virus (i.e., influenza, coronavirus, etc.) spread through manipulating the conditions of i) its diffusion, ii) the virus survival outside the host, and iii) the immunity of host population [ ] . meteorological conditions, such as temperature, humidity, wind speed and direction, atmospheric pressure, solar radiation (including ultraviolet (uv) spectrum) and precipitation amount and intensity depend on the latitude and the elevation of the location, thus creating distinct climatic zones in the planet. while in some regions, such as temperate climate zones, human influenza peaks have clear seasonal cycles, in others it is not as predictable [ ] [ ] [ ] [ ] [ ] . an array of studies, investigating the relationship between climatic factors and the activity of influenza all over the world, concluded that at the high latitudes of the world the peaks of influenza correlate with cold and dry weather conditions (i.e., winter season), while around the equatorial zone, it is more common during the months of high humidity and precipitation [ ] [ ] [ ] [ ] [ ] [ ] [ ] . essentially, it depends on explicit threshold conditions based on monthly averages of specific humidity and temperature. when specific humidity drops below - g/kg and temperature drops below - °c, the peak of influenza is stimulated during the cold-dry season, however, for tropical and subtropical (always humid and warm) regions, it is likely to prevail during the high precipitation (≥ mm) months the possible origins of the new coronavirus sars-cov genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding when darkness becomes a ray of light in the dark times: understanding the covid- via the comparative analysis of the dark proteomes of sars-cov- , human sars and bat sars-like coronaviruses novel coronavirus (sars-cov- ) epidemic: a veterinary perspective the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak an interactive web-based dashboard to track covid- in real time interim analysis of pandemic coronavirus disease (covid- ) and the sars-cov- virus in latin america and the caribbean: morbidity, mortality and molecular testing trends in the region epidemiological, socio-demographic and clinical features of the early phase of the covid- epidemic in ecuador. medrxiv severe acute respiratory syndrome a novel coronavirus from patients with pneumonia in china structure, function, and antigenicity of the sars-cov- spike glycoprotein structural basis for the recognition of the sars-cov- by full-length human ace crystal structure of sars-cov- main protease provides a basis for design of improved α-ketoamide inhibitors a pneumonia outbreak associated with a new coronavirus of probable bat origin genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding. the lancet return of the coronavirus: -ncov. viruses genome composition and divergence of the novel coronavirus ( -ncov) originating in china analysis of therapeutic targets for sars-cov- and discovery of potential drugs by computational methods disease and diplomacy: gisaid's innovative contribution to global health global initiative on sharing all influenza data -from vision to reality pre-fusion structure of a human coronavirus spike protein cryo-em structures of mers-cov and sars-cov spike glycoproteins reveal the dynamic receptor binding domains angiotensin-converting enzyme is a functional receptor for the sars coronavirus sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor a new coronavirus associated with human respiratory disease in china receptor recognition by novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars the proximal origin of sars-cov- . virological a novel angiotensin-converting enzyme-related carboxypeptidase (ace ) converts angiotensin i to angiotensin - epithelial cells lining salivary gland ducts are early target cells of severe acute respiratory syndrome coronavirus infection in the upper respiratory tracts of rhesus macaques a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury high expression of ace receptor of -ncov on the epithelial cells of oral mucosa a promoter-level mammalian expression atlas sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor article sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor the spike glycoprotein of the new coronavirus -ncov contains a furin-like cleavage site absent in cov of the same clade host factors in coronavirus replication human coronaviruses: a review of virus-host interactions sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus a structural analysis of m protein in coronavirus assembly and morphology epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan epidemiological and clinical features of the novel coronavirus outbreak in china. medrxiv clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study temporal dynamics in viral shedding and transmissibility of covid- presumed asymptomatic carrier transmission of covid- potential presymptomatic transmission of sars-cov- interferon-stimulated genes and their antiviral effector functions rig-i in rna virus recognition rna recognition and signal transduction by rig-i-like receptors recognition of viral single-stranded rna by toll-like receptors mechanisms of innate immune evasion in re-emerging rna viruses viral innate immune evasion and the pathogenesis of emerging rna virus infections immunopathogenesis of coronavirus infections: implications for sars pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology middle east respiratory syndrome interaction of sars and mers coronaviruses with the antiviral interferon response sars and mers: recent insights into emerging coronaviruses dysregulation of immune response in patients with covid- in wuhan plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome mers-cov infection in humans is associated with a pro-inflammatory th and th cytokine profile interleukin- receptor blockade is associated with reduced mortality in sepsis patients with features of the macrophage activation syndrome: re-analysis of a prior phase iii trial a multicenter, randomized controlled trial for the efficacy and safety of tocilizumab in the treatment of new coronavirus pneumonia (covid- ) effects of chloroquine on viral infections: an old drug against today's diseases chloroquine is a potent inhibitor of sars coronavirus infection and spread in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) baricitinib as potential treatment for -ncov acute respiratory disease covid- : consider cytokine storm syndromes and immunosuppression. the lancet novel immunodominant peptide presentation strategy: a featured hla-a* -restricted cytotoxic t-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory syndrome coronavirus nucleocapsid protein association of human leukocyte antigen class ii alleles with severe acute respiratory syndrome in the vietnamese population epidemiological and genetic correlates of severe acute respiratory syndrome coronavirus infection in the hospital with the highest nosocomial infection rate in taiwan in human-leukocyte antigen class i cw and class ii dr genotypes are associated with resistance to severe acute respiratory syndrome (sars) infection association of human leukocyte antigen class ii alleles with severe middle east respiratory syndrome-coronavirus infection a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster lack of peripheral memory b cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study two-year prospective study of the humoral immune response of patients with severe acute respiratory syndrome profile of specific antibodies to the sars-associated coronavirus antibody responses to sars-cov- in patients of novel coronavirus disease a serological assay to detect sars-cov- seroconversion in humans. medrxiv reinfection could not occur in sars-cov- infected rhesus macaques the convalescent sera option for containing covid- drugmaker takeda is working on coronavirus drug breadth of concomitant immune responses prior to patient recovery: a case report of non-severe covid- a tale of two viruses: does heterologous flavivirus immunity enhance zika disease? evasion of antibody neutralization in emerging severe acute respiratory syndrome coronaviruses antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus neutralizing antibody response and sars severity anti-severe acute respiratory syndrome coronavirus spike antibodies trigger infection of human immune cells via a ph-and cysteine protease-independent fcγr pathway severe acute respiratory syndrome (sars) coronavirus-induced lung epithelial cytokines exacerbate sars pathogenesis by modulating intrinsic functions of monocyte-derived macrophages and dendritic cells dysregulated type i interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in sars-cov-infected mice licensed dengue vaccine: public health conundrum and scientific challenge dengue vaccine efficacy: not a zero sum game critique of world health organization recommendation of a dengue vaccine an updated roadmap for mers-cov research and product development: focus on diagnostics identification of a novel coronavirus in patients with severe acute respiratory syndrome assays for laboratory confirmation of novel human coronavirus (hcov-emc) infections genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan covid- ) technical guidance: laboratory testing for novel coronavirus ( -ncov) in suspected human cases specific primers and probes for detection novel coronavirus. novel primers and probes for detection of novel coronavirus in coronavirus detection of novel coronavirus ( -ncov) by real-time rt-pcr detection of novel coronavirus ( -ncov) in suspected human cases by rt-pcr protocol: real-time rt-pcr assays for the detection of sars-cov- detection of second case of -ncov infection in japan rt-pcr protocol for the detection of -ncov centers for disease control and prevention. real-time rt-pcr panel for detection -novel coronavirus. coronavirus in california | covid- testing. carbon health xpert® xpress sars-cov- has received fda emergency use authorization. cepheid. cdc. coronavirus disease (covid- ): information for laboratories: -ncov coronavirus update | hologic molecular test receives fda emergency use authorization. hologic. genmark receives fda emergency use authorization for its eplex® sars-cov- test -ncov cdc-qualified probe and primer kits for sars-cov- new york sars-cov- real-time reverse transcriptase (rt)-pcr diagnostic panel coronavirus disease (covid- ) | labcorp covid- : genesig new coronavirus ( -ncov) nucleic acid detection kit fda oks cellex's antibody-based test for covid- flexible testing options for sars-cov- coronavirus mesa biotech covid- test receives fda emergency use authorization | genomeweb neumodx secures fda emergency use authorization for coronavirus test qiagen launches qiastat-dx test kit for detection of sars-cov- coronavirus in europe following ce marking loopmediated isothermal amplification of dna development and clinical performance of high throughput loop-mediated isothermal amplification for detection of malaria development of reverse transcription loop-mediated isothermal amplification (rt-lamp) assays targeting sars-cov- . biorxiv recent advances and perspectives of nucleic acid detection for coronavirus potential rapid diagnostics, vaccine and therapeutics for novel coronavirus ( -ncov): a systematic review sars-cov- diagnostic pipeline development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis pm : . labs scramble to spot hidden coronavirus infections mers-cov diagnosis: an update covid- coronavirus rapid test cassette bioeasy novel coronavirus ( -ncov) test kits antibody testing for covid- : a report from the national covid scientific advisory panel immunological assays for sars-cov- : an analysis of available commercial tests to measure antigen and antibodies antibody tests in detecting sars-cov- infection: a meta-analysis evaluation of nine commercial sars-cov- immunoassays test performance evaluation of sars-cov- serological assays immunity and immunopathology to viruses: what decides the outcome? the trinity of covid- : immunity, inflammation and intervention rapid detection of novel coronavirus sars-cov- using a crispr-based detectr lateral flow assay live cell imaging of single rna molecules with fluorogenic mango ii arrays hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series cr ip t ce pt e d us cr ip t ac ce pt us the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan who- -ncov-clinical- . -eng clinical characteristics of coronavirus disease in china risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease /fulltext?utm_campaign=tlcoronavirus &utm_source=twitter&utm_medium=social. the lancet clinical management of severe acute respiratory infection ( sari) when covid- disease is suspected: interim guidance management of critically ill adults with covid- if clinically indicated:" is it? a rapid advice guideline for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (standard version) diagnostic utility of clinical laboratory data determinations for patients with the severe covid- severe acute respiratory syndrome-related coronavirus -the species and its viruses, a statement of the coronavirus study group clinical characteristics of coronavirus disease in china correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases relation between chest ct findings and clinical conditions of coronavirus disease (covid- ) pneumonia: a multicenter study performance of radiologists in differentiating covid- from viral pneumonia on chest ct as deaths mount, china tries to speed up coronavirus testing. the new york times fielddeployable viral diagnostics using crispr-cas clinical diagnosis of samples with -novel coronavirus in wuhan. medrxiv detection of novel coronavirus ( -ncov) by real-time rt-pcr differential diagnosis of illness in patients under investigation for the novel coronavirus (sars-cov- ) hiv- did not contribute to the -ncov genome covid- in patients with hiv: clinical case series presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the new york city area a trial of lopinavir-ritonavir in adults hospitalized with severe covid- enfermedad por coronavirus (covid- ) and hiv: asuntos y acciones claves novel coronavirus infection and pregnancy pregnancy and perinatal outcomes of women with severe acute respiratory syndrome middle east respiratory syndrome coronavirus (mers-cov) infection during pregnancy: report of two cases & review of the literature clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records clinical manifestations and outcome of sars-cov- infection during pregnancy coronavirus in pregnancy and delivery: rapid review coronavirus disease (covid- ) and pregnancy: what obstetricians need to know guidelines for pregnant women with suspected sars-cov- infection analysis of the pregnancy outcomes in pregnant women with covid- in hubei province novel corona virus disease (covid- ) in pregnancy: what clinical recommendations to follow? isuog interim guidance on novel coronavirus infection during pregnancy and puerperium: information for healthcare professionals pediatric patients with coronavirus disease in china characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding angiotensin-converting enzyme inhibits lung injury induced by respiratory syncytial virus clinical and ct features in pediatric patients with covid- infection: different points from adults are children less susceptible to covid- ? cancer patients in sars-cov- infection: a nationwide analysis in china surgical treatment strategy for digestive system malignancies during the outbreak of novel coronavirus pneumonia sars-cov- transmission in patients with cancer at a tertiary care hospital in wuhan, china delayed initiation of adjuvant chemotherapy among patients with breast cancer health management of breast cancer patients outside the hospital during the outbreak of novel coronavirus disease managing oncology services during a major coronavirus outbreak: lessons from the saudi arabia experience stress, depression, the immune system, and cancer clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study care for critically ill patients with covid- the role of ultrasound lung artifacts in the diagnosis of respiratory diseases is there a role for lung ultrasound during the covid- pandemic? mortality and morbidity in acutely ill adults treated with liberal versus conservative oxygen therapy (iota): a systematic review and meta-analysis the search for optimal oxygen saturation targets in critically ill patients: observational data from large icu databases practical recommendations for critical care and anesthesiology teams caring for novel coronavirus ( -ncov) patients the impact of high-flow nasal cannula (hfnc) on coughing distance: implications on its use during the novel coronavirus disease outbreak exhaled air dispersion during high-flow nasal cannula therapy versus cpap via different masks staff safety during emergency airway management for covid- in hong kong noninvasive ventilation in critically ill patients with the middle east respiratory syndrome. influenza other respir viruses noninvasive ventilation for patients with hypoxemic acute respiratory failure ventilation with lower tidal volumes versus traditional tidal volumes in adults for acute lung injury and acute respiratory distress syndrome. cochrane database syst rev treatment for severe acute respiratory distress syndrome from covid- beyond low tidal volume ventilation: treatment adjuncts for severe respiratory failure in acute respiratory distress syndrome optimal plateau pressure for patients with acute respiratory distress syndrome: a protocol for a systematic review and metaanalysis with meta-regression prone position for acute respiratory distress syndrome. a systematic review and meta-analysis formal guidelines: management of acute respiratory distress syndrome low-dose and short-term application of corticosteroid treatment in patients with severe covid- pneumonia: single-center experience from wuhan characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical predictors of mortality due to covid- based on an analysis of data of patients from wuhan, china. intensive care med conservative fluid management or deresuscitation for patients with sepsis or acute respiratory distress syndrome following the resuscitation phase of critical illness: a systematic review and meta-analysis colloids versus crystalloids for fluid resuscitation in critically ill people effect of reduced exposure to vasopressors on -day mortality in older critically ill patients with vasodilatory hypotension: a randomized clinical trial scandinavian ssai clinical practice guideline on choice of inotropic agent for patients with acute circulatory failure vasopressors for hypotensive shock water, sanitation, hygiene and waste management for covid- impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand hand-hygiene mitigation strategies against global disease spreading through the air transportation network rational use of face masks in the covid- pandemic advice on the use of masks in the community, during home care and in healthcare settings in the context of the novel coronavirus (covid- ) outbreak wearing face masks in the community during the covid- pandemic: altruism and solidarity. the lancet. ; effectiveness of surgical and cotton masks in blocking sars-cov- : a controlled comparison in patients rational use of face masks in the covid- pandemic research and development on therapeutic agents and vaccines for covid- and related human coronavirus diseases remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial. the lancet systematic review of the efficacy and safety of antiretroviral drugs against sars, mers or covid- : initial assessment a trial of lopinavir-ritonavir in adults hospitalized with severe covid- an exploratory randomized controlled study on the efficacy and safety of lopinavir/ritonavir or arbidol treating adult patients hospitalized with mild/moderate covid- (elacoi) efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical trial a pilot study of hydroxychloroquine in treatment of patients with moderate covid- hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial observational study of hydroxychloroquine in hospitalized patients with covid- association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in new york state the effect of chloroquine, hydroxychloroquine and azithromycin on the corrected qt interval in patients with sars-cov- infection clinical trials on drug repositioning for covid- treatment the antiviral effect of interferonbeta against sars-coronavirus is not mediated by mxa protein what's new | coronavirus disease covid- . covid- treatment guidelines effectiveness of convalescent plasma therapy in severe covid- patients the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory metaanalysis effectiveness of convalescent plasma therapy in severe covid- patients treatment of critically ill patients with covid- with convalescent plasma effect of convalescent plasma therapy on viral shedding and survival in covid- patients from sars to mers, thrusting coronaviruses into the spotlight recent advances in the vaccine development against middle east respiratory syndrome-coronavirus memory t cell responses targeting the sars coronavirus persist up to years post-infection immunogenicity of candidate mers-cov dna vaccines based on the spike the spike protein of sars-cov -a target for vaccine and therapeutic development receptor-binding domain of sars-cov spike protein induces long-term protective immunity in an animal model yeast-expressed recombinant protein of the receptor-binding domain in sars-cov spike protein with deglycosylated forms as a sars vaccine candidate immunoinformatics-aided identification of t cell and b cell epitopes in the surface glycoprotein of -ncov a sequence homology and bioinformatic approach can predict candidate targets for immune responses to sars-cov anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection a double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge ade and dengue vaccination safety and immunogenicity of an anti-zika virus dna vaccine -preliminary report mrna vaccines -a new era in vaccinology mrna as a transformative technology for vaccine development to control infectious diseases mrna vaccine delivery using lipid nanoparticles first fda-approved vaccine for the prevention of ebola virus disease, marking a critical milestone in public health preparedness and response could enhanced influenza and pneumococcal vaccination programs help limit the potential damage from sars-cov- to fragile health systems of southern hemisphere countries this winter? global influenza seasonality: reconciling patterns across temperate and tropical regions epidemiology of seasonal influenza in the middle east and north africa regions, - : circulating influenza a and b viruses and spatial timing of epidemics. influenza other respir viruses influenza seasonality: timing and formulation of vaccines roles of humidity and temperature in shaping influenza seasonality seasonality of influenza and its association with meteorological parameters in two cities of pakistan: a time series analysis environmental predictors of seasonal influenza epidemics across temperate and tropical climates influenza epidemics in the united states global patterns in seasonal activity of influenza a/h n , a/h n , and b from to : viral coexistence and latitudinal gradients seasonality of influenza in the tropics: a distinct pattern in northeastern brazil influenza surveillance in pune, india, - epidemiological and virological influenza survey in dakar, senegal: - quantifying the role of weather on seasonal influenza influenza seasonality: underlying causes and modeling theories stability of sars coronavirus in human specimens and environment and its sensitivity to heating and uv irradiation an explanation for the seasonality of acute upper respiratory tract viral infections epidemic influenza and vitamin d -dihydroxyvitamin d is a potent suppressor of interferon γ-mediated macrophage activation seasonal variation in host susceptibility and cycles of certain infectious diseases influence of extreme weather and meteorological anomalies on outbreaks of influenza a (h n ) key: cord- -moekkw x authors: grace, sara title: policing social distancing: gaining and maintaining compliance in the age of coronavirus date: - - journal: nan doi: . /police/paaa sha: doc_id: cord_uid: moekkw x drawing on motivational posturing theory (mpt) and procedural justice theory (pjt), this article makes recommendations for how best to secure compliance with social distancing regulations. applying those theories to—mostly observational—data from a study on the use and impact of penalty notices for disorder, the influences on cooperation during police–citizen encounters are explored. whilst focusing on the english data/regulations, as both mpt and pjt have been tested internationally, the conclusions have relevance beyond these shores. the article proposes a sixth posture—compulsion, a form of resistant compliance—to the five set out by mpt. focusing attention not just on whether compliance is achieved but how recognizes the risk to future legitimacy posed by only achieving compliance through coercion or the threat thereof. lessons from the research are applied to policing social distancing, with regards to: securing compliance during interactions, self-regulation and enforcement action, and how to preserve police legitimacy. the health protection (coronavirus, restrictions) (england) regulations give police in england the power to issue £ on-the-spot fines (up to £ , for subsequent offences ) to enforce new rules on social distancing which aim to prevent the spread of the covid- . officers may also use powers of arrest and remove people to their home. the college of policing and npcc ( , p. ) have called on forces to be consistent and adopt an 'inquisitive, questioning mind-set', only using enforcement powers as a last resort. this is underpinned by a four-step approach: engage with people, explain the risks they are posing to themselves and others, encourage them to adhere to the regulations and, if they do not, enforce the law using on-the-spot fines, arrest, and/or prosecution. policing social distancing is a very particular and peculiar circumstance. however, there are some parallels with policing antisocial behaviour through existing dispersal powers and penalty notices for disorder (pnds). new rules prohibited public gatherings of more than two *lecturer in criminology, university of salford, salford, uk. e-mail: s.k.grace@salford.ac.uk fines were initially set at £ , up to £ for subsequent offences but were increased on may . policing, volume , number , pp. - doi: . /police/paaa v c the author(s) . published by oxford university press. all rights reserved. for permissions please e-mail: journals.permissions@oup.com people except in certain limited circumstances and imposed restrictions on movement 'without reasonable excuse' (emphasis added, see sections and , correct as at may ). whilst the regulations give a non-exhaustive list of such exceptions, the law lacks the specificities of government advice. for example, guidance, but not the law, initially limited people to just 'one form of exercise a day' (cabinet office, ) (see section ( )(b), correct as at may ). and, just as there may be disagreement over, for example, whether any given behaviour is 'likely to cause harassment, alarm or distress' (in breach of section of the public order act and punishable by pnd), so too conflict may occur over whether a person has a 'reasonable excuse' to circumvent restrictions on movement. given these parallels, existing research on the use and impact of pnds can offer some insight into how best to achieve compliance with the new rules. this article brings together research on motivational posturing theory (mpt) and procedural justice theory (pjt) to analyse data on: policing in the night-time economy (nte)-the first application of mpt in that context -and the use of pnds, before applying these findings to policing social distancing. the article is structured into three parts: first, it sets out the literature on why people comply with authorities. secondly, it outlines the findings from a study on the use of pnds (grace, a )-drawing, especially on observations of police-citizen interactions in the nte and document analysis of pnds, as well as interviews and surveys with pnd recipients-to explore what influences, in particular, short-term compliance with the police during encounters, as well as payment of pnds and future offending (i.e. mid-and long-term compliance). in doing so, the article answers calls to draw on observational research in developing our understanding of procedural fairness and its influence on compliance with the police (radburn and stott, ) . observations allow for consideration of the dynamic nature of police-citizen interactions and examination of how, when, and why people move from more to less compliant postures (and back). based on this analysis, it is proposed that in addition to the five motivational postures set out by braithwaite ( a) , there is a sixth: compulsion. finally, based on the findings from this research, as well as broader literature on procedural justice and motivational posturing theories, recommendations are made for how we might best police social distancing to secure compliance and legitimacy. whilst the focus here is on the regulations in england and data drawn from that context, mpt and pjt are empirically driven theories which have been tested internationally-in particular, in the uk, usa, australia, and mainland europe-and so the conclusions have relevance beyond these shores. when assessing compliance we are concerned with both when people comply and why. to take the first of these, there are three frames of interest when considering compliance with the coronavirus regulations: short-term compliance with officers during police-citizen encounters; mid-term compliance with (i.e. payment of) the fine (if issued); and long-term compliance with the law/future cooperation with the police. of particular importance here (and for the police) are compliance with officers during police-citizen encounters and long-term compliance, both with social distancing rules and with the police once those rules are lifted. public messaging on the risk posed by coronavirus, and in turn the risk this poses to the national health service, seeks to encourage (voluntary) compliance on normative grounds, whereas instrumental thinking underpins the enforcement strategy. to weight the rational choice in favour of compliance, it is well publicized that breach of the rules could result in a fixed searches of various databases in may , including proquest, jstor, emerald insight, scopus, and google/google scholar for the search terms motivational posture/motivational posturing and night-time economy/nte returned no results. penalty notice (fpn). there are incentives to accept the notice (such as not getting a criminal record or having to appear in court and a lower fine for quick payment) and disincentives to subsequent breach of the rules, with fines increasing for each offence up to a maximum of £ , . on summary conviction, fines are unlimited. fines thus serve as a general deterrent, with specific measures aimed at deterring repeat offenders. the government will surely hope that as people adapt to the new regulations, compliance becomes habitual; people get used to living within the new rules, adopting new ways of working and connecting with people online for example. however, there are questions about whether, and for how long, people might be willing to accept these new ways of living. early in the lockdown, there were already concerns that a minority were 'breaking the rules or pushing at boundaries' of acceptable behaviour (hancock, ) . as time passes, lockdown fatigue may set in making it harder to ensure voluntary compliance. disparities between law and guidance, as well as changes to the guidance, may also lead to confusion over what is/is not acceptable, making voluntary compliance all the more difficult to achieve (police federation, ). indeed, 'the government was forced to issue a swift correction [following an announcement of changes to the guidance on may ] when dominic raab [foreign secretary] advised the public to break the law' (dearden, ) . the challenge for the police, who have been tasked with enforcing the regulations, is both how to gain and maintain compliance. and, crucially, how to do that in a manner that does not cause long-term harm to their legitimacy. procedural justice and motivational posturing theories offer some guidance for how police forces might achieve those goals. normative compliance is related to legitimacy. there is a wealth of research on pjt which demonstrates that perceptions of procedural justice-which regards the process of decision-making rather than the decision itself-are related to perceptions of police legitimacy which, in turn, encourage voluntary compliance, both with the regards to willingness to cooperate with the police (both in the short-and long-term) and willingness to obey the law (hough et al., ; reisig et al., ; tyler, ) . the procedural justice literature outlines four antecedents to procedural fairness: participation (or 'voice'): allowing people to give their account of events and have their views considered. neutrality: demonstrating that decisions are unbiased, based on the facts of the case. respect: treating people with dignity and respect. trustworthy motives: demonstrating sincerity, benevolence, and sharing public concerns. emerging research suggests perceptions of distributive fairness-i.e. assessments of equitability, whether people feel they been treated similarly to others and received an outcome they feel they deserve-are related to perceptions of procedural justice (maxwell et al., ; mclean, ; , and thereby, in turn, legitimacy (and compliance). there is some debate in the literature about what is a predictor of legitimacy and what is a constituent element thereof (e.g. jackson and bradford, ; tankebe et al., ) . for our purposes, it is sufficient to note that perceptions of distributive and procedural justice (as well as police effectiveness and police lawfulness) have been found to be central to police legitimacy and that police legitimacy has been found to predict compliance. motivational posturing theory 'the starting point for motivational posturing theory is that authorities which make regulatory demands threaten our freedom' (braithwaite, , p. ) . the threats to freedom posed by the coronavirus regulations are clear to see; they restrict our freedom of movement and assembly, but also more broadly our ability to, amongst other things, earn a living and achieve our goals. our motivational postures are how we cope with those threats. they reflect the degree of distance individuals wish to place between themselves and an authority (here, the police), which, in turn, reflects the legitimacy we ascribe them; whether we feel aligned with their goals and trust their means of achieving those goals. people may either have attitudes of deference or defiance. however, even those who defer to regulations may do so either because they think their purpose is sound (commitment) or because they have 'the force of law' (capitulation) (braithwaite, , p. ) . defiant attitudes include: resistance, where the individual doubts the intentions of the regulator; disengagement, where the individual is disenchanted with the system, believing there to be no point in challenging authority, and game-playing. a disengaged posture could reflect a perceived lack of legitimacy (in pjt terms) and a concomitant defiance of the decisions of the authority. game-playing shares that same disenchantment, but rather than the fatalism of the disengaged, game-players are combative, seeking to 'beat the authority at its own game' (braithwaite, , p. ; a; b) . these five postures load onto two factors or supra-dimensions and people may be high/low on either dimension (braithwaite, ) . the first, resistance-cooperation, is bipolar with commitment and capitulation at one end and resistance at the other. the second is unipolar, disengagement and game-playing both reflecting dismissiveness. braithwaite ( b, p. ) has previously noted that postures are not mutually exclusive but are 'not likely to be equally strong in any one individual at any one time . . . the assumption of co-existence remains [however] plausible'. in the research presented here, resistant attitudes were often coupled with compliant postures (and behaviour). as such, a sixth posture-compulsion-is proposed. it is hypothesized that compulsion would fit into the existing model as set out in table (braithwaite, a; ; . compulsion lies between capitulation and resistance; it is compliant behaviour, coupled with a resistant demeanour, that is, where people are coerced into accepting officers' decisions through either the threat or reality of enforcement action, but where they continue to express grievance at officers' actions. whilst those who capitulate can be said to acquiesce, accepting the authority of the decision maker, the compelled do not 'go quietly' (discussed further below). unlike the resistant, however, they do ultimately comply. regulation poses a threat to our three selves (braithwaite, ) . the moral self is the sense that oneself is a 'good', law-abiding person, someone who does the 'right' thing. the democratic collective self (or grievance self; braithwaite, ) values justice and fair treatment. the status-seeking self seeks to achieve our personal goals. blocks, such as those posed by the coronavirus regulations, pose a threat to our status-seeking self. mpt posits that a strong moral self will lead to compliance, whereas a strong grievance self (and weak moral self) leads to resistance. dismissiveness, be it in the form of disengagement or game-playing, 'pits a strong status-seeking self against a weak moral self' (braithwaite, , p. ) . to ensure compliance authorities must, therefore, engage and buttress the moral self. to address resistance requires procedurally fair treatment, through which the moral self is acknowledged and restored. coronavirus presents a unique moment in our social history, there is no guide to effectively police social distancing; instead we must draw from existing research in other contexts. mpt tells us about the 'signals those being regulated send to regulators around legitimacy and compliance' (braithwaite, , p. ) . pjt tells us about how people assess fair decision-making processes and thus what a fair process entails. these are, therefore, complementary theoretical frameworks that can offer a guide to practitioners to recognize both when their legitimacy may be contested and how they might respond to restore legitimacy when policing covid- . this research aims to explore whether and why people comply (or not) with the police; taking lessons from policing in the nte (in the first known application on mpt in that context), and the use of pnds, and applying them to this new context: policing coronavirus. in doing so, this article proposes a way forward for gaining and maintaining compliance in these unchartered waters. data analysed here were originally gathered for a study on the use and impact of pnds (grace, a) . field notes from -h observations of police working in the nte in one english city between january and july were reanalysed to select case studies on police-citizen encounters (some of which involved numerous people) with sufficient detail to assess compliance. this included cases where pnds were issued (grace, a, table . ) . motivational postures are empirically derived 'composite narratives made up of attitudes, beliefs, emotions, expectations and norms . . . [however, they are] not hidden from view' they are statements to be seen (braithwaite, , p. ) . they can, therefore, be inferred through observation and, indeed, it is this same inference that authorities (in our case the police) would be guided to act on when drawing on mpt in practice. mpt and pjt provide complementary (empirically driven) theoretical frameworks to assess compliance. data analysis was both inductive and deductive, moving between theory and data in an iterative fashion, exploring links between the theoretical categories (silverman, ) . case studies were initially subject to analytic induction whereby behaviour was coded for compliance/noncompliance, then within those 'core groups' (bryman, ) , whether it suggested postures of commitment or capitulation (compliance) or resistance, disengagement, or game-playing (noncompliance). the co-existence of resistant compliance/ deference commitment-accepts the purpose of the regulations, sharing the same goals and accepts the authority of the regulator capitulation-accepts the authority of the regulator, but does not necessarily share the same goals enforced selfregulation compulsion-accepts the purpose of the regulations, but does not accept they have broken them, thinks power is being used inappropriately/poor decisions are being made negotiated selfregulation resistance-accepts the need for a system of regulation and authority of the regulator, but thinks power is being used inappropriately/poor decisions are being made discretionary use of enforcement powers dismissiveness disengagement-does not share the norms/values of the regulator, mistrusts their motives and questions the need for a system of regulation, withdraws and does not follow the rules non-discretionary use of enforcement powers game-playing-does not share the norms/values of the regulator and enjoys finding loopholes to work around the regulations. behaviour from people who complied with officers' directions led to the creation of an additional compliant posture-compulsion-explained in the findings below. data were also subject to thematic analysis to understand the common drivers for compliant/non-compliant behaviour. whilst the analysis presented here focuses on observation data, and short-term compliance, these are complemented with a document analysis of pnd tickets (n ¼ ) as well as a survey of pnd recipients (n ¼ ) and semi-structured interviews with survey respondents, with some examination of mid-and long-term compliance (see grace ( a) for further details). the analysis presented here is limited, not least because observation data were not originally collected for the purpose of assessing motivational postures or procedural fairness. however, given the novelty of social distancing rules, reanalysis of existing (albeit limited) data from other contexts provides a useful means of developing an evidence-based approach. the particular value of the current research lies in its use of observation data, which is rare both in studies of mpt and pjt. observation provides a means to consider the 'dialogic and relational' character of legitimacy (bottoms and tankebe, , p. ) . by observing 'interactions in situ', the dynamic nature of compliance-which is necessarily lacking from the 'thin' data provided by existing, largely survey-based research on procedural justice (harkin, , p. ; radburn and stott, , p. )-can be reviewed. document analysis of officers' evidence on pnds issued for drunk and disorderly and breach of section of the public order act (offences largely committed in the nte, n¼ ) found that whether pnds were issued on-the-spot or following arrest was strongly related to offenders' compliance (v ¼ . , df ¼ , p < . , u ¼ À . ). only three non-compliant people were issued with pnds on-the-spot; two were initially arrested, and the other was issued the day after the offence. compliance was the main driver in where tickets were issued (grace, ) . officers cannot issue fines to non-compliant people. non-compliance was highly correlated with suspect demeanour; only four of the people who were non-compliant displayed no aggression towards officers at any stage (grace, a) . indeed, officers were one of the victims in % of section and drunk and disorderly offences and the sole victim in % (n ¼ ). the importance of demeanour-and its relationship with compliance-was supported by observation data; of the pnds issued during observations were issued to people who were abusive to, and noncompliant with, officers. evidence from the case studies presented below offers some insight into why people do/do not comply, and thus how officers might avoid such 'conflict spirals' (tedeschi and felson, , p. ) , whereby individuals respond aggressively to police intervention and officers respond with arrest. motivational posturing in the nte: a sixth posture? of the case studies, people complied at some stage in and, perhaps unsurprisingly, all except one (of the four) case(s) where people did not appear to comply at any stage related to incidents where, for various reasons, the end of the encounter was not observed. in the final one, officers were called to another incident, leaving a pair of (still disgruntled) men who had refused to go home as requested by officers. most people's posture changed (sometimes more than once) during an encounter. whilst overall cases involved people who demonstrated either commitment (n ¼ ) and/or capitulation (n ¼ ) at some stage, only two were committed throughout, both of whom had approached the police for help. a further were categorized as demonstrating a sixth (new) posture-compulsion. with regards to defiant postures, resistance (at any stage) was demonstrated in of the case studies. only two cases involved disengagement from/dismissal of authority, with people refusing to engage with officers (both were arrested). game-playing-the desire to evade justice by finding loopholes and winning concessions-was similarly rare. that is not to say it is rare in practice just that (by virtue, if it is successful) it is hard to detect via police observations. game-playing could be seen in those who tried to walk/run away when they saw the police approaching (n ¼ ). but also, perhaps too, in those who seemed to 'turn on the charm' in an attempt to win leniency (n ¼ ). postures changed, sometimes more than once, during most encounters (n ¼ ). observation case -a man apprehended for urinating in the doorway of a block of flats-offers a good example of how people could move between postures. initially, officers asked him 'how he'd feel if someone did that in his house, he drunkenly agreed he was out of order'. accepting that the behaviour was wrong, he, therefore, demonstrated commitment. officers told him such behaviour could lead to a fine. misunderstanding them to mean he was going to be fined, he replied '"fine, give me a ticket then" in a resigned manner'. in light of an (ongoing) lecture, his posture seemed to shift then to one of capitulation-he accepted that the behaviour was wrong, but was merely resigned to, rather than accepting of, the possibility of a fine. when faced with this capitulation, the officers reacted angrily telling him 'well i was about to say as you'd been alright we were going to let you go, but if you want a ticket we'll give you one'. in response to their change in approach, he became more resistant, questioning their decision, repeatedly saying 'but i haven't told you to p-off or f-off' (self-censoring swearwords). he was thus resistant, in that he was pushing back against officers' decision to issue a pnd, but ultimately he was still complying with their requests, suggesting a posture of compulsion. in most cases where people's postures became more resistant (n¼ ), this was as they sought to argue their case and/or resist arrest. where people moved to more deferent postures (n ¼ ), they were convinced or cajoled into compliance, accepting officers' decisions (voluntarily desisting, dispersing, and/or accepting a pnd) or else they were coerced into doing this with the threat or reality of a pnd or arrest. the former approach was associated with postures of commitment or capitulation, whereas the latter was associated with (what i have termed) a posture of compulsion. to distinguish between commitment and capitulation, as operationalized in this study: commitment was willing compliance, where people seemed to accept the behaviour/actions of officers as the right ones in the circumstances, complying without any resistance. whereas capitulation was an acquiescence to the police, an acceptance that (even if they might disagree) the police had the authority to behave/act as they were. the 'sixth posture', compulsion was created due to the numerous cases involving a simultaneous co-occurrence of compliance with resistance. whilst capitulation suggests an acceptance of the regulator's authority, compulsion was associated with challenging/questioning authority. postures of compulsion share with resistance the same sense of grievance and protest at the regulator's (here, the police's) behaviour but are distinct both behaviourally and attitudinally. behaviourally, the compelled comply, the resistant defy. for example, in contrast to observation case who-whilst pushing back against their decision-answered officers' questions, accepting an on-the-spot pnd, in case , having been evicted from a bar, a woman refused officers' requests to go home, repeatedly swearing at them until she was eventually arrested. attitudinally, resistance and compulsion are both associated with a strong grievance, but the former is associated with a weak moral self (braithwaite, , p. ) . compulsion, however, was associated with a strong grievance and a strong moral self. indeed, the grievance stemmed from officers' failure to treat them in a distributively and procedurally fair way and recognize them as a person who had behaved in a morally (if not necessarily legally) acceptable way; for the compelled resistance thus manifest as an appeal to, rather than a rejection of, or attack on, officers. the role of distributive and procedural (in)justice in (non-)compliance in the nte where people were convinced or cajoled into compliance, this was associated with processes that reflect values of procedural fairness: listening to people's accounts of events, empathizing, being respectful, explaining their response etc. thus, for example, in observation case , the man was arrested after refusing to move on and being abusive towards an officer as he sought to find out if they had arrested his friend. his arrest points to an initially resistant posture and refusal to heed officers' warnings. on arrival at the station he became jovial, telling officers 'i'm too old for all this'; rather than an expression of genuine remorse, this seemed to be a move from resistance to game-playing, looking to charm officers into treating him more leniently. this more compliant behaviour led to him being de-arrested and issued with an on-the-spot pnd in the police van. after which he asked after his friend, but was told: [he] couldn't discuss it as it was confidential . . . just like [earlier] . . . he couldn't tell him as perhaps his friend wouldn't want him to know . . . the man replied 'to be fair if your colleague had told us that at the time we'd be alright, but he wound us up'. having initially been arrested, case moved from a defiant to compliant posture, capitulating to the officer's decision when treated with procedural fairness-the officer explaining his actions and treating the man with respect. during observations, being told they were not going to be arrested or else that they would 'only' receive a pnd/dispersal order (when a more serious punishment may have been anticipated) was often coupled with a shift from compulsion to capitulation. people no longer sought to 'state their case', their case had been heard. the research highlighted the context-specific nature of respect. officers sometimes swore at/in conversation with people, but, as this mirrored the individuals' language, it was 'well-received'. tone is everything, but this is difficult to capture in survey-based research. notably, one survey respondent agreed the officer was polite but elaborated in the interview that they were 'aggressively polite', their politeness was seen as a means of exerting authority rather than as a mark of respect (interview ). respect is not just expressed through (polite) words but through body language and tone of voice and most importantly by listening to the individual and explaining why officers were taking the action they were. positive engagement operationalized officers' respect for the offender, the neutrality of their decision-making and their trustworthiness. resistant behaviours-both compulsion (compliance) and resistance (noncompliance)-manifested as calls to have their version of events heard. voice or the denial thereof was central to resistance. it was common, both in interviews and during observations for people to comment 'i-or if they were talking about a friend, they-haven't done anything!' people would say this even where they had quite clearly broken the law. instead, disagreement stemmed from a belief that their behaviour was not sufficiently serious to warrant (that/any) action, a rejection of the (implied) label 'offender' (they did not need to be punished, a warning would have sufficed), that others had done the same or worse, and, more rarely, complaints that they had been provoked by officers. similarly, participants in snow's ( , p. ) study of (mostly traffic) fpn recipients and wells and savigar's ( ) research on driving offenders found that people might accept they 'technically' broke the law but distinguish themselves and/or their circumstances as undeserving of punishment/justifiable. people resist the police when they feel 'wronged'. they appear to take cues on distributive fairness, from the procedural fairness of the treatment they (do or do not) receive. whether police actions (and outcomes, where pnds were issued) were seen as distributively fair and/or favourable depended on the circumstances of the offence as well as the way officers presented their decision to intervene/take action. procedural fairness may then help inform judgements about distributive fairness by informing people's understanding of officers' reasoning and motives. officers sometimes 'sold' their decisions. for example, in case , a man who was stopped for urinating in public was told he could get a ticket, but as he had been discreet and his attitude was 'spot on' he would not this time, but that if they saw him again he would be in trouble. decisions were also sold by presenting formal action as the only/'least worst' outcome. such sales pitches might generate a sense that officers are acting with neutrality and trustworthiness as well as appealing to the individual's moral self and promoting a sense of voice/participation as officers are essentially saying 'i am recognising you as a person who "only" needs this (less serious) intervention'. this might also appeal to game-players who will feel that they have won a concession. however, attempts at a sales pitch did not always 'hit the mark'. in case , a woman received a drunk and disorderly pnd and written direction to leave the area after slapping a doorman who had ejected her from a bar. she was told she could be arrested and charged with assault but instead would 'just' get a pnd. she was compelled to accept these punishments, but demonstrated ongoing grievance, arguing that she had been warranted in her actions due to the bouncer's behaviour towards her. the importance of distributive fairness, and its relationship with procedural fairness, found here is supported by research from mclean ( mclean ( , and maxwell et al. ( ) . procedural fairness might encourage a sense of distributive fairness (and vice versa), however, a procedurally fair process cannot overcome the (legitimate) sense of unfairness that comes from being treated differently to others, that is, experiences of distributive unfairness. whilst distributive and procedural fairness might be conceptually distinct, they are inherently linked. apparent distributive unfairness raises concerns about officers' neutrality, their motives, and their trustworthiness (i.e. their procedural fairness). the sense of distributive unfairness might be particularly acute during policecitizen interactions which happen in public places if people can see they are being treated differently to others. for example, in case , two men resisted officers on the grounds that they had been held back, whilst the group they had argued with had been allowed to walk off without comment. long-term compliance: a(nother) special case? a survey of pnd recipients (n ¼ ) -who received tickets for a range of offences, including section , drunk and disorderly, theft, and possession of cannabis-found that, in keeping with the observation data, procedural and distributive justice were significantly associated with short-term compliance (measured as self-reported willingness to accept the officer's decision). however, contrary to much of the pjt literature, neither procedural nor distributive justice were associated with perceptions of (legal) legitimacy. nor were measures of procedural or distributive fairness directly associated with payment of the pnd (mid-term compliance) or long-term compliance, measured as self-reported reoffending (grace, a, pp. - ) . whilst % of respondents agreed they were more wary of being caught breaking the law (n ¼ ), % agreed that, were they in the same situation again they would behave the same way (n ¼ ), and % admitted that they had committed the same offence subsequently (n ¼ ), with repeat offending most commonly reported by respondents who had received pnds for possession of cannabis, drunk and disorderly, and public urination. this tension between pnds on the one hand, providing an awareness of the possibility of being punished, whilst on the other, not necessarily affecting behaviour was highlighted in interview (on-the-spot, s pnd for public urination, paid): i haven't done it again, i er, that's a lie [sounds incredulous, as though he is surprised at himself] i have done it again, i'm just really careful to look out for police officers beforehand . . .. the distinction between the pnd survey and existing literature (discussed above) with regards to the role of procedural justice in long-term compliance may, of course, simply reflect deficiencies in data gathered from a small convenience sample. equally, however, these findings do mirror jackson et al.'s ( ) and bradford et al.'s ( ) findings for traffic offences where, similarly compliance was-unlike in other contexts-not directly related to procedural fairness and (thereby) legitimacy. jackson et al. ( , p. ) reasoned that traffic offences' failure to fit with the existing model might reflect that such offences are not seen as 'truly criminal'. whilst people might be generally law-abiding, traffic offences were not seen as 'real' law. for traffic offences, compliance was driven by personal morality and, to a lesser extent, perceived risk of being caught. disorder offences and cannabis possession might too present a 'special case' with regards to the (lack of) influence of procedural justice on police legitimacy and longterm compliance. legitimacy rests, in part, on normative alignment, but this may be harder to achieve for disorder given the contested nature of 'order'. distributive fairness might also be more important in contexts where whether behaviour is 'wrong' is contested and police responses vary. months, and sometimes years, after the ticket had been issued, some survey respondents and interviewees still felt passionately that they had been harshly treated (grace, a, pp. - ) . as summed up by one survey respondent: i was treated like the scum of the earth. i'm i've worked my whole adult life in public services. i've never treated anyone so disrespectfully over something so trivial (on , on-thespot, urinating in public, paid). these findings highlight fpns' potential for generating long-term grievances against the police. however, it must be recognized that the ongoing anger of survey respondents may well have been the reason they chose to participate in the research; this was not a representative sample. the possible distinction between crime and disorder in the applicability of the pjt model needs to be explored through further research, using larger, representative samples. the focus in this article is on short-and long-term compliance as these are more pressing issues for policing social distancing; however, it is worth noting that both the ticket analysis and survey data suggest that whether or not people pay their pnd, that is, their mid-term compliance, may be driven by their ability to pay (grace, a, b) . document analysis of pnd tickets found that students ( %, n ¼ ) and the employed ( %, n ¼ ) were significantly more likely to pay their pnd than unemployed recipients ( %, n ¼ ) (v ¼ . , df ¼ , p < . , cramer's v ¼ . ). similarly, a survey of pnd recipients (n ¼ ) found that ability to pay was the only factor associated with whether the pnd was paid or registered as a fine. neither procedural nor distributive justice were associated with whether people paid (grace, a, pp. - ) . this was a small, convenience sample, which overrepresented those that paid their pnd as compared to national data, so these findings should be treated with caution, but they do highlight concerns about the choice of financial penalties as an enforcement strategy-particularly the use of fpns-given their inequitable impact. the burden of punishment will fall more heavily on those who are less well off (i.e. those already likely to be most detrimentally affected by coronavirus). this was starkly highlighted by one survey respondent who described the fine as 'exploiting[,] my fine was £ suddenly £ i was [on] £ per fortnight jobseekers [employment benefit] . . . i thought fair enough i will do a few days in prison' (sn , in custody, theft pnd, unpaid). people's ability to pay could, therefore, lead to very different outcomes. whilst whether or not people pay fixed penalties is not an immediate concern for police forces, such distributive unfairness could offend the democratic collective self and encourage resistant and/or dismissive postures making it harder for officers to secure voluntary compliance in the short-and/or long-term. the research presented here suggests proposals for policing social distancing, both during encounters and with regards to longer-term compliance with the coronavirus regulations. it also highlights the ways in which policing social distancing may impact on police legitimacy beyond the virus. these lessons will be considered in turn. existing research on motivational postures and pjt is supported by the data presented here: when officers act in ways that are perceived as being procedurally fair, people are more likely to cooperate/comply with them, procedural fairness discourages resistant postures. this further highlights the importance of a procedurally fair approach. analysis of observational research allows for consideration of the relational and interactive nature of 'compliance'; exploring when and why people move between different motivational postures. if authorities can understand people's motivational postures, they can tailor their response to increase the likelihood of compliance. mpt sets out five postures, whilst this research proposes a sixth: 'compulsion'. whether there is a distinct sixth posture that people hold in relation to authorities remains to be tested empirically via survey research. what this observational research suggests is that when trying to assess others' motivational postures-as the police would be tasked with doing during encounters-it may be useful to think of six. in this extended model, there are three compliant postures, which might be best summarized as signalling: this is fair (committed), this is fair enough (capitulated), and this is not fair (compulsion). resistant postures also signalled that sense of unfairness, but this was coupled with a defiance of officers, for example, refusing to answer questions, heed warnings, etc., whereas the compelled (ultimately) do as told. in policing the coronavirus regulations, if the police focus purely on achieving compliance, rather than how (and why) that compliance achieved, they might secure cooperation in the short-term but, according to the wider evidence on mpt and pjt, negatively impact on perceptions of police legitimacy (see further below). this sixth posture 'compulsion' therefore helps focus attention not just on whether compliance is achieved but how, recognizing the risk to future legitimacy posed by only achieving compliance through coercion or the threat thereof. the college of policing and npcc ( ) have adopted a four-step strategy of: engage, explain, encourage, and enforce. whilst four stages are set out, fundamentally they boil down to: step onepersuade and step two-enforce. persuasion-or, to fit the existing enforcement model (table ) , what we might term, negotiated self-regulationshould bolster the moral self and encourage postures of commitment (and compliance). where officers are met with resistance, procedural fairness, that is, demonstrating neutrality and trustworthiness, giving people a voice and behaving respectfully, may make recourse to coercive measures to enforce compliance less likely. the terms engage, explain, and encourage highlight the strategy's roots in procedural fairness; however, the guidance focuses largely on officers as information-givers, for example, they will 'educate people' and, amongst other things, 'emphasise the benefits to the nhs by staying at home' (brown, , p. ) . whilst this explanation will be important, procedural fairness requires a two-way dialogue. it will be equally (if not more) important that officers listen to people's accounts for why they appear to be circumventing regulations and, recognizing the subjectivity of the concept of a 'reasonable excuse', appreciate that people may not be intentionally breaking the rules. to enforce social distancing rules, officers have been given the power to issue fpns. this research, however, questions officers' ability to issue such fines on-the-spot to (non-compliant) pedestrians. the dynamics may be different when stopping people in vehicles. when issuing pnds, people who failed to follow informal warnings were more likely to be arrested; non-compliant people do not/cannot accept tickets. for those displaying compulsion, who only comply once threatened with and/or issued with an fpn, mpt (as well as the, albeit very limited, data here) would suggest a 'sales pitch'-highlighting the potential (more severe) sanctions (e.g. prosecution and much higher fine) they are avoiding-might appeal to their inner (status-seeking) game-player, encouraging a posture of capitulation (over compulsion). however, observations in the nte suggested that such sales pitches may not always 'hit their mark', especially where people have a strong (and perhaps justified) sense of distributive unfairness because they can see others not being punished. such as, for example, where the police walk past a group of middle-aged people to intervene in a group of young men playing football at a public park. selective law enforcement is not only routine but also necessary to the functioning of the police and the criminal justice system as a whole (goldstein, ) . in keeping with existing laws, not all breaches of the coronavirus regulations will be visible; officers will receive reports from third parties and come across (potential) breaches during patrols. officers will have the discretion to decide when, and where, to intervene, who to fine and/or arrest. whilst there is a notable gap between the law and the more comprehensive (and far more widely publicized) government guidance, 'even the most precisely worded rule of law needs interpreting in concrete situations' (reiner, , p. ). officers will, understandably, rely on their existing 'working rules' and cultural values to navigate this vacuum; despite calls for consistency, enforcement action may, therefore, fall more heavily on some groups/locations than others, with, as we have seen, differences between forces (charman, ; npcc, ) . where officers meet resistance, cultural norms may encourage them to punish those who fail the 'attitude test' (loftus, , p. ) . this research suggests, however, that such resistance, rather than coming from a rejection of the rules, may instead reflect people's feelings that have behaved acceptably in the circumstances and that officers have failed to take on board (what they see as relevant) mitigation and, as a result, mis-labelled them as an 'offender'. their resistance is thus a plea to be recategorized as a law-abiding citizen and have their moral self appeased. existing cultural norms may encourage officers to focus attention on 'the usual suspects' (medina ariza, ) . conversely, the need to prioritize public health may lead them into interactions with people who normally avoid police censure. such people may have a strong moral self and thus be particularly aggrieved by police attention, leading to resistance. equally, in the absence of a history of conflict, they could be less likely to come to the encounter with a posture of resistance or dismissiveness and be better placed to navigate it in a way that wins leniency. they could also be more inclined to interpret officers' treatment as procedurally fair and/or receive such procedurally fair treatment (sargeant et al., ) . initial data show that, in england, , fpns were issued between march and may , % to men and % to people aged under (npcc, ). whether fpn use mirrors the disproportionality seen in stop and search is difficult to gauge as % of tickets omitted ethnicity data. however, elsewhere, in new york and new south wales, for example, 'minority communities are disproportionately targeted by ramped-up policing that has accompanied the enforcement of lockdown measures' (letin, ) . new powers may thus exacerbate existing distributive unfairness in police attention and existing tensions. in policing social distancing, there is a risk of resistance not just from the individual(s) initially approached, but from bystanders (and subsequently the wider community), creating the potential for public disorder and/or collective disorder. this was seen in a manchester case; an officer threatened to use incapacitant spray on a person accused of breaching social distancing rules (busby, ) . the democratic self will be attuned to how, where, and when these new social distancing rules are enforced. in that case, the person's neighbours (one of whom filmed parts of the encounter, which was later published (lachey, ) ) started to resist the officer and ultimately there were a group of people and a second police car at the scene. complaints can be heard from neighbours that the officers' intervention, particularly his threat to use pava (incapacitant spray), was excessive. voice will be central to policing social distancing with legitimacy; officers need to be open to suspects' explanations for any assumed breaches of the rules. threats of force, as seen in the manchester case, may be met with resistance, not least because whether people's behaviour falls within (the permitted) 'reasonable excuses' is subjective. if officers' assessments of what is 'reasonable' fail to match those held by the communities they police, resistance is likely to follow. if they consistently do this, there is potential for major rioting (reicher and stott, ) . engaging with communities to develop a shared understanding of 'reasonable excuses' and explaining the reason for police interventions when they occur should help operationalize neutrality and trustworthiness as well as the distributive fairness (perceived deservedness) of receiving police attention. wherever possible, officers should abide by the regulations themselves, that is, keeping a safe distance ( m), not gathering in groups, etc. this is not only necessary for officers' safety but to operationalize respect, by minimizing the risk to citizens (a point that was noted by the videographer in the manchester video, who commented they were 'all risking corona [virus] because of him [the officer]'). by respecting the rules, they are seeking to enforce, officers can further demonstrate neutrality and trustworthiness, appeasing the democratic collective self. in the short term, whilst procedurally and distributively fair policing may encourage voluntary compliance, for those who refuse to heed officers' informal directions, my research suggests it is unlikely that officers will be able to issue them with fines on-the-spot; only (of ) non-compliant offenders were issued with pnds on-the-spot, were initially arrested, the other received a ticket the next day. non-compliant people are unlikely to willingly accept fines, although they may be compelled to do so. in those cases, where people remain non-compliant despite officers' attempts at persuasion, arrest remains an option but a decision needs to be taken about the relative risks/ rewards of enforcing the rules via arrest given the risk this poses to officers' health and the risk that officers inadvertently become super-spreaders during subsequent contacts with the public as well as the risk to legitimacy posed by compulsion. forces should heed the npcc's suggestion that enforcement action be a last resort. as platts-fowler ( , pp. and ) notes with regards to riots 'arrests in the imminent or early stages of unrest, of people deemed to be doing little wrong by their peers, become symbolic'. to return to manchester case, the force's quick public response-that the officer's actions were wrong, and he was now under investigation-should appeal to local citizens' democratic collective self as well as reducing the likelihood that the police will be cast as an 'out group' (reicher and stott, , p. ) . achieving compliance with social distancing rules mpt and pjt have developed largely separately, however, the importance of-what braithwaite terms-the moral self is also supported by procedural justice literature which (whilst highlighting the relationship between legitimacy and compliance) has found personal morality to be the strongest predictor of law-abiding behaviour (hough et al., ) . this relationship is particularly strong with regard to traffic offences, where police legitimacy was not related to compliance (bradford et al. ; jackson et al., ) . the best route to compliance with the social distancing rules is, therefore, by bolstering people's normative alignment with the regulations. officers can do this to an extent through their strategy of 'engage, explain, encourage' but promoting moral alignment with the rules is not the sole remit of the police (and is therefore largely beyond the scope of this article). suffice it to say, such wide-scale posturebuilding activity was reflected, for example, in the state support for, and promotion of, the (initially community-led) weekly 'clap for carers'. conversely, news that the prime minister's most senior advisor dominic cummings had travelled miles so as to isolate in closer proximity to suitable childcare, whilst, at the same time, the government were instructing people to 'stay home' might undermine commitment and promote dismissive postures, making defiance more likely and the regulations harder to police (bbc, ) . indeed, that this news may have bred a sense of disjuncture between the government and the people was perhaps best illustrated by the (usually pro-conservative) daily mail front page, which asked '. . . the question the whole country is asking . . . what planet are they on?' (groves, ) . the above section suggests means of dealing with 'pockets of resistance' from small groups. however, there is a risk that over time, growing resistance and/or dismissiveness would see a mass evasion of the rules. this would suggest that most people are no longer committed to them, thus questioning their legitimacy. this is reminiscent of the mass evasion of the poll tax in the s (hoggett and burns, , p. ) : the crucial thing about the poll tax . . . was that it offered everybody the opportunity of making an individual act of defiance. in this way 'not paying' became a direct and immediate personal statement, a 'fingers up' to the 'powers that be', a focus for the suppressed hatred that so many people felt for thatcherism. there is a very real risk, particularly in light of the news of, and public response to, dominic cummings' apparent breach of the coronavirus regulations (bbc, a), that mass defiance of social distancing rules becomes similarly symbolic. in such an event, just as with poll tax, the rules, rather than the policing thereof, may need to be revised. public anger rests on an apparent distributive unfairness in the application of the rules, that it is one rule for us (the people) and another for them (the elite) (bbc, b); being seen to address this inequity will be important in (re-)building commitment. as set out in table , mpt suggests that effective regulation requires different enforcement strategies depending on the regulatee's posture. this reflects an approach of responsive regulation, which proposes an enforcement pyramid (j braithwaite, (j braithwaite, , : [beginning] with respectful and cheaper strategies at the base. this allows virtuous actors to voluntarily comply with reminders about standards, while rational actors calculate that it is in their interests to comply. (healy, , p. ) the responses of the regulatee to interventions drawn from the base of the pyramid are the ones that determine if, how far and when the regulator escalates up the pyramid. (drahos and krygier, , p. ) research on deterrence in fields as a disparate as corporate crime and gang violence have highlighted the value of having multiple levers to pull, with multiple treatments being more effective than any single intervention (j braithwaite, ; schell-busey et al., ) . 'an integral part of . . . [responsive regulation] is to provide opportunities for dialogue' (braithwaite et al., , p. ) . procedural justice is thus important not only in individual encounters but also in the design of the regulatory system; key stakeholders from the community should be involved in developing the enforcement strategy and enforcement should be coupled with education. enforcement options for the coronavirus regulations are limited to fpn or prosecution (and a fine on conviction). a more reintegrative and/or restorative, tiered, approach-drawing on existing powers, using (different) community resolutions (nearer the bottom of the pyramid) and conditional cautions (nearer the top)-is likely to present a better deterrent than solely financial penalties. the introduction of deferred fpns-cancelled on completion of the conditions set out, operating in much the same way as existing pnds with an education optioncould offer a better interim measure, reducing the unnecessary criminalization that would occur from using conditional cautions. a restorative approach would see conditions which require offenders to contribute to the coronavirus relief effort in some way. this could appeal to the individual's moral self, allowing them to 'do the right thing' and make a recognized, valuable contribution. being more distributively fair than financial penalties-which disproportionately affect poorer people-this might also appeal to the democratic collective self (although distributive fairness also depends on whether powers are used disproportionately against some groups). it might, too, enable officers to engage with offenders' statusseeking self. if someone is breaking the rulesgoing for a drive because they were bored, for example, as in one early case (williams, )-giving them a community resolution (in that case a legitimate reason to travel, by delivering supplies, for example) satisfies the offender's desire to find loopholes. their status-seeking self may also value the social capital to be gained from contributing to much-needed relief efforts. avoiding more severe penalties might also appeal to their sense of competition. adopting a partnering approach such as this is the alternative to domination when trying to secure compliance for the dismissive (murphy, ) . financial penalties and prosecution could then be reserved for those who fail to meet these conditions. the challenge of policing social distancing: preserving legitimacy the wider evidence on procedural justice highlights that perceptions and experiences of procedural justice affect police legitimacy, which, in turn, is related to future willingness to cooperate with the police and to comply with the law; the impact of policing coronavirus may, therefore, be felt long after the regulations are lifted. from the existing mpt and pjt literature, as well as the research presented here, a number of different hypotheses follow about how policing social distancing will affect police legitimacy. in the absence of lockdownspecific evidence, the following (empirically derived) hypotheses might serve as a (temporary) guide for how to police social distancing in a manner that can best preserve legitimacy. in sum, if officers act with distributive fairness (follow the rules and apply them evenhandedly) and procedural fairness-listen to people (allow them a voice), treat them with respect, and demonstrate neutrality and trustworthiness by explaining their actions-this will promote a sense of procedural fairness and, in turn, police legitimacy, encouraging compliance at the scene. whether this will promote future cooperation with the police and long-term compliance with the law in general-as seen in other police legitimacy research (reisig et al., ) -is unknown. early research, however, suggests that-as with traffic offences (bradford et al., ; jackson et al., ) and, as suggested here, disorder offences-voluntary (long-term) compliance with the coronavirus regulations may not be related to legitimacy . social distancing rules may be contested. the key to long-term compliance would seem to lie in building public commitment to the regulations (which is largely outside of the remit of the police). compliance may, therefore, rest on the legitimacy of these rules specifically, rather than the police or law in general. the regulations serve an expressive function, communicating to people both how they ought to behave and setting expectations about how others will behave . ordinarily, 'law-abiding' people, balancing competing pressures, will sometimes choose to break rules in an attempt to satisfy other (seemingly to them, legitimate) goals, (unlawfully) using a mobile phone to call home whilst driving in order to be a 'responsible parent', for example (wells and savigar, , p. ) . the prime minister's defence of dominic cummings' breach of the regulations, praising him for acting on his 'instincts' as a 'parent', may thus undermine commitment to social distancing rules providing, as it does, a state-sanctioned 'alternatively constructed "good" citizen' beyond the simply lawabiding one and, thereby, providing justification for defiance of the rules (wells and savigar, , p. ; bbc, b) . during interactions with the public, officers should be attuned to people's motivational postures. procedural and distributive fairness should reduce resistance. distributive justice may also reduce dismissiveness (but this hypothesis is previously untested). personal morality is the strongest predictor of compliance. officers can bolster the moral self by appealing to people as 'good citizens' during encounters, treating them with procedural fairness and more generally by public education campaigns promoting the virtue of adhering to the rules. a lack of clarity in the rules, such as that seen in the move from a message to 'stay at home, protect the nhs, save lives' to 'stay alert, control the virus, save lives' will likely make officers' job more difficult (department of health and social care, ; police federation, ). the above hypotheses should be tested; there is an urgent need for research in this field. direct observations will not be possible-due to the current restrictions-analysis of body-worn camera footage and citizen journalism would provide a means to assess (the dynamic nature of) compliance in situ. panel surveys would allow for examination of the factors which affect legitimacy and/or compliance over time . data on where, when, and against whom enforcement powers are used should also be collected; it will be necessary to consider the both how the powers granted by the new regulations and existing powers (such as pnds and other out of court disposals) are used in policing social distancing. the above hypotheses follow from the research presented; however, the wider evidence suggests perceptions of police effectiveness and lawfulness will also impact on legitimacy (jackson and bradford, ; tyler, ) . these should be examined also. in future it would be worth comparing the policing social distancing with other scenarios, to consider whether issues of fairness, legitimacy, and compliance play(ed) out differently in that new context (as they appeared to in the pnd survey discussed here, and prior research on traffic offences; jackson et al., ) . whether the sixth posture-compulsion-is evident in other contexts should also be tested. it may be that compulsion, whilst useful for assessing compliant behaviour in situ, is less applicable when measuring people's attitudes to authority more generally. this concept, and the operationalization thereof, should be examined through further research. the purpose of these new powers is the promotion of public health. that fact should be at the forefront of any/all attempts to formally enforce social distancing regulations. there is no blueprint for policing in the age of coronavirus, the dynamics will be different to other circumstances with which the police are familiar, but we can learn lessons from when police forces have successfully maintained legitimacy and gained compliance. whilst tasked with enforcing the rules on social distancing, in practice, lessons from existing research on the use of pnds, procedural justice and mpt suggest that it is (physical distancing and) social alignment that should be the goal. a pjt/mpt informed approach provides a model, rather than a script for working, (as ever) officers will need to tailor their approach to the person(s) before them. in doing this, these theories suggest that, in the short term, officers should be attuned to the different motivational postures people are demonstrating, adjusting their response accordingly. if forces want to (gain and) maintain legitimacy, then it is at the best commitment they should seek, or at least capitulation, that is, willing compliance 'this is fair' (capitulation) or 'fair enough' (capitulation). the posture of compulsion has been introduced here to reflect the constraint-based (unwilling) compliance that officers should seek to avoid: compulsion would be suggested by people who continue to challenge officers' assessment that they are in breach of the rules, arguing that they have not done anything wrong. enforcing the rules through the threat or use of an fpn or arrest should, in such cases, be avoided and further dialogue sought. compulsion is likely to damage legitimacy long after regulations are lifted. procedural justice can reduce such resistance and enhance legitimacy. perceptions of distributive justice are related to procedural justice (see also grace, a; mclean, mclean, , . voice is central: allow people to tell their side, explain their actions/motivations, by doing so (i.e. by being procedurally fair), officers demonstrate they are being distributively fair (i.e. evenhanded/ proportionate). enforcement should be reserved for those with dismissive postures, those with an unwavering attitude of 'you can't tell me what to do'. even here, the value of financial penalties is questioned; better to first seek punishments based on principles of restorative justice. whilst officers have been given powers to enforce the regulations, coercion and voice offer very different means of achieving the same ends, with very different consequences for police legitimacy in the long term. persuading-from a safe distance-rather than coercing compliance is a prudent, less-resource intensive and, fundamentally, safer approach than resort to coercive powers. heavy-handed enforcement risks triggering resistance in individual police-citizen encounters, but also more broadly within communities leading to collective disorder (reicher and stott, ) . the police have been given a difficult job, but it is vital they get it right. whilst (long-term) voluntary compliance with social distancing rules may rest on building public commitment to the regulations, in the short-term, the research suggests that procedural and distributive justice will be key to reducing resistance during police-citizen encounters and policing social distancing with legitimacy and by consent. dull compulsion or perceived legitimacy? assessing why people comply with the law in nigeria dominic cummings row: the families who stayed away in lockdown beyond procedural justice: a dialogic approach to legitimacy in criminal justice the dog that never quite barked: social identity and the persistence of police legitimacy obeying the rules of the road: procedural justice, social identity, and normative compliance the essence of responsive regulation search of donald campbell: mix and multimethods responsive regulation tensions between the citizen taxpaying role and compliance practices, centre for tax system integrity a new approach to tax compliance dancing with tax authorities: motivational postures and non-compliant actions closing the gap between regulation and the community taxation threat, motivational postures and responsive regulation coronavirus: policing the instruction to stay at home.' briefing paper no. social research methods, th edn. oxford uk lockdown: police apologise after man threatened with pepper spray guidance: coronavirus outbreak faqs: what you can and can't do police socialisation, identity and culture: becoming blue. london: palgrave macmillan. college of policing and npcc ( ). 'covid- -policing brief in response to coronavirus legislation coronavirus: police attack government's "lack of clarity and mixed messages" on lockdown changes promotional material: coronavirus: stay at home, protect the nhs, save lives -web version regulation, institutions and networks police discretion not to invoke the criminal process: low-visibility decisions in the administration of justice crime, violence, justice and social order: monitoring contemporary security issues swift, simple, effective justice? examining the use and impact of penalty notices for disorder identifying the aims of penalty notices for disorder and whether these have been realised in practice what planet are they on?.' daily mail coronavirus: public urged to follow "mission-critical" rules police legitimacy, ideology and qualitative methods: a critique of procedural justice theory patients as regulatory actors in their own health care the revenge of the poor: the anti-poll tax campaign in britain legitimacy, trust and compliance: an empirical test of procedural justice theory using the european social survey blurring the distinction between empirical and normative legitimacy? a methodological commentary on "police legitimacy and citizen cooperation in china pre--print of why do people comply with the law? legitimacy and the influence of legal institutions the lockdown and social norms: why the uk is complying by consent rather than compulsion. british policy and politics at lse greater manchester police threaten to pepper spray then arrest a man moving a tree for his mum may). 'coronavirus is the ultimate demonstration of the real-world impact of racism police occupational culture: classic themes, altered times status influences on perceptions of procedural justice: a test of the group value model among intimate partner violence arrestees the importance of outcome fairness: revisiting the role of distributive justice revisiting the role of distributive justice in tyler's legitimacy theory police-initiated contacts: young people, ethnicity, and the "usual suspects turning defiance into compliance with procedural justice: understanding reactions to regulatory encounters through motivational posturing' fixed penalty notices issued under covid beyond the loot": social disorder and urban unrest pfew position on lockdown guidance procedural justice": concepts, critiques and opportunities policing the coronavirus outbreak: processes and prospects for collective disorder the politics of the police the construct validity and refinement of process-based policing measures is dissatisfaction with police inevitable? testing an integrated model of motivational postures and procedural justice in police-citizen contacts police leniency in traffic enforcement encounters: exploratory findings from observations and interviews what works? a systematic review of corporate crime deterrence doing qualitative research: a practical handbook receiving an on the spot penalty: a tale of morality, common sense and law-abidance public cooperation with the police in ghana: does procedural fairness matter? viewing things differently: the dimensions of public perceptions of police legitimacy a multidimensional model of police legitimacy: a cross-cultural assessment violence, aggression and coercive actions procedural justice policing keeping up, and keeping on: risk, acceleration and the law-abiding driving offender coronavirus: police turning parts of uk into "dystopia" after prosecuting shoppers and people driving "due to boredom i would like to thank professor christopher birkbeck, jamie grace, and the anonymous reviewers for their feedback on earlier drafts of this article. i would also like to thank dr sarah charman and dr matthew jones for their feedback on the preceding blog. finally, i would like to thank professor kristina murphy for offering her insights into mpt when i was first developing my ideas on 'the sixth posture'. key: cord- -t akdu x authors: bahrami, afsane; ferns, gordon a title: genetic and pathogenic characterization of sars-cov- : a review date: - - journal: nan doi: . /fvl- - sha: doc_id: cord_uid: t akdu x the first case of coronavirus disease (covid- ) caused by severe acute respiratory syndrome coronavirus (sars-cov- ) was reported in december . this virus belongs to the beta-coronavirus group that contains a single stranded rna with a nucleoprotein within a capsid. sars-cov- shares % nucleotide identity to sars-cov. the virus is disseminated by its binding to the ace receptors on bronchial epithelial cells. the diagnosis of covid- is based on a laboratory-based reverse transcription polymerase chain reaction (rt-pcr) test together with chest computed tomography imaging. to date, no antiviral therapy has been approved, and many aspects of the covid- are unknown. in this review, we will focus on the recent information on genetics and pathogenesis of covid- as well as its clinical presentation and potential treatments. mers-cov s protein s s sars-cov s protein ´ a orf a mers-cov ( constitute the viral envelope [ ] . accessory proteins appear to promote the adaptation of covs to human host cells [ ] . genomic analysis of ten genome of sars-cov- isolated from nine patients demonstrated . % nucleotide identity [ ] . another report found that . - . % sequence similarity in sample of five infected patients [ ] . phylogenetic analysis demonstrates that sars-cov- shares and . % nucleotide identity to mers-cov and sars-cov, respectively [ , , ] . the sars-cov- constitutes a clade among the sub-genus sarbecovirus [ ] . bioinformatics analysis of the viral genome from one covid- patient shared and % sequence similarity with bat sars-like-covzxc and human sars-cov, respectively [ ] . however, the external subunit of spike rbd of sars-cov- has only % amino acid (aa) identity with other sars-associated covs [ ] . the s-protein of sars-cov- is longer ( aa) than for other viruses such as sars-cov ( aa) and bat sars-like covs ( aa). the s-glycoprotein of sars-cov- has been found to have three short insertions at the n-terminal end, with four variations in the receptor binding site within the rbd compared with sars-cov [ ] . notably, sars-cov- orf b codifies a new short protein. moreover, its novel orf sequence possibly encode a secreted protein with an α-helical structure with a β-sheet(s) consisting of six strands [ ] . the high levels of genetic identity ( . %) between the sars-cov- and bat-cov ratg does not indicate the precise variant that may have led to the outbreak in humans, although it has been suggested that the likelihood that the novel cov has derived from bats is very probable [ ] . sars-cov- and ratg differ with respect to the number of major genomic properties, in which sars-cov- harbors a polybasic (furin) cleavage site insertion at the connection of the two subunits of the s-protein, s and s [ ] . the n-protein is hidden within phospholipid bilayers and coated via two distinctive forms of s-proteins including the spike glycoprotein trimmer which is present in all covs, as well as the hemagglutinin-esterase (he) solely found in certain covs. for instance, sars-cov- does not appear to have the he gene. the m and e proteins are found inside the s-glycoproteins within the viral envelope [ ] . the s, e, m, n and orf a genes of sars-cov- are predicted to be , , , and nucleotides in length, respectively. moreover, sars-cov- has been predicted to contain an orf gene, of nucleotide size, situated between the m and n corresponding orf genes [ ] . the sars-cov sequence reveals serine substituting for glycine in the residue at position of the nsp protein in bat sars-like and sars-cov. this aa substitution could promote local stiffness of the polypeptide chain for steric impact and potency of the serine side-chain to constitute h-bonds. beside, serine is a nucleophile that can establish structural environments, like those at active sites of enzyme. mutations in the nsp protein were reported to affect the replication of sars-cov- in infected cells [ , ] . it has been reported that the single n t variant in sars-cov- 's s-protein may enhance binding affinity for the ace cellular receptor [ ] . furthermore, a single n r mutation in sars-cov- rbd promotes its ace -receptor binding and, thus potentially enhances human-to-human transmission [ , ] . by studying the crystal structure of sars-cov- rbd binding to the human ace receptor has shown that the ace receptor-binding ridge in sars-cov- rbd results in a more compact conformation, leading structural alterations at the rbd/ace interface versus the sars-cov [ ] . overall, sars-cov- binding affinity for ace is - -times greater than for other sars-associated covs [ ] . a missense mutation at the position of s protein (aspartate to glycine, d g mutation), in the spike protein of sars-cov- , which has emerged as a predominant clade in europe ( % sequences) and is spreading worldwide ( % sequences). the d g mutation promotes viral infectivity and transduction of multiple human cell types and mitigates neutralization sensitivity to individual convalescent sera [ ] [ ] [ ] [ ] . lipids play important roles at different stages in the covs life cycle. covs recruit intracellular membranes of the host cells to produce new compartments, or double membrane vesicles, which are used for the replication of the virion particle genome [ ] . recently, an important lipid processing enzyme, known as cpla α has been reported to be related to the formation of double membrane vesicle and cov's amplification [ ] . it has been demonstrated that the enzyme, phospholipase a group iid, is involved in anti-inflammation or proresolving lipid mediator regulation which may lead to worse outcomes in a sars-cov infection animal model by modulating the immune response [ ] . it has been shown that there is a distinct insert that includes basic aas in the s /s priming loop of sars-cov- , which is not found in sars-cov or any sars-associated covs. it may substantially alter the entry pathway of sars-cov- compared with other viruses of the β-covs lineage b [ ] . in a recent report it was shown that sars-cov- 's s-protein entry into /human ace receptor cells is primarily mediated via endocytosis, and that pikfyve, a tpc and cathepsin l are crucial for virus entry. pikfyve is the key enzyme in the early endosome involved in the synthesis of pi( , )p and its main downstream effector, tpc . the s protein of sars-cov- could also stimulate syncytia in /human ace cells independently of exogenous protease [ ] . in a study of sars-cov- infected patients, it was found that severely affected cases had lower numbers of blood lymphocytes, percentages of monocytes, basophils and eosinophils as well as increased leukocytes numbers and neutrophil-lymphocyte-ratio. in most patients with unfavorable progression of covid- , elevated concentrations of infection-associated markers and inflammatory cytokines was observed. the frequency of t cells was significantly lower, and less effective in severely affected subjects. both t helper (th) cells and suppressor t cell numbers in patients with covid- were below the reference range. the percentage of naive helper t cells was increased, and memory helper t cells and regulatory t cells reduced in severe conditions [ ] . furthermore, simultaneous to the infection with sars-cov- , cd + t lymphocytes are quickly over-activated to switch to the pathogenic th cells producing gm-csf. the cytokines environment activates inflammatory cd + cd + monocytes, leading to over-expression of il- and enhances the inflammatory response. regarding the increased infiltrations of inflammatory cells that have been found in lungs of severe sars-cov- infected patients [ , ] , these population of abnormal and noneffective pathogenic th cells and inflammatory granulocytes may go to the pulmonary circulation and by immune stimulation, lead to functional impairment of the lungs and eventually death [ ] . inflammasomes are very large intracellular poly-protein signaling complexes which are constitute in the cytosol as an inflammatory immune reaction to endogenous danger stimuli [ ] . nlrp responds to wide spectra of pathogens and endogenous signals, and is involved in the molecular pathway of various auto-inflammatory disorders [ ] . it has been reported that the sars-cov can induce the nlrp inflammasome in macrophages through orf b. whereas sars-cov infects macrophages or monocytes, sufficient orf b may be present to impact on the autophagy-lysosome pathway, and nlrp inflammasomes. sars-cov replicates efficiently in lung epithelial cells. these cells also amplify nlrp and support assembly of nlrp inflammasomes. in sars-cov patients, the full effect of the orf- b on these inflammatory cascades was observed in the lung epithelium. interestingly, orf b may be involved in the 'cytokine storm' or 'cytokine cascade' and inflammasome induction which happens within intensive sars-cov infection [ ] . sars-cov- infection stimulates the immune response in two stages. in the early stages, a particular adaptive immune response is necessary to eradicate the virus and to impede progress to a more severe condition. the protective immune response at this phase requires that the host should have excellent general health and a suitable genetic context which provides antiviral immunity [ ] . although, when the immune response protection is disabling, virus will disseminate and great damage to the affected tissues occurs, particularly in organs with a high levels of ace receptor expression. the injured cells activate innate inflammation within the lungs which is mainly mediated through pro-inflammatory macrophages/monocytes. lung inflammation is the major reason for the fatal respiratory disease at the severe stage of covid- [ ] . in viral infections, host antiviral micrornas participate in the regulation of immune response to virus and are capable of targeting viral genes and interfere with replication, mrna expression and protein translation of virion particle gene. sardar et al. predicted the antiviral host-micrornas specifically for covid- . they reported a list of six micrornas related to covid- including hsa-let- a, hsa-mir , hsa-mir , hsa-mir b, hsa-mir and hsa-mir which has been previously reported to be related to other viral infections, such as hiv [ ] . virion particles spread from the respiratory mucosa, by binding to the ace receptors on ciliated bronchial epithelial cells, and after that may engage with other cells [ ] . in one report from wuhan, the average incubation period of sars-cov- infected patients was . days, but it this differed between individuals [ , ] . until now, most patients with covid- have initially presented with mild manifestations in other words dry cough, sore throat and fever which spontaneously resolve. although, some patients have developed other more severe disease such as organ failure, septic shock, pulmonary edema, dyspnea, myalgia, fatigue and acute respiratory distress syndrome [ ] . in contrast to sars-cov, patients infected with sars-cov- , development of upper respiratory tract signs and manifestations are less common, suggesting that sars-cov- may target cells in the lower airway [ ] . among cases with severe dyspnea, more than % have required intensive care. some covid- cases do not present with fever or radiologic abnormalities on admission, which makes initial diagnosis difficult [ ] . the main characteristics of covid- on preliminary ct examination including bilateral multi-lobar groundglass opacities with a peripheral/posterior distribution and patchy consolidation, primarily in the lower lobes and fewer inside the right middle lobe [ ] . the main reported laboratory test abnormalities in cases with severe covid- infection include: increased levels of liver enzymes (ldh, alt and ast), total bilirubin, creatinine, cardiac troponin, d-dimer, prothrombin time, procalcitonin and crp [ ] . the histology of liver specimens of sars-cov infected patients have revealed a remarkable liver injury with an increase in mitotic cells, along with eosinophilic bodies as well as balloon-like hepatocytes [ ] . cardiac involvement is another prominent manifestation of covid- and is closely related to a poor outcome [ ] . in a recent systematic review, the incidence rate of diarrhea varied from to % in covid- patients. it may develop earlier, or following the respiratory symptoms. findings of several studies showed that viral rna shedding is detect for a longer time period compared with nasopharyngeal swabs [ ] . in an investigation on covid- patients, of whom . % had severe disease with comorbidities of hypertension, . % diabetes mellitus, . % coronary heart diseases and . % cerebrovascular disease [ ] . another study, of patients with covid- , found that % and % had history of hypertension and diabetes, respectively [ ] . analysis of covid- cases, showed that older age (odds ratio [or] = . ; % ci: . - . ), male gender (or . ; % ci: . - . ) and hypertension as a comorbidity (or . ; % ci: . - . ) are related with more severe disease on admission [ ] . moreover, patients with cancer were more vulnerable to severe events from covid- such as admission to the intensive care unit needing invasive ventilation, or death [ ] . it has been reported that the highest viral load in throat swabs occurs at the time of development of symptoms. however, viral shedding was reported to occur before the onset of symptoms, and a major proportion of transmissibility happened before first symptoms in the index case [ ] . furthermore, severe covid- cases tend to have an increased viral load and a long virus-shedding time [ ] . at present, the diagnosis of covid- is largely based on guideline agreement that includes laboratory tests and chest ct imaging technique [ , ] . pcr testing of asymptomatic or mild symptomatic contacts can be used in the evaluation of peoples who have been in contact with a covid- case [ ] , and the who has not accepted the results of a chest ct without rt-pcr conformation in the diagnosis of covid- [ ] . chest ct is a routine imaging tool for the diagnosis of pneumonia, which is relatively easy and rapid to perform. chest ct shows typical radiographic characteristics in almost all covid- cases, such as peripheral/posterior distribution and patchy consolidation, and/or interstitial alterations with a peripheral distribution, so may provide benefit for diagnosis of covid- [ ] . respiratory tract samples were collected for the diagnosis and screening of patients with sars-cov- pneumonia; in the - days of the initiation of symptoms, patients with covid- have increased viral loads in their upper and lower respiratory tracts [ , ] . for suspected cases, real-time fluorescence (rt-pcr) was performed to detect the positive nucleic acid of sars-cov- in sputum, throat swabs and secretions of the lower respiratory tract specimens [ ] . a nasopharyngeal and/or an oropharyngeal swab are frequently recommended for screening or diagnosis of early infection [ , ] . a single nasopharyngeal swab has become the preferable swab as it is welltolerated by the patient and safer for the operator. serological testing detects presence of igg, igm or both. a positive elucidation has been defined as a positive lgm, or convalescent sera with a higher lgg titer >four-times in comparison with the acute phase. sars-cov- igg and igm are detected in whole blood, plasma, serum or specimens. antibodies increase late in the course of illness; the mean duration of sars-cov- igm antibody detection was reported to be days, whereas igg detection about week following the appearance of symptoms [ ] . in contrast to respiratory samples which may disturb from false-negative results because of the sampling factors, the presence of antibodies in blood uniformly is detectable. specimens are easier to gather versus respiratory samples, such as fewer risks to the operator. the serological assay is very easy, rapid, availability of elisa platforms, requires no instrumentation and can provide results in just min [ ] . based on the recommendation of who, covid- management protocols have mostly highlighted infection prevention, patient early detection and monitoring, and best supportive care [ , ] . no specific antiviral treatment is currently recommended for covid- due to lack of evidence. many treatment regimens have been assessed for covid- , some showing promising preliminary results. a total of trials on covid- have been registered to date in the clinicaltrial.gov (updated july ). several pharmacotherapeutic agents have been used including lopinavir/ritonavir, hydroxychloroquine and ifn-β- a (table ) . results from several in vitro and clinical studies demonstrated that chloroquine phosphate, an old agent for the treatment of malaria, had significant efficacy and acceptable safety for treatment of covid- [ , ] . findings of an open-label nonrandomized clinical trial among infected patients indicated that hydroxychloroquine treatment significantly reduced viral load in covid- cases and its effectiveness is promoted by azithromycin [ ] . in a systematic review including six published articles highlighting the potency of chloroquine in attenuation the replication of sars-cov- -associated virus [ ] . but several other studies demonstrated no evidence of a strong antiviral function, or clinical benefit of the hydroxychloroquine for the treatment of patients with severe covid- [ , ] . the combination of lopinavir/ritonavir (lpv-r) is extensively used for treating hiv-infected patients. lpv-r has been suggested for treatment of covid- . a total of covid- patients were randomly assigned to receive lpv-r (n = ) or standard-care (n = ). treatment with lpv-r was not different from standard care regarding the time to clinical improvement, mortality rate at days, as well as detection of viral rna at different time points [ ] . arbidol as a wide-spectrum antiviral compound that can inhibit viral fusion of influenza. in one study, patients with laboratory-confirmed sars-cov were randomly divided into two arms: cases received lpv-r ( mg/ mg, two per day) and patients were administrated arbidol ( . g a; three per day). no difference was observed concerning fever duration between the two arms. weeks after the intervention, no viral load was found in cases received arbidol, while the viral load was detectable in . % of lpv-r group patients. moreover, no adverse side effects were reported in either arm [ ] . nelfinavir (nfv) is a potent hiv- protease inhibitor that received us fda approval in for treatment of hiv infection. the antiviral activity of nfv against sars-cov- was reported in vero e cells [ ] . by using an integrative computational drug-discovery method, nfv was introduced as a potential inhibitor of sars-cov- main protease [ ] . the main protease of covs (mpro) is an important protein necessary for the proteolytic maturation of the virion particle [ ] . therefore, targeting mpro is considered to havepotential as a treatment for covid- through suppression of the polypeptide cleavage virus [ ] [ ] [ ] . concerning the results of molecular docking, natural polyphenols such as hesperidin, rutin, diosmin, apiin and diacetyl-curcumin have been reported to have acceptable efficacy to target sars-cov- mpro than nfv [ ] . cytokine-directed antagonists, in other words adalimumab (tnf-α) and cmab (il- ) against sars-cov- have been evaluated in clinical trials. the variety of cytokines such as type-i ifn-i contribute to the 'cytokine storm' and pathology of sars-cov- . therefore, targeting the upstream origin of cytokine generation could be a promising therapeutic approach [ ] . utilizing an in silico model, it has been shown that antipolymerase agents including sofosbuvir, idx- , ribavirin (rbv) and remidisvir (gs- ; rdv) can target rna-dependent rna polymerase of sars-cov- [ ] . the first severe-infected patient with sars-cov- in the usa was cured by reception of intravenous rdv [ ] . due to adverse side effects, the appropriate dose of rbv in clinical setting should be given with caution. in previous experience, for example in pandemic influenza a (h n ), and avian influenza a (h n ), passive immunization has been successful for treating of infectious complications [ ] . a remarkable reduction in viral load and mortality was observed by using convalescent plasma therapy against severe acute viral respiratory infections, such as those created by covs [ ] . patients who have recovered from sars-covs infection often have high titers of neutralizing antibody and may be a precious source of convalescent plasma. the fda has also approved the administration of plasma from recovered individuals for treatment of severe covid- patients [ ] . monoclonal antibodies sars-cov-specific human monoclonal antibody (mab) can bind potently with sars-cov- region. but, some of the most powerful sars-cov-particular neutralizing antibodies (i.e., m ) that target the ace binding site of sars-cov did not bind to sars-cov- s-protein, indicating that the disparity in the rbd of sars-cov and sars-cov- has an important effect impact on the cross-reactivity of these mabs, and so novel mabs that specifically target sars-cov- rbd need to be designed [ ] . effective sars-cov- vaccines are urgently needed in order to reduce infection severity, viral shedding as well as human-human transmission, so assisting the control of the cov outbreaks. because s-protein and associated fragments, in other words rbd of sars-and mers-covs are the main targets for designing vaccines, it is speculated that homologous regions of sars-cov- can also be applied as prime targets for designing vaccines against this novel covs [ ] . in addition, other conserved regions of sars-cov- including two subunits of the s-protein, m-protein as well as n-protein, can be applied as another potential target for design and development of effective vaccines. antiviral vaccines can be categorized into two broad groups: dna-and rna-based vaccines, in which individuals are injected with genetically engineered plasmid containing the dna molecule encoding the antigen against which an immune response is eligible, thus the cells machinery creates the antigen, leading to immunological response; and peptide-or protein-based vaccines that include whole-inactivated virus, individual viral proteins or subdomains, and purified or recombinant proteinaceous antigens proteins from the virus, all of which are manufactured in vitro. the candidate vaccines that have recently entered clinical development include: mrna- , ad -ncov, ino- and lv-smenp-dc and pathogen-specific aapc ( table ) . several platforms have progressed to development with potential for rapid development, including dna-and rna-based platforms, followed by those for developing recombinant-subunit vaccines. rna and dna vaccines can be made quickly because they do not require culture or fermentation, instead using synthetic processes [ , ] . even with such promising platforms, sars-cov- vaccine development faces serious challenges. although the virus's s glycoprotein is a promising immunogen for protection, optimization of antigen design is crucial to obtaining an optimum host immune system response. another concern is the possible exacerbation of lung disease, either directly or because of antibody-dependent enhancement due to the type helper t-cell response. furthermore, as with naturally acquired infection, the optimal duration of immunity is unknown; similarly, whether single-dose vaccines will confer lengthy immunity is doubtful. in the early phases of the epidemic, early detection assists management of the disease and preventive approaches such as masks, hand hygiene compliances, prevention of public contact, voluntary home quarantine, early diagnosis, contact tracing, intelligence social distance and travel restrictions have been recommended to decrease transmission. other approaches include limiting events that may facilitate superspreader potential including religious services (marriages and funerals) [ ] . many dimensions of the sars-cov- and corresponding disease are unknown. for instance, the role of ace receptors in sars-cov- pathogenesis remains uncertain. future studies should be concentrate on profound understating of replication, pathogenesis and biological properties applying the relevant biological methods in other words reverse genetics and molecular techniques. genome wide association studies may provide an opportunity for the identification of potential genetic factors contributed in the development of covid- . although host genetic studies are expensive and complex, more studies are required to determine the role of host genetics (such as variation in hla genes) in the immune response to covs, and the clinical outcome of covs-mediated disease. understanding of the sar-cov- viral genetics during the time and geography specially review regarding to the number and repetition of viral mutations and recombination rates and their association with viral infectivity, transmissibility, severity of disease and clinical manifestation, viral load and disease outcome are important knowledge gaps that navigate our research timetable. until now, no unique antiviral therapy has been approved; so treatment is mainly based on symptomatic therapy and best supportive care. the zoonotic link of sars-cov- infection has not been definitively proven; although, phylogenetic analysis shows that sars-cov- is very similar to sars-like bat covs. lessons from other human outbreaks from pathogenic viruses such as sars-cov, mers-cov and influenza viruses are very informative and valuable. different wide-spectra antivirals agents previously used for treatment of influenza, sars-and mers-covs are under assessment for repurposing either monotherapy or in combinations to treat covid- cases. sars-cov- is a novel human pathogen, and may interact with host antiviral defense via a specific pathway. altogether, the infection and development of sars-cov- relies on the interplay between the virus and the patient's immune response. investigations of the area of sars-cov- -host interplay provide response to many crucial questions in virus pathogenesis, disease control and prevention. at present, covid- is leading to substantial global concerns. development of valid, accurate and appropriate serological tests is urgently needed. it will be essential to quickly design and develop effective therapeutic regimen and vaccines to prevent or stop infection of this novel covs. the covid- has caused more infections and deaths compared with either sars or mers. according to r values, it is deemed that sars-cov- is more infectious than sars or mers. as imposition of globalization, covs will cause spreads and outbreaks with various mutant strains similarly in the coming years. with promotion of scientific collaboration, which is as a consequence of globalization, we may have more powerful means of combating covs, in which we characterize the genome structure and pathogenesis of sars-cov- infection very well in the near future. a present treatment is mainly supportive, but trials of vaccines and antivirals are in progress. differences in the length of the spike as it is longer in sars-cov- are likely to play a major role in the pathogenesis and treatment of this virus. robust coordination and collaboration between researchers, vaccine developers, international regulators, policymakers, financiers, national public health institutes and governments will be required to ensure that potential late-stage vaccine candidates can be produced in adequate amount with high safety and efficacy as well as equitably provided to all affected areas, specially low-resource regions. ) and multiple lineage-specific accessory proteins at the -end. • phylogenetic analysis demonstrates that severe acute respiratory syndrome coronavirus (sars-cov- ) shares and . % nucleotide identity to middle east respiratory syndrome cov and sars-cov, respectively. • the s-protein of sars-cov- is longer than for other viruses such as sars-cov and bat sars-like covs. • virion particles spread from the respiratory mucosa, by binding to the ace receptors on ciliated bronchial epithelial cells, and after that may engage with other cells. • the s-glycoprotein mediates binding of the virus to the sensitive human cell surface receptors, followed by fusion of the virus and host cell membranes to assist viral entrance. • sars-cov- infection stimulates the immune response via two stages. at the incubation and nonalarming stages, a particular adaptive immune response is needed to eradicate the virus and to impede progress to severe condition. • the injured cells activate innate inflammation within the lungs, which is mainly mediated through pro-inflammatory macrophages/monocytes. lung inflammation is the major reason for the fatal respiratory disease at the severe stage of coronavirus disease (covid- ) infection. • the main characteristics of covid- on preliminary computed tomography (ct) examination including bilateral multi-lobar ground-glass opacities with a peripheral/posterior distribution and patchy consolidation. • at present, the diagnosis of covid- is largely based on laboratory tests pcr and chest ct imaging technique. although, no specific antiviral treatment for covid- is currently advised due to lack of evidence. • several pharmacotherapeutic agents have been used for treatment of covid- patients consisting lopinavir/ritonavir, hydroxychloroquine and ifn β- a. • effective sars-cov- vaccines are urgently needed in order to decrease infection severity, viral shedding as well as human-human transmission. the most advanced candidates have recently moved into clinical development, including mrna- , ad -ncov, ino- and lv-smenp-dc, and pathogen-specific. all authors contributed to data collection, drafting or revising the article, gave final approval of the version to be published, and agree to be accountable for all aspects of the work. this study was supported by birjand university of medical sciences. the authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. no writing assistance was utilized in the production of this manuscript. sars and mers: recent insights into emerging coronaviruses jumping species -a mechanism for coronavirus persistence and survival a tug-of-war between severe acute respiratory syndrome coronavirus and host antiviral defence: lessons from other pathogenic viruses evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission covid- in singapore -current experience: critical global issues that require attention and action pandemic potential of -ncov coronavirus as a possible cause of severe acute respiratory syndrome a novel coronavirus from patients with pneumonia in china fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin sars-cov- viral load in upper respiratory specimens of infected patients the reproductive number of covid- is higher compared to sars coronavirus coronavirus endoribonuclease activity in porcine epidemic diarrhea virus suppresses type i and type iii interferon responses a pneumonia outbreak associated with a new coronavirus of probable bat origin a new coronavirus associated with human respiratory disease in china the m, e, and n structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles pre-fusion structure of a human coronavirus spike protein bat-to-human: spike features determining 'host jump' of coronaviruses sars-cov, mers-cov, and beyond host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein structure, function, and evolution of coronavirus spike proteins predicting the receptor-binding domain usage of the coronavirus based on kmer frequency on spike protein mechanisms of coronavirus cell entry mediated by the viral spike protein cryo-em structure of the -ncov spike in the prefusion conformation coronaviruses: an overview of their replication and pathogenesis evidence that tmprss activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response role of the spike glycoprotein of human middle east respiratory syndrome coronavirus (mers-cov) in virus entry and syncytia formation angiotensin-converting enzyme is a functional receptor for the sars coronavirus efficient activation of the severe acute respiratory syndrome coronavirus spike protein by the transmembrane protease tmprss receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus return of the coronavirus: -ncov efficient assembly and release of sars coronavirus-like particles by a heterologous expression system infectious bronchitis virus e protein is targeted to the golgi complex and directs release of virus-like particles the cytoplasmic tails of infectious bronchitis virus e and m proteins mediate their interaction a structural analysis of m protein in coronavirus assembly and morphology molecular interactions in the assembly of coronaviruses the membrane m protein carboxy terminus binds to transmissible gastroenteritis coronavirus core and contributes to core stability characterization of the coronavirus m protein and nucleocapsid interaction in infected cells origin and evolution of pathogenic coronaviruses genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding statement in support of the scientists, public health professionals, and medical professionals of china combatting covid- china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin full-genome evolutionary analysis of the novel corona virus ( -ncov) rejects the hypothesis of emergence as a result of a recent recombination event • the coronavirus disease , although closely related to batcov ratg sequence throughout the genome (sequence similarity . %), shows discordant clustering with the bat sars-like coronavirus sequences the spike glycoprotein of the new coronavirus -ncov contains a furin-like cleavage site absent in cov of the same clade there are a peculiar furin-like cleavage site in the spike protein of the coronavirus disease , lacking in the other sars-like covs complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in wuhan covid- : the role of the nsp and nsp in its pathogenesis structural basis of severe acute respiratory syndrome coronavirus adp-ribose- -phosphate dephosphorylation by a conserved domain of nsp structural basis for receptor recognition by the novel coronavirus from wuhan functional assessment of cell entry and receptor usage for lineage b β-coronaviruses, including -ncov diarrhea during covid- infection: pathogenesis, epidemiology, prevention and management evolutionary and structural analyses of sars-cov- d g spike protein mutation now documented worldwide the d g mutation of sars-cov- spike protein enhances viral infectivity global spread of sars-cov- subtype with spike protein mutation d g is shaped by human genomic variations that regulate expression of tmprss and mx genes the d g mutation in sars-cov- spike increases transduction of multiple human cell types sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum inhibition of cytosolic phospholipase a α impairs an early step of coronavirus replication in cell culture critical role of phospholipase a group iid in age-related susceptibility to severe acute respiratory syndrome-cov infection structural modeling of -novel coronavirus (ncov) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to sars-cov and related sars-like coronaviruses characterization of spike glycoprotein of sars-cov- on virus entry and its immune cross-reactivity with sars-cov dysregulation of immune response in patients with covid- in wuhan pathological findings of covid- associated with acute respiratory distress syndrome pulmonary pathology of early phase novel coronavirus (covid- ) pneumonia in two patients with lung cancer pathogenic t cells and inflammatory monocytes incite inflammatory storm in severe covid- patients role of the nlrp inflammasome in cancer nlrp inflammasome as a treatment target in atherosclerosis: a focus on statin therapy sars-coronavirus open reading frame- b triggers intracellular stress pathways and activates nlrp inflammasomes covid- infection: the perspectives on immune responses pathological findings of covid- associated with acute respiratory distress syndrome comparative analyses of sar-cov genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis clinical, laboratory and imaging features of covid- : a systematic review and meta-analysis early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan clinical characteristics of coronavirus disease in china coronavirus disease (covid- ): a systematic review of imaging findings in patients laboratory abnormalities in patients with covid- infection sars-associated viral hepatitis caused by a novel coronavirus: report of three cases association of cardiac injury with mortality in hospitalized patients with covid- in wuhan, china clinical characteristics of coronavirus disease in china clinical characteristics of patients infected with sars-cov- in wuhan host susceptibility to severe covid- and establishment of a host risk score: findings of cases outside wuhan cancer patients in sars-cov- infection: a nationwide analysis in china temporal dynamics in viral shedding and transmissibility of covid- viral dynamics in mild and severe cases of covid- radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study laboratory testing for coronavirus disease (covid- ) in suspected human cases: interim guidance covid- ): situation report - ct imaging features of novel coronavirus ( -ncov) viral load of sars-cov- in clinical samples virological assessment of hospitalized patients with covid- beijing union medical college hospital on 'pneumonia of novel coronavirus infection' diagnosis and treatment proposal (v . ) comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-pcr assays profiling early humoral response to diagnose novel coronavirus disease (covid- ) diagnostic performance of covid- serology assays clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial a systematic review on the efficacy and safety of chloroquine for the treatment of covid- a pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease- (covid- ) no evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe covid- infection a trial of lopinavir-ritonavir in adults hospitalized with severe covid- arbidol monotherapy is superior to lopinavir/ritonavir in treating covid- nelfinavir is active against sars-cov- in vero e cells nelfinavir was predicted to be a potential inhibitor of -ncov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation structure of mpro from covid- virus and discovery of its inhibitors identification of natural compounds with antiviral activities against sars-associated coronavirus anti-sars coronavirus c-like protease effects of isatis indigotica root and plant-derived phenolic compounds immunomodulatory and anti-sars activities of houttuynia cordata identification of potent covid- main protease (mpro) inhibitors from natural polyphenols: an in silico strategy unveils a hope against corona potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody anti-hcv, nucleotide inhibitors, repurposing against covid- first case of novel coronavirus in the united states convalescent plasma to treat covid- : possibilities and challenges the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis covid- : fda approves use of convalescent plasma to treat critically ill patients an emerging coronavirus causing pneumonia outbreak in wuhan, china: calling for developing therapeutic and prophylactic strategies the covid- vaccine development landscape developing covid- vaccines at pandemic speed covid- and community mitigation strategies in a pandemic key: cord- -auqh vtr authors: nan title: emerging respiratory disease - coronaviruses date: - - journal: dis mon doi: . /j.disamonth. . . sha: doc_id: cord_uid: auqh vtr nan coronaviruses -an overview coronaviruses (cov) are a diverse group of viruses capable of infecting humans, and a wide range of animals. cov affect multiple systems, and can cause respiratory, gastrointestinal, hepatic, and neurological illnesses, ranging from mild sickness to death. cov are classified into multiple genera, including alpha, beta, gamma and delta coronaviruses. [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . of note, cov seem to be able to adapt to new hosts and changing environments; this may be related to cov ability to mutate and recombine [ , , , ] , perhaps contributing to novel viruses with varying human pathogenicity. coronaviruses (order nidovirales, family coronaviridae, genus coronavirus) are large, enveloped, single stranded, positive-sense rna viruses, capable of infecting a variety of animals, including bats, mice, birds, dogs, pigs, cattle, and humans. identified many decades ago, coronavirus ( figure [ ]from the latin corona (translation "crown" or "halo") represents the appearance of cov virions as they are viewed through an electron microscope [ , [ ] [ ] [ ] [ ] . the virus appearance is created by viral spikes (s), peplomers that populate the surface and determine host tropism ( figure ) [ ] [ ] [ ] . [ ] . typically cov are considered to be highly species-specific. in immunocompetent hosts, infection elicits the immune response of neutralizing antibodies and cell-mediated immune responses that attempt to kill infected cells [ , , ] . coronaviruses, members of the coronaviridae family were identified and grouped based upon their serological crossreactivity, and genomic sequence homology. host ranges are diverse, and can include canines, felines, swine, mice, camels, bats, birds, and humans. [ , , , [ ] [ ] [ ] [ ] [ ] across the four genera of coronaviruses are alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus [ , , , ] there is a high frequency of recombination and rate of mutation which are believed to allow covs to adapt to new hosts and environments [ , [ ] [ ] [ ] [ ] [ ] [ ] . sars cov [ , , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] is a good illustration of this; studies revealed it originated from animalsbats as the natural reservoir [ ] [ ] [ ] [ ] , , [ ] [ ] [ ] , and palm civet as the intermediate host [ ] [ ] [ ] . this underscores the infection risk in human animal interactionsoccupational, or adventure or travel, as well as environmental incursion and changing habits expected with climate change, which can pose significant risks to human, as well as animal health. as an animal pathogen, coronaviruses can lead to highly virulent respiratory, enteric, and neurological diseases, in addition to hepatitis, resulting in epizootics of respiratory diseases and/or gastroenteritis. as a human virus the range of disease is broad, from cold like to severe multisystem involvement (these cov infections are associated with short incubation periods ( - days), such as those found in sars [ , , , , , , ] . several coronaviruses are capable of causing fatal systemic diseases in animals, including feline infectious peritonitis virus (fipv), swine hemagglutinating encephalomyelitis virus (hev), some strains of avian infectious bronchitis virus (ibv) and mouse hepatitis virus (mhv). these particular cov can replicate in liver, lung, kidney, gut, spleen, brain, spinal cord, retina, as well as other tissues [ , , ] . according to the cdc, the first case of sars cov was reported in asia in early [ ] . further investigation notes november the first case of an atypical pneumonia emerged in china (guangdong province) where ultimately the causative agent was determined to be a newly discovered coronavirus. by an epidemic of similarly severe, atypical pneumonias, was emerging from hong kong, guangdong, and toronto, ontario. the following is the timeline of initial events that transpired referable to sars cov. on february china reported to the world health organization (who) that cases of atypical pneumonia of unknown etiology had been identified in guangdong province since november ; five people had died. as of february a physician from guangdong province, who was ill with an atypical pneumonia, travelled to hong kong, staying overnight in a hotel. the etiology causing his illness was identified as severe acute respiratory syndrome coronavirus (sars cov); it was likely transmitted to at least additional persons. these transmissions/infections subsequently initiated outbreaks in hong kong, singapore, viet nam, and canada [ ] [ ] [ ] [ ] [ ] , ] symptoms characteristic of this aggressive atypical pneumonia included an onset of illness associated with high fever (temperature greater than . °f [ . °c]), headacheoften severe, an overall feeling of discomfort, and body aches, again often severe. some persons may have had respiratory symptoms at the outset. approximately % to % percent experienced diarrhea. after to days, sars patients may develop a dry cough. most patients develop pneumonia. given the prior outbreaks of highly pathogenic avian influenza in that same region of china, it was first considered to be an emerging flu virus. other pathogens, including members of the paramyxoviridae family, and human metapneumovirus (hmpv) were considered as causative of this new clinical illness which became known as severe acute respiratory syndrome or sars. after international collaboration among multiple research facilities, a previously unknown pathogen was ultimately determined to be causative of sars -a new coronavirus -sars cov [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . whiles sars cov is a significant pathogen capable of causing profound illness, even death, historically coronaviruses were one cause of 'the common cold.' known as endemic human betacoronaviruses hcov-oc and hcov-hku . coronaviruses affecting humans (hcovs) historically were associated with mild illness. found in group (hcov- e) and group (hcov-oc ) they are a widespread cause of mild respiratory illnesses [ ] , although occasionally these cov cause serious infections of the lower respiratory tract in children and adults, including necrotizing enterocolitis in newborns [ ] [ ] [ ] [ ] [ ] . early research into the sars co-v genomic sequence demonstrated that this new cov does not belong to any of the known groups of coronaviruses, previously described human coronaviruses hcov-oc and hcov- e [ ] [ ] [ ] [ ] [ ] . in fact it appears sars cov is only somewhat related to these hcov. the sars-cov genome appears to be equidistant from those of all known coronaviruses. moreover, sars cov closest relatives appear to be the murine, bovine, porcine, and human coronaviruses in group and avian coronavirus ibv in group . research on the sars cov suggests this new virus represents a fourth group or lineage of coronavirus -group [ ] . genomic sequence analysis seems to support the hypothesis that of sars-cov is an animal virus for which the normal host is still unknown and that developed the ability to productively infect humans or has the ability to cross species barriers [ ] . the genome shows that sars-cov is neither a mutant of a known coronavirus, nor a recombinant between known coronaviruses. as the virus passes through human beings, sars-cov maintains genotype, and is adapted to the human host [ ] . testing allows genetic analysis to distinguish different strains of sars-cov, allowing epidemiological studies [ ] . not surprisingly there are also economic, as well as health implications -coronaviruses cause important diseases in domestic animals, as well as in human populations. toronto during and in the aftermath of their sars outbreak saw a significant, albeit temporary decline in tourism and business related visits, as well as lost conference and trade show related commerce. recognizing the importance of animalhuman pathogen crossover, opportunities to reduce the spread of contagion, and to identify potential risks is critical to prevent or at least reduce the likelihood of sars, mers, and influenza outbreaks such as the avian influenza outbreaks of the 's and early 's and the swine flu outbreak in . sars co-v ( figure ) [ ] can be detected in extracts of lung and kidney tissue by virus isolation or pcr; bronchoalveolar lavage specimens by virus isolation, electron microscopy and pcr; and sputum or upper respiratory tract swab, aspirate, or wash specimens by pcr [ , , ] . sars-associated coronavirus rna was detected in nasopharyngeal aspirates by rt-pcr in % at initial presentation (mean . days after onset of illness) and in % at day [ ] . in stool samples, viral rna was detected in % of patients two weeks after the onset of illness. % of urine samples were positive for viral rna [ ] . viral rna was also detected at extremely low concentrations in plasma during the acute phase and in feces during the late convalescent phase, suggesting that the virus may be shed in feces for prolonged periods of time [ , ] . the timelines of events as noted by cdc concluded towards the end of with removal of travel warnings to china and ontario. by the end of , according to the cdc report of who data, reports of sars infections from countries and regions revealed , persons with probable sars resulting in deathswith an estimated case fatality rate just below % (higher in elderly, infirm patients). in the united states, eight sars infections were documented by laboratory testing and an additional probable sars infections were reported. by the cdc issued a "notice of embargo of civets" as a sars-like virus had been isolated from civets (captured in areas of china where the sars outbreak originated). cdc also banned the importation of civets. the civet is a mammal with a catlike body, long legs, a long tail, and a masked face resembling a raccoon or weasel. sars cov was detected in animal handlers of civets. the ban on civets is currently still in effect. by the national select agent registry program declared sars-coronavirus a select agent. a select agent is a bacterium, virus or toxin that has the potential to pose a severe threat to public health and safety [ , ] . in spite of significant effort to develop countermeasures for coronaviruses, three are as of yet no licensed therapeutics that have shown consistent effectiveness against mers cov or sars cov. [ ] . intensive careproviding ventilator, circulatory and other organ system support to preserve renal, hepatic and neurological function, as well as prevention of secondary infection is critical. during the sars cov pandemic of immune based therapies have been tried, with equivocal results. ribavirin and interferon combinations showed some clinical improvements in non human primate studies, but unlike actual clinical experiences with mers and sars, where the illness, let alone treatment are rarely initiated rapidly after infection, the trials provided interventions soon after viral challenge [ ] [ ] [ ] [ ] [ ] . during sars cov epidemics, various combinations of therapies were trialed [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] , but no scaled, controlled approaches were conducted, making recommendations on current antivirals with or without interferon combination therapy, of concern, and questionable [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . ribavirin is a potent nucleoside analogue used with varying degrees of success against rna viruses, but there is the potential for adverse side effects including hemolytic anemia, metabolic derangements. interferon can also elicit adverse effects, although they have demonstrated value against viral infection [ ] [ ] [ ] [ ] . corticosteroids have been tried in sars cov infectionthey resulted in increased viral load, admissions to intensive care unit, and mortality [ , ] . during sars cov, convalescent plasma, hyperimmune globulin were shown to be relatively safe, and possibly effective for reducing mortality [ ] [ ] [ ] [ ] . convalescent plasma, when administered within days of illness, did decrease mortality in sars cov patients, according to one study [ ] . they found this was a time critical issueadministration had to be given within a week period. the challenge of course is in identifying cases and contacts rapidly and immediate utilization of such therapies for a chance at optimal effect. donor supply, technical capacity in regions where sars, mers or other emerging threats are likely to occur, safety of end product and other challenges can limit the potential of this therapeutic option. monoclonal antibodies (mabs) offer promise, and have demonstrated efficacy in the treatment of cancer and autoimmune diseases, as well as respiratory syncytial virus (rsv) [ , , ] . trials are ongoing to determine the use of mabs for ebola virus disease, hiv -primary and secondary prevention [ ] . unfortunately the costs, as well as research and development timelines are longer than for polyclonal antibody preparations. nevertheless, in spite of rigorous testing, regulatory and cost issues associated with mabs, their potential as therapies for mers and other potentially deadly diseases continue to drive research in this area. antiviral research into adenine analogues that can disrupt viral rna replication [ ] are being developed as well as a nucleoside analogues with the potential to work against filoviruses, coronaviruses, and other rna viruses [ ] . ideally an antiviral that covers a broad range of coronaviruses will be developed based upon the genetic sequence of these viruses and their life cycle. but the development of such an antimicrobial and other interventions still remains in the future. of note, extensive research is also being conducted towards developing vaccines. towards that end, not unlike vaccines directed towards other pathogens, research has focused on viral structure [ , ] , and replication mechanisms ( figure [ ]/ (table ) [ ] . not surprisingly, as with other pathogens, such as dengue [ ] [ ] [ ] [ ] [ ] where there remain unknowns, such as protective immunity, cross protection against a variety of strains, and other technical difficulties, there are a variety of challenges to overcome in developing an effective vaccine against sars or other coronaviruses. for example, in developing a live sars cov vaccine, it will be necessary to address the various coronavirus strains to recombine with each other, with the potential of attenuated parts of the genome being replaced with non-attenuated components of the genome, resulting in a pathogenic virus. one approach being considered is the use of reverse genetics; it may eliminate the risk of recombination between coronavirus strains [ , [ ] [ ] [ ] [ ] , , ] . as suddenly as sars cov emerged, it has seemingly gone quiescent. however another significant, and previously unknown or not described coronavirus respiratory disease has emerged. in the next section the newest member of cov discovered that causes human illness will be discussed. it is the middle east respiratory syndrome coronavirus (mers-cov, mers), which is part of the beta group of coronaviruses. avian influenza a (h n ) virus human infections with the emerging avian influenza a h n virus from wet market poultry: clinical analysis and characterization of viral genome human infection with a novel avian-origin influenza a(h n ) virus global concerns regarding novel influenza a (h n ) virus infections a detailed epidemiological and clinical description of human cases of avian-origin influenza a (h n ) virus infection in shanghai radiological findings of chest in patients with h n avian influenza from a hospital avian influenza: critical considerations for primary care physician animal -human interface h n cdc emerging h n influenza a (novel reassortant avian-origin) pneumonia: radiologic findings initial computed tomography findings of pneumonia in patients with human infected avian influenza (h n ) chest x-ray and ct findings of early h n avian influenza cases thoracic imaging features of patients with h n subtype avian influenza virus infection human infection with a novel avian-origin influenza a (h n ) virus: serial chest radiographic and ct findings analysis of the clinical characteristics and treatment of two patients with avian influenza virus (h n ) severe acute respiratory syndrome: radiographic review of probable cases in toronto the emerging infectious disease emergence of avian influenza a (h n ) virus causing severe human illness china chest xray and computed tomography (ct) findings of early h n avian influenza cases middle east respiratory syndrome coronavirus (mers -cov_ infection pulmonary pathologic findings of fatal pandemic influenza a/h n viral infections. arch patholo influenza a (h n ) virus associated pneumonia: high resolution computed tomography -pathologic correlation cdc guidance on testing for h n interim guidance on the use of antiviral agents for treatment of human infections with avian influenza a h n the biology of coronaviruses coronaviruses post sars: update on replication and pathogenesis delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel middle east respiratory syndrome coronavirus: implications for pathogenesis and treatment virus taxonomy; ninth report of the international committee on taxonomy of viruses discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacornavirus evidence of the recombinant origin of a bat severe acute respiratory syndrome osars) like coronavirus and its implications on the direct ancestor of sars coronavirus molecular epidemiology of human coronavirus oc reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination isolation and characterization of viruses related to the sars coronavirus from animals in southern china cdc/national institutes of health public domain coronavirus image severe acute respiratory syndrome coronavirus like virus in chinese horseshoe bats viruses and bacteria in the etiology of the common cold mandell, douglas, and bennett's principles and practice of infectious diseases spectrum of clinical illness in hospitalized patients with "common cold" virus infections coronavirus pneumonia following autologous bone marrow transplantation for breast cancer survival of human coronaviruses e and oc in suspension after drying on surfaces: a possible source of hospitalacquired infections the sars coronavirus: a postgenomic era sars coronavirus: a new challenge for prevention and therapy a newly discovered human pneumovirus isolated from young children with respiratory tract disease identification of a novel coronavirus in patients with severe acute respiratory syndrome severe acute respiratory syndrome: identification of the etiological agent coronavirus as a possible cause of severe acute respiratory syndrome the genome sequence of the sars-associated coronavirus characterization of a novel coronavirus associated with severe acute respiratory syndrome viral zoonoses -a threat under control? comparative full-length genome sequence analysis of sars coronavirus isolates and common mutations associated with putative origins of infection comparative analysis of the sars coronavirus genome: a good start to a long journey chinese university of hong kong molecular sars research group. coronavirus genomic-sequence variations and the epidemiology of the severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study update on sars research and other possibly zoonotic coronaviruses the severe acute respiratory syndrome vaccines to prevent severe acute respiratory syndrome coronavirus-induced disease modjarrad k treatment strategies for middle east respiratory syndrome coronavirus treatment with interferon-alpha b and ribavirin improves outcome in mers cov infected rhesus macaques ifn alpha a or ifn beta in combination with ribavirin to treat middle east respiratory syndrome coronavirus pneumonia: a retrospective study oral ribavirin for the treatment of noninfluenza respiratory viral infections: a systematic review interferon in oncological practice e: review of interferon biology, clinical applications, and toxicities the use of corticosteroid as treatment in sars was associated with adverse outcomes: a retrospective cohort study effects of early corticosteroid treatment on plasma sars associated coronavirus rns concentrations in adult patients feasibility, safety, clinical and laboratory effects of convalescent plasma therapy for patients with middle east respiratory syndrome coronavirus infection: a study protocol the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of sever acute respiratory infections of viral etiology: a systematic review and exploratory meta analysis potent neutralization of mers cov by human neutralizing monoclonal antibodies to the viral spike glycoprotein exceptionally potent neutralization of middle east respiratory syndrome coronavirus by human monoclonal antibodies rewiring the severe acute respiratory syndrome coronavirus (sars-cov) transcription circuit: engineering a recombination-resistant genome nucleotide prodrug gs is a broad spectrum filovirus inhibitor that provides complete therapeutic protection against the development of ebola virus disease evd in infected non human primates id week biocryst announces nature publication demonstrating efficacy of bbcx in a non human primate model of filovirus infection zabel p molecular mechanisms of severe acute respiratory syndrome (sars) recent developments in anti-severe respiratory syndrome coronavirus chemotherapy emerging respiratory viruses: challenges and vaccine strategies safety and immunogenicity from a phase i trial of inactivated severe acute respiratory syndrome coronavirus vaccine a sars dna vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a phase i clinical trial viral hemorrhagic fever viruses in novel viruses, emerging pathogens -the pandemic threat continues next generation dengue vaccines: a review of candidates in preclinical development evaluation of commercially available anti-dengue virus immunoglobulin m tests protective efficacy of the recombinant, live attenuated, cy tetravalent dengue vaccine in thai schoolchildren: a random controlled phase b trial cells in dengue virus infection in vivo reverse genetics of sars related coronavirus using vaccinia virus based recombination published this newly identified respiratory viral illness was caused by a novel coronavirus, which was initially designated as human betacoronavirus [ - ], but was eventually named middle east respiratory syndrome coronavirus (mers cov). reminiscent of, and worth considering as a caution for greater vigilance towards emerging pathogens, the suddenness that sars cov emerged as a new cause of severe pulmonary illness, has been replicated in this new aggressive respiratory illness mers cov. unlike sars cov, it has not caused the thousands of cases over a short period of time as with other cov, including sars cov, the exact epidemiology, including whether there are larger numbers of mild illness, remains unknown. males over yrs of age seem to be at higher risk of severe disease symptoms and death among those infected. while the greatest spike in cases occurred near key: cord- - tr authors: benjamin, elliot title: progressive politics and humanistic psychology in the trump/coronavirus era date: - - journal: j humanist psychol doi: . / sha: doc_id: cord_uid: tr in this article, the author discusses the relationship of progressive politics to humanistic psychology in the trump/coronavirus era. the harsh realities of personal fears and severe challenges to our mental health evoked by both the united states presidency of donald trump and the coronavirus pandemic are described initially. then, a number of self-care practices that are consistent with the basic values of humanistic psychology and that we can undertake to help us meet these harsh realities are illustrated. next, the author describes his own personal engagement and self-care in the world of progressive politics and humanistic psychology in the context of the resisting trump movement. the article concludes with the author suggesting that perhaps it may be worthwhile for politically like-minded others to also consider finding ways of merging their progressive politics with humanistic psychology in order to enhance their self-care through these turbulent times in the trump/coronavirus era. in the present article, i want to focus on the merging of progressive politics and humanistic psychology during the tremendously stressful and dangerous times in which we are currently living, which i refer to as the trump/ coronavirus era. the merging that i describe in this article is based on my own relevant experiences, primarily in the united states, but they may very well have applications to various countries in other parts of the world. i have published a number of articles and given a number of talks related to the merging of progressive politics and humanistic psychology in the context of the resisting trump movement (benjamin, a (benjamin, , b (benjamin, , . in the concluding section of one of my articles (benjamin, ) , i summarized my view that many of the statements and policies of united states president donald trump are completely antithetical to the basic premises of humanistic psychology that involve engaging in genuine and empathic relationships with people: under the current dangerous leadership and rhetoric of us president donald trump, the destructive effects on the mental health of much of our country's population are becoming increasingly apparent. furthermore, president trump's various political activities, especially inclusive of his dangerous rhetoric, may very well have led to significant increases in violence, and they run completely counter to the basic values of humanistic psychology that promote genuine, empathic relationships between human beings. (pp. - ) my above summary describing the detrimental effects of trump's leadership and rhetoric on mental health, as well as its apparent stimulation of significant increases in violence (benjamin, ) , is supported by a number of quantitative statistical studies as conveyed by various authors: (fein et al., ; finkelstein et al., ; folley, ; haverluck, ; macias, ; panning, ) . however, the concerns that myself and others have previously written about in regard to the "destructive effects on the mental health of much our country's population" under the "dangerous leadership and rhetoric of us president donald trump" (benjamin, , pp. - ) are currently greatly increased due to the current coronavirus pandemic crisis. nevertheless, i believe that the merging of progressive politics and humanistic psychology in the context of the resisting trump movement, now applied in our current trump/coronavirus era, may therapeutically enhance our mental health while literally saving the united states and the world from the point of disaster with no escape (benjamin, a (benjamin, , b (benjamin, , c (benjamin, , d . to support my contention about the value of this merging of progressive politics and humanistic psychology, i will make use of my own relevant experiences in the resisting trump movement with a current focus on the coronavirus pandemic crisis. there have been a number of disturbing reports about the significant detrimental effects on the mental health of a large segment of the u.s. population, directly related to our present political climate under what i have referred to as the "dangerous leadership and rhetoric" of president donald trump (benjamin, ) . one of these disturbing reports conveyed the following: trump's behaviors during the campaign (e.g. misogyny, and ethnic bigotry, prejudice, and discrimination), and his subsequent success have ignited and perpetuated feelings and beliefs characterized by fear of and hostility toward particular groups, and major shifts in beliefs and perspectives that reveal potentially significant challenges people could face as a result of the disruption of a particular worldview. . . . specifically, the demonstrated threats to human rights and civil liberties have raised disturbing challenges for many american citizens and undocumented immigrants in the form of deep concern at being led and governed by an individual who does not promote public safety, equality, and human dignity in language and behavior. (krippner & pitchford, , pp. - ) the prevalent anxiety that many americans have experienced since the election of trump has been referred to as "trump anxiety disorder" and described as follows: symptoms were specific to the election of trump and the resultant unpredictable sociopolitical climate. . . . though not an official diagnosis, the symptoms include feeling a loss of control and helplessness, and fretting about what's happening in the country and spending excessive time on social media. . . . trump is driving the nation into a mental crisis. "two-thirds of americans say they are stressed about the future of our nation-including a majority of democrats and republicans," an apa press release issued last year revealed. "more than half of americans ( percent) say the current political climate is a very or somewhat significant source of stress, and nearly half ( percent) say the same about the outcome of the election." . . . "we're surrounded by conversations, news and social media that constantly remind us of the issues that are stressing us the most." (haverluck, , pp. - ) furthermore, as i have previously described, the precarious mental health of president trump himself may very well be a significant factor related to these detrimental mental health effects: a significant factor in this detrimental mental health phenomenon in the united states is directly related to the questionable mental health of president trump himself, as strikingly described in terms like malignant, pathological, hedonistic, and narcissistic by a number of well-respected psychiatrists and psychologists in the book the dangerous case of donald trump (lee, ) . (benjamin, , p. ) however, these disturbing reports pale by comparison with what the whole world is now facing with the current coronavirus pandemic crisis, and the united states is doubly challenged by what i have referred to as the "deadly duo": trump and the coronavirus (benjamin, a (benjamin, , b (benjamin, , c . the deadly worldwide consequences of the coronavirus have been described excessively, and there have also been a number of descriptions of the detrimental effects on mental health in the united states from this crisis (benjamin, d; graham, ; holcombe, ; hunter, ; kaur, ) . some of these descriptions are as follows: along with these feelings of disorientation, it may seem like it's getting harder to concentrate and taking longer to complete tasks, as if our brains are just working more slowly. . . . "it's a perfect storm between changes in environment, loss of social anchors and increases in cognitive stress. . . . and then on top of that, most of us are not getting the quality sleep that we used to" . . . "often if you're feeling stressed or you're feeling anxious, those thoughts and feelings can show up and either make it more difficult to fall asleep or more difficult to stay asleep." . . . that sleeplessness, in turn, can further cognitive impairment, attention and concentration issues and short-term memory loss. . . . "we've lost all of the routine of a typical week, and that means having weekends as a boundary or as a separation or something to look forward to. . . . now the weekend is the same as a weekday. because work is home and home is work for many people, some may find themselves working longer hours or into the weekends. gone are the happy hours, concerts or sporting events that once separated weekdays from weekends, causing the days to just drag on. . . . for those who still need to go into work, routines may look a lot different. and there's the added mental strain of remembering to socially distance, wear masks and avoid touching surfaces. all of that can contribute to a sense of disorientation." . . . we're multitasking a lot more. many people are finding themselves balancing multiple responsibilities, such as homeschooling children or caring for an elderly family member-all while holding down a full-time job or coping with the stress of a layoff. . . . "our working memory is a limited resource. . . . we can easily tax it by trying to engage it in too many activities at once or trying to multitask in our mind." the pandemic is becoming a source of chronic stress given that it's been going on for weeks, or even months for some people. . . . high stress levels impair our concentration and attention, and can affect short-term memory. (kaur, , pp. - ) "we've lost that sense of certainty, that sense of safety, that sense of predictability and so it stands to reason that all of that leaves us feeling dislocated and unsure about what's going to happen next." . . . people all over the world are grieving the sudden loss of loved ones, and the intensity of those losses is clear. but grief can come from the loss of anything we're attached to deeply: the loss of economic stability, the loss of our ability to move around freely, the ability to participate in life's milestones in person. (hunter, , p. ) across the country, seniors' lives are being upended as continuing care retirement communities take aggressive steps to protect residents from covid- , the illness caused by the novel coronavirus. . . . without regular contact with other people, older adults can become lonely or depressed. a change in someone's health status that might have been noticed if they didn't show up for dinner can now go unobserved. without stimulation, motivation and cognition can decline. (graham, , pp. , ) it could put strain on families, send children home to abusive situations, make those living alone feel isolated and threaten people's sense of purpose by keeping them from work. . . . and those experiencing financial insecurity in the midst of the pandemic have an added stress that is difficult to resolve. . . . the experience of staying home together through a pandemic can be considered a collective trauma. . . . people in quarantine show signs of confusion, depression and anger. (holcombe, , p. ) it is well-known that cognitive stimulation is significantly related to preventing cognitive decline (eckroth-bucher, ; krell-roesch et al., ) , and the related detrimental consequences to mental health from the coronavirus are likely spreading throughout the world. in particular, in china, there are studies that have reported detrimental mental health consequences that include anxiety, depression, sleep-related symptoms, and fears of being quarantined and isolated from the world (huang & zhao, ; wilder-smith & freedman, ) . however, as described in the next section, there are also a number of self-care recommendations from health care professionals that may offset at least some of the detrimental mental health consequences from the coronavirus, and some of these recommendations are consistent with the basic premises of humanistic psychology (c. r. rogers, ) . mental health professionals have recommended a number of self-care practices to offset the detrimental mental health consequences of the coronavirus. these recommended self-care practices include developing self-awareness, self-acceptance, and self-compassion, practicing mindfulness, meditation, and/or yoga, connecting with others "virtually," engaging in constructive and cathartic self-expression, limiting the frequency of getting news updates, limiting social media time, obtaining professional "virtual" mental health assistance, getting adequate sleep, keeping up with proper nutrition, getting outside as much as possible, engaging in regular physical activity, spending enough alone-time if living with someone, focusing on the joys in the little things in life, maintaining a sense of daily structure as much as feasible, and taking frequent breaks (graham, ; holcombe, ; hunter, ; kaur, ; k. rogers, ; villano, ; willingham, ) . a number of these self-care practices have been well-established as beneficial practices to mental health in a variety of circumstances (brenner, ; kabat-zinn, ; c. r. rogers, ; schneider et al., ) . the following illustrates some of these recommendations that are consistent with the basic premises of humanistic psychology that involve self-awareness, self-expression, creativity, authenticity, and empathy: [senior] communities have responded by having staff check in regularly with vulnerable residents, offering to arrange video visits with family members, organizing zoom interest groups for residents and creating programming, such as exercise sessions broadcast over closed-circuit, in-house television stations. (graham, , p. ) being present in our sadness is important while at the same time holding as much gratitude or joy as we can. . . . it's really important for us to be present to the loss as we're moving through it, but it's also important to stay present to the restoration, to the moving forward, to the finding the meaning in our living, to allowing moments of joy to come in to release some of the anguish. . . . crying and screaming are healthy expressions of grief, therapists say, and dancing and singing can also be restorative expressions of emotion. . . . one important element of taking care of yourself is setting boundaries. being able to say, "today is not the day" when someone comes to you with something you can't presently deal with . . . noting that women often struggle with feelings that taking care of yourself is somehow selfish. it's not. (hunter, , pp. - ) since action can allay our anxieties, you may want to also consider what you can do to help others who may be more affected by the outbreak than you. service workers, medical workers, hourly workers and people in the restaurant or entertainment industries may have their livelihoods paralyzed or have to put themselves in disproportionate danger. . . . if you can't seem to get a handle on your thoughts, professional help can be an option. (willingham, , pp. - ) "just having someone to talk to, someone who can help you work through some of these difficult issues, is invaluable. . . . now more than ever, therapists are becoming indispensable for giving people the tools they need to get through any situation." (villano, , p. ) meditation is one tool that can help our immune systems functioning optimally. . . . "awareness by itself heals. awareness without conceptual intervention restores self-regulation." . . . in a review of studies on the effects of mindfulness-based stress reduction [(mbsr)] and mindfulness-based cognitive therapy (mbct), researchers found that people who received this therapy were less likely to respond to stressful situations with negative thoughts or unhelpful emotional reactions. those participants were also more likely to focus on the present moment and less likely to experience ruminating thoughts. breathing meditations can also reduce muscle tension and your heart rate, which are signs of stress. . . . breathing meditations are another tool you can add to your coping toolkit, which may also include journaling, baking or virtually connecting with others. (k. rogers, , pp. - ) the above self-care recommendations are certainly very valuable and have a great deal of potential to benefit many people who are desperately trying to find ways to constructively deal with not only the corona virus pandemic crisis but also the trump-induced mental health crisis, as described in the preceding section. however, there is one particular self-care recommendation that has not been mentioned by the above authors, and this is one that i personally have gotten much value from and i will discuss in the next section. in this section, i will endeavor to put all the above threads together: self-care, humanistic psychology, progressive politics, the resisting trump movement, and the coronavirus, and i will do so through conveying my own continuous involvement in each of these five threads. however, i experience these five threads as interconnecting without any kind of firm boundaries, and therefore my portrayal of my relevant experiences in this regard will encompass all these threads simultaneously. to begin with, my involvement with progressive politics ever since the november, u.s. presidential election has been completely immersed with the resisting trump movement. and since , i have been involved in writing articles and giving talks to promote the merging of humanistic psychology with progressive politics via the resisting trump movement (benjamin, a (benjamin, , b (benjamin, , . however, the recent advent of the horrific coronavirus pandemic crisis has brought things to a whole new level, and i have described my thoughts related to the connections between trump and the coronavirus (benjamin, a (benjamin, , b (benjamin, , c with some preliminary excursions into how these connections can also relate to humanistic psychology (benjamin, d) . for example, i originally had written about the "dangerous leadership and rhetoric" of president trump (benjamin, ) but this is now extended to the apparent stimulation of hate crimes against asian americans related to trump for a period of time designating the coronavirus as the "chinese virus" (benjamin, d; somvichian-clausen, ) . but the question i want to focus on at this point is how my involvement in progressive politics through the resisting trump movement in the current trump/coronavirus era goes together with my self-care in the context of humanistic psychology. and much of the answer to this question is related to my involvement with the grass roots progressive politics resisting trump indivisible movement, which like everything else in these coronavirus times, has currently transformed into "virtual" connections. i take part in both the relatively small weekly zoom meetings with my local bangor, maine indivisible group, and in the large monthly national indivisible conference calls. in regard to my self-care, the weekly bangor indivisible meetings consists of only about a dozen people, and i am quite active in voicing my thoughts and feelings, both personal and political. my thoughts and feelings that i have conveyed to my indivisible colleagues have been largely focused on what it takes to defeat trump in the november u.s. presidential election, which now means electing joe biden to be president (benjamin, e) . for the past year indivisible was not favorable to biden, as biden was not nearly progressive enough to satisfy the progressive leanings of virtually all indivisible members, which i certainly understand and empathize with. however, true to their commitment to defeat trump, indivisible has now endorsed biden, with over % of indivisible members voting in favor of the endorsement (seitz-wald, ). i have stimulated discussions in my bangor indivisible group related to how indivisible could induce former bernie sanders supporters to support biden, inclusive of my personal disclosure about my communications with my son in this regard (benjamin, e) . i have expressed my concerns, reinforcing the similar concerns expressed by others in the group, about trump trying to postpone the november presidential election and/or eliminating or minimizing mail-in vote ballots to help him get reelected, through not supporting the continuation of the u.s. post office (bunch, ). i have sparked continued discussions about the sexual assault allegation against biden, taking into account biden's defense of these allegations and the evidence for and against him (bradner & lee, ; cillizza, ; dem, ) . thus, in the midst of the coronavirus pandemic restrictive environment that we are now required to live through, i have been able to maintain my political/personal connections in a way that has nourished me and made me feel less isolated and more part of the progressive political world. my continued involvement in the indivisible movement, and in particular with my local indivisible group virtually, has been a very important part of my self-care as i live through the trump/coronavirus era, and is part and parcel of the basic values of humanistic psychology that involve selfexpression, authenticity, and empathy. furthermore, i have continued my writings regarding the connections of humanistic psychology to progressive politics and the resisting trump movement, inclusive of this present article, as i have received constructive feedback and interest from professional humanistic psychology circles in response to my ideas, and what i have to say, about humanistic psychology. taken together, the affirming responses that i have received, and am receiving, from indivisible and professional humanistic psychology circles have the effect of making me feel connected to an idealistic group of people to whom i can relate, which is nourishing my sense of self-care through these turbulent times. this goes hand-in-hand with my personal good fortune to be involved in a continuous loving harmonious (nonsocial distancing) relationship with my wife, as well as with the continuation of my artistic/therapeutic mode of day-to-day functioning, inclusive of my engaging in pure mathematics as a hobby, playing the piano by myself and playing piano/flute with my wife, writing psychology/political articles, enjoying our family dog and cat, engaging in my disciplined mindfulness meditation practice, exercising at home regularly and taking walks, and separating the weekends from the weekdays through continuing to experience homey, fulfilling, and intimate weekends with my wife (benjamin, d) . this all goes along with stringently practicing social distancing and taking the utmost precautions when i am out in public, while the coronavirus pandemic is still raging, as i recently turned years and i certainly am not taking my good health for granted (benjamin, d) . but all things considered, i am grateful to still be alive and well and have the opportunity to be writing this essay and have it published in a professional humanistic psychology journal. in this way, the five threads of self-care, humanistic psychology, progressive politics, the resisting trump movement, and the coronavirus are all woven together for me, with permeable boundaries that are working well to keep me functioning effectively through these trying times. it may be worthwhile for politically like-minded others to also consider finding ways of merging their progressive politics with humanistic psychology in order to enhance their self-care through these turbulent times in the trump/ coronavirus era. in this regard, i find the following wise and inspiring words from esteemed humanistic psychology elder maureen o'hara ( ) to be timely and relevant (benjamin, d) : i believe that despite the looming threats which often appear to block out the light of hope, we are in fact witnessing a transformative insurgency at the core of which is a new consciousness. there are "persons of tomorrow" everywhere engaged in large and mostly small creative and effective initiatives addressing the multiple challenges humanity faces in the st century. . . . it is urgent that as an alternative to the current narratives of despair, fear and division we promote narratives of hope and solidarity not just with other humans but with all the species on the planet. these narratives already exist in the hearts and minds of those who are making a difference. we are in this together. the culture our descendants will inhabit will be created by the actions, stories and choices we make now. (o'hara, , pp. , ) in this essay, i have discussed the relationship of progressive politics to humanistic psychology in the trump/coronavirus era. there are harsh realities of personal limitations and challenges to our mental health that we are all facing during these turbulent times. however, there are also a number of self-care practices that we can undertake to help us get through these times, and a number of these practices are consistent with the basic values of humanistic psychology. for me personally, i am continuing to engage in the world of progressive politics and humanistic psychology in the context of the resisting trump movement, and along with my good fortune to have a fulfilling personal life, i am consequently undertaking sufficient self-care to be able to function effectively through the crisis that is challenging all of us with our very survival. along these lines, it may be worthwhile for politically like-minded others to also consider finding ways of merging their progressive politics with humanistic psychology in order to enhance their self-care through these turbulent times in the trump/coronavirus era. the author declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. the author received no financial support for the research, authorship, and/or publication of this article. building progressive bridges, resisting trump, and humanistic psychology: part building progressive bridges, resisting trump, and humanistic psychology: part the merging of humanistic psychology and progressive politics with an application to the dangerous leadership and rhetoric of president donald trump: part the deadly duo: part : trump and the coronavirus the deadly duo: part : trump, the coronavirus, and a lesson from the spanish flu epidemic the deadly duo: part : the devastation accelerates-but perhaps with a bit of a silver lining? trump the coronavirus pandemic, asian american xenophobia, and humanistic psychology an integrative miracle: sanders working with biden to defeat trump biden denies sexual assault allegation destroy the post office and you destroy democracy: maybe that's trump's plan? the philadelphia inquirer joe biden just missed a golden opportunity to address the tara reade allegations tara reade's apparent lies are a betrayal to all survivors preserving cognition through an integrated cognitive stimulation and training program the constitution demands it: the case for the impeachment of donald trump a quantitative approach to understanding online antisemitism hate crimes rose by percent in counties where trump hosted campaign rallies in : study. the hill expert report predicts up to two more years of pandemic misery in shutting out threat, seniors in retirement communities feel isolated trump anxiety disorder" is soaring long-term social distancing may be traumatic: here is what to expect and what to do generalized anxiety disorder, depressive symptoms and sleep quality during covid- epidemic in china: a web-based cross-sectional survey that uncomfortable coronavirus feeling: it could be grief coming to our senses: healing ourselves and the world through mindfulness the pandemic is messing with our conception of time quantity and quality of mental activities and the risk of incident mild cognitive impairment humanistic psychology, trauma studies and post-traumatic growth trump again shifts estimated us coronavirus death toll the dangerous case of donald trump: psychiatrists and mental health experts assess a president coronavirus model projects , deaths in us, nearly double its last estimate the-number-of-hate-groups-in-americareached-a-twenty-year-high-thanks-to-trump?detail=emailll trump anxiety disorder: the trump effect on the mental health of half the nation and special populations on becoming a person take a breath: how the simple set of meditative breathing helps us cope. the philadelphia tribune the handbook of humanistic psychology: theory, research, and practice indivisible, the progressive group never keen on biden, endorses the former vp. nbc news now trump's use of the term "chinese virus" for coronavirus hurts asian americans, says expert can your marriage survive the coronavirus? cnn isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus ( -ncov) outbreak how to keep coronavirus fears from affecting your mental health ( ), levenson et al. ( ) , and benjamin ( a benjamin ( , b benjamin ( , c and the references therein. . see benjamin, e. ( a benjamin, e. ( , b benjamin, e. ( , elliot benjamin has a phd in mathematics from the university of maine, and a phd in psychology from saybrook university with a concentration in consciousness and spirituality. he is currently a psychology mentor/phd committee chair at capella university and was previously a mathematics professor for years. he has published four books and nearly articles in the fields of humanistic and transpersonal psychology, philosophy/spirituality and awareness of cult dangers, parapsychology, the creative artist and mental disturbance, progressive politics, pure mathematics, and mathematics enrichment. he lives in maine, is married, enjoys playing the piano, tennis, and ballroom dancing, and has an author's website that can be viewed at www.benjamin-philosopher.com key: cord- -k l unc authors: lu, li; lankala, srinivas; gong, yuan; feng, xuefeng; chang, briankle g. title: forum: covid- dispatches date: - - journal: cult stud crit methodol doi: . / sha: doc_id: cord_uid: k l unc covid- pandemic is the first truly global crisis in the digital age. with death count worldwide reaching , merely months after its first outbreak in china in late december and . million cases reported in countries and territories as of july , this ongoing pandemic has spread far beyond domain of world health problem to become an unprecedented challenge facing humanity at every level. in addition to causing social and economic disruptions on a scale unseen before, it has turned the world into a site of biopolitical agon where science and reason are forced to betray their impotence against cultish thinking in the planetary endgame depicted in so many dystopian science fictions. it is in this context that this forum offers a set of modest reflections on the current impacts incurred by the covid- virus. blending ethnographic observations with theory-driven reflections, the five authors address issues made manifest by the crisis across different regions, while keeping their sight on the sociopolitical problems plaguing our life both individually and collectively. taken together, they provide a grounded documentary for the archive that the covid- virus is making us to construct. the apparition of these faces in the crowd. -ezra pound, "in a station of the metro" the french word envoi is polysemic, defined as dispatch, the action of sending, something that is sent, a poetic dedication or dedication of a literary work, and the marking of the beginning of a process. this article is a dispatch from hubei, china, based on the author's -month stay in his hometown qianjiang, a small city in the middle of hubei, during the coronavirus pandemic. firsthand observations sent from the epicenter give us a clear picture of what the coronavirus has done. moreover, this article argues that the coronavirus marks a spectral moment in which a repressed trauma returns. there have been fierce debates on the origins of the coronavirus and the political, economic, and social significances of the pandemic. popular representations of the coronavirus which isolate, stigmatize, and terrify the other are symptoms of a returning trauma, which is caused by bodily memories of being victims in past disasters. a derridean reading of the envoi highlights the inherent failure of sending: what is sent can always be held up by a malfunctioning in the process of the sending or postal system, and the meaning of the trauma is lost. this traumatic failure results in a repetition in representation and the return of what is sent to the writer/sender. proposing a supplement, this article foregrounds bodily knowledge acquired through social and political trauma by virtue of fear of the coronavirus. this fear of what is familiar reminds us of the feeling of the uncanny. according to freud and derrida, the uncanny is related to the spectral working of a hidden desire that repeatedly returns as a haunting body, representation, and history. this line of thinking helps us to better understand conflicting representations of the coronavirus. the coronavirus is a ghost. this is not merely a metaphorical proposition; this is accurate in the sense that the coronavirus instantiates our phantasms, fears, and desires toward ghosts. in this regard, derrida's specters of marx provides us with a basic framework for understanding the coronavirus as a ghost. the first teaching of derrida is that ghosts do not come at just any time but in spectral moments that do not belong to time. by pointing precisely to the c scxxx . / cultural studies <span class="symbol" cstyle="symbol">↔</span> critical methodologiesli et al. present or now-time, derrida ( ) regards spectral time as "a disjointed now that always risks maintaining nothing together in the assured conjunction of some context whose border would still be determinable" (p. ). second, a ghost is a phenomenon in the game of repetition and difference. neither exclusively situated in life nor in death, neither visible nor invisible, a ghost is "the frequency of a certain visibility. but the visibility of the invisible. and visibility, by its essence, is not seen, which is why it remains epekeina tes ousias, beyond the phenomenon or beyond being" (derrida, , p. ) . third, to "make oneself fear" is essentially ineluctable in the experience of a ghost. one becomes frightened of a ghost "on the condition that one can never distinguish between the future-to-come and the comingback of a specter" (derrida, , p. ) . in other words, what one fears is not the ghost, but the fear, imagination, and one's subject inspired by the ghost. finally, "a ghost never dies, it remains always to come and to come-back" (derrida, , p. ) . whatever repression the dead may suffer, the return of the dead is anticipated, and "this being-with specters would also be, not only but also, a politics of memory, of inheritance, and of generations" (derrida, , p. xviii) . in light of derrida's framework on specters, once the coronavirus finds a host, it starts to live a ghostly life. the coronavirus pandemic irrupted during a time of turmoil. as the chinese president xi jinping has expressed, the world is experiencing profound shifts unseen in a century. while the trend of globalization is markedly receding, nationalism, popularism, and isolationism are on the rise. the eulogic discussions of "chimerica," a popular term coined by the british epidemiologist neil ferguson in , are being replaced by the theories and practices of the china-u.s. decoupling. the trade dispute between china and the united states puts an end to the chinese ideal of great harmony in the world. in addition, as his campaign slogan "america first" shows, donald trump epitomizes the idea of american exceptionalism. in traditional chinese thinking, famine, natural disasters, and plague happen when the political order or legitimacy are out of joint. during this disjointed moment, a plague was anticipated, even fabricated before it came. according to a widely circulated story in the we-media during the height of the coronavirus, wang yongyan, an academician specializing in chinese medicine at the chinese academy of engineering, predicted half a year ago that a plague would come after the dongzhi (winter solstice), one of the chinese solar periods. in addition, he predicted that the plague would last until next spring. in hindsight, rumors about a new virus were spreading right after the dongzhi. or, simply put, divination went hand in hand with the plague during a time of disjointing, disjunction, or disproportion. while scientists are still trying to track down patient zero, conspiracy theories about the origins of coronavirus have been spreading. bat soup and biological warfare are on the top of the list of suspected criminals. like ghosts, the coronavirus takes shape in the game of visibility and invisibility. in this game, ways of seeing determine how a virus can be understood. approximately made up of . microns, the coronavirus can only be seen under an electron microscope, made visible with the help of scientific equipment and representations. in contrast, a poet like ezra pound sees the invisible through his gifted imagination. his imaginative inspiration and aesthetic reflection allow his keen observation to become a line of poetic beauty and philosophical complexity. through this form of observation, an invisible apparition becomes visible in the faces of the crowd. similarly, the depiction of a fictional killer-virus called wuhan- in dean koontz's novel the eyes of darkness, re-gained popularity among those who regard it as an imaginative depiction of the coronavirus. in line with this imaginative depiction, mr. wang, well-trained in traditional chinese medicine, claimed that his prediction was based on his reading of the xiang (image) of the sky, earth, plants, animals, and human beings. visible to the naked eye, xiang functions as the visible traces from which an invisible plague becomes visible to an expert in traditional chinese medicine. in other words, with scientific support, talent, and training, people are able "to see this invisibility, to see without seeing, thus to think the body without body of this invisible visibility" (derrida, , p. ) . in this way, the ghostly nature of the coronavirus lies in the different frequencies of its visibility. however, despite our faith in being able to depict, and make distinctions between, the invisible and the visible, the way of seeing the coronavirus, especially in this time of turmoil, is politically conditioned and manipulated. when i took a night bullet train to wuhan with my family for vacation, it felt like an ordinary chinese family reunion trip during the spring festival: carriages packed with passengers, luggage, excitement, anxiety, and weariness in the air. one of the reasons for the peaceful atmosphere was that china and the united states had signed a trade agreement a few days before, sending a false message to the world that rationality and peace would return. one thing was markedly noticeable on the train: most passengers wore a facial mask for fear of an officially unidentified but unofficially sarslike virus. to my surprise, a line of masked faces was greeted at the exit by the smiling faces of relatives or friends, the indifferent faces of railroad workers, and the shrewd faces of barkers at the hankou railway station. this lack of consistency indicates that aspects of the coronavirus were kept secret. furthermore, this scenario at the station reminded me of a horrifying scene in the film the cassandra crossing, an eye-opening disaster thriller for my generation directed by george p. cosmatos. in this harrowing film, an international express carrying a virus-infected terrorist approaches a station at night. when the train reached the station, the passengers, who were kept from the truth, were confronted with members of the u.s. army in white biological hazard protective suits lined up on both sides of the platform. in both cases, the dynamic of the visibility and the invisibility of a virus was of political significance. the facial masks and the protective suits were used not only to protect people from a virus but also to make the secret of the virus both visible and invisible. in other words, political manipulation complicates the ways that a virus is seen and how the coronavirus, in particular, is seen as a political ghost. the coronavirus pandemic frightened people because it looked like the return of a specter, namely sars. because of its fatality and residua, sars remains an unresolved trauma for many chinese. at the early stages of the coronavirus pandemic, what was most frightening was its assumed high fatality rate. similarly, the short notice given for the lockdown of wuhan, a huge city of more than million residents, sent a clear message to everyone that the novel coronavirus was the grim reaper. corona, the brand of the first car i owned and of the beer i had on my first visit to a mexican restaurant, was colored by images of a fearful virus, deserted streets, calm officials on tv news channels, and panicking crowds in wuhan hospitals caught on video by the we-media. unlike the countries who proposed or actually enacted herd immunity, the chinese authorities imposed very tough immunity measures, a lesson learned from the sars pandemic, when highways, the railway station, and docks in my hometown were closed overnight. nursing homes were under quarantine; no visitors were allowed in. local authorities advised avoiding public gatherings, including public square dancing and playing majiang. the most popular forms of social activity, especially for retired people, were no longer available. after the initial panic, it was discovered that the fatality rate of the coronavirus was much lower than sars. according to the world health organization, the sars mortality rate worldwide was about %. in early february, the chinese authorities claimed that the coronavirus mortality rate in wuhan was about %. subsequently, what elicited fear in the population was the future-to-come, particularly in the form of social unrest. on one hand, stricter quarantine measures were implemented: all roads were quickly blocked with cranes or tankers or stones; vehicles' use was not allowed, unless a special permit was issued; all grocery shops, markets, restaurants, and hotels were shut down; residents were not allowed to exit their residential areas except for grocery shopping at an arranged supermarket. in addition, central and local authorities watched closely for other concerns, such as food shortages and the inflation of prices. thanks partly to its rich agricultural products in a land of fish and rice, the impact of the coronavirus on food supply and prices did not affect my hometown. however, under the restrictions put in place, my hometown looked like a ghost town, and the uncertainty of the future frightened people of all social strata. in fact, what people fear most is that the coronavirus will never die and will come back again and again, either in the form of a future-to-come or a return of the dead. regardless, despite the medical or political ambition to eradicate the coronavirus, we might have to accept the fact that the virus will co-exist with us forever. for instance, the coronavirus has been mutating, and the way the coronavirus replicates itself in the cells of other organisms is ubiquitous. this mechanism of repetition and difference functions both literally and metaphorically. on one hand, the coronavirus reproduces itself through difference. merely a collection of genetic materials that seems to think with/like a human once it infects its host, the virus induces a feeling of the uncanny, a topic to which i will return later. in addition, news sources reported that infected patients tested positive again after they had been released from the hospital. robert redfield, director of the u.s. centers for disease control and prevention, admitted that some deaths from coronavirus have been discovered posthumously (cnn, ) . in other cases, the coronavirus acted like a whimsical tyrant who inadvertently signed a death sentence. for example, the only cases of death in my residential area was an old couple who lived in an apartment very close to that of my parents. they got infected by their son and daughter who came back from wuhan. what remained a mystery was that the son and the daughter had stayed with their parents for more than days, much longer than the latent period of coronavirus. days after they were hospitalized, they died one after another. on the other hand, the coronavirus reproduces difference in its host organisms. the neighborhood my mother lives in is an acquittance community and an aging society. cadres and volunteers from the neighborhood committee have diligently attended to the needs of the old. aware of the higher fatality rate of the old, an ageist exhortation to quarantine was broadcast repeatedly through a portable loudspeaker placed at the gate of the neighborhood committee building. as stigmatized targets, senior residents were susceptible to the emotion of shame and, for this reason, chose to stay at home. the use of broadcasts and the instigation of shame illustrates how the coronavirus (re)produces, moderates, and polices the line between the public and private spheres. the coronavirus also changed the affective, moral, and power economy of the family. the spring festival is supposed to be the perfect time for a temporary family reunion of joy and harmony. when the lockdown continued longer than everyone expected, generational conflicts broke out. in extreme cases, the political infected families while they were trying to contend with the coronavirus during quarantine. for example, fang fang, a veteran chinese writer who lived in wuhan, posted her thoughts on life in quarantine on her or her friend's weibo account. those posts were later collected and published under the title wuhan diaries. public opinion on those posts varied and eventually led to a political debate between left-wing and right-wing netizens, eventually affecting family members who conflicted in their attitudes toward the wuhan diaries. along with the coronavirus, the memory of personal, generational, and political traumas returned. sars, the cultural revolution, natural disasters, and national humilities were recurring themes in representations of the coronavirus. the suffering and trauma in the epicenter deserve an envoi/dedication, and efforts have been made to achieve this goal, such as daily national and international coverage, fang fang's wuhan diaries, and we-media postings. in these kinds of representation, a rhetoric of "suffering as sublime" is usually at play. in addition, stigmatizing the suffering of others, or blaming the other for one's suffering, is another kind of dedication. both kinds of representations of the coronavirus attempt to take the moral higher ground by attempting to fix the coronavirus as a mere object awaiting to be represented. no matter what position the representation takes toward the coronavirus and its significances, the will to truth turns a dedication quickly into a testimony and even a perjury. a virus is an infectious agent that replicates only within a host organism. for the host, a coronavirus is a deadly stranger and an intimate family member at the same time. familiar, frightening, and secretive, the coronavirus reminds us of the uncanny, as discussed by freud. in his pioneering study, freud focused on the unsettling psychological state of the uncanny. distinct from the feeling of fear, the uncanny is a kind of terrifying feeling that is associated with something known and familiar. after an etymological investigation of the german words heimliche/unheimliche, and a close reading of hoffmann's story "the sand-man," freud ( ) unearthed the origins of the uncanny: "it may be true that the uncanny [unheimlich] is something which is secretly familiar [heimlich-heimisch], which has undergone repression and then returned from it, and that everything that is uncanny fulfills this condition" (p. ). he also associates the feeling of the uncanny "with the omnipotence of thoughts, with the prompt fulfillment of wishes, with secret injurious powers and with the return of the dead" (freud, , p. ) . following the lead of freud, derrida worked on the concept of the uncanny to engage with marx's concepts of repetition, specter, and fear. refuting the claims that the tenants of marxism have died, derrida emphasizes the strange familiarity of the specter of marxism in the age of advanced capitalism. as derrida insists, the specter of marxism will continue to return from the future to visit us, to live with us, and to alert us. similarly, derrida ( ) interprets the uncanny through the concept of absolute hospitality, in which "one may deem strange, strangely familiar and inhospitable at the same time (unheimlich, uncanny)" (p. ). remaining structurally open to future interpretation, the uncanny in derrida's account presupposes a materialism without substance, a messianic without messianism. derrida's understanding of the uncanny is critical to my reading of the coronavirus as a ghostwriter of envoi. as a ghostwriter, the coronavirus is a ghost who writes from the future. as a stranger and a family member, it writes with and in the place of the host. by writing an envoi, a kind of writing haunted by failure and repetition, the coronavirus makes itself visible and frightening in a spectral moment. however, the envoi is not exclusively governed by a ghostly logic that is followed by and instantiated through the coronavirus. in critiquing the tendency to unearth an ultimate truth, eve kosofsky sedgwick & frank ( ) regard affects as a possible way out of the binary opposition of truth and falsehood in representation. by invoking the power of the performativity of shame, they highlight the negative affects neglected by identity politics, dismissed and stigmatized: without positive affect, there can be no shame: only a scene that offers you enjoyment or engages your interest can make you blush. similarly, only something you thought might delight or satisfy can disgust. both these affects produce bodily knowledges. (sedgwick & frank, , p. ) in their view, shame is neither subversive nor mandatory; it works with other affects, drives, and representations to adapt the body to its situation. foregrounding bodily knowledge acquired through trauma commits us to thinking differently about representation and the envoi in question. fear of the coronavirus is not only the fear of a returning trauma as a ghostly logic in representation. more importantly, the coronavirus writes itself and writes about bodily memories of trauma in a constant play of materialization: inscribing fear in itself and on the body of the host permanently. with the end of the lockdown in hubei, the coronavirus pandemic is almost over in china. however, the coronavirus has been sending, and will keep sending, its fearful envoi. the enduring sign of the coronavirus pandemic for indians was not related to medicine or public health. it was the unprecedented exodus of migrant workers from metropolitan centers to their native rural districts, sometimes hundreds of miles away (mukhopadhyay & naik, ; petersen & chaurasia, ) . the scale of this migration was vast and is still being understood. it certainly provokes disturbing questions about urbanity and the fragility of a political compact that kept people in their place through calibrated deprivation (dahdah et al., ) . but for our purposes here, i will explore the ways in which it underscores the varying effects of the pandemic on different classes of people and the diversity of its signification. the virus in india is both a medical event to be dealt with through appropriate public health measures and a mediated discourse that has developed its own ramifications and responses. i argue that both forms of the virus have had tragic and miserable consequences, but on different classes and groups of people. like the televised persian gulf war of that jean baudrillard found to be a distinct and distorted signifier of the actual fighting on the ground, the virus itself is not the same phenomenon once it is transformed into a signifier for other meanings and purposes. the novel coronavirus later named covid- emerged in the public consciousness as a distinct problem with the rapid rise in infections in several indian states by february . in march, the government of india mandated an immediate "lockdown" of the entire country. this new term burned itself into the national consciousness and its many vernaculars almost instantly, as its meaning became physically apparent. it involved the physical arrest of people wherever they happened to be at the moment, and the prohibition of all commerce, traffic, and circulation. it was announced with a -day notice period by the prime minister, in an eerie echo of a similar announcement in of the withdrawal of paper currency. that tragic farce had laid a historical precedent for this second tragedy to come. as a deeply iniquitous society and economy were forced to a halt, the effect was expectedly unequal. metropolitan indian citizens soon learned to cope with the new hardships of "work-from-home," homeschooling, online classes and meetings, and such social-media-driven innovations as cooking and cleaning without domestic servants and entertaining themselves in their houses and apartments. the government also encouraged the adoption of derivative coping mechanisms as soon as they were observed in other countries: applauding medical workers from the safe confines of apartment balconies and terraces; singing, chanting and clanging metal plates and dishes with utensils in cacophonous, solidarity of the gated classes; lighting lamps and candles; and waving mobile phone flashlights at appointed times (krishnan, ) . however, the actual effect of the virus became inseparable from the effect of the "lockdown." the sudden impoverishment of the majority of the country's population led to starvation, medical neglect, and a national panic. while invisible to the citizens in its first few weeks, it became impossible to ignore, when workers across indian cities started to simply walk back to their native villages. their exit from cities also emphasized the fragility of urban belonging: that in a crisis, indian cities were fundamentally empty shells, drawing people not through cosmopolitan attractions or civic rewards but by rural misery. at this point, the virus was still largely a media phenomenon, while the "lockdown" was what had directly affected most indians: the sudden disappearance of work, wages, commerce, and circulation magnified the precarity of urban existence. the largely informal national economy quickly unraveled in a crisis. this crisis was exacerbated by the role of the virus in continuing the ideological and political discourses of the chaotic period immediately preceding the lockdown. the use of the virus to carry out "politics by other means" can be seen in other polities as well, but its entanglement with indian politics is particularly useful as a means to understand the virus as a set of signifying practices. the context of this political use of the virus as a signifier is also inseparable from the highly mediatized nature of indian politics and society. the virus emerged as a discursive phenomenon in india at a crucial juncture in a national conflict over changes to the country's citizenship laws. with the rise to national power of the ruling rashtriya swayamsevak sangh (rss, or the national volunteers organization-a fascist group founded in ), india's national government had been attempting since to achieve its political goal of abolishing its secular and liberal constitution through a steady dismantling of public institutions (roy, ) . this conflict worsened in with the re-election of the rss-controlled government headed by the current prime minister, and the consequent repeal of laws that had hitherto guaranteed the autonomy of the occupied territory of kashmir. this was followed by a critical change to citizenship laws to specifically exclude muslims from gaining indian citizenship and institute a new "citizens' register" to determine afresh the legal status of all residents. with reports of the parallel construction of detention camps outside major cities, the fascist inspiration and ominous intent of the new laws became clearer and more immediate. protests and political resistance to the new measures emerged across the country, and were met with violent responses from the police and rss groups. matters had reached a head when the nationwide lockdown was suddenly imposed. except in a few indian states such as kerala, with still functioning local health systems, the lockdown did not involve any public initiative to test or prevent the spread of the virus. instead, in keeping with the ruling ideology of our time, citizens were mandated to protect themselves, on pain of being brutalized by the police if they failed. in this chaotic sauve qui peut scenario, the rhetoric of basic preventive measures took on ominous ideological connotations depending on who you were and where you lived. as it became clear that only access to clean running water, adequate space, and a home to live in would guarantee the efficacy of the public health guidelines, medical advice became meaningless for much of the country's population, especially the inhabitants of vast informal urban settlements in the metropolitan cities. in effect, a dual situation emerged: a parallel virus had infected the classes who lived in gated urban communities and formal neighborhoods and who followed its progress in daily primetime news trackers. positive cases, testing ratios, death rates, and other numbers soon flew across television and website screens in macabre charts, graphs, and complex animations, as breathless studio anchors enthusiastically tracked the competitive fatalities across states, regions, cities, and countries. as the formal state and civil society response to the virus grew more and more into a media discourse, its actual effect on the population was determined by existing social conditions and ideological practices than by the ideals of public health. in the early period of its spread, the illusion of its control was maintained through the interpellation of the mass television audience as ideal national subjects. in a series of televised speeches, the prime minister exhorted citizens to planned acts of mass discipline, such as the applause, noise-making, and lamp-lighting exercises mentioned earlier. it took several costly weeks for the citizens to realize that this national son-et-lumière had only served to deafen and obscure a different and more real virus that had silently spread illness and death among urban populations who did not have houses or apartments with balconies. a starved public health system soon proved inadequate and unprepared. because this real crisis was not mediated or televised, there was no appropriate or meaningful response to it. the easy congruity of the eagerly adopted virus prevention measures with the practice of caste-based rituals of discrimination was not lost on most indians (george, ) . this fortunate coincidence enabled the easy normalization of virus prevention as a legitimization of existing hierarchical practices. the convenient prescription of social distancing appeared to keep the privileged class of wealthy and respectably middle-class white-collar workers as far away as possible from the physical contact or proximity of their social inferiors. the pandemic thus seemed tailor-made for defenders of hindu caste hierarchies, a righteous and suitably scientific legitimation of social discrimination. the fantasy of caste purity would have remained an abhorrent social remnant if it had not become part of state policy in the last few years. but in the context of the stateled legitimation of religious hierarchies and the consequent onslaught on emancipatory laws, this entanglement of the virus with caste and with the violent hate crimes against muslims acquired a dangerous dimension. it is this distrust of and disgust with a compromised public health system that drove so many indians streaming out of cities and into the relative safety of their impoverished rural communities. the alienation of muslims as a national other has been a part of the basic doctrine of india's current ruling group ever since its founders, awed by the nazi policy of extermination, adopted a similar goal for the erasure of non-hindu communities in india. the mass protests and popular uprising against the rss's attempts to irrevocably alter the basic structure of the country's republican constitution had reached a tipping point when the covid- epidemic was suddenly deemed emergent enough to impose an unprecedented "lockdown," in effect a de facto police state across the country. the imposition of the lockdown allowed police to destroy protest sites, detain protestors, and unleash a reign of terror across indian cities. caught in the initial crossfire were members of an apolitical muslim religious group, the tablighi jamaat, whose convention in delhi had been interrupted by the lockdown. jamaat members trapped in the organization's premises by the curfew were found to be infected with the virus. the consequent media narrative of the discovery of the infection among the jamaatis veered into the fantastical, with nightly news anchors debating the strategies of a "corona jihad" that was to be waged by militant muslims using the virus as a weapon (perrigo, ) . this dog-whistle narrative of muslim bodies as unclean spreaders of a foreign disease dovetails with similar narrative frames used to portray hindus from laboring and working castes as well. the manufacture of conspiracies surrounding the coronavirus can be seen across the world and is not unique to india. a disturbingly large proportion of americans, for example, appear to believe that the virus has been manufactured to enable mind-control through vaccination and g cellular signals by a ruling elite (fisher, ) . on rare occasions, these conspiracies do spiral out into real effects such as the bombing of cellular towers in britain and the anti-vaccination movement in the united states. in india, however, the covert encouragement of such theories by the state itself, to legitimize the hatred toward muslims, exacerbates and normalizes the rumors as mainstream prime time news which is then amplified and shared through an organized social media campaign (ellis- petersen & rahman, ) . the vilification of the muslim other serves two purposes, one of furthering the state's broader agenda of religious and caste purity, and the other more immediate goal of providing a scapegoat for the inescapable rise in infections and deaths due to the virus and the inability of the state and society to understand the crisis. the brutal police crackdown that accompanied the lockdown and the violence of its imposition across the country were a small reminder of the routinization of the "lockdown" as a way of life in the occupied valley of kashmir, part of the only muslim-majority state in the indian union. the effects of the police state as a normalized entity have been multiplied since the abrogation in of constitutional laws guaranteeing the region's autonomy, even if such laws were honored more in the breach in preceding decades (zia, ) . the uncanny resemblance of a public health curfew to a military occupation is not coincidental, but the result of the colonial origins of both, and of the state institutions they represent. the symbiotic existence of caste-based discrimination, the extermination of a religious minority, and the colonial occupation of an entire province within the same body politic is made possible by the continuous interpellation of the mass of people to become national citizen-subjects. this call to obedience, broadcast daily through primetime television and magnified through the near-mandatory use of mobile phones, is the only sign of a nation-state that is otherwise absent in the real world. the failure to stop the spread of the real virus is obscured as the interpellated citizen is urged, cajoled, and threatened to participate in the simulacral fight against a mediated virus in a purely semiotic realm. the washing of hands without the precious reality of running water, the maintenance of "social distance" in the absence of space, the exhortation to "work from home" for a population that is not housed, and the discourses of online socialization and commerce are all much more than signs of mere denial: they are the components of this new semiotic space, enabling the call to national belonging in a new domain, bereft of its mooring in the world. from a broader historical perspective, the coronavirus epidemic does not appear to have affected indians as much as the far greater fatalities caused by more prosaic diseases, hunger, and the increasingly toxic air and water (rukmini, ) . what has caused the greatest pain and panic is the response to the epidemic. this response has been not to the virus itself, but to a simulacral virus that appears to occupy the same space and shares the same name as covid- , but which is a mere signifier, pointing to other, older evils. like baudrillard's hyperreal war, it has surpassed the real virus itself and has come to occupy its place. it cannot be wished away or prevented with a vaccine, it needs a response in kind: of new counter-signs and counter-discourses. a catastrophic pandemic unseen in a century, the current raging of covid- around the globe has undoubtedly produced a unique symbolic site for global, regional, and national imaginations. as the earliest epicenter of this infectious illness, china has witnessed the proliferation of discourses about the evolution of the pandemic on various media platforms, through which the chinese public has the rare chance to reflect on important issues regarding identity construction, social reformation, and nation building. while much attention has been paid to the stigmatization of china in euro-american politics, media, and everyday whisper that label the natural coronavirus as a cultural and ethnic fault (fu, ) , what has been overlooked is how china has portrayed other countries in this global health crisis, especially those surrounding nation-states in the same geopolitical area. east asia, or the sinosphere in the broader sense, with the collective memory of fighting sars in , is thought to have responded to covid- more efficiently than many western countries (salmon, ) . how, then, is the east asian encounter with covid- depicted in the chinese public discourse? how does such depiction envisage china's relations with neighboring countries and its position in the area? in this essay, i discuss the ways in which the coronavirus pandemic has been appropriated by the chinese public for a (re)imagination of east asia. by exploring the evolving representations of its neighboring countries throughout the epidemic on chinese media platforms including weibo, wechat, and zhihu, i argue that the talk of the regional responses to covid- envisions a china-centered union of selected east asian countries in parallel with the historical tributary system of the sinosphere. through the expression of the nostalgia for imperial china, the discursive reconstruction of the east asian identity is a ratification of china's contemporary ambition to reclaim its geopolitical dominance. synchronized with the rapid transmission of the coronavirus in china and east asia between january and march , the chinese public in this early phase drew close attention to the unfolding of the epidemic in its nearby countries, and japan and south korea in particular. with the disease breakout involving diamond princess (japan) and shincheonji church of jesus (south korea) frequently making news headlines, the discussions of how those countries responded to covid- flourished online, which, in combination with the continuous debates over china's own pandemic threat management, contributed to the imagination of the covid- rampancy as a regional challenge that china and its neighbors faced together. central to the discursive formation of this imagined community was the celebration of the incessant interaction and cooperation between china and some east asian countries to combat the virus collectively. in the wake of the outbreak when china was threatened by the crumbling of its health care system, the countries under the spotlight-japan and south korea-were widely appraised for the sympathetic and supportive approaches they took to help china overcome the severe shortage of medical resources. the media reports of japanese and south korean governments leading the international aids to china (gong, ) were echoed by numerous warm anecdotes on social media championing the heartfelt support from their people. perhaps the most well-known story of this kind, a japanese institution wrote a chinese-language verse on the boxes of masks it donated to the province of hubei: "rivers low, mountains high; the same moon in the sky" (trans. zhao, ) ("山川异域，风 月同天"), which immediately went viral online because of its signification of the long-lasting friendship between china and japan. according to account of the expedition to the east by the great master (唐大和上东征传) written by omi no mifune (淡海三船) (see wong, ) , this sentence was from an ancient poem written on the edges of the buddhist robes japanese missions (遣唐使) brought to tang china as the tribute from prince nagaya (長屋王). given its profound roots in the history of japanese envoys to imperial china learning from the chinese culture and civilization, this verse went beyond re-fostering the traditional sino-japanese solidarity. analogizing japan's mask donation with ancient japanese envoys' gifts, it also evoked the retrospective commemoration of the hierarchy between china and japan in history which almost vanishes in the modern era. therefore, the popularity of this verse may indicate the aspiration for the reoccurrence of such bi-lateral relations. indeed, this was only one example of the ubiquitous imaginary of the pan-east asian cooperation and exchange of goods and information as a modern emulation of the tributary system through which imperial china maintained its diplomatic and trade relations to neighboring countries and consolidated its dominance in the region for over a millennium. after china started to keep the pandemic under control and resume the production of medical supplies, this metaphor was further perpetuated in an attempt to accentuate that china's supplies of medical goods and anti-epidemic lessons to nearby countries drastically outnumbered what it was initially given. on weibo, china's return of masks and respirators to its neighbors was often explicitly compared with the "vassals' gifts" chinese emperors assigned to tributary states in posts like this: tribute is both the highest form of alliance and an advanced way of investment, but (this time) it is based on masks! recently, xinwu district in wuxi, jiangsu province donated , to toyokawa, aichi prefecture in japan in return for the , masks, protective clothing and other anti-epidemic materials toyokawa donated to xinwu district in february. (weibo source, march , ) this nostalgic use of metaphor implies a crucial undertone of sinocentrism of the public imagination of the community comprising china and bordering countries fighting against the coronavirus. the tracing of the origin of east asian solidarity to the past is suggestive of the ambition of the present. the chinese public not only fantasizes about a reunion of china, japan, and south korea for covid- but more importantly yearns for the recovery of their nation's leadership and centrality in this battle. as the coronavirus expands rampantly to the rest of the world from march onward, chinese media coverage quickly catches up with the shift of the epicenters from east asia to europe and north america and reformulates the pandemic as a global health crisis. against the depiction of how covid- created chaos, helplessness, and dysfunction in western societies stands the stark contrast of east asia as a safer zone where the outbreaks have been largely contained with success. with the similar control of cases less than , , japan and south korea remain at the heart of this imagined safe zone in company with china even though the reality has seen even fewer confirmed cases in other parts of asia as well as the recent resurgence of virus spreading in all these three countries. this rhetoric is in concert with the prevalence of online deliberations about why east asia as an area has performed better than other parts of the globe in the containment of the virus. at the core of these discourses lies the construction of an east/west binary which frames the global responses to the pandemic into a competition in which "we" (the east/ east asia) have triumphed "them" (the west/euro-america). although china and neighboring countries diverge in the official approaches to handle the pandemic, their relative efficiency in virus containment in comparison with the west is considered to be guided uniformly by the cultural values they share as part of the "confucius east." in particular, collectivism-the principles of prioritizing community interests to personal interests, pursuing social harmony, compliance to authority, avoid causing inconvenience to others-has been glorified as the main drive for the people in east asia to more effectively cope with the governmental strategies in contact tracing, testing, social distancing, and mask wearing. similarly, the regional cooperation in the pandemic management is regarded as a manifestation of these values. for example, the reflections on how south korea has set a model of disease control using mass tracing and testing tend to recognize the smooth uptake of this procedure facilitated by koreans' collectivist mind-set that downplays individual privacy and complies with the data-mining measures to track and publicize their locations, activities, and close contacts. meanwhile, other popular discussions blame the religiosity of the shincheonji church members whose gatherings caused the initial covid outbreak in south korea, which is reflected from the titles of zhihu posts that describe the diffusion of the virus through "hallelujah" such as "the occupation of south korea by covid- , everything has to start from 'hallealia'" and "south korean cult hallelujah devastated the country." apparently, these titles have no intention to mask the underlying tone mocking at the role of christianity in the acceleration, not mitigation, of disease spreading, which further serves as a foil to the power of confucianism to help south korea navigate away from the disaster. in fact, satire targeting at christianity represents the broader criticism of western cultural values in hindering the efficacious enforcement of restrictive and surveilling measures against the coronavirus. the east asian identity is thus reaffirmed through the clashes between the eastern and western civilizations. however, it is worth noting that the narratives about the east asian conquest of covid- are again permeated with the metaphor of the tributary system delineating china as the leader and role model in this imagined "safe zone." not only does the attribution of the regional success to confucianism call up the historical chinese centrality in the sinosphere but the emphasis on china's ability to offer lessons and instructions from its early experience for its neighbors to benefit from also ratifies the restoration of the "teacher/student" relation between imperial china and pre-modern japan and korea. far from a total reenactment of the historical sinosphere, this chinese imaginary of east asia engages with a purposeful selective process that amplifies china's solidarity with some east asian countries but simultaneously mutes others in the same region. as remarked earlier, a majority of the online narratives about the cooperative responses to covid- in east asia revolves around china, japan, and south korea, with less frequent inclusion of singapore as well as occasional reference to such countries as mongolia and myanmar. this emphasis on forming a coalition with japan and south korea is compatible with china's longterm agenda of promoting and dominating the china-japan-south korea union (中日韩一体化), which was recently reiterated by the three governments' consensus to speed up the negotiation of the free trade zone (中日韩自贸 区) (wang, ) . in this sense, the covid- crisis has offered a discursive site for the chinese state to rebuild this trilateral bond and remodel its significant neighbors whose national images, due to the respective disputes around diaoyu islands and thaad (terminal high altitude area defense), have been negative in china for almost a decade. while the china-japan-south korea triangle is romanticized in connection with other small countries, the alienation of some confucius societies from this imagined "cooperative" east asia is quite striking, especially given the outstanding results some of them have produced in the prevention of disease transmission. the first excluded category includes taiwan, hong kong, and macau-the territories outside the mainland in the great china area. whereas macau is often forgotten by the media as it has always been, both taiwan and hong kong are widely criticized and mocked for their attempt to politicize the pandemic as a weapon to confront beijing and increase international recognition. the second group pertains to north korea and vietnam-the authoritarian states that have close political and ideological bonds with china. for instance, north korea has been constantly questioned and satirized because of the lack of transparency in the disclosure of its epidemic circumstances. vietnam's outstanding handling of the virus which led to only confirmed cases and death was nearly silenced in the mainstream media coverage. in the unusual reference to vietnam in some zhihu conversations, vietnam's success was rarely celebrated but considered as a "threat" to china's leadership in containing the pandemic in the area. the trivialization and exclusion of these countries/ regions from the chinese imagination of east asia as a collective force fighting against covid- is not unexpected. in the first place, the negative attitudes toward them (except macau) reflects a backlash against the restrictive, noncooperative methods those governments have enforced to block the virus from mainland china (e.g., full border closure; ban on exports of medical supplies), which signifies their resistance to be incorporated into the modern tributary system chinese people have aspired. yet for taiwan and hong kong, this exclusion repeats the endeavor of chinese official propaganda to erase the distinction between them and the mainland and disavow their political autonomy. instead of being completely out of the picture, their responses to the coronavirus are mainly discussed as part of the chinese experience to consolidate the national identity. for north korea and vietnam, the negative impression may partly result from china's ongoing diplomatic conflicts with them in recent years regarding the south china sea and denuclearization, respectively. nevertheless, the shaking of the "socialist brotherhood" on the matter of covid- also implies the reluctance of the chinese public to articulate a regional identity around the axis of a shared political regime. in fact, assimilating itself with ideological and political allies is likely to obscure the focus of this imaginary on china's historical and cultural alignment with japan and south korea. as covid- begins to shift both the scholarly and media focus on an international scale to reconsidering the dark sides of globalization (chan & haines, ) and mourning for the disruption of european union (trofimov & pancevski, ) , china's reversed agenda of imagining a regional union is stunningly intriguing. on one hand, the eagerness to build solidarity with east asian countries represented by japan and south korea might be a strategy to react to the racialization of covid- as a "chinese virus" and the demonization of china as a "public enemy" and "trouble maker" in the euro-american political and media agenda (viala-gaudefroy & lindaman, ). by articulating china's resemblance (and collaboration) with the bordering democratic capitalist states (rather than the "socialist brothers") in the "confucius-inspired" success of halting the virus, the public discourse strives to construct a collective identity of the east so as to brush off china's label of the other imposed by the western imagination. ironically, this consolidation of the eastern identity also serves as a repercussion to otherize the west as the loser to the coronavirus. on the other hand, the rise of this east asian imaginary centering around china's historical and cultural bonds with japan and south korea has far-reaching implications for china's geopolitical strategies beyond the covid- pandemic and the realm of public health. rested upon the trope of the imperial tributary system, this imagination reflects how the chinese public discourse echoes the state ambition to recuperate the historical dominance of china in the sinosphere, which is part of chinese communist party's long-term project of "the great revival of the chinese nation" (中华民族伟大复兴), or in xi jinping's term, the "chinese dream" (中国梦). incorporating japan and south koreathe most important american allies in east asia-into the imagined tributary network might serve the specific purpose of weakening the u.s. hegemony in the region (see ikenberry, ) , whereas the tactic exclusion of north korea and vietnam indicates the indifference of many chinese to the state's political and ideological "comrades" (whose traditional alliance with china has often proven itself unstable and delusionary in the changeable economic and political dynamics in east asia). more importantly, this selective reimagination of the eastern union expresses the chinese public's nostalgic ideal of the nation's revival, which dreams of a return to the middle kingdom, the empire that reunites and leads east asia through culture and history. during the year , which is anticipated to be the warmest year in human history, we failed to stop the rampant spread of a coronavirus called covid- and its disastrous impact on societies and individual lives. unlike its "cousin" sars, which broke out in early and vanished into thin air largely because of rising temperatures, the current respiratory epidemic has yet to show any sign of amelioration with the arrival of summer. news photos have shown audiences an incredibly bleak, bizarre, and somewhat surreal picture of life during the pandemic. streets are evacuated. stores are closed. public services are paralyzed. modernized cities have become empty and ghostly quiet. only scattered people equipped with medical face masks walk anxiously in this futurist, apocalyptic scene. to use timothy morton's concept, the covid- pandemic has become a "hyperobject," a phenomenon that possesses an ahuman time scale and an extremely diffused quality in occupying space. in such a space-time reconfiguration, or, in plain language, during this type of disaster, humankind becomes an obsolete idea, as humans no longer play a meaningful role in the space-times created by and for "hyperobjects." unfortunately, such a concept bares relevance in light of the uncontrollable proliferation of the coronavirus across the globe at this juncture. worse still, some epidemiologists warn that a new round of outbreak will likely occur soon in the coming fall. a possible scenario could repeat the conditions after the / fukushima daiichi nuclear disaster, when breathing with face masks, people eventually became accustomed to a state of emergency as the conditions for living and dying in the anthropocene. "[p]oison has become a normal feature of daily life, the second nature we have to inhabit" (berardi, , p. ) . while one can attribute the deterioration of nature to neoliberalism and its disastrous governance, this essay, rather, speculates on what foregrounds the involutional relationship between humans and the earth beyond the "nature-culture" divide. whether one is willing to admit or not, viruses are neither creation ex nihilo nor culturally and politically constructed representation. instead, they are beings that have always been part of earth's composition. in a prophetic book, the natural contract, the late philosopher michel serres ( ) describes the evolution of the earth's composition. in ancient law and modern science, nature was treated as an objective reference point, because it had no subject. existing objectively "out there," the earth was a space that did not depend on humans but only acted passively in relation to causality. yet, witnessing the ecological crisis arising in the th century, humans realized that the earth has been affected by our behavior and is now behaving like an aberrant subject! in recent scholarship, this subject has been referred to as gaia, the capricious goddess of the earth (see latour, , p. ) . the earth is full of action and so is covid- . as described in news reports, the coronavirus looks for and hijacks its hosts; it finds easy purchase on, and takes control of, human bodies; it kills many, but not all, of its hosts so as to keep moving, spreading, replicating, and surviving. it would be impossible to talk about the virus without referring to those actions. cited by the washington post, a virologist came up with a vivid analogy for viruses by comparing them with destructive burglars. "they break into your home, eat your food, use your furniture and have , babies" (kaplan et al., ) . as the word "object" refers to entities that are inanimate and subject to chains of causality, viruses, in this sense, hardly fit into this definition. for instance, covid- remains mostly enigmatic, not least because it is considered strikingly sneaky-"the virus doesn't really want to kill us. it's good for them, good for their population, if you're walking around being perfectly healthy," said another virologist in the same washington post article (kaplan et al., ) . besides doing things such as breaking-into, eating, and having-babies, the virus is further endowed with intentions-it does not want to kill us! however, the coronavirus should not be mistaken for a subject, especially a subject-agent, which is historically associated with liberal humanism since the enlightenment and which is deeply rooted in the "nature-culture" divide, an ontological regime referred to by latour as "the modern constitution" (see latour, b) . the idea of the subject as a product of euro-american modernity is indivisible from its aim to achieve individual sovereignty and autonomy. in a politico-legal sense, bounded individualism is the most evolved form of this idea in the wake of the global expansion of capitalism. faced with an unprecedentedly active earth in the late th century, nonetheless, this anthropocentric conception of the subject-agent has been confronting exponential challenges, among which the current coronavirus pandemic constitutes the latest one. to be clear, the term "subject" is a mismatch for covid- , not because it is agentless and incapable of doing the same things that humankind does. the contrary is true: the state of being of the virus-what it is-can unfold only through its actions and long after its performances. at stake for the virus and humans is that there are "no pre-constituted subjects and objects, and no single sources, unitary actors, or final ends" (haraway, , p. ) far from being a de-animated object, or an anthropomorphized subject, gaia, the increasingly "rioting" earth, is a collective of actions that distributes agency in heterogeneous and surprising ways. as a result, "we must not believe in advance that we know whether we are talking about subjects or objects, men or gods, animals, atoms, or texts" (latour, a, p. ) , and also viruses until their actions are captured, and rendered into shapeswhether the shape of a human or of a virus. the story of the human-centered history is being replaced by an explosion of narratives about the increasingly animated and animating earth. however, the dualism of the subject versus the object, unfortunately, is still perniciously conserved in the mainstream reaction to the covid- pandemic. when societies are forced to act on the pandemic, the virus is almost exclusively treated as an object subject to the chain of causality. this tendency is clearly reflected in the mobilization of wartime rhetoric and discourses in conjunction with governments' anti-epidemic measures. for instance, when visiting wuhan right after its lockdown, sun chunlan, china's vice premier, warned that the country was facing "wartime conditions." likewise, only month later, president donald trump declared a national state of emergency over the coronavirus outbreak in the united states. in this antagonistic discourse, contending with the virus, a not-yet-tamed and potentially threatening other, is framed as a relationship between humans and their enemies. for those who believe humans and only humans make history, a self-proclaimed war on the virus is unavoidable! peace, accordingly, is only imaginable to be reached, or more precisely restored, to an already existing order, established primarily for humans. mobilized to describe the relationship between covid- and humans, "war" is a terrible and even dangerous choice in terminology, due to its undertone of human exceptionalism. in fact, nearly % of the cells in a human body is "part of a vast community of companion species, particularly bacteria and viruses" (smart & smart, , kindle ) . unfortunately, most humans have yet to learn the meaning of living and becoming-with these beings who are made by and making humans at the same time. in her book staying with the trouble: making kin in the chthulucene, donna haraway ( ) invites readers to contemplate our troubling present, the chthulucene, an emerging regime of naturecultures, as opposed to the "nature-culture" divide. contrasting to the discourse of the anthropocene and the capitalocene, both of which are conceived as human-induced condition, the "chthulucene" is, first and foremost, concerned with earth beings who live in "manifold forms and manifold names in all the airs, waters, and places of earth"-they are monsters which "demonstrate and perform the material meaningfulness of earth processes" (haraway, , p. ) . the vicious coronavirus is evidently one of these monsters. despite the havoc it is creating in the present, the epidemic is a manifestation of the biotic and abiotic powers inherent in earthly actors and is part of "ongoing multispecies stories . . . in times that remain at stake" (haraway, , p. ) . as implied by the title, one of the valuable lessons of haraway's book is that, for humans in particular, there might be no better option other than to stay with troubles, of which humans are never innocent. staying with the troubles demands caring for all the threads that bind us together and make our existence possible in the first place-humans are made by countless earth beings and vice versa. it also means that we are required to weave unexpected and even dangerous connections with others, in haraway's ( ) words, making kin as oddkin "in unexpected collaborations and combinations . . . we become-with each other or not at all" (p. ). this insight is particularly useful for thinking about viruses. because viruses have "no cellular machinery of their own, they become intertwined with ours. their proteins are our proteins" (kaplan et al., ) . in this sense, the evolution of humans and viruses is inseparable from the process of involution of the two into one. in other words, becomingwith means that, by definition, a "we" always precedes an "i," a "you," or a "they." the so-called "asymptomatics" provide an excellent example of this point. asymptomatics refer to those who test positive for covid- but, confusingly, do not suffer from illness or show any symptom of the disease. asymptomatic infections or carriers are possibly greater in number than those with symptoms. at this point, it is impossible to decide which of the two types is more typical of covid- infections, because, as a researcher at the university of oxford says, "there is not a single reliable study to determine the number of asymptomatics" (shukman, ) . in the same news report, neil hall, a biomedical expert, suggests considering asymptomatic cases of the coronavirus as the "dark matter" of the epidemic, as invisible and not-yet identified dark matter is believed to make up most of the matter in the universe. despite the fact that no conclusion has been reached about the enigmatic phenomenon of asymptomatics, the differences that manifest among patients reveal that the virus, and the particular cases of infection, should be examined as specific units. in other words, between the virus and humans, the specificity of an encounter matters. unlikely to be autopoietic systems that reproduce autonomous units, the virus and an infected body constitute a collectively produced, sympoietic system that does not have self-defined spatial or temporal boundaries. in these cases, and from a non-anthropocentric, philosophical point of view, the idea of bounded individualism has to be discarded for good. beyond the divide between the subject and the object, what emerges are ontologically heterogeneous practitioners who are involved in each other's lives. besides evolution, living also relies on involution. without any intention of "romanticizing" covid- and the current pandemic, staying with the trouble, as articulated by haraway ( ) , is "to make kin in lines of inventive connection as a practice of learning to live and die well with each other in a thick present" (p. ). the coronavirus does not happen as a matter of fact, which "passively" waits to be discovered, investigated, tamed, or neutralized by "active" humans. what we call the covid- pandemic manifests itself as a differentiating and relational effect because it matters by bringing into being various relations between humans, and between humans and their oddkin. in this view, science is only one practice among many others to capture the efficacy of its mattering. in addition to biomedical measures, a more critical question for the coronavirus crisis is "what method does the matter demand" (thompson, , p. ) ? proposed by haraway for living in the chthulucene, the string figure might also serve as an appropriate method and image for the pandemic, characterized by its exceptional contagiousness and interactivity. consisting of "passing on and receiving, making and unmaking, picking up threads and dropping them," the string figure is all about "becoming-with each other in surprising relays" (haraway, , p. ) . crucial to this method is that it does not guarantee what is obtained turns out to be good in the end, because living itself has become so dangerous in this very thick present-agencies are distributed, conflicting, and entangled in a myriad of practitioners, human and non-human alike. in this pandemic, we are all playing the game of string figures with our oddkin. it is not beneficial to judge in advance who is a subject and who is an object, or which one is active and which one passive, as all participants might be capable of something that matters in one way or another. for example, one thing that the respiratory disease teaches us is that not only breathing matters but also the manner how one breathes matters to others. life and death happen inside specific connections and their mattering in mundane, and even fleeting, encounters. making covid- matter requires us to reanimate "what is coming into states of matter and mattering in bodies, stories, acts, and events" (stewart, , p. ) , in other words, in the vicissitudes of our ordinary lives. for the future of this thick present, one key is to stop imagining the crisis of the coronavirus as something wholly predicated on effective vaccines and scientific solutions. instead, humans must learn to connect and also care for threads, some of which are obvious, some elusive, some vicious and dangerous, and some fictional. we may need to discard terms such as "overcoming" or "solution," and turn to terms like "participation" concerning all that we are uncertain of but have to live and become with, together, in the "metamorphic zone" called the earth (latour, , p. ). what does it mean, the plague? it is life, that is all. the most abundant biological entities on earth, viruses are forever and everywhere. suspended between living and being dead, they are simply there, a slimy strip of ribonucleic acid (rna), as biologists tell us. poorer in life than tardigrades, incapable of movement, and having no logistic of their own, they ride on and feed off others to replicate themselves, to become the viruses that they are. as smart schoolchildren know, they are transmissible and must be so transmitted as to go viral, to become the viruses as we know them. dependent entirely on carriers, that is, exploiting others' hospitality, without which they have no life (but also no death either), viruses exemplify transmissibility. they live and thrive, as it were, only if their hosts are susceptible, in motion, and in contact and they die or die down when susceptible hosts are either unavailable or no longer hospitable. defined, that is, made finite, by transmissibility, and yet transcending its barren finitude through parasitism, viruses exist and operate like pure media, self-generating and selfgenerated by being entirely coterminous with the channel through which they flow and multiply. interpolating and encoding themselves in the metabolic cycle of others, thereby reproducing themselves passive-actively, they mediate by colonizing others and, in so doing, mediate themselves by proxy, going about so energetically and indiscriminately as to cause the demise and thus thwarting unwittingly their own propagation. if viruses communicate anything, if their shadowy occupation of host bodies sends any message, it is their very own communicability, their ability to disseminate themselves over a large population with effort less than minimal. although all over creation and in abundance, most of the viruses cause us no harm and we pay them little attention, even though they populate our body and capitalize on its resources. they become a matter of grave concern when they infect us, when they not only put themselves inside (in-ficere) our body and stain its normal functioning, but also threaten to afflict as many people as their "infectivity" attacks. more dangerous and less tamable than most microbes, viruses invade our body and compromise it at the cellular level. they do not just make us sick; they bring about plague. once seen as a cause of infection, viruses accrue significance and take on the label "pathogens." to refer to viruses as pathogens implies that they are "medicalized," that they not only enter into a relation with humans who regard them as toxic and virulent, but are also seen as a problem to be addressed in a methodical, systematic, that is, "scientific," manner. it is through this medicalization that viruses are individuated and identified as a distinct biological entity and, having been so captured and given a name-for example, h n , mers-cov, sars-cov- , covid- , and the like-by what might be called the "clinical gaze" and its taxonomic procedures, they enter into sciences and become a focus of medical research, made all the more pressing if and when they create public health crisis. more than one hundred years after martinus beijerinck gave the name contagium virum fluidum (contagious living fluid) to the incitant of tobacco mosaic first discovered by adolf mayer and dimitri ivanovsky, viruses are now actively collected, classified, and manipulated by scientists in highly restricted spaces called laboratories, most of which, like the viruses housed carefully therein, are hidden from public eyes. while slimy poisons were once thought to be sent down by god to punish us for our sins, we now see viruses not only as an object of scientific investigation but also as a medical challenge that nature poses to us as biological creatures on earth. like birds, bats, and rats, we are all equal opportunity hosts to killer germs. not all viruses are fully pathogenic, but pathogenic viruses are ever ready to go viral when the conditions are ripe. however, although viral infection may break out and spill over, it does not mean that there is a pandemic. "pandemics," as virologists tell us, "begin when a brandnew virus infects a human who also at that point is able to transmit the virus to other humans" (buettner, ) . two points should be noted without delay. first, pandemics are not created by transmission of viruses from some source to humans, but from humans to humans. breakouts of viral infections among members of a primate community deep in the amazon rainforests, for example, may be large scale and may disturb ecological balance alarming to conservationists, but they do not for all that count as pandemics in the sense that the term is properly used. viruses might infect one or more individuals, but humans are responsible for creating the conditions that transform infections to outbreaks and outbreaks into pandemics. pandemics, in other words, are not natural or biological phenomena; they name a human crisis, a contagious malady plaguing humans who are both agents and patients at the same time. contagious diseases are disastrous to all, locked, as we are, in the same bubble in which microbes live and grow, but pandemics are decidedly more pernicious in that we become, often unknowingly, the source and the cause of our own infestation. second, pandemics are "declared." as is the case with catastrophic events in history, like wars, famines, or mass cultural anomaly as bizarre as the chinese sorcery scare of , whose duration and identity result from an act of punctuation and sense-making entirely sociopolitical in nature, pandemics too begins with a performative act that announces their beginning and, having made them to begin in this way, determines when they reach their end, even though the viruses and their carriers may still be with(in) us (see kuhn, ) . naming not microbial activities in nature but a crisis for humans, pandemics are events made real, public, and urgent, as just said, by a performative-a speech act, to be exact-whose authority in pronouncing their beginning and end depends on the very force that makes the declaration authoritative and forceful in the first place. brought into being by discourse and public communications, pandemics are social constructions; they signal a state of emergency-appearing, first, as physical ailments on the part of individuals, subsequently identified and ratified by medical and scientific community as a real health problem, and finally materialized by authoritative broadcast and public acknowledgment, thereupon becoming a public policy issue to be addressed by political leadership, all these over a determinate territory. once established as such, a pandemic individualizes a collective paroxysm, making it a public enemy by giving it a face, a name, a certain life span in the social calendar, without which the havocs wreaked by the virus would not be the crisis its name designates and invokes. it is in this declarative nature of pandemics that we can see how viruses, once medicalized and publicly acknowledged, are inevitably entangled with science, history, culture, and politics. socially constructed by a decision, by a cut or break into regular time, they mark a "zone of exception," a temporal heterotopic, as it were, where we, individually and collectively, stand to one another as equal subjects to illness, unfreedom, and death in the unending drama of man against nature and its hostile elements. viruses are viruses are viruses. they have no political content; operating according to the laws of physics, chemistry, and biology, they come and go on their own rules and on their own times, as nature dictates. in sharp contrast, pandemics are biopolitical phenomena; they are moments of discontinuity or rupture in social order, shot through from start to finish with forces and factors that shape culture, history, and economy, which in turn determine what they mean and how they come about and come to pass. moreover, and importantly, a pandemic is not a single, monolithic event; it is a series of localized epidemics, each with its own point of origin, its own history, its own epidemiological pattern and impacts. further still, all these factors crisscross one another in a complex, nonlinear fashion, amassing multiple agents and stakeholders in such a critical fashion that the language of war is often used by the authority in charge to quell the infectious assault. pandemics force social changes precisely because the changes they incur invite resistance. it is for this reason, perhaps for this reason alone, that pandemics inevitably appear as a site of social contestations, politicizing and politicized by the heterogeneous constructions barely betrayed by the name of a single virus. it is for this reason too that pandemics assert themselves as a sign of generalized cultural and economic strife, a symptom of social struggle underlying the health terror that a viral breakout unfailingly induces. covid- is a novel virus, novel in that scientists do not fully understand how it afflicts the body and therefore cannot predict its epidemiological paths. to control its spread, we have no choice but to employ methods developed from past experiences, such as quarantine/isolation, social distancing, face coverings, and contact tracing, to name a few now well-known. because viruses are infectious, to control its spread is, understandably, to separate and to isolate. this means that people be kept away from one another. instead of gathering or being together, we make ourselves scare; better yet, we isolate ourselves, even if begrudgingly. more than that, the injunction of isolation leads straightaway to insulation in that the ultimate, foolproof means of isolation is to literally atomize ourselves, to turn ourselves into windowless monads. indeed, all the mitigation measures we hear about of late-quarantine, mask wearing, hand washing, and social distancing-are in reality anti-social measures. don't reach out and don't touch anyone! cover up your face! just as social distancing-a contradiction in terms of sorts-means keeping physical distance, and just as mask wearing reduces mutual recognition based on simple vision to its unnatural minimum, (self-)isolation and quarantine all but eliminate human contact of all kinds. when the plagues struck, we were all lepers; when covid- strikes, we are all windowless monads. pandemics are born of communicable diseases, yet for this reason, they force us to be incommunicable. flattening individuals and bringing to a halt exchange and commerce of every kind, they turn a society into one that is against society. if there is a history of pandemics, it is a history of anti-social history. neither alive nor dead, neither this nor that, viruses are by nature improper. never proper, that is, never being (of) themselves, they appropriate-always ready to make others their own. they are pure media, as suggested earlier. viruses are pure because they mediate unconditionally. however, inasmuch as unconditional mediation performed by viruses leads to the demise of their host, upon whom they depend for their parasitic reproduction, viruses end up annihilating themselves by their very nature; they are always already their own collateral casualties. rendering themselves nil by simply being and subsisting as themselves, pure media are no (longer) media. unconditional mediation ends all mediations. by bringing society to go against itself, viruses commit suicide, so to speak, by killing their host, by the unconditional abuse of others' hospitality. and, alas, weat least some of us-are spared. covid- is a new virus. but, unlike the known flu viruses, or h n , sars, and the like, covid- is considered "novel," not the least because, as indicated earlier, it frustrates scientists' understanding. "it has been like nothing else on earth," says an infectious-disease expert, who falls victim to the virus; "i knew i had the disease; it couldn't have been anything else," but "i don't understand what's happening in my body" (yong, ) . there are many things, inanimate or living, on earth that are like nothing we know so far, and there are many things happing in our body that we do not understand at all. covid- can justifiably be called "novel," but isn't every virus novel in its own way and at some moment in time? isn't being novel the normal course of event in life and in life sciences as well? "there is novelty here," remarks a prominent epidemiologist karl friston upon leaving a lab meeting about covid- , but he quickly adds, "so this, from my point of view, is just an average day" (kosner, ) . being novel is the very characteristic of all viruses and many other things in nature as well. the novelty of covid- may not be as novel as we think. what is possibly novel about covid- is the fact that it gives us the first pandemic in our truly globalized age. the global village, in which we now live, is so hyper-connected-not only by technology but also through affluence, commerce, and global travel-that an infectant can travel from one city to another as fast as jet streams flow. connectivity translates qualitative diversity into measurable multiplicity, reducing distance and difference for the formation of the common, which in turn strengthens connectivity. to be alive, as few would disagree, is to be connected, literally and in every other sense. but this means that we must live in and with the risks that global connectivity brings to us. to be connected brings with it the possibility of being stranded in harm's way. as covid- makes clear, "connectivity is the killer" (kosner, ) . after all, life depends on maintaining boundaries and keeping differences. deadly viruses are deadly because they breach them. as infection rate rises, so does anxiety. and bleak scenes spread as wide as the virus goes. deserted streets, boardedup stores, closed factories, shot-down public transportations; remote learning, work-from-home; stock markets crashed . . . and, worse yet, "i just lost my job." individual solation leads quickly to desolation across the board. and economy bears the brunt of a colossal coronal attack. shortly after covid- spread out of wuhan, china, to europe in january , stories about the economic plight began to top the list of topics in public forums and news media. the future we face seems to lie in one of the two choices: to die from hunger or to die from the disease (餓死 或病死), as the expressions go in chinese media. it is not for no reason that a policy brief released in june by the united nations on the impact of the pandemic is given the title "the world of work cannot and should not look the same after this crisis" (guterres, ) . the address on the launch of this brief, given by the secretary-general antónio guterres ( ) , begins as follows: the covid- pandemic has turned the world of work upside down. every worker, every business and every corner of the globe has been affected. hundreds of millions of jobs have been lost . . . many small and medium-sized enterprises-the engine of the global economy-may not survive. after painting a depressing picture of the future and explaining how difficult it will be for the world economy to return to "normal," guterres's ( ) address makes a hardly perceptible turn when he says "let's not forgot the pre-covid- world was far from normal." it seems then that, rather than shattering the world of work as we know it, the covid- pandemic simply exposes in higher resolution the "tremendous shortcomings, fragilities and fault lines" that have been eroding society and economy from the bottom-up for decades. the pre-covid- world, in which we thought we lived a normal life, is not as normal as we think (see guterres, ) . to save the economy under siege is to "return to normal" as soon as possible, so cry the bureaucrats and journalists alike. but what is "normal" in this case? what does "being normal" mean exactly? is the world, old or new, ever normal? there are norms regulating life, but has there ever been a "normal life" as such? the so-called normal life, a life before covid- , to which we pray to return, is in truth one of recollection, a romantic one at that, as the un policy brief readily admits. just as a viral infection may display more than one symptom on the part of its victims, embody more than one single illness, and create more than one single public health challenge, life, as it is actually lived, is hardly reducible to one normal life. in fact, the socalled normal life is the one that brought us the pandemic in the first place. to live is to live normally; to return to normal is what living is all about. the so-called new normal is both new and not so new, which is to say, it is neither really new nor really normal. perhaps the world has never been and will never be normal, whatever our idea of "being normal" means. if a pandemic can turn the world upside down, it is because life has been turning and turning again. and anything that returns cannot be entirely new. humans have been haunted by viruses since time immemorial. from the prehistoric pandemics in northeastern china , years ago, uncovered at sites now called hamin mangha and miaozigou, to the justinian plague ( - ad) that may have helped to bring down feudalism, or the small pox outbreak that finally toppled the aztec empire before hernán cortés returned to the region in the spring of , viral infections have tormented the lands and their people over millennia. traveling with host animals and humans, viruses had gone global long before globalization became a fact. there are known pandemics in the last years, all displaying the same pattern of spiking in seasonal waves after the initial attacks. covid- , and some of its coronal cousins, will undoubtedly expand the list. to those who are living through its assault, the impacts brought about by covid- are more or less clear and more or less measurable. but what is the meaning of covid- when the current pandemic is over? will it be remembered? if so, in what way and to what extent? if the history of pandemics has taught us anything, it is that history tends to repeat itself, that viral outbreaks are an ineliminable part of the natural history, in which humans are a part and in which no "zone of being" is free from viral infection. recall the spanish flu of , the worst pandemic during the last two centuries. it is estimated to have wiped out million people worldwide, meanwhile infecting million, a third of the world's population at the time. however, despite its short distance of mere one hundred years from us, few people today know much about it, and still fewer are able to understand or feel the impact it had at that time. its centenary a short time ago passed noiselessly, certainly not for lack of stories or records. like the many plagues before it, the spanish flu, it seems, never quite made itself into what reinhart koselleck ( ) calls the "the space of experience" (p. ). failing to make its way into collective memory, it is also helpless in figuring into our "horizon of expectation" (koselleck, , p. ) . if the spanish flu faded largely from memory, all the woes caused by covid- are, likewise, likely to dissipate in time, regardless of how we feel and say about it now. there was a pre-coronavirus world, and there will be a post-coronavirus world, but viruses, known or novel, will outlast our worlds. viruses are everywhere and forever. so, plagues will never disappear for good (camus, , p. ) . but what then does it mean, the pandemic? it is life, that is all. a troubled memory, fading, under the vast indifference of the sky. until the gate of oran closes again. assembled in this forum, the five short essays provide some modest reflections on the coronavirus pandemic and its still unfolding consequences. committed to a variety of disciplinary perspectives and interests, the authors did not set out by pursuing any preset direction or common agenda supposedly carried out collectively in our intellectual labor. rather, what unifies the diverse inquiries in these essays is the shared awareness about the confusion in the public discourse that constantly fails to distinguish a coronavirus called covid- from the covid- pandemic, or as briankle reminds us in his essay, from "a series of localized epidemics." this alertness constitutes a common ground in addressing specific issues or phenomena in these essays. this forum is anything but comprehensive. if it can contribute to the discussion of the crisis, it is most likely because all the essays refuse to bind the pandemic exclusively with the coronavirus and to position the virus and humanity in rigid opposition to each other. in her multispecies ethnography, anna tsing tells a marvelous story about matsutake mushrooms. "when hiroshima was destroyed by an atomic bomb in ," says she, "it is said, the first living thing to emerge from the blasted landscape was a matsutake mushroom" (tsing, , p. ) . when human history temporarily comes to a halt in disasters, matsutake, and also viruses in our case, may well survive and continue to thrive with their own stories. histories are being made every day by humans and non-humans alike; however, the future for those histories to converge has still yet to come. as demonstrated in the essays gathered here, while governments and the public are desperate to frame the virus in their own social and political narratives, the virus also works hard to inscribe its historicity on the earth and humans too. if a message must be dispatched out to all at this juncture, it is that for a future of collaborative survival, the stake of living together has nothing to do with harmony and conquest, but is derived from "disturbance-based ecologies" (tsing, , p. ) , that is, plagues. plagues are life, that is all. the author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. the author(s) received no financial support for the research, authorship, and/or publication of this article. gong yuan https://orcid.org/ - - - xuefeng feng https://orcid.org/ - - - x notes . in a trilogy of contemporary essays, baudrillard ( ) argued that the war in the desert was a new phenomenon, because it was defined and shaped by its discursive aspect as a form of television programming, regardless of what happened on the ground. . that earlier announcement called "demonetisation" led to a vast contraction of commerce and an immiseration of a majority of the population which has still not recovered, and is now widely considered an unnecessary exercise of personal whimsy. for an analysis of the economic consequences, see ghosh et al. ( ) . . the decline of indian agriculture is not adequately discussed in the celebration of urban growth. its effects are however inescapable and directly lead to the growth of informal settlements in cities (balakrishnan, ; jaffrelot & thakker, ) . . mediatization, or the analysis of events with their mediated construction as the starting point, is a phenomenon that has grown in importance across cultural contexts, as media theorists attempt to understand the increasing influence of media forms on culture, especially with the virtualization of human interaction and the redefinition of community through the use of social media and mobile communication. for a fuller discussion, see couldry and hepp ( ) . discontents: an indian history ( ), jayal ( ) traces the current shift in the discourse of indian citizenship from an egalitarian rights-based model to a new regime predicated on religious and cultural identity, given shape through the concomitant technocratic frames of transactional welfare and biometric identity. . four short essays provide further context and narrate the response: shankar et al. ( ) . . partha chatterjee's ( chatterjee's ( , insightful categorization of indian society separates the distinct ontological domain of a small formal "civil society" that includes rights-bearing citizens, from the vast undifferentiated mass of the population that constitutes "political society" and which forms the actual locus of democratic practice. . the current indian government has dramatically increased the acquisition and use of big data in governance, including a reliance on biometric identification for access to welfare programs and the use of mobile phones for access to services: part of the government's covid- response was in the form of a mandatory mobile application that purported to use location tracking to show active virus infections in the user's vicinity. an analysis of its invasive nature can be found in a working paper by deb ( ). . societies always declared war on problems they cannot solve: war on drugs, war on poverty, and the like. it is no surprise to see donald trump refers to covid- as an "invisible enemy" and calls himself a war-time president in his speeches on the covid- pandemic. similar examples abound across the board throughout history. it is widely recognized by epidemiologists today that the model developed by john snow based on the cholera outbreaks between and in england is too linear to be of any use in contemporary pandemics. like the global climate instability or financial market volatility, pandemics are nonlinear phenomena, displaying a high degree of uncertainty that defies simple causal explanation. on this, see kosner ( ) . . it is therefore not surprising that we observe donald trump repeatedly refers to covid- as wuhan virus or kung flu in reaction to his rise and fall in poll and public opinion as he tries to find scapegoat, in this case, china, for his sorry failure in handling the crisis. a virus is always more than a virus when it enters the body politic. india's brutally uneven development patterns are mapped in routes migrant workers are taking home. scroll the gulf war did not take place bifo covid- : straight answers from top epidemiologist who predicted the pandemic the plague. vintage diseasescape: coping with coronavirus, mobility, and politics. global-e the politics of the governed: reflections on popular politics in most of the world lineages of political society: studies in postcolonial democracy cdc director says some coronavirus-related deaths have been found posthumously conceptualizing mediatization: contexts, traditions, arguments the covid- crisis in india: a nascent humanitarian tragedy. books & ideas public policy imperatives for contact tracing in india specters of marx: the state of the debt, the work of mourning and the new international coronavirus conspiracy theories targeting muslims spread in india. the guardian why coronavirus conspiracy theories flourish, and why it matters. the new york times the standard edition of the complete psychological works of sigmund freud as coronavirus spreads, so does racism and xenophobia covid- lockdown and the pandemic of caste demonetisation decoded: a critique of india's currency experiment chinese-japanese-s. korean relations evolve to meet the challenge of covid- . global times the world of work cannot and should not look the same after this crisis the companion species manifesto staying with the trouble: making kin in the chthulucene american hegemony and east asian order by revealing magnitude of migrant worker phenomenon, covid- points to rural distress. the indian express reconfiguring citizenship in contemporary india the coronavirus isn't alive. that's why it's so hard to kill sediments of time: on possible histories karl friston takes on the pandemic with the brain's arsenal high on talk, low on substance: modi's speech showed india is ill-prepared for covid. the caravan soulstealers: the chinese sorcery scare of the pasteurization of france we have never been modern agency at the time of the anthropocene migrant workers distrust a state that does not take them into account it was already dangerous to be muslim in india. then came the coronavirus india racked by greatest exodus since partition due to coronavirus. the guardian india: portents of an ending: modi, the rss and the rise of the hindu far right. the nation how covid- compares against other killer diseases in india why east beat west on covid- : east asia has handled and contained the pandemic far better than the west on nearly all metrics shame in the cybernetic fold: reading silvan tomkins the natural contract the demagogue and his labyrinth. the baffler coronavirus: the mystery of asymptomatic "silent spreaders posthumanism: anthropological insights mattering compositions labyrinth of linkages: cinema, anthropology, and the essayistic impulse coronavirus crisis threatens to split an already fractured eu the mushroom at the end of the world: on the possibility of life in capitalist ruins donald trump's "chinese virus south korea agree to continue push for free-trade deal despite ongoing tensions across region. south china morning post buddhist pilgrim-monks as agents of cultural and artistic transmission: the international buddhist art style in east asia, ca covid- can last several months the popularity of "rivers low, mountains high; the same moon in the sky" and its english translation the hindu rashtra comes of age. contending modernities li lu is an associate professor of literary theory at the school of chinese language and literature and a research associate at the center for literary theory at beijing normal university. he teaches courses on marxian aesthetics, critical theory, and translation theories.srinivas lankala teaches in the department of communication at the english and foreign languages university, hyderabad. he works in the areas of semiotics and critical theory, and engages with questions of politics, history, and nationalism. key: cord- -xj md authors: li, lian yong; wu, wei; chen, sheng; gu, jian wen; li, xin lou; song, hai jing; du, feng; wang, gang; zhong, chang qing; wang, xiao ying; chen, yan; shah, rushikesh; yang, he ming; cai, qiang title: digestive system involvement of novel coronavirus infection: prevention and control infection from a gastroenterology perspective date: - - journal: j dig dis doi: . / - . sha: doc_id: cord_uid: xj md an epidemic of an acute respiratory syndrome caused by severe acute respiratory syndrome coronavirus (sars‐cov‐ ) in wuhan, china, now known as coronavirus disease (covid‐ ), beginning in december , has attracted an intense amount of attention worldwide. as the natural history and variety of clinical presentations of this disease unfolds, extrapulmonary symptoms of covid‐ have emerged, especially in the digestive system. while the respiratory mode of transmission is well known and is probably the principal mode of transmission of this disease, a possibility of the fecal‐oral route of transmission has also emerged in various case series and clinical scenarios. in this review article, we summarize four different aspects in published studies to date: (a) gastrointestinal manifestations of covid‐ ; (b) microbiological and virological investigations; (c) the role of fecal‐oral transmission; and (d) prevention and control of sars‐cov‐ infection in the digestive endoscopy room. a timely understanding of the relationship between the disease and the digestive system and implementing effective preventive measures are of great importance for a favorable outcome of the disease and can help climnicians to mitigate further transmission by taking appropriate measures. currently, available data show that gastrointestinal involvement in covid- is relatively infrequent compared with mers and sars. among the patients enrolled in the case series reported, had diarrhea (average . %, range %- . %), and had nausea or vomiting symptoms (average . %, range %- %) ( table ) . , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] a recent study found that almost half of patients with covid- showed liver involvement to some degree, with variable degrees of elevated alanine aminotransferase and aspartate aminotransferase. although the exact cause remains obscure, it may be related to direct liver damage caused by covid- or antiviral drugs. the involvement of the digestive system in covid- may be underestimated as most patients initially develop respiratory symptoms. gastrointestinal symptoms were not recognized or were neglected at the early stage of this epidemic outbreak until the first case was reported in the usa, when coronavirus rna was identified in the patient's stool sample. moreover, it is necessary to find ways to prevent transmission through the sewage system. gastrointestinal manifestation in patients with severe acute respiratory syndrome coronavirus (sars-cov- ) infection above, by adopting single-cell rna-sequencing technology from two cohort samples, a recent study has shown that ace is highly expressed in cholangiocytes rather than the hepatocytes or other interstitial cells. therefore, during the diagnosis and treatment of patients with sars-cov- , clinicians should pay special attention to their liver function. however, another study pointed out that ace also participated in the prevention of inflammation of the intestine by regulating innate immunity, cellular cytotoxicity, and energy metabolism ( figure ). nevertheless, it is necessary for clinicians to note that the digestive system may be invaded by sars-cov- and evolve into an alternative source of infection. although there been no solid evidence to confirm that sars-cov- can be transmitted through the fecal-oral route, this possibility exists as the virus has been successfully isolated in a stool or anal swab of patients with covid- , which is almost as accurate as a pharyngeal swab. , moreover, sars-cov- was also detected in the stool sample of patients in rehabilitation, which stays positive longer than in the swab. table and figure . sars-cov- is a serious threat to human health worldwide due to its strong ability for human-to-human transmission. in the early days of the disease outbreak, medical staff focused on screening for respiratory symptoms. however, as the disease progresses and understanding unfolds, digestive symptoms related to covid- have also been identified. a literature review has shown that the sars-cov- and the sars that broke out in belong to the same β-coronavirus family and possess highly similar genomes. in addition, the receptors for both sars and sars-cov- is ace . therefore, it is not difficult to understand why sars-cov- may give rise to digestive system symptoms similar to those induced by sars-cov. a recent case series in china has confirmed that sars-cov- nucleic acid which is negative in throat swabs can still be detected in the feces of three covid- patients, two of whom manifested diarrhea before treatment. nevertheless, as it remains unknown whether the virus in the digestive system is derived from cellular fragments from the respiratory system or consists of replicates in the digestive tract, it is sensible to take early steps to prevent fecal-oral transmission both in the hospital and in the community. additional clinical case reports and laboratory studies are needed to confirm the existence of this transmission route. more importantly, efforts should be made to formulate the clinical protocols and develop antiviral drugs targeting the digestive system in the future. all authors have no conflicts of interest or financial ties to disclose. none. lian yong li https://orcid.org/ - - - clinical characteristics of covid- patients with digestive symptoms in hubei, china: a descriptive, crosssectional, multicenter study enteric involvement of severe acute respiratory syndrome-associated coronavirus infection severe acute respiratory syndrome vs. the middle east respiratory syndrome clinical features of patients infected with novel coronavirus in wuhan a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study epidemiologic and clinical characteristics of novel coronavirus infections involving patients outside wuhan, china washington state -ncov case investigation team. first case of novel coronavirus in the united states the first case of novel coronavirus pneumonia imported into korea from wuhan, china: implication for infection prevention and control measures importation and human-tohuman transmission of a novel coronavirus in vietnam clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical characteristics of novel coronavirus infection in china [epub ahead of print structure analysis of the receptor binding of -ncov the digestive system is a potential route of -ncov infection: a bioinformatics analysis based on single-cell transcriptomes / . . . v .full.pdf profiling ace expression in colon tissue of healthy adults and colorectal cancer patients by single-cell transcriptome analysis ace expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism specific ace expression in cholangiocytes may cause liver damage after -ncov infection fecal specimen diagnosis novel coronavirus-infected pneumonia novel coronavirus infection and gastrointestinal tract persistence and clearance of viral rna in novel coronavirus disease rehabilitation patients clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study prevention and control program on novel coronavirus infection in children's digestive endoscopy center peking union medical college hospital. diagnosis and clinical management of novel coronavirus infection: an operational recommendation of peking union medical college hospital (v . ) genome composition and divergence of the novel coronavirus ( -ncov) originating in china potent neutralization of novel coronavirus by recombinant ace -ig three cases of novel coronavirus pneumonia with viral nucleic acids still positive in stool after throat swab detection turned negative digestive system involvement of novel coronavirus infection: prevention and control infection from a gastroenterology perspective key: cord- -mivxm oh authors: groneberg, david a; poutanen, susan m; low, donald e; lode, hartmut; welte, tobias; zabel, peter title: treatment and vaccines for severe acute respiratory syndrome date: - - journal: lancet infect dis doi: . /s - ( ) - sha: doc_id: cord_uid: mivxm oh the causative agent of severe acute respiratory syndrome (sars), which affected over individuals worldwide and was responsible for over deaths in the – outbreak, is a coronavirus that was unknown before the outbreak. although many different treatments were used during the outbreak, none were implemented in a controlled fashion. thus, the optimal treatment for sars is unknown. since the outbreak, much work has been done testing new agents against sars using in-vitro methods and animal models. in addition, global research efforts have focused on the development of vaccines against sars. efforts should be made to evaluate the most promising treatments and vaccines in controlled clinical trials, should another sars outbreak occur. severe acute respiratory syndrome (sars) is an infectious disease characterised by substantial morbidity and mortality, first recognised after an outbreak in - . , the who issued a global alert on sars on march , after receiving reports from china's guangdong province, hong kong, and vietnam regarding clusters of respiratory illness of unknown aetiology. one of the first reports was made by who scientist carlo urbani, who was called to investigate cases of pneumonia of unclear aetiology in a hospital in hanoi; he later died of sars. following the who alert, probable sars cases were also reported from other regions in china, and other asian countries including singapore, taiwan, indonesia, thailand, and the philippines. other countries, including canada, the usa, and germany also identified cases. in retrospect, sars originated in guangdong at the end of . it first spread to other regions in asia and then international travel facilitated its spread to other continents. a cumulative total of probable cases of sars were recorded during the period from november , to july , , with deaths in countries. soon after sars was identified as a new disease, the who initiated a collaborative global network striving to work together to identify the aetiological agent of sars. in unprecedented time, a novel coronavirus-sars coronavirus-was identified as the probable causative agent of sars - (figure ) and koch's principles were demonstrated to be fulfilled by this agent. , this virus belongs to the coronavirus family-enveloped, positive-sense rna viruses associated with respiratory disease in human beings and animals. , evidence suggests that sars coronavirus originated from sars-like viruses in animals in the southern chinese province of guangdong; the most frequently implicated animal is the himalayan palm civet, an animal found in food markets and eaten as a delicacy. , sars coronavirus is organised into - open reading frames (orfs) containing approximately nucleotides. , , in total, sars-coronavirus sequences derived from different sars epidemic phases have been analysed and genotypes characteristic of each phase have been identified. , the different sars-coronavirus orfs represent typical viral genes such as protease and replicase, spike, envelope, membrane, and nucleocapsid, all of which may represent potential therapeutic targets (figure ). in common with all infections caused by coronaviruses, after infection sars coronavirus induces the synthesis of Ј coterminal sets of subgenomic mrnas in target the causative agent of severe acute respiratory syndrome (sars), which affected over individuals worldwide and was responsible for over deaths in the - outbreak, is a coronavirus that was unknown before the outbreak. although many different treatments were used during the outbreak, none were implemented in a controlled fashion. thus, the optimal treatment for sars is unknown. since the outbreak, much work has been done testing new agents against sars using in-vitro methods and animal models. in addition, global research efforts have focused on the development of vaccines against sars. efforts should be made to evaluate the most promising treatments and vaccines in controlled clinical trials, should another sars outbreak occur. cells. in laboratory settings, sars coronavirus is able to infect macaque monkeys, mice, ferrets, and domestic cats. clinically, sars is characterised by systemic symptoms such as fever and myalgia, followed by respiratory symptoms including a non-productive cough and dyspnea. laboratory findings include lymphopenia, and chest radiographs commonly exhibit unilateral or bilateral infiltrates. approximately % of cases deteriorate, requiring intubation and mechanical ventilation. the overall mortality rate has been reported to be about %. however, sars mortality rates in those over years old have been reported to be as high as %. affected children seemed to have milder symptoms with no reports of death. at the time of the - outbreak, physicians shared their personal experiences supporting or rejecting various treatments for sars. because of the rapid progression of the outbreak, multicentre, randomised, controlled interventional trials were not possible, and the success of various treatments remains largely anecdotal. thus, a consensus on therapeutic strategies has not yet been reached. since the outbreak, global research efforts have focused on testing new agents against sars with in-vitro methods and animal models. in addition, much effort has been placed on developing effective vaccines against sars. this review summarises the clinical experience of the use of various treatments during the outbreak and provides an overview of the data, both in vitro and in vivo, supporting, or otherwise, the effectiveness of these treatments and those that have been proposed since the outbreak. in addition, we summarise the progress made to date regarding sars vaccines. a summary of the pharmacological agents that have been used or proposed for the treatment of sars is shown in figure . during the - outbreak, suspected sars cases were usually treated initially with broad-spectrum antibacterial drugs effective against typical bacterial causes of acute community-acquired pneumonia. the administration of broad-spectrum antibiotics-eg, respiratory fluoroquinolones, second-generation cephalosporins, or third-generation cephalosporins-plus a macrolide is recommended at the first signs of the sars, because the initial features of the disease are nonspecific. however, after sars coronavirus is identified as the causative agent, antibiotics may be withdrawn, because there is no evidence that antibiotics are clinically beneficial in the treatment of sars. even before the causative agent of sars was discovered, treatment with ribavirin was used empirically to treat patients with sars. ribavirin is a synthetic nucleoside with broad-spectrum antiviral activity. clinical studies that have assessed the effectiveness of ribavirin in sars range from anecdotal case reports and retrospective case series to one randomised clinical trial with multiple treatment arms. however, none of these studies definitively determine whether or not ribavirin is effective against sars. case reports and case series suggest that combined treatments including ribavirin may be beneficial to some extent; however, in all of these studies, the effect of ribavirin is confounded by the concomitant use of other agents. for example, studies describe clinical and radiological improvements in patients treated with ribavirin and steroids, , but, without a control group, it is difficult to determine whether the improvements result from ribavirin, steroids, the combination of both, or the natural course of the illness. one study showed that the delayed initiation of combined therapy with ribavirin and steroids was among the risk factors associated with severe complicated disease, suggesting that ribavirin might be beneficial, but it is difficult to delineate the role of delaying the use of ribavirin from the delay in the use of steroids. the results of a randomised clinical study in guangdong, involving multiple different treatment arms, suggest that ribavirin given at a low dose ( - mg/day) was less effective compared with an early and aggressive use of steroids with interferon alfa. however, the lack of a control arm in this study does not allow for one to make definitive conclusions about whether or not ribavirin has any positive effect on sars compared with no treatment. invitro testing showed that ribavirin was not able to inhibit sars-coronavirus replication at clinically achievable concentrations. , this finding, combined with postmortem findings demonstrating high viral loads in most patients despite treatment with ribavirin, suggests that if ribavirin has any effect against sars coronavirus, it is likely to have only a small beneficial effect at best. this is important when the side-effects that have been associated with ribavirin use are considered. knowles and co-workers reported common adverse events in people with suspected or probable sars who were treated with ribavirin. % of these people had evidence of haemolytic anaemia; hypocalcaemia and hypomagnesaemia were reported in % and % of the people, respectively. the combination of the protease inhibitors lopinavir and ritonavir was used less frequently during the sars outbreak compared with ribavirin. the lopinavir/ ritonavir combination was first considered a potentially useful treatment after in-vitro studies showed it had antiviral activity against sars coronavirus. , chan and colleagues compared outcomes in people who received lopinavir/ritonavir as initial treatment, and as rescue therapy, with matched controls; all patients were given ribavirin and steroids according to a standardised protocol. the addition of lopinavir/ritonavir as initial treatment was associated with a statistically significant reduction in the overall death rate and intubation rate compared with matched controls (pϽ · ). however, the subgroup that received lopinavir/ritonavir as rescue therapy did not show a significant difference in these endpoints. chu and co-workers also assessed treatment with lopinavir/ritonavir compared with historic controls; all patients were also treated with ribavirin and steroids in a similar protocol to that of chan and collegues. adverse events (development of acute respiratory distress syndrome [ards] or death within days) were significantly lower in the lopinavir/ritonavir group than in the historic controls (pϽ · ). in addition, a significant reduction in the need for rescue pulsed steroids for severe respiratory deterioration (pϽ · ) and significantly lower nosocomial infections were also noted in those treated with lopinavir/ritonavir, compared with controls (pϽ · ). by multivariate analysis, it was demonstrated that the lack of treatment with lopinavir/ritonavir, age years old or greater, and positive hepatitis b carrier status were independent predictors of an adverse outcome including death or the development of ards requiring intensive care within days of onset of illness. based on these studies, lopinavir/ritonavir appears to be a promising anti-sarscoronavirus agent. other protease inhibitors have been studied in vitro for potential antiviral effects in sars. for example, yamamoto and colleagues screened a set of compounds that included antiviral drugs already widely used, and found that nelfinavir strongly inhibited sarscoronavirus replication. nelfinavir inhibited the cytopathic effect induced by sars-coronavirus infection, and the expression of viral antigens was much lower in infected cells treated with nelfinavir than in untreated, infected cells. in addition, barnard and colleagues found that two protease inhibitors-calpain inhibitor vi (val-leu-cho) and calpain inhibitor iii (z-val-phe-ala-cho)-inhibited sars coronavirus, suggesting that other protease inhibitors may also be useful in the treatment of sars. the membrane-associated carboxypeptidase angiotensinconverting enzyme (ace ), is a cellular receptor for sars coronavirus, interacting with the s domain of the spike protein. thus, peptides and small compounds that bind to ace , are possible agents for the treatment and prevention of sars. in addition, a soluble form of the receptor, antibodies to it, or the receptorbinding domain of the spike protein, may be candidate treatments. indeed, sui and co-workers searched a nonimmune human antibody library and successfully identified an anti-s human monoclonal antibody, r, that potently neutralises sars-coronavirus infection and efficiently inhibits syncytium formation by blocking binding to ace . r was shown to compete with soluble ace for association with the s domain of the spike protein and bound to it with high affinity. theoretical reasoning and in-vitro evidence suggest that fusion inhibitors are promising treatment candidates for sars. , peptides derived from the heptad repeat regions and of hiv- gp -a transmembrane protein involved in the fusion of hiv and target cellsare the basis for anti-hiv fusion inhibitors. based on similarities between the heptad repeat regions of gp in hiv- and the heptad regions in the spike protein of sars coronavirus, a common mechanism mediating fusion between each virus and target-cell membranes was postulated. , liu and colleagues tested two sets of peptides corresponding to the heptad regions in the spike protein for inhibitory activity against sars coronavirus, and found that one peptide-cp inhibited sars-coronavirus infection in vitro. it has been postulated that cp binds to heptad region of the spike protein and interferes with the conformational changes needed to allow fusion with target cells. rna interference (rnai) treatment is a process by which small interfering rnas (sirna) are administered, leading to degradation of mrna with identical sequence specificity. this technology has been used to silence genes in cultured cells and in animals, and to target hiv, hepatitis b, and hepatitis c viral infections. [ ] [ ] [ ] to explore the possibility of interrupting sars-coronavirus replication with sirnas, specific sirnas targeting the spike gene in sars coronavirus were synthesised. these sirnas effectively and specifically inhibited gene expression of the spike protein in sars-coronavirusinfected cells. another study assessed the in-vitro efficiacy of six sirna molecules targeting different sites of the replicase a region of the sars-coronavirus genome. judged by morphological changes, three of the molecules markedly inhibited the cytopathic effects caused by viral infection and replication. the three sirnas also inhibited the infection and replication of different strains of sars coronavirus, indicating that sirnas targeting the replicase a region may be an option for future clinical use. in-vitro studies have shown that glycyrrhizin, a component of liquorice roots, is able to inhibit sarscoronavirus replication. glycyrrhizin inhibits hiv replication in vitro and has been used clinically in the treatment of hepatitis c and hepatitis b with some success. the mechanism of glycyrrhizin-induced inhibition of viral replication-and specifically sarscoronavirus replication-is unclear, but possibly involves inhibition of replication through an antiviral effect of nitric oxide (no). glycyrrhizin upregulates expression of inducible no synthase and production of no in mouse macrophages. in addition, preliminary results by cinatl and colleagues show that glycyrrhizin induces no synthase in vero cells used to cultivate sars coronavirus. cinatl and colleagues showed that sars-coronavirus replication is inhibited when deta nonoate-a no donor compound-is added to the culture medium. this finding has been further corroborated by keyaerts and co-workers using a different no donor compound, s-nitroso-n-acetyl-penicillamine. keyaerts and colleagues also report their findings on the use of inhaled no gas to treat a number of people with sars. their results suggest an associated immediate improvement in oxygenation and a lasting effect after termination of inhalation of no, which is known to be a potent mediator of airway inflammation. , niclosamide wu and colleagues screened a set of marketed drugs that were not registered for antiviral use to determine if any had in-vitro activity against sars coronavirus. they found that niclosamide, an existing antihelmintic drug, was able to inhibit replication of sars coronavirus. the underlying mechanism by which the drug exerts this effect is unclear, but the study shows that niclosamide does not interfere with the virion's attachment to, or entry into, cells, nor does it appear to inhibit the protease activity. new compounds continue to be tested, with the goal of finding more potential candidate treatments for sars. for example, from over agents tested, wu and colleagues found compounds with potent anti-sars-coronavirus activity. more compounds are likely to be discovered in the future. during the - sars outbreak, systemic steroids became a mainstay of sars therapy in many centres. the rationale for their use was based on the paradoxical finding that, despite a fall in sars-coronavirus viral load and a rise in sars-specific igg typically seen during the rd week of illness, a clinical deterioration was observed in some people. in addition, pathological findings consistent with bronchiolitis obliterans organising pneumonia and ards led to the hypothesis that immune hyperactivity resulting from cytokine dysregulation may be a component of sars that could be reduced by steroid treatment. in most cases, steroids were administered as adjunctive therapy to ribavirin treatment. if the patient's review respiratory condition worsened clinically, pulsed, highdose steroids were added. however, most studies were confounded by the concomitant use of other agents, and none of the studies contained a control group. thus, whether or not steroids have a beneficial effect in the treatment of sars cannot be readily determined. in some studies, treatment regimens containing steroids seemed to be associated with chest radiographic improvements, fever defervescence, and improvement in oxygenation rates earlier than patients not treated with steroids. , , however, in a study by hsu and colleagues, adding steroids was not associated with clinical improvement, although the dose of steroids in this study was lower than in those where benefit was seen. ho and co-workers retrospectively compared the clinical and radiographic outcomes of people with probable sars who received ribavirin, of whom initially received pulsed, highdose steroids and of whom initially received lowdose steroids. pulsed, high-dose steroids were also given to any patient as rescue therapy in the presence of deteriorating respiratory status. the cumulative steroid dose, intensive care unit admission rate, need for mechanical ventilation, and mortality rates were similar in both groups after days. however, those people initially given pulsed steroids required less oxygen and had earlier radiographic improvement. in addition, they required substantially less rescue pulsed steroids. this study suggests that early initiation of pulsed steroids may have a role in the treatment of sars. however, definitive studies are needed and the potential benefits of steroids must be compared with the associated risks, such as the development of avascular necrosis, secondary sepsis, and fatal aspergillosis, some of which have been described in people with sars. , in beijing, hong and du evaluated people with sars who had received steroids and ribavirin, and who presented with largejoint pain, potentially caused by avascular necrosis, between march and may . both plain radiographs and magnetic resonance imaging examination were completed on the same day. people were identified with avascular necrosis. the mean time to diagnosis of avascular necrosis was days after the onset of sars, or days after steroid use. interferons type interferons have been shown to inhibit sarscoronavirus replication in in-vitro studies. , [ ] [ ] [ ] because of initial reports describing these in-vitro results, interferons were used clinically during the latter part of the outbreak. loutfy and colleagues described their clinical experience with interferon alfacon -a recombinant, non-naturally occurring type interferon containing common aminoacids from several natural interferon alfa subtypes-in people with probable sars treated in an open-label study in toronto. people with sars who received treatment with steroids alone were compared with nine people who received steroids plus interferon alfacon . the group treated with interferon alfacon had significantly improved oxygen saturation levels (p= · ) and a more rapid resolution of radiographic lesions. in addition, this group exhibited substantially less elevation in creatine kinase levels and a trend towards a more rapid normalisation of lactate dehydrogenase levels. however, this group also received higher doses of steroids, so it is difficult to determine whether or not the beneficial effects were due to the interferon alfacon . haagmans and co-workers investigated the prophylactic use of interferons in a macaque model. days before inoculation with sars coronavirus, macaques were given pegylated interferon alfa. substantially reduced viral replication, viral excretion, viral antigen expression by type pneumocytes, and pulmonary damage were noted in the treated macaques compared with untreated macaques. post-exposure treatment with pegylated interferon alfa yielded intermediate results. these results suggest that interferons have a role in the treatment of sars. because most patients develop antibodies against sars coronavirus and survive the disease, passive and active immunisation are viewed as possible effective means to prevent and/or treat sars. indeed, the development of various vaccines is one of the most important goals of ongoing sars research. one of the initial proposals to treat sars was to use sera from people convalescing from sars as passive immunotherapy. this passive immunisation was attempted with anecdotal success. since then, prior infection and passive transfer of murine neutralising antibodies have been shown to prevent replication of sars coronavirus in the respiratory tract in mice. technological advances enabling the development and purification of human monoclonal antibodies can be exploited to create specific monoclonal antibodies in large-scale production. indeed, monoclonal antibodies obtained from immortalised b lymphocytes isolated during convalescence from people with sars have been shown to neutralise virus infection in vitro and to prevent virus replication in a mouse model of sarscoronavirus infection. in addition, ter meulen and colleagues showed that prophylactic administration of a human igg monoclonal antibody reactive with whole inactivated sars coronavirus was able to reduce replication of sars coronavirus in the lungs of infected ferrets, completely prevent the development of sars-coronavirus-induced macroscopic lung pathology, and stop the shedding of virus in pharyngeal secretions. although passive immunisation strategies appear promising, the ideal approach to ensure rapid control of future outbreaks of sars is to generate an effective and safe vaccine. there are numerous teams worldwide working on the creation of vaccines using inactivated sars coronavirus, recombinant subunits, recombinant dna, and viral vectors. given the potential for antibody-directed viral enhancement and disease exacerbation, as reported for vaccines directed against another coronavirus (feline infectious peritonitis coronavirus), it is important that all vaccines created be carefully evaluated before being used clinically. of all of the vaccines in development, most work relates to viralvectored vaccines and dna vaccines. to date, three different viral-vectored vaccines have been described with successful results reported in animal models. [ ] [ ] [ ] gao and colleagues reported using three adenoviralbased vectors expressing codon-optimised sarscoronavirus spike, membrane, and nucleocapsid proteins. intramuscular vaccination with all three vaccines at day and day was shown to induce broad, virus-specific immunity in rhesus macaques. all six vaccinated macaques had antibody responses against the spike protein and t-cell responses against the nucleocapsid protein. in addition, all vaccinated animals showed strong neutralising-antibody responses to sars-coronavirus infection in vitro. challenge tests to determine whether or not this immune response was able to prevent, or reduce the severity of, infection with sars coronavirus were not completed. bisht and co-workers constructed recombinant forms of the highly attenuated modified vaccinia virus ankara (mva) containing the gene encoding the full-length sars-coronavirus spike protein and assessed whether expression of the spike protein alone in mva could raise neutralising antibodies and protectively immunise mice. both intranasal and intramuscular administration of the vaccine to balb/c mice at and weeks led to the production of serum antibodies against the spike protein that neutralised sars coronavirus in vitro. weeks after the second immunisation, vaccinated animals and control animals were challenged with sars coronavirus. those given the vaccine had reduced titres of sars coronavirus in the respiratory tract. likewise, the passive transfer of serum from mice immunised with the vaccine to naive mice led to a reduction in sars-coronavirus replication. these findings suggest that this mva-based vaccine is a promising sars-coronavirus vaccine candidate. bukreyev and colleagues reported their successful experience with the mucosal immunisation of african green monkeys with an attenuated parainfluenza virus expressing the sars-coronavirus spike protein. the complete sars-coronavirus spike protein gene was incorporated into a recombinant attenuated parainfluenza virus that is being developed as a live attenuated, intranasal paediatric vaccine against human parainfluenza virus type . four african green monkeys were vaccinated with a single dose of the vaccine, administered via the respiratory tract, and four other monkeys were vaccinated with a control. all monkeys were challenged with sars coronavirus days after immunisation. neutralising serum antibodies were noted in all of the vaccinated animals. after sarscoronavirus challenge, viral shedding was documented in all of the control animals but not in any of the vaccinated animals. the authors concluded that a vectored mucosal vaccine expressing the sarscoronavirus spike protein alone may be highly effective for the prevention of sars in a single-dose format. dna vaccines are also an attractive option for sars vaccines. thus far, three experimental studies have been published addressing dna vaccination in sars. [ ] [ ] [ ] yang and colleagues showed that giving mice a sars-coronavirus dna vaccine encoding the spike glycoprotein induced t-cell responses, neutralisingantibody responses, and protective immunity. alternative forms of the spike protein were assessed and all were found to induce substantial neutralisingantibody titres and strong immune responses mediated by cd and cd cells. in addition, a reduction in viral replication in the lungs by more than six orders of magnitude was noted after sars-coronavirus challenge; the protection was shown to be mediated by a humoral, but not a t-cell-dependent, immune mechanism. these findings show that dna vaccines based on the spike glycoprotein may lead to effective immune responses with protective immunity in animal models. kim and co-workers reported the generation and characterisation of dna vaccines targeting the nucleocapsid protein of sars coronavirus by antigen linkage to calreticulin, which has been shown to enhance mhc class i presentation to cd (+) t cells. with a murine model, it was shown that the vaccination with this dna vaccine leads to the generation of a more potent nucleocapsid-specific humoral and t-cellmediated immune responses, compared with nucleocapsid dna alone. in addition, mice vaccinated with the dna vaccine were capable of substantially reducing the titre of challenging vaccinia virus expressing sars-coronavirus nucleocapsid protein. in a similar study by zhu and colleagues, immunisation of mice with a nucleocapsid-based dna vaccine led to nucleocapsid-specific antibodies and specific cytotoxic t-cell activity. challenge tests were not completed. together, the data presented on potential vaccines reflect enormous international efforts. because a vaccine usually takes - years of clinical development after review entering phase i clinical trials before being licensed, it is not expected that any of these vaccines will be available for clinical use in the near future. however, given the pace and amount of progress to date, the period of time before clinical production of a sars vaccine may be substantially shortened compared with other vaccines. whether or not sars will re-emerge is a matter of debate. , however, in the event that sars does recur, the most promising-and immediately available-agents for the treatment of the syndrome seem to be type interferons, steroids, and lopinavir/ritonavir, based on the available data on agents already clinically approved. however, by the time another outbreak arrives, many of the other promising agents-eg, sars-coronavirusspecific receptor-binding inhibitors, fusion inhibitors, and sirnas-may have been approved for clinical use. the choice of agents will need to be determined based on the available data at that time. ideally, the most promising agents would be given in a controlled clinical trial. the difficulties in designing and implementing controlled clinical trials-which limited the ability of researchers to do such trials during the past sars outbreak, and which will continue to pose problems in the event of future outbreaks of sars or other novel pathogens-have been summarised. [ ] [ ] [ ] the best solution to facilitate the implementation of clinical trials in future outbreaks would be the establishment of an international collaborative clinical-trials group with access to appropriate contingency funds, and an internationally accepted ethics review board. until then, research based on in-vitro studies and in-vivo animal models should be continued to determine the best agent, or combination of agents, worthy of further clinical consideration. we declare that we have no conflicts of interest. data for this review were identified by searches of medline, current contents, and references from relevant articles; numerous articles were identified through searches of the extensive files of the authors. search terms were "severe acute respiratory syndrome", "sars", "treatment", "coronavirus", "infection", "sars coronavirus", "vaccination", and "antiviral". english language papers were reviewed. severe acute respiratory syndrome: global initiatives for disease diagnosis the aetiology, origins, and diagnosis of severe acute respiratory syndrome summary of probable sars cases with onset of illness from world health organization multicentre collaborative network for severe acute respiratory syndrome diagnosis. a multicentre collaboration to investigate the cause of severe acute respiratory syndrome coronavirus as a possible cause of severe acute respiratory syndrome identification of a novel coronavirus in patients with severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome morphology and morphogenesis of severe acute respiratory syndrome (sars)-associated virus newly discovered coronavirus as the primary cause of severe acute respiratory syndrome koch's postulates fulfilled for sars virus nidovirales: a new order comprising coronaviridae and arteriviridae the structure and replication of coronaviruses the biology and pathogenesis of coronaviruses isolation and characterization of viruses related to the sars coronavirus from animals in southern china wild animals could be source of sars the genome sequence of the sars-associated coronavirus characterization of a novel coronavirus associated with severe acute respiratory syndrome molecular evolution of the sars coronavirus during the course of the sars epidemic in china epidemiological and genetic analysis of severe acute respiratory syndrome the molecular biology of coronaviruses mice susceptible to sars coronavirus virology: sars virus infection of cats and ferrets severe acute respiratory syndrome: clinical outcome and prognostic correlates epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in hong kong children hospitalized with severe acute respiratory syndrome-related illness in toronto antiviral treatment of sars: can we draw any conclusions? the broad-spectrum antiviral ribonucleoside ribavirin is an rna virus mutagen a cluster of cases of severe acute respiratory syndrome in hong kong a major outbreak of severe acute respiratory syndrome in hong kong clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study description and clinical treatment of an early outbreak of severe acute respiratory syndrome (sars) in guangzhou, pr china severe acute respiratory syndromerelated coronavirus is inhibited by interferon-alpha glycyrrhizin, an active component of liquorice roots, and replication of sars-associated coronavirus severe acute respiratory syndrome-associated coronavirus in lung tissue common adverse events associated with the use of ribavirin for severe acute respiratory syndrome in canada role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study hiv protease inhibitor nelfinavir inhibits replication of sars-associated coronavirus inhibition of severe acute respiratory syndrome-associated coronavirus (sarscov) by calpain inhibitors and beta-d-n -hydroxycytidine angiotensin-converting enzyme is a functional receptor for the sars coronavirus novel peptide inhibitors of angiotensin-converting enzyme substrate-based design of the first class of angiotensin-converting enzyme-related carboxypeptidase (ace ) inhibitors potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s protein that blocks receptor association interaction between heptad repeat and regions in spike protein of sars-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors cloaked similarity between hiv- and sars-cov suggests an anti-sars strategy inhibiting severe acute respiratory syndrome-associated coronavirus by small interfering rna modulation of hiv- replication by rna interference interference of hepatitis c virus rna replication by short interfering rnas short interfering rna-directed inhibition of hepatitis b virus replication silencing sars-cov spike protein expression in cultured cells by rna interference inhibition of sars-associated coronavirus infection and replication by rna interference effect of glycyrrhizin, an active component of licorice roots, on hiv replication in cultures of peripheral blood mononuclear cells from hiv-seropositive patients long-term treatment of chronic hepatitis c with glycyrrhizin [stronger neo-minophagen c (snmc)] for preventing liver cirrhosis and hepatocellular carcinoma lamivudine and glycyrrhizin for treatment of chemotherapy-induced hepatitis b virus (hbv) hepatitis in a chronic hbv carrier with non-hodgkin lymphoma induction of inducible nitric oxide synthase and proinflammatory cytokines expression by o,pЈ-ddt in macrophages inhibition of sars-cov infection in vitro by s-nitroso-nacetylpenicillamine, a nitric oxide donor compound role of nitric oxide in allergic inflammation and bronchial hyperresponsiveness role of nitric oxide in chronic allergen-induced airway cell proliferation and inflammation inhibition of severe acute respiratory syndrome coronavirus replication by niclosamide small molecules targeting severe acute respiratory syndrome human coronavirus pro/con clinical debate: steroids are a key component in the treatment of sars lung pathology of fatal severe acute respiratory syndrome clinical features and short-term outcomes of patients with sars in the greater toronto area severe acute respiratory syndrome (sars) in singapore: clinical features of index patient and initial contacts high-dose pulse versus nonpulse corticosteroid regimens in severe acute respiratory syndrome fatal aspergillosis in a patient with sars who was treated with corticosteroids sars: prognosis, outcome and sequelae avascular necrosis of bone in severe acute respiratory syndrome role of interferons in the treatment of severe acute respiratory syndrome inhibition of sars coronavirus infection in vitro with clinically approved antiviral drugs interferon-beta a and sars coronavirus replication interferon alfacon- plus corticosteroids in severe acute respiratory syndrome: a preliminary study pegylated interferon-alpha protects type pneumocytes against sars coronavirus infection in macaques how the sars vaccine effort can learn from hivspeeding towards the future, learning from the past treatment of severe acute respiratory syndrome with convalescent plasma prior infection and passive transfer of neutralizing antibody prevent replication of severe acute respiratory syndrome coronavirus in the respiratory tract of mice an efficient method to make human monoclonal antibodies from memory b cells: potent neutralization of sars coronavirus human monoclonal antibody as prophylaxis for sars coronavirus infection in ferrets caution urged on sars vaccines a review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination effects of a sars-associated coronavirus vaccine in monkeys mucosal immunisation of african green monkeys (cercopithecus aethiops) with an attenuated parainfluenza virus expressing the sars coronavirus spike protein for the prevention of sars severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice nucleic acid vaccines: an overview a dna vaccine induces sars coronavirus neutralization and protective immunity in mice generation and characterization of dna vaccines targeting the nucleocapsid protein of severe acute respiratory syndrome coronavirus induction of sars-nucleoproteinspecific immune response by use of dna vaccine sars-one year later seasonality of infectious diseases and severe acute respiratory syndrome-what we don't know can hurt us clinical trials and novel pathogens: lessons learned from sars preparing to prevent severe acute respiratory syndrome and other respiratory infections collateral damage: the unforeseen effects of emergency outbreak policies support from the deutsche atemwegsliga and the german research foundation (dfg gr / - ) to dag is gratefully acknowledged. key: cord- -bc hr fr authors: sirpilla, olivia; bauss, jacob; gupta, ruchir; underwood, adam; qutob, dinah; freeland, tom; bupp, caleb; carcillo, joseph; hartog, nicholas; rajasekaran, surender; prokop, jeremy w. title: sars-cov- -encoded proteome and human genetics: from interaction-based to ribosomal biology impact on disease and risk processes date: - - journal: j proteome res doi: . /acs.jproteome. c sha: doc_id: cord_uid: bc hr fr [image: see text] sars-cov- (covid- ) has infected millions of people worldwide, with lethality in hundreds of thousands. the rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. in this review, we address the insights gained for the sars-cov- proteome, which we have integrated into the viral integrated structural evolution dynamic database, a publicly available resource. integrating evolutionary, structural, and interaction data with human proteins, we present how the sars-cov- proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. the most noteworthy human genetic potential of sars-cov- is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. this inhibition has the potential to not only regulate about % of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. as we understand more of the dynamic and complex biological pathways that the proteome of sars-cov- utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. the sars-cov- (covid- ) pandemic has impacted every component of life, including research and medicine. in just a few months from the onset of infections to writing of this review, papers/objects have been published on sars-cov- ( figure ). this body of literature primarily focuses on infectious diseases, the respiratory system, public environmental occupational health, biochemistry molecular biology, virology, immunology, pharmacology, microbiology, and healthcare science services, to name a few fields ( figure a ). title extraction of these papers reveals mainly clinically connected terms ( figure b) . the extensive infectious disease and clinical base of this literature has yielded knowledge of viral entry, replication, immune response, and transmission. however, in a short window of time, biochemical and molecular biology insights into sars-cov- have yielded a smaller body of literature that continues to grow ( out of the items), taking more time for data generation than clinical descriptions. of these biochemistry/molecular biology items, are primary articles ( figure c ). title and abstract word extraction from these biochemistry/molecular biology items, followed by counting mentions of all human ( ) or sars-cov- proteins, shows a heavy focus on ace and spike (s) proteins ( figure d ). the virus primarily enters cells through the interaction of the sars-cov- surface glycoprotein, spike (s), interacting with the human encoded ace , similar to that of the sars virus. , from the abstract/title terms, we identified / usages of ace and / of spike. other human proteins with repeated mentions include tmprss ( titles/ abstract), ace ( / ), furin ( / ), dpp ( / ), and c ( / ). additional sars-cov- proteins with mentions include nsp (rna-directed rna polymerase, / ), nucleocapsid (n, / ), membrane (m, / ), envelope (e, / ), nsp ( clpro/mpro, / ), nsp ( / ), nsp ( ′-o-methyltransferase, / ), orf ( / ), nsp ( / ), nsp (guanine-n methyltransferase, / ), nsp (papain-like protease, / ), and nsp (uridylate-specific endoribonuclease, / ). only nsp and nsp for sars-cov- have no mentions within any of these titles or abstracts for biochemical linked papers on sars-cov- . overall this suggests a few papers specifically related to sars-cov- proteins have been published; however, a large body of literature exists for the original sars and other coronaviruses that can give interpretation of the diverse functions performed by the viral-coded proteins and how they interact with human biology. the advancement of knowledge of the sars-cov- proteome has been slower than clinical insights due to the need for experimental work that is slow and that is being hampered by social isolation. the base-pair single-stranded rna genome of sars-cov- (ncbi nc_ . ) has a base-pair ′ utr, multiple protein-coding segments, and a base-pair ′ utr. sars-cov- has a % genomic similarity with sars-cov, a known human pathogen, with both known to enter cells through the binding of human ace . , in addition to sars-cov and sars-cov- , five other coronaviruses are capable of human-to-human transmission and infection (hku , nl , oc , e, and mers-cov). hundreds of coronaviridae family member genomes have been sequenced in human and other vertebrate hosts, , and many structures have been solved for coronaviridae species proteins, allowing for systematic assessments of the knowledge base. our group implemented a sequence-to-structure-to-function analysis , to understand sars-cov- proteins, developing a robust understanding of protein conservation, structure, and molecular dynamics. the data generated for each protein was then developed into the viral integrated structural evolution dynamic database (vistedd), a publicly released database of multiple tools for the virus. the database can be accessed at https://prokoplab.com/vistedd/. these tools consist of educational resources for the proteins coded by sars-cov- (molecular videos, d protein model prints, amino acid details of conservation, and dynamics), the mapping of critical sites to each protein, and the insights into how sars-cov- interacts with human proteins. generating this database has given our team a diverse understanding of sars-cov- , particularly for host protein interactions of each of the viral proteins. multiple studies have begun building systemic insights for sars-cov- infections. multiple groups have performed systematic data assessment of ace expression and protein staining, suggesting the physiological cell types that can be targeted by the virus. they have shown expression in many tissues throughout humans, with expression within the lung found on the apical surface of polarized bronchial secretory epithelia cells. − once the virus enters the cells, it results in the alteration of broad biological pathways, including translation, splicing, protein homeostasis, and nucleic acid metabolism. epithelial organoid cultures exposed to the virus produce a robust change in rna expression patterns for cytokine and interferon intracellular immune responses that give rise to tissue signals. single cell profiling within the lungs of patients shows the intracellular cytokine/interferon response results in the recruitment of macrophages in severe cases and t-cells in moderate cases, with a high potential for therapeutic intervention. , over activation of the cytokine/interferon response is connected to poor outcomes within patients, correlating with macrophage activation syndrome. additional adverse outcomes for the activation of apoptosis within lymphocytes have been observed and may contribute to the noted lymphopenia. proteomics and metabolomics of patient sera show the same macrophage dysfunction, while also elucidating platelet and complement dysregulation with the identification of severity classifiers. − in totality, the physiological response to the virus is likely mediated by a combination of immune system activation and the direct human interaction partners, altering cellular processes. an understanding of these detailed biological interactions can shed light on potential therapeutic opportunities while building a fundamental knowledge of viral biology. to date, few studies have been performed that systematically look at mapping how the sars or coronavirus proteins physically interact with human proteins. structural level insights for coronavirus proteins are surprisingly deficient of human interaction partners. a few of these proteins have been targeted for interaction assessments, such as the nucleocapsid protein , (shown below). it has been speculated that the understanding of virus−host interactions represents a major untapped potential of viral inhibitors. a review highlights the literature of viral−host interactions for coronaviruses, focused on synergizing the knowledge of independent experiments for virus receptors, translation, membrane dynamics, immune regulation, cell cycle control, and replication. the more recent work by gordon et al. covering the systematic affinity purification of different sars-cov- proteins within human cells has elucidated many mechanisms and drug compounds for the regulation of viral processes. bringing this data together with our vistedd tools, we provide a current snapshot of sars-cov- viral proteins ( figure ). orf ab is a large protein that is proteolytically cleaved to produce different proteins, many involved in rna replication. the nmr structure of gdt has been solved, and sequences have been identified by basic local alignment search tool (blast). nsp interacts with proteins of the alpha dna polymerase ( figure ) and is involved in regulating endonucleolytic rna cleavage of mrna, allowing the virus to enrich viral rna within a cell. , nsp has been shown to interact with ribosomal subunits, resulting in the inhibition of translation, ′ mrna capping changes, and mrna destabilization. − from a sars-cov yeast two hybrid screen, nsp was identified to interact with immunophilins, showing that it alters the intracellular immune response. expression of nsp drives changes in interferon signaling. these processes make nsp a potential virulence factor. − see prokoplab.com/ nsp for additional information. the protein has no solved protein structure, with itassergenerated predictions that are mostly ( %) coiled, and sequences have been identified by blast. all of the protein interaction partners are acetylated ( figure ). the protein has been suggested to be dispensable to viral replication but does impact rates of replication. see prokoplab.com/nsp for additional information. the protein has hundreds of solved x-ray crystal structures with a c zinc finger, and sequences have been identified by blast. the papain-like proteinase cleaves the first four nsp proteins, where inhibition can block viral replication. the proteinase can cleave proteins and has been shown to have deubiquitinase activity. − this deubiquitinase function has been linked to the regulation of immune system cytokine response, , specifically the type-i interferon signaling pathway, and has connection to virulence. see prokoplab. com/papain_like_proteinase for additional information. the protein has no solved protein structure, with itassergenerated predictions that are mostly ( %) coiled, and sequences have been identified by blast. nsp interacts with several proteins involved in mitochondrial import for inner membrane insertion (figure ). nsp and nsp interact and form within the membrane and are involved in transcription complex assembly anchoring. , the complex is involved in the double membrane secretory vesicle formation , in the endoplasmic reticulum, conferring with human protein interaction partners. see prokoplab.com/nsp for additional information. nsp has hundreds of solved x-ray crystal structures, with the protein found in a dimer form with a cysteine protease function, , and sequences have been identified by blast. the enzyme cleaves most of the proteins of the larger rep protein with a highly conserved specificity, where inhibition is one of the most studied interventions. − see prokoplab.com/ c-like_proteinase for additional information. the protein has no solved protein structure, with itassergenerated predictions that are mostly ( %) coiled, and sequences have been identified by blast. nsp interacts with multiple proteins involved in atp hydrolysis-coupled cation transmembrane transport ( figure ). the protein is likely transmembrane-localized, along with nsp /nsp , and is involved in autophagosome formations. − the few papers discussing nsp suggest a major future area of understanding and pharmaceutical intervention potential. see prokoplab. com/nsp for additional information. there are several solved structures for nsp that interact with nsp /nsp ( nur, ahm, and ub ), − and sequences have been identified by blast. the nsp protein interacts with multiple small gtpases of the ras complex, many of which are prenylation-regulated ( figure ). the nsp /nsp /nsp complex is a viral rna-directed rna polymerase unit, where nsp is enhanced through the binding of nsp /nsp . see prokoplab.com/nsp for additional information. there are several solved structures for nsp that interact with nsp /nsp ( nur and ub ), − and sequences have been identified by blast. the nsp protein interacts with proteins involved in translation, snrna ′-end processing, s rna binding, and ribonucleoproteins ( figure ). in addition to the information provided for nsp , nsp has been suggested to also interact with the orf protein. see prokoplab.com/nsp for additional information. nsp has many known protein structures, with the protein requiring dimerization to function, and sequences have been identified by blast. nsp interacts with multiple proteins of structural constituents of the nuclear pore ( figure ). nsp and nsp interact with the nuclear factor-κb repressing factor (nkrf) and may cause an interleukin (il)- /il- -mediated chemotaxis of neutrophils and an overexuberant host inflammatory response. nsp is involved in viral rna synthesis and rna binding, which likely evolved from a protease. , see prokoplab.com/nsp for additional information. nsp has many known protein structures, including those interacting with nsp and nsp , and contains two zinc binding motifs; sequences have been identified by blast. nsp stimulates nsp ′− ′ exoribonuclease/ mismatch excision , and nsp ′-o-methyltransferase activities. , the interface of interaction with nsp and nsp overlaps, suggesting a dynamic regulation process that may involve the linkage of functions through a spherical dodecameric structure. a peptide-based inhibition of the nsp interaction has been proposed as a potential viral regulator. see prokoplab.com/nsp for additional information. nsp is a little-known small . kda peptide with few interaction partners. nsp has multiple known protein structures with a zinc active site and a structure that interacts with nsp /nsp , − and sequences have been identified by blast. nsp is involved in the replication of plus-strand rna through complement strand synthesis and then viral rna synthesis. the enzyme is highly targeted for therapeutic inhibition of viruses. it is also known as rdrp and is the target of the drug remdesivir. see prokoplab.com/rna-directed_rna_polymerase for additional information. nsp has multiple known protein structures with a zinc active site, and sequences have been identified by blast. nsp interacts with multiple proteins involved in the centrosome−golgi apparatus and centrosome ( figure ) and has a rna and a dna duplex-unwinding ability to separate strands with ′ to ′ polarity. − see prokoplab.com/helicase for additional information. nsp has multiple known protein structures with a zinc active site, and sequences have been identified by blast. nsp has an s-adenosyl-l-methionine (sam)-binding pocket and an exoribonuclease function that is involved in rna capping, − and it interacts with nsp and is known to interact with the human ddx rna helicase to enhance the virus replication. see prokoplab.com/guanine-n _ methyltransferase for additional information. nsp has multiple known protein structures, and sequences have been identified by blast. nsp is a mn +dependent toric monomer to the hexamer enzyme involved in uridylate-specific cleavage , that may be regulated by nsp / nsp , and it interacts with the retinoblastoma protein to impact the cell cycle and is also known as nendou. see prokoplab.com/uridylate-specific_endoribonuclease for additional information. nsp has multiple known protein structures with na, mg, and s-adenosyl-l-methionine (sam), and sequences have been identified by blast. nsp is an sam-based enzyme for the methylation of ribose ′-oh in viral rna capping , and interacts with nsp . the protein is a critical component in the inhibition of the host type-i interferon response and is also known as ′-o-mtase. see prokoplab.com/ -omethyltransferase for additional information. the spike surface glycoprotein has multiple known protein structures that are heavily glycosylated and form a trimer complex , and is a known structure of the interaction with the dimer of heterodimers ace /slc a ( m ); sequences have been identified by blast. s is a class-i viral fusion protein and drives the specificity of cell targets through the interaction with ace to enter human cells. , following binding to the receptor, s undergoes a conformational change to allow viral entry. for the protein to function correctly, it must be proteolytically cleaved by trypsin and, upon cell-binding proteases such as tmprss , elevate entry through the mediating tropism. s is of interest to the development of immunizations and rapid detection of coronaviruses, as its surface is exposed. , see prokoplab. com/spike for additional information. orf a has no solved protein structure, with itassergenerated predictions, and sequences have been identified by blast. orf a is a three transmembrane helix protein where the extracellular component localizes the protein to the golgi apparatus with a caveolin- binding potential and is involved in the formation of viral particles. , orf a has been shown to impact the cell cycle. see prokoplab.com/ a for additional information. the envelope protein (e) has no solved protein structure, with itasser-generated predictions, and sequences have been identified by blast. e is required for viral particle formation with transmembrane helix-forming pentameric αhelical bundles with channel activity that can contribute to the membrane permeability. see prokoplab.com/e for additional information. the membrane protein (m) has no solved protein structure, with itasser-generated predictions, and sequences have been identified by blast. m has human interaction partners that are involved in the mitochondrial matrix ( figure ) and is a critical component of viral membranes that are involved in viral budding. see prokoplab.com/m for additional information. orf has no solved protein structure, with itassergenerated predictions, and sequences have been identified by blast. two of the interaction partners are involved in the transcription-dependent tethering of rna polymerase ( figure ). orf can function toward the inhibition of beta interferons through the regulation of the signal transducer and activator of transcription (stat ) and endoplasmic reticulum (er) stress and can interact with nsp . see prokoplab.com/orf for additional information. orf a has multiple known protein structures, and sequences have been identified by blast. orf a has protein interaction partners involved in ribosomal large subunit biogenesis ( figure ) and localizes to the er and golgi network. it can regulate the cell cycle in g /g progression. see prokoplab.com/ a for additional information. orf has no solved protein structure, with itassergenerated predictions, and sequences have been identified by blast. orf has multiple interaction partners involved in the er lumen (figure ) and is a protein shared with sarsr-batcov, with a high positive selection. see prokoplab.com/ orf for additional information. the nucleocapsid protein (n) has multiple known protein structures, and sequences have been identified by blast. n has protein interaction partners involved in mrna binding, the ribonucleoprotein complex, and the mrna surveillance pathway (figure ) and is critical for the viral replication in multiple processes, including viral rna stability, replication, and packaging. the protein is modified within the cell, including phosphorylation and adpribosylation. , the protein consists of three domains, with the n-terminal domain involved in rna binding, the internal dynamic multimer structured unit, and the c-terminal domain, an acidic dimerization region. − the protein can interact with rna by serving as a rna chaperone while also interacting with the m protein and human hnrnpa through the internal multimerization domain. , see prokoplab.com/n for additional information. orf has no solved protein structure, with itassergenerated predictions, and is unique to sars-cov- . very little is known of its molecular function or cellular expression. see prokoplab.com/orf for additional information. ■ sars-cov- risk factors and genetics based on human protein interactions sars-cov- infection exhibits more adverse effects and outcomes in those with other comorbidities, including hypertension, diabetes mellitus, and coronary heart disease. the other risk factors for mortality include older age, elevated d-dimer levels, and a higher sequential organ failure assessment (sofa) score. the mortality associated with sars-cov- infection is tied to the patient's progression to multiorgan dysfunction. the elderly are particularly susceptible to severe sars-cov- infection, which is most likely due to the immunosuppression and underlying comorbidities associated with advanced age. advanced age has been shown to have a depressive effect on both the innate and the adaptive immune system, known as immunosenescence. this is associated with decreased phagocytosis and the bactericidal effects of neutrophils and is also associated with the downregulation of cytokine signaling , and innate immune receptors. with sars-cov- infection, emphasis is placed on the adaptive immune system to aid in clearing virally infected cells. the elderly population has been shown to have a shift toward inhibitory pathways, particularly in cd + t cells and to a lesser degree in cd + t cells, which may play a role in allowing disseminated viral spread. this reduction of t cell activity is also joined by the involution of the thymus with age, leading to less naive t cell output, which further depresses immune functions. these accumulative effects on the immune system render the elderly population particularly susceptible to dispersed viral infection at baseline levels, which may ultimately result in viral sepsis. with the immunosenescence and increased prevalence of comorbidities associated with older age, it makes sense that this population is being hit the hardest by sars-cov- ; however, many younger adults who lack the above immunosenescence have also been killed from the infection, some of whom displayed no prior medical history. this aspect points to the idea that genetics may play a role in determining the severity of sars-cov- infection. the immune response to sars-cov- infection in severe cases characteristically induces lymphopenia, particularly of cd- + t cells, and increases il- , il- , il- , and interferon (ifn)-γ levels. this work is backed by multiple proteomic studies identifying biomarkers of severity that connect to the immune system. , the cytokine storm induced by sars-cov- is not a new phenomenon and has been demonstrated in the pathogenesis of other novel human coronaviruses, including mers and sars-cov- . similar consequences in severe coronavirus infections appear to stem from the cytokine storm of proinflammatory chemokines and cytokines, eventually resulting in acute respiratory distress syndrome (ards) and multiorgan dysfunction. a previous study on sepsis and cytokine storm indicates the presence of genetic variants in multiple pathways that have a polygenetic contribution. in many patients with sars-cov- that have severe infection, the identification of hyperferritinemic sepsis often occurs. fever developed at day , sepsis developed at day , admission to the intensive care unit occurred at day (for acute respiratory distress syndrome), and death occurred at day . critically ill patients, defined as those with septic shock, multiple organ dysfunction/failure, and/or respiratory failure, accounted for approximately % of the study population, yet the study population displayed a case fatality rate of . % in early reports from wuhan, china. hyperferritinemia on day and day predicts mortality long before the development of sepsis and intensive care unit admission. hyperferritinemia has been suggested to have genetic associations through pathogenic variants in genes targetable by il rap and anti-c antibodies. type- interferonopathies, like heterozygous null variants in irf , have been shown to result in severe manifestations of seasonal influenza virus. similar monogenetic variants likely exist that lead to the individual risk of severe disease onset from sars-cov- in previously healthy patients. much of the genetics around the immune activation leading to a cytokine storm and hyperferritinemic sepsis remains poorly defined and requires future initiatives and cohorts to define these genetic contributions adequately. initial sars-cov- infection is commonly associated with fever, cough, malaise, and fatigue. in more severe cases, disseminated intravascular coagulation has been noted with elevated d-dimer levels in the serum of severe covid- patients, placing them into thromboembolic risk. recent recommendations have been made to utilize thromboprophylaxis or full-anticoagulation therapy for patients in the thromboembolic risk category. a specific protein−protein interaction was discovered between sars-cov- 's orf and the tissue plasminogen activator (tpa) protein of hosts. the tpa, which is encoded by the plat gene, plays a crucial role in thrombolysis by catalyzing the conversion of plasminogen to plasmin, the major enzyme involved in lysis of blood clots. increased the activity of tpa can lead to excessive bleeding, whereas decreased activity is associated with thromboembolus formation, increasing the chances of pulmonary embolism, stroke, and myocardial infarction. the extent to which orf interacts with tpa is not well understood, but its involvement may render a patient at risk for thromboembolism, as has been seen in the clinical setting. in a study by ladenvall et al., it was found that the discovered eight single nucleotide polymorphisms and the alu insertion polymorphism at the plat locus were not significant contributors to plasma tpa levels. this finding indicates that inherited variants of the plat gene may not be directly involved with the coagulopathy in sars-cov- patients; however, the polymorphisms may render the host's tpa protein to a tighter binding by orf , yielding greater repression during infection, placing the patient at higher risk for thromboembolism. it has also been shown that sepsis involves upregulation of platelet adhesion molecules and increased circulation of platelet−leukocyte aggregates. this may point toward more of an immune-system-catalyzed coagulopathy, resulting in the presentation of strokes, pulmonary embolisms, myocardial infarctions, and microvascular injury, which impact severe sars-cov- patients. as coagulopathy has mainly been investigated in both viral and bacterial sepsis, there may be a dual effect of both the immune-mediated response and the protein−protein interaction of orf with the host tpa in cases of sars-cov- infection. further investigation is warranted to determine the extent of the interaction of orf with the host tpa to determine if it plays into the pathogenesis of sars-cov- -related coagulopathy. sars-cov- has been associated with cardiac dysfunction, including myocardial infarction and heart failure. the underlying mechanisms for cardiac injury currently being hypothesized are indirect cardiac injury from the cytokine storm and inflammatory response, severe hypoxia as a result of ards, and direct viral invasion of cardiomyocytes. interestingly, ace , the host receptor for sars-cov- , is expressed in the heart, indicating direct viral invasion could be a potential cause of myocardial dysfunction. sars-cov- 's nonstructural protein (nsp ) was found to interact with the e -ubiquitin ligase mindbomb homologue (mib ). this ubiquitin ligase is a positive regulator of the delta-mediated notch signaling pathway, which is involved in multiple processes during cardiac development. mutations in the mib have been associated with left ventricular noncompaction (lvnc) characterized by left ventricular trabeculations and reductions in cardiac systolic function. lvnc can range from being asymptomatic to presenting heart failure, depending on the extent the mutation has on the notch pathway. the prevalence of lvnc in the general population is estimated to be around / to / . patients with the asymptomatic form of lvnc may be at higher risk for exacerbation of cardiac dysfunction following sars-cov- due to involvement of this pathway, especially if they are unaware that they have this mutation. this may play a role in the cardiac dysfunction seen in younger sars-cov- patients who lack underlying comorbidities. aside from cardiac development, the notch pathway has also been implemented in cardiac repair, which was demonstrated in rat models where the notch and notch pathways were upregulated, thereby reducing postmyocardial infarctions in the setting of heart failure. the mechanism behind the repair process is still under investigation; however, the disruption of the notch signaling pathway by the interaction of nsp with mib may prove to play a role in the cardiac involvement of sars-cov- infection. furthermore, although vertical transmission of sars-cov- has not been seen, neonates who have tested positive for the infection may need to have their cardiac function assessed over time due to mib 's role in cardiogenesis and repair. while we present a detailed assessment of two interaction partners' connections to pathology and risk factors, many more likely exist. we postulate that if function of any protein diverges from normal biology to contribute to sars-cov- biology, it could result in a similar disease state within the cell as a loss of function or deleterious genetic mutation. thus, to journal of proteome research pubs.acs.org/jpr reviews understand the sars-cov- -connected diseases through the human protein interactions, we assessed clinvar, a database of clinically identified variants. a query of the sars-cov- human interaction partners through clinvar reveals protein-based variants within the list ( figure a ). in total, of the queried genes have a clinvar submission. of these clinvar-connected genes, there are a total of that have a clinical annotation of pathogenic (pathogenic or likely pathogenic), with a total of different variants ( figure b ). the gene with the most pathogenic variants is fbn , which is known to interact with sars-cov- nsp and is involved in autosomal dominant familial thoracic aortic aneurysms and aortic dissections and marfan syndrome. a further analysis of clinical disorders connected with those genes with or more pathogenic-associated variants, excluding fbn (pkp , acadm, ppt , wfs , col a , pcnt, fbn , bcs l, ngly , cyb r , acad , neu , gnb , nars , tcf , npc , pigo, cdk rap , cenpf, ggcx, fkbp , tbk , fbln , exosc , por, gpaa , and rhoa), reveals a high connection to cardiac, neurological, diabetic, and syndromic biology. the sars-cov- orf has the most genes connected by interactions to pathogenic clinvar returns from queried genes, followed by protein m, nsp , nsp , and orf c ( figure c ). orf is connected to genes associated to human genetic diseases (col a , ngly , neu , npc , fkbp , dnmt , plod , smoc , il ra, adam , sil , lox, pofut , tor a, hyou , edem , emc , and hs st ), with significant enrichment of these genes to protein folding (false discovery rate (fdr) = . ) and endoplasmic reticulum lumen (fdr = . × − ). while only associated with pathogenic interaction partners, the nucleocapsid (n) protein has interesting disease genetics based on previous observations of a process known as viral-induced genetics. the nucleocapsid (n) protein has the potential to impact and change cellular landscapes through the direct regulation of ribosomal biology. the protein−protein interaction map by gordon et al. supports the hypothesis that sars-cov- n proteins interact with multiple mrna-binding proteins and ribonucleoprotein complex proteins ( figure ). in multiple viruses, proteins have been shown to interact with these complexes to regulate a process known as nonsense-mediated decay (nmd). nmd is a cellular process involved in the removal of mrna that does not conform to the bulk of cellular mrna, where proteins accumulate on the transcript and direct the cellular degradation of the mrna. the process is primarily used within cells to degrade mrna molecules with nonsense and frameshift genetic variants and those with improper splicing to prevent the cell from producing truncated proteins that can drive dominant-negative or deleterious gain of function outcomes. viral rna is usually suppressed and degraded within cells through nmd, acting as a cellular immune system process. − thus, an evolutionary arms race has arisen where a virus can propagate more efficiently if it has a protein that can suppress nmd, keeping its rna levels elevated. − multiple lines of evidence for both sars-cov- and sars-cov suggested that the n protein is used to suppress nmd and evade cellular immune processes. nearly all of the coronaviruses and the larger nidovirales order genomes contain the n protein, which has been shown to interact with multiple ribosomal proteins, including crucial nmd factors. directly inhibited by nmd, with the n protein expression blocking this inhibition. positive-sense single-stranded rna viruses, including coronaviruses, are likely targets of nmd due to their many overlapping reading frames, retained introns, and long ′ utrs present within the cytoplasm of human cells. the n protein interacts with three proteins annotated to the mrna surveillance pathway (upf , pabpc , and pabpc ) and several proteins involved in mrna binding and the ribonucleoprotein complex that are all known to have cellular interactions (figure ). while the fine details of the n protein interaction on the factors are poorly understood, the three mrna surveillance genes are well-connected to nmd biology. pabpc is known to be critical for nmd, with its removal suppressing nmd. , from plants to humans, upf is considered a key regulator of nmd through its recruitment of multiple proteins to rna. − the regulation switch of upf is known to be regulated/activated through phosphorylation at various sites to allow its protein interactions, − while the n protein has been shown in multiple viral species to be phosphorylated − and likely dynamic in modifications throughout the rna replication and viral lifecycle. , these phosphorylation switches and the interaction of n to nmd proteins are potential sites of pharmaceutical or biological regulation that have been undervalued to this point. other notable interactions of the n protein are ras gtpaseactivating protein-binding protein homologues (g bp / ) and casein kinase alpha (csnk a ), suggesting the regulation of stress granule formation. nmd is found at the intersection of a variety of cellular pathways beyond mrna surveillance and viral control. notably, it is closely associated with the integrated stress response requiring translation initiation factor eif s for function. cellular stresses such as hypoxia and er stress lead to the inhibition of nmd via phosphorylation of eif s . this phosphorylation typically induces stress granule formation as well, which has been cited to aid viral replication in some cases and weaken them in others. when g bp is depleted within cells, there is a significant impairment of the replication for coronaviruses and respiratory syncytial viruses (rsvs). , multiple viruses have been shown to regulate phosphorylation of eif s at varying time points of infection with connection into nmd regulation. stress granule formation can enhance nmd inhibition, such as hypoxic conditions modulating upf and eif s . , the interaction of sars-cov- n protein human interactors promotes the inhibition of nmd and enhancement of both viral replication and truncated host polypeptides that can enhance viral pathogenicity (figure ) . the regulation of nmd by viral proteins is crucial for allowing the viral rna to survive, but nmd processes within cells also regulate multiple endogenous transcripts, several in normal biology, and some based on genetic disease regulation. many genes, including isoforms with early truncation (frameshifts and nonsense codons) and genes involved in amino acid homeostasis, tumorigenesis, and cell cycle control, are activated when nmd is inhibited within a cell. − in total, this amounts to about % of transcripts within a cell that are regulated by nmd processes and could be altered within the cell by sars-cov- . on top of this, most individuals contain at least one gene where a nonsense or frameshift variant within the genome is being suppressed, being either inherited or somatic. assessments of human genomes reveal that every person has at least one variant regulated by nmd. recently, our group has shown a complex involvement of this regulation with rare human variants, driving adverse outcomes through a process we have termed viral-induced genetics (vig). in a patient with an epstein−barr virus (ebv) infection, they had an adverse immune response of classical hyperferritinemic sepsis like that of severe sars-cov- patients. this individual has both whole-exome sequencing in addition to multiple bloodbased rnaseq experiments performed throughout their clinical course. sequencing revealed a heterozygous splicing variant in the gene rnaseh b, which is associated with recessive aicardi−goutieres syndrome and has been connected to type-i ifn-mediated autoimmune disease. , rnaseq of the patient, when healthy, showed that the splicing variant was present at very low levels, suggesting that the copy was being inhibited through nmd. while the patient was healthy for years of life, the ebv was shown by rnaseq to inhibit nmd, resulting in the presence of the splice variant, which resulted in a dominant-negative rnaseh b protein that drove cell dysfunction. this suggests that many human variants within genes connected to the immune system and viral response, which are usually suppressed by nmd and result in no cellular dysfunction, are activated by the virus through the inhibition of nmd and can give rise to severe viral outcomes. just like in a computer virus, the antivirus of the computer is often targeted. when additional computer code contains a risk to system failure that is inhibited by the antivirus, if the antivirus is shut down, the other system vulnerabilities become present and often contribute to the computer failure. the full extent of these variants and the disease process remain to be elucidated but is a promising avenue for exploration of viral-induced outcomes in sars-cov- . the sars-cov- pandemic represents a unique challenge to scientists. unlike previous pandemics, our knowledge of the genome and its coded proteins was gleaned within weeks of the outbreak, now with thousands of sequences within a short window. this level of insight has allowed for a pivot to a more robust insight into the viral proteome and how it interacts with host proteins. the advancement of protein-based bioinformatics and previous coronavirus research studies have proved useful in defining the function of each protein coded by the virus. here, we show how many of these viral proteins interact with human proteins connected to biological pathways and disease connections, including numerous risk factors from immune to cardiovascular systems. most notably, we highlight literature on the role of the viral nucleocapsid (n) protein in nmd regulation, where the inhibition of nmd allows for viral rna stability while simultaneously activating genetics of cellular processes and viral-induced genetics. while we have seen thousands of publications on sars-cov- and other coronaviruses, the details of a proteome-wide knowledge base of sars-cov- -coded proteins limit our ability to expand into the incredible potential of preventing and mitigating the current pandemic and future pandemics with a larger therapeutic toolset. characterization of coding/noncoding variants for shroom in patients with ckd molecular modeling in the age of clinical genomics, the enterprise of the next generation sars-cov- (covid- ) structural and evolutionary dynamicome: insights into functional evolution and human genomics expression of the sars-cov- cell receptor gene ace in a wide variety of human tissues ace receptor expression and severe acute respiratory syndrome coronavirus infection depend on differentiation of human airway epithelia receptor ace and tmprss are primarily expressed in bronchial transient secretory cells hca lung biological network. sars-cov- entry factors are highly expressed in nasal epithelial cells together with innate immune genes proteomics of sars-cov- -infected host cells reveals therapy targets single-cell landscape of bronchoalveolar immune cells in patients with covid- eils, r. covid- severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis imbalanced host response to sars-cov- drives development of covid- transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in covid- patients proteomic and metabolomic characterization of covid- proteomic fingerprints for potential application to early diagnosis of severe acute respiratory syndrome the sars coronavirus nucleocapsid protein-forms and functions nucleocapsid phosphorylation and rna helicase ddx recruitment enables coronavirus transition from discontinuous to continuous transcription virus-host interactomes-antiviral drug discovery host factors in coronavirus replication novel beta-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein from the severe acute respiratory syndrome coronavirus sars coronavirus nsp protein induces template-dependent endonucleolytic cleavage of mrnas: viral mrnas are resistant to nsp -induced rna cleavage suppression of host gene expression by nsp proteins of group bat coronaviruses a two-pronged strategy to suppress host protein synthesis by sars coronavirus nsp protein severe acute respiratory syndrome coronavirus protein nsp is a novel eukaryotic translation inhibitor that represses multiple steps of translation initiation severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp and rational design of an attenuated strain unique sars-cov protein nsp : bioinformatics, biochemistry and potential effects on virulence coronavirus nonstructural protein : common and distinct functions in the regulation of host and viral gene expression protein structure and sequence reanalysis of -ncov genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and hiv- the nsp proteins of mouse hepatitis virus and sars coronavirus are dispensable for viral replication identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity a noncovalent class of papain-like protease/deubiquitinase inhibitors blocks sars virus replication deubiquitinating activity of the sars-cov papainlike protease the papain-like protease from the severe acute respiratory syndrome coronavirus is a deubiquitinating enzyme severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme sars coronavirus papain-like protease inhibits the tlr signaling pathway through removing lys -linked polyubiquitination of traf and traf coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of sting-mediated signaling sars coronavirus papain-like protease inhibits the type i interferon signaling pathway through interaction with the sting-traf -tbk complex the papain-like protease determines a virulence trait that varies among members of the sars-coronavirus species structure and cleavage specificity of the chymotrypsin-like serine protease ( clsp/nsp ) of porcine reproductive and respiratory syndrome virus (prrsv) mutation in murine coronavirus replication protein nsp alters assembly of double membrane vesicles localization and membrane topology of coronavirus nonstructural protein : involvement of the early secretory pathway in replication replication is supported by a reticulovesicular network of modified endoplasmic reticulum c-like proteinase from sars coronavirus catalyzes substrate hydrolysis by a general base mechanism dissection study on the severe acute respiratory syndrome c-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors coronavirus main proteinase ( clpro) structure: basis for design of anti-sars drugs biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus c-like proteinase the substrate specificity of sars coronavirus c-like proteinase topology and membrane anchoring of the coronavirus replication complex: not all hydrophobic domains of nsp and nsp are membrane spanning coronavirus nsp proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate evolutionary analysis of sars-cov- : how mutation of non-structural protein could affect viral autophagy coronavirus nsp restricts autophagosome expansion structure of the sars-cov nsp polymerase bound to nsp and nsp co-factors insights into sars-cov transcription and replication from the structure of the nsp -nsp hexadecamer nonstructural proteins and of feline coronavirus form a : heterotrimer that exhibits primer-independent rna polymerase activity the sars-coronavirus nsp +nsp complex is a unique multimeric rna polymerase capable of both de novo initiation and primer extension the nonstructural protein (nsp ) of the sars coronavirus interacts with its orf accessory protein severe acute respiratory syndrome coronavirus nsp dimerization is essential for efficient viral growth virus-host interactome and proteomic survey of pmbcs from covid- patients reveal potential virulence factors influencing sars-cov- the nsp replicase protein of sars-coronavirus, structure and functional insights the severe acute respiratory syndrome-coronavirus replicative protein nsp is a single-stranded rna-binding subunit unique in the rna virus world crystal structure of nonstructural protein from the severe acute respiratory syndrome coronavirus reveals a novel fold with two zinc-binding motifs rna ′-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp / nsp exoribonuclease complex structural basis and functional analysis of the sars coronavirus nsp -nsp complex in vitro reconstitution of sars-coronavirus mrna cap methylation crystal structure and functional analysis of the sars-coronavirus rna cap ′-o-methyltransferase nsp /nsp complex coronavirus nsp , a critical co-factor for activation of multiple replicative enzymes dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp coronavirus nsp /nsp methyltransferase can be targeted by nsp -derived peptide in vitro and in vivo to reduce replication and pathogenesis molecular anatomy of viral rna-directed rna polymerases multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase the severe acute respiratory syndrome (sars) coronavirus ntpase/helicase belongs to a distinct class of ′ to ′ viral helicases the human coronavirus e superfamily helicase has rna and dna duplex-unwinding activities with ′-to- ′ polarity structure-function analysis of severe acute respiratory syndrome coronavirus rna cap guanine-n -methyltransferase functional screen reveals sars coronavirus nonstructural protein nsp as a novel cap n methyltransferase characterization of the guanine-n methyltransferase activity of coronavirus nsp on nucleotide gtp the cellular rna helicase ddx interacts with coronavirus nonstructural protein and enhances viral replication crystal structure and mechanistic determinants of sars coronavirus nonstructural protein define an endoribonuclease family crystal structure of a monomeric form of severe acute respiratory syndrome coronavirus endonuclease nsp suggests a role for hexamerization as an allosteric switch structural and biochemical characterization of endoribonuclease nsp encoded by middle east respiratory syndrome coronavirus binding of the methyl donor s-adenosyl-l-methionine to middle east respiratory syndrome coronavirus ′-o-methyltransferase nsp promotes recruitment of the allosteric activator nsp coronavirus nonstructural protein is a cap- binding enzyme possessing (nucleoside- ′o)-methyltransferase activity ribose ′-o-methylation provides a molecular signature for the distinction of self and non-self mrna dependent on the rna sensor mda assembly of coronavirus spike protein into trimers and its role in epitope expression cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer the coronavirus spike protein is a class i virus fusion protein: structural and functional characterization of the fusion core complex coronavirus spike proteins in viral entry and pathogenesis structure of sars coronavirus spike receptor-binding domain complexed with receptor characterization of severe acute respiratory syndrome-associated coronavirus (sars-cov) spike glycoprotein-mediated viral entry mechanisms of coronavirus cell entry mediated by the viral spike protein severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody severe acute respiratory syndrome coronavirus orf a protein interacts with caveolin severe acute respiratory syndrome coronavirus a protein is a viral structural protein the severe acute respiratory syndrome coronavirus a is a novel structural protein g phase cell cycle arrest induced by sars-cov a protein via the cyclin d /prb pathway nucleocapsid-independent assembly of coronavirus-like particles by co-expression of viral envelope protein genes structure and inhibition of the sars coronavirus envelope protein ion channel expression of sars-coronavirus envelope protein in escherichia coli cells alters membrane permeability coronavirus particle assembly: primary structure requirements of the membrane protein severe acute respiratory syndrome coronavirus open reading frame (orf) b, orf , and nucleocapsid proteins function as interferon antagonists severe acute respiratory syndrome coronavirus orf antagonizes stat function by sequestering nuclear import factors on the rough endoplasmic reticulum/golgi membrane orf- , induces caspase- mediated, er stress and jnk-dependent apoptosis structure and intracellular targeting of the sars-coronavirus orf a accessory protein sars coronavirus a protein blocks cell cycle progression at g /g phase via the cyclin d /prb pathway severe acute respiratory syndrome (sars) coronavirus orf protein is acquired from sars-related coronavirus from greater horseshoe bats through recombination selective replication of coronavirus genomes that express nucleocapsid protein the coronavirus nucleocapsid is a multifunctional protein the severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by − - -mediated translocation sequence comparison of the n genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein the nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its n-terminal domain and multimerization properties modular organization of sars coronavirus nucleocapsid protein coronavirus nucleocapsid protein is an rna chaperone characterization of protein-protein interactions between the nucleocapsid protein and membrane protein of the sars coronavirus the sars-cov nucleocapsid protein: a protein with multifarious activities clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study effect of age on human neutrophil function innate immunosenescence: effect of aging on cells and receptors of the innate immune system in humans altered cytokine production in the elderly cutting edge: impaired toll-like receptor expression and function in aging signaling pathways in aged t cells -a reflection of t cell differentiation the effect of age on thymic function human coronavirus infections: causes and consequences of cytokine storm and immunopathology molecular immune pathogenesis and diagnosis of covid- understanding the inflammatory cytokine response in pneumonia and sepsis: results of the genetic and inflammatory markers of sepsis (genims) study adults with septic shock and extreme hyperferritinemia exhibit pathogenic immune variation understanding human autoimmunity and autoinflammation through transcriptomics covid- ) in china: a systematic review and meta-analysis changes in blood coagulation in patients with severe coronavirus disease (covid- ): a meta-analysis thromboembolic risk and anticoagulant therapy in covid- patients: emerging evidence and call for action tissue plasminogen activator genetic variation at the human tissue-type plasminogen activator (tpa) locus: haplotypes and analysis of association to plasma levels of tpa the coagulopathy of acute sepsis covid- presenting as stroke pulmonary embolism in patients with covid- : time to change the paradigm of computed tomography covid- and the cardiovascular system: implications for risk assessment complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases novel coronavirus outbreak research team. epidemiologic features and clinical course of patients infected with sars-cov- in the cardiovascular burden of coronavirus disease (covid- ) with a focus on congenital heart disease associated with acute respiratory distress syndrome receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus notch signaling in cardiac development and disease mutations in the notch pathway regulator mib cause left ventricular noncompaction cardiomyopathy activation of notch signaling in cardiomyocytes during post-infarction remodeling vertical transmission of coronavirus disease (covid- ) from infected pregnant mothers to neonates: a review viral-induced genetics revealed by multi-dimensional precision medicine transcriptional workflow applicable to covid- nucleocapsid protein recruitment to replication-transcription complexes plays a crucial role in coronaviral life cycle interplay between coronavirus, a cytoplasmic rna virus, and nonsense-mediated mrna decay pathway nonsense-mediated mrna decay (nmd) mechanisms the nonsense-mediated decay rna surveillance pathway the host nonsense-mediated mrna decay pathway restricts mammalian rna virus replication nonsense-mediated mrna decay: novel mechanistic insights and biological impact beyond quality control: the role of nonsense-mediated mrna decay (nmd) in a combined proteomics/genomics approach links hepatitis c virus infection with nonsense-mediated mrna decay virus escape and manipulation of cellular nonsense-mediated mrna decay rna virus evasion of nonsense-mediated decay how retroviruses escape the nonsense-mediated mrna decay an interactome map of the nucleocapsid protein from a highly pathogenic north american porcine reproductive and respiratory syndrome virus strain generated using silac-based quantitative proteomics function of a retrotransposon nucleocapsid protein the cellular interactome of the coronavirus infectious bronchitis virus nucleocapsid protein and functional implications for virus biology interaction of pabpc with the translation initiation complex is critical to the nmd resistance of aug-proximal nonsense mutations a conserved role for cytoplasmic poly(a)-binding protein (pabpc ) in nonsense-mediated mrna decay upf is required for nonsense-mediated mrna decay (nmd) and rnai in arabidopsis mammalian staufen recruits upf to specific mrna ′utrs so as to elicit mrna decay nmd factors upf and upf bridge upf to the exon junction complex and stimulate its rna helicase activity interactions between upf , erfs, pabp and the exon junction complex suggest an integrated model for mammalian nmd pathways upf phosphorylations create binding platforms for smg- and smg- :smg- during nmd binding of a novel smg- -upf -erf -erf complex (surf) to the exon junction complex triggers upf phosphorylation and nonsense-mediated mrna decay a post-translational regulatory switch on upf controls targeted mrna degradation phosphorylation of the porcine reproductive and respiratory syndrome virus nucleocapsid protein phosphorylation and subcellular localization of transmissible gastroenteritis virus nucleocapsid protein in infected cells severe acute respiratory syndrome coronavirus nucleocapsid protein expressed by an adenovirus vector is phosphorylated and immunogenic in mice phosphorylation of the mouse hepatitis virus nucleocapsid protein effects of phosphorylation of avian retrovirus nucleocapsid protein pp on binding of viral rna regulation of hepadnavirus reverse transcription by dynamic nucleocapsid phosphorylation nonsense-mediated mrna decay at the crossroads of many cellular pathways valiente-echeverría, f. strategies for success. viral infections and membraneless organelles innate immune evasion by human respiratory rna viruses mouse hepatitis coronavirus replication induces host translational shutoff and mrna decay, with concomitant formation of stress granules and processing bodies hypoxic inhibition of nonsense-mediated rna decay regulates gene expression and the integrated stress response possible roles in the control of translation and mrna degradation. cold spring harbor perspect nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise nonsense-mediated rna decay regulation by cellular stress: implications for tumorigenesis nonsense-mediated mrna decay factors act in concert to regulate common mrna targets nonsense-mediated mrna decay in health and disease the rules and impact of nonsense-mediated mrna decay in human cancers a novel rnaseh b splice site mutation responsible for aicardi-goutieres syndrome in the faroe islands genetically defined autoinflammatory diseases rare adar and rnaseh b variants and a type i interferon signature in glioma and prostate carcinoma risk and tumorigenesis key: cord- -quuju h authors: kumar, aishwarya; gupta, puneet kumar; srivastava, ankita title: a review of modern technologies for tackling covid- pandemic date: - - journal: diabetes metab syndr doi: . /j.dsx. . . sha: doc_id: cord_uid: quuju h objective: science and technology sector constituting of data science, machine learning and artificial intelligence are contributing towards covid- . the aim of the present study is to discuss the various aspects of modern technology used to fight against covid- crisis at different scales, including medical image processing, disease tracking, prediction outcomes, computational biology and medicines. methods: a progressive search of the database related to modern technology towards covid- is made. further, a brief review is done on the extracted information by assessing the various aspects of modern technologies for tackling covid- pandemic. results: we provide a window of thoughts on review of the technology advances used to decrease and smother the substantial impact of the outburst. though different studies relating to modern technology towards covid- have come up, yet there are still constrained applications and contributions of technology in this fight. conclusions: on-going progress in the modern technology has contributed in improving people's lives and hence there is a solid conviction that validated research plans including artificial intelligence will be of significant advantage in helping people to fight this infection. ever since the first report of coronavirus disease at wuhan, china in december , it has affected over countries and territories around the world with two million cases and more than , deaths as on april . with this growing crisis, companies & researchers over the world are looking for the ways to address the challenges of this virus, to mitigate the spread and develop a cure for this disease. in this baffling battle, science and technology is playing a vital role. for example, early in the outbreak when china initiated its response to virus it focused on artificial intelligence (ai) by relying on like facial recognition cameras to track the infected patients with travel history, robots to deliver food and medicines, drones to disinfect public places, to patrol and broadcast audio messages to public encouraging them to stay at home [ ] . ai has been used extensively to discover new molecules on the way to find aid for covid- . many researchers are using ai to find new drugs and medicines for the cure, along with some computer science researchers focusing on detecting the infectious patients through medical image processing like x-rays and ct scans [ ] . ai is even developing tracking software's like monitoring bracelets that helps in classification of peoples breaching the quarantine rule. smart phones and ai enhanced thermal cameras are also being used for detecting fever and infected people [ ] . countries like taiwan infused the national medical insurance database with inputs from the immigration and customs database, hence confronting the coronavirus patients on the basis of their travel history and symptoms [ , ] . in all, ai is used to identify, track and forecast outbreaks, it is helping in diagnosing the virus. it is used in processing the healthcare claims. the drones and robots are used to deliver food and medicine supplies as well as in sterilizing public places. ai is helping to develop drugs and coronavirus vaccine using super computers [ ] . this present study focuses on the use of artificial intelligence advances in the fight against the coronavirus epidemic. it gives a thorough review of the technology advances used to decrease and smother the substantial impact of the outburst. the motivation for the present study is not only limited to assess the effect of the portrayed procedures but also to prescribe their utilization as well. this paper shows the reader the applications of ai and presents an underlying picture of how modern technology could react to the covid- pandemic. technology refers to techniques, frameworks and devices which are the after effect of scientific information being utilized for practical purposes. artificial intelligence can be characterized as machine learning (ml), natural language processing (nlp), and computer vision applications. these abilities instruct computers to use huge information based models to design, depict, and predict. in table , we discussed various applications of modern technology in the covid- epidemic. to combat coronavirus, ai majorly focuses on diagnosis of the patients and virus, medical imaging process, disease tracking and its prediction. on the other hand, it also covers alerting, creating awareness and social control through the internet. following are some ways where technology is being used in the fight against covid- . the overall pandemic of covid- significantly challenges open clinical frameworks. with restricted clinical assets, treatment needs are controlled by the severity of the patient. though numerous mild outpatients rapidly turned into serious or critical stage, it's more significant to recognize them early and give opportune treatment for optimizing treatment procedure and lessening mortality. ai capacities can be valuable to analyze, predict and clarify (treat) covid- contaminations, and help oversee financial effects. so far, most clinical utilizations of artificial intelligence to the covid- reaction have concentrated on diagnosis dependent on clinical imaging. the quality of the present diagnostic methods at the initial introduction of the disease has been questioned. in recent writings, it has been discovered that a few research works use artificial intelligence to help analyze computational tomography (ct) scans, while other research works use patient's clinical information to predict the advancement of the infection [ , ] . lives can be saved, expansion of the ailment might be curbed and huge data could be generated from ai models with the quick and precise diagnosis of covid- . scientists working on ai applications show that it can give extra time to radiologists and do a diagnosis quicker and less expensive than with coronavirus regular tests. for this purpose, the doctors can use x-rays as well as ct scans, computed tomography [ ] . table explains different artificial intelligence applications in ct diagnosis of covid- . coronavirus tests are short in supply and costly, however, all emergency clinics have x-rays (or ct) machines. with the assistance of deep learning, radiologists can diagnose covid- using x-ray pictures. covid-net an artificial intelligence application is created to analyze covid- symptoms in chest x-rays utilizing information of different lung conditions and covid- from patients [ ] . in a diagnostic study, an ai platform was established using inception migration neural network for extracting covid- symptoms using ct images, achieving . % accuracy [ ] . an initial detection model was created to recognize covid- pneumonia from influenza-a viral pneumonia and sound cases with pulmonary ct pictures utilizing deep learning systems. the patient's infected parts were proportioned by using a -d deep learning model. this study showed . % accuracy of the model [ , ] . jin et al. developed a deep learning model that can precisely identify corona virus symptoms from the community acquired pneumonia (cap) and other lung diseases. a d deep learning framework using chest ct was constructed using a neural network (cov-net) [ ] . for coronavirus diagnosis; a deep learning model was proposed which straightforwardly accepts ct scans information as input and implements lung division, diagnose covid- and finds abnormal slices. furthermore, the study trusts that the diagnosis outcomes of ai framework can be quantitatively clarified in the initial picture to mitigate the disadvantage of deep neural systems as a black box [ ] . an automated tool was created to quantifying the symptoms of this virus in the lungs of the patient and to observe the growth of the infection or reaction to cure, using a deep learning method. the capability of ai in diagnostics isn't yet practiced, though chinese hospitals have installed ''ai-assisted" radiology technology. reverse. transcription polymerase chain reaction (rt-pcr) tests are the key methodology used for diagnosing coronavirus, yet they have restrictions as far as specimen assortment, time required for the study, and execution [ ] . specific abnormality in images and designs in ct scans showing covid- symptoms has been discovered [ ] . artificial intelligence can be used to track illness will spread of covid- with time and place. ongoing discoveries recommended that covid- has respiratory patterns which are different from seasonal influenza and regular cold, eminently that they display tachypnea (fast breathing) [ ] . forecast of tachypnea could be a first-order diagnostic feature that may add to enormous scope screening of potential patients [ ] . different proposition have been made to use cell phones in covid- identification, either utilizing implanted sensors to recognize covid- side effects or phone based surveys to channel high-risk patients dependent on reactions to key questions [ ] . berlin utilizes an epidemiological sir model that considers containment measures by governments, for example, lockdowns, quarantines, and social distancing solutions [ ] . a likewise expanded sir model, considering general public health measures against the pandemic and utilizing information from china, has been pre-published and made accessible in r for [ ] . gleamviz epidemiological model is used to track the spread of the infection [ ] . similarly, metabiota [ ] offers an epidemic tracker [ ] and a near-term forecasting model of infection spread, which they used to make forecasts. tracking the spread of covid- can be significant information for general public health authorities to design, plan, and deal with the pandemic [ ] . a novel methodology was proposed dependent on features contained in patients' clinical data and blood tests to assist doctors in identifying high-risk patients as early as they can under these circumstances, thus improving the forecasting of patients and lessening the mortality of those that are seriously sick [ ] . in lieu of this, a forecast model dependent on the xgboost calculation was made to predict mortality risk and distinguish key features which can be estimated in clinics. the researchers found out three key clinical pointers (lactic dehydrogenase, lymphocyte and high-affectability c-receptive protein) for assessing a patient's mortality. a plus point of this method is its interpretability, the three indicators identified by the methodology correspond to the most significant factors in the pathophysiological progress of covid- , specifically cell injury, cell immunity, and inflammation [ ] . a corresponding report meant to forecast if existing covid- patients would require a long stay in hospitals or not, based on a u-net subsidiary trained on ct imaging data [ ] . these two methodologies can help in recognizing the patients that may require escalated and long-term care, helping clinics deal more adequately. at last, while both of these investigations were constrained in scope and information, they establish significant roads of research that can be supplemented and stretched out with clinical information from approaching cases the world over. computational biology includes the development & use of data analytics, mathematical modeling and computational simulation procedures to study biology. computational biologists are assisting with battling coronavirus through disease modeling and finding another medication for this pandemic. disease dynamics modeling contributes in understanding the effect of parameters that rules the spread of the infection, and the impact that mediations can have in controlling this spread [ ] . as soon as virus advances in the deceased body, both lungs start showing ground glass and infiltrates. numerous data driven drug repurposing (drug repositioning) approaches have been proposed with the point of identifying illnesses, conditions or groups of patients that could be treated with existing medications not known for this disease [ ] . when virus rna genome first enters a cell, it mingles with the host's protein-production, utilizing it to make proteins that can duplicate rna molecules. these rna-replicating proteins, called "polymerases," make a target for treatments [ ] . proteins have a d structure, which is evaluated by their genetically encoded amino acid sequence, and this structure impacts the role and purpose of the protein [ ] . there are two primary ways to deal with the forecast task: template modeling, which predicts structure utilizing similar proteins as a template sequence, and the other is template free modeling, which predicts structure for proteins that have unknown related structure [ ] . the alphafold model depends on an enlarged resnet architecture and uses amino acid sequences, and also features taken out from parallel amino acid sequences using several sequence arrangements, to foresee the distance and the dispersal of angles between amino acid residues [ ] . this framework has been applied to anticipate the structures of six proteins identified with sars-cov- (sars-cov- membrane protein, protein a, nsp , nsp , nsp , and papain-like proteinase) [ ] . it is projected that these predictions will help to see coronavirus capacities and possibly lead to future improvement of cures against covid- . group of specialists at the massachusetts institute of technology are building an approach to obstruct the novel coronavirus that causes covid- by making a "decoy" receptor, or protein, that could be taken as a medication. coronaviruses cause sickness by binding the body's ace receptors. the mit specialists are utilizing an ai model trained on data about the ace receptor to simulate the connection between the baits and the virus [ ] . some research focuses to find novel compounds for use in focusing on sars-cov by utilizing an exclusive pipeline to discover inhibitors for the c-like protease [ ] . such models utilize three sorts of information: the crystal structure of the protein, the co-crystalized ligands, and the homology model of the protein. for each info type, various models including generative auto-encoders and generative adversarial networks are utilized [ ] . the researchers investigate potential applicants using a reinforcement learning approach with a prize capacity that consolidates factors, for example, measures of medication, likeness, novelty, and assorted variety. though national and worldwide associations have utilized social media platforms to communicate with the general population, but apparently this is leading to a crisis in which populaces can become overwhelmed with information, and the propagation of misinformation is progressively common. who's reaction to fighting this infodemic is using its information network for epidemics (epi-win) stage for imparting data to key partners [ ] . apart from that, the facebook promotions with content identified with the infection is analyzed. the facebook ad library [ ] scans all commercials utilizing the catchphrases "coronavirus" and "covid- " and gathered outcomes across nations, with most in the us ( %) and the eu (italy made up % of the ad showcases). a system for covid- detection utilizing information found from smartphones' sensors, for example, cameras, microphones, temperature and inertial sensors is proposed in [ ] . on the other hand, sound information received from a cell phone's microphone is utilized for cough type detection [ ] . this information is significant for ai calculations to learn and foresee the contamination threat of every being, subsequently helping in early identification of high-risk cases for quarantine purpose, thus diminishing the spread of the infection to the helpless populations [ ] . a few drones are utilized to trail people, not applying facemasks, while others are utilized to broadcast information to bigger crowds and furthermore to sanitize open spaces. small-multi-copter [ ], a shenzhen-based innovation, has assisted with decreasing the infection transmission hazard in city-wide transport of clinical supplies and quarantine materials through drones. to battle the spread of the novel coronavirus spread in india, the administrations launched aarogya setu [ ] mobile application that trails coronavirus cases around and helps in battling the infection on an individual level. it helps in tracking the coronavirus contamination by utilizing the cell-phone's gps framework and bluetooth and give data that will help in deciding whether you have been close to a covid- tainted individual or not. researchers are investigating each possible choice for fighting the coronavirus pandemic, and modern technology represents to a captivating road. while technology advances have entered into our day by day lives with numerous victories, they have additionally added to helping people in the very intense battle against covid- . the papers talk about the troubles while using these algorithms in real world clinical practices. likewise, there is an interest for a future work on building up a benchmark framework to assess and look at the current techniques. the present models acquired extraordinary accuracy in recognizing covid- symptoms with different kinds of viral pneumonia utilizing radiology pictures but lacks transparency and interpretability. it can be conclude that there is a wide scope of potential utilizations of modern technologies covering clinical and cultural difficulties made by the coronavirus pandemic; but not many of them are right now develop enough to show operational effect. nil the uses of drones in case of massive epidemics contagious diseases relief humanitarian aid: wuhan-covid- crisis artificial intelligence in the battle against coronavirus ( covid- ): a survey and future research directions a novel ai-enabled framework to diagnose coronavirus covid using smartphone embedded sensors: design study response to covid- in taiwan big data analytics mapping the landscape of artificial intelligence applications against covid- a deep learning algorithm using ct images to screen for corona virus disease (covid- ) automatic detection of coronavirus disease (covid- ) using xray images and deep convolutional neural networks development and evaluation of an ai system for covid- diagnosis covid-net: a tailored deep convolutional neural network design for detection of covid- cases from chest radiography images a deep learning algorithm using ct images to screen for corona virus disease (covid- ) deep learning system to screen coronavirus disease development and evaluation of an ai system for covid- diagnosis serial quantitative chest ct assessment of covid- : deep-learning approach real-time reverse transcription-polymerase chain reaction assay for sars-associated coronavirus correlation of chest ct and rt-pcr testing in coronavirus disease evaluation and treatment coronavirus (covid- ) abnormal respiratory patterns classifier may contribute to large-scale screening of people infected with covid- in an accurate and unobtrusive manner identification of covid- can be quicker through artificial intelligence framework using a mobile phone-based survey in the populations when cities/towns are under quarantine world-wide covid- outbreak data analysis and prediction a time-dependent sir model for covid- with undetectable infected persons a machine learning-based model for survival prediction in patients with severe covid- infection. medrxiv prepr xgboost: a scalable tree boosting system machine learning based ct radiomics model for predicting hospital stay in patients with pneumonia associated with sars-cov- infection: a multicentre study impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand baricitinib as potential treatment for -ncov acute respiratory disease understanding covid- : what does viral rna load really mean? using ai for scientific discovery what is the protein folding problem ? why is protein folding important multi-scale context aggregation by dilated convolutions deep residual learning for image recognition covid- and the raas -a potential role for angiotensin ii ? potential covid- c-like protease inhibitors designed using generative deep learning approaches how to fight an infodemic use of a smartphone thermometer to monitor thermal conductivity changes in diabetic foot ulcers: a pilot study poster abstract: a comprehensive approach for cough type detection on the coronavirus (covid- ) outbreak and the smart city network: universal data sharing standards coupled with artificial intelligence (ai) to benefit urban health monitoring and management we would like to thank editor, associate editor for their valuable suggestion which greatly helped in the improvement of the earlier version of the manuscript. diagnosis using radiology images• ai is used to extract radiological features for timely and accurate covid- diagnosiswang et al. [ ] , narin [ ] , wang et al. [ ] , xu et al. [ ] yes [ yan, zhang, goncalves et al. [ ] , qi et al. [ ] no [ ]• he machine learning-based ct radiomics models showed feasibility and accuracy for predicting hospital stay in covid- patients computational biology and medicines perspective• benevolentai used to search for baricitinib, which is predicted to reduce the ability of the virus to infect lung cells.richardson et al. [ ] no • cough type detection using an extensive set of acoustic features applied to the recorded audio from a relatively large population of both healthy subjects and patient key: cord- -m kfom x authors: kyriakopoulos, anthony m.; papaefthymiou, apostolis; georgilas, nikolaos; doulberis, michael; kountouras, jannis title: the potential role of super spread events in sars-cov- pandemic; a narrative review date: - - journal: arch acad emerg med doi: nan sha: doc_id: cord_uid: m kfom x coronaviruses, members of coronaviridae family, cause extensive epidemics of vast diseases like severe acute respiratory syndrome (sars) and coronavirus disease- (covid- ) in animals and humans. super spread events (sses) potentiate early outbreak of the disease and its constant spread in later stages. viral recombination events within species and across hosts lead to natural selection based on advanced infectivity and resistance. in this review, the importance of containment of sses was investigated with emphasis on stopping covid- spread and its socio-economic consequences. a comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the “potential role of sses on severe acute respiratory syndrome coronavirus (sars-cov- ) pandemic” and were published before (th) of august . overall, ninety-eight articles were found eligible and reviewed. specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus (sars-cov- ) epidemics, in contrast to the partially effective general restriction measures. the effect of sses on previous sars epidemics has been documented in detail. however, the respective potential impact of sses on sars-cov- outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective sse preventive strategies, which may lead to overt global community health benefits. this is crucial for sars-cov- pandemic containment as the vaccine(s) development process will take considerable time to safely establish its potential usefulness for future clinical usage. severe acute respiratory syndrome (sars) has periodically emerged as epidemics and its natural history could be utilized as a "compass" to comprehend and manage the current pandemic of sars-cov- . sars-cov- the etiologic agent of the novel coronavirus disease (covid- ) , be-although the prediction and subsequently the prevention of sses seems to be complicated, the virus, host, environmental, and mass behaviors determine relative approaches to prevent and control sses; core community health programs can inhibit and decrease the incidence and the effect of sses ( ) . nevertheless, horizontal austerity measures, such as recommending or compelling individuals to self-isolate at home, which might cause serious social and psychological burden, and quarantine, also leading to loss of income due to social distancing, are associated with negative psychological and religious effects, which can be long lasting ( ) , thereby leading to serious instability of the global society. prolonged social isolation and loneliness are associated with increased mortality ( ) . currently, limited piece of information exists regarding the effect of sses on coronavirus epidemics. the aim of this narrative review is to mainly focus on the potential impact of sses on large outbreaks of coronavirus. the development of an emergency sars-cov- vaccine has its potential usefulness and/or limitations and may result in severe health outcomes, which prompts better screening for sses in order to control coronavirus pandemics. to avoid, in most respects, literature selection bias ( ) , multiple electronic sources: medline/pubmed, scifinder, science direct and goggle scholar as well as researchgate and general (google) were investigated via queries with a nonrestricted time frame reaching the th of august . initial investigation of sses and sars, sses and mers, and sses and covid- , gave narrative results from pubmed. the selected literature, which is included in the study, is presented in table . same items were also searched in all other mentioned sources. the scope of the study was not only to investigate the transmission of sars-cov- due to sses, its comparison with sars-cov- and mers-cov, but also to assess the general global impact due to sses by covid- . therefore, further literature investigation was performed using the same electronic sources. further investigation was made on: a) the prevention of sses by coronaviruses causing sar- , mers and covid- , b) the socio-economic relation of sars-cov- , mers and covid- due to sses, c) the austerity caused by sses of covid- , and d) the relation of sses containment to future vaccination programs. for further investigation, the following items were searched: "sars, mers and covid- epidemic prevention", "sars mers and covid- infectivity and pathogenicity", "coronavirus sse prevention", sse coronavirus crisis and socio-economics", "holy cup reli-gion and transmission of pathogens and sses", and "coronavirus immunity and vaccination". studies providing an adequate determination of an sse related to sars, mers and covid- were primarily screened and selected by two reviewers (authors) blinded to one another. the results were thereafter cross-matched and duplicates were removed. based on this primary search, the socio-economic impact of coronavirus, produced by sses, was extrapolated by two other reviewers (authors). following this initial selection stage, further screening was performed by all reviewers, using the previously described search items to identify parameters determining the global impact of covid- due to sses. identified parameters included the global impact of immunity and vaccination, the holy cup and religion transmission, and the austerity caused by covid- and other coronavirus epidemics due to restrictions applied. all search results were cross-matched to remove duplicates and thereafter, exclusion and inclusion criteria were applied. after removing the duplicates, review was conducted on titles and abstracts. also, a decision was made to remove "news press opinions". computational model methodologies producing contradictory results, studies with wrong interpretation of sses, and studies with non-clear-cut results were also removed. studies using the interpretation "a super spreading individual, known as the index case, produces a cluster of sars, mers, and covid- secondary infections" were included. a second exclusion criterion was applied. in this stage, peer reviewed literature of recent dates, studies assessing sars, mers, and covid- epidemiology measures, studies on covid- restriction measures producing social and economic austerity, articles discussing the perspective for future vaccination and population immunity, and finally genetic studies on coronaviruses causing sars, mers, and covid- . by following the described methodology, on medline/pubmed: a) articles were found on sars and mers and sse, and b) articles were found on covid- and sses. out of: a) of the articles on sars and mers and sse, and b) out of the articles on covid- and sse were deemed relevant hits. after applying the exclusion criteria, articles from the first category, and from the second category were included in the study. suitable articles found by searching, which were selected and reviewed for each part, are illustrated in figure . further investigation in all other electronic sources described, using the same method- ( ) original research description of sse importance in covid- epidemic ! severe acute respiratory syndrome; ∧ middle east respiratory syndrome; &coronavirus disease- ; *super spread events; **when clearly indicated in article, the type of study is also mentioned. ology, increased the number of the included literature to a) and b) , for their respective categories of search. studies included from pubmed in these categories of searches are briefly described and listed in table . further, assessing the general global impact of sses related to covid- , using all the mentioned sources, via the same methodology, led to the inclusion of a) articles related to genetic analysis of sars-cov- and mers-cov and sars-cov- , b) articles related to super spread events, c) articles related to austerity, d) articles related to infectivity and pathogenicity of sars, mers and covid- , e) articles related to prevention of sses concerning human coronaviruses, f) articles related to socio-economic impact, and g) articles related to immunity and future vaccination. table illustrates the initial numbers of hits using all search items in all sources, and the final number of articles reviewed in each category. the involvement of sses in sars extensive outbreaks ( , , , ( ) ( ) ( ) ( ) ( ) , necessitates urgent elucidation as global tranquility is disturbed by covid- pandemic. epidemiological research has proposed that the outbreak was related to a seafood market in wuhan (hubei, china), underlining the ongoing risk of viral transmission from animals to induce severe diseases in humans. metagenomic rna sequencing of bronchoalveolar lavage fluid from a patient with pneumonia identified a novel rna virus strain from the coronaviridae family (called sars-cov- ); and phylogenetic analysis (by introducing the widely used in silico protein screening) ( ) ( ) ( ) ( ) of the complete viral genome ( , nucleotides) disclosed that the virus was most closely connected ( . % nucleotide similarity) with a group of sars-like coronaviruses (genus betacoronavirus, subgenus sarbecovirus) formerly isolated from bats in china ( ) ( ) ( ) ( ) ( ) . ( , , , ) , that closely related sars-like viral genes were traceable in chinese bat populations. authors claimed that these viruses were capable of infecting humans, by selective adaptations or adjustments, and thereby, causing a new epidemic ( ) . enhancement of virulence is also attributed to these adaptations due to acquisition of spike protein via adaptive mutations ( ) . continuous viral random mutations are possible through in- termediate host transmission, until a deadly virus develops, as illustrated in figure . recent evidence revealed that recombination within intermediate hosts has contributed to development of sars-cov- ( , ). asian outdoor markets could constitute the ideal places for continuous viral mutation exchanges ( ) . as presented in table , the best way to circumvent continuous virus production is targeted surveillance; to at least stop the overspreading by sses ( , , , ) . this has also been proposed by menachery et al. ( ) . sars-cov- is accountable for the unprecedented covid- pandemic ( ) , and the interplaying mechanisms involved in the pathophysiology of covid- include sars-cov- virulence, host immune response, and complex inflammatory reactions ( ) . emerging data, also, imply that the reser-voirs of sars-cov- infection may be similar to covid- ( , , , , ) , as remarkable similarities exist between sars and swine acute diarrhea syndrome (sads) in topographical, temporal, environmental and etiological backgrounds. however, the increasing coronavirus variety and spread in bats were recognized as a potential target to diminish future epidemics that might impend livestock, community health, and financial progress ( ) . probably, identification of animal and insect vectors that transmit the disease, identification and control of alternative routes of transmission like fecal-oral route, and identification of super spreader patient groups could help minimize the epidemiological extent compared to the one observed for sars-cov- infection worldwide. lessons from sars epidemic taught us that the key to control is minimizing the time from the diagnosis of infection to prompt hospital isolation and diminishing the probability table : key clinical and laboratory screening functions to appropriately forecast, prevent, and confront sars! coronavirus , and future coronavirus epidemic waves to estimate the probability of a major outbreak, use simulations of stochastic compartmental epidemic models. use of diagnostic tests to detect asymptomatic susceptibility and pre-symptomatic infectivity estimation of super spread events of current and previous coronavirus epidemics introduction of individual reproductive number. integrated and computational analysis of the influence of individual variation by binomial distribution and use of branching process analysis of disease data. genetic characterization of inpatient viral isolates to identify intermediate animal hosts facilitating the infection next generation sequencing of samples and cultured viral isolates to obtain full sequence and phylogenetic analysis application. environmental detection and continuous sewage monitoring rt-qpcr# screening on sewage systems, vectorsÙĹ and potential air transmission. autopsies and detection of serology conversion of potential vectors. heptad repeat region screening for positive selection computer simulation models to detect positive selection events e.g. codeml branch-site test coupled with bayes empirical bayes procedure, and mixed effects model of evolution. receptor recognition analysis of ace-ii+ to identify origin of crossspecies and human to human transmissions coronaviruses genetic sequencing and phylogenetic analysis of ace-ii to provide origin and efficiency of cross-species and human to human transmission and identification of intermediate hosts. !severe acute respiratory syndrome; #reverse transcriptase quantitative polymerase chain reaction; +angiotensin-converting enzyme-ii. fecal -oral frequent contact with wild animal reservoirs (including domestic animals) and birds** airborne and fecal -oral construction area workers air particles sewage system workers*** fecal -oral *in both community and hospital environments. **including slaughter houses, pet shops, animal and bird collectors and breeders, cow, and pig farmers. ***including workers coming in contact with environment contamination. !human immunodeficiency virus, #methicillin resistant staphylococcus aureus. of another sse ( ). the typically recognized - rule or the so-called "pareto rule", states that % of efforts lead to % of results ( ) . more specifically, this comprises a principally convenient state when tackling infectious diseases and is applied to investigate infection transmission, and initially among cattle farms. in this regard, woolhouse et al. ( ) reported that targeted actions concerning disease control and prevention in % of the farms that mainly supplied the basic reproduction number (ro) decreased spread by % ( ) . focusing on the covid- virus, ro is a sign of virus transmissibility, denoting the average figure of novel infections caused by an infectious individual in a totally naive population. for r > , the number of infected people tends to increase, whereas for r < , transmission is likely to stop; ro represents a chief model in the epidemics, signifying the risk of an infectious mediator with regard to epidemic spread ( ) . recent data indicate that the estimated mean ro for covid- is almost . , with a median of . and the interquartile range (iqr) of . , which is substantially higher than who's estimation of . . however, due to biased methodology, ro for covid- is expected to be about - , which is approxi-mately consistent with the who estimate ( ) . sses appear to be a main limitation of the ro concept. ro, when calculated as a mean or median value, does not include the heterogeneity of transmission between infected individuals ( ); two infective agents with equal r estimates might have noticeably diverse patterns of transmission. moreover, the goal of a health care system is to achieve ro < , which is probably only phenomenally feasible in certain conditions without scheduled prevention, recognition, and response to sses ( ) . naturally, epidemics follow the aforementioned / rule ( ) . specifically, in human population, due to heterogeneous exposure to infectious agent, the % core population may transmit the disease, widely. for sars, the rate might have been even lower than % ( ). the increased infectious potential of a small population subgroup seems to be related to immunodeficiency, such as in hemodialysis, cancer, immunosuppressive therapies ( , , , ) . additionally, facilitation of disease spread and transmission due to vector exposure has been investigated in relation to cockroaches ( ) . possible mechanical transportation by rats and cat ( , ) and air transmission ( ) in sars-cov- have also been studied. other animals capable of being sars-cov- carriers (excluding mice and rats), like pigs, ferrets, cats, and nonhuman primates have recently been introduced ( ), and contamination of sewage with sars-cov- , has probably preceded covid- outbreak in france ( ) . all these agents may contribute to a minimum of % of the total transmission potential ( ), maybe even more ( , ) . table displays possible super spreader groups; thus, indicating screening targets to prevent sses. sars epidemic taught us that control programs were inefficient in controlling the epidemic within a population, and failed to identify and provide a targeted infection diagnosis in groups causing potential sses ( , ) . on the other hand, sars-cov- having the ability to cause a pandemic rather than an epidemic, resulted in an increased number of cases and deaths; albeit having a lower mortality rate than sars coronavirus ( ) . sses during covid- may involve not only one city, but also a whole country or many countries, requiring investigation of their effects on a national or international level ( , , ). preventing and decreasing covid- -related sses necessitates the decryption of the mechanism through which sars-cov- spreads through super spreader individuals, for example within healthcare facilities ( , ) . healthcare facilities are essential for prevention and control of sses ( ) . sse prevention may enable us to even overcome initial low covid- virus infectiveness. the capability of the virus to produce sses troubles the epidemiological attempts to restrict viral spread only by isolating individuals at high risk and performing obsolete isolation at home for the general population as carried out in countries such as greece ( ) . during the sars epidemic in china (beijing) and singapore, the vast majority of infected individuals were barely infective and only % of the population was highly infectious, in contrast to many published sars models ( , ) . other ways of potential coronavirus transmission between hosts may provide explanations for enormous outbreaks ( ) . it should not be disregarded that coronaviruses cause both respiratory and intestinal infections and share common evolutionary roots with hepatitis viruses ( , ) . passing the cross-species barrier and genetic adaptation within hosts may promote virulence of coronaviruses in humans ( ) . this, prompts to specifically identify potential super spreader groups within populations through targeted diagnosis. some of these groups are listed in table . for this purpose, a usual infection must be distinguished from a super spread infection ( , ) . during sars epidemic, the coronavirus infectiousness mostly occurred in the late stages of infection ( , ) , whereas in covid- , viruses are transmitted even in pre-symptomatic stages ( ) . as with influenza a virus subtype h n transmission ( ) , accurate diagnosis of covid- in potentially asymptomatic super spreaders may help contain the magnitude of large outbreaks ( ) . in the case of diamond princess cruise ship, an earlyassessed r of . (âl'Ĺ times higher than the r in the epicenter of the outbreak in wuhan, china) was decreased to an assessed effective ro of . following on-board isolation and quarantine processes ( ) . similarly, in china (wuhan) the application of non-pharmaceutical interventions in the society, including a cordon sanitaire of the town; interruption of community transport, school, and most employment; and termination of all community events decreased the ro from . to . over a -week period ( ) . nevertheless, these strategies could not be maintained. emerging research evidence ( ) regarding sewage contamination that preceded paris covid- epidemic is pointing to the reports of from the health department of hong kong ( , ) , the noble work by ng ( ) , and urge for extensive environmental monitoring ( , ) to prevent future covid- relapses. however, the flow of genetic variation may be even more complex as illustrated in figure . therefore, advanced clinical and laboratory monitoring is required to prevent sses and thereafter, new coronavirus epidemics. assembly of key functions and screening techniques of reference centers is presented in table . newer therapeutic agents and protocol applications are promising ( ) , although probably carrying the possibility of resistance state ( ) . first, these also require specific diagnostic and surveillance strategies to overcome any unknown adverse epidemiology consequences ( ) . inhibiting wild meat markets and related consumption of wild meat by creating vivid campaigns could be a critical for interrupting the introduction of coronaviruses crossing from animals to the human population, as was the case for sars ( , , ) and middle east respiratory syndrome (mers) ( ) epidemics, and probably now for covid- pandemic ( - ) . furthermore, the food production process requires radical reconsideration, concerning the industrial environment of current food production and serious violations of natural ecosystems ( ) . current industrial procedures for preparing food increasingly favor conditions where viral evolution produces new mutations and increased rates of mutations ( ) , thus raising the probability of new and more infectious viral strains. in sars and mers epidemics, the role of sses in vigorously distributing the epidemics has been substantially proven ( ) ( ) ( ) ( ) ( ) . the new covid- epidemiology evidence also adequately highlights the important role of sses in homeland of china ( , , ) , although surprising evidence from neighboring countries show the unlikely role of sse in the spread of the disease ( ). the coronaviridae family is characterized by a positive-sense single-stranded rna genome. mouse hepatitis virus is a representative member of the family ( ) . additionally, human hepatitis e virus also has a positive-sense single stranded rna genome and shares a common evolution pathway with coronaviruses ( ) . hepatitis-related incidents were described for sars ( ) . the genetic recombination of these viruses within arbitrary intermediate hosts produced contagious strains that are extremely pathogenic to humans ( , ) . in this respect, the relation of sars-cov genetic sequences isolated from human, civets, and bats permitted us to find the reason for such a dangerous epidemic, which affected people on a worldwide scale in ( ) . moreover, the unpredictable epidemic of mers-cov posed a serious risk to the health of communities worldwide. these underscored the necessity for further research of the virus epidemiology and pathophysiology to develop successful therapeutic and preventive medications against mers-cov infection ( ) . while sars-cov- is genetically and structurally connected with mers-cov, it has its own exclusive structures which are responsible for its quick spread throughout the world ( ). specifically, variations in coronavirus pathogenicity within different species ( ) make the understanding of sars epidemics even more unclear through their capability to overcome the barrier for cross species transmission, which also alters their infectivity status ( , ) . as a result, boosting the pathogenic behavior of coronavirus strains, within species ( ) , and across species barriers ( ) , which is a reflection of their positive adaptation to rapid recombination events ( ) . the recent mers epidemic revealed the tendency of the strain to genetically adapt and produce greater outbreaks ( ) as occurred in sars epidemic in ( ) . however, mainly for socioeconomic reasons, alarm signals were ignored until recently ( ) . a new phylogenetic analysis technique employed on clustered covid- strains displayed a geographic variation preference in infectivity and pathogenesis ( ) . this is probably due to predominating strain's tendency to cause an sse as an outcome of a multi-factorial epidemic process presented in figure ( , ) . marked sses for covid- have already been fully characterized and warrant urgent investigation ( , ) . as presented in tables and , each way of transmission should be investigated. heterogeneity of epidemic characteristics across nations ( ) implies that in this way we may minimize coronavirus transmission. therefore, salvation of national economic catastrophes will also be achieved in this way ( ) . thus, the whole biomedical science machinery needs to perform targeted diagnosis of sses and share the obtained experience. subsequently, central authorities will no longer need excessive non-specific contact measures, which will in turn normalize both societal and economic activities. on the other hand, improper understanding of how covid- spreads resulted in societal imbalance due to arbitrary restriction of social and religious life including holy communion cup. it has been consecutively demonstrated by expert research that the holy cup (chalice) and the holy cloth are not sources or pathways, for potential spreading of infectious diseases including human immunodeficiency virus (hiv) ( ), hepatitis b virus (hbv) ( ) as well as other communicable pathogens ( ) . specifically, a review ( ), considered other relative studies. in this review, the possibilities that the shared communion cup can act as a vehicle for indirect transmission of human immunodeficiency virus, since it was detected in the saliva of infected individuals, was investigated. it was emphasized that although for bacterial contamination, the alcoholic content of the wine, the material that the cup is made of, or the practice of partially rotating the cup, cannot stop the occasional transmission of microbes, the microbial transmission was considerably reduced by the intervening use of a cloth to swab the lip of the cup between communicants. notably, it was emphasized that transmission means not an obligatory inoculation or infection. furthermore, it was also emphasized that out of the epidemiology of microbes transmitted via saliva, particularly for the transmission of the herpes viruses, the indirect transmission is rare, and indeed transmission is highly possible by other means than by the saliva. it was also emphasized that neither hepatitis b virus nor human immunodeficiency virus infection can be transmitted by saliva, rendering their indi-rect transmission also less likely by inorganic objects. finally, the study concluded that no episode of disease transmission has ever been reported as a result of the shared communion cup use, and that there was not any scientific evidence that the communion cup practice should be abandoned due to the possible risk of spreading of any infection ( , ) . likewise, kingston et al. ( ) , by considering relative papers, also concluded that there is no evidence that the holy communion cup spreads infections. moreover, more recent estimations also demonstrated that no infections have ever been observed as a result of religious rituals including christian common communion chalice practice ( ) ; whereas, data of previous studies implied that saliva could play a role in hbv transmission, are likely to be trivial ( ) . similarly, recent evidence indicate that, although hbv dna and hcv rna can be discovered in the saliva of infected patients, they seem unlikely to transmit infection ( ) . it should be noted that, as in the case of coronavirus ( , ) , hbv also exists in many body fluids including saliva, nasopharyngeal fluid or tears by measures of qualitative and pcr methods ( ) . the detection of hbv dna in saliva motivated our study group to investigate the potential viral transmission through the holy communion cup. two successive retrospective studies were conducted to investigate the role of holy communion as an independent risk factor of hbv dispersion. the first preliminary study included patients from our registry of those with chronic hepatitis b under entecavir (jannis kountouras-personal communication) treatment ( ) , and in the next step, the relative registry of another department of the same hospital was incorporated. other parameters studied, the substantial independent categorical variable to evaluate our hypothesis was the patients' occupation, thereby introducing two sub-groups; priests and non-priests. this classification was performed based on a standard active and perpetual exhibition (at least once weekly) of priests to many people's saliva, as a part of the grounded process of the holy communion cup. the control group comprised of the aggregate of orthodox priests in greece ( , ) and the rest general population ( , , ) at that timeframe. approval of the institutional ethics committee was obtained and all predispositions of the helsinki declaration were fulfilled. the reservoir database did not include any personified information (name, id number, etc.) and thus no informed consent was required. pearson's chi-squared test with degree of freedom was performed to evaluate whether there was a statistically significant difference between the frequencies of hbv infection in case and control groups and statistical significance was set at p < . . the first single-centre registry included patients and one ( . %) of them was a priest. chronic hepatitis b was significantly more frequent among non-priests compared to priests (x ( , n= )= . , p < . ). the extended sample (n= ) included the registry of another department and an aggregate of four ( . %) priests were diagnosed with chronic hepatitis b. likewise, the chi-square test revealed that non-priest subjects were more likely to suffer from chronic hepatitis from hbv infection compared to priests (x ( , n= ) = , p < . ). in conclusion, both of our analyses indicated a lower prevalence of hbv chronic hepatitis among priests when compared to other occupations. currently, vaccines for covid- are in pre-clinical development, and no final clinical phase has been ended due the recent emergence of the disorder. many global entities have stated their plans to produce a vaccine for covid- . according to the who, candidate vaccines are being produced for covid- as of march , ( ) . importantly, for production of highly effective and safe covid- vaccines, features such as the possibility of the induction of antigen-dependent enhancement (ade) and additional severe opposing effects previously detected with sars and mers should be considered. ade is a phenomenon that occurs when non-neutralizing antibodies against proteins of a virus increase, also increasing virus infectivity ( ) . in this regard, coronaviruses can escape the immunity provided by inactivated or recombinant protein vaccines via fast evolution ( ) . the problem with live attenuated vaccines is that the coronavirus can recover its virulence via serial passages in cell culture or in vivo ( ) . moreover, vaccination in animals and humans could facilitate, rather than inhibit, the pathogenesis of the targeted viruses. this can be the consequence of an ade phenomenon. this underlines a mechanism by which specific antibodies facilitate infection with the targeted virus, or cell-based augmentation, a process resulting in an allergic inflammatory response induced by immunopathology ( , ) . many experimental sars-cov- vaccines have been formulated from whole inactivated viruses, due to their advantage of large-scale production, multiple epitope presentation and high conformation stability ( ) . one such vaccine uses viruses from ay a strain of sars-cov- , which are double inactivated using formalin and uv irradiation, the socalled double-inactivated virus (div) vaccine ( ) . although div had initially been demonstrated to induce neutralizing antibodies and to protect against sars-cov- viral replication, both in tissue culture and in young mice, it soon became apparent that older mice suffered from vaccine-induced immune pathologies, including failure to contain viral replication, augmented clinical disease and associated symptoms, and increased inflammatory response and eosinophilic influx ( , ) . in this respect, there is an overlap between the immunopathologic responses connected with coronavirus disease and vaccination, and the role of t helper (th) cells in immune augmentation and eosinophilic lung immunopathology; host th polarized inflammatory reactions portray an important role in the pathophysiology of covid- pneumonia and edema ( , ) . eosinophilic pathology, indicating increased pathogenesis and disease severity in the elderly, has been attributed to the nucleocapsid (n) protein, despite the incorporation of multiple sars-cov- antigens in the div ( , ) . this is on grounds that the n protein is a strong modulator of innate immunity, also acting as an interferon antagonist, and therefore, it has the capability to induce inflammation with subsequent immune pathology in situations of heterologous viral challenge or in immune senescence, where patients fail to mount effective immune responses against the disease ( , ) . the route of transmission is important to be established for sars cov- . as seen with other important infectious diseases of a) air borne transmission such as tuberculosis ( ), b) orofecal transmission such as hev ( ) and c) blood transmission such as hbv and hepatitis d virus ( ) , even if efficient vaccination is established, understanding of sses is still important. recent research data on the immune receptors used by coronaviruses, which reflect their ability to propagate in the human population, imply that complex immune reactions are responsible for a cell to cell transmission. in addition to ace-ii receptor, as is the case with sars-cov, mers-cov ( ) and possibly for sars-cov- ( , ), viruses use complex receptor recognition systems common to immunopathology damage mechanisms in coronavirusinfected individuals, which clearly define the clinical outcome ( ) . therefore, application of vaccines that may interfere with antibody-mediated infection by coronaviruses ( ) without true epidemiologic containment of coronaviruses, to restrict genetic adaptation events and inevitably producing an sse, may be a miscellaneous attempt. however, synergy of sse prevention measures with proper vaccination can provide a robust attempt for disease containment. this study aimed to perform a literature review. although effort was made to decrease the risk of bias of results via double-blind screening of literature and employment of multiple electronic search engines, bias cannot be eliminated due to incomplete retrieval of identified research and biased estimations of included literature conclusions and methods used. outcome of the study may also contain biased estimations originating from wrong interpretation of super spreading individuals in literature reviewed for sars, mers, and covid- outbreaks. although the importance of sses in covid- was recognized by this study, more data from future accumulated epidemiology studies are needed to justify these findings. taken all together, management of sses is mandatory to yield efficient control over sars-cov- . this is achievable through early diagnosis of pre/asymptomatic infected individuals within potential super spreading groups. prevention of outbreaks is more essential, especially due to the lack of efficient vaccination and therapeutic protocols, which necessitates efficient monitoring, as sars-cov- virus follows complex infectious patterns. the sars-cov- epidemiological models that do not take sses into consideration seem to lead to confusing results with high uncertainty. sars-cov- causes prolonged "pandemics" through complex adaptation routes. currently, in addition to the high technology utilized for diagnosis, clinical observation is indispensable to deeply comprehend sses and prohibit further outspread of covid- . reference laboratories with efficient and accredited molecular and serological diagnosis must be inter-linked between countries. all these parameters could contribute to avoiding a second blind unjustified response that characterized the first covid- pandemic spread. understanding the epidemiology of covid- through sses could be preventive for future epidemics. a systematic meta-analysis research methodology, when covid- epidemiology data accumulate further, would be advisable to confirm the conclusions of this study. this study did not involve the participation of any humans or animals as it was based only on literature research. ak inspired the conception and drafted the initial manuscript. jk revised substantially the manuscript, intellectual content and provided disclosed data for hbv investigation. ak and jk made the primary double-blind search. ap, jk, ak, mn, and ng, made all other searches. ap contributed to the immunology aspect of manuscript. ap and ng aided in the clinical part and preparing the final version of the manuscript. md contributed to bibliographical search and revision of the manuscript. all authors contributed to the english editing of the manuscript. âȂČ genomic and protein structure modelling analysis depicts the origin and infectivity of -ncov covid- , sars and mers: are they closely related? clinical microbiology and infection receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus superspreading and the effect of individual variation on disease emergence transmission dynamics of the etiological agent of sars in hong kong: impact of public health interventions the role of superspreading in middle east respiratory syndrome coronavirus (mers-cov) transmission the role of super-spreaders in infectious disease network analysis of mers coronavirus within households, communities, and hospitals to identify most centralized and super-spreading in the arabian peninsula identifying and interrupting superspreading eventsâȂŤimplications for control of severe acute respiratory syndrome coronavirus . emerging infectious diseases the psychological impact of quarantine and how to reduce it: rapid review of the evidence loneliness and social isolation as risk factors for mortality why systematic review rather than narrative review? psychiatry investigation possible role of an animal vector in the sars outbreak at amoy gardens. the lancet coronaviruses post-sars: update on replication and pathogenesis superspreading sars events soluble receptor potentiates receptor-independent infection by murine coronavirus heterogeneities in the transmission of infectious agents: implications for the design of control programs identification of a novel antibody associated with autoimmune pancreatitis helicobacter pylori and autoimmune pancreatitis: role of carbonic anhydrase via molecular mimicry? challenge in the pathogenesis of autoimmune pancreatitis: potential role of helicobacter pylori infection via molecular mimicry in silico screening of chinese herbal medicines with the potential to directly inhibit novel coronavirus a new coronavirus associated with human respiratory disease in china a sars-like cluster of circulating bat coronaviruses shows potential for human emergence genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding. the lancet the population genetics of mutations: good, bad and indifferent the deadly coronaviruses: the sars pandemic and the novel coronavirus epidemic in china convalescent plasma in covid- : possible mechanisms of action covid- âȂŤ toward a comprehensive understanding of the disease time course quantitative detection of sars-cov- in parisian wastewaters correlates with covid- confirmed cases fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin cannabidiol as prophylaxis for sars-cov- and covid- ? unfounded claims versus potential risks of medications during the pandemic amplification of the basic reproduction number in cattle farm networks the reproductive number of covid- is higher compared to sars coronavirus the current treatment landscape of irritable bowel syndrome in adults in hong kong: consensus statements outbreak of severe acute respiratory syndrome (sars) at amoy gardens, kowloon bay, hong kong main findings of the investigation legislative council select committee to inquire into the handling of the severe acute respiratory syndrome outbreak by the government and the hospital authority of hong kong environmental transmission of sars at amoy gardens sars-cov- (covid- ) phylogenetic network analysis of sars-cov- genomes evolutionary biology of human hepatitis viruses presymptomatic transmission of sars-cov- âȂŤ singapore transmission during presymptomatic phase, japan. emerging infectious diseases detecting presymptomatic infection is necessary to forecast major epidemics in the earliest stages of infectious disease outbreaks covid- outbreak on the diamond princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures evolving epidemiology and impact of nonpharmaceutical interventions on the outbreak of coronavirus disease structure of the rna-dependent rna polymerase from covid- the mechanism of resistance to favipiravir in influenza the heptad repeat region is a major selection target in mers-cov and related coronaviruses current status and development strategy for community-supported agriculture (csa) in china transmission characteristics of mers and sars in the healthcare setting: a comparative study pathogen cross-transmission via building sanitary plumbing systems in a full scale pilot test-rig sars: future research and vaccine predicting super spreading events during the severe acute respiratory syndrome epidemics in hong kong and singapore the sars outbreak and its impact on infection control practices covid- super-spreaders: definitional quandaries and implications reconstruction of transmission pairs for novel coronavirus disease (covid- ) in mainland china: estimation of superspreading events, serial interval, and hazard of infection inferring super-spreading from transmission clusters of covid- in hong kong, japan, and singapore sars-associated viral hepatitis caused by a novel coronavirus: report of three cases a review of sars-cov- and the ongoing clinical trials molecular epidemiology, evolution and phylogeny of sars coronavirus. infection molecular characteristics, functions, and related pathogenicity coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus genotype and phenotype of covid- : their roles in pathogenesis bat origin of human coronaviruses the impact of sars epidemic. washington, d.c.: national academies press estimating the global economic costs of sars memorandum on the infections hazards of the common communion cup with especial reference to aids the hazard of infection from the shared communion cup infections associated with religious rituals saliva and viral infections commentary: a review of risk of hepatitis b and c transmission through biting or spitting transmission routes of -ncov and controls in dental practice saliva: potential diagnostic value and transmission of -ncov high levels of hepatitis b virus dna in body fluids from chronic carriers experience of entecavir administration in patients with chronic hepatitis b. annals of gastroenterology the possible of immunotherapy for covid- : a systematic review introduction to modern virology animal coronavirus vaccines: lessons for sars identification of the mechanisms causing reversion to virulence in an attenuated sars-cov for the design of a genetically stable vaccine a double-inactivated severe acute respiratory syndrome coronavirus vaccine provides incomplete protection in mice and induces increased eosinophilic proinflammatory pulmonary response upon challenge avoiding pitfalls in the pursuit of a covid- vaccine successful vaccination strategies that protect aged mice from lethal challenge from influenza virus and heterologous severe acute respiratory syndrome coronavirus a double-inactivated whole virus candidate sars coronavirus vaccine stimulates neutralising and protective antibody responses increase in methicillin-resistant staphylococcus aureus acquisition rate and change in pathogen pattern associated with an outbreak of severe acute respiratory syndrome the potential role of th immune responses in coronavirus immunopathology and vaccine-induced immune enhancement. microbes and infection th responses in cytokine storm of covid- : an emerging target of jak inhibitor fedratinib specific epitopes of the structural and hypothetical proteins elicit variable humoral responses in sars patients the role of super-spreading events in mycobacterium tuberculosis transmission: evidence from contact tracing laboratorybased surveillance for hepatitis e virus infection hepatitis b and hepatitis d virus infections in the central african republic, twenty-five years after a fulminant hepatitis outbreak, indicate continuing spread in asymptomatic young adults carcinoembryonic antigen-related cell adhesion molecule is an important surface attachment factor that facilitates entry of middle east respiratory syndrome coronavirus virus cell-to-cell transmission clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study'. the lancet interaction of severe acute respiratory syndrome-associated coronavirus with dendritic cells understanding the super-spreading events of sars in singapore super-spreading events of sars in a hospital setting: who, when, and why super-spreaders in infectious diseases all authors agree to publish this manuscript. all data used for this manuscript are available upon request all authors declare that they have no competing interests. no funding or grant was received for this study. we thank our families for providing moral assistance to accomplish this study. key: cord- -t zf k authors: brüssow, harald title: the novel coronavirus – a snapshot of current knowledge date: - - journal: microb biotechnol doi: . / - . sha: doc_id: cord_uid: t zf k another animal to human transmission of a coronavirus occurred in december on a live animal market in the chinese city of wuhan causing an epidemic in china, reaching now different continents. this minireview summarizes the research literature on the virological, clinical and epidemiological aspects of this epidemic published until end of february . in late december , chinese physicians identified a series of pneumonia cases in wuhan, an -million inhabitant megacity and traffic hub in central china. the infections were epidemiologically associated with a seafood 'wet' market in the city. 'wet' market means that live and dead animals are sold, raising the suspicion of another zoonotic virus infection that had spilled over into the human population similar to the severe acute respiratory syndrome (sars) epidemic in , which also started from a live animal market. in sars, the viral source was traced back to a bat coronavirus with civets as potential intermediate host. the novel wuhan virus figures under different names ( -ncov for novel coronavirus in the research literature, sars-cov- by the international committee on taxonomy of viruses, covid- as disease denominator by who), all names indicating that it represents a coronavirus. one might argue whether 'new' instead of 'novel' coronavirus is not a better term since it is not completely different, but related to the sars coronavirus, while others find that sars-cov- suggests a too close relations with the sars virus possibly leading to some confusion (jiang et al., ) . as the wuhan virus name changed, so changed the character of the epidemic and this overview can only provide a snapshot of the scientific research literature on this topic at the moment of this writing ( february ). within a record time of less than a month, the novel coronavirus was identified, isolated and sequenced by three groups of chinese scientists. a large consortium coordinated by w. tan from the chinese centers for disease control and prevention (chinese cdc) obtained eight complete viral genome sequences from nine patients either by direct rna isolation and sequencing from bronchoalveolar lavage fluid (balf) or from classical virus isolation on human airway epithelial cells (lu et al., ) . the eight genomes showed sequence identity of . %, i.e. only four nucleotides differed out of the nucleotide-long single-stranded rna genomes. this level of viral genomic identity isolated from different human subjects is unusual for an rna virus that has been circulating for a long time in the human population. this observation suggests a recent single spill-over event from an animal source into humans. geneticists estimated that this event might have occurred in november . the closest relatives of the new virus are coronaviruses isolated from bats in eastern china, but they shared only . % sequence identity with the new isolates. therefore, viral taxonomists consider the novel coronavirus as a new viral species belonging to clade of the sarbecovirus group, acronym for sars comprising betacoronaviruses. with the sars virus, the new isolates shared even less, namely % sequence identity. while bats are still considered the most likely source for this novel coronavirus, bats were already hibernating at the time of onset of this epidemic and no bats were sold at the huanan food market in wuhan, suggesting an intermediate animal host where adaptation to human transmission might have occurred. live hedgehogs, badgers, snakes and turtledoves were sold at the huanan market. claims were made, but were not (yet) substantiated that snakes or pangolins were intermediate hosts for creating the coronavirus by recombination events. w. tan and colleagues, who now constitute the china novel coronavirus investigating and research team, described subsequently the isolation of further coronaviruses from three patients in wuhan who tested negative for viral and four bacterial respiratory pathogens. these viruses were closely related to those of the earlier nine patients. in human airway epithelial cells, the cytopathic effect of this virus was a lack of cilium beating . another group led by y.-z. zhang from the zoonosis group of the chinese cdc in beijing determined the genome of a closely related coronavirus by deep metatranscriptomic sequencing of the bronchoalveolar fluid of a patient working at the seafood market of wuhan (wu et al., c) . analysis of the cell receptor interacting viral s (spike) gene showed indications of a recombination event. protein modelling suggested the human angiotensin-converting enzyme ii (ace ) protein as receptor. z.-l. shi from the wuhan institute of virology, and collaborators, presented a detailed characterization of the viruses detected in seven patients from wuhan suffering from severe pneumonia. six of them were professionally associated with the local food market . metagenomics of balf yielded coronaviruses that shared . % sequence identity between the patients and the other coronavirus isolates from wuhan. using primers corresponding to a region in the s gene, these scientists developed a sensitive and outbreakspecific pcr test providing a diagnostic tool for the virus detection in balf or alternatively oral swabs of patients. for one patient, the researchers demonstrated an igm seroconversion followed by an igg seroconversion when using elisa technique with the viral nucleocapsid as target antigen. three patients showed specific igm responses indicating an acute infection. this serological evidence is important since the full set of koch's postulates for the identification of a new pathogen has not yet been fulfilled. from one patient, they isolated a virus that caused cytopathic effects on the established vero cell line after days of incubation. the virus-infected cells were stained with specific antibodies and were observed by fluorescence microscopy, allowing the establishment of a virus neutralization test. all patients developed neutralizing serum antibodies. while hela cells could not be infected with the novel coronavirus, this cell line became susceptible when expressing the ace protein of human, bat and civet (but not of mouse) origin indicating that this novel coronavirus uses this protein as a cell receptor, as did the sars coronavirus from the epidemic. zhang et al. ( a) compared novel coronavirus genomes isolated from patients in three chinese cities (wuhan, zhejiang and guangdong) and thailand, all of whom had contact to wuhan. the genomes were very similar but could still be classified into six genogroups, suggesting that mutations had accumulated within patients during the current outbreak. curiously, the most basal genogroups were detected in guangdong, and not wuhan, isolates. another group did an in-depth annotation of the genomes of the novel coronaviruses with sars virus and identified amino acid substitutions affecting all predicted proteins of the viral genome (wu, peng et al., b) . one study focused on the cases of patients hospitalized in wuhan before january , all of whom had laboratory-confirmed -ncov infection (huanget al., ) . at this earliest phase of the outbreak, patients were mostly males ( %), half of whom had underlying diseases and % of whom were exposed to the huanan seafood market. common presenting symptoms were fever ( %), cough ( %) and myalgia or fatigue ( %). dyspnoea (laboured or difficult breathing) developed in %; acute respiratory distress syndrome (ards) was seen in %; % of patients needed to be transferred to an intensive care unit (icu); and % died. the patients showed lymphopenia (a reduction of lymphocytes in the circulating blood) and signs of a 'cytokine storm'. a follow-up study investigated patients at jinyintan hospital in wuhan between january and january . all patients had pcr-confirmed -ncov infection (chen et al., ) . during this next phase of the epidemic, fewer patients had had an exposure to the huanan seafood market ( %), but they were still predominantly male ( %). the average age was years, and again, half of them suffered from chronic diseases. the predominant clinical manifestations in these patients were fever ( %), cough ( %) and shortness of breath ( %). imaging techniques showed bilateral pneumonia in % of the cases. seventeen per cent developed ards, which worsened in %, leading to death from multiple organ failure. in a third report, patients with confirmed novel coronavirus infection were admitted between january and at zhongnan hospital of wuhan . this report differed from the previous two in important respects. in this cohort, only % of the patients reported having had an exposure to the huanan seafood market, and the gender ratio was not significantly biased. the presenting symptoms were fever ( %), fatigue ( %) and dry cough ( %), followed by anorexia, myalgia and dyspnoea. bilateral shadows, or ground glass opacities, were revealed by imaging techniques in the lungs of all patients. overall, % of the patients needed a transfer to icu and % died. half of the patients showed comorbidities (hypertension, cardiovascular disease and diabetes). most notably, % were possibly infected in the hospital, including healthcare workers. until february , only nine cases of -ncov infections were reported in infants under year in china, all of whom had had infected family members. all infants had a mild form of disease (wei et al., ) . for planning public health measures, basic transmission data for the novel coronavirus are essential. the first confirmed cases from wuhan provided data for a first epidemiological analysis (li et al., a) , but it should be kept in mind that the virus might evolve during the epidemic and change its properties. over the three early phases of the infection (< jan , jan - , jan - ), no change in average age was seen ( - years); no cases < years of age were observed. male dominance among the patients disappeared, and the degree of 'wet' market exposure in the patients dropped over time. in addition, patient contact with persons showing respiratory symptoms was reported in fewer than % of the cases. these scientists calculated a mean incubation period of . days displaying a long tail ( th percentile: . days). comparisons of index cases and secondary cases in five clusters yielded a 'serial interval' of days. from onset of illness to a medical visit, and then to hospital admission, and days elapsed respectively. the wuhan epidemic showed a doubling time of days. from the cluster analysis, a basic reproduction number of . was estimated, i.e. each case led on average to . new infections. another report investigated a case of a family from shenzhen visiting relatives in wuhan . one wuhan relative had developed fever, cough and dyspnoea four days before the arrival of family members from shenzhen. four further relatives developed respiratory symptoms which led to hospitalization in two. from the six shenzhen family visitors, the four adults developed symptoms (fever, cough, weakness and diarrhoea) during the days of their wuhan visit, while two children remained unaffected. notably, a family member who remained in shenzhen contracted the disease four days after the return of the visitors from wuhan to shenzhen. the data are evidence for efficient human-to-human virus transmission. the virus was detected in most nasopharyngeal and half of the throat swabs, a single serum sample, but no urine or stool sample of this family cluster. of importance for easy sampling and virus diagnostics, % of hospitalized patients from hongkong were positive for pcr virus detection in self-collected saliva (te et al., ) . the viral load ranged from to viral copies per ml saliva and decreased over the duration of hospitalization, but in one patient, it was still detectable days after hospitalization. another study extended the epidemiological analysis to infected patients living outside of wuhan, but who had a recent travel history to wuhan (backer et al., ) . this cohort allowed an estimation of the mean incubation period to . days. upper estimates range up to days, which is important to determine the appropriate duration of quarantine. the novel coronavirus is spreading rapidly. on january , the first patient was reported on the west coast of the united states. the patient developed respiratory symptoms after a family visit to wuhan (holshue et al., ) . during hospitalization, the patient developed diarrhoea and the stool was weakly virus-positive. this observation is important since it could indicate a gut tropism in addition to lung tropism, not unusual for coronavirus. one might therefore count on a changing symptomatology in the unfolding of the current epidemic, necessitating public health measures against faecal-oral transmission (danchin et al., ) . this scenario is not unlikely, since the ace host receptor for the novel coronavirus is highly expressed on gut enterocytes (liang et al., ) . some change in symptomatology was already seen for chinese patients outside of wuhan. among the first -ncov patients from beijing, upper airway congestion was the dominant finding (chang et al., a) . disease in laboratory-confirmed patients from zhejiang province showed mostly mild to moderate disease; % had diarrhoea, and only one patient needed icu (xu et al., ) . when analysing cases, an overall case fatality rate (cfr) of . % was calculated. however, when the analysis was limited to cases outside of the hubei province (where wuhan is located), the cfr was only . % (wu and mcgoogan, ) , possibly suggesting change of the epidemic to milder diseases with larger chains of transmission (vetter et al., ) . on january , two citizens of germany developed symptoms and became -ncov-positive after meeting a chinese business partner, who only became ill on the flight back to china. two further subjects developed symptoms who had contact with one of the infected germans notably before this person developed symptoms. this report suggests that infected persons can infect contact persons during the incubation period (rothe et al, ) . wu and leung ( a) estimated the national and global spread of the novel coronavirus on the basis of the air and train traffic data from and to wuhan, accounting for the strict metropolitan-wide quarantine measure imposed on wuhan on january by using an infection metapopulation model. according to this calculation, sufficient numbers of infected subjects had already been exported to major chinese cities ( infected subjects to five cities) to start secondary local epidemics. the peak of the wuhan epidemic was predicted for april and that of local epidemics peaks in other chinese cities would lag by - weeks. if transmissibility could be reduced by % through restrictions of people's mobility, then the magnitude of the epidemic could be reduced by % and the peak of the epidemic would be delayed by one month. one major unknown factor of this model is the seasonality of the novel coronavirus infections, respiratory infections being typical winter infections declining with the warming of the seasons. research, available only as preprint (lai et al., ) , estimated that more than infected subjects from wuhan travelled to international destinations, with thailand and japan leading the list. public health measures must therefore also be taken in these countries to contain the international spread of the epidemic. the epidemic has also reached europe with an unexplained focus in northern italy. particularly, worrisome will be the spread of infections to african countries where many regions have close economic connections with china, but insufficient hospital and public health resources to assure efficient containment measures (gilbert et al., ) . risk of transmission to africa and south america is, however, by some epidemiologists considered to be low (haider et al., ) . it is currently unclear whether transmission will be muted in agro-economies with lower population densities. so far, chinese physicians have developed an empirical treatment and triage algorithm based on their experience with patients from wuhan (zhang, et al., b) . this triage scheme proposes a separation of patients into those receiving home treatment and those receiving treatments for regular community acquired pneumonia. suspected viral pneumonia cases are tested for the novel coronavirus under isolated observation; in case of dyspnoea and hypoxia development, supplemental oxygen supply will be given. the viral pneumonia patients were treated with arbidol, approved in russia and china for influenza treatment. when the diagnosis of the novel coronavirus has been confirmed, a patient has been transferred to a specially designated hospital. the efficacy of arbidol against coronavirus is not, however, well substantiated scientifically or clinically. emergency conditions call for a need for speed in drug development. a promising approach is the repurposing of drugs tried against coronaviruses from previous outbreaks with sars or middle east respiratory syndrome (mers) coronavirus (li and de clercq, ) . mers, in contrast with sars, is a coronavirus zoonosis of likely bat origin with camels as intermediate hosts that is still circulating. the four non-structural proteins that were preclinically explored as antiviral targets against sars and mers coronaviruses are reasonably well conserved in the novel coronavirus, raising hopes for this approach. however, patient enrolment for a mers treatment trial with lopinavir (an antiretroviral proteinase inhibitor)/ritonavir (cytochrome p inhibitor to prolong the half-life of lopinavir) and interferon-b b (miracle) is still ongoing. numerous clinical trials have been registered in china to test different compounds or combinations of compounds against the new coronavirus infection. test drugs range from antiviral nucleotide analogs over viral protease inhibitors to traditional chinese herbal medicine (e.g. forsythia derivative lian qiao) (maxmen, ) . it is important to start the tests now to get the informative patients enrolled and tested before the current epidemic stops. who suggests a shared standard clinical protocol for these trials to make the outcomes comparable. with virus neutralization tests now at hand, chinese researchers have already done in vitro efficacity tests against the novel coronavirus . the most promising effects were observed with the nucleotide analog remdesivir and the anti-malaria compound chloroquine. both showed inhibition of the novel coronavirus in the low micromolar concentration range. remdesivir acts on viral rna transcription at the postviral entry level, while chloroquine needs to be applied at the beginning of the infection; chloroquine's action on lysosome membranes might interfere with the viral entry-fusion events. it is of note that the nucleotide analog remdesivir had a better activity against mers coronavirus than the protease inhibitor lopinavir combined with ritonavir, and this both in cell culture and in mouse infections. in the mouse mers infection model remdesivir improved pulmonary function, reduced lung viral loads and decreased severe lung pathology (sheahan et al., ) . in addition, remdesivir given prophylactically to mers virus-challenged rhesus monkeys significantly reduced viral titres in the lung and prevented lung pathology as assessed by histology or by x-ray radiographs when compared to control animals (de wit et al., ) . treatment with remdesivir h after viral challenge had a more limited protective effect in rhesus monkeys. in early february, two randomized, placebocontrolled clinical trials testing the therapeutic efficacy of remdesivir were started in china. one trial will enrol patients with mild or moderate novel coronavirus disease (clinicaltrials.gov: nct ) and the other patients with severe disease (clinicaltrials.gov: nct ). the enrolment is planned to be completed by end of april and may respectively. the importance of evidence-based treatments proven in controlled clinical trials must be stressed since in the sars epidemic untested drug treatment seems to have done more harm than no treatment (a. danchin, personal communication) . therapeutics directed against immunopathological host responses might have a treatment value in view of the 'cytokine storm' seen in some patients with novel coronavirus infections. vaccines against mers and sars are currently not available. as in the case of the sars epidemic, the current epidemic must be fought with public health measures. as a first measure, the chinese authorities have closed the 'wet' seafood market in wuhan. due to the close contact of live animals with humans, these markets offer ideal conditions for the transmission of zoonotic infections. after two coronavirus infections having emerged from chinese 'wet' food markets, strict hygiene measures are clearly warranted. however, consuming meat and other products of wild animals has a long tradition in china. there is a philosophy of medicine food homology, ('eaten when hungry is food, eaten when ill is medicine') such that in china pangolin products, for example are reputed to help against rheumatism; 'meridian obstruction'; liver disease; and to improve eyesight (li and li, b) . more recently, consumption of meat of wild animals has become a sign of social status. it will not be easy to eradicate these false medical beliefs. interdiction might create black markets; therefore, some scientists recommend strictly controlling, instead of forbidding, this market. protecting the healthcare workers against nosocomial infection is another urgent need, since patient care will already represent a heavy burden to the health system and any reduction in health personnel would cause further problems. face masks are insufficient protection for them; n masks, goggles and protective gowns are needed for medical personnel (chang et al., b) . for the general public, frequent hand washing, cough and sneezing etiquette and wearing masks when visiting public places are recommended . however, scientific evidence is lacking for the effectiveness of wearing masks by the uninfected person in contrast to the proven effectiveness of hand washing against respiratory infections. the sars epidemic was contained by means of syndromic surveillance; isolation of patients; and quarantine of contacts. these measures will also play an important role in the current epidemic which, due to its sheer size, will necessitate more draconian measures such as limiting the movement of persons to and from hotspots of infection, resulting in the lockdown of wuhan and of particular small cities in italy and germany. who has declared the novel coronavirus epidemic as a public health emergency. this expanding epidemic will be a stress test for existing health systems, including those of industrialized countries. it should also be a further motivation to strengthen fundamental research in trans-species viral infections and on potential zoonosis impacts, particularly from bats, under changing environmental conditions. from the viewpoint of citizens, when it comes to the protection of lives, one might ask whether one should not put the same spending on public health and preventive research as on the spending on defence budgets. incubation period of novel coronavirus ( -ncov) infections among travellers from wuhan a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiologic and clinical characteristics of novel coronavirus infections involving patients outside wuhan, china protecting health-care workers from subclinical coronavirus infection epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study a new transmission route for the propagation of the sars-cov- coronavirus. medrxiv preprint preparedness and vulnerability of african countries against importations of covid- : a modelling study ) passengers' destinations from china: low risk of novel coronavirus ( -ncov) transmission into first case of novel coronavirus in the united states clinical features of patients infected with novel coronavirus in wuhan ) a distinct name is needed for the new coronavirus assessing spread risk of wuhan novel coronavirus within and beyond china therapeutic options for the novel coronavirus ( -ncov) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia game consumption and the novel coronavirus diarrhoea may be underestimated: a missing link in novel coronavirus genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding more than clinical trials launch to test coronavirus treatments transmission of -ncov infection from an asymptomatic contact in germany comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov consistent detection of novel coronavirus in saliva covid- : a puzzle with many missing pieces remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro a novel coronavirus outbreak of global health concern clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china novel coronavirus infection in hospitalized infants under year of age in china prophylactic and therapeutic remdesivir (gs- ) treatment in the rhesus macaque model of mers-cov infection characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study genome composition and divergence of the novel coronavirus ( -ncov) originating in china a new coronavirus associated with human respiratory disease in china clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series origin and evolution of the novel coronavirus therapeutic and triage strategies for novel coronavirus disease in fever clinics a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus from patients with pneumonia in china none declared. key: cord- -vq uhj i authors: da silva, severino jefferson ribeiro; silva, caroline targino alves da; guarines, klarissa miranda; mendes, renata pessôa germano; pardee, keith; kohl, alain; pena, lindomar title: clinical and laboratory diagnosis of sars-cov- , the virus causing covid- date: - - journal: acs infect dis doi: . /acsinfecdis. c sha: doc_id: cord_uid: vq uhj i [image: see text] in december , a novel beta (β) coronavirus eventually named sars-cov- emerged in wuhan, hubei province, china, causing an outbreak of severe and even fatal pneumonia in humans. the virus has spread very rapidly to many countries across the world, resulting in the world health organization (who) to declare a pandemic on march , . clinically, the diagnosis of this unprecedented illness, called coronavirus disease- (covid- ), becomes difficult because it shares many symptoms with other respiratory pathogens, including influenza and parainfluenza viruses. therefore, laboratory diagnosis is crucial for the clinical management of patients and the implementation of disease control strategies to contain sars-cov- at clinical and population level. here, we summarize the main clinical and imaging findings of covid- patients and discuss the advances, features, advantages, and limitations of different laboratory methods used for sars-cov- diagnosis. t he recent emergence of a novel coronavirus in the human population has caused dramatic and unprecedented impact of the economy and prompted mobilization of public health authorities around the world to counter the rapid spread of the virus. coronaviruses (covs) are members of the coronaviridae family and are an important group of viruses that infect a large number of animals including mammalian and avian species. the coronavirinae subfamily is divided into four genera based on genetic features: alphacoronavirus (α-covs), betacoronavirus (β-covs), gammacoronavirus (γ-covs), and deltacoronavirus (δ-covs). the α-covs (hcov- e and hcov-nl ) and β-covs (hcov-oc and hcov-hku ) cause human infection and have been associated with mild respiratory diseases. in the st century, however, three β-covs have emerged from animal reservoirs to cause severe disease in humans: severe acute respiratory syndrome coronavirus (sars-cov), the middle east respiratory syndrome coronavirus (mers-cov), and the pandemic severe acute respiratory syndrome coronavirus (sars-cov- ). , the genome of covs consists of a single-stranded positive sense (+ssrna) of around kb in size. the genomic rna is capped at the ′ end and has a poly(a) tail at the ′ end, allowing it to act as an mrna for translation of the replicase polyproteins. , the ′ terminal region of the genome encodes a polyprotein that is cleaved into nonstructural proteins involved in the transcription and replication process, and the ′ terminal region encodes viral structural proteins. in december , the world was on alert due to a cluster of severe pneumonia cases of unknown origin in wuhan, hubei province, china. this outbreak was epidemiologically linked to a wholesale animal and seafood market where live and freshly slaughtered animals were kept and sold. of the initial patients hospitalized with pneumonia, two-thirds had a history of direct exposure to this market. on the basis of the clinical presentation and the link with the animal market, similar to sars epidemiology, a cov was suspected as the causative agent and therefore pan-cov pcr primers were used to test the samples followed by sequencing. the causative agent was identified as a novel cov, eventually named sars-cov- , and the respiratory syndrome associated with the infection was designated as coronavirus disease- (covid- ) by the world health organization (who). the sars-cov- genome has about % sequence identity to sars-cov (with whom it is classified into the species severe acute respiratory syndrome-related coronavirus) and % to mers-cov. the most closely related virus to sars-cov- found so far is a cov isolated from bats, named ragt cov, whose nucleotide identity is %, suggesting that sars-cov- is also of bat origin. however, it is not clear whether sars-cov- jumped to humans directly from bats or through an intermediate host. the rapidly increasing numbers of covid- prompted who to declare first a public health emergency of international concern (pheic) on january , and then a pandemic on march , . as of july , , more than million cases of covid- and deaths have been reported in countries and territories around the world. most of the cases have been reported by the usa, followed by brazil, india, russia, south africa, mexico, and peru. different from the other highly pathogenic covs, sars-cov- has acquired the ability to establish sustained humanto-human transmission. its basic reproductive number (r ), i.e., the number of secondary infections generated from one infected individual, is estimated to be between . and . , with a mean of . . ultimately, this metric will require further investigations and may vary across settings and locations. on the basis of the travel history and symptom onset of patients in china, the mean incubation period of covid- has been calculated to be . days, ranging from to up to days. clinically, the spectrum of covid- manifestations ranges from asymptomatic and mild to severe infections requiring oxygen therapy and ventilation support. , , since its emergence, a wide variety of methods have been developed for the purpose of the rapid and accurate diagnosis of covid- . on the basis of clinical criteria alone, sars-cov- cannot be reliably distinguished from infections with other pathogens that cause similar symptoms, including influenza, seasonal cov, adenovirus, bocavirus, human metapneumovirus, parainfluenza, respiratory syncytial virus rhinovirus, bordetella pertussis, legionella pneumophila, myco-plasma pneumonia, , and even the mosquito borne dengue virus. in this context, the laboratory-based diagnosis assumes a role for the clinical management of patients and the implementation of disease control measures. here, we review the clinical features, laboratory methods, and imaging findings that are used for covid- diagnosis. in addition, we explore the next steps of the methods under development for covid- diagnosis. a rapid presumptive diagnosis based on clinical assessment and epidemiological characteristics is critical to ensuring appropriate patient care and controlling viral transmission, thus contributing to disease control. as mentioned and as with other respiratory viral infections, the signs and symptoms of covid- are nonspecific and the clinical spectrum of disease can range from no symptoms to severe pneumonia and death. asymptomatic infection has been reported in many settings, but some patients develop clinical disease at a later stage of infection. the proportion of truly asymptomatic infections is unclear, but some estimates indicated that up to % of infections do not result in overt clinical signs of disease. a recent mathematical model suggested that undocumented infections might be major drivers of sars-cov- spread in the world. according to who criteria, a person is suspected of being infected with covid- in three scenarios: (i) a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, shortness of breath) and a history of travel to or residence in a location reporting community transmission of covid- disease during the days prior to symptom onset; (ii) a patient with any acute respiratory illness who has been in contact with a confirmed or probable covid- case in the last days prior to symptom onset; and (iii) a patient with severe acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, shortness of breath, and requiring hospitalization) and in the absence of an alternative diagnosis that fully explains the clinical presentation. if a patient then tests positive with a laboratory diagnostic, then the infection becomes a confirmed overall, % of laboratory-confirmed covid- patients develop mild to moderate disease, which includes nonpneumonia and pneumonia cases, % have severe disease (dyspnea, tachypnea, blood oxygen saturation ≤ %, and pao /fio ratio of % of the lung field within − h), and % of cases reach critical state (respiratory failure, septic shock, and/or multiple organ dysfunction/failure). risk factors for severe covid- include age ≥ years and people with preexisting concurrent conditions such as cardiovascular disease, hypertension, diabetes, chronic respiratory disease, immunodeficiencies, cancer, and obesity. − accurate estimates of the covid- case fatality rate are still lacking, but it is believed to be around % and can be as high as . % in patients > years of age. however, this number is dependent on the level of testing in countries, testing accuracy, and death-reporting policies. interestingly, men have a much higher risk of death than women. , table summarizes the clinical signs and symptoms of covid- patients seen in several studies. in general, the most common clinical manifestations are fever, dry cough, fatigue, sputum production, dyspnea, sore throat, headache, myalgia or arthralgia, and chills ( figure ). less common symptoms include nausea or vomiting, nasal congestion, diarrhea, hemoptysis, and conjunctival congestion. in children, sars-cov- infection is generally mild and in some cases asymptomatic; however, when presented, the main symptoms include fever (about %), cough ( %), and pharyngeal erythema ( . %). more recently, several studies have been suggested that covid- infection was associated with cutaneous manifestations in patients. − major manifestations observed in covid- patients including different types of lesions such as purpuric, papulovesicular, livedoid, urticarial, maculopapular, and thromboticischemic. a recent study in european covid- patients reported that . and . % of patients had olfactory and gustatory dysfunctions, respectively. these disorders persisted after the resolution of other symptoms. finally, a single retrospective case series in wuhan, china, reported neurologic manifestations in of hospitalized patients ( . %) with a laboratory-confirmed diagnosis of covid- . these symptoms were more common in severe cases, along with acute cerebrovascular events, headache, dizziness, and impaired consciousness. it is unclear whether the neurologic manifestations were caused by sars-cov- directly or by pulmonary disease or other organ damage indirectly or by cytokines. since this study included only hospitalized patients in a single location, the true percentage of neurological manifestations in covid- needs further evaluation. imaging techniques such as chest x-rays, pulmonary computed tomography (ct) scans, and lung ultrasounds are important tools in the early diagnosis of pneumonia in patients with covid- . although chest x-rays are less expensive and more convenient for follow up in pneumonia cases, the technique has low-resolution and projection overlapping, which could lead to many false-negative covid- cases. reports indicate that covid- patients submitted to chest ct scans on admission presented abnormal results (about %), showing bilateral multiple ground-glass and patchy opacity. a clinical laboratory findings and biomarkers in covid- patients. several studies have reported hematologic and blood chemistry alterations in patients infected by sars-cov- . , major laboratory findings in covid- patients identified by meta-analysis include leukopenia, leukocytosis, decreased albumin levels, increased levels of creactive protein, lactate dehydrogenase (ldh), creatinine kinase, and biliarubin, and a high erythrocyte sedimentation rate (esr). increased levels of creatine kinase and lactate dehydrogenase were associated with myalgia. a growing body of evidence suggests that sars-cov- infection can trigger the overproduction of cytokines in some patients, known as a cytokine storm, which is associated with poor outcomes. , − as for other severe viral infections, the exacerbated production of proinflammatory cytokines may be involved in some of the pathophysiology of covid- , including pulmonary edema and lung failure and damage to the liver, heart, and kidneys. compared to healthy adults, covid- patients had higher levels of il- β, il- ra, il- , il- , il- , il- , basic fgf, g-csf, gm-csf, ifn-γ, ip- , mcp- , mip- a, mip- b, pdgf, tnf-α, and vegf. serum biomarkers associated with severe disease included il- , il- , il- , g-csf, ip- , mcp- , mip- a, and tnf-α. a recent retrospective study of confirmed covid- cases ( fatal and discharged cases) in wuhan, china, identified several serological markers that were more elevated in lethal cases than in survivors: elevated ferritin, il- , myoglobin, creactive protein, and cardiac troponin. together, these findings suggest that covid- mortality might be due to infection-driven hyperinflammation. diagnostic virology of covid- . laboratory virology tests are essential for a correct diagnosis and the population level prevalence of covid- , given the number of asymptomatic cases or nonspecific clinical symptoms. results from these tests guide clinicians and health officials in the management, control, and prevention of covid- . several analytical parameters are used to determine the performance of covid- assays, including clinical sensitivity, clinical specificity, positive predictive value (ppv), negative predictive value (npv), and overall accuracy. the confirmation of a sars-cov- infection in the laboratory can be achieved by direct and indirect virology methods. while direct detection is more specific, indirect methods allow a greater opportunity for virus detection after the acute phase of the disease. in direct tests, the clinical sample is examined directly for the presence of particles, virus antigens, or viral nucleic acids, whereas indirect methods detect the serological response against the infection (figure ). samples. the world health organization (who) recommends that all procedures performed with covid- be done only by trained professionals and should take place in a laboratory with an appropriate level of biosafety. nonpropagative diagnostic assays, such nucleic acid amplification tests (naats), sequencing, and some serological tests (e.g., elisa type assays) can be performed in biosafety level (bsl- ) laboratories provided that the initial processing (before virus inactivation) of samples takes place in a validated biological safety cabinet. however, procedures that involve propagative virus work, such as virus culture, isolation, or neutralization assays, should be performed in laboratories equivalent to bsl- using validated practices. the work team must use appropriate personal protective equipment including eye protection (goggles or a disposable face shield), a respirator or facemask, a long-sleeved gown, and gloves and follow all standard operating procedures regarding sample collection and handling. respirators that offer a higher level of protection such as n respirators or powered air-purifying respirators should be used instead of a face mask when performing an aerosol-generating procedure. samples from patients with a suspected or confirmed case must be transported to un , a code referring to "biological substance category b"; however, virus-infected cultures or isolates must be transported as category a -un , "an infectious substance that affects humans". , specimens for diagnosis. choosing the correct sample for diagnosis tests is an essential step in a reliable diagnosis. sars-cov- infection can be detected in a variety of clinical specimens, such as nasopharyngeal or oropharyngeal aspirates or washes, nasopharyngeal or oropharyngeal swabs, sputum, tracheal aspirates, and bronchoalveolar lavage. − the median duration of sars-cov- shedding in respiratory samples is (irq, − ) days in survivors, but shedding can last for up to days. given the invasiveness and requirements for equipment and skilled labor, the collection of specimens other than sputum from the lower respiratory tract should be considered only in special situations. a nasopharyngeal swab collected with a fiberplastic shaft swab is the preferred choice for swab-based sars-cov- testing because it provides reliable results while not being too invasive. calcium alginate swabs and wooden shaft swabs are not recommended because they may contain substances that inactivate some viruses and inhibit pcr testing. when collection with a nasopharyngeal swab is not possible, oropharyngeal swabs, nasal midturbinate swabs, or anterior nares (nasal swab) swabs are also acceptable alternatives. swabs should be placed immediately after collection into sterile tubes containing to ml of a viral transport medium to preserve viral integrity. upon collection and with the appropriate storage medium, specimens can be stored at − °c for up to h. in cases of delayed testing or shipping, samples should be stored at − °c or below. inadequate sample collection, handling, and storage are important variables that may result in false-negative test results. in addition to respiratory tract specimens, sars-cov- can also be detected in other samples such as stool, anal swabs, and blood but not in urine. , , sars-cov- detection in blood is not frequent and is associated with disease severity. , the detection rate of sars-cov- rna in fecal specimens is similar to that of pharyngeal swabs; , however, importantly, fecal viral shedding appears to occur for a longer period of acs infectious diseases pubs.acs.org/journal/aidcbc review time. sars-cov- detection in stool is not associated with the presence of gastrointestinal symptoms or the severity of illness. − despite high virus rna levels in feces, successful isolation of sars-cov- from patient stool has been reported. the isolation of sars-cov- from urine and ocular secretions from infected patient has been described. , viral shedding in human breast milk and semen has been detected, , while in tears it has either been undetected or acs infectious diseases pubs.acs.org/journal/aidcbc review detected at very low frequency. serum and plasma samples are used for serological assays, especially week postinfection. the median seroconversion time for total anti-sars-cov- antibodies, igm and then igg, were days , , and , respectively. virus isolation. sars-cov- was first isolated from bronchoalveolar lavage from a patient with pneumonia in vero e and huh cells. the viral identity was confirmed by immunofluorescence using the now-known cross-reactive anti-sarsr-cov rp n antibody, rt-qpcr, and metagenomics sequencing. the cellular infectivity of the isolated virus was confirmed by virus neutralization assay using sera from convalescing patients. culture-based methods for sars-cov- detection have been used in research and public health laboratories in different parts of the world, but virus isolation is not recommended as a routine diagnostic procedure because it has low sensitivity, it is time-consuming, and it requires bsl- containment. sars-cov- is also culturable in several cell lines, including human airway epithelial, , vero e , vero ccl- , and huh- cells. , , , vero e cells express high levels of angiotensin-converting enzyme (ace ), which has been identified as a key a cell receptor for sars-cov- infection. similar to sars-cov- and mers-cov, sars-cov- isolation is enhanced in an engineered vero e that expresses tmprss (transmembrane serine protease ) levels that are -fold higher than in human normal lung tissue and other human cell lines, suggesting that tmprss protease is important for sars-cov- infection. recently, zang and colleagues demonstrated that tmprss and tmprss promote sars-cov- entry into enterocytes. harcourt and co-workers studied the susceptibility of several cell lines such as vero ccl- , vero e , hek- t, a , and huh- as well as the big brown bat kidney cell line (efk b) to support the productive replication of sars-cov- . no cytopathic effect (cpe) was observed in any of the cell lines except in vero e and vero ccl cells, in which the virus grew to > pfu/ml at h postinfection. huh- and hek- t cells showed only modest viral replication, whereas no virus replication was detected in either a or efk b cells. sars-cov- produced distinct plaques in vero e cells, but plaques in vero ccl- cells were not as clear, suggesting that vero e cells might be the best choice for the propagation, quantification, and study of plaque phenotypes of different sars-cov- strains. however, should virus isolation be attempted, vero e cells clearly stand out as a cell line that supports infection and virus production. a recent cross-sectional study used sars-cov- rt-qpcr confirmed specimens and evaluated their ability to infect vero cell lines. for the study, patient samples were incubated on vero cells (ccl- ) during days, and then the cytopathic effect was evaluated. of these, samples ( . %) demonstrated viral growth, but there was no growth in samples with a ct value > , which suggests using samples with low ct values for successful viral isolation. electron microscopy. human cov was first isolated in from a patient with a common cold. later, the virus was named "coronavirus" due to the virus' appearance under the electron microscope that resembles the solar corona. cov particles are pleomorphic, and their surfaces are covered with a distinct layer of projections, which corresponds to the long spike protein. given the virus' distinctive morphology, electron microscopy has been used to observe and identify virus particles after isolation in culture systems in the initial outbreak in wuhan and subsequently by others. , , the first attempts to recover sars-cov- virions with the characteristic fringe of surface spike proteins from the first covid- case in australia failed, but adding trypsin to the cell culture medium immediately allowed the visualization of the virus with characteristic cov morphology, with particles of − nm diameter displaying prominent spikes ( − nm) on the surface. real-time rt-qpcr. the gold standard diagnostic test for sars-cov- infection is viral rna detection by reverse transcription quantitative real-time polymerase chain reaction (rt-qpcr) given its sensitivity, specificity, and speed. rt-qpcr shows better performance than serology because it can identify positive cases in the early stage of infection, even during the incubation period of the disease and after symptoms have disappeared. many laboratory-developed tests based on the rt-qpcr assay have been published or are in development for sars-cov- detection. some of these developed assays are specific to the pandemic strain of the virus, and others also recognize genetically similar strains such as sars-cov. molecular targets for sars-cov- rt-qpcr include the genes that encode the nucleocapsid (n), envelope (e), spike (s), and rna-dependent rna polymerase proteins given their high degree of genetic conservation (figure ) . , most assays use two targets in the viral genome, but in the event of reagent shortages, rt-qpcr screening with only one set of primers instead of two may be considered after thorough validation in the individual laboratory. performing a sample preheating step instead of rna extraction can also be considered during a shortage of viral nucleic acid extraction kits. in a study with oropharyngeal swab samples ( positive and negative for sars-cov- ) in denmark, it was found that heating for min at °c resulted in a sensitivity, specificity, and accuracy of . , . , and . %, respectively, as compared with magna pure rna-extracted samples. although some laboratories have recommended heat inactivation of the virus ( − °c for − min) before rna extraction to protect laboratory personnel, this procedure adversely affects the efficacy of rt-qpcr for sars-cov- detection. high rates of false-negative sars-cov- rt-qpcr results and prolonged nucleic acid conversion have been reported in some studies, which have implications for returning to normal activities and covid- control. − in addition to in-house tests, many molecular assay kits have been approved by the food and drug administration's (fda) and have been made commercially available for the detection and amplification of the sars-cov- rna genome (https:// www.fda.gov/medical-devices/emergency-situations-medicaldevices/emergency-use-authorizations). however, diagnostic laboratories should rigorously validate these commercial kits before routine use since the analytical sensitivity of some commercial rt-qpcr tests differs substantially, which could lead to false-negative results. two of the most widely used assays in the western world have been developed by charite, hospital germany and the u.s. cdc. nalla and co-workers compared the performance of the charité(n, polymerase, and e targets) and the cdc (n , n , and n targets) primer/probe sets side-by-side using clinical samples. it was found that all assays were highly specific to sars-cov- , with no cross-reactivity with other respiratory viruses. the cdc n and the charitéhospital e-gene primer/probe sets performed equally well and were the most sensitive assays for detecting sars-cov- . we anticipate acs infectious diseases pubs.acs.org/journal/aidcbc review that this list will grow as several new rt-qpcr assays are being developed to promote the accurate and rapid detection of sars-cov- . the results demonstrated that the median duration between the onset of symptoms to nucleic acid conversion was days (iqr, − ) and that the longest duration was days after the onset of symptoms. it was found that higher viral loads (inversely proportional of the ct value) can be observed in upper respiratory samples soon after symptom onset and that the peak occurs within the first week of illness onset of covid- confirmed patients. , in another study, the authors evaluated the viral shedding patterns demonstrated in patients with mild and severe covid- disease using specimens from patients, including individuals classified as mild cases and classified as severe cases. the results showed that the viral load of severe cases was around times higher when compared with that of mild cases, indicating that higher viral loads might be associated with severe clinical findings. in addition, it was revealed that the ct values of severe cases were significantly lower than those of mild cases in infected patients at the time of admission and that early viral clearance was observed in patients classified as mild cases ( days after onset). sars-cov- -positive rt-qpcr detection has also been demonstrated even after the resolution of covid- symptoms. , for this reason, the cdc has recommended obtaining at least two negative upper respiratory tract samples, collected in intervals of h or longer, to document sars-cov- clearance. on the other hand, the viral shedding in asymptomatic patients with covid- also has been investigated. , zhou and co-workers analyzed the viral shedding pattern in patients that were confirmed to have covid- using rt-qpcr but were asymptomatic during admission to the hospital. subsequently, the study divided the patients into groups: patients who remained asymptomatic during hospitalization (aps) and patients who presented symptoms after admission to the hospital (apis). the results demonstrated that the median ct value of aps ( . , interquartile range [iqr] . − . ) was higher than when compared to apis ( . , iqr . − . ), showing a lower viral load in aps. also, it was found that the duration of viral shedding remained similar in the two patient groups, which reflects the possibility of sars-cov- transmission in the community during the asymptomatic period. in addition, the study findings revealed that the viral load of aps peaked during the first week after admission to the hospital while that of apis peaked during the second week of covid- infection. these findings alert professionals and health authorities to the possibility of transmission during the asymptomatic period of patients with covid- disease. however, further scientific studies with more patients are required to elucidate the real role of asymptomatic patients in the transmission chain. reverse transcription loop-mediated isothermal amplification (rt-lamp). the recent increase in the number of covid- cases in the world has encouraged a global effort to develop point-of-care platforms for diagnosing sars-cov- . reverse transcription loop-mediated isothermal amplification (rt-lamp) is perhaps one of the most promising platforms for rapid development and accessible sars-cov- testing and has many advantages, compared to rt-qpcr, such as high specificity and sensitivity, simple operation, rapid amplification, and low cost,. , rt-lamp assays have been developed for other covs of the same genus (betacoronavirus), including sars-cov , and mers-cov. , not surprisingly, several studies have already demonstrated the use of rt-lamp for sars-cov- detection. − crispr/cas-based diagnostic methods. the clustered regularly interspaced short palindromic repeats (crispr)/cas machinery has recently been adapted as a poc tool for the rapid detection of nucleic acids (dna or rna). , overall, this crispr machinery is programmed to cleave specific sequences in the dna/rna target where the results can be easily observed by combination with a lateral-flow strip. initially, zhang's team developed a crispr/cas-based platform called specific high-sensitivity enzymatic reporter unlocking (sherlock) that, combined with isothermal preamplification to detect strains of single-strand rna viruses, identifies mutations and human genotype dna, and distinguishes pathogenic bacteria. , more recently, using the same knowledge, they adapted a protocol using the sherlock system for sars-cov- detection. on the other hand, mammoth bioscience company developed another platform based on the crispr/cas system named the endonuclease-targeted crispr trans reporter (de-tectr) to detect any rna or dna target, which has now been used to detect the sars-cov- rna genome from respiratory swab rna extracts. the suitability of detectr technology for the detection of sars-cov- was evaluated using patient specimens, including patients with covid- infection and patients with other viral respiratory infections, and then compared with the cdc rt-qpcr as a reference method to confirm covid- infection. the sars-cov- detectr test had % positive predictive agreement and % negative predictive agreement when compared with rt-qpcr results. despite these promising results, crispr/cas-based diagnostic methods are not widely used by diagnostic laboratories and need further implementation. taken together, these results highlight the great potential of crispr-based diagnostic methods as a rapid, specific, portable, and accurate detection platform for the detection of the sars-cov- genome in patient samples. sensors. sensors represent another alternative detection method with rapid and high throughput. since the emergence of sars-cov- , several research groups from different parts of the world have also focused on alternative sensing modalities based on sensors for the diagnosis of sars-cov- that reduce the use of expensive laboratory equipment, trained laboratory personnel, and extensive sample preparation and provide fast and accurate results. in this context, qiu and co-workers developed a dual-functional plasmonic biosensor combining the plasmonic photothermal (ppt) effect and localized surface plasmon resonance (lspr) to detect sars-cov- . in another study, the authors used a field-effect transistor (fet)based sensor to detect sars-cov- from patient samples. in general, these recent research findings are based on technologies previously used for the detection of other viral pathogens that now can be adapted for the detection of sars-cov- . for instance, due to its high sensitivity and specificity, simple operation, low cost, and other advantages, the sensors using programmable biomolecular components named the toehold switch developed in response to previous ebola and zika outbreaks represent another powerful platform for detecting the sars-cov- genome. − genome sequencing. whole genome sequencing was used to identify potential etiological agents involved in the index cases of the covid- pandemic in wuhan. in addition to unequivocally confirming the diagnosis of a sars-cov- infection, regular sequencing of a percentage of patient samples from clinical cases can be used to monitor changes in the viral genome over time and trace transmission patterns. for this purpose, several sequencing protocols based on sanger and next-generation sequencing (ngs) are being applied to rapidly generate the genome sequences. , , lu and colleagues used a combination of sanger, illumina, and oxford nanopore minion sequencing technologies to obtain the whole-genome sequences of sars-cov- from six patient specimens from wuhan, china. holshue and colleagues reported the first case of the novel coronavirus in the united states and used a combination of the sanger method, illumina, and minion to generate the whole-genome sequences. whole-genome sequencing using minion technology coupled with phylogenetic analyses and travel history allowed the identification of sars-cov- entry routes into latin america during its emergence in brazil. as of july , , genome sequences had been deposited in genbank (https://www.ncbi. nlm.nih.gov/genbank/sars-cov- -seqs/), including complete genome sequences from different countries around the world and partial genome sequences. sars-cov- has evolved continuously since its emergence. the binding regions of primers and probes should be monitored continuously for matching to the virus genome as more sequence information becomes available. in this scenario, artesi and colleagues reported that changes within the sars-cov- primer binding region negatively affected the performance of commercial rt-qpcr assays (unpublished data, https://www.medrxiv.org/content/ . / . . . v ). in another study, rana and co-workers analyzed the whole genome sequence of patients with covid- and found variations in the primer and probe binding sites that could produce false-negative results. a comprehensive bioinformatics analysis of sars-cov- sequences from around the world identified the presence of mutations/ mismatches in the primer/probe binding regions of assays out of rt-qpcr assays studied, including the charite-orf b reverse primer and the us-cdc-n- probe. however, it should be noted that except at the ′ end, rt-qpcr can tolerate mismatches at the ′ extremity or in the middle of a primer. thus, oligonucleotide binding regions should be continuously monitored by bioinformatics and also by wet-laboratory experiments in order to identify changes that may influence rt-qpcr performance. , , taken together, whole genome sequencing and bioinformatics will be important in global efforts to combat the pandemic, with the resulting analyses being used to guide a wide range of studies, including diagnostics, , , molecular epidemiology studies, viral evolution, − elucidatation of possible hosts of the virus, , − identification of targets for drugs and vaccines, , molecular determinants involved in virulence and pathogenicity, , and factors related to the host's immune response to the virus. , serology. serological methods are being increasingly used and can be used for diagnosis, contact tracing, and herd immunity assessment, and vaccine efficacy evaluation. seroepidemiologic studies can assist in the investigation of the ongoing pandemic and the retrospective assessment to determine the attack rate or the progress of the pandemic through antibody detection. these studies can assist health authorities and governments in making sound decisions with respect to the implementation of public health measures during the course of the current pandemic. population-based serosurveys for sars-cov- has been applied in several sites to assess the burden of covid- and more accurately determine sars-cov- prevalence and transmission dynamics. − moreover, serology can also be useful in situations where rt-qpcr is negative and there is a strong epidemiological link to covid- infection. in these cases, paired serum samples collected in the acute and convalescent phase can be of diagnostic value. the adaptive immune response to sars-cov- infection has been studied, , , , despite several knowledge gaps in this area. long and co-workers studied the antibody responses to sars-cov- in patients with covid- in china. seroconversion for igm and igg occurred simultaneously or sequentially, and the median day of seroconversion for both immunoglobulins was days after covid- onset. the seroconversion rate for igg reached % days after symptom onset. in a related work, zhao and colleagues showed that the median seroconversion times for total antibodies, igm, and igg were , , and days after sars-cov- infection. severe patients tend to have higher antibodies titers than patients with mild covid- . , to investigate the antibody responses to sars-cov- in convalescing individuals, robbiani and co-workers analyzed plasma samples collected an average of days after the onset of symptoms from convalescing individuals. most convalescent plasmas obtained from recovered patients did not contain high concentrations of neutralizing activity. a related study with convalescing patients detected serum neutralizing antibodies in out of patients, and there was a strong correlation among neutralization antibody titers, the numbers of virus-specific t cells, and anti-s-rbd igg but not with anti-np igg. notably, the antibody response and viral clearance can be delayed in immune-compromised individuals and people posteriorly infected with sars-cov- . in the past few months, a variety of serological tests have been designed to detect sars-cov- , mainly enzyme-linked immunosorbent assays (elisa), immunofluorescence assays (ifa), chemiluminescence enzyme immunoassays (clia), and lateral flow assays (lfa). of these serological methods, elisa, clia, and lfa are used for the first-line screening of patient samples with covid- . most serological assays are based on the sars-cov- nucleocapsid protein (n), transmembrane spike protein (s), or s receptor-binding domain (rbd) because of their high antigenicity. − as mentioned before, sars-cov- enters host cells using its spike protein and represents the main target of neutralizing antibodies produced by the host. in this context, several studies have demonstrated that serological tests using the s antigen are more sensitive than those using n-antigen-based antibody assays. instead of a single antigen, some companies have combined n-and s-based antigens to develop serological assays for sars-cov- detection. cross-reactivity between sars-cov- and sars-cov- has been reported against the n protein but not against the s subunit of the s protein. cross-reactive antibodies between sars-cov- and sars-acs infectious diseases pubs.acs.org/journal/aidcbc review cov- have been detected in both the rbd region located in the s subunit and also in non-rbd regions. anderson and colleagues analyzed patient samples with sars-cov- and sars-cov- infections and showed that there is no detectable cross-neutralization by sars-cov- patient serum against sars-cov- , despite significant cross-reactivity between the n proteins from the two viruses many elisa-based assays have been developed to evaluate the human antibody response (iga, igm, and igg) against sars-cov- . , − cross reactivity to other coronaviruses has been reported, and therefore test results should be interpreted in light of the local epidemiological scenario. for example, it has been shown that igm elisa allows a higher detection efficacy than rt-qpcr after . days of symptom onset, and the combined use of igm elisa and rt-qpcr increases the positive detection rate to . % when compared with a single rt-qpcr test ( . %). the median time of appearance of igm and iga antibodies in plasma was days, while igg was detected days after symptom onset. in the same study, sars-cov- n elisa did not show any cross-reactivity with other covs, with the exception of sars-cov- , a virus that has not been in circulation since the to outbreak. perera and co-workers developed an elisa based on the receptor-binding domain (rbd) of the sars-cov- s protein to detect igg and igm antibodies in human sera and compared the elisa results with confirmatory microneutralization and % plaque reduction neutralization tests (prnt ). they found that prnt were more sensitive than microneutralization to detecting antibodies against sars-cov- , indicating that elisa should be used for screening and prnt should be used for confirmation in large-scale seroepidemiological studies. a magnetic chemiluminescence enzyme immunoassay (mclia) has also been developed for virus-specific antibody detection. in a study with covid- patients, sera from these patients did not cross react with the sars-cov spike antigen, but some cross-reactivity was found with the sars-cov nucleocapsid antigen. many lateral flow assays (lfa) have been developed to detect sars-cov- − and have obtained emergency use authorization from the fda (https://www.fda.gov/medicaldevices/emergency-situations-medical-devices/emergency-useauthorizations). a combined igm/igg assay seems to be a better choice in terms of performance and sensitivity to either antibody alone (igm or igg). recently, li and colleagues developed a rapid lfa to simultaneously detect igm and igg antibodies against sars-cov- within min in human blood. the assay uses the receptor binding domain of the sars-cov- s protein as the antigen. they validated the assay with blood samples previously screened by rt-qpcr, including positive and negative samples. the assay had a sensitivity of . % and a specificity of . % compared to rt-qpcr. in addition, several studies have been used to evaluate the clinical sensitivity of serological tests with covid- patient samples collected on different days after the onset of symptoms. − pan and colleagues evaluated a commercial lateral flow immunochromatographic test targeting viral igm or the igg antibody and compared it with rt-qpcr. the sensitivity of the assay for sars-cov- detection was . % in early-stage patients ( − days after onset), . % in intermediate-stage patients ( − days after onset), and . % in late-stage patients (more than days after onset). in similar study, tang and co-workers compared the diagnostic performance of two sars-cov- commercial serologic tests using specimens from pcr-confirmed sars-cov- patients and control specimens from different days after disease onset (< , − , − , and ≥ days). both assays had poor diagnostic sensitivity during the first days of symptoms, generating a high rate of false-negative results. the time of sampling since the onset of symptoms must be taken into account when performing the serological diagnostic test, and false-negative results can lead to the false assumption that a person is not infected, consequently bringing about serious challenges and implications for the spread or containment of the disease. most patients will seroconvert only in the second week after infection, and thus negative serological test results obtained during the first days of the disease should be interpreted with caution. as opposed to classical serum neutralization assays such as the microneutralization and plaque reduction neutralization test (prnt), pseudovirus neutralization assays for sars-cov- can be performed in biosafety level facilities. pseudovirusbased neutralizing assays for sars-cov- have been developed using vesicular stomatitis virus (vsv) and lentiviral pseudovirus systems. , such systems will facilitate the study of covid- humoral immunity and the development and evaluation of vaccines and therapeutics against sars-cov- once the reliability and cross reactivity have been assessed. antigen detection tests represent another alternative to detecting sars-cov- . antigen detection assays are developed to directly detect viral particles in biological samples such as nasopharyngeal secretions from infected patients. in this context, some rapid antigen assays have been proposed to detect sars-cov- . , − a fluorescence lfa antigen test based on the n protein has been developed and validated using nasopharyngeal and oropharyngeal samples from suspected covid- cases ( positive by rt-qpcr). compared with rt-qpcr, the test achieved a sensitivity of . % and % specificity. however, some commercially available point-of-care tests have very low sensitivity, which hinders their use in covid- diagnosis. , for the validation of serological tests, robust test validation with adequate clinical samples representative of a real-world scenario (e.g., timing from disease onset, different disease severities, different geographical locations, and patient age) is of paramount importance. particular attention should be paid to the low specificity of some assays and the high possibility of false-positive results. a low specificity of serological assays may have important consequences in terms of both diagnosis and population surveillance of covid- patients at the individual level and population level. , at the individual level, the risks posed by false-positive results can be of great concern. for instance, people who have never been infected may return to work or travel because they are considered to be immune to sars-cov- infection. at the population level, false-positive results may increase the prevalence of covid- disease and provide a distorted picture of the higher population immunity and lower mortality rate than what is actually happening, which can negatively affect seroepidemiological surveillance studies. thus, the independent validation of covid- serological tests using samples from different stages of the disease is urgently needed to encourage health care professionals and governments to make sound decisions. differential diagnosis. since the clinical manifestations of covid- are similar to those of other respiratory diseases, differential diagnosis is of paramount importance in assisting physicians in the therapeutic management of patients and health officials in establishing disease control policies. in an effort to do so, respiratory pathogens in patients suspected of covid- in italy have been investigated. here, researchers tested the nasopharyngeal swabs of suspected causes using sars-cov- rt-qpcr and a commercial multiplex respiratory cartridge that detects and differentiates viral and bacterial pathogens. only patients were confirmed to be infected with sars-cov- , and ( . %) were positive for other respiratory pathogens, including ( . %) positive for influenza a and ( . %) positive for influenza b. other pathogens detected in the patient samples were common cold cov (h-cov e, h-cov nl , and h-cov hku ), rhinovirus, enterovirus, metapneumovirus, adenovirus, mycoplasma pneumoniae, streptococcus pneumoniae, and legionella pneumophila. these results highlight the diagnostic differential and demonstrate the importance of using a spectrum of molecular kits for the rapid detection of respiratory pathogens in order to improve the clinical management and treatment of patients infected with covid- . in another study, yan and co-workers reported the cases of two patients in singapore who initially had moderate symptoms including myalgia, a mild cough, and diarrhea and presented with thrombocytopenia and a normal chest radiograph. dengue was suspected, and a rapid serological test for dengue produced false-positive results. as patient symptoms worsened, they were later diagnosed with covid- by rt-qpcr. taken together, these findings suggest that special attention is needed in the differential diagnosis between arboviruses and sars-cov- infection, especially in countries where is there a circulation of denv, zikv, and chikv. moreover, coinfection with sars-cov- and other respiratory viruses, such as common cold cov, influenza, and metapneumovirus, have been reported, highlighting the need for repeat testing based on clinical indications. − the rapid spread of sars-cov- around the world, with mounting cases of fatal pneumonia and the economic crisis, is a global concern. diagnostics represent one of the most powerful tools in mitigating these effects until a vaccine can be established. this needed is further highlighted by overlapping symptoms from other pathogens that can confound diagnosis based only on clinical criteria. as we have reviewed, many approaches have been established for the diagnosis of sars-cov- , and we anticipate the coming months to bring about many more innovative strategies. critically, the development of inexpensive point-of-care diagnostic platforms will accelerate the global response to the current pandemic, especially in countries with health systems devoid of adequate laboratory infrastructure. it will be important that widespread diagnostic development and validation continue in the coming months and that the large-scale implementation of these sars-cov- diagnostic platforms is successful as this pandemic evolves. reliable, easy-to-use assays will be absolutely critical, especially as the disease moves through low-and middle-income countries. ( ) wang, c., horby, p. w., hayden, f. g., and gao, g. f. ( ) a novel coronavirus outbreak of global health concern. lancet ( ), − . ( ) huang, c., wang, y., li, x., ren, l., zhao, j., hu, y., zhang, l., fan, g., xu, j., gu, x., cheng, z., yu, t., xia, j., wei, y., wu, w., xie, x., yin, w., li false-positive dengue serology in singapore who. report of the who-china joint mission on coronavirus disease (covid- ) covid- : four fifths of cases are asymptomatic, china figures indicate substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov ) characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention cancer patients in sars-cov- infection: a nationwide analysis in china predictors of mortality for patients with covid- pneumonia caused by sars-cov- : a prospective cohort study factors associated with hospitalization and critical illness among , patients with covid- disease likelihood of survival of coronavirus disease cutaneous manifestations in covid- : the experiences of barcelona and rome cutaneous small-vessel vasculitis associated with novel coronavirus sars-cov- infection (covid- ) cutaneous manifestations in covid- : a first perspective cutaneous manifestations of covid- : a review of the published literature olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease neurologic manifestations of hospitalized patients with coronavirus disease relation between chest ct findings and clinical conditions of coronavirus disease (covid- ) pneumonia: a multicenter study clinical characteristics of patients infected with sars-cov- in wuhan diagnosis of the coronavirus disease (covid- ): rrt-pcr or ct? initial clinical features of suspected coronavirus disease in two emergency departments outside of hubei clinical course and risk factors for mortality of adult inpatients with covid- in wuhan clinical, laboratory and imaging features of covid- : a systematic review and meta-analysis th responses in cytokine storm of covid- : an emerging target of jak inhibitor fedratinib the cytokine release syndrome (crs) of severe covid- and interleukin- receptor (il- r) antagonist tocilizumab may be the key to reduce the mortality covid- : consider cytokine storm syndromes and immunosuppression ) pathological findings of covid- associated with acute respiratory distress syndrome correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases. radiology , e . ( ) cdc. interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease (covid- ) detection of sars-cov- in different types of clinical specimens sars-cov- viral load in upper respiratory specimens of infected patients ) cdc. interim guidelines for collecting, handling, and testing clinical specimens from persons for coronavirus disease virological assessment of hospitalized patients with covid- profile of rt-pcr for sars-cov- : a preliminary study from covid- patients comparison of different samples for novel coronavirus detection by nucleic acid amplification tests detectable -ncov viral rna in blood is a strong indicator for the further clinical severity fecal specimen diagnosis novel coronavirus-infected pneumonia prolonged presence of sars-cov- viral rna in faecal samples characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding the presence of sars-cov- rna in feces of covid- patients prolonged viral shedding in feces of pediatric patients with coronavirus disease prolonged presence of sars-cov- viral rna in faecal samples infection of bat and human intestinal organoids by sars-cov- sars-cov- isolation from ocular secretions of a patient with italy with prolonged viral rna detection detection of sars-cov- in human breastmilk clinical characteristics and results of semen tests among men with coronavirus disease evaluation of coronavirus in tears and conjunctival secretions of patients with sars-cov- infection ( ) a novel coronavirus from patients with pneumonia in china remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro analysis of ace in polarized epithelial cells: surface expression and function as receptor for severe acute respiratory syndrome-associated coronavirus sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor enhanced isolation of sars-cov- by tmprss -expressing cells ) tmprss and tmprss promote sars-cov- infection of human small intestinal enterocytes predicting infectious sars-cov- from diagnostic samples cultivation of a novel type of common-cold virus in organ cultures virology: coronaviruses virus isolation from the first patient with sars-cov- in korea identification of coronavirus isolated from a patient in korea with covid- isolation and rapid sharing of the novel coronavirus (sars-cov- ) from the first patient diagnosed with covid- in australia ) ecdc. rapid risk assessment: coronavirus disease (covid- ) pandemic: increased transmission in the eu/eea and the uk − eighth update an alternative workflow for molecular detection of sars-cov- -escape from the na extraction kit-shortage potential false-negative nucleic acid testing results for severe acute respiratory syndrome coronavirus from thermal inactivation of samples with low viral loads false negative tests for sars-cov- infection -challenges and implications antibody responses to sars-cov- in patients with covid false-negative of rt-pcr and prolonged nucleic acid conversion in covid- : rather than recurrence detection of novel coronavirus ( -ncov) by real-time rt-pcr -novel coronavirus ( -ncov) real-time rrt-pcr panel primers and probes comparative performance of sars-cov- detection assays using seven different primer/probe sets and one assay kit rapid random access detection of the novel sars-coronavirus- (sars-cov- , previously -ncov) using an open access protocol for the panther fusion development of a laboratory-safe and low-cost detection protocol for sars-cov- of the coronavirus disease improved molecular diagnosis of covid- by the novel, highly sensitive and specific covid- -rdrp/hel real-time reverse transcription-polymerase chain reaction assay validated viral load of sars-cov- in clinical samples viral dynamics in mild and severe cases of covid- . the lancet temporal dynamics in viral shedding and transmissibility of covid- viral dynamics of sars-cov- across a spectrum of disease severity in covid- clinical features and dynamics of viral load in imported and nonimported patients with covid- epidemiologic features and clinical course of patients comparisons of viral shedding time of sars-cov- of different samples in icu and non-icu patients factors associated with prolonged viral rna shedding in patients with covid- time kinetics of viral clearance and resolution of symptoms in novel coronavirus infection discontinuation of transmission-based precautions and disposition of patients with covid- in healthcare settings (interim guidance) viral dynamics in asymptomatic patients with covid- prevalence of asymptomatic sars-cov- infection: a narrative review loop-mediated isothermal amplification (lamp) for the diagnosis of zika virus: a review development and validation of reverse transcription loop-mediated isothermal amplification (rt-lamp) for rapid detection of zikv in mosquito samples from brazil evaluation of real-time reverse transcriptase pcr and real-time loop-mediated amplification assays for severe acute respiratory syndrome coronavirus detection a rapid and specific assay for the detection of mers-cov rapid and visual detection of novel coronavirus (sars-cov- ) by a reverse transcription loop-mediated isothermal amplification assay development of reverse transcription loop-mediated isothermal amplification (rt-lamp) assays targeting sars-cov- development of a novel reverse transcription loop-mediated isothermal amplification method for rapid detection of sars-cov- development of a reverse transcription-loop-mediated isothermal amplification as a rapid early-detection method for novel sars-cov- rt-lamp for rapid diagnosis of coronavirus sars-cov- nucleic acid detection with crispr-cas a/c c multiplexed and portable nucleic acid detection platform with cas , cas a, and csm a protocol for detection of covid- using crispr diagnostics crispr-cas -based detection of sars-cov- diagnostic methods and potential portable biosensors for coronavirus disease dual-functional plasmonic photothermal biosensors for highly accurate severe acute respiratory syndrome coronavirus detection causative virus (sars-cov- ) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor paper-based synthetic gene networks rapid, low-cost detection of zika virus using programmable biomolecular components toehold switches: de-novo-designed regulators of gene expression ( ) first case of novel coronavirus in the united states genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan revista do instituto de medicina tropical de sao paulo sequence mismatch in pcr probes may mask the covid- detection in nepal presence of mismatches between diagnostic pcr assays and coronavirus sars-cov- genome assay optimization for molecular detection of zika virus evaluation of who listed covid- qpcr primers and probe in silico with sers-cov- full genome sequences emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments the establishment of reference sequence for sars-cov- and variation analysis genomic diversity of sars-cov- in coronavirus disease patients the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak -an update on the status fullgenome evolutionary analysis of the novel corona virus ( -ncov) the proximal origin of sars-cov- genomic variance of the -ncov coronavirus a guideline for homology modeling of the proteins from newly discovered betacoronavirus covid- : the role of the nsp and nsp in its pathogenesis nonstructural proteins ns b and ns are likely to be phylogenetically associated with evolution of -ncov ) a sequence homology and bioinformatic approach can predict candidate targets for immune responses to sars-cov- preliminary identification of potential vaccine targets for the covid- coronavirus (sars-cov- ) based on sars-cov immunological studies seroprevalence of anti-sars-cov- igg antibodies in prevalence of sars-cov- specific neutralising antibodies in blood donors from the lodi red zone in lombardy seroprevalence of immunoglobulin m and g antibodies against sars-cov- in china neutralizing antibodies against sars-cov- and other human coronaviruses detection of sars-cov- -specific humoral and cellular immunity in covid- convalescent individuals patterns of igg and igm antibody response in covid- patients early virus clearance and delayed antibody response in a case of covid- with a history of co-infection with hiv- and hcv ) structure, function, and antigenicity of the sars-cov- spike glycoprotein novel antibody epitopes dominate the antigenicity of spike glycoprotein in sars-cov- compared to sars-cov protocol and reagents for pseudotyping lentiviral particles with sars-cov- spike protein for neutralization assays cross-reactive antibody response between sars-cov- and sars-cov infections lack of cross-neutralization by sars patient sera towards sars-cov- analysis of the first cluster of cases in a family of novel coronavirus pneumonia in gansu province profiling early humoral response to diagnose novel coronavirus disease (covid- ) sars-cov- seroconversion in humans: a detailed protocol for a serological assay, antigen production, and test setup serological assays for severe acute respiratory syndrome coronavirus (sars-cov- ) test performance evaluation of sars-cov- serological assays diagnostic performance of rapid igg/igm antibody tests and the euroimmun iga/igg elisa in covid- patients development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis clinical performance of two sars-cov- serologic assays serological immunochromatographic approach in diagnosis with sars-cov- infected covid- patients severe acute respiratory syndrome coronavirus -specific antibody responses in coronavirus disease clinical performance of different sars-cov- igg antibody tests evaluation of two automated and three rapid lateral flow immunoassays for the detection of anti-sars-cov- antibodies establishment and validation of a pseudovirus neutralization assay for sars-cov- characterization of spike glycoprotein of sars-cov- on virus entry and its immune cross-reactivity with sars-cov evaluation of novel antigen-based rapid detection test for the diagnosis of sars-cov- in respiratory samples evaluation of rapid antigen test for detection of sars-cov- virus development of a portable, ultra-rapid and ultra-sensitive cell-based biosensor for the direct detection of the sars-cov- s microfluidic immunoassays for sensitive and simultaneous detection of igg/igm/antigen of sars-cov- within min ) diagnostic accuracy of serological tests for covid- : systematic review and metaanalysis coinfection with covid- and coronavirus hku -the critical need for repeat testing if clinically indicated coinfection of influenza virus and severe acute respiratory syndrome coronavirus (sars-cov- ) coinfection with sars-cov- and human metapneumovirus sars-cov- and influenza virus co-infection epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in emerging novel coronavirus ( -ncov) pneumonia china: a descriptive, cross-sectional, multicenter study prevalence and clinical presentation of health care workers with symptoms of coronavirus disease in dutch hospitals during an early phase of the pandemic clinical and virologic characteristics of the first patients with coronavirus disease (covid- ) in the united states clinical features, laboratory characteristics, and outcomes of patients hospitalized with coronavirus disease (covid- ): early report from the united states key: cord- -pjcskj m authors: piazza, kelly senters; diaz, gustavo title: light in the midst of chaos: covid- and female political representation() date: - - journal: world dev doi: . /j.worlddev. . sha: doc_id: cord_uid: pjcskj m the promotion of gender equality and the empowerment of women are global policy priorities across countries and development institutions. research on gender and politics shows that exceptional environments can activate stereotypes of women as honest, trustworthy, and competent lawmakers in public health and, in doing so, can generate increased public support for female political candidates. we argue that the – coronavirus pandemic has the potential to produce this outcome, as recent public opinion polls highlight widespread discontent with male-led governments’ responses to the pandemic and elevated concerns surrounding public health. recent positive media reports of female world leaders’ responses to the pandemic provide further reason to suspect a forthcoming increase in political support for female candidates. we posit that such an outcome may prove essential not only for enhancing development and improving long-standing gender inequities but also for alleviating the pandemic’s disproportionately allocated hardships. the promotion of gender equality and the empowerment of women is formally recognized as a global policy priority both by the world's countries and by leading development institutions. not only is gender equality morally and ethically just, but scholars and development practitioners agree that the empowerment of women engenders positive political, economic, and social yields for societies writ large. as such, government and nongovernment actors have developed wide-ranging initiatives in pursuit of this goal with varying degrees of success. operating under the belief that political empowerment is an important precursor to gender equality in wide-ranging development metrics, political scientists have worked to understand the factors underlying women's political representation. their research finds that factors ranging from electoral gender quotas (sacchet, ; wylie, ) to proportional representation electoral systems (that permit multiple electoral winners) boost women's electoral prospects (ahn, kim, & kang, ; githens, lovenduski, & norris, ; matland, ; salmond, ) . the caveat is that these factors are less impactful in enhancing women's political representation in the absence of accompanying public support for female candidates (franceschet & piscopo, ) . recent research suggests that exceptional environmentsinvolving conflict and including political corruption scandals accompanied by downturns in public trust as well as public health crises -can generate the public support for female political representation that public policies or institutions alone may not. such unique environments may promote female candidates either because they increase the demand for desirable qualities associated with women or because they focus voters' attention on issues that women are perceived to be especially competent in addressing. we argue that the - coronavirus pandemic may have fostered an environment capable of promoting female representation through both mechanisms. in this piece, we overview key findings from related research and introduce preliminary insight into contemporary global attitudes related to the coronavirus. both help us to weigh in on whether the coronavirus pandemic may lead to favorable electoral outcomes for female candidates. the literature on gender stereotypes asserts that female politicians are perceived to be more empathetic, compassionate, honest, trustworthy, and liberal than their male counterparts (alexander & andersen, ; dollar, fisman, & gatti, ; funk, hinojosa, & piscopo, ; huddy & terkildsen, ; mcdermott, ; world development j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / w o r l d d e v morgan, ) . exceptional environments that are deficient in these areas may generate demands for female inclusion. recent and ongoing scholarship on the exceptional environments associated with conflict and political corruption revelation explores the validity of this claim, seeking to understand the connection between gender stereotypes relating to qualities and personality traits and electoral dynamics. regarding conflict, both a robust literature on peace-building and security council resolution concede that women are fundamental to post-conflict resolutions (see zuckerman & greenberg, ) . underlying calls for increased female representation in post-conflict states is the ''women and peace" hypothesis that women hold more pacific or compromising attitudes than men, plausibly a function of ''traditionally female characteristics such as empathy and caring" (brounéus, ; tessler, nachtwey, & grant, ; tessler & warriner, ) . additionally, some accounts suggest that women improve the process and outcome of peace talks because they build trust and bridge divides (o'reilly, ) . speaking on corruption, funk et al., discern that gender stereotypes work to the political benefit of female political candidates in exceptional latin american environments penetrated with perceived corruption and political distrust. they find that latin american political parties nominate more women when the public lacks trust in the national legislature under the presumption that voters will look more favorably upon female candidates due to their association with the desirable qualities of honesty and trustworthiness. ongoing research corroborates this conclusion, finding that revealing corruption in brazilian municipalities increases the number of women contesting mayoral offices, especially in places where male incumbents were revealed to engage in malfeasance (diaz & piazza, ) . both studies suggest that political environments that spark public distrust, such as those plagued with corruption, can activate gender stereotypes relating to qualities or personality traits that render female candidates more attractive than their male counterparts. similar to post-conflict and corruption-laden environments, the - coronavirus pandemic has ushered in a deficiency in public trust around the world. poor public perceptions of both government responses to covid- and government truthfulness abounded in march and april and were especially acute in countries with male leaders. according to data from the international survey on coronavirus (fetzer et al., ) , as of april , , less than % of respondents in countries ranging from the united kingdom to brazil to indonesia perceived their governments' reactions to the pandemic to be sufficient. per this same source, more than % of respondents in countries ranging from the united states to chile to nigeria perceived their governments to be untruthful in communications regarding the pandemic. though causal tests remain outstanding, other data from the international survey on coronavirus suggests corresponding high levels of distrust in government in a subset of countries, including the united states, colombia, venezuela, and russia. more than % of respondents in these countries have indicated a distrust in government to take care of its citizens in light of the raging pandemic. in line with the previously reviewed literature, the meager levels of public trust in government following from the - coronavirus pandemic may increase demands for female representation, compel political parties to field female candidates, and potentially improve female candidates' chances of electoral success. aside from qualities or personality traits, the literature on gender stereotypes acknowledges differences in perceived issue competencies across male and female politicians. whereas male politicians are perceived as proficient policymakers in the ''high politics" areas of the economy, agriculture, employment, fiscal affairs, crime, and security (herrnson, lay, & stokes, ; lawless, ) , female politicians are generally considered to be especially adept policymakers in the ''low politics" areas of education, health, and other issues relating to ''children and family" (alexander & andersen, ; herrnson, lay, & stokes, ; huddy & terkildsen, ; leeper, ) . recent research has moved beyond documenting these stereotypes to demonstrating their influence on electoral behaviors. most pertinent to this paper, piazza & schneider, assess whether the exceptional environment stemming from the - zika epidemic and the accompanying priming of the ''women's issue" of (infant) health resulted in an electoral boost for female candidates. their difference-in-difference analyses show that if the number of cases of zika per , residents increases by % in the two months leading up to the brazilian municipal elections, then the vote share for female mayoral candidates is predicted to increase by . %. they find that this effect is especially pronounced in brazilian municipalities with high incidences of the zika virus among pregnant women. the authors attribute these results to popular perceptions of female candidates' unique competencies in the area of public health and, more specifically, in infant health and family planning. like the zika virus, the - coronavirus pandemic has primed the ''women's issue" of public health around the world. public opinion polls from mid-march conducted in diverse contexts including the united states, canada, and italy point in this direction. on the basis of mid-march social media surveys, nelson et al., find that . % of americans expressed concerns of getting sick from covid- , and . % expressed concerns of not being able to get medical care. an angus reid institute poll conducted march - found that a similar share of canadians ( %) perceived the coronavirus outbreak to be a serious threat to their country, with % expressing personal concerns about getting sick from the novel coronavirus and % expressing concern for their friends and family members. an ipsos survey of , italian adults conducted from march to march found that % of italians perceived the coronavirus as a threat to italy, with % expressing a perceived personal threat. we interpret the common concern with the - coronavirus pandemic across these diverse global contexts as a strong signal that the public health crisis and evaluations of incumbent responses to it will factor into upcoming electoral decisions world-wide. insofar as both these public health concerns predominate and endure in the lead up to electoral contests and global publics interpret these concerns to correspond with ''women's issues," research on the - zika virus epidemic suggests that female candidates may experience an electoral boost in upcoming political contests. we identify two critiques to our argument. first, research from economics and law finds that organizations appoint more women to ''glass cliff" leadership positions in moments of crisis (ashby, ryan, & haslam, ; haslam & ryan, ) . ryan, haslam, and kulich, selection strategies in politics. in line with this research, the coronavirus pandemic may increase female representation not due to their perceived trustworthiness or competence in public health but because party leaders are more likely to assign women to leadership positions with high risk of failure in moments of crisis. second, though intimately connected with public health, the - coronavirus pandemic is less directly related to the types of health in which women are perceived to have a comparative advantage. this means that the coronavirus pandemic may not increase support for female candidates in the same way that the zika epidemic did. while these critiques are valid, we believe that media reports of female leadership in response to the coronavirus mitigate them and bolster our argument. reports praising german chancellor angela merkel's sciencebased response, widespread testing, transparency, stringent social distancing policies, travel restrictions, and relational appeals to the public to induce compliance and new zealand prime minister jacinda arden's clarity, compassion, strict national lockdown, travel restrictions, and pervasive testing (mahdawi, ) have fostered the narrative that female executives have more effectively, efficiently, and impressively handled the coronavirus pandemic (cherneski, ) . whether a function of over competence, the disproportionate hurdles women need to overcome to be elected in the first place, or a disposition to seek out advice from experts in moments of crisis, the contemporary dynamics suggest that female world leaders are handling the virus in an impressive manner (mahdawi, ; yancey-bragg, ) . there are compelling reasons to suspect that these narratives instill gender stereotypes relating to trustworthiness and/or competence in public health, and insofar as they do, it is plausible to anticipate an improvement in female candidates' prospects in upcoming electoral contests. to summarize, research suggests that exceptional environments may activate gender stereotypes that improve the electoral prospects of female candidates. though distinct from other exceptional climates in its global reach and magnitude, we argue that the - coronavirus pandemic also has the potential to produce an outcome favorable to prospective female politicians. recent public opinion polls highlight both general discontent with how politicians have managed the pandemic and widespread concerns surrounding the ''women's issue" of public health. contemporary public opinion, along with the positive media coverage of female leaders in times of crisis, may lead both party elites and voters to turn towards female candidates. in the midst of chaos, an increase in women's political representation could establish an important foundation from which to protect recent development advances and achieve related goals. it may also prove fundamental in alleviating the pandemic's disproportionately allocated hardships. according to grown and sánchez-páramo, '' there is a high risk that gender inequalities will widen during and after the pandemic and that gains in women's and girls' accumulation of human capital, economic empowerment, and voice and agency, painstakingly built over the past decades, will be reversed" (grown & sánchez-páramo, ) . substantiating grown and sánchez-páramo's fear, recent reports indicate that the coronavirus has hit economic sectors with high female employment shares (e.g. the service and ''essential worker" sectors) especially hard, intensified women's domestic responsibilities, and increased violence against women (alon, doepke, olmstead-rumsey, & tertilt, ; bahn, cohen, & van der meulen rodgers, ; campbell, ; cherneski, ; gausman & langer, ; graves, ; grown & sánchez-páramo, ; o'donnell, peterman, & potts, ; wenham, smith, & morgan, ) . these consequences may be especially pronounced for women of racial and ethnic minority groups, who bear the brunt of enforcement sanctions, job losses, and the adverse public health effects of the virus itself (kirby, ) . in the event that the - coronavirus pandemic increases public support for female political candidates who exude qualities of trustworthiness and uphold their mandates in the realm of public health, there may be some promise for relief. under chancellor angela merkel's leadership, began developing a test for the virus (blackburn & ruyle, ) and required healthcare providers to immediately report suspected cases of covid- to public health authorities (wieler & gottschalk, ) . from the outset, national responses were science-based, and information collected was made transparent. within a month, tests were widely available at no cost to probable carriers of the virus and swiftly rolled out (wieler & gottschalk, ) . shortly thereafter, merkel adopted stringent social distancing policies, mandated the closure of schools and retail businesses, limited public gatherings, and operated with travel restrictions (blackburn & ruyle, ) . in an effort to induce compliance with these policies, merkel ''asked citizens to consider how their behavior impacts those they love" (cherneski, ) . as a result, the number of daily confirmed cases in germany has, at the time of this writing, diminished both in terms of the number of daily confirmed cases and deaths. since the pandemic's outbreak, the media has frequently touted new zealand prime minister jacinda ardern's successes in curtailing the coronavirus. prior to new zealand's first reported case of covid- , prime minister jacinda ardern banned travel from china (blackburn & ruyle, ) . in late-march, one month after new zealand's first reported case, new zealand implemented a strict national lockdown that closed schools and non-essential businesses, banned social gatherings, and mandated a -day self-isolation period for travelers entering the country (blackburn & ruyle, ) . ardern evoked compliance by compelling the country's citizens to 'be kind to each other' (cherneski, ) . as a result, new zealand was, as of mid-june , considered to be coronavirus free. low female political representation in the us: an institution-based explanation gender as a factor in the attribution of leadership traits the impact of covid- on gender equality legal work and the glass cliff: evidence that women are preferentially selected to lead problematic cases a feminist perspective on covid- and the value of care work globally. gender, work & organization how leadership in various countries has affected covid- response effectiveness the women and peace hypothesis in peacebuilding settings: attitudes of women in the wake of the rwandan genocide an increasing risk of family violence during the covid- pandemic: strengthening community collaborations to save lives evidence-loving rockstar chief medical officers: female leadership amidst covid- in canada women can't win: electoral double standards in the face of corruption are women really the ''fairer sex? corruption and women in government global behaviors and perceptions at the onset of the covid- pandemic gender quotas and women's substantive representation: lessons from argentina women to the rescue: the gendered effects of public discontent on legislative nominations in latin america sex and gender disparities in the covid- pandemic different roles, different voices: women and politics in the united states and europe women's domestic burden just got heavier with the coronavirus the coronavirus is not gender-blind, nor should we be the road to the glass cliff: differences in the perceived suitability of men and women for leadership positions in succeeding and failing organizations women running ''as women": candidate gender, campaign issues, and voter-targeting strategies gender stereotypes and the perception of male and female candidates evidence mounts on the disproportionate effect of covid- on ethnic minorities. the lancet respiratory medicine women, war, and winning elections: gender stereotyping in the post-september th era the impact of prejudice on female candidates: an experimental look at voter inference the secret weapon in the fight against coronavirus: women. the guardian women's representation in national legislatures: developed and developing countries voting cues in low-information elections: candidate gender as a social information variable in contemporary united states elections gender and the latin american voter. the latin american voter us public concerns about the covid- pandemic from results of a survey given via social media a gender lens on covid- : pandemics and violence against women and children why women? inclusive security and peaceful societies the electoral buzz: rational prospective voting and the politics of the zika epidemic in brazil politics and the glass cliff: evidence that women are preferentially selected to contest hard-to-win seats why gender quotas don't work in brazil? the role of the electoral system and political finance proportional representation and female parliamentarians further tests of the women and peace hypothesis: evidence from cross-national survey research in the middle east gender, feminism, and attitudes toward international conflict: exploring relationships with survey data from the middle east covid- : the gendered impacts of the outbreak party institutionalization and women's representation in democratic brazil emerging covid- success story: germany's strong enabling environment female world leaders are handling the coronavirus crisis ''in a really impressive manner the gender dimensions of post-conflict reconstruction: an analytical framework for policymakers the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord- -deuvq wf authors: sahasranaman, anand; kumar, nishanth title: network structure of covid- spread and the lacuna in india's testing strategy date: - - journal: nan doi: nan sha: doc_id: cord_uid: deuvq wf we characterize the network of covid- spread in india and find that the transmission rate is . , with daily case growth driven by individuals who contracted the virus abroad. we explore the question of whether this represents exponentially decaying dynamics or is simply an artefact of india's testing strategy. testing has largely been limited to individuals travelling from high-risk countries and their immediate contacts, meaning that the network reflects positive identifications from a biased testing sample. given generally low levels of testing and an almost complete absence of testing for community spread, there is significant risk that we may be missing out on the actual nature of outbreak. india still has an apparently low current caseload, with possibly a small window of time to act, and should therefore aggressively and systematically expand random testing for community spread, including for asymptomatic cases. this will help understand true transmission characteristics and plan appropriately for the immediate future. : the spread of covid- in india (till march , ) . a) change in cumulative caseload over time shows sharp rise of cases in march . b) state-wise distribution of cases in india reveals maharashtra to have the highest burden of cases. the key parameter to characterize an outbreak is the transmission rate, which is a measure of the average number of individuals infected by an individual carrying the virus. a commonly used metric of transmission is the basic reproductive number , which is the transmission rate given that the population has no immunity from past exposures or vaccination, nor any deliberate intervention in disease transmission [ ] . when > , the number of infections grows and spreads in the population, but not for < . is generally modelled from data on the spread of the disease, with the assumption that the dynamic of spread is underway in the community and that the measure therefore parametrizes the extent of intra-community spread. in this work, we look at the data on each individual case of covid- infection and attempt to create the network structure of infections for india. essentially, we attempt to identify how each individual was infected -whether the individual carried the infection from abroad (level ), or if it was local transmission in the country from an individual who had been infected abroad (level ), or if it was community transmission between individuals in the country (level ). using this characterization of individual infections, we create the network of covid- infections in india, and compute the transmission rate as the average number of neighbours of a node in the network. we also simulate different scenarios of transmission using a simple susceptible-infected-recovered (sir) epidemiology model [ ] , to highlight potential pathways of spread. the model considers a system of we use march , as the date on which significant interventions happened in india to restrict the spread of disease, including the suspension of almost all visas for tourists entering the country, in addition to measures adopted by a number of states closing schools and colleges, as well as malls and movie halls. as of this date, we find that there were cases of individuals who had contracted the virus, and we were able to identify the sources of infection in of these cases. because case numbers in india are still close to , we find that newspapers are still tracking individual case histories; and we use these newspaper reports and wikipedia to construct the data set on individual transmission [ , . out of these cases, we identified ( %) as level , ( %) as level or local transmission, and only one ( %) as level or community transmission (fig. a) . a day (fig. a) . this anomaly is resolved when we assess the network structure, which reveals that a majority of infections still being identified are those who contracted the virus abroad ( %, fig. in countries where the virus has seen community spread, has been estimated in the region of . − , which indicates exponential growth dynamics [ ] . while there is emerging research suggesting a degree of climate determination in the spread of covid- as well as a correlation with geographical latitude, these results are very new and need confirmation [ , ] . therefore, in the absence of clinching evidence relating to environmental factors, we ask the question of what is driving this discrepancy in transmission rates between india and other countries experiencing community spread. to answer this question, we must first turn our attention to testing processes on the ground to identify cases of covid- in india. it has been widely reported that the testing in india has been focused on (and limited to) citizens who have travelled from a set of high-risk countries and those who have come in contact with these cases [ ] [ ] . there has been no systematic testing process in place for testing the extent of community spread in india [ ] . given this bias in testing, it should be no surprise that among the observed cases of covid- in the country, a majority are travellers from high-risk countries and their immediate contacts with local transmission (as reflected in the networks structure of infections, fig. b ). recently the indian council for medical research (icmr) confirmed that limited testing on community spread had been initiated - , tests of people without travel history or contact with infected persons were to be done, though details of the randomization process in selecting these cases are not available [ ] . while this is a start, it must be kept in mind that the actual network of spread will continue to reflect the same bias until community testing becomes a significant part of the testing strategy. consolidated data from icmr tells us that india has so far tested a total of , samples [ ] , or tests people per million population, which is very low compared to other countries that have been testing for community spread [ ] , and creates the risk of missing such transmission in case it is already underway in the country. india currently has over covid- positive cases, but is yet to hit the kinds of caseload spikes seen in china, the us and europe [ ] . given this shrinking window of opportunity and the significant lacuna in testing, india must, aggressively and systematically, proceed to widen the scope of testing for possible community transmission immediately. in this context, icmr has just announced the introduction of tests for asymptomatic direct and high-risk contacts of a confirmed case [ ] . however, given the tremendous void in testing for community spread so far, there is a need for larger scale random testing of both symptomatic and asymptomatic cases, in order to better understand the extent of spread in the broader community. this is particularly critical because if indeed community transmission is underway in india, we could see significant proportions of the population being infected by covid- before the epidemic recedeswe simulate these possibilities for = . (which is at the lower end of transmission rates from global evidence on covid- ) and = . (which is close to the median transmission rate from evidence so far) and find that with community spread, we could see maximum infection caseloads of % and % of the population respectively (figs. a and b). a b epidemic spread models used by the uk and us predict much higher infection rateswith = . , they estimate that up to % of the population of the us/uk would be infected in the absence of intervention [ ] . even if we assume that maximum infection load in india peaks at %, (about million people) and even if only % of these cases are most severe requiring intensive care, this means that the indian health system would need to cater for million icu beds, but it is estimated that there are only around , icu beds in indiaor icu bed for people [ ] . given the state of the indian health system, it is essential that we do as much as possible to test randomly for community spreadboth symptomatic and asymptomatic -and attempt to unearth the gravity of spread in india as soon as possible, especially while the current restrictions on international travel, closure of places of gathering (schools, colleges, malls, temples, workplaces etc.), household quarantines, and other social distancing measures that are already in place. briefing by who director-general tedros adhanom ghebreyesus - coronavirus pandemic coronavirus in india: tracking country's first covid- cases; what numbers tell. india today mohfw the reproduction number contributions to the mathematical theory of epidemics-i coronavirus pandemic in india coronavirus cases rise to , italian tourists among them: government coronavirus update: new case reported from ghaziabad, india now has patients coronavirus: delhi resident tests positive for coronavirus, total people infected in india j&k man tests positive for coronavirus; infected in india coronavirus: more positive cases in india, total goes up to , says health ministry ndtv. of family in kerala get coronavirus, total positive cases in india coronavirus update: new cases reported, india now has covid- patients fresh coronavirus cases emerge from punjab, bengaluru; takes total to coronavirus: two test positive in pune; confirmed cases in india. indiatvnews coronavirus: all schools, colleges in kerala to shut down in march; more test positive coronavirus update: more test positive for covid- in maharashtra, number rises to the new indian express. cases reach in india as jaipur person tests positive, one critical in kerala coronavirus cases in maharashtra; budget session to be curtailed the times of india. one more tests positive for covid- uttar pradesh tally is nine sixth case of coronavirus reported in delhi coronavirus update: indian national evacuated from italy with tests positive for covid- two more test positive in yavatmal; maharashtra count rises to four new coronavirus cases confirmed in mumbai, maharashtra total cases at . india today second case of coronavirus confirmed in hyderabad coronavirus: -year-old from jaipur tests positive for covid- , has travel history of spain. india today the reproductive number of covid- is higher compared to sars coronavirus spread of sars-cov- coronavirus likely to be constrained by climate. medrxiv the indian express. one covid- positive infects . in india, lower than in hot zones india needs a more aggressive testing regimen for coronavirus: experts public-health experts raise concerns about india's restricted testing for covid- is india testing enough for coronavirus cases? will know if india is going through community transmission of covid- : icmr worldometers strategy of covid testing in india impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand key: cord- -t jngq authors: ramshaw, rebecca e.; letourneau, ian d.; hong, amy y.; hon, julia; morgan, julia d.; osborne, joshua c. p.; shirude, shreya; van kerkhove, maria d.; hay, simon i.; pigott, david m. title: a database of geopositioned middle east respiratory syndrome coronavirus occurrences date: - - journal: sci data doi: . /s - - - sha: doc_id: cord_uid: t jngq as a world health organization research and development blueprint priority pathogen, there is a need to better understand the geographic distribution of middle east respiratory syndrome coronavirus (mers-cov) and its potential to infect mammals and humans. this database documents cases of mers-cov globally, with specific attention paid to zoonotic transmission. an initial literature search was conducted in pubmed, web of science, and scopus; after screening articles according to the inclusion/exclusion criteria, a total of sources were selected for extraction and geo-positioning. each mers-cov occurrence was assigned one of the following classifications based upon published contextual information: index, unspecified, secondary, mammal, environmental, or imported. in total, this database is comprised of unique geo-positioned mers-cov occurrences. the purpose of this article is to share a collated mers-cov database and extraction protocol that can be utilized in future mapping efforts for both mers-cov and other infectious diseases. more broadly, it may also provide useful data for the development of targeted mers-cov surveillance, which would prove invaluable in preventing future zoonotic spillover. middle east respiratory syndrome coronavirus (mers-cov) emerged as a global health concern in when the first human case was documented in saudi arabia . now listed as one of the who research and development blueprint priority pathogens, cases have been reported in countries across four continents . imported cases into non-endemic countries such as france, great britain, the united states, and south korea have caused secondary cases [ ] [ ] [ ] , thus highlighting the potential for mers-cov to spread far beyond the countries where index cases originate. reports in animals suggest that viral circulation could be far more widespread than suggested by human cases alone [ ] [ ] [ ] . to help prevent future incidence of mers-cov, public health officials can focus on mitigating zoonotic transfer; however, in order to do this effectively, additional research is needed to determine where spillover could occur between mammals and humans. previous literature reviews have looked at healthcare-associated outbreaks , importation events resulting in secondary cases , , occurrences among dromedary camels , , or to summarize current knowledge and knowledge gaps of mers-cov , . this database seeks fill gaps in literature and build upon existing notification data by enhancing the geographic resolution of mers-cov data and providing occurrences of both mammal and environmental detections in addition to human cases. this information can help inform epidemiological models and targeted disease surveillance, both of which play important roles in strengthening global health security. knowledge of the geographic extent of disease transmission allows stakeholders to develop appropriate emergency response and preparedness activities (https://www.jeealliance.org/ global-health-security-and-ihr-implementation/joint-external-evaluation-jee/), inform policy for livestock trade and quarantine, determine appropriate demand for future vaccines (http://cepi.net/mission) and decide where to deliver them. additionally, targeted disease surveillance will provide healthcare workers with updated lists of the methods and protocols summarized below have been adapted from previously published literature extraction processes [ ] [ ] [ ] [ ] [ ] , and provide additional context surrounding our systematic data collection from published reports of mers-cov. data collection. we identified published reports of mers-cov by searching pubmed, web of science, and scopus with the following terms: "middle eastern respiratory syndrome", "middle east respiratory syndrome", "merscov", and "mers". the initial search was for all articles published about mers-cov prior to april , , and was subsequently updated to february , . these searches were conducted through the university of washington libraries' institutional database subscriptions. we searched the web of science web of science core collection (the subscribed edition includes science citation index expanded, -present; social sciences citation index, -present; arts & humanities citation index, -present; emerging sources citation index, -present). we searched the standard scopus database and the standard, freely available pubmed database; these products have a single version that is consistent across institutional subscriptions or access points. in total, this search returned , related abstracts, which were collated into a database before a title-abstract screening was manually conducted (fig. . flowchart) . articles were removed if they did not contain an occurrence of mers-cov; for example, vaccine development research or coronavirus proteomic analyses. non-english articles were flagged for further review and brought into the full text screening stage. the accompanying supplementary file highlight the title and abstract screening process and the inclusion and exclusion criteria. full text review was conducted on , sources. to meet the inclusion criteria, articles must have contained both of the following items: ) a detection of mers-cov from humans, animals, or environmental sources, and ) mers-cov occurrences tagged with spatial information. additionally, extractors attempted to prospectively manually remove articles containing duplicate occurrences that were already extracted in the dataset. extractors only prospectively manually removed articles if it was clear the articles contained data we were confident had already been extracted and had high-quality data. we excluded sources based on full text review. in addition, we reviewed citations and retroactively added relevant articles to our database if they were not already included. we retroactively added and subsequently marked ten articles for extraction using this process. in total, we extracted peer-reviewed sources reporting detection of mers-cov that included geographic and relevant epidemiological metadata. geo-positioning of data. google maps or arcgis was used to manually extract location information at the highest resolution available from individual articles. we evaluated spatial information as either points or polygons. the geography was defined as a point if the location of transmission was reported to have occurred within a × km area. point data are represented by a specific latitude and longitude. a point references an area smaller than × km in order to be compatible with the typical × km resolution of satellite imagery used for global analyses. the geography was defined as a polygon if the location of transmission was less clear, but known to have occurred in a general area (e.g. a province), or the location of transmission occurred within an area greater than × km (e.g. a large city). we used contextual information to determine location in instances where the author's spelling of a location differed from google maps or arcgis. maps provided by authors were digitized using arcgis. we used three different types of polygons: known administrative boundaries, buffers, and custom polygons. relevant administrative units were sourced from the global administrative unit layers curated by the food and agricultural organization of the un for known administrative boundaries of governorates, districts, or regions, and paired with the occurrence record. buffers were created to encompass areas in cities and regions without corresponding administrative units. to ensure that buffers encompassed the entirety of the area of interest, google maps was used to determine the required radius. in areas with unspecified boundaries (e.g. table mountain national park and the border region between saudi arabia and uae) arcgis was used to generate custom polygons, which were assigned a unique code within a defined shapefile for ease of re-identification. this database is publicly available online , . each of the rows represents a unique occurrence of mers-cov. rows containing an index, unspecified, or imported case represent a single case of mers-cov. rows containing mammal and secondary cases may represent more than one case but are still unique geospatial occurrences. table shows an overview of the content available in the publicly available dataset. in addition, online-only table lists occurrences by geography, origin, shape type, and publication and online-only table provides citations of the data. index unspecified mammal import secondary absent environmental www.nature.com/scientificdata www.nature.com/scientificdata/ . pathogen: name the pathogen identified (e.g. mers-cov, bat coronaviruses, and other mers-cov-like pathogens). . pathogen_note: miscellaneous notes regarding pathogen. . patient_type: index, unspecified, na, secondary, import, or absent. • index: any human infection of mers-cov resulting after direct contact with an animal and no reported contact with a confirmed mers-cov case or healthcare setting. • unspecified: cases that lacked sufficient epidemiological evidence to classify them as any other status (e.g. serosurvey studies). • na: non-applicable field; case was not a patient (e.g. mammal) • secondary: defined as any cases resulting from contact with known human infections. cases reported after the index case can be assumed to be secondary cases unless accompanied by specific details of likely independent exposure to an animal reservoir. • import: cases that were brought into a non-endemic country after transmission occurred elsewhere. • absent: suspected case(s) ultimately confirmed negative for mers-cov. . transmission_route: zoonotic, direct, unspecified, or animal-to-animal. • zoonotic: transmission occurred from an animal to a human. • direct: only relevant for human-to-human transmission. • unspecified: lacked sufficient epidemiological evidence to classify a human case as zoonotic or direct. • animal-to-animal: transmission occurred from an animal to another animal. . clinical: describes whether the mers-cov occurrence demonstrated clinical signs of infection. denoted by yes, no, or unknown. • yes: clinical signs of infection were present/reported. clinical signs among humans may range from mild (e.g. fever, cough) to severe (e.g. pneumonia, kidney failure). clinical signs among camels include nasal discharge. • no: clinical signs of infection were not present/reported. • unknown: subject(s) may or may not have been demonstrating clinical signs of infection. for example, some authors did not explicitly mention symptoms, but individuals reportedly sought medical care. another example being when a diagnostic serosurvey was conducted during an ongoing outbreak. the term "unknown" was used when articles lacked sufficient evidence for extractors to definitively label as "yes" or "no". . diagnostic: describes the class of diagnostic method that was used. pcr, serology, or reported. . diagnostic_note: more detailed information related to the specific test used (e.g. rk , igg, or igm serology). . serosurvey: describes the context if serological testing was used. • diagnostic: testing of symptomatic patients. • exploratory: historic exposure determined among healthy asymptomatic individuals. . country: iso code for country in which the case occurred. . origin: open-ended field to provide more details on the specific in-country location of mers-cov case. . problem_geography: this field was utilized if the mers-cov case was reported in a location that could cause uncertainty when determining exact geographic occurrence (e.g. hospital, abattoir). . lat: latitude measured in decimal degrees. . long: longitude measured in decimal degrees. . latlong_source: the source from which latitude and longitude were derived. . loc_confidence: states the level of confidence that researchers had when assigning a geographic location to the mers-cov case (good or bad). an answer of 'good' meant the article stated clearly that the case occurred in a specific geographic location and no assumptions were required on part of the researcher. an answer of 'bad' meant the article did not clearly state the specific geographic location of the mers-cov case, but the researcher was able to infer the location of occurrence. the field site_notes was utilized to detail the logic behind researchers' decisions when inference was required. . shape_type: the geographic shape type assigned to the mers-cov occurrence (point or polygon). . poly_type: if the mers-cov occurrence was assigned a shape_type of polygon, was it admin (gaul), custom, or buffer? . buffer_radius: if a mers-cov occurrence was assigned a buffer, what is the radius in km? . gaul_year_or_custom_shapefile: file path used to reach the necessary shape file in arcgis. users of this dataset can find custom shapefiles created for this dataset at: https://cloud.ihme.washington.edu/index. php/s/dgoykyqnbjg f /download . poly_id: a standardized and unique identifier assigned to each gaul shapefile. . poly_field: which type of polygon was used to geo-position the occurrence? (e.g. if admin polygon was used, enter adm _code) . site_notes: miscellaneous notes regarding the site of occurrence. . month_start: month that the occurrence(s) began. if the article provided a specific month of illness onset, the month was assigned a number from - ( = january, = february, etc.). if the article did not provide a specific month of illness onset, then researchers assigned a value of 'na' . month that the occurrence(s) ended, defined as the date a patient tested negative for mers-cov. if the article provided a specific month for recovery, the month was assigned a number from - ( = january, = february, etc.). if the article did not provide a specific month of symptom onset, then researchers assigned a value of 'na' . . year_start: year that the occurrence(s) began. if the year of illness onset was not provided in the article, the ihme standard was used: (year_start = publication year - ). year that the occurrence(s) ended. if the article did not provide a specific year for recovery, the ihme standard was used: (year_end = publication year - ). . year_accuracy: if years were reported, this field was assigned a value of ' ' . if assumptions were required, this field was assigned a value of ' ' . all data extracted from the original search (october to april , ) was reviewed independently by a second individual to check for accuracy. challenging extractions from the updated search (may , to february , ) were selected for group review during bi-weekly team meetings. upon extraction completion, all data were checked to ensure they fell on land and within the correct country. while the protocol implemented above was designed to reduce the amount of subjective decisions made by extractors, total elimination was not possible. wherever a subjective decision had to be made, the extractor utilized the various notes fields in order to document the logic behind decisions. these decisions were subsequently reviewed by other extractors. the techniques described here can be applied to collect and curate datasets for other infectious diseases, as has been previously demonstrated with dengue and leishmaniasis . additionally, since these data were collected independently through published reports of mers-cov occurrence, they may be used to build upon existing notification data , . our ability to capture occurrences in this dataset is contingent on the data contained within published literature. therefore, this dataset does not represent a total count of all cases. instead, this dataset's value lies within its geo-precision. data were extracted with a focus on obtaining the highest resolution possible. these data may be merged with other datasets, such as who or oie surveillance records, and are intended to complement, not replace, these resources. together, published reports and notification data can provide a more comprehensive snapshot of current disease extent and at-risk locations. an important consideration, whether using the literature data alone, or in combination with other databases, is the potential for duplication. various pieces of metadata can be used to evaluate where potential duplicates could lie, such as common date fields (month_start, month_end, year_start, year_end) or consistent geographic details (lat, long, poly_id, shape_type) or shared epidemiological tags (patient_type). researchers may wish to consider further steps, such as fuzzy matching of geographic data (e.g. matching a point with an overlapping buffer) or temporal data (e.g. matching a precise month with an overlapping month interval). we acknowledge this duplicate-removal process will not catch all matching records, but it will likely catch several. we recommend occurrences are layered from top to bottom in the following order: index (green), unspecified (orange), mammal (yellow), import (blue), secondary (purple). points were plotted using their assigned latitudes and longitudes, and shape files were created for polygons. buffers were also plotted using assigned latitudes and longitudes, after which each buffer's custom radius was drawn. higher resolution geographies (points, buffers, governorates) were plotted on top of lower resolution geographies (countries, regions). www.nature.com/scientificdata www.nature.com/scientificdata/ this approach because it will allow researchers to remove several duplicates without erroneously deleting any two occurrences that are truly unique (i.e. not duplicates). essentially, we recommend a sensitive approach above a more specific approach, as the latter simply risks culling too many records that aren't actually duplicates. when merging with other databases, consistency in metadata tagging is essential. for the who disease outbreak news data feed , for instance, nomenclature for case definitions is slightly different, with who definitions of "community acquired" and "not reported" comparable to "index" and "unspecified" respectively. in addition, it is important to recognize what information is beyond the scope of these additional databases. again, when comparing to the who dataset, it is important to recognize that serologically positive cases do not meet the case definition used in the who database. these adjustments need to be identified on a dataset-to-dataset basis. among cases tagged as index or unspecified. occurrences tagged as index are coloured green, those tagged as unspecified are coloured orange. points were plotted using their assigned latitudes and longitudes, and shape files were created for polygons. buffers were also plotted using assigned latitudes and longitudes, after which each buffer's custom radius was drawn. higher resolution geographies (points, buffers, governorates) were plotted on top of lower resolution geographies (countries, regions). points were plotted using their assigned latitudes and longitudes, and shape files were created for polygons. buffers were also plotted using assigned latitudes and longitudes, after which each buffer's custom radius was drawn. higher resolution geographies (points, buffers, governorates) were plotted on top of lower resolution geographies (countries, regions). www.nature.com/scientificdata www.nature.com/scientificdata/ this database can be combined with other covariates (e.g. satellite imagery) to produce environmental suitability models of mers-cov infection risk and potential spillover on both global and regional scales as achieved with other exemplar datasets [ ] [ ] [ ] [ ] . this information can be useful in resource allocation aimed at improving disease surveillance and contribute towards a better understanding of the factors facilitating continued emergence of index cases. the addition of sampling techniques and prevalence data may improve this dataset. researchers were ultimately unable to add these data due to inconsistencies in the way literature reported sampling techniques and prevalence date by geography. an attempt to extract these data using the current approach would have led to sporadic inclusion of this information and would not have been comprehensive for the entire dataset. moving forward, we recommend authors report sampling technique and prevalence data at the highest resolution geography possible, as seen in miguel et al. . we encourage continued presentation of paired epidemiological and geographic metadata that would allow for more detailed analysis in the future. this database may also be utilized in clinical settings to provide an evidence-base for diagnoses when used in conjunction with patient travel histories. additionally, it can be used to identify geographies for surveillance, particularly areas where mers-cov has been documented in animals but not humans (e.g. ethiopia and nigeria). identifying locations for surveillance will, in turn, inform global health security. while models will increase the resolution at which these questions can be addressed, datasets such as this provide an initial baseline. a major limitation of this database is the potential for sampling bias, which stems from higher frequency of disease reporting within countries where there exists strong healthcare infrastructure and reporting systems. this database does not attempt to account for such biases, which must be addressed in subsequent modelling activities where such biases are of consequence. similarly, another limitation is potential duplicate documentation of singular occurrences. this can happen when the same occurrence is assigned different geographies (e.g. point, polygon) in multiple publications. even though extractors made efforts to prospectively manually identify duplicate occurrences, this was challenging because the process relied upon papers providing sufficient details for extractors to determine a duplicate occurrence (e.g. geography, patient demographics, dates of occurrence, diagnostic methods, etc.). however, the majority of papers did not report such details for each occurrence. in those instances, it was impossible for extractors to discern whether occurrences may have been duplicates from a previous artic le. even case studies inconsistently reported patient details and demographic information. these are some examples of challenges faced by extractors when we attempted to identify duplicates. without sufficient contextual clues, extractors lacked evidence to determine duplicity and thus likely extracted some unique occurrences more than once. despite efforts to remove duplicate occurrences from the database, it is possible that some remain. geographic uncertainty is similarly problematic for analyses such as this. in some cases, polygons, as opposed to points, are utilised as a geographic frame of reference, reflecting the uncertainty in geotagging in the articles themselves. for some occurrences, there is a strong assumption that the geography listed corresponds to the site of infection. while the use of km × km as the minimum geographical unit allows for some leeway in this precision, it is possible that even with the point data (often corresponding to household clusters) these may not map directly with true infection sites. this must be considered in any subsequent geospatial analysis. finally, this database represents a time-bounded survey of the literature. while all efforts were made to be comprehensive within this period, articles, and therefore data, will continue to be published. efforts to streamline ongoing collection processes are still to be fully realized . regardless, we hope that this dataset provides a solid baseline for further iteration. isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome coronavirus (mers-cov) clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: a report of nosocomial transmission enhanced mers coronavirus surveillance of travelers from the middle east to england control of an outbreak of middle east respiratory syndrome in a tertiary hospital in korea molecular evolution of mers coronavirus: dromedaries as a recent intermediate host or long-time animal reservoir? middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation presence of antibodies but no evidence for circulation of mers-cov in dromedaries on the canary islands comparative analysis of eleven healthcare-associated outbreaks of middle east respiratory syndrome coronavirus (mers-cov) from to assessing the risk of observing multiple generations of middle east respiratory syndrome (mers) cases given an imported case risk of mers importation and onward transmission: a systematic review and analysis of cases reported to who a systematic review of mers-cov seroprevalence and rna prevalence in dromedary camels: implications for animal vaccination a rapid scoping review of middle east respiratory syndrome coronavirus in animal hosts what have we learned about middle east respiratory syndrome coronavirus emergence in humans? a systematic literature review. vector borne zoonotic dis middle east respiratory syndrome coronavirus (mers-cov) infection: epidemiology, pathogenesis and clinical characteristics geopositioned middle east respiratory syndrome coronavirus occurrences. database - . institute for health metrics and evaluation (ihme) database of geopostioned middle east respiratory syndrome coronavirus occurrences global database of leishmaniasis occurrence locations the contemporary distribution of trypanosoma cruzi infection in humans, alternative hosts and vectors a global compendium of human dengue virus occurrence a global compendium of human crimean-congo haemorrhagic fever virus occurrence a comprehensive database of the geographic spread of past human ebola outbreaks food and agricultural organization of the united nations. the global administrative unit layers (gaul): technical aspects global distribution maps of the leishmaniases updates to the zoonotic niche map of ebola virus disease in africa the global distribution of crimean-congo hemorrhagic fever the global distribution and burden of dengue risk factors for mers coronavirus infection in dromedary camels in a supervised learning process to validate online disease reports for use in predictive models critical contribution of laboratories to outbreak response support for middle east respiratory syndrome coronavirus international health regulations ( ) facilitate communication for in-flight contacts of a middle east respiratory syndrome case first confirmed case of middle east respiratory syndrome coronavirus infection in the kingdom of bahrain: in a saudi gentleman after cardiac bypass surgery. case rep event based surveillance of middle east respiratory syndrome coronavirus (mers-cov) in bangladesh among pilgrims and travelers from the middle east: an update for the period middle east respiratory syndrome coronavirus antibodies in dromedary camels middle east respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study definitive diagnosis in suspected middle east respiratory syndrome coronavirus cases characteristics of traveler with middle east respiratory syndrome complete genome sequence of middle east respiratory syndrome coronavirus (mers-cov) from the first imported mers-cov case in china imported case of mers-cov infection identified in china mers-related betacoronavirus in vespertilio superans bats prevalence and genetic diversity analysis of human coronaviruses among cross-border children no mers-cov but positive influenza viruses in returning hajj pilgrims, china two deletion variants of middle east respiratory syndrome coronavirus found in a patient with characteristic symptoms human neutralizing monoclonal antibody inhibition of middle east respiratory syndrome coronavirus replication in the common marmoset complete genome sequence of middle east respiratory syndrome coronavirus isolated from a dromedary camel in egypt cross-sectional surveillance of middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels and other mammals in egypt mers coronavirus neutralizing antibodies in camels mers coronaviruses in dromedary camels seroepidemiology for mers coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in egypt systematic, active surveillance for middle east respiratory syndrome coronavirus in camels in egypt middle east respiratory syndrome coronavirus: epidemiology and disease control measures geographic distribution of mers coronavirus among dromedary camels first cases of middle east respiratory syndrome coronavirus (mers-cov) infections in france, investigations and implications for the prevention of human-to-human transmission clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection a case of imported middle east respiratory syndrome coronavirus infection and public health response laboratory investigation and phylogenetic analysis of an imported middle east respiratory syndrome coronavirus case in greece cluster of middle east respiratory syndrome coronavirus infections in iran epidemiological and clinical characteristics of patients with middle east respiratory syndrome coronavirus in iran in health care associated middle east respiratory syndrome (mers): a case from iran influenza virus but not mers coronavirus circulation in iran phylogenetic analysis of merscov in human and camels in middle east respiratory syndrome coronavirus specific antibodies in naturally exposed israeli llamas, alpacas and camels the prevalence of middle east respiratory syndrome coronavirus (mers-cov) antibodies in dromedary camels in israel detection of coronaviruses in bats of various species in italy investigation of an imported case of middle east respiratory syndrome coronavirus (mers-cov don't forget the migrants": exploring preparedness and response strategies to combat the potential spread of mers-cov virus through migrant workers in sri lanka high prevalence of middle east respiratory coronavirus in young dromedary camels in jordan. vector borne zoonotic dis arabia: an index case investigation middle east respiratory syndrome coronavirus (mers-cov) serology in major livestock species in an affected region in jordan stillbirth during infection with middle east respiratory syndrome coronavirus antibodies against mers coronavirus in dromedary camels mers-cov antibodies in humans, africa no serologic evidence of middle east respiratory syndrome coronavirus infection among camel farmers exposed to highly seropositive camel herds: a household linked study serological evidence of mers-cov antibodies in dromedary camels (camelus dromedaries) in laikipia county occurrence of the middle east respiratory syndrome coronavirus (mers-cov) across the gulf corporation council countries: four years update emergence of mers-cov in the middle east: origins, transmission, treatment, and perspectives laboratory-confirmed case of middle east respiratory syndrome coronavirus (mers-cov) infection in malaysia: preparedness and response dromedary camels in northern mali have high seropositivity to mers-cov middle east respiratory syndrome coronavirus (mers-cov) infections in two returning travellers in the netherlands middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels in nigeria lack of serological evidence of middle east respiratory syndrome coronavirus infection in virus exposed camel abattoir workers in nigeria asymptomatic mers-cov infection in humans possibly linked to infected dromedaries imported from oman to united arab emirates middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels the middle east respiratory syndrome coronavirus (mers-cov) zoonotic origin and transmission of middle east respiratory syndrome coronavirus in the uae imported case of middle east respiratory syndrome coronavirus (mers-cov) infection from oman to thailand serologic evidence for mers-cov infection in dromedary camels contact tracing the first middle east respiratory syndrome case in the philippines effectiveness of the middle east respiratory syndrome-coronavirus protocol in enhancing the function of an emergency department in qatar high proportion of mers-cov shedding dromedaries at slaughterhouse with a potential epidemiological link to human cases isolation of mers coronavirus from a dromedary camel mers-cov infection of alpaca in a region where mers-cov is endemic middle east respiratory syndrome coronavirus (mers-cov) rna and neutralising antibodies in milk collected according to local customs from dromedary camels occupational exposure to dromedaries and risk for mers-cov infection risk factors for primary middle east respiratory syndrome coronavirus infection in camel workers in qatar during - : a case-control study mers-cov outbreak in jeddah-a link to health care facilities a case of long-term excretion and subclinical infection with middle east respiratory syndrome coronavirus in a healthcare worker a comparative study of clinical presentation and risk factors for adverse outcome in patients hospitalised with acute respiratory disease due to mers coronavirus or other causes a family cluster of middle east respiratory syndrome coronavirus infections related to a likely unrecognized asymptomatic or mild case acute management and long-term survival among subjects with severe middle east respiratory syndrome coronavirus pneumonia and ards acute middle east respiratory syndrome coronavirus: temporal lung changes observed on the chest radiographs of patients acute myocarditis associated with novel middle east respiratory syndrome coronavirus an outbreak of middle east respiratory syndrome (mers) due to coronavirus in al-ahssa region, saudi arabia antibody response and disease severity in healthcare worker mers survivors brief report: family cluster of middle east respiratory syndrome coronavirus infections characteristics and outcomes of middle east respiratory syndrome coronavirus patients admitted to an intensive care unit in jeddah, saudi arabia clinical and laboratory findings of the first imported case of middle east respiratory syndrome coronavirus to the united states clinical aspects and outcomes of patients with middle east respiratory syndrome coronavirus infection: a singlecenter experience in saudi arabia clinical course and outcomes of critically ill patients with middle east respiratory syndrome coronavirus infection co-circulation of three camel coronavirus species and recombination of mers-covs in saudi arabia community case clusters of middle east respiratory syndrome coronavirus in hafr al-batin, kingdom of saudi arabia: a descriptive genomic study description of a hospital outbreak of middle east respiratory syndrome in a large tertiary care hospital in saudi arabia descriptive epidemiology and characteristics of confirmed cases of middle east respiratory syndrome coronavirus infection in the makkah region of saudi arabia detection of the middle east respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient epidemiological, demographic, and clinical characteristics of cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study evidence for camel-to-human transmission of mers coronavirus exposures among mers case-patients first confirmed cases of middle east respiratory syndrome coronavirus (mers-cov) infection in the united states, updated information on the epidemiology of mers-cov infection, and guidance for the public, clinicians, and public health authorities hospital outbreak of middle east respiratory syndrome coronavirus human infection with mers coronavirus after exposure to infected camels, saudi arabia identified transmission dynamics of middle east respiratory syndrome coronavirus infection during an outbreak: implications of an overcrowded emergency department impact of middle east respiratory syndrome coronavirus (mers-cov) on pregnancy and perinatal outcome lack of middle east respiratory syndrome coronavirus transmission from infected camels longitudinal study of middle east respiratory syndrome coronavirus infection in dromedary camel herds in saudi arabia transmission and evolution of the middle east respiratory syndrome coronavirus in saudi arabia: a descriptive genomic study spread, circulation, and evolution of the middle east respiratory syndrome coronavirus an observational, laboratory-based study of outbreaks of middle east respiratory syndrome coronavirus in jeddah and riyadh, kingdom of saudi arabia multifacility outbreak of middle east respiratory syndrome in taif, saudi arabia epidemiology of a novel recombinant middle east respiratory syndrome coronavirus in humans in saudi arabia mers coronavirus in dromedary camel herd, saudi arabia mers cov infection in two renal transplant recipients: case report mers-cov in upper respiratory tract and lungs of dromedary camels middle east respiratory syndrome (mers) coronavirus seroprevalence in domestic livestock in saudi arabia middle east respiratory syndrome coronavirus (mers-cov): a cluster analysis with implications for global management of suspected cases middle east respiratory syndrome coronavirus in al-madinah city, saudi arabia: demographic, clinical and survival data middle east respiratory syndrome coronavirus in children middle east respiratory syndrome coronavirus infection during pregnancy: a report of cases from saudi arabia middle east respiratory syndrome coronavirus infection in dromedary camels in saudi arabia middle east respiratory syndrome coronavirus transmission in extended family middle eastern respiratory syndrome corona virus (mers cov): case reports from a tertiary care hospital in saudi arabia molecular epidemiology of hospital outbreak of middle east respiratory syndrome notes from the field: nosocomial outbreak of middle east respiratory syndrome in a large tertiary care hospital-riyadh, saudi arabia outbreak of middle east respiratory syndrome at tertiary care hospital patient characteristics infected with middle east respiratory syndrome coronavirus infection in a tertiary hospital predictors of mers-cov infection: a large case control study of patients presenting with ili at a mers-cov referral hospital in saudi arabia presence of middle east respiratory syndrome coronavirus antibodies in saudi arabia: a nationwide, crosssectional, serological study presentation and outcome of middle east respiratory syndrome in saudi intensive care unit patients report of middle east respiratory syndrome coronavirus (mers-cov) infection in four patients with hematological malignancies treated at king fahad medical city risk factors for middle east respiratory syndrome coronavirus infection among healthcare personnel spontaneous intracranial hemorrhage in a patient with middle east respiratory syndrome corona virus successful recovery of mers cov pneumonia in a patient with acquired immunodeficiency syndrome: a case report surveillance and testing for middle east respiratory syndrome coronavirus, saudi arabia the critical care response to a hospital outbreak of middle east respiratory syndrome coronavirus (mers-cov) infection: an observational study the first case of the korean middle east respiratory syndrome outbreak travel-related mers-cov cases: an assessment of exposures and risk factors in a group of dutch travellers returning from the kingdom of saudi arabia treatment outcomes for patients with middle eastern respiratory syndrome coronavirus (mers cov) infection at a coronavirus referral center in the kingdom of saudi arabia middle east respiratory syndrome coronavirus transmission among health care workers: implication for infection control histopathology of middle east respiratory syndrome coronovirus (mers-cov) infection -clinicopathological and ultrastructural study the calm before the storm: clinical observations of middle east respiratory syndrome (mers) patients the prevalence of middle east respiratory syndrome coronavirus (mers-cov) infection in livestock and temporal relation to locations and seasons assessing the detection of middle east respiratory syndrome coronavirus igg in suspected and proven cases of middle east respiratory syndrome coronavirus infection cross-sectional study of mers-cov-specific rna and antibodies in animals that have had contact with mers patients in saudi arabia a cohort-study of patients suspected for mers-cov in a referral hospital in saudi arabia conveyance contact investigation for imported middle east respiratory syndrome cases recovery from the middle east respiratory syndrome is associated with antibody and t-cell responses outbreak of middle east respiratory syndrome-coronavirus causes high fatality after cardiac operations prevalence of antibodies against the middle east respiratory syndrome coronavirus, influenza a and b viruses among blood donors, saudi arabia serological evidence of coronavirus infections in native hamadryas baboons (papio hamadryas hamadryas) of the kingdom of saudi arabia hematologic, hepatic, and renal function changes in hospitalized patients with middle east respiratory syndrome coronavirus middle east respiratory syndrome coronavirus and pulmonary tuberculosis coinfection: implications for infection control outcome of strict implementation of infection prevention control measures during an outbreak of middle east respiratory syndrome outbreak of middle east respiratory syndrome coronavirus in saudi arabia: a retrospective study sero-prevalence of middle east respiratory syndrome coronavirus (mers-cov) specific antibodies in dromedary camels in tabuk, saudi arabia seroepidemiology of middle east respiratory syndrome (mers) coronavirus in saudi arabia ( ) and australia ( ) and characterisation of assay specificity risk factors for primary middle east respiratory syndrome coronavirus illness in humans middle east respiratory syndrome coronavirus disease in children close relative of human middle east respiratory syndrome coronavirus in bat rooting the phylogenetic tree of middle east respiratory syndrome coronavirus by characterization of a conspecific virus from an african bat mers outbreak in korea: hospital-to-hospital transmission a case report of a middle east respiratory syndrome survivor with kidney biopsy results an unexpected outbreak of middle east respiratory syndrome coronavirus infection in the republic of korea atypical presentations of mers-cov infection in immunocompromised hosts clinical implications of cases of middle east respiratory syndrome coronavirus infection in a south korean outbreak emergency cesarean section in an epidemic of the middle east respiratory syndrome: a case report epidemiologic features of the first mers outbreak in korea: focus on pyeongtaek st. mary's hospital epidemiological investigation of the th confirmed middle east respiratory syndrome coronavirus case with an indefinite mode of transmission during the pyeongtaek outbreak in korea extensive viable middle east respiratory syndrome (mers) coronavirus contamination in air and surrounding environment in mers isolation wards detection of severe acute respiratory syndrome-like, middle east respiratory syndrome-like bat coronaviruses and group h rotavirus in faeces of korean bats high fatality rates and associated factors in two hospital outbreaks of mers in daejeon, the republic of korea infectivity of an asymptomatic patient with middle east respiratory syndrome coronavirus mers epidemiological investigation to detect potential mode of transmission in the th mers confirmed case in pyeongtaek mers-cov outbreak following a single patient exposure in an emergency room in south korea: an epidemiological outbreak study middle east respiratory syndrome in persons, south korea middle east respiratory syndrome-coronavirus infection: a case report of serial computed tomographic findings in a young male patient outbreaks of middle east respiratory syndrome in two hospitals initiated by a single patient in daejeon successful treatment of suspected organizing pneumonia in a patient with middle east respiratory syndrome coronavirus infection: a case report surveillance operation for the st confirmed case of middle east respiratory syndrome coronavirus in response to the patient's prior travel to jeju island transmission among healthcare worker contacts with a middle east respiratory syndrome patient in a single korean centre host susceptibility to mers-cov infection, a retrospective cohort study of the korean mers outbreak a study of the probable transmission routes of mers-cov during the first hospital outbreak in the republic of korea a middle east respiratory syndrome screening clinic for health care personnel during the middle east respiratory syndrome outbreak in south korea: a single-center experience evaluation and clinical validation of two field-deployable reverse transcription-insulated isothermal pcr assays for the detection of the middle east respiratory syndrome-coronavirus serologic responses of mers-coronavirus-infected patients according to the disease severity the clinical and virological features of the first imported case causing mers-cov outbreak in south korea mers-cov antibody responses year after symptom onset neurological complications during treatment of middle east respiratory syndrome impact of middle east respiratory syndrome outbreak on the use of emergency medical resources in febrile patients hospital outbreaks of middle east respiratory syndrome zero transmission of middle east respiratory syndrome: lessons learned from thailand family cluster of middle east respiratory syndrome coronavirus infections further evidence for bats as the evolutionary source of middle east respiratory syndrome coronavirus a phylogenetically distinct middle east respiratory syndrome coronavirus detected in a dromedary calf from a closed dairy herd in dubai with rising seroprevalence with age acute middle east respiratory syndrome coronavirus infection in livestock dromedaries antibodies against mers coronavirus in dromedary camels clinicopathologic, immunohistochemical, and ultrastructural findings of a fatal case of middle east respiratory syndrome coronavirus infection in the united arab emirates epidemiological investigation of middle east respiratory syndrome coronavirus in dromedary camel farms linked with human infection in abu dhabi emirate middle east respiratory syndrome coronavirus antibody reactors among camels in dubai middle east respiratory syndrome coronavirus during pregnancy polyphyletic origin of mers coronaviruses and isolation of a novel clade a strain from dromedary camels in the united arab emirates prevalence of middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels in abu dhabi emirate time course of mers-cov infection and immunity in dromedary camels transmission of middle east respiratory syndrome coronavirus infections in healthcare settings response to emergence of middle east respiratory syndrome coronavirus diversity of middle east respiratory syndrome coronaviruses in dromedary camels based on full-genome sequencing identification of diverse viruses in upper respiratory samples in dromedary camels from united arab emirates mers-cov in pregnancy some epidemiological studies on mers coronavirus in dromedaries in the united arab emirates -a short communication emerging and reemerging diseases in the world health organization (who) eastern mediterranean region-progress, challenges, and who initiatives melinda gates foundation opp# and s.i.h. was supported by opp curated and catalogued the database. s.s. provided managerial support. all authors participated in interpreting and summarizing the results. r.e.r. wrote the first draft of the manuscript. all other authors critically reviewed the manuscript had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis s.i.h. and d.m.p. are members of the editorial board of scientific data. supplementary information is available for this paper at https://doi.org/ . /s - - - .correspondence and requests for materials should be addressed to d.m.p.reprints and permissions information is available at www.nature.com/reprints. open access this article is licensed under a creative commons attribution . international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons license, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons license, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this license, visit http://creativecommons.org/licenses/by/ . /.the creative commons public domain dedication waiver http://creativecommons.org/publicdomain/zero/ . / applies to the metadata files associated with this article. key: cord- - alqfkd authors: revzin, margarita v.; raza, sarah; warshawsky, robin; d’agostino, catherine; srivastava, neil c.; bader, anna s.; malhotra, ajay; patel, ritesh d.; chen, kan; kyriakakos, christopher; pellerito, john s. title: multisystem imaging manifestations of covid- , part : viral pathogenesis and pulmonary and vascular system complications date: - - journal: radiographics doi: . /rg. sha: doc_id: cord_uid: alqfkd infection with severe acute respiratory syndrome coronavirus (sars-cov- ) results in coronavirus disease (covid- ), which was declared an official pandemic by the world health organization on march , . the infection has been reported in most countries around the world. as of august , there have been over million cases of covid- reported worldwide, with over covid- –associated deaths. it has become apparent that although covid- predominantly affects the respiratory system, many other organ systems can also be involved. imaging plays an essential role in the diagnosis of all manifestations of the disease, as well as its related complications, and proper utilization and interpretation of imaging examinations is crucial. with the growing global covid- outbreak, a comprehensive understanding of the diagnostic imaging hallmarks, imaging features, multisystemic involvement, and evolution of imaging findings is essential for effective patient management and treatment. to date, only a few articles have been published that comprehensively describe the multisystemic imaging manifestations of covid- . the authors provide an inclusive system-by-system image-based review of this life-threatening and rapidly spreading infection. in part of this article, the authors discuss general aspects of the disease, with an emphasis on virology, the pathophysiology of the virus, and clinical presentation of the disease. the key imaging features of the varied pathologic manifestations of this infection that involve the pulmonary and peripheral and central vascular systems are also described. part will focus on key imaging features of covid- that involve the cardiac, neurologic, abdominal, dermatologic and ocular, and musculoskeletal systems, as well as pediatric and pregnancy-related manifestations of the virus. vascular complications pertinent to each system will be also be discussed in part . online supplemental material is available for this article. (©)rsna, describe in detail the key imaging features of the varied pathologic manifestations of this infection that involve the pulmonary and peripheral and central vascular systems. all medical professionals, including radiologists, have been given the daunting task of recognizing the varied presentations and complications of covid- to ensure prompt diagnosis and thereby limit viral spread, as well as provide appropriate care to patients with the goal of improving recovery. coronaviruses are nonsegmented enveloped rna viruses with a single-strand linear positive-sense rna ( , ) . six types of coronavirus have been identified that cause human disease. four of these cause mild respiratory symptoms whereas the other two, middle east respiratory syndrome (mers-cov) coronavirus and severe acute respiratory syndrome coronavirus (sars-cov- ), have previously resulted in epidemics with high mortality rates ( ) . although the genome of sars-cov- is % identical to that of sars-cov- , it is more similar to the genome of bat coronaviruses ( % identical) ( ) . both sars-cov- and sars-cov- have similar receptor-binding gene regions, thus for cell entry both viruses use the same angiotensin-converting enzyme (ace ) receptor ( ) . currently, two different types of sars-cov- have been identified. however, the implications of this finding are uncertain ( ) . covid- is generally diagnosed with the results of a real-time reverse transcription-polymerase chain reaction (rt-pcr) test of a nasopharyngeal specimen obtained with a swab. however, this test may obtain false-negative results owing to a variety of factors, including insufficient viral load, improper collection of viral samples, and technical errors during the swabbing procedure ( , ) . more than million confirmed cases of co-vid- have been reported to date around the world, within all continents except for antarctica, and the incidence has been steadily rising ( ) . in the united states, covid- has been reported in all states, the district of columbia, and at least four territories ( ) . the cumulative incidence varies by state and is likely dependent on a number of factors, including population density and demographics, the extent of testing and reporting, and the initiation of mitigation strategies. in the united states, outbreaks in long-term care facilities and homeless shelters have underscored respiratory illness is the most commonly associated manifestation of sars-cov- . this is due to abundant ace receptor expression in the lung parenchyma, specifically on the acinar side of lung epithelial cells (pneumocytes) within the alveolar spaces, allowing virus entry. this correlates with the observation that the earliest lung injury is often seen in the distal airways. chest radiography and chest ct may be performed as adjuncts in cases of an initial negative rt-pcr test with persistent high clinical suspicion for disease. similar to those at chest radiography, the most suspicious ct features for covid- infection in the lungs include multifocal bilateral peripheral ggos, with or without focal consolidations, in lung regions close to pleural surfaces, including the fissures. patients admitted to the icu with barotrauma as a result of intubation or as a complication of ards may develop pneumothoraces or pneumomediastinum, further complicating the pulmonary manifestations of covid- infection. in december , a novel coronavirus, severe acute respiratory syndrome coronavirus (sars-cov- ), was identified as the cause of a cluster of pneumonia cases in wuhan, a city in the hubei province of china. in the first few months of , infection with this novel coronavirus led to a global pandemic that has now affected almost every country in the world, and, by august , over million cases had been documented ( , ) . although sars-cov- disease (or coronavirus disease ) primarily manifests as a lung infection, with symptoms ranging from those of a mild upper respiratory infection to severe pneumonia and acute respiratory distress syndrome (ards), other multisystemic manifestations of this disease and related complications are becoming more commonly recognized ( ) . in this article, we provide an inclusive review of this potentially life-threatening and highly contagious infection, with emphasis on clinical presentation, the pathophysiology of the virus, and the role of imaging in diagnosing and monitoring the viral infection and its related complications. we provide a system-by-system review of the key imaging features of the various pathologic manifestations known to date, as well as offer relevant prognostic information that can be inferred from imaging findings. in part of this article, we discuss general aspects of the disease, with an emphasis on virology, the pathophysiology of the virus, and clinical presentation of the disease. in addition, we receptor of the host, with subsequent fusion of the viral and cell membranes (endocytosis), resulting in viral cell entry and depletion of ace receptors on the cell surface ( ) . once within a cell, the virus activates the intracellular immune system, which causes immune and nonimmune cells to release large amounts of proinflammatory cytokines that activate a cytokine storm and result in damage to the host ( ) (fig ) . antibodies to the virus are induced in those patients with sars-cov- infection. however, it is unknown whether all patients with sars-cov- infection mount a protective immune response and how long any protective effect will last. preliminary data on protective immunity are beginning to emerge ( , ) . the incubation period for covid- is believed to be less than days following exposure, with most cases manifesting - days after exposure ( , ( ) ( ) ( ) . the clinical presentation spectrum varies and includes mild to moderate symptoms ( %), severe symptoms ( %- %), and critical illness ( %). there is increasing evidence that many patients with covid- are asymptomatic yet are able to transmit the virus to others. on the basis of data from several most recent metaanalyses, it has been estimated that approximately %- % of patients with confirmed covid- are asymptomatic. however, it is important to recognize that a large percentage of patients with no symptoms at the time of detection will become symptomatic later. for a more accurate estimation of patients with confirmed covid- who remain asymptomatic throughout the disease course, longitudinal data must be collected over a sufficient period of time to allow distinction between asymptomatic and presymptomatic cases ( , ) . in addition, various studies have reported that children are likely to have a higher proportion of asymptomatic infection than adults. however, the largest meta-analysis and systematic review studies to date report that only approximately %- . % of confirmed pediatric cases are asymptomatic ( , ) . as with the adult population, the accuracy of this reported data remains unclear, as there are significant concerns regarding potential selection bias and testing error. the most common symptoms at presentation are fever, cough, and shortness of breath. mild to moderate disease is generally characterized by constitutional symptoms and the possible development of mild pneumonia, while symptoms of severe disease include dyspnea and hypoxia, as well as more than % lung involvement at the risk of exposure and infection in group settings ( ) . the main mode of transmission is person to person. however, other sources of transmission have also been implicated ( ) ( ) ( ) . person-toperson transmission is thought to occur mainly through respiratory droplets that are released in a cough or sneeze or during conversation. droplets typically do not travel more than ft (about m) and are not thought to linger in the air, although this notion has been challenged ( ) ( ) ( ) . environmental contamination also plays a role in viral transmission and occurs through droplet accumulation on frequently touched surfaces, with subsequent spread to susceptible mucous membranes within the mouth, nose, and eyes ( ) ( ) ( ) . men are disproportionately more commonly affected by an infection with sars-cov- , and the in-hospital mortality rate among male patients is significantly higher compared with that of female patients ( ) . there is uncertainty regarding the time interval during which an individual with covid- is infectious. it appears that the virus can be transmitted before the development of symptoms and throughout the course of illness. however, definitive data are not yet available, as most information on this subject comes from studies that evaluated the presence of viral rna in respiratory and other specimens, which may not correlate with infectivity. transmission of sars-cov- from asymptomatic individuals (or individuals within the incubation period) has been well documented ( ) ( ) ( ) ( ) ( ) . however, the extent to which asymptomatic and presymptomatic transmission occurs and their relative contribution to the spread of the pandemic remain unknown. the length of time an individual remains infectious is also uncertain. the duration of viral shedding is variable, and there appears to be a wide range, which may be dependent on the severity of illness ( ) ( ) ( ) . the life cycle of the virus within the host consists of the following five steps: (a) attachment, (b) penetration (viral entry to the cell), (c) biosynthesis (viral replication), (d) maturation (assembly and accumulation), and (e) release (through cell destruction). ace has been identified as a functional receptor for sars-cov- ( ) . in the human body, ace expression is high in the lung (expressed on lung epithelial cells), heart, gastrointestinal system, kidney, pancreas, spleen, bladder, cornea, and blood vessels ( , ) . sars-cov- enters a human cell by binding its spike or s protein to the ace imaging within - hours of symptom onset. critically ill patients are diagnosed with respiratory failure, shock, or multiorgan dysfunction ( ) ( ) ( ) ( ) ( ) ( ) . although most symptoms are respiratory in nature, clinical features of the disease may vary, with both typical and atypical presentations (table ) . recovery time appears to be around weeks for mild infections and - weeks for severe disease ( ) . the sars-cov- virus has the potential to cause complications in every body system. ards is a major complication of severe covid- , seen in %- % of patients with severe symptoms, and typically develops within - days after the onset of dyspnea. up to % of patients with ards will require mechanical ventilation ( , ) . ards is usually seen in patients greater than years of age and/or those with risk factors (discussed in the following section) ( ) . cardiac complications include arrhythmias (including atrial fibrillation), acute myocarditis, cardiomyopathy, and shock ( , ) . abdominal and/or pelvic solid organ injury is also commonly seen. thromboembolic complications, including pulmonary embolism (pe), peripheral venous and arterial thrombosis, and acute stroke (seen also in patients older than years without risk factors) have all been reported ( - ). individuals of any age can acquire sars-cov- infection, although adults middle-aged and older are most commonly affected, and older adults are more likely to experience severe disease ( , , ) . older age is also associated with increased mortality ( , , ) . eighty-seven percent of patients diagnosed with covid- are - years of age ( ) , and % percent of reported deaths have occurred in those aged greater than or equal to years. children are significantly less affected and exhibit a milder spectrum of disease. an increased risk of developing severe illness and increased mortality have been reported in patients with underlying cardiovascular disease, diabetes mellitus, hypertension, chronic lung disease, cancer (particularly hematologic malignancies, lung cancer, and metastatic disease), obesity, and chronic kidney disease ( , ( ) ( ) ( ) . the centers for disease control and prevention also includes immunocompromised status and liver disease as potential risk factors for severe illness, although specific data regarding risks associated with these conditions are limited. common laboratory test findings in those patients admitted to the hospital with covid- include lymphopenia and elevated aminotransaminase, lactate dehydrogenase, and inflammatory marker figure . illustration shows the proposed mechanism of sars-cov- cell entry and activation of the immune system. sars-cov- enters human cells by attaching to a cell surface receptor (ace ) and by utilizing a human enzyme called transmembrane serine protease (tmprss ). once bound to the receptor, sars-cov- undergoes endocytosis and enters into the cell, along with the ace receptor. this process reduces the number of ace receptors on cells, leading to an increase of angiotensin ii (angii) levels in the blood. angiotensin ii triggers an inflammatory pathway involving nf-κb and interleukin -signal transducer and activator of transcription protein (il- -stat ), particularly in nonimmune cells including endothelial and epithelial cells. this pathway forms a positive feedback cycle, named il- amplifier (il- amp), resulting in its excessive activation and therefore the cytokine storm and ards. part of this pathway involving nf-κb, il- -stat , or both is enhanced with age, which could be the reason why older patients are more at risk for death following covid- diagnosis compared with other age groups. s = viral spike protein subunit , s = viral spike protein subunit ,tnf-a = tumor necrosis factor-α. levels (eg, ferritin, c-reactive protein, and erythrocyte sedimentation rate) ( , , ) . lymphopenia is particularly common and is characterized by a lymphocyte count less than /microl. up to % of patients have leukocytosis (> / microl) and % of patients have leukopenia (< /microl) ( ) . in those patients who require treatment in the intensive care unit (icu) for pneumonia and/or other multisystem manifestations, serum procalcitonin levels are more likely to be elevated ( , ) . several laboratory test features, including elevated d-dimer levels (> . mg/ ml) and severe lymphopenia, have been associated with higher mortality rates (table ) ( , ) . respiratory illness is the most commonly associated manifestation of sars-cov- . this is due to abundant ace receptor expression in the lung paren-chyma, specifically on the acinar side of lung epithelial cells (pneumocytes) within the alveolar spaces, allowing virus entry (fig ) ( ). this correlates with the observation that the earliest lung injury is often seen in the distal airways ( ) . as discussed previously, alveolar damage is also attributable to the release of cytokines and chemokines that allow fluids to fill the pulmonary interstitium and acini, and the hypercoagulable state associated with covid- that results in micro-and macrothrombosis of the pulmonary vasculature ( ) . chest radiography is typically the first-line imaging modality performed in patients with suspected covid- infection. at patient admission, initial posteroranterior or anteroposterior (ap) chest radiographs are obtained, usually with the use of an intervening glass door to minimize exposure to the technologist (this technique provides adequate quality for chest radiograph acquisition when compared with that of conventional methods) ( ) . pulmonary consolidations and other pneumonia-related changes may be diagnosed when interpreting images obtained using this technique, as well as changes related to ards in patients who are critically ill. at early stages of disease and in mild cases, findings at chest radiography may be normal. wong et al ( ) found that initial chest radiography findings were abnormal in % of patients who required hospital admission, and in % of patients who had already been hospitalized ( ) . chest radiography and ct.-the most commonly reported findings of covid- at chest radiography include lung consolidation and ground-glass opacities (ggos) ( ) . reticular opacities may accompany areas of ggos and can be well depicted on standard chest radiographs. viral pneumonias, including covid- , typi-cally produce lung opacities in more than one lobe. additionally, evidence of multifocal airspace disease on chest radiographs can be indicative of covid- pneumonia, most frequently in a lower lung distribution and bilateral (fig ) . peripheral lung involvement is one of the most specific features of this infection, although it may resemble other inflammatory processes with multifocal, patchy, or confluent distribution of findings, such as organizing pneumonia (fig ) . a pattern of diffuse lung opacities may also be seen with covid- infection, as well as a number of other infectious and/or inflammatory processes, such as ards. during the disease course, lung opacities may rapidly evolve into a diffuse coalescent or consolidative pattern within - weeks after symptom onset, often peaking around - days after initial clinical presentation ( fig ) ( , ) . pleural effusions, lung cavitation, and pneumothorax are rare findings in covid- and, when depicted on chest radiographs, should raise suspicion for other potential causes ( ) ( ) ( ) . in young and middle-aged patients, the extent of ggos at chest radiography have been shown to correlate with the need for hospitalization and performing intubation. toussie et al ( ) reported that patients with ggos depicted in at least two lung zones are more likely to require hospitalization and those with ggos in three zones were more likely undergo intubation ( ) . on the basis of the pattern and distribution of the opacities and the presence or absence of certain clinical signs (such as obesity), the authors developed a chest radiography severity scoring system that could be used as a prognostic factor of outcomes in young adult patients with covid- (fig ) . advancements in new technologies such as artificial intelligence have allowed the utilization of automated assessment and tracking of covid- pulmonary disease severity on chest radiographs. the results of this artificial intelligence-based longitudinal assessment could potentially be used for the prediction of patient prognosis (with respect to the likelihood of requiring intubation or death) ( ) . chest radiography and chest ct may be performed as adjuncts in cases of an initial negative rt-pcr test with persistent high clinical suspicion for disease. the american college of radiology advises against using ct as a first-line tool in the diagnosis of covid- , recommending that it be used sparingly and reserved for symptomatic hospitalized patients with specific clinical indications, such as assessment of complications ( , ) . chest radiography is a less sensitive modality for the detection of covid- lung disease when compared with that ct, with a reported baseline chest radiography sensitivity of % ( ). the longitudinal assessment of covid- pneumonia progression in a -year-old man who presented to the emergency department with dyspnea and dry cough. (a) ap chest radiograph obtained at hospital admission at the time of symptom onset shows bilateral pulmonary opacities (arrows) at the periphery of the right mid lung and at the left lung base. (b) ap chest radiograph obtained on day of hospitalization shows progression of multifocal opacities bilaterally, which now involve more than two lobes, and interval development of bibasilar consolidations. these findings correspond to a higher severity score and carry a worse prognosis. in addition, there is mild pulmonary edema, suggestive of fluid overload. note that the patient had undergone intubation. (c) ap chest radiograph obtained on day of hospitalization shows progression of the multifocal bilateral peripheral opacities. true sensitivity and specificity of ct for detection of covid- remains relatively unknown. one study showed that radiologists identified cases of covid- versus other viral pneumonias correctly %- % of the time on the basis of typical ct features ( ) . however, the results of this study should be treated with caution, as the control and covid- -positive groups evaluated in this study came from two different institutions (the cases of covid- came from china and control cases from the united states) ( ). pulmonary us.-pulmonary us is another imaging modality that has been shown to be useful in the evaluation of critically ill patients with covid- , as it can be performed at the bedside and allows detection of pneumonia ( ) . the most commonly depicted features of lung involvement at us include the presence of b-line artifacts, an irregular thickened pleura, and subpleural consolidations (fig , movies , ) ( ). b-line artifact distribution corresponds to subpleural thickened interlobular septa, as demonstrated at ct. b-line artifacts are vertically oriented, highly dynamic, and hyperechoic artifacts that originate from the pleura or from areas of consolidation that usually manifest in pa-tients with alveolar-interstitial syndrome ( ) ( ) ( ) . these lines indicate accumulation of fluid in the pulmonary interstitial space (lung rockets) or alveoli (ground glass). when multiple, they are associated with pulmonary edema of cardiogenic, noncardiogenic, or mixed origin and are indicative of lung interstitial syndrome. b-line artifacts usually move with lung sliding. absence of lung sliding should raise concern that the lung is not inflated or that there may be a pneumothorax. hanced ct pulmonary angiography is performed to assess for possible pe in patients who develop acute dyspnea or acute deterioration of respiratory symptoms, or those in whom d-dimer markers are significantly elevated. the utilization of pulmonary scintigraphy (ventilation-perfusion scanning) in patients with suspected covid- pneumonia should be limited, unless deemed essential for medical management. if ventilation-perfusion scanning is deemed necessary, the ventilatory phase of the examination should be eliminated and only the perfusion phase should be performed ( ) . dual-energy ct has also been shown to be helpful for the evaluation of lung perfusion abnormalities ( ) . chest ct and reporting.-the role of chest ct in covid- is constantly evolving, with respect to clinical evaluation and treatment decisions. whereas the th chinese novel coronavirus pneumonia diagnosis and treatment plan incorporates ct into the criteria that clinically define covid- , the american college of radiology and the society of thoracic radiology, among others, advocate its use only in cases that require problem solving ( , , ) . the suitability of chest ct has also been assessed in various scenarios by the fleischner society, which deemed ct a major tool for diagnosis in patients with worsening symptoms or those in an environment that is resource constrained, with respect to rt-pcr testing availability ( ) . the recent radiological society of north american expert consensus statement on reporting proposed standardized nomenclature and an imaging classification for covid- pneumonia that involves four categories: typical appearance, indeterminate appearance, atypical appearance, and negative for pneumonia (table ) ( ) . in an attempt to pursue standardized reporting, a covid- reporting and data system (co-rad) based on a five-point scale of suspicion for . although subpleural involvement has been frequently documented, subpleural sparing may also be present (fig ) ( ) . there are two types of ggos that have been described: pure type and a mixed pattern, which is characterized by the presence of both ggos and areas of consolidation (fig ) . at ct, ggos with or without consolidation are typically depicted in a peripheral, posterior, and diffuse or lower-lung zone distribution ( , ) . pure-type ggos, the most commonly observed pattern, usually develop between days and after symptom onset, peaking at - days ( , ( ) ( ) ( ) . therefore, a negative chest ct examination should not be used to exclude the possibility of covid- , particularly early in the disease process ( ) . later in the disease course, the frequency of consolidation increases (fig ) . in fact, wang et al ( ) noted that after symptom onset, the predominant imaging abnormality becomes a mixed pattern of ggos, which typically peaks during days - of the illness and has been shown to be the second most prevalent pattern thereafter. as discussed previously, similar temporal changes have been observed on plain radiographs (fig ) ( ) . pulmonary vascular abnormalities such as vessel enlargement and regional mosaic perfusion patterns are also commonly found in covid- pneumonia ( ) . other more atypical or infrequent signs described in patients with covid- , such as the halo and reverse halo (or atoll) sign, usually manifest later in the disease course and are often absent at the time of symptom onset (figs , ) ( ) . the halo sign describes a nodule or mass surrounded by ground glass opacification, while the reverse halo (or atoll) sign is defined as a crescent or complete ring of consolidation that surrounds a focal area of ggo (figs , ) ( ) . both appearances may be embedded within an area of consolidation. however, it is important to note that these findings are not specific, as they have been previously described in early stages of opportunistic invasive fungal infections in immunocompromised patients (eg, aspergillosis, mucormycosis), as well as in immunocompetent patients diagnosed with nonfungal endemic infections, cryptogenic organizing pneumonia, vasculitis, neoplasm, and inflammatory diseases ( ) . unifocal unilateral lesions are uncommon and found only in % of patients with covid- (fig ) ( ) . the development of gelatinous mucus secretions may be responsible for lung collapse that can coexist with adjacent areas of consolidation. contrast-enhanced ct aids in the differentiation of collapsed atelectatic lung from pneumonia by demonstrating parenchymal lung enhancement within atelectatic lung and absent or markedly diminished lung enhancement in the setting of pneumonia (fig ) . bronchial wall thickening was described in %- % of patients with co-vid- (fig ) ( ) . pleural effusion, cavitation, pulmonary nodules, tree-in-bud opacities, and lymphadenopathy have not been reported in patients with covid- and can be useful in differentiating covid- pneumonia from other conditions ( ) . in normal lung, subsegmental vessels are usually inconspicuous within the subpleural regions. however, it has been shown that many patients with covid- exhibit tortuous and dilated distal vessels in the subpleural lung ( ) . these findings should not be confused with pulmonary vascular thickening (or thick vessel sign) within pulmonary opacities in covid- pneumonia, which has been reported to range from % to % in patients with covid- ( , , ) . pulmonary vascular thickening is a nonspecific sign and can be seen in other conditions, including pulmonary hypertension, pulmonary venoocclusive disease, hepatopulmonary syndrome, and portopulmonary hypertension ( ). one of the most common respiratory complications of covid- infection is ards (fig ) . while ards is a clinical diagnosis that has a grading system based on the degree of hypoxia, imaging plays a supportive role in its diagnosis and management. it has been suggested that abnormal pulmonary vasoregulation may play a large role in patients with covid- infection before the onset of radiologic or clinical manifestations that would suggest ards, and may be even more pronounced when ards does occur ( , ) . the presence of disordered vasoregulation is supported by the frequency of pronounced dilatation of vasculature within regions of diseased lung, leading to significant ventilation and perfusion mismatches early in the disease. perfusion abnormalities in the setting of covid- pneumonia, most optimally assessed at dual-energy ct, may suggest an underlying vascular process. chest radiography and ct can aid in the identification of additional underlying causes of ards symptoms, such as superimposed bacterial pneumonia or congestive heart failure, although findings are frequently nonspecific. in the acute phase of ards, chest radiography may demonstrate bilateral airspace opacities with air bronchograms (fig ) . unless pulmonary edema is also present, septal lines and pleural effusions are not expected findings. in the acute exudative phase of ards, within the first week, ct demonstrates diffuse ggos in a posterior and basal predominance, and a crazy-paving pattern may also be depicted ( fig ) . the crazy-paving appearance is thought to be attributable to superimposition of thick interlobular septa on ggos and was detected in % of patients with covid- ( ) . in the subsequent subacute phase of ards, consolidations may develop posteriorly or anteriorly if the patient is prone, with reversible bronchiectasis (figs , ) . in the late phase of ards, more patients admitted to the icu with barotrauma as a result of intubation or as a complication of ards may develop pneumothoraces or pneumomediastinum, further complicating the pulmonary manifestations of covid- infection (figs - ) . in fact, patients with covid- who require mechanical ventilation were found to be at increased risk of barotrauma when compared with patients with ards alone and patients without covid- . barotrauma was associated with a longer length of hospital stay and was an independent risk factor for death in patients with covid- ( ). pe is another complication of covid- infection, described in further detail in the "peripheral and central vascular manifestations of co-vid- " section. in recently published studies, the incidence of pe in patients with covid- who underwent pulmonary ct angiography was reported to be between % and % ( , , ) . currently, there are conflicting results as to whether there is increased probability of pe in patients with covid- who are receiving intensive care or require mechanical ventilation when compared with those who are not admitted to the icu ( , ) . a notable risk factor for the development of pe is obesity, with recent data showing that patients with a body mass index greater than kg/m are . times more likely to develop pe. additionally, african american patients are at higher risk of developing pe when compared with other ethnic groups ( ) . with respect to the location and distribution of thrombi, pe is more commonly found in the segmental and lobar branches and less commonly in the central pulmonary arteries (fig ) ( ) . long-term effects of the disease and followup long-term imaging sequelae have not been well established at this point and are still under investigation. organ-specific vascular manifestations and complications will be discussed in the corresponding part article in a future issue of radiographics. manifestations of covid- there is growing evidence of coagulopathy related to covid- , which may predispose patients to both venous and arterial thromboembolism and result in deep venous thrombosis (dvt), pe, limb ischemia, stroke, and myocardial infarction ( ) ( ) ( ) . although the pathogenesis and incidence of thrombotic complications are not clearly understood, coagulopathy has been noted to be a poor prognostic indicator and is associated with higher mortality ( , , , ) . the most common pattern of coagulopathy observed in patients hospitalized with covid- is characterized by elevated d-dimer and fibrinogen levels ( ) and correlates with a parallel rise in inflammatory marker levels, including but not limited to levels of c-reactive protein, tumor necrosis factor-α, and various interleukins ( fig ) ( , ( ) ( ) ( ) . initial data have demonstrated that co-vid- -associated coagulopathy manifests with features of both sepsis-induced coagulopathy and thrombotic microangiopathy ( , ( ) ( ) ( ) . multiple factors, including inflammatory cytokine release, critical illness, platelet activation, and endothelial dysfunction, play a role. this is further evidenced by recent histologic data that have demonstrated diffuse alveolar damage, microthrombi formation, and occlusion of small pulmonary vessels ( ) . however, it is still uncertain whether covid- has other unique characteristics that result in direct activation of coagulation. as seen in other infections that result in sepsis-induced coagulopathy, the primary infection of covid- initiates cellular injury and results in an inflammatory response, which includes production of inflammatory cytokines, endothelial activation, and recruitment of neutrophils and mononuclear cells. the activation of coagulation is a host immune response that contributes to the compartmentalization of pathogens in an attempt to prevent dissemination. however, endothelial cell dysfunction results in excess thrombin production and disrupted fibrinolysis, which results in a hypercoagulable state. following cellular injury, tissue factor, which is a critical initiator of the extrinsic coagulation pathway, is expressed on macrophages, monocytes, and endothelial cells and plays a central role in the development of coagulopathy and disseminated intravascular coagulation. additionally, fibrinolysis is suppressed in sepsis ( , ) . compared with the typical pattern of sepsisinduced coagulopathy, patients with covid- figure . covid- complicated by pneumothorax and pneumomediastinum in a -year-old man who underwent intubation with increased oxygen requirements. posteroranterior chest radiograph obtained in the prone position shows moderate-size right pneumothorax and small left apical pneumothorax (black arrows). pneumomediastinum is evident by the presence of air around the aortic arch and beneath the heart (red arrows). the endotracheal tube and feeding tube are in place. a large amount of subcutaneous emphysema is depicted bilaterally (white arrows). the patchy bilateral hazy opacities are compatible with covid- pneumonia. are diagnosed with less prominent thrombocytopenia ( ) . additionally, prothrombin time and partial thromboplastin time remain near normal and fibrinogen levels are elevated until later in the disease process when they decrease and patients subsequently develop disseminated intravascular coagulation ( , ( ) ( ) ( ) . additionally, authors of a recent study have suggested that a small subset of severe co-vid- cases demonstrate complement-mediated microvascular injury and thrombosis, consistent with activation of the alternative pathway and lectin pathway cascades ( ) . it is also important to note that hypoxia itself can stimulate thrombosis through an increase in blood viscosity and a hypoxia-inducible transcription factor-dependent signaling pathway. additionally, ards may be a potential cause for hypoxic pulmonary vasoconstriction, pulmonary hypertension, and right ventricular failure ( ) . aside from hemostatic derangements, underlying comorbidities (cancer, obesity, etc) and immobility and the use of mechanical ventilation, central venous catheters, and extracorporeal circuits contribute to thrombotic risk. in addition, current investigational medications for treating covid- may have adverse drug-drug interactions with antiplatelet agents and anticoagulation therapy ( ) . to summarize, the pathophysiology of the hypercoagulable state found in association with covid- disease is extremely complex and multifactorial in nature, with many varied factors playing a role in its occurrence (fig ) . it is important to note that the existing evidence is primarily derived from a few small retrospective analyses, and further evaluation with large prospective cohort studies must be conducted to better understand this illness. duplex us, mr angiography, and ct angiography, as well as mr and indirect or combined ct venography are the primary noninvasive modalities for the diagnosis of arterial and venous thrombosis and thromboembolism in patients with covid- ( , ) . however, it is important to note that these disease processes may also be detected at routine contrast-enhanced ct performed in the portal venous phase, particularly when the main or large branch vessels are affected. taking into consideration that many multiorgan and multisystem complications of covid- are caused by or directly associated with vascular thrombotic events, careful assessment of the vasculature is essential in the evaluation of all imaging examinations performed in patients with covid- . the risk of venous thromboembolism (vte), which is already greater in all critically ill patients, is higher in those with critical illness due to sars-cov- infection ( ) . an ever-increasing number of published studies have assessed the risk of vte in patients with covid- , with reported incidences of dvt ranging from % to % ( , ( ) ( ) ( ) . the incidence was found to be much higher if both symptomatic and asymptomatic patients were assessed and in patients with prolonged hospital stays in the icu (cumulative incidence rates were as high as % at days of hospitalization) ( ) . the wide range of reported incidences can be explained by the fact that vte remains largely underdiagnosed in patients with severe covid- , as only symptomatic patients generally undergo imaging. this is in part due to the contagious nature of covid- , as its high transmissibility rate complicates the workup of patients with infection. in an attempt to minimize exposure to radiologic technologists and transport personnel, only symptomatic patients are typically eligible to undergo imaging, often using abbreviated protocols and portable machines that may result in a limited evaluation. additionally, the concern over shortages of personal protective equipment (ppe) influenced the number and types of examinations that were offered to this group of patients. underdiagnosis of complications of vte in patients with co-vid- is a significant issue, as many of these patients who are severely ill already have ards and its complications (including hypoxic pulmonary vasoconstriction, pulmonary hypertension, and right ventricular failure), and further insult from a pe may be fatal. it is important to note that veins of any caliber may be affected, and therefore all vessels should be scrutinized for potential thrombus. elevated d-dimer levels, commonly found in patients with covid- , do not currently warrant routine investigation for acute vte in the absence of clinical manifestations or other supporting information ( ) . however, in patients with high clinical suspicion for vte, there should be a low threshold for ordering diagnostic tests to evaluate for dvt and/or pe. the imaging examinations performed to diagnose dvt or pe in patients with covid- may not be requested or performed, potentially owing to patient instability. moreover, performing imaging examinations may be challenging in patients with severe ards who require prone positioning. investigating for pe as well as lower and upper extremity dvt may not always be feasible owing to these clinical and positioning issues. although deterioration of right ventricular function in this setting may be a critical finding that justifies the need for establishing a diagnosis of pe, it could also be argued that the prognosis of patients with ards who require prone positioning is so grave that investigation for an underlying vte may not alter the clinical course. preventive and therapeutic use of antithrombotic agents is helpful toward mitigating the occurrence thrombotic and hemorrhagic events in these high-risk patients ( ) . lower and upper extremity doppler us is the first-line imaging modality for diagnosis of peripheral venous thrombosis and can be performed at the bedside. occlusive and partially occlusive thrombi and their potential associations with central lines can be readily diagnosed . noncompressible veins, echogenic clot, and minimal or absent flow within a distended vein are the us hallmarks of acute or subacute dvt (figs - ) . superinfection may result in thrombophlebitis and can be diagnosed by the demonstration of hyperemia in the wall of an otherwise thrombotic vessel at color doppler us. in cases of incomplete and/or inadequate thrombus evaluation or extension of thrombus into a more central vessel, ct and mr venography can be employed (fig ) . the presence of a filling defect within a vessel, with or without occlusion, is the characteristic finding of venous thrombosis. us, absence of flow within an arterial segment is diagnostic of an occlusive thrombus. abnormal waveforms (stump waveforms), character- the authors of only a few studies to date have evaluated the frequency of peripheral arterial thrombosis in patients with covid, with a reported incidence of . % ( ) . the authors of a few reported cases of lower extremity arterial thrombosis have suggested a link between preexisting peripheral arterial disease and the development of arterial thromboembolism. it has been hypothesized that acute and progressive thrombosis may be attributable to a combination of the hyperinflammatory state induced by covid- superimposed on a preexisting condition ( , ) . doppler us and ct angiography of the extremity vessels are both instrumental in the evaluation of peripheral arterial thrombosis. at ized by a low amplitude and high-resistance pattern with absence of diastolic flow, can aid in identification of a more distal occlusion. alternatively, tardus parvus waveforms within more distally recanalized vessels are findings suggestive of a more proximal significant stenosis or occlusion (fig ) . reconstituted flow, sometimes with collateralization, may be depicted distal to an occlusion. peripheral and central arterial thromboembolism may also be the result of atrial fibrillation. ct angiography aids in the assessment of the extent of thrombosis and its potential complications such as ischemia to a related structure or organ. an abrupt cutoff of the affected vessel may be readily detected at ct angiography (figs - , movie ). the few reported cases ( ) of peripheral arterial thromboembolism associated with covid- have involved both upper and lower extremity arteries, and carotid and vertebral artery involvement have been described as well. the larger central arterial system may also be involved (eg, floating thrombi may be visualized in the aorta and aortic arch) ( fig ) ( ) . it is important to keep in mind that covid- can affect more than one organ or structure, and every organ and vessel should be scrutinized when assessing for complications . it is also essential to recognize that patients with covid- may develop thrombosis of various vascular systems, and there could be concomitant involvement of one or more venous or arterial vascular beds. therefore, if evidence of thrombosis is detected, careful assessment of the entire imaged vascular system, as well as correlated organ or structure, is essential. sars-cov- is a novel coronavirus that has rapidly resulted in a worldwide pandemic and has been the cause of extreme morbidity and mortality. it primarily affects the respiratory system but may also impact a multitude of other systems in the human body, resulting in multiorgan injury and, in some cases, failure. imaging plays a significant role in the detection, diagnosis, and assessment of virus-induced injury, as well as its associated complications. a recognition and understanding of the pathophysiology of the virus and its effects on the immune system and coagulation is paramount toward improving radiologists' ability to accurately identify key imaging findings and promptly recognize possible complications, specifically those affecting the pulmonary and vascular systems, thereby minimizing the number of diagnostic misses and misinterpretations. appropriate application of the described chest radiography and ct scoring systems in the evaluation of lung involvement, including automated assessment, may increase the consistency of reported findings and aid in risk stratification, as well as offer prognostic information. owing to the complexity of the viral pathophysiology and its targeting of multiple organ systems, the recognition of one complication should prompt intense scrutiny for others, particularly if the patient is critically ill. a thorough knowledge of diagnostic imaging hallmarks, atypical imaging features, multisystem manifestations, and evolution of imaging findings is essential to optimize patient care. in a and b) . (c-f) sagittal (c), coronal (d), and axial (e, f) ct angiographic images show a large thrombus extending from the abdominal aorta into the superior mesenteric artery origin (arrow in c), which resulted in bowel ischemia, evidenced by thickening of the watershed splenic flexure of the large bowel (arrow in d). note the multifocal bilateral wedge-shaped renal cortical infarcts (arrows in e). note also a nonocclusive thrombus in the left profunda femoris artery (white arrow in f), indicative of a concurrent presence of a peripheral thrombosis. there is normal opacification of the patent right profunda femoris artery (black arrow in f). this case demonstrates multifocal multisystem manifestations of covid- complicated by coagulopathy that resulted in injury to various organs and systems. it is an example of the need for increased awareness among radiologists to thoroughly evaluate all covered anatomy for covid-related complications. covid- coronavirus pandemic saving mothers' lives: reviewing maternal deaths to make motherhood safer: - -the eighth report of the confidential enquiries into maternal deaths in the united kingdom comorbidities and multiorgan injuries in the treatment of covid- novel coronavirus: what neuroradiologists as citizens of the world need to know tissue distribution of ace protein, the functional receptor for sars coronavirus: a first step in understanding sars pathogenesis covid- ) outbreak: what the department of radiology should know a pneumonia outbreak associated with a new coronavirus of probable bat origin the genetic sequence, origin, and diagnosis of sars-cov- detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction sars-cov- viral load in upper respiratory specimens of infected patients tubal ectopic pregnancy geographic differences in covid- cases, deaths, and incidence: united states prevalence of sars-cov- infection in residents of a large homeless shelter in boston surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient aerosol and surface stability of sars-cov- as compared with sars-cov- stability and inactivation of sars coronavirus comorbidities, clinical signs and symptoms, laboratory findings, imaging features, treatment strategies, and outcomes in adult and pediatric patients with covid- : a systematic review and meta-analysis transmission of -ncov infection from an asymptomatic contact in germany a familial cluster of infection associated with the novel coronavirus indicating possible person-to-person transmission during the incubation period presumed asymptomatic carrier transmission of covid- clinical characteristics of asymptomatic infections with covid- screened among close contacts in nanjing covid- transmission within a family cluster by presymptomatic carriers in china viral dynamics in mild and severe cases of covid- viral load dynamics and disease severity in patients infected with sars-cov- in zhejiang province, china factors associated with prolonged viral rna shedding in patients with coronavirus disease (covid- ) functional assessment of cell entry and receptor usage for sars-cov- and other lineage b betacoronaviruses single-cell rna-seq data analysis on the receptor ace expression reveals the potential risk of different human organs vulnerable to -ncov infection expression of sars-cov- receptor ace and tmprss in human primary conjunctival and pterygium cell lines and in mouse cornea structural basis of receptor recognition by sars-cov- covid- : a new virus, but a familiar receptor and cytokine release syndrome virological assessment of hospitalized patients with covid- treatment of critically ill patients with covid- with convalescent plasma early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical characteristics of coronavirus disease in china a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster prevalence of asymptomatic sars-cov- infection: a narrative review proportion of asymptomatic coronavirus disease : a systematic review and metaanalysis clinical characteristics of children with covid- : a meta-analysis persons evaluated for novel coronavirus: united states clinical features of patients infected with novel coronavirus in wuhan, china epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention clinical characteristics of covid- in new york city epidemiological and clinical aspects of covid- ; a narrative review profile of rt-pcr for sars-cov- : a preliminary study from covid- patients illinois department of public health. covid- statistics cardiovascular disease, drug therapy, and mortality in radiographics.rsna.org acute pe associated with covid- pneumonia detected with pulmonary ct angiography acute pe and covid- pneumonia: a random association? coagulopathy and antiphospholipid antibodies in patients with covid- neurologic manifestations of hospitalized patients with coronavirus disease incidence of thrombotic complications in critically ill icu patients with covid- large-vessel stroke as a presenting feature of covid- in the young covid- : consider cytokine storm syndromes and immunosuppression radiographics update: venous thrombosis and hypercoagulability in the abdomen and pelvis-findings in covid- characteristics of hospitalized adults with covid- in an integrated health care system in california cancer patients in sars-cov- infection: a nationwide analysis in china clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study obesity in patients younger than years is a risk factor for covid- hospital admission clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china d-dimer levels on admission to predict in-hospital mortality in patients with covid- frequency and distribution of chest radiographic findings in patients positive for covid- gross examination report of a covid- death autopsy policies and guidelines for covid- preparedness: experiences from the university of washington ct imaging features of novel coronavirus ( -ncov) ct features of coronavirus disease (covid- ) pneumonia in patients in wuhan, china chest ct findings in coronavirus disease- (covid- ): relationship to duration of infection essentials for radiologists on covid- : an update-radiology scientific expert panel portable chest x-ray in coronavirus disease- (covid- ): a pictorial review coronavirus disease (covid- ): a systematic review of imaging findings in patients clinical and chest radiography features determine patient outcomes in young and middle age adults with covid- automated assessment of covid- pulmonary disease severity on chest radiographs using convolutional siamese neural networks. medrxiv advocacy-and-economics/acr-position-statements/ recommendations-for-chest-radiography-and-ct-for-suspected-covid -infection ct should not be used as first-line tool against coronavirus, acr warns following pandemic declaration performance of radiologists in differentiating covid- from non-covid- viral pneumonia at chest ct radiological society of north america expert consensus statement on reporting chest ct findings related to covid- : endorsed by the society of thoracic radiology, the american college of radiology, and rsna-secondary publication is there a role for lung ultrasound during the covid- pandemic? sonographic signs and patterns of covid- pneumonia bedside lung ultrasound in the assessment of alveolar-interstitial syndrome lung ultrasonography and cardiac surgery: a narrative review re: ventilation-perfusion scans during the coronavirus disease (covid- ) outbreak pulmonary vascular pathology in covid- co-rads: a categorical ct assessment scheme for patients suspected of having covid- -definition and evaluation henry ts; six signatories. a role for ct in covid- ? what data really tell us so far the role of chest imaging in patient management during the co-vid- pandemic: a multinational consensus statement from the fleischner society time course of lung changes at chest ct during recovery from coronavirus disease (covid- ) temporal changes of ct findings in patients with covid- pneumonia: a longitudinal study novel coronavirus ( -ncov) pneumonia the diagnostic value of halo and reversed halo signs for invasive mold infections in compromised hosts chest ct manifestations of new coronavirus disease (covid- ): a pictorial review chest ct features and their role in covid- radiology perspective of coronavirus disease (covid- ): lessons from severe acute respiratory syndrome and middle east respiratory syndrome coronavirus disease (covid- ): role of chest ct in diagnosis and management relation between chest ct findings and clinical conditions of coronavirus disease (covid- ) pneumonia: a multicenter study ct findings in diseases associated with pulmonary hypertension: a current review covid- does not lead to a "typical" acute respiratory distress syndrome imaging of diffuse lung disease in the intensive care unit patient high incidence of barotrauma in patients with covid- infection on invasive mechanical ventilation acute pe in patients with covid- at ct angiography and relationship to d-dimer levels acute pe and covid- diagnosis, prevention, and treatment of thromboembolic complications in covid- : report of the national institute for public health of the netherlands covid- and thrombotic or thromboembolic disease: implications for prevention, antithrombotic therapy, and follow-up: jacc state-of-the-art review venous thrombosis and hypercoagulability in the abdomen and pelvis: causes and imaging findings abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia the procoagulant pattern of patients with covid- acute respiratory distress syndrome hypercoagulability of covid- patients in intensive care unit: a report of thromboelastography findings and other parameters of hemostasis thromboinflammation and the hypercoagulability of covid- advance in the management of sepsis-induced coagulopathy and disseminated intravascular coagulation difference of coagulation features between severe pneumonia induced by sars-cov and non-sars-cov complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases cardiovascular considerations for patients, health care workers, and health systems during the covid- pandemic indirect ct venography at kvp with sinogram-affirmed iterative reconstruction compared to kvp with filtered back projection: assessment of image quality and radiation dose combined direct and indirect ct venography (combined ctv) in detecting lower extremity deep vein thrombosis confirmation of the high cumulative incidence of thrombotic complications in critically ill icu patients with covid- : an updated analysis prevalence of venous thromboembolism in patients with severe novel coronavirus pneumonia incidence of venous thromboembolism in hospitalized patients with covid- d-dimer is associated with severity of coronavirus disease : a pooled analysis rhabdomyolysis as a presentation of novel coronavirus disease venous thrombosis and arteriosclerosis obliterans of lower extremities in a very severe patient with novel coronavirus disease: a case report severe arterial thrombosis associated with covid- infection this journal-based sa-cme activity has been approved for ama pra category credit tm . see rsna.org/learning-center-rg. key: cord- -tk oggi authors: hosseini, elahe seyed; kashani, narjes riahi; nikzad, hossein; azadbakht, javid; bafrani, hassan hassani; kashani, hamed haddad title: the novel coronavirus disease- (covid- ): mechanism of action, detection and recent therapeutic strategies date: - - journal: virology doi: . /j.virol. . . sha: doc_id: cord_uid: tk oggi novel coronavirus sars-cov- , designated as covid- by the world health organization (who) on the february , , is one of the highly pathogenic β‐coronaviruses which infects human. early diagnosis of covid- is the most critical step to treat infection. the diagnostic tools are generally molecular methods, serology and viral culture. recently crispr-based method has been investigated to diagnose and treat coronavirus infection. the emergence of -ncov during the influenza season, has led to the extensive use of antibiotics and neuraminidase enzyme inhibitors, taken orally and intravenously. currently, antiviral inhibitors of sars and mers spike proteins, neuraminidase inhibitors, anti-inflammatory drugs and ek peptide are the available therapeutic options for sars-cov- infected individuals. in addition, chloroquine, which was previously used for malarial and autoimmune disease, has shown efficacy in the -ncov infection treatment. in severe hypoxaemia, a combination of antibiotics, α-interferon, lopinavir and mechanical ventilation can effectively mitigate the symptoms. comprehensive knowledge on the innate and adaptive immune responses, will make it possible to propose potent antiviral drugs with their effective therapeutic measures for the prevention of viral infection. this therapeutic strategy will help patients worldwide to protect themselves against severe and fatal viral infections, that potentially can evolve and develop drug resistance, and to reduce mortality rates. recent pharmaceutical strategies to treat coronavirus - improve immune system to fight with covid- - abbreviations [ ] [ ] introduction over the last two decades, three coronaviruses have periodically crossed animal species such as bats, transmitted to human populations, and caused an ever-increasing outbreak of a large-scale pandemic [ , ] . the previously reported viral zoonotic pathogens include sars-cov (severe acute respiratory syndrome coronavirus) and mers (middle east respiratory syndrome coronavirus) [ , ] , that can cause severe respiratory disease in human [ , ] . sars-cov- , a novel coronavirus (which causes covid- ) , has fast spread like a pandemic since its outbreak in wuhan, china, in december [ ] . it causes an acute and deadly disease with a % j o u r n a l p r e -p r o o f mortality rate. however, this novel coronavirus is usually associated with a mild to severe respiratory disease in humans [ , , ] . this virus has the ability of jumping between species, and causing a variety of diseases as a strange and complex pathogen [ ] . due to the frequent interaction between humans and animals, a virus is a common source of zoonotic infection. covid- , due to its human-to-human transmission, has become a health emergency of global concern [ , ] . currently, we have no sufficient evidence to propose that a specific wildlife animal is the virus origin. a proper study of the viral source, evolution, mode of zoonotic transmission and infectivity, would help to prevent further infections. [ , ] . coronaviruses (covs) belong to the nidovirales order, coronaviridae family, which comprises of two subfamilies, namely orthocoronavirinae and letovirinae (international committee on taxonomy of viruses) [ , ] . covs are genotypically classified into four genera: alpha coronaviruses (a), beta coronaviruses (b), gamma coronaviruses (g), and delta coronaviruses (d), according to their phylogenetic and genomic data. further, β-coronavirus is subdivided into four viral lineages of a to d [ , ] . coronavirus is an enveloped and non-segmented virus, which has a large positive-sense single-stranded rna virus genome ( - kb) , capped and polyadenylated [ ] . coronavirus also has crown-shape spikes projecting from its surface ( - nm in size), from which its name derived [ ] . the cov spike (s) glycoprotein attaches to cellular receptors on the host cell and mediates viral entry resulting in interspecies transmission and pathogenesis [ , ] figure ). it seems that the high sequence identity in sars-cov- and pangolin-cov may be due to coincidental convergent evolution [ ] . phylogenetic analysis of rbd region of the spike protein, has also led to a further presumption that the identity of sars-cov- rbd to pangolins-cov rbd might be result of accidental mutations followed by natural selection, and/or recombination events in pangolins [ ] (figure ). most common clinical symptoms of covid- disease are dry cough, fever and shortness of breath in the majority of patients. some patients also experience other signs such as sore throat, headache, myalgia, fatigue and diarrhea [ , ] . in the initial phase of the disease, patients can j o u r n a l p r e -p r o o f be afebrile, only presenting with chills and respiratory symptoms. although most cases appear to be mild, all patients have new pulmonary signs as ground-glass lung opacity on chest x-ray [ , ] . the symptoms in patients with mild pneumonia are fever, cough, sore throat, tiredness, headache or myalgia [ ] . they do not obviously show any of the serious symptoms or complications. some patients were reported to have upper respiratory infection (uri), bilateral patchy opacity in lung [ ] , decreased white blood cell or lymphocyte number [ ] and increased alt, ast, ldh, ck-mb, crp and esr in these stages of infection [ ] . patients with severe pneumonia, suffer from acute respiratory distress syndrome (ards) and refractory hypoxemia. ncov- can cause severe pulmonary infection, respiratory failure, along with organ damage and dysfunction. in case of extra-pulmonary system dysfunctions, such as derangements in hematologic and digestive system, the risk of sepsis and septic shock will be serious, resulting in considerable increase in fatality rate. the findings showed that the disease is mild in the majority of patients ( %) and only a few of them develop severe pneumonia, pulmonary edema, ards, or different organ damages with case morality rate of . %. in children, infection generally presents with much milder clinical symptoms or even asymptomatic, compared with adult. according to previous studies, pregnant women do not seem to have a severe disease, while older patients are at a high risk of developing critical illness [ , ] . the case fatality rate (cfr) increased in % of patients older than with a history of chronic diseases, such as high blood pressure, diabetes, heart diseases, respiratory diseases, cerebrovascular diseases, endocrine system disorders, digestive system disorders and cancers . in most of cases, the cause of death is respiratory failure, septic shock or several organ failure [ ] . in fact, increased c-reactive protein (crp) is an important factor of impaired immunity, characterized by lymphopenia. so, sars-cov- is more probably to affect older people with chronic disease due to their poorer immune function [ ] . covid- has also been found to infect more males (average age of . years) than females [ ] . the less susceptibility of females to viral infections is likely associated with the protective role of x chromosome and sex hormones, which result in stronger immune response to virus [ ] . ct imaging findings of patients with covid- revealed that most of cases had ground-glass opacities, which may manifest as crazy paving pattern, organizing pneumonia and architectural distortion. on x-rays or chest ct imaging of the examined patients, j o u r n a l p r e -p r o o f early diagnosis is the most important step to manage and treat covid- . the diagnostic tools are generally molecular methods, serology and viral culture. initial laboratory investigations of hospitalized patients consist of a complete blood count, coagulation testing and serum biochemical test such as creatine kinase (ck), lactate dehydrogenase, procalcitonin, and electrolytes [ , ] . based on laboratory tests, most patients showed a significant decrease in total number of lymphocytes, suggesting that lymphocytes (particularly t lymphocytes) are likely target of sars-cov- . in the covid infection, virus particles begin to spread through the respiratory tract and infect the surrounding uninfected cells. this leads to initiate a cytokine storm and consequently trigger a series of sever immune responses. this process results in some changes in immune cells, particularly lymphocytes, and then leads to immune system dysfunction [ ] . hence, the decreased number of the circulating lymphocytes could be considered as a diagnostic marker for sars-cov- infection and its severity [ ] . previous studies reported that there is a correlation between elevated level of pro-inflammatory cytokines like il b, il , il , ifnγ, ip , and mcp , and cytokines such as ifnγ, tnfα, il , and il , in sars-cov and mers-cov infection respectively, with pulmonary inflammation and lung injury. notably, the high value of cytokines like il b, ifnγ, ip , and mcp , may activate t helper cells (th ) response. this cytokine storm is probably associated with disease severity. however, in sars-cov infection, enhanced secretion of t helper (th ) and cytokines like il and il , reduce peripheral white blood cells and immune cells such as lymphocytes, probably leading to suppression of the inflammatory response and immune system function followed by serious lung damage, which differs from sars-cov infection [ ] . these findings suggest that sever and uncontrolled inflammatory response have a more damaging effect on covid- induced lung injury than viral pathogenicity. therefore, in sars-cov- pneumonia, it is vital to control cytokines or chemokines to detect the impact of coronavirus on their production in the critical phase of the disease [ , ] . rt-pcr (reverse-transcription polymerase chain reaction) or real-time pcr and genome sequencing for respiratory or blood specimens are the next methods to confirm covid- infection (table ) . together with its time-consuming process and the problems associated to performance of rt-pcr kit are the main obstacles to control this epidemic [ ] . chest ct, compared to rt-pcr, is a fast, sensitive, easy to perform and more accurate and reliable tool for screening and diagnosis of covid- [ ] . chest ct can also show pulmonary abnormalities in covid- patients with early negative rt-pcr results [ , ] . in the primary stage of pneumonia itself, ct images can demonstrate several small ground-glass opacity as well as some interstitial changes [ ] , remarkable in the lung periphery [ ] [ ] . crispr-cas -based sherlock system consists of two rna guides, which are combined with a cas protein, and form a sherlock system to recognize the presence of covid- viral rna. at first the team used synthetic fragments of sars-cov- rna as a pattern for designing two rna guides, which are able to bind to their complementary sequences in covid- rna. in order to visual readout, they used a paper strip (as a paper strip in pregnancy test) for dipping into a prepared sample. then, appearance of a line on the paper strip indicates the existence of virus in the sample [ , ] . also, another research group has recently proposed a rna-targeting crispr system to target rna genome of sars-cov- in the laboratory, to limit its ability to reproduce [ ] . this crispr cov- patients, particularly to target their lung, which is main infected organ [ ] . before therapeutic application of crispr/cas d system to patients, it is necessary to determine the safety and efficacy of this system in clearance of -ncov and other viruses in animals. if researchers find this therapeutic strategy secure and beneficial, then it would be applied to kill the viruses that have the potential to evolve and also develop drug resistance [ ] . since the emergence of -ncov, due to its rapid spread and being a serious threat to human health, researchers have made great efforts to understand the pathogenetic characteristics of this virus to develop effective drugs. due to appearance of the -ncov during the influenza season, orally and intravenously antibiotics and neuraminidase inhibitors such as oseltamivir having been widely used as an experimental treatment for -ncov in china [ , ] . however, there is no reliable evidence that shows oseltamivir is an effective treatment in -ncov [ ] . at present, there is no antiviral drug assumed to provide protection against covid- infection; also it will take long time to develop and a vaccine and gets approval for it. [ ] . nowadays, griffithsin, as an inhibitor of sars and mers spike, remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [ ] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and ek peptide [ ] , the clinical potential to be applied against the -ncov infection [ , ] . chloroquine shows its inhibitory effects against -ncov through increasing endosomal ph required for virus cell fusion, also affecting the glycosylation of cellular receptors of sars-cov [ ] . chloroquine is a cheap and safe anti-viral medicine, which is orally administrated and widely distributes all over body especially in the lungs [ ] . also, remdesivir, which has a structure chemically similar to hiv reverse-transcriptase inhibitors, is currently in the phase of clinical trials for -ncov [ ] . the spike (s) protein is a promising target for the development of antivirals drugs, due to its major role in the virus-receptor interaction. griffithsin, a medicine targeting the oligosaccharides on the surface of different spike proteins [ ] , has also been tested in phase i trials for the treatment of hiv and sars-cov [ ] . however, the efficacy of spike inhibitors for the treatment of -ncov should be re-evaluated [ ] . there are multiple mechanisms of action for nucleoside analogues (adenine or guanine derivative), including lethal mutagenesis, inhibition of rna biosynthesis, or rna chain premature termination [ ] . they inhibit synthesis of viral rna in human coronaviruses by targeting the rna-dependent rna polymerase [ ] . favipiravir (t- ), a guanine analogue, is an antiviral drug targeting the viral rna-dependent rna polymerase of rna viruses such as ebola, influenza, yellow fever, j o u r n a l p r e -p r o o f chikungunya, norovirus and enterovirus. it has been recently proposed to be effective also against coronaviruses, in vitro [ ] . using fabiravir and ribavirin combined with oseltamivir, for the treatment of coronaviruses diseases such as in severe influenza, is better than oseltamivir alone [ ] . at present, lopinavir/ritonavir and ifn-alpha are in the initial phase of clinical trials in patients infected with -ncov [ , ] . according to the guidelines [ ] , lopinavir ( mg/ mg bid po) used to treat hiv/aids infection and ritonavir as a booster, as well as ifnalpha ( million u bid inh) usually utilized for treatment of hbv, are recommended as antiviral therapy [ , ] . a scholar's report from hong kong illustrated that use of the combination of lopinavir/ritonavir (lpv/rtv) (anti-hiv drugs) with ribavirin, reduces the risk of acute respiratory distress syndrome (ards) or death in treated patients [ ] . further researches are needed to understand whether these inhibitors can effectively block the -chymotrypsin-like and papain-like proteases of -ncov [ ] . in addition, remdesivir, earlier used against the ebola virus, has been presently determined as antiviral drug for treating mers/sars and related zoonotic bat covs in the cell cultures and animal models [ ] [ ] [ ] . based on animal experiments, remdesivir effectively decreases the virus titer of mice infected with mers-cov and improves the lung tissue damage, in comparison to other cases treated with a compound of lopinavir/ritonavir and interferon-β [ ] . remdesivir has also been recently suggested to inhibit -ncov [ ] by terminating the viral rna transcription in early stage [ , ] . another decade, another coronavirus a novel coronavirus outbreak of global health concern. the lancet origin and evolution of pathogenic coronaviruses sars and mers: recent insights into emerging coronaviruses molecular epidemiology, evolution and phylogeny of sars coronavirus. infection novel coronavirus: from discovery to clinical diagnostics. infection, genetics and evolution a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster. the lancet a novel coronavirus from patients with pneumonia in china clinical features of patients infected with novel coronavirus in wuhan, china. the lancet human coronavirus: host-pathogen interaction. annual review of microbiology pneumonia of unknown cause-china. emergencies preparedness, response, disease outbreak news novel wuhan ( -ncov) coronavirus. american journal of respiratory and critical care medicine nsp of coronaviruses: structures and functions of a large multi-domain protein discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus structure, function, and evolution of coronavirus spike proteins. annual review of virology from sars to mers, thrusting coronaviruses into the spotlight. viruses coronavirus genomics and bioinformatics analysis. viruses predicting the receptor-binding domain usage of the coronavirus based on kmer frequency on spike protein. infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases dengue viruses and promising envelope protein domain iii-based vaccines genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan. emerging microbes & infections diagnosis and treatment recommendations for pediatric respiratory infection caused by the novel coronavirus epidemiology, genetic recombination, and pathogenesis of coronaviruses molecular evolution of human coronavirus genomes a novel coronavirus associated with severe acute respiratory syndrome identification of a novel coronavirus in patients with severe acute respiratory syndrome return of the coronavirus: -ncov. viruses isolation of a novel coronavirus from a man with pneumonia in saudi arabia coronavirus infections and immune responses the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak-an update on the status covid- : epidemiology, evolution, and cross-disciplinary perspectives on the origin and continuing evolution of sars-cov- epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study. the lancet the continuing -ncov epidemic threat of novel coronaviruses to global health-the latest novel coronavirus outbreak in wuhan first case of novel coronavirus in the united states clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study. the lancet respiratory medicine a pneumonia outbreak associated with a new coronavirus of probable bat origin clinical characteristics of novel coronavirus infection in china. medrxiv prevalence of comorbidities in the middle east respiratory syndrome coronavirus (mers-cov): a systematic review and meta-analysis sex-based differences in susceptibility to severe acute respiratory syndrome coronavirus infection sexual dimorphism in innate immunity an ultrasensitive, rapid, and portable coronavirus sars-cov- sequence detection method based on crispr-cas . biorxiv comparative analysis of primer-probe sets for the laboratory confirmation of sars-cov- . biorxiv molecular diagnosis of a novel coronavirus ( -ncov) causing an outbreak of pneumonia the infection evidence of sars-cov- in ocular surface: a single-center crosssectional study. medrxiv clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan identification of coronavirus isolated from a patient in korea with covid- . osong public health and research perspectives cross-species transmission of the newly identified coronavirus -ncov advances in virus research chest ct for typical -ncov pneumonia: relationship to negative rt-pcr testing use of chest ct in combination with negative rt-pcr assay for the novel coronavirus but high clinical suspicion ct imaging features of novel coronavirus ( -ncov) novel coronavirus (covid- ) outbreak: a review of the current literature. ejmo a protocol for detection of covid- using crispr diagnostics crispr-based surveillance for covid- using genomicallycomprehensive machine learning design. biorxiv virus against virus: a potential treatment for -ncov (sars-cov- ) and other rna viruses transcriptome engineering with rna-targeting type vi-d crispr effectors a systematic review of therapeutic agents for the treatment of the middle east respiratory syndrome coronavirus (mers-cov). travel medicine and infectious disease clinical management of respiratory syndrome in patients hospitalized for suspected middle east respiratory syndrome coronavirus infection in the paris area from comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings a pan-coronavirus fusion inhibitor targeting the hr domain of human coronavirus spike. science advances abelson kinase inhibitors are potent inhibitors of severe acute respiratory syndrome coronavirus and middle east respiratory syndrome coronavirus fusion unique synergistic antiviral effects of shufeng jiedu capsule and oseltamivir in influenza a viral-induced acute exacerbation of chronic obstructive pulmonary disease the chinese prescription lianhuaqingwen capsule exerts anti-influenza activity through the inhibition of viral propagation and impacts immune function. bmc complementary and alternative medicine drug treatment options for the -new coronavirus ( -ncov) new insights into the antiviral effects of chloroquine. the lancet infectious diseases anti-malaria drug chloroquine is highly effective in treating avian influenza a h n virus infection in an animal model chloroquine is a potent inhibitor of sars coronavirus infection and spread remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro coronaviruses-drug discovery and therapeutic options treatment of middle east respiratory syndrome with a combination of lopinavir/ritonavir and interferon-β b (miracle trial): statistical analysis plan for a recursive two-stage group sequential randomized controlled trial new nucleoside analogues for the treatment of hemorrhagic fever virus infections comparative effectiveness of combined favipiravir and oseltamivir therapy versus oseltamivir monotherapy in critically ill patients with influenza virus infection the novel chinese coronavirus ( -ncov) infections: challenges for fighting the storm broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses a randomized, controlled trial of ebola virus disease therapeutics broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent rna dependent rna polymerase therapeutic efficacy of the small molecule gs- against ebola virus in rhesus monkeys initiation, extension, and termination of rna synthesis by a paramyxovirus polymerase coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease therapeutic options for the novel coronavirus ( -ncov). potential benefits of precise corticosteroids therapy for severe -ncov pneumonia clinical evidence does not support corticosteroid treatment for -ncov lung injury. the lancet clinical features predicting mortality risk in patients with viral pneumonia: the mulbsta score single-cell rna expression profiling shows that ace , the putative receptor of wuhan -ncov, has significant expression in the nasal, mouth, lung and colon tissues, and tends to be co-expressed with hla-drb in the four tissues repurposing of clinically developed drugs for treatment of middle east respiratory syndrome coronavirus infection the financial support for the current research was provided by research deputy of kashan university of medical sciences, kashan, iran. not applicable esh, hhk and nrk provided direction and guidance throughout the preparation of this manuscript. hhb, hn and hhk conducted the literature and drafted the manuscript. other authors reviewed the manuscript and made significant revisions on the drafts. all authors read and approved the final version. the authors declared that they have no competing interests. not applicable. key: cord- -dgysimh authors: al-jabir, ahmed; kerwan, ahmed; nicola, maria; alsafi, zaid; khan, mehdi; sohrabi, catrin; o'neill, niamh; iosifidis, christos; griffin, michelle; mathew, ginimol; agha, riaz title: impact of the coronavirus (covid- ) pandemic on surgical practice - part (surgical prioritisation) date: - - journal: int j surg doi: . /j.ijsu. . . sha: doc_id: cord_uid: dgysimh the coronavirus (covid- ) pandemic represents a once in a century challenge to human healthcare with . million cases and , deaths thus far. surgical practice has been significantly impacted with all specialties writing guidelines for how to manage during this crisis. all specialties have had to triage the urgency of their daily surgical procedures and consider non-surgical management options where possible. the pandemic has had ramifications for ways of working, surgical techniques, open vs minimally invasive, theatre workflow, patient and staff safety, training and education. with guidelines specific to each specialty being implemented and followed, surgeons should be able to continue to provide safe and effective care to their patients during the covid- pandemic. in this comprehensive and up to date review we assess changes to working practices through the lens of each surgical specialty. the rapid spread of covid- around the world ( . million cases and over , deaths brings new challenges for the international medical and surgical community [ ] ; the unprecedented strain it has put on units around the world has unfortunately been accompanied by an increasing number of covid- infections and subsequent deaths amongst medical colleagues [ ] . it is therefore important to follow the latest guidelines for surgical management of patients in order to reduce the risk of infection for patients and medical personnel. in part , the authors have reviewed the current evidence and offered general recommendations for changes to surgical practice to minimise the effect of the covid- pandemic on surgical units. prioritisation of surgical services during this pandemic must be a careful balance of patient needs and resource availability and the european association of urology guidelines office offer the following suggestions for factors that must be taken into account [ ] oncological surgery with the disruption of normal surgical practices due to workforce shortages as well as resource limitations due to covid- , it is important to rationalise all surgeries undertaken. this is especially important in cancer surgery where the surgeon must balance risk of potential viral transmission to the surgical team as well as of possible progression of cancer in the patient [ ] . in the first instance, patients should be transferred to hospitals with greater capacity to cover procedures, with the suggestion of setting up local 'covid- free' surgical hubs for the continuation of oncological surgery. in cancer patients, general considerations must also be taken into account. it is routine that most complex elective surgical procedures receive ward-based care post-operatively. occasionally, patients may develop postoperative complications requiring itu admission and/or re-operation, which may prove to be a challenge with the increasing numbers of covid- patients requiring level care. it is recommended that length of stay (los) be decreased to a minimum, especially in critical care [ , ] furthermore, the nhs has identified the cancer patients which are most at risk during the outbreak and who are likely to become seriously or critically unwell if they were to contract the virus. these include: patients on active chemo-or radiotherapy; immunotherapy or any antibody treatments; or immune system modulation therapy (eg. protein kinase inhibitors or post-transplantation immunosuppressants). this group also includes patients with blood or bone marrow cancers ie. leukemia, lymphoma or myeloma. further to the above, factors such as age above , pre-existing cardiovascular and/or respiratory disease have been associated with a worse prognosis. following a multidisciplinary team (mdt) discussion, clinicians are encouraged to clearly outline the risks and benefits with patients before commencing or continuing any cancer treatment [ ] . surgical teams are encouraged to offer telephone or video consultations when possible, cancel follow ups which are deemed non-essential in an attempt to minimise patient contact. in cases where patients must attend hospital appointments, time patients spend in services should be minimised. they should have a scheduled appointment time and should be advised not to arrive early [ ] . surgeons are encouraged to maximise breast conserving surgery when possible, as definitive mastectomy and/or reconstruction should be deferred when possible if radiotherapy options are available. surgeons should also consider alternative, non-surgical therapy where possible. suggestions for prioritisation are in table additionally, lu et al [ ] recommended prioritising breast disease care according to benign or malignant disease. for benign disease, they use the bi-rads grading score and advise that patients with score < are suitable for a -month deferral. patients grading ≥ should have a biopsy, reviewed in - weeks then re-assessed. for malignant disease, with a bi-rads grade ≥ and highly suspicious for malignancy, a core needle biopsy or fine needle aspirate should be arranged urgently. in hospitals in phase or , neoadjuvant therapy is given priority over surgical intervention and is to be administered in a day chemotherapy unit to avoid unnecessary admissions. they also recommend postponing follow-up adjuvant chemotherapy in patients who have recently had surgery for early stage breast cancer. for more at risk patients (such as the elderly or immunosuppressed) with a low tumour burden, a reduced dose (≥ % of the standard dose) is recommended. finally, where possible, adjuvant radiotherapy should be delayed by - months to avoid nosocomial transmission [ ] . for patients with stable remission, they recommend that reviews should be conducted every months instead of -monthly. in locally advanced resectable colon cancer, surgeons are urged to consider neoadjuvant chemotherapy and revisit the idea of surgery in - months. there should also be consideration of further chemotherapy in patients with rectal cancer which have shown a clear response to neoadjuvant chemotherapy. this may also be considered in locally advanced or recurrent rectal cancer requiring pelvic exenteration, in an attempt to delay the operation for a few months. diverting stomas should be utilised or give preference for stoma formation over anastomosis to reduce the risk of postoperative complications (e.g. anastomotic leak) [ ] . suggestions for prioritisation are given in table . guanyu et al [ ] note that sars-cov- has been identified in many faecal specimens and advise extra precautions during colorectal surgery where laparoscopically generated aerosols may mix with blood or intestinal contents during anastomoses. additionally, they note that whilst fever is a main sign of covid- , it is also a primary manifestation of anastomotic leak and advise surgeons to carefully consider this possibility depending on patient risk factors. in thoracic cancer, care must be taken to differentiate between the symptoms of covid- (which are predominately respiratory in nature) or severe acute respiratory distress syndrome and progression in lung cancer. furthermore, patient groups must be very carefully selected for surgery as any reduction in lung reserves may severely affect the risk of complications and morbidity and mortality should they later be infected with covid- . suggestions for prioritisation are given in table . trauma and orthopaedics is a key speciality where operations will be required to continue despite a patient's covid- status. for this reason, extensive planning is required to ensure that optimal injury care is provided regardless of a patient's infection status. trauma coordinators are required to plan for a potential surge in intensive care capabilities, where patients with suspected or confirmed covid- should be grouped in a separate area from patients without the virus, while ensuring optimal care is not compromised. policies should be decided in each centre regarding the restriction of elective appointments and procedures [ ] . some suggestions for case prioritisation are seen in table . examples of these patients include hip fractures and infected prostheses. these patients will require hospital admission and urgent surgical management that cannot be postponed. efficient treatment is essential to avoid prolonged hospital stay both before and after surgery. a lead attending physician must be allocated to coordinate the flow of patients from the emergency department through to operating room (or) scheduling. it is advised that daily trauma conferences should be held to update on problems faced and logistics of dealing with said issues. elective theatre capacity and rehabilitation services should be utilised to minimise preoperative delay and postoperative stay in hospital. elderly patients will be seen frequently in trauma and orthopaedics; therefore measures must be taken to shield these patients from covid- during their stay in hospital. anaesthetic guidelines must be developed for patients requiring surgery who may be covid- positive. examples of these patients include ligamentous injuries of the knee. non-operative management must be explored first to avoid hospital admission. a clinical decision must then be made when faced with a serious injury taking into account the availability of available clinicians and resources, as well as the potential impact on society. as resources become more strained, nonoperative care will be emphasised, where possible, to reduce the number of inpatients in hospital and resulting burden on the hospital system. this will also mean more beds are available for obligatory inpatients. many trauma patients may be clinically suitable for day-case surgery such as simple periarticular fractures. by utilising day-case trauma surgery, unnecessary admissions can be avoided thus reducing the likelihood of patients being exposed to a hospital environment while freeing up beds for obligatory inpatient cases. due to covid- , the only day-case procedures likely to take place are urgent cases therefore careful consideration and prioritisation of these patients is essential to ensure the necessary staff and theatre space is available. first contact and fracture clinics these patients will be outpatients therefore any hospital or clinic attendance must be kept to an absolute safe minimum. emergency departments are likely to be under immense pressure therefore trauma and orthopaedic surgeons may take pressure off the emergency services by utilising a fracture clinic. whilst the emergency departments may continue to care for patients who require resuscitation or a full trauma team, fracture clinics may be asked to take patients directly from ed triage with fractures, wounds and minor injuries prior to examination or diagnosis. surgery must not be scheduled by a junior clinician without approval from an experienced attending. managers can play to become fully integrated in regional and hospital planning. as mentioned previously, intensive care triage and resource allocation are essential when a surge in patients requiring urgent treatment is seen. regarding management of critically injured patients, it is advised that the standards of care for these patients is adapted in that the criteria for early triage to palliative care services is implemented for patients with low chances of survival [ ] . furthermore, senior staff such as trauma attendings should triage patients using a uniform triage policy rather than clinical judgement alone for trauma and icu patients. if resources in a care centre become sufficiently limited, exclusion from treatment may be decided based on the probability of the patient surviving to ensure resource allocation is efficient [ ] . an essential element of surgical service planning is the delivery of emergency general surgery. it is important to ensure that this continues as normal wherever possible for both patients infected with covid- or not [ ] . one suggestion is to set up dedicated 'clean' and 'dirty' emergency operating rooms to avoid nosocomial infections in covid-negative patients. operations or procedures should be performed if conservative management has failed, may cause harm to the patient, is likely to prolong hospital stay, or increase the likelihood of readmission at a later stage [ ] . surgeons should also be wary of a possible reduction in the availability of blood products. the uk has already seen resources beginning to deplete due to both increased usage as well as a reduction in blood donors due to social distancing and quarantine measures [ ] . it is therefore advisable for individual centres to monitor regional blood availability and if required, support a restrictive transfusion strategy both in ors and icu where necessary [ ] or intraoperative cell salvage [ ] . suggestions for prioritisation are given in table . incision and drainages should continue to be performed in cases of superficial soft tissue abscess, including perianal abscesses, under local anaesthesia where possible. in cases where infection is deep seated (ie. muscle involvement), incision and drainage should be performed in the or, in an attempt to avoid extension of the disease and shorten hospital stay. this classification includes, but is not limited to, perirectal abscesses (ischiorectal, intersphincteric, supralevator). if an operating room is not available, percutaneous drainage should be considered [ ] . spinelli et al. [ ] warn that cases of covid- may present with abdominal symptoms resembling acute pancreatitis. in fact, furong et al. [ ] suggest that high angiotensinconverting enzyme (ace ) receptor expression in the pancreas may be a cause of mild pancreatitis in patients infected with sars-cov- and advise clinicians to remain vigilant of this phenomenon. in cases of progression to necrotising pancreatitis during the covid- pandemic, percutaneous and interventional radiology (ir) drainage strategies should be favoured over endoscopy and laparoscopic or open operative methods [ ] . emergency operations should be performed in closed loop bowel obstruction and obstructions due to incarcerated hernias, bowel perforations and intestinal ischemia cases. conservative management should be attempted in bowel obstruction secondary to adhesions [ ] . appendicitis, if uncomplicated, may be treated with a trial of intravenous (iv) antibiotics with an aim to switch to oral alternatives. attention must be given to cases with an appendicolith present, or in cases where there is disease extension outside of the right iliac fossa. such cases have a - % failure rate and may constitute a longer than necessary hospital stay. this risk must be assessed against or availability. patients with complicated appendicitis should be treated with iv antibiotics followed by an oral switch. depending on the patient's clinical status, defined abscesses should be drained percutaneously or operated on. in cases where non-surgical management fails, surgery must be performed urgently [ ] . management of diseases of the biliary tree remain mostly unchanged. pain control is crucial in cholelithiasis and chronic cholecystitis. an elective cholecystectomy should be performed at a later stage. in cases of refractory pain, an emergency laparoscopic cholecystectomy should be performed. this is also true for acute cholecystitis cases; if the patient is fit and there is an emergency theatre available, they should be operated on in an attempt to minimise hospital stay. if there is limited operating room availability or the patient is not fit for a laparoscopic operation, then treatment should be with iv antibiotics. in cases where iv antibiotics have failed, a cholecystostomy may be performed. patients with choledocholithiasis who fail to pass their stone should undergo an endoscopic retrograde cholangio-pancreatography (ercp) with sphincterotomy. an elective cholecystectomy should be performed at a later stage [ ] . uncomplicated diverticulitis management remains unchanged ie. iv antibiotics followed by an oral switch. hinchey grade and cases should undergo percutaneous drainage as well as receive antibiotic treatment. hinchey and classifications should undergo a laparotomy with bowel resection and primary anastomosis or colostomy formation, as appropriate [ ] . transplant surgery covid- is having a significant impact on organ donation services world-wide. as the pandemic evolves, the transplant community faces various challenges, from allocation of resources and consenting patients, to optimizing immunosuppressive medication in patients with suspected covid- infections [ ] . currently, there is a limited amount of data to draw firm conclusions on the effect of covid- on organ transplantation. however, the immunosuppressive agents used may pose an increased risk of developing severe infections, placing these patients in an extremely vulnerable category. in the uk, transplant patients have been advised to stay at home and avoid face to face contact for weeks. additionally, transplant units should take measures to reduce the need for hospital attendance in these vulnerable patients by postponing nonurgent appointments or conducting them virtually as well as delivering immunosuppressive medication to a patient's home. it is important to note that levels of immunosuppression should be reviewed regularly. however, adjusting the level of immunosuppression should be undertaken with care as this could jeopardise the viability of the transplanted organ [ ] . guidance on acute transplantation during this pandemic is currently being developed and is adapting on a regular basis. transplant units are encouraged to take into account the availability of intensive care beds as this will affect feasibility and safety of undertaking organ transplantation. during the covid- outbreak, transplant decisions should be made on a case by case basis by balancing the risk of infection due to immunosuppression and hospital stay against the risk of organ failure. acutely however, recipients with an active infection or are recovering from an infection should not undergo transplantation. ultimately, if a unit has a significant number of covid- cases and has limited resources available, with a potential for negative impact on patient care, transplant services should be temporarily halted and reevaluated at regular intervals [ ] . alterations must be made to the consenting process during this pandemic with several additional factors needing to be taken into consideration when consenting patients for both living organ donation and solid organ transplantation. these include: • risk of transmission of sars-cov- from donor to recipient this should consider language barriers and disabilities to reduce the risk of miscommunication [ ] . local transplant services are taking drastic measures, making adaptations based on the resources available and the desires of donors and recipients. it is recommended that each centre should use their clinical judgement based on the circumstances of their individual centre. some kidney transplant centres have closed live donor programs due to the risk of patients contracting covid- and limited access to critical care beds, while others are conducting risk-benefit analyses on a case by case basis [ ] [ ] [ ] . there are a limited number of case reports relating to the effects of covid- on renal transplant patients [ ] [ ] [ ] [ ] [ ] . guillen et al [ ] report a case of a -year-old male who had undergone renal transplantation in . they expressed concern that sars-cov- may present in an atypical fashion in immunocompromised patients (diarrhoea, nausea and vomiting). there is also some discrepancy in the literature regarding the management of immunosuppression. zhu et al [ ] reported a case of a patient being successfully treated by initially stopping immunosuppressive medication followed by the introduction of a reduced regimen. similar findings were reported in two larger case series [ , ] . in contrast, wang et al [ ] successfully treated a patient without altering immunosuppressive therapy. a similar trend is seen in liver transplantation where clinicians should use their clinical judgement, taking into account resource availability in their respective centres. some centres in the uk are aiming to run a reduced service, accommodating those with severe disease (expected to die within the next months without transplantation or a united kingdom model for end-stage liver disease score > ) [ ] . decisions to perform heart and lung transplants should also be undertaken at a local level. routine surveillance such as biopsies and bronchoscopies should be postponed in patients who are more than months from transplantation, have not suffered previous episodes of rejection and are clinically stable. in heart transplant patients, it is recommended that non-invasive methods to assess rejection should be employed. such as gene expression profiling. for lung transplant patients, more emphasis should be placed on home spirometry data to be evaluated in virtual consultations. criteria should also be developed so that patients can notify the healthcare team if there is a significant decline in lung function [ ] . most patients who have undergone transplant surgery require immunosuppression to prevent graft rejection. however, this requires a careful balance as it can also result in an increased risk of developing covid- or severe complications. in suspected covid- cases, all other causes of symptoms such as fevers and cough should be excluded. this includes but is not limited to cytomegalovirus, pneumocystis, pneumonia and urinary sepsis. clinicians should also take into account atypical presentations of covid- and have a low threshold for testing. management is then categorised based on patients who do not require hospital admission, those who are unwell and admitted to hospital and patients who are progressively deteriorating and require ventilatory support (figure ) [ ] . cardiothoracic practice will be inevitably affected by covid- . in the uk and us all elective and non-urgent procedures have been postponed with resources being redirected to the emergency and urgent cardiothoracic service. furthermore, cardiothoracic surgeons possess generic skills which are mostly transferable to itu, making them prime candidates for redeployment. nhs england has issued guidance on management of cardiothoracic procedures based on the phase of the covid- pandemic [ ] . these phases include preparation, escalation, crisis (compensated and uncompensated), resolution, recovery and normal working ( table ). in summary, the elective cardiothoracic surgery service will be greatly reduced throughout the pandemic. surgeons are encouraged to use telephone and video conferencing to limit face-to-face appointments and to delay non-urgent referrals and follow ups. cardiothoracic surgeons can greatly support the itu service and attempts should be made to make senior staff available for redeployment [ ] . the vascular society of great britain and ireland have issued guidance for clinicians on the impact of covid- on vascular surgery services [ ] . these include general principles, outpatient appointments, elective and emergency vascular surgery, alongside trainee advice. regarding outpatients, only urgent cases should be seen, and virtual clinics considered. regarding surgical procedures, most arterial surgery is either classified as urgent or emergency and should therefore continue where possible. elective procedures, venous surgery, and asymptomatic conditions requiring intervention should be deferred. nhs england have classed acute & critical limb ischaemia, symptomatic aortic aneurysm & dissection and unstable carotid plaques as all still being emergency procedures and essential but the threshold for abdominal aortic aneurysm (aaa) should be weighed against the risk of rupture [ ] . where possible, ruptured aaas should be treated via endovascular aneurysm repair (evar) to reduce dependency on high dependency units (hdu). in patients with critical leg ischaemia or diabetic foot, urgent intervention is required in those with an immediately threatened leg(s), including an interventional radiological approach or amputation (as opposed to debridement). the american college of surgeons have similarly provided guidelines for the triage of vascular surgery patients (table ) [ ] . ahmed et al [ ] categorise urological surgeries into: oncological, emergency and benign and offer suggestions for prioritisation. these include the recommendation for liberal usage of local anaesthesia and day-case surgery wherever possible to minimise the impact on both resource usage and workforce shortages with anaesthesists being redeployed. furthermore, they suggested the setting up of parallel urological services with 'cold' hospitals dealing with oncological and emergency work and 'hot' hospitals operating on suspected covid- patients. additionally, whilst the extent of urinary viral shedding is not yet fully understood, there is some early evidence that sars-cov- viral rna is detectable in urine suggesting precautions must still be undertaken in urological services [ ] . moreover, there is some evidence that sars-cov- especially targets the cells of the urinary tract as they strongly express angiotensin-converting enzyme receptors -a known method of entry into the human host [ ] . this is one possible explanation for the recorded rates of acute kidney injuries in patients with covid- . additionally, sighinolfi et al [ ] warn urologists to consider covid- as a differential diagnosis in urosepsis as many of the symptoms (namely fever, leukopenia, tachycardia and tachypnoea) overlap. when prioritising patients, oncological surgeries must be a key priority. this is a major part of urological services with prostate cancer accounting for . % of all cancers [ ] , and recommendations are presented in table to be used in conjunction with guidelines issued by the eau guidelines office [ ] . due to the complex considerations that must be taken into account for these patients, a robust multidisciplinary team, consisting of urologists, oncologists, urological-specialist radiologists, anaesthetists and infectious disease clinicians, must be utilised for surgical prioritisation [ ] . the majority of benign surgeries may be delayed and where they should be prioritised, this is highlighted in table . principles for urological surgery during the covid- outbreak include as previously described in part , including the use of telephone triage and self-isolation prior to admission. simonato et al [ ] advise avoiding laparoscopy/robotic surgery where possible and where surgery is unavoidable, it should be performed only by experienced urological surgeons to decrease the risk of postoperative complications as well as reduce or time. additionally, they advise that enhanced recovery after surgery (eras) programmes be used to reduce length of stay in hospital as well as to reduce complications and admissions to already overstretched critical care units. furthermore, they advise regular correspondence with patients' relatives and to discharge patients who require catheters with video or photographic tutorials for catheter management in addition to virtual follow-up clinics. whilst there have been no publication of guidelines by any professional association for the management of stone surgery during the covid- pandemic, there have been some guidance published by proietti et al [ ] suggesting telephone triage of patients followed by prioritisation based on stone size and location, the presence of any obstructive uropathy, patient symptoms, presence of any stents or nephrostomy tubes and any other complicating factors such as renal failure or a solitary kidney. additionally, desouky [ ] suggests that despite reports in the media, nonsteroidal anti-inflammatory drugs (nsaids) should continue to be used as analgesia and as treatment for renal colic due to high effectiveness. similar considerations for prioritisation of surgery must also be undertaken for patients due to undergo robotic surgery. the eau robotic urology section have issued guidelines for both rationalisation and alterations to operative technique, with the aim of maximising protection for healthcare workers and minimising collateral damage to patients requiring treatment for non-covid- conditions [ ] . they also recommend that operations only be undertaken by the most experienced operators and that the minimum amount of staff necessary should be present in the or with all unnecessary personnel excluded (including fellows and students). there are specific recommendations for the prioritised ophthalmic operations (table ). when possible and safe, these operations should be performed as day cases. the surgical procedure with the less postoperative follow-up visits and the faster recovery period should be chosen. local anaesthetic is also preferred to general anaesthesia wherever possible [ ] . despite the cancellation of ophthalmic operations and outpatient clinics, all patients should be contacted to address any concerns they may have and to be given appropriate advice regarding management and awareness of red flag symptoms. patients should be stratified as low, medium or high risk and contacted by letter, by telephone, by through virtual clinics or remain face to face, depending on the severity and resources available in the eye department [ ] . moorfields eye hospital have also published guidance on ophthalmological risk stratification and implementation [ , ] . in order to further reduce the risk of acquiring covid- infection, patients should spend as little time in the department, and come into contact with as few patients and staff, as possible. necessary actions include reducing the number of anti-vegf injections per outpatients list and preference given to longer acting anti-vegf injections; no clinical review for ongoing anti-vegf injections; and stagger arrival times so that they do not occur at the same time. moreover, it is recommended that not all ophthalmology staff should be present. instead, staff could be reorganised into two teams, taking turns every two weeks. the team working from home should be on stand-by and be prepared to cover for any sick colleague from the active team. only senior-level clinicians capable of making decisions should see patients, and any administrative work should be undertaken from home where possible [ ] . the use of ppe in ophthalmology should follow local governmental recommendations. other specific recommendations are that surgical masks can be worn for multiple patients examined under the slit lamp, and that slit lamps can be modified with plastic breath shields to prevent droplet transmission of the virus. following these recommendations, reused masks should not be taken off between patients and there should be no contact between the mask and hands or clothes, to avoid contamination. it is also important to disinfect the plastic breath shields with alcohol before and after every consultation [ ] . plans for urgent elective cases should be made prior to surgery; neurosurgical teams should see if these plans can be delivered without access to icu. day case surgery and short length stay as routine are encouraged i.e. single night stay. critical care beds should only be reserved for patients who may require invasive monitoring or ventilatory support. for emergencies, the threshold for usual acceptance may change. due to the current situation, decision making will be challenging, hence ultimate decision should be shared by at least attendings, and multi-disciplinary teams should comprise of senior members only [ ] . the british neuro-oncology society offers suggestions for prioritisation of neuro-oncology (table ) . for outpatient referrals, only mri confirmed malignant brain tumour patients should be seen. for any mri confirmed non-malignant brain tumours, referral bodies should be followed up for confirmation. elective surgery for non-malignant brain tumour patients who are asymptomatic should be postponed. contact must be minimised during consultations. furthermore, chemotherapy and radiotherapy must be minimised and triaged for those who are most likely to benefit. if standard treatment is not offered, reasons must be outlined in the records [ ] . neuro-oncological treatment for glioma patients young adult patients with high grade malignant glioma should undergo maximal safe glioma resection; carmustine (bcnu) wafer may be used safely with no risks of contamination. radiological investigations alone should be used to generate treatment plans for the elderly and for patients with comorbidities [ ] . for low grade glioma patients, the bnos suggests a delay of - months [ ] . mohile et al [ ] suggested that only chemotherapy regimens which increase the interval between doses should be considered for patients with idh-wildtype gliomas, and the use of cytotoxic chemotherapy, immunotherapy and other tumour treatments should be evaluated against the potential risks of infection and immunosuppression. for patients with grade and grade idh-mutated gliomas, a similar decision-making plan to idh-wildtype patients may be followed and p/ q co-deletion glioma patients should delay therapy. mgmt methylated glioma patients may benefit from standard radiotherapy and chemotherapy courses hence temozolomide and radiation should be considered. on the other hand, mgmt unmethylated glioma patients are unlikely to benefit from temozolomide hence shorter radiotherapy courses with the aim of avoiding adjuvant and/or concurrent chemotherapy may be optimal for these cases [ ] . strict ppe must be followed by technicians involved in the care of patients undergoing chemotherapy and radiotherapy and toxicity tests should be done at the longest safe interval to reduce patient risks of covid- infections. cancer treatment must be stopped until recovery for any patients who test positive for covid- and treatment risk-benefit ratio should be evaluated for these patients. all malignant brain tumour patients should be followed up, preferably via remote tele-consultation at the surgeon's discretion. the following are adapted from guidelines published by the bnvg/sbns for the neurosurgical management of neurovascular conditions during the covid- epidemic [ ] . cta should be performed prior to transfer to neurosurgery, if possible. if no aneurysm is found and the patient has perimesencephalic sah, then an attending neuroradiologist should confirm perimesencephalic pattern and negative cta. it is encouraged to not transfer these patients or perform dsa. if no aneurysm is found and the patient has non-perimesencephalic sah, then good cta quality needs to be confirmed, which should be repeated if inadequate. an attending neuroradiologist should confirm the absence of an aneurysm and the adequacy of cta. a dsa should be done to address any concerns. otherwise, it is reasonable to repeat a cta at week locally. if an aneurysm is found: • world federation of neurological surgeons (wfns) grading score - : current provided guidelines should still be followed for transfer and treatment. • wfns - : neurosurgical treatment will still be beneficial for low grade patients. patients with poor prognostic factors are likely to undergo conservative treatment at their local hospital. • aneurysmal clot: this should be treated at the discretion of a senior neurosurgeon, although a higher treatment threshold may be followed. transfer patients to emergency surgery if they present with ich causing mass effect. those with ich but absent mass effect should undergo cta/mra: urgent treatment should be provided for ruptured or symptomatic cases from cortical venous reflux, and with regards to spinal fistulas, only cases with rapid neurological deterioration should be treated. treatments for unruptured aneurysms (also including giant aneurysm) should be postponed, unless there is cranial nerve iii palsy. all avms and davfs treatments should also be postponed. guidelines have been published by nhs england and nhs improvement for the management of neurotrauma patients during the covid- epidemic [ ] . categories to consider for neurotrauma patients include: national and local head injury guidelines should still be followed for these patients (fig ) [ , ] . treatment for emergency patients should be expedited. an anaesthetic guideline for covid- positive patients is required. contingency plans should be made for supply chain issues. this includes patients with easily reversible conditions e.g. extra-axial haematoma (extradural/subdural) with mass/clinical effect. during times of very limited care, withdrawal of treatment may occur earlier after decisions of futility are made for patients with brain injuries which are considered to be unsurvivable. overall, most neurosurgical spine and head procedures are safe to perform with strict ppe. if possible, pcr testing for covid- should be done for suspected patients prior to treatment. cranial and spinal drilling should be performed with slower speeds and more thorough irrigations of stationary drills should be done to reduce bone skull aerosol [ , ] . furthermore, to prevent blood splashing in a negative pressure operating room, surgeries should be performed as gently as possible [ ] . in addition, endonasal procedures should be avoided as they produce significant droplet aerosol; in wuhan, despite the use of n masks, ent surgeons were the worst affected by bone aerosol [ ] . oral and maxillofacial surgery nhs england and nhs improvement have published guidelines for the treatment of acute omfs and trauma patients (table ) [ ] . they suggest that senior members of the team should make decisions regarding patient care at the first point of contact with the patient, thus ensuring that unnecessary admissions are avoided, and nosocomial infections are minimised. additionally, a suggested model is that admission from the emergency room be directed to omfs clinics before any examination or treatment which is a divergence from normal practice where initial treatment is started by emergency physicians. in addition to this, they suggested the organisation of a temporary 'clean' minor operating theatre and dressings clinic within a triage clinic room to provide immediate services such as suturing of wounds and lacerations, abscess drainage and any urgent procedures that can be performed under local anaesthesia. non-operative care should be considered for patients with injuries which can be managed conservatively (this includes condylar fractures). for patients requiring surgical treatment, including mandibular and midfacial fracture patients and for cases involving cervicofacial infections, teams should work towards expediting the pre-operative and operative care. to reduce post-operative stay, elective rehabilitation services are suggested. the british association of head & neck oncologists (bahno) have also published guidelines for head and neck cancer management during the covid- epidemic [ ] . all non-malignant cancer treatments should be postponed, and tele-consultations should be done to assess the severity of any referrals of unclear urgency. priority should be given to malignant cancer patients and to those are older than years of age with/without comorbidities. ppe must be strictly followed during consultations and diagnostics work up should be kept to the minimum required to make informed and safe treatment plans. for any nasal endoscopy procedures, as per the advice of ent uk, aerosol generating procedure (agp) level of protection must be followed; theatre clothes and full ppe should be worn and endoscopy should be carried by remote video monitoring instead of eyepiece [ ] . with regards to surgical cancer treatment, it is encouraged to postpone surgical procedures which require itu admission at the discretion of senior surgeons. furthermore, day case surgeries should be prioritised, and their length reduced, if possible. with regards to nonsurgical cancer treatment, palliative chemotherapy should be delayed in asymptomatic patients. all patients should be followed up by telephone. however, it is suggested to minimise patient contact by delaying clinic appointments by the longest interval possible at the discretion of the senior surgeons. furthermore, caprioglio et al [ ] offer recommendations for the management of orthodontic emergencies which involve assessment of the patient over telemedicine devices then advising the patient step by step for self-management. although fever, cough and shortness of breath are commonly advertised as the symptoms suggestive of covid- , numerous reports emerged to reveal anosmia, an ent presentation, as a symptom of covid- and in some cases was present as an isolated symptom. hence, it was recommended that patients presenting with anosmia should be treated as a suspected case of covid- and healthcare workers should don ppe before making contact [ ] . ent surgeons were identified to be among those at an increased risk of contracting covid- from their patients due to working for prolonged periods of time in close proximity to their patients' faces as well as due to the presence of several aerosol-generating procedures (agps) in ent. the first hospital doctor fatality during this epidemic was an otolaryngologist and this highlights the risks faced by ent doctors [ ] . ent uk has generated a list of procedures that they consider to be agps. examination of the upper aerodigestive tract can be considered as an agp, especially if it triggers coughing, sneezing or pharyngeal reflexes, as well as operative procedures on the aerodigestive tract. it is recommended that all agps (e.g. nasal endoscopy, nasal cautery, foreign body removal, biopsies, tracheostomy tube changes and emergency care provided for acute tonsillitis, quinsy and epistaxis etc.) are carried out wearing full ppe, including ffp respirator, which could be substituted with ffp or n respirator in cases of unavailability of ffp respirator. it has also been recommended that all otolaryngeal examinations and operative procedures that are unnecessary are avoided [ ] . guidelines for the acute surgical care of quinsy, acute tonsillitis and epistaxis have been revised to minimise the risk posed to ent surgeons whilst providing uncompromising patient care. for example, revised guidelines recommend treating quinsy on history alone where possible, reserving oral examination for severe cases; it also recommends betadine gargles in the management of quinsy, reserving drainage for severe cases [ ] . tracheostomy guidelines have also been revised due to an anticipated increase in requests to perform tracheostomies on suspected or confirmed covid patients as well as due to tracheostomy being an agp which poses a considerable risk to the operator [ ] . additionally, rokade et al [ ] has described the innovative use of microscope drape in endoscopic sinus surgery while hellier et al [ ] has described the novel use of microscope drape in mastoidectomy, in both cases to reduce aerosolization in these operative procedures which are considered to be agps. suggestions for prioritisation are given in table . the british association of plastic surgery (bapras) and nhs england has provided advice to its members to help aid the management of plastic surgery patients during covid- (table ). the association has provided a plastic and reconstructive surgery escalation policy [ ] . this provides hospitals with recommendations on how to cope with an increase in covid- prevalence. with high prevalence, emergency surgery should be limited, and all elective surgery should be stopped. all emergency injuries should be triaged to outpatient clinics and minor operations should be performed in outpatient clinics. for the management of burns, breast reconstruction and melanoma specific guidelines have been formulated and to cope with the expected drastic reduction of clinical and surgical facilities advice has been created to guide local services. for patients with a suspected melanoma diagnosis, a referral letter is still required, which will be reviewed at a multidisciplinary team (mdt). the advice will be given on the basis of the photograph. the patient may then be sent directly for surgery to remove the lesion and phoned with the results once the pathology has been analysed [ , ] . nhs england have also set out specific guidelines for the management of burn injuries during the covid- epidemic [ ] . the recommendation guidelines for the management of patients with burns includes considering the burn patient into four categories. firstly, obligatory inpatients are those with large burns that will need continued admission and surgical management. however, treatment must be expedited to avoid pre-operation delay and minimize the length of stay. secondly, non-operative patients are those that can be reasonably managed without an operation. during the epidemic it is vital to consider non-operative care for burns to avoid unnecessary admissions. thirdly, day-case patients are those that can be undertaken for a large number of conditions. lastly, first contact and clinics patients are the outpatient attendances that should be kept to the safe minimum. the guidelines highly support non operative care to reduce the inpatient and operative burden on the nhs. many burn related procedures can be considered as day cases and should be considered. to avoid unnecessary admissions, senior presence is vital for the management of burn patients and will help reduce the ed workload as a whole, so the ed can focus on other medical patients. for facial plastic surgery, bapras have adopted the baoms guidance with their four main recommendations of ppe (full ppe including ffp mask for face to face exams and treatment), avoid (clinics, contact, transfer and surgery), restrict (visits, generation of aerosols and staff numbers) and abbreviate (time waiting in rooms and treatment) [ ] for breast reconstruction, the american society of plastic surgery has provided guidelines to manage breast reconstruction during covid- . all delayed breast reconstruction, planned secondary or revision breast reconstruction procedures should be postponed. for those patients who were considering immediate reconstruction, the society has advised plastic surgeons to err on the side of caution and delay reconstruction due to the potential risks and complications that may occur postoperatively. the decision to delay should take into account the age and comorbidities of the specific patient and the local-regional and individual institutional factors [ , ] . the american college of surgeons states that the principle of paediatric surgery during the covid- pandemic is to provide appropriate surgical care to children with urgent surgical issues (table ) while utilising patient care resources effectively in addition to protecting healthcare workers. non-urgent surgery should only be performed if necessary to avoid prolonged hospitalisation or further hospital readmissions [ ] . nhs england has also made a further recommendation to continue with elective paediatric surgeries only if patients are asa grade , with the exception of cancer cases [ , ] . paediatric surgical services should focus on the effective management of emergency cases with any elective procedures being postponed wherever possible. this will allow for better access to theatres and increase in the staff capacity, with the aims of decreasing the preoperative period and ensuring an early discharge. the paediatric surgical team should ensure continuous management of urgent surgical cases while minimising the risk of transmission of infection. such strategies could include the reorganisation into two groups, one that is active within hospitals, and one that works remotely in isolation, and the use of telemedicine. whenever possible and safe, the presence of parents during surgery should be considered [ ] . there is emerging evidence that paediatric patients suffer complications from preventable conditions due to late access to medical care. in response to this evidence, the royal college of paediatrics and child health has emphasised the importance of acute paediatric services and primary care forming agreed pathways for acute paediatric diseases. they also emphasised the importance of primary care workers having accessible and immediate advice from attendings in hospital and community-based paediatrics, to ensure prompt diagnosis and management [ ] . due to covid- , all surgical specialties have had to limit their surgical practices and rationalize the surgeries which are performed. selection of patients for urgent surgery during the pandemic is vitally important to ensure patients have postoperative reserves to combat any possibility of later being infected with covid- . surgeons from all specialties have been asked to consider non-surgical treatment where safe and possible to avoid unnecessary hospital admissions and to avoid patient harm. all surgery specialists have been asked to limit their follow up to telephone and video where possible. the delivery of emergency surgery during covid has become difficult due to a reduced workforce and hospital supplies. for example, all surgical specialties must carefully consider the need for postoperative supplements including blood transfusions. surgical consent has been tailored to minimize person to person contact, with written and online documentation being utilized where possible. due to evolving circumstances, guidelines for preoperative evaluation, intraoperative and postoperative management are subject to constant change. it is therefore advised to follow national guidelines to ensure the latest recommendations are implemented across centres. all surgical specialties have been affected by the covid- pandemic. all specialties have had to triage the urgency of their daily surgical procedures and consider non-surgical management options where possible. surgeons are having to adapt to new guidelines among covid- to continue to provide vital emergency surgery within their specialty. with guidelines specific to each specialty being implemented and followed, surgeons should be able to continue to provide safe and effective care to their patients during the covid- pandemic. • supratentorial symptomatic brain metastases. • hydrocephalus patients with rare brain tumours -suggestions of using endoscopic third ventriculostomy or ventriculoperitoneal shunt to delay surgery (except for germ cell tumours and pineoblastoma). • patients with low grade glioma who can reasonably be monitored with mri -a -month interval scan should be added to ensure no tumour progression in cases delayed by - months. • tumours of skull base in patients with minimal symptoms. • for high grade glioma patients, it has been suggested to consider reducing the course and fraction of radiotherapy and chemotherapy if there is no significant worse prognosis. oral therapy regimens are preferred, if possible, instead of iv administration. • for mgmt unmethylated glioblastoma patients, chemotherapy may be excluded; monitor patients for any deterioration. • whole brain radiotherapy patients. • stereotactic radiosurgery patients with brain metastasis. • patients with radiotherapy for other rare malignant tumours including anaplastic astrocytoma, pineoblastoma and primitive neuroectodermal tumour. • radiotherapy and chemotherapy patients with low grade glioma who can safely be monitored for an initial period. • patients with atypical meningioma or recurrent meningioma receiving radiotherapy. world health organization declares global emergency: a review of the novel coronavirus (covid- ) covid- and italy: what next? eau guidelines office rapid reaction group, an organisation-wide collaborative effort to adapt the eau guidelines recommendations to the covid- era management of cancer surgery cases during the covid- pandemic: considerations clinical guide for the management of noncoronavirus patients requiring acute treatment: cancer clinical guide for the management of cardiothoracic surgery patients during the coronavirus pandemic american college of surgeons, covid- guidelines for triage of breast cancer patients the treatment proposal for the patients with breast diseases in the central epidemic area of coronavirus disease urgent intercollegiate general surgery guidance on covid- american college of surgeons, covid- guidelines for triage of colorectal cancer patients several suggestion of operation for colorectal cancer under the outbreak of corona virus disease in china american college of surgeons, covid- guidelines for triage of thoracic cancer patients american college of surgeons committee on trauma, maintaining trauma center access & care during the covid- pandemic: guidance document for trauma medical directors clinical guide for the management of trauma and orthopaedic patients during the coronavirus pandemic management of patients with urgent orthopaedic conditions and trauma during the coronavirus pandemic royal college of surgeons in ireland, royal college of surgeons of edinburgh, royal college of physicians and surgeons of glasgow, clinical guide to surgical prioritisation during the coronavirus pandemic covid- pandemic: perspectives on an unfolding crisis: covid- pandemic: perspectives on an unfolding crisis american college of surgeons, covid- guidelines for triage of emergency general surgery patients covid- outbreak in northern italy: viewpoint of the milan area surgical community emergency preparedness, resilience and response guidance for uk hospital transfusion teams clinical guide for the management of general surgical patients during the coronavirus pandemic highly ace expression in pancreas may cause pancreas damage after sars-cov- infection organ donation during the coronavirus pandemic: an evolving saga in uncharted waters covid- : information for transplant professionals transplant society guidance for clinicians on consent for solid organ transplantation in adults and living organ donation in the context of the covid- pandemic covid- ) guidance for patients with kidney disease the renal association, covid- : challenges for renal services bulletin number : organ and tissue donation and transplantation directorate case report of covid- in a kidney transplant recipient: does immunosuppression alter the clinical presentation? successful recovery of covid- pneumonia in a renal transplant recipient with long-term immunosuppression covid- in a kidney transplant patient identification of kidney transplant recipients with coronavirus disease coronavirus disease pneumonia in immunosuppressed renal transplant recipients: a summary of confirmed cases in guidance for cardiothoracic transplant and ventricular assist device centers regarding the sars cov- pandemic guidance on the management of transplant recipients diagnosed with or suspected of having covid triage considerations for patients referred for structural heart disease intervention during the coronavirus disease (covid- ) pandemic: an acc /scai consensus statement covid- virus and vascular surgery clinical guide for the management of vascular surgery patients during the coronavirus pandemic american college of surgeons, covid- guidelines for triage of vascular surgery patients global challenges to urology practice during covid- pandemic persistence and clearance of viral rna in novel coronavirus disease rehabilitation patients single-cell rna-seq data analysis on the receptor ace expression reveals the potential risk of different human organs vulnerable to -ncov infection covid- : importance of the awareness of clinical syndrome by urologists global cancer statistics : globocan estimates of incidence and mortality worldwide for cancers in countries covid- and urology: a comprehensive review of the literature network (run), pathways for urology patients during the covid- pandemic endourological stone management in the era of the covid- urology in the era of covid- : mass casualty triage eau robotic urology section (erus) guidelines during covid- emergency recommendations for tiered stratification of urologic surgery urgency in the covid- era triaging office-based urologic procedures during the covid- pandemic considerations in the triage of urologic surgeries during the covid- how to prioritize urological surgeries during epidemics: lessons learned from the toronto sars outbreak in the royal college of ophthalmologists, glaucoma management plans during covid- the royal college of ophthalmologists, management of ophthalmology services during the covid pandemic the royal college of ophthalmologists, management plans for children and young people with eye and vision conditions during covid- ophthalmological risk stratification & implementation guidance moorfields risk stratification for paediatric ophthalmology the royal college of ophthalmologists, protecting patients, protecting staff the royal college of ophthalmologists, ppe and staff protection requirements for ophthalmology sbns covid- bulletin # covid- treatment pathways and guidance sbns guide for the neurosurgical management of neurovascular conditions during the covid- pandemic clinical guide for the management of neurotrauma patients during the coronavirus pandemic clinical guideline [cg ], national institute for health and care excellence (nice) preliminary recommendations for surgical practice of neurosurgery department in the central epidemic area of coronavirus infection experiences of practicing surgical neuro-oncology during the covid- pandemic precautions for endoscopic transnasal skull base surgery during the covid- clinical guide for the management of patients requiring oral and maxillofacial surgery during the coronavirus pandemic maxillofacial trauma management during covid- : multidisciplinary recommendations approaches to the management of patients in oral and maxillofacial surgery during covid- pandemic british association of head and neck oncologists, bahno statement on covid- management of orthodontic emergencies during -ncov anosmia as a potential marker of covid- infection -an update practical aspects of otolaryngologic clinical services during the novel coronavirus epidemic: an experience in hong kong guidelines for changes in ent during covid- pandemic adult tonsillitis & quinsy guidelines bla covid- tracheostomy guidelines ioannidis, fess in the covid era: the microscope drape method to reduce aerosolization mastoidectomy in the covid era -the microscope drape method to reduce aerosolization clinical guide for the management of patients requiring plastic treatment during the coronavirus pandemic advice for managing melanoma patients during coronavirus pandemic clinical guide for the management of acute burns patients during the coronavirus pandemic asps statement on breast reconstruction in the face of covid- pandemic developing a virtual fracture clinic for hand and wrist injuries british society for surgery of the hand, covid- resources for members american college of surgeons, covid- guidelines for triage of pediatric surgery patients clinical guide for the management of paediatric patients during the coronavirus pandemic clinical guide for the management of paediatric critical care patients during the coronavirus pandemic british association of paediatric surgeons, covid- information for paediatric surgeons delayed access to care for children during covid- : our role as paediatricians -position statement the following additional information is required for submission. please note that failure to respond to these questions/statements will mean your submission will be returned. if you have nothing to declare in any of these categories, then this should be stated. please enter the name of the registry, the hyperlink to the registration and the unique identifying number of the study. you can register your research at http://www.researchregistry.com to obtain your uin if you have not already registered your study. this is mandatory for human studies only. . name of the registry: n/a . unique identifying number or registration id: . hyperlink to your specific registration (must be publicly accessible and will be checked): please specify the contribution of each author to the paper, e.g. study design, data collections, data analysis, writing. others, who have contributed in other ways should be listed as contributors. the guarantor is the one or more people who accept full responsibility for the work and/or the conduct of the study, had access to the data, and controlled the decision to publish. please note that providing a guarantor is compulsory.corresponding author: ahmed al-jabir senior author: riaz agha key: cord- -s qthxx authors: aven, terje; zio, enrico title: globalization and global risk: how risk analysis needs to be enhanced to be effective in confronting current threats date: - - journal: reliab eng syst saf doi: . /j.ress. . sha: doc_id: cord_uid: s qthxx in the last - years, technological innovation has enabled the advancement of industry at a global scale, giving rise to a truly global society, resting on an interdependent web of transnational technical, economic and social systems. these systems are exposed to scenarios of cascading outbreaks, whose impacts can ripple to very large scales through their strong interdependencies, as recently shown by the pandemic spreading of the coronavirus. considerable work has been conducted in recent years to develop frameworks to support the assessment, communication, management and governance of this type of risk, building on concepts like systemic risks, complexity theory, deep uncertainties, resilience engineering, adaptive management and black swans. yet contemporary risk analysis struggles to provide authoritative societal guidance for adequately handling these types of risks, as clearly illustrated by the coronavirus case. in this paper, we reflect on this situation. we aim to identify critical challenges in current frameworks of risk assessment and management and point to ways to strengthen these, to be better able to confront threats like the coronavirus in the future. a set of principles and theses are established, which have the potential to support a common foundation for the many different scientific perspectives and ‘schools’ currently dealing with risk handling issues. currently the world is suffering as a result of the coronavirus, which among other catastrophic consequences has also led to the implementation of different forms of social isolation as measures of mitigation. this is affecting directly the fundamental element exposed to the health risk, which is also the principal actor in the globalized industrial, economic and social world: people. as a result of people's isolation, many industrial, social and cultural systems have suspended or significantly reduced their production and services, with future effects still to be seen. the coronavirus case demonstrates that the development of disastrous events has dramatically changed during recent years, because of globalization, pushed by technological innovation and strong industrialization. our society now relies on an interdependent web of transnational technical, economic and social systems, which has allowed the massive and wide transportation and distribution of people, materials, products, services, for an unprecedented improvement of welfare in most regions of the world. at the same time, however, the interconnected systems are inevitably exposed to potential scenarios of cascading outbreaks, whose effects can ripple to very large scales through their strong interdependencies. the vulnerabilities are massive and disturbing. the underlying systems have complex features, interactions among the system elements lead to complex dynamics, and surprises occur (turner and pidgeon , meadows , helbing , mcdaniel and driebe . classical risk assessments do not work in these situations, as a potential disaster in such complex systems cannot be foreseen by looking at the chain of events that may occur (leveson ) . the global financial crisis of a few years ago is an example: one bank, lehman brothers, filed for bankruptcy in (mishkin ) , with losses that extended far beyond its own financial value or its thousands of employees who lost their jobs; the effects rippled throughout the global financial system, bringing it to its knees and spreading to other major sectors like the car industry. the main lifeline systems today are all tightly connected in large and intricate networks of dependency and with interdependent links to other sectors and across national borders. with respect to the above , a major issue for risk analysts and managers is how to deal with hazards and threats with a potential for extreme consequences and large uncertainties. we know that in these cases, accurate predictions of what is coming cannot be made and, in fact, the coronavirus case has shown that the world's risk management and governance systems are not working as intended. we have not been effective in protecting people from this virus. as risk scientists, it is necessary to reflect on thisis the reason mainly about unfortunate circumstances or poor risk handling by authorities and agencies? do we, as a risk science community, also bear a responsibility for this failure? have we provided the proper concepts, principles, approaches, methods and models for adequately assessing, communicating, managing and governing the risk? in recent years, various perspectives and approaches have been proposed in the literature, to try to meet the challenges of assessing and handling risk in relation to such extreme situations and complex systems. these perspectives and approaches, which to a large extent can be viewed as scientific schools, include what we will refer to as 'safety science' (highlighting sociotechnical aspects, complexity theory, and resilience analysis), 'risk governance and systemic risk frameworks', 'post-normal science', quality management and 'risk science' (highlighting 'broad' perspectives on risk with an emphasis on uncertainties, knowledge and potential surprises (black swans)). these perspectives and approaches all produce knowledge relevant to the proper assessment, communication and handling of risks subject to large uncertainties. but is the message the same? is the separation between these schoolsas reflected by differences in scientific pillars and preferred journals, conferences, societies, etc. -hampering the development of authoritative guidance to help policy-makers, managers and decisionmakers to properly assess, communicate and handle risk? is there a potential for joining forces, to build a new generation of risk, safety and resilience frameworks for the benefit of society and us all? the present paper discusses all these issues, motivated by the pandemic outbreak that the whole world is experiencing and the consequences that it is suffering because of the coronavirus, covid- . the main aim of the paper is to provide new reflections and knowledge on the proper assessment and handling of risk of the types addressed above, by critically reviewing current perspectives and approaches, and pointing to areas with the potential for enhancements, so that we can be better able to confront global, highly uncertain and large consequence threats like the coronavirus in the future. a key topic discussed is the tension between using scientific methods and models, on the one hand, and applying the precautionary principle, on the other, as we have seen also in the context of the scientific and political debates for the coronavirus. in fact, in relation to the coronavirus case, politicians have to a large extent referred to the precautionary principle (and still are), to justify the implementation of many specific measures. in this respect, we seek to bring new insights about this principle and associated ideas of risk handling, by relating it to the particular case of the global risk of coronavirus and the perspectives of the different scientific schools of risk assessment, management and governance mentioned above. the reminder of this paper is structured in the following way. first, in section , we discuss the general issues involved in preparing for and managing disasters. then, in section , we describe the coronavirus case from a risk assessment and management perspective, addressing relevant specific features and challenges. in section , we summarize and reflect on current perspectives and approaches (schools) for assessing and handling risks of this type, using the classification referred to above. from this basis, in section , we discuss what we can do to improve the way we assess, communicate and handle risks like those of the coronavirus type. finally, section provides some conclusions. in general terms, a disaster is any occurrence that causes damage, destruction, ecological disruption, loss of human life, human suffering, or the deterioration of health and health services on a scale sufficient to warrant an extraordinary response from outside the affected community or area (who, ) . such situations may include natural disasters, such as droughts, earthquakes, floods or storms, and epidemics; or industrial accidents, such as nuclear or chemical ones (lehtveer and hedenus , lidskog and sjödin , and xu et al . the former are addressed within the concept of disaster management (akgün et al ) , but studies of epidemic disaster management are quite rare, compared to those of earthquakes, floods and other disasters, and are mostly focused on predicting the impact of an epidemic if one were to start. the latter (industrial disasters) are typically dealt with by formalized frameworks of technical risk assessment and management, to inform decisions on the design and operation of adequate preventive and mitigative barriers. the physical setting in which disasters may occur has dramatically changed over recent years, because of globalization pushed by technological innovation and strong industrialization. new factors are driving the occurrence and the consequences of disasters, among which population density, urbanization, globalization and climate change are perhaps the most evident. these factors are proving catalysts for the acceleration of pandemic disasters. for example, climate change might play a role in the birth and transmission of specific diseases; the huge trend of urbanization of the world's population, along with the substantial growth in population itself, is a factor that can accelerate epidemic outbreaks into pandemic disasters, through social globalization. all this renders our socio-technical-economic systems vulnerable to a pandemic like the one we are facing today, and more difficult the risk management of disasters and crises in general. disaster management comprises, in general, a set of activities that are performed before, during and after a disaster, with the goal of preventing loss of human life, reducing the impact of the disaster on the economy and re-establishing a normal, or even improved, state of affairs (altay and green iii ) . disaster risk management seeks to identify and adopt adequate measures of prevention, mitigation, preparedness, emergency response and recovery (pettit and beresford ) . various studies have shown that risk management of disasters can save lives and offer relief to those hit by the disaster (pettit and beresford , akgün et al ) . the objectives of disaster preparedness for control and containment of an outbreak of an epidemic or pandemic relate, then, to reducing the rate at which vulnerable individuals become infected, reducing the mortality rate for those already infected and increasing the immunization capacity of the population. the preparation measures for control and containment must build the capabilities to launch quarantine programs over entire geographic regions, where possible. they must provide medical supplies and life commodities. they can be adopted both for prevention of the spread after the initiation of an infectious disease (pre-event measures) or for control and containment of a confirmed outbreak (post-event measures). in the former case, a predetermined amount of medical supplies should be kept in stock and ready to be used at the outbreak of the epidemic. for the specific case of the coronavirus, the european union (eu) has created a stockpile of medical equipment (such as ventilators and protective masks) to help eu countries fight the covid- pandemic. the stockpile includes medical items, such as intensive care medical equipment, for example ventilators, and personal protective equipment, such as reusable masks, and laboratory supplies; its current main aim is to help those eu states that face shortages of the equipment needed to treat infected patients and to protect health care workers (https://ec.europa.eu/commission/presscorner/detail/en/ip_ _ ). in general, the management of the risk of disasters, such as epidemic/pandemic outbreaks, calls for preparedness and a prompt response to control them. certain protocols should be prepared and, then, followed; supplies and human resources (medical and other personnel, particularly in the case of epidemics and pandemics) should be adequately prepared and effectively made available and utilized, for the containment effort to be successful. for example, if a smallpox attack happens, vaccination of the affected population should take place within four days, while, in the case of an anthrax outbreak, the distribution of antibiotics should take place within two days of the event (lee, ) . this calls for an emergency supply chain (sometimes also called a humanitarian supply chain) that is properly designed, managed and operated, to successfully handle the many logistics issues that arise. this entails that financial resource allocation, vital commodities' and medical supplies' stockpiling capacities and locations be optimized, based on an a priori risk assessment, and the logistics operations during emergency for their management transportation and distribution be carried out in conjunction with the available information on the evolution of the disaster, in order to contain its spread and hopefully keep it below critical proportions. governmental agencies and health institutions must be prepared in advance for the control and containment of disasters of epidemic outbreaks. to prepare, they must take risk-informed decisions on contingency plans to be set up so as to ensure the availability of emergency medical stocks and well-trained personnel, their appropriate deployment, and the availability of different types of vehicles for the transportation of essential medical supplies and commodities, etc. an evident common ground and connection exists between the technical risk assessment & management and the disaster management, stemming from the four stages that meet their purpose: prevention/mitigation, protection/preparation, response, and recovery. prevention/mitigation comprises all activities for avoiding the occurrence of the accident/disaster and reducing its probability. protection/preparation relates to all safety measures and activities that are designed and planned to be put into action when the accident/disaster occurs, in order to reduce its impact and minimize losses. response is obtained through the activities of emergency and crisis management implemented during the aftermath of the accident/disaster, to prevent additional damage and loss. finally, recovery is the phase of restoring the back-to-normal situation after the accident/disaster. the four stages of disaster management, thus, match those of resilience management (zio ) or business continuity zio , xing et al ) , typical of engineered systems and industrial companies, respectively. in spite of the importance of taking a risk-informed approach to disaster preparedness, and all the associated logistics operations for disaster control and containment, the scientific community has not yet produced well-established approaches that explicitly incorporate risk assessment as a systemic framework for holistically dealing with the problem of disaster preparedness. this paper is motivated by the pandemic outbreak that the whole world is experiencing because of the coronavirus, covid- . as of april , , . gmt, there are , confirmed cases of coronavirus globally. sadly, there have been , deaths. the current coronavirus pandemic has raised the importance of preparing for disasters, but, unfortunately, once again, only after the factonce the covid- epidemic outbreak in china had escalated to a global pandemic. and although some claim this event to be a black swan (a surprising, unforeseen extreme event), there are aspects that lead to a different perspective on the matter, which make it not surprising at all, in our globalized world, but actually very likely to occur in, say, a ten-year horizon, having in mind the rather high number of similar events in recent years. a set of characteristics defines the risk of global crises that we are exposed to, such as that due to the coronavirus outbreak, and these shape the way we address it. in the specific case of the current pandemic, the probability of and the risk related to the occurrence of the outbreak of such a crisis and of its severity have been judged too low in spite of clear evidence. large uncertainties and weak knowledge have partially caused this, leading to an insufficient level of preparedness in all countries and from all points of view: material, organizational, financial, political and cultural. what has not helped the preparedness is the individual and regionally collective "optimistic bias", which often determines the attitude to risk and the policy measures that follow. from the point of view of individual attitude, the optimistic bias leads people to ignore the risks: it is the superwoman/superman attitude of "it won't happen to me", in most cases supported by the illusion of having control over things. it has led some people to feel that they will avoid the covid- disease and, therefore, they can even ignore protective measures, including confinement (bako and zio ) . this is somewhat fed by certain erroneous, or incomplete at best, communication, e.g. that which fosters the belief that the virus is really only dangerous for old and sick people. communication should, instead, be clear on the fact that nobody can escape infection by the new coronavirus and that the physical reaction to the disease differs from individual to individual, as it is conditioned by a number of factors, mostly unknown. from the point of view of collective communities, it has again to a large extent been an "it won't happen to me" attitude, until it is suddenly revealed that the pandemic is real and there will be a high number of cases and also deaths in this region/country/area. another characteristic refers to the perception that people have of different risks. irrespective of whether there is more or less risk, tangible hazards like those arising from activities like car driving are perceived to be less severe than intangible hazards, like those related to epidemics or nuclear accidents. in the specific case of the coronavirus, the high speed at which it spreads makes it legitimate to feel worried and, so, legitimate questions arise: how does this novel pandemic compare to the "normal" or accepted risk of infectious death? what is the "worst case" scenario? should we panic and shun other people who may be carrying what might kill us? and, although it is rational to advocate that there is no need to become paranoid and fearful, but, on the contrary, there is a need to evaluate the risk and manage it scientifically, this is difficult to do in practice because:  the risk level depends on the characteristics of the virus, including how it spreads to people  a number of factors affect the behavior of the virus and of people, and all are highly uncertain because of lack of knowledge on the physics of the virus and uncertainty in the actions and reactions of people, at all levels  uncertainty affects the effectiveness of measures put in place to control the pandemic. so, the rational and logical approach to dealing with the risk of the occurring pandemic (as with any other risk, for that matter) is not to panic but to limit one's own personal and potential exposure and to minimize both the size and scale of the potentially exposed population. but the risk values produced to guide the decisions on how to do that cannot be exact, as they are based on weak and even potentially erroneous knowledge related to, for example, the spread of the virus and the actuation and respect of the measures implemented. and if risk were judged based on how it is perceived (also biased by "street" news and politics), then intangible hazards would receive the highest attention, as is the case for operating nuclear power plants and today's pandemic. so, professional risk numbers are not enough to deal with situations like the coronavirus crisis. policies crave to be science-based, but science does not have clear answers in cases like this, characterized by large uncertainties due to a weak knowledge base on the phenomenon and the factors involved. and the communication of the risk becomes difficult itself: how to explain what risk is in situations of large uncertainties and little knowledge? how can one say that it is small or large, relating it to uncertainties and knowledge? a risk professional may say that the risk is low (e.g. in the early phases of the outbreak), but the uncertainties are large: how can this be communicated, so that it is properly understood and used for decision making? in a case like this, when the stakes involved and uncertainties are so large, there are no alternatives but to give weight to the precautionary principle. the health experts have been crystal clear about the need for some type of societal lockdown, and politicians, faced with a potential for catastrophic events with thousands and even millions of deaths, have had no other choice than to follow the recommendations of the experts and even to take the precautionary measures some steps further. while trying to limit the spread and control of the pandemic, the healthcare systems have been pushed to the edge of their capacity. the expected economic and social costs are, however, enormous, and this brings strong pressure to lift the measures and reopen everything as soon as possible. in support to this, real-time tests are performed, and extensive research is conducted, to find ways of treating the patients and developing efficient vaccines against the virus, while some form of adaptive, learning-based risk management policy is applied in basically all countries (duffey and zio a and b). we imagine that we are confronted with the coronavirus pandemic, in its early stages of development. authorities must make decisions and take countermeasures to control the pandemic. these decisions and countermeasures imply public investments and can be restrictive for people's activities. the potential impacts of the pandemic are huge and the uncertainties are large concerning the actual evolution of the outbreak and its consequences, as well as the effects of the possible interventions. predictions on the scenarios of the evolution of the spread of the virus are highly desirable, but the influencing factors are many and the models of the phenomena involved need to be based on many assumptions, for most of which there is no absolute justification. this is because the physical, medical, social and economic phenomena involved are not really understood, in spite of the fact that there is field experience and considerable knowledge on such types of viruses, in general, and also on how to best handle their spread and the risks they carry. for situations like this, characterized by large uncertainties, the traditional textbook approaches to risk assessment and management cannot be used. formal risk assessments cannot be applied as is, to accurately predict scenarios of evolution and estimate their consequences, accounting for the effects of alternative countermeasures. thus, the decision-making remains intrinsically dynamic and adaptation to the evolution of the situation is inevitable, as shown by the different decision strategies taken back and forth by the authorities of the countries affected by the covid- pandemic. this motivates a reflection on the approaches to risk assessment and management for different types of risk problems. there are, indeed, many ways of categorizing risk problems. many relate to the severity of the consequences (the stakes involved) and their degrees of uncertainty (e.g. funtowicz and ravetz , renn , aven . from the perspective of these two dimensions, the pandemic situation that we are addressing corresponds to a high risk problem (large consequences with high uncertainty), and the traditional approach to risk assessment and management just does not work. as mentioned in section , different 'schools' exist, to meet this type of situation. in the following, we briefly recall some of these, the main aim being to show that, in fact, they all provide useful perspectives for and approaches to how to meet the challenges of assessing and managing risk in relation to critical situations of the kind that we are experiencing due to the coronavirus pandemic. post-normal science ravetz , ravetz ) acknowledges the need for an alternative and supplementary approach to science and policy making, when the stakes involved and the related uncertainties are largeand, typically, with different values in dispute and decisions urgently needed on which actions to take. this requires extending beyond the traditional perspective that science is not only certain but also value-free, calling for the need of new methods capable of going beyond numbers through different aspects of knowledge and information, dialogue and participation. the post-normal science emphasizes uncertainty and qualitative analysis, and a scheme for how to perform such analysis has been proposedthe nusap system (funtowicz and ravetz , , van der sluijs . nusap uses five categories for the management and communication of uncertainty in science for policy: numeral, unit, spread, assessment and pedigree. through nusap, a qualitative study of the quality and strength of the knowledge base behind the relevant scientific information and risk findings can be made, to inform policy making. . it is undoubted that pandemics, like the one we are experiencing, do pose systemic risk and, from this perspective, must be assessed and managed. system thinking, based on seeing wholes and interconnections, is, then, needed if we are to identify potential surprises and the unforeseenas stressed by many scholars of organizational theory, accident analysis, and the quality discourse (turner and pidgeon , deming , hollnagel et al , leveson )and effectively deal with their consequences. risk governance and systemic risk frameworks rely on three main categories of strategies for handling risk: risk-informed (based on risk assessments), robustness/resilience (based on the cautionary and precautionary principles) and discursive strategies (renn ). the strategy to apply in practice, to confront a systemic risk such as that brought by a pandemic, is normally a combination of these three types of strategies, with robustness/resilience as a main instrument for dealing with uncertainties (including potential surprises and the unforeseen), and dialogue for addressing differences in values. acknowledging complexity and dealing with uncertainties and the potential for surprises, through robustness and resilience-based approaches are key features of the risk governance school. this leads to safety science, and its roots in the 'sociotechnical perspectives on safety', which builds on three pillars (aven and ylönen ): i) a holistic view is needed to manage safety, using knowledge and experiential insights from different fields and disciplines (including technology and social sciences); ii) it is not possible to predict with sufficient accuracy and manage with sufficient control the behaviour of complex systems, their vulnerabilities and their response to accidents and disasters; and iii) robustness and resilience, thus, need to be accommodated, in addition to risk analysis. along these lines of thought, a rich body of literature on resilience has arisen in recent years, as a supplement to the traditional quantitative risk assessment approach, which has shown strong limitations when confronted with the analysis of complex systems and interconnected activities subject to large uncertainties regarding events' occurrences and consequences' evolution. the underlying idea is that, by strengthening the resilience of the system, the safety is improved without the need to calculate all probabilities and risks. we do not need to identify all eventshazards and threatsthat can occur as we have to do in traditional, quantitative risk assessments based on probabilistic methods. theories are developed providing a rationale for moving from 'safety-i', where the focus is on ensuring that 'as few things as possible go wrong', to 'safety-ii', where the aim is to ensure that 'as many things as possible go right' (hollnagel et al ) . in contrast somewhat to this perspective, the high reliability organizations (hros) tradition emphasizes the importance of failures, and that high performance and reliability can be achieved even in complex organizations if properly managed; five principles are highlighted therein: preoccupation with failure, reluctance to simplify, sensitivity to operations, ccommitment to resilience and deference to expertise (weick and sutcliffe ) . potential surprises are also a key focus of the quality discourse (deming , bergman ), with its distinction between 'common-cause variation' and 'special-cause variation'. the former variation relates to 'normal' system variation, whereas the latter is associated with the unusual variation, the surprises (the black swans). understanding the system causes is seen as the key to improving the system. risk science is the final school to be mentioned in this brief overview. it is based on the idea that the concepts, principles, approaches, methods and models for assessing, communicating, managing and governing risk form a distinct science (sra , a ,b, aven . this science provides guidance for all types of situations, including those characterized by the potential for severe consequences and large (deep) uncertainties, like the one we are facing in the covid- pandemic. it provides knowledge about risk fundamentals, for example related to what risk is, how to characterize risk, what methods are suitable for analyzing risk, how to treat uncertainties in risk assessment, how to understand and use the precautionary principle, the difference between professional risk judgments and risk perception, how to best deal with risk related to potential surprises and the unforeseen (black swans), and how to understand the link between risk and resilience. all the other schools can be viewed as providing knowledge to this science. a broad perspective on risk is adopted (sra , aven ), which sees uncertainty as a main component of risk and stresses the importance of knowledge and its strength when assessing and describing risk. the perspective allows for the inclusion of many safety, security, resilience and quality issues and is applicable to all domains (engineering, health, business, etc.). in addition, many different risk management frameworks have been developed to deal with specific issues and domains, for example enterprise risk management (erm) and business continuity management (bcm), in the case of commercial activities. bcm is of special relevance in this context, as it highlights disaster and crisis management, resilience and recovery planning (zeng and zio ) . as a final note on the perspectives taken above on risk, resilience, robustness, safety and security, these follow fundamental work by the society for risk analysis (sra), see sra ( sra ( , a . there are other perspectives than these, as for example that by the us national academy of sciences which defines risk as part of resilience (see e.g. linkov and trump , linkov et al , galaitsi et al. . we also refer to ale et al ( a,b) , jongejan ( ) and aven ( ) for discussions related to the nexus between risk and resilience. it is beyond the scope of the present paper to discuss the justification and rationale of the different perspectives, but one key point should be made clear: the difference is to large extent rooted in different conceptual understandings and terminology. there is a broad recognition of the importance of resilience to meet uncertain and unknown types of threats and disturbances. recent works on resilience and risk analysis and management in relation to covid- (e.g. hynes et al , golan et al , aven and bouder ) demonstrate this by their focus on system response measures and policies to prepare, absorb, recover and adapt. however, the resources are limited and what measures and policies to implement is challengingconsiderations of what will or can happen are needed, as well as overall judgments of what is acceptable levels of risk and vulnerabilities. risk science as referred to above provides one framework for conceptualising and understanding these phenomena; resilience analysis and management others, see the above references. for the purposes of the present paper, such differences in perspectives just underscore the point being made in the coming section: there are many 'schools' providing knowledge on how to handle risk when the uncertainties are large, which to varying degree work together. the overview in the previous section has shown that there are many perspectives and schools providing knowledge on how to understand, assess, communicate and handle risk, in relation to hazards and threats with the potential for extreme consequences, where the uncertainties are large. these perspectives and schools are founded on different scientific fields, developing in, to a large extent, separate activities, such as conferences, research activities, scientific journals and educational programs. yet, we argue here that the similarities and overlaps in the fundamental ideas are stronger than their differences. specifically, we highlight the following theses as common to all these perspectives and schools: a) uncertainty is a key element of all the relevant frameworks. b) an important source of uncertainty is potential surprises and the unforeseen. c) it is essential to distinguish between uncertainty and ways of measuring uncertainty. d) risk assessments provide knowledge about what type of events may occur, how often they may occur and what could be the consequences of these events if they were to occur. e) risk perception reflects aspects like fear and dread, but could also include conscious judgments of uncertainties. f) robustness and resilience are fundamental strategies to deal with the uncertainties. g) sciences about activities, events, processes developing in the world (for example, about the global spread of a virus) are supported by all perspectives and schools through their process of generation of knowledge on how to understand, assess, communicate and handle the risk (vulnerabilities, resilience, etc) and the uncertainties associated with these activities, events, processes. h) precautionary thinking is necessary in cases when the stakes involved are high and there are large (scientific) uncertainties, but the degree of precaution remains a political issue more than a science issue. as a matter of fact, scientific work can be regarded as a precautionary measure to reduce the uncertainties. i) adaptive, learning-based risk handling is suitable and advisable, given the occurrence of the hazard or threat. j) prevention of the occurrence of the potential crises-initiating hazards and threats remains a major priority. k) science informs decision-makers; it does not prescribe what is the best policy, arrangement or measure. l) openness, transparency, dialogue and participation are general features of prudent risk-handling frameworks. acknowledging uncertainty as a key component of risk is critical if we are to properly understand, assess and communicate risk. the traditional approaches to risk assessment and management jump more or less directly to the uncertainty measurement toolprobabilitythe result being that key aspects of uncertainty are not given the attention they require. all the schools discussed in section see this challenge and provide broader frameworks for allowing the analysts to take some steps back from the operational measurement tool and look more deeply into the knowledge supporting the analyses and the uncertainty measures used. risk assessments cannot produce accurate predictions of what is coming; rather, they help us to see what we know and what we do not know. they report the knowledge we have and are used as instruments for gaining new knowledge by, for example, studying how assumptions and model parameters influence key risk metrics. in the current coronavirus case, we have seen a number of models used to estimate the number of deaths, with uncertainty intervals showing the dependencies on key assumptions. however, seldom or never have we seen communicated the actual meaning of these uncertainty intervals and their dependencies on the knowledge basis supporting the evaluation of these intervals. at an early stage of the development of the coronavirus epidemic, many people raised their concerns. however, some experts indicated that lay people's concerns were the result of risk perceptional factors and biases, well-known from the scientific literature on this topic (e.g. kahneman et al , kahneman . the point made was that coronavirus hits all the 'hot buttons': a risk situation which is characterized by features like unknown, new and delayed effects, lack of control and catastrophic potential, commonly summarized by the two dimensions: newness and dread. the implication is that the risk is amplified, and there is a potential for overreaction. but how can we conclude that the response is an overreaction? at the time of concern, we are still faced with considerable uncertainties, and overreaction is a human attitude which reflects that. there is no ground truth to be used as reference for what is or is not an adequate response in such uncertain situations. lay people's risk perception can also include conscious judgments of uncertainties, partly ignored by the professional risk judgments. the insights provided by the different schools referred to above acknowledge that the experts' assessments have limitations and other knowledge sources can also provide valuable input to the overall risk considerations and should be considered. when faced with uncertainties, robustness and resilience-based strategies are important, as we do not know what will happen next. we need to be ready to tackle different types of scenarios, also surprising ones. at the same time, we need to build on the available knowledge and strengthen it to better understand what is happeningwe adapt and learn. the schools discussed in section support this approach to tackling risks, based on adaptation and learning, by providing concepts, principles, approaches, methods and models for how to do this. the perspectives differ partly on terminology and tools but remain similar on the fundamental ideas. inevitably, there is always a balance to be made between measures to create values, on the one hand, and measures to protect, on the other. science does not give us the formula for finding the right balance. it provides relevant knowledge and is, thus, informing the decision-maker, but it does not prescribe what should be done. the authorities in different countries have all labelled their policies "science-based", indicating that their policies are determined by the science findings. this type of notion is misleading, as the policies are at best science-informed. as we know, science produces justified claims about the world, but claims are not facts nor the truth. policies also reflect values, in particular related to how to give weight to uncertainties. in the case of large uncertainties, there is a considerable leap between insights provided by science and the considerations and policies derived by the political institutions. when faced with high stakes and large (scientific) uncertainties, precautionary measures will be and should be given weight in informing the decisions, as in the risk handling related to the coronavirus. the point is simply that we will avoid very high losses, and, given the uncertainties about the virus and the process of its spread, this leads to extraordinarily cautious policies. all governments now seem to have adopted such policies. some scholars are skeptical about the use of the precautionary principle/approach, indicating that it is not rational and scientific. however, the principle, as interpreted here as a guiding perspective, is in no way non-scientific: because of the uncertainties, there is not sufficient knowledge available to guide us differently on a solid basis. a key precautionary measure becomes, then, research to strengthen the knowledge base. it is acknowledged that different situations call for different approaches for assessing and handling risk -"simple" problems with no or very limited uncertainties require different strategies than those required by problems with high stakes involved and large uncertainties, as considered in this paper. all schools referred to in section acknowledge this, although the different ways of classifying the "problems" vary. uncertainty is, however, a common feature in all classification systems used. these schools also highlight the importance of openness, transparency, dialogue and participation for dealing with situations of the kind discussed in this paper (high stakeslarge uncertainties). there are always some limitations to this in practice, for example on the extent of openness that one can really achieve/obtain, but in many ways these features characterize an ideal in our democratic societies and we should be concerned when they are threatened in any way. finally, we conclude this section with some reflections about the actual risk handling in the coronavirus case. today, the world is faced with an extreme crisis as a result of the coronavirus. thus, we can conclude that the risk handling has failed. the failure can be traced back to i) the origin of the virus, ii) the lack of early control, and iii) the mitigation measures adopted, given its spread. the first type of failure is difficult to analyze at this stage, but thorough investigations and efforts are needed to see whether there are some fundamental problems in our societies, creating this type of threat. openness and international cooperation are required to meet this challenge, but it could be difficult to obtain necessary changes in activities that are grounded in traditional and cultural practices. nonetheless, this issue is a major concern. is it possible to avoid such a virus occurring? nothing would be better than the solution to this question. secondly, it was a failure that the signals and warnings were not taken seriously, which led to a delay in actuating measures for the control of the spread. the health organizations have warned governments and politicians for years that a serious pandemic is likely to occur. national and global risk assessments all point to pandemics as a major risk. yet the signals and warnings were to a large extent ignored. as such, the coronavirus pandemic is not to be seen as a black swan; its occurrence is not a surprising event relative to our knowledge. maybe we could classify the event as a known unknown, indicating that there was knowledge that a serious pandemic could occur quite soon, but when it would occur was unknown to us. surely there is a need to improve the way the world deals with this type of alarms and warnings. international cooperation is needed to develop relevant tools and institutions to look into this. thirdly, governments struggle to justify investments in preparedness measures. there are many threats that we must be protected from and using a lot of public money for something that might happen requires a strong economy and strict prioritizations. however, for pandemic risks, the evidence has been strong and clear, but still the coronavirus spread has been enormous, whereas its mitigation has been weak in many respects. the problems that we are facing have demonstrated the extreme degree of vulnerability that our societies face today because of globalization. necessary equipment is not available locally. all countries now depend on deliveries from specific producers often far away. following the coronavirus case, fundamental pillars for how we have organized the world will be questioned. more decentralized systems will challenge the globalist perspective. one of the reviewers of the original version of this paper questioned the above conclusion that the risk handling in this case has failed. the point made was that some risks were taken and accepted, and the potential consequences were known, see also discussions in ale et al ( a,b) . yes, decision-making about risk acceptance is an important task of risk management and governance, but it also makes sense to challenge this decisionmaking with respect to the outcomes and its rationale. we should question why many risk aspects where accepted and key vulnerabilities not reduced or eliminated. that is exactly what this paper and many others are doing. it is about scrutinizing the current risk handling in order to identify weaknesses and look for ways that it can be improved. the risk management and governance is not based on a destiny perspective, expressing that serious events will occur if we have calculated a probability for these events to occur. an ultimate goal of risk management and governance is to avoid disasters. above, we have pointed to some issues that we consider critical for being able to do this. it is about improving current approaches for risk handling. we also point to the need for the sciences and schools dealing with these challenges to do their job together, supporting the actual risk handling in the world. this is about risk analysts and scientists to make constructive reflections on systems and processes of the world, and on how to improve the handling of these and of their risks, in line with the ideas of science and quality management. in this paper, we have taken the dramatic world crisis of the coronavirus pandemic to reflect on the current frameworks for risk assessment and management and what they can offer in these situations of high stakes and large uncertainties. we have recognized that the contemporary frameworks struggle to provide authoritative unified societal guidance to adequately handle these types of risks. this is clearly shown by the coronavirus case, in which the risk handling has failed in the identification and prevention of the origin of the virus, in the lack of early control and in the efficacy of the decision-making about the mitigation measures to be adopted once the spread had started. we have highlighted that the existing scientific perspectives and schools related to risk share a number of fundamental principles and theses. they all consider uncertainty as a key element and view risk assessment as providing knowledge on what is known and what is not known about the occurrence and consequences of dangerous events, in the different risk situations. recognition is given to the fact that risk perception reflects human feelings, like fear and dread, but could also include conscious judgments of uncertainties different from those of the risk professionals. precautionary thinking, robustness and resilience are necessary approaches to develop adequate policies to address situations of high stakes and large uncertainties. the level of precaution, the decisions on how robust and resilient to be, remain political decisions, which can be informed by science and scientific knowledge: science does not prescribe the best policy of risk handling, but it can provide information for its definition by the decision-makers. it is time to initiate processes to obtain stronger integration of these perspectives and schools. only then, it is likely that we will be able to provide guidance for risk handling that really can have an impact. how to proceed is, however, difficult, given the way academic fields and societies work. the current crisis has been an eye-opener for many of us in different ways; perhaps it can also be that in relation to this challenge. we do hope so. certainly, prevention remains a main priority ("if you think that safety is expensive, try an accident", kletz, ) , and the capabilities for adaptive, learning-based risk handling are required in the event of an occurrence of the hazard or threat. these aspects need to be dealt with in the current setting of our highly vulnerable world, where factors like population density, urbanization, globalization and climate change influence the uncertain occurrence of disasters and their uncertain consequences. for this, more openness, transparency, dialogue and participation at all levels are needed for prudent risk-handling, to be better able to confront global threats like the coronavirus in the future. risk based facility location by using fault tree analysis in disaster management h ( a) precaution, resilience, faith, and covid- h ( b) resilience or faith or/ms research in disaster operations management an emerging new risk analysis science: foundations and implications the science of risk analysis the covid- pandemic: how can risk science help? risk management and governance some foundational issues related to risk governance and different types of risks a risk interpretation of sociotechnical safety perspectives conceptualistic pragmatism: a framework for bayesian analysis? the new economics. nd analysing recovery from pandemics by learning theory: the case of covid- prediction of covid- infection, transmission and recovery rates: a new analysis and global societal comparisons uncertainty and quality in science for policy science for the post-normal age the need to reconcile concepts that characterize systems withstanding threats trends and applications of resilience analytics in supply chain modeling: systematic literature review in the context of the covid- pandemic globally networked risks and how to respond from safety-i to safety-ii: a white paper resilience engineering: concepts and precepts bouncing forward: a resilience approach to dealing with covid- and future systemic shocks white paper on risk governance. towards an integrative approach. author: o. renn with annexes by p. graham. geneva: international risk governance council how prepared is prepared enough? thinking, fast and slow judgment under uncertainty: heuristics and biases what went wrong? case histories of process plant disasters and how they could have been avoided analyzing dispensing plan for emergency medical supplies in the event of bioterrorism nuclear power as a climate mitigation strategytechnology and proliferation risk a new accident model for engineering safer systems engineering a safer world: systems thinking applied to safety risk governance through professional expertise. forestry consultants' handling of uncertainties after a storm disaster tiered approach to resilience assessment the science and practice of resilience systemic risks: theory and mathematical modeling complexity, uncertainty and surprise: an integrated view thinking in systems: a primer over the cliff: from the subprime to the global financial crisis. no. w emerging systemic risks: final report to the oecd futures project emergency relief logistics: an evaluation of military, nonmilitary and composite response models contributing to disaster management as an individual member of a collectivity: resilient ethics and ethics of resilience. psyarxiv what is post-normal science? precaution and the governance of risk systemic risks: the new kid on the block glossary society for risk analysis risk analysis: fundamental principles core subjects of risk analysis man-made disasters. nd ed risk governance experiences with the nusap system for multidimensional uncertainty assessment in model-based foresight studies managing the unexpected: resilient performance in an age of uncertainty. nd ed risk reduction and emergency preparedness: who six-year strategy for the health sector and community capacity development dynamic business continuity assessment using condition monitoring data natural disasters and social conflict: a systematic literature review an integrated modeling framework for quantitative business continuity assessment the future of risk assessment the authors are grateful to two reviewers for their useful comments and suggestions to the original version of this paper. the work has been carried out by terje aven and enrico zio, based on close collaboration on all aspects of the paper. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord- -all j od authors: clark, m. a. title: bovine coronavirus date: - - journal: british veterinary journal doi: . /s - ( ) - sha: doc_id: cord_uid: all j od summary this review aims to summarize current data describing the characteristics of bovine coronavirus (bcv) and the three clinical syndromes with which this virus is associated. the first half of this paper consists of a general description of the virus, commencing with a brief outline of the methods used for in vitro growth. the structure of the virus is then described in more detail, with particular reference to the structure and functions of the four major viral proteins. this is followed by an outline of the unique replication strategy adopted by coronaviruses. the second half of this review discusses the clinical significance of the virus, beginning with a detailed account of bcv-induced neonatal calf diarrhoea, the clinical syndrome with which this virus is most commonly associated. the clinical and epidemiological importance of bcv respiratory tract infection is then discussed, and finally the evidence supporting the aetiological role of bcv in outbreaks of winter dysentery in adult cattle is examined. bovine coronavirus (bcv) was first reported by mebus et al. ( mebus et al. ( , a , and is now widely recognized as an important cause of neonatal calf diarrhoea. the virus also infects the bovine respiratory tract and has been associated with winter dysentery in adult cattle. there has been a single report of accidental transmission of bcv from experimentally inoculated calves to a human investigator (storz & rott, ) , but until further evidence becomes available the zoonotic potential of bcv must remain open to question. bovine coronax rus belongs to antigenic group of the coronaviridae family of viruses (coronaviruses), and for further information on bcv and other members of this family readers should refer to the recent reviews published by babiuk et al. ( ) , siddell ( ) , spaan et al. ( , ) , holmes ( ) and lai ( ) . despite problems in virus isolation, bcv has now been grown in both tracheal and gut organ cultures (stott et al., ; bridger et al., a, b; mcnulty et al., ) and also in a large number of cell lines including human rectal tumour- (hrt- ), vero, madin darby bovine kidney (mdbk) and madin darby canine kidney (mdck ) (laporte et al., ; dea et al., b; schultze et al., b) . addition of exogenous trypsin enhances or promotes the growth of bcv in many cell lines including vero, bovine foetal thyroid (bfty), bovine foetal brain (bfb) and bovine embryonic lung (bel) (dea et al., b; toth, ) . virus growth in early passages in cell culture is typically without the production of a recognizable cytopathic effect (cpe) . later passages may result in a marked cpe characterized by syncytia formation and cell detachment, the precise cpe varying with both the virus strain and the host cell type. plaques are observed when inoculated cultures are overlayed with agarose, and the addition of trypsin may enhance both cpe and plaque formation vautherot, ; hirano et al., ; st. cyr-coats & storz, ; payne & storz, ) . at present colostrum deprived gnotobiotic or conventional calves are the only animal models of bcv enteric infection. dea et al. ( a) failed to demonstrate bcv replication in other species, although a number of groups have demonstrated encephalitis in neonatal mice following inoculation with bcv via the intranasal or preferably the intracerebral route (kaye et al., ; akashi et al., ; gerna et al., ; barthoid et al., ) . bovine coronavirus particles are pleomorphic to rounded in shape, varying in diameter from to nm and with a mean diameter of about nm. well preserved virions present a characteristic appearance when negatively stained preparations are examined under the electron microscope (em). the virus envelope is seen as a distinct pair of electron dense shells from which the spike (s) glycoproteins (gps) radiate to form a fringe of surface projections (spikes or peplomers). these petal shaped spikes are about nm long and lie external to a second fringe of shorter projections formed by the haemagglutinin-esterase (he) gps. both types of surface projection may be lost during sample storage and preparation, so virions which either partially or completely lack these surface projections are also frequently observed (sharpee et al., ; bridger et al., b; dea et al., a; roseto et al., ) . bovine coronavirus particles possess four major structural proteins: the nucleo- & brian, ; brian et al., ; deregt et al., deregt et al., , vautherot & laporte, ; st. cyr-coats et al., ) . the n protein lies internal to the virus envelope and is associated with the viral rna, the m gp spans the viral envelope whilst the s and he gps project from the envelope (fig. ) . a number of minor structural and non-structural proteins have also been described (babiuk et al., ; cox et al., ; abraham et al, b) . the n protein is non-glycosylated, has a molecular weight (mw) of - kda and can form disulphide-linked trimers (mw kda) under non-reducing conditions. the gene encoding the n protein has been sequenced in the mebus (m) and f strains of bcv (lapps et al., ; cruciere & laporte, ) : only minor sequence differences were detected between these two viruses. the encoded protein is rich in serine residues, and these may be phosphorylated. the n protein is also rich in basic amino acids, which are concentrated in regions representing the sites of genomic rna binding. many molecules of the n protein are associated with the genome to form a long, flexible, helical nucleocapsid. the m gp exists as a series of species which have different levels of glycosylation on an identical protein backbone. it is thought to originate as an unglycosylated precursor protein with a mw of about kda. subsequent addition of one or two oligosaccharide side chains, each with a mw of about kda, results in species with mws of about and kda. the carbohydrates are joined by o-linked glycosidic bonds (king & brian, ; deregt et al., ) . the gene encoding the m gp of m strain bcv has been sequenced by lapps et al. ( ) , and analysis of sequence data for this and other coronaviruses has led to the proposal that the m gp has three distinct domains. a kda hydrophilic amino-terminal (n-terminal) domain lies external to the virus envelope, and contains all the carbohydrate present in the protein. the central domain forms three hydrophobic tz-helices which span the lipid bilayer three times whilst the carboxy-terminal (c-terminal) domain lies on the inner surface of the viral envelope and interacts with the nucleocapsid. the s gp exists either as an uncleared kda precursor or as two cleavage products which migrate on polyacrylamide gel electrophoresis (page) as a single band ( kda) or as two closely related bands ( and kda). in the majority of cell lines the s gp is present as the cleaved form, but when the virus is grown in cells such as bovine foetal spleen (bfs) or bfb, exogenous trypsin is required for cleavage st. cyr-coats et al., ) . the genes encoding the s gp of six different strains of bcv have been sequenced, and have been found to be highly consewed (abraham et al., a; boireau et al, ; parker et al., b; zhang et al., ) . the encoded protein contains amino acids and potential n-linked glycosylation sites. a peptidase cleavage site has been identified at amino acids - , allowing cleavage of the s precursor into s and $ subunits which represent the n-terminal and c-termi,lal cleavage products respectively. the $ subunit contains a c-terminal hydrophobic s-helix which anchors the sgp in the virus membrane, whilst two amphipathic at-helices form the stalk which supports the outer bulbous s subunit. the s gp has several important functions, the first of which is to bind to the host cell receptor during initiation of infection. both isolated s gp and intact virions agglutinate mouse, rat and adult chicken red blood cells by binding to a receptor on the erythrocyte surface which contains a modified sialic acid residue, n-acetyl- -o-acetylneuraminic acid (neu , ac.,). it has been postulated that the same residue may act as a receptor on the target cell membrane during the infection process (vlasak et al., b; schultze et al.. schultze et al.. , a . the s gp is also important in membrane fusion events: at the start of infection it induces fusion of the virus envelope with the cell membrane and later in infection it induces cell-to-cell fllsion resulting in the spread of virus between cells and the formation of syncytia. cleavage of the s gp is required for activation of its cell fusion activity, which is mediated by the $ subunit payne & storz, ; st. cyr-coats et al., ; yoo et al, a) . the s gp contains important neutralizing epitopes, and monoclonal antibodies (mabs) directed against this protein neutralize the virus both in vitro and in vivo (deregt <, td., b) . strongly neutralizing mabs have been mapped to two regions on the s subtmit, and a further two regions have been defined by non-neutralizing mabs on each of the $ and $ subunits (deregt & babiuk, ; deregt et al., a; vautherot et al., ; yoo et al., yoo et al., , b . the he gp is a disulphide linked dimer with a mw of - kda. it is reduced by -mercaptoethanol to two identical monomers, each with a mw of kda. the gene encoding the he gp has been sequenced in the quebec and m strains of bcv, the reported sequences differing by only two bases which lead to a change in just one amino acid (parker et al., ; kienzle et al., ) . the encoded protein contains amino acids, nine potential sites for n-linked glycosylation and a c-terminal membrane anchoring domain. the primary translation product has a mw of . kda. this protein is glycosylated to yield a kda monomer, which rapidly undergoes dimerization by the formation of disulphide bonds before further glycosylation yields the mature gp (deregt et al, ; hogue et al., ; parker et al., a) . bovine coronavirus induces both haemagglutination and haemadsorption, the latter term referring to the process by which erythrocytes are adsorbed to the membranes of infected cells (sharpee et al., ; kienzle et al., ; payne & storz, ) . it was initially proposed that the he gp was the sole haemagglutinating protein of bcv (king & brian, ; king et al., ) but it has now been demonstrated that both the s and the he gps cause haemagglutination by binding to surface receptors containing neu , acz (schultze et al, a, b) . the he gp is in fact a less potent haemagglutinin than the s gp, as it only agglutinates erythrocytes from mice and rats and not those from adult chickens which bear fewer surface receptors (schultze et al., a) . at present it is unclear why bcv contains two receptor-binding proteins, particularly since many coronaviruses lack the he gp. in common with the s gp, the he gp contains important neutralizing epitopes, and mabs directed against the he gp neutralize the virus both in vitro and in vivo (deregt et al., b) . two independent epitopes (a and c) and a third overlapping epitope (b) have been defined on this protein; strongly neutralizing mabs all mapped to epitope a (deregt & babiuk, ; parker et al., parker et al., , a vautherot et al., ) . the he gp also contains a receptor destroying enzyme (rde) which cleaves an ester linkage to release -o-acetyl residues from sialic acids and which therefore inactivates the erythrocyte receptor (neu , ac,.,) for bcv. activation of this enzyme causes the virus to elute from erythrocytes when the temperature is raised to °c (vlasak et al., a, b; parker et al., a; vautherot et al., ; schultze et al., b; storz et al., ) . the rde is probably involved in the early stages of virus replication, as enzyme inhibition greatly reduces viral infectivity (vlasak et al., a) . the he gp of bcv bears both a structural and functional resemblance to the he protein of type c influenza viruses. an amino acid sequence homology of. . % has been demonstrated between the he protein of bcv and the ha subunit of the influenza c virus he protein (kienzle et al, ) , and the he proteins of both viruses induce haemagglutination, bind to receptors containing neu , ac,_, and possess a receptor destroying acetylesterase enzyme (vlasak et al, a, b; schultze et al, schultze et al, , a storz et al., ) . on the basis of these observations it has been proposed that coronaviruses may have acquired the he gene from the influenza c viruses by a non-homologous recombination event (luytjes et al., ) . the bcv genome consists of a single strand of non-segmented rna of positive sense (guy & brian, ) . it is about - kb in size, and is organized into seven regions which each contain one or more open reading frames. the regions are separated by reinitiation sites (junction sequences), and these contain the signal for the transcription of the subgenomic messenger rnas. the ' end of the genome encodes for non-structural proteins including the viral rna polymerase enzyme, whilst the gene order for the structural proteins is: '-he-s-m-n- ' (spaan et al, ) . the bcv isolates studied to date all belong to a single serotype as polyclonal sera have only detected very minor antigenic variations (bridger et al., b; dea et al., ; ei-ghorr et al., ; heckert et al., c; tsunemitsu et al., ) . monoclonal antibodies have detected variations on the n, s and he proteins and some isolates also vary in their physicochemical properties and in their ability to produce a cpe and form plaques in cultured cell monolayers (dea et al., a; vautherot & laporte, ; vautherot et al., ; st. cyr-coats & storz, ; czerny & eichhorn, ; deregt et al., b; ei-ghorr et al., ; clark et al., ; hussain et al, ) . the unique replication strategy of coronaviruses has been described in several recent reviews (siddell, ; spaan et al., ; holmes, ; lai, ) . studies on bcv indicate that this virus replicates in a manner similar to that of the other coronaviruses (doughri et al., ; tektoff et al., ; keck et al., ; hofmann et al., ) , and the aim of this section is therefore merely to highlight the most important aspects of coronavirus replication. it seems likely that bcv attaches via both the s and he gps to receptors (possibly neu , acz) on the target cell membrane (vlasak et al., b; schultze et al., a, b ). the precise mechanism by which the virus then enters the cell is uncertain. uptake may be achieved either by direct fusion of the virus envelope with the plasma membrane of the cell, or by endocytosis followed by fusion of the virus envelope with the membranes of endocytic vesicles (payne & storz, ; payne et at, b; yoo et al., a) . once inside the cell virus replication occurs entirely within the cell cytoplasm. the genomic rna first attaches to ribosomes and directs the synthesis of rna dependent rna polymerase. this enzyme directs transcription of a complementary full length (-) strand of rna from the genomic (+) strand. the (-) strand rna serves as a template for synthesis of full length genomic rna and also seven subgenomic mrnas, which form a ' nested set with common ' ends. each mrna contains all the nucleotide sequence of the next smallest mrna plus an extra gene at the ' end which is referred to as the unique region. the ' ends also have a common leader sequence of - bases, and it has been suggested that this leader sequence originates from the ' end of the (-) strand rna by a discontinuous leader primed transcription mechanism. in this model, leader rna transcribed from the ' end of the (-) strand rna would separate from the rest of the template but still remain bound to the polymerase enzyme. the leader sequence-polymerase complex would then bind by base pairing at specific non-coding regions called reinitiation sites on the (-) strand rna, where it would act as a primer for synthesis of the rest of the mrna. it is likely that this proposed model of mrna synthesis is still incomplete, particularly since it has recently been demonstrated that the mrnas themselves undergo replication through a (-) strand copy of each mrna (hofmann et al., ) . only the unique regions of the mrnas are translated, and most contain a single open reading frame which codes for only one protein. translation of the mrnas coding for the non-structural and n proteins occurs on free ribosomes in the cell cytoplasm, whilst the m, s and he gps are synthesized on ribosomes at the rough endoplasmic reticulum (rer). the m gp is only glycosylated once it reaches the golgi apparatus, whereas the s and he gps are glycosylated at the rer during protein synthesis and the carbohydrate side chains subsequently modified during transport through the golgi apparatus. virus assembly occurs by budding at the membranes of the rer and golgi apparatus, the site of assembly being determined by the restricted intracellular transport of the m gp. the n protein interacts with newly synthesized genomic rna to form fragile nucleocapsids, which align on the cytoplasmic surface of the membranes of the rer and golgi due to an interaction with the m gp. in these membranes the host cell proteins are replaced by viral gps, and whole virions are pinched off and released into the lumen. most bcv particles are released from intact cells using the normal cell secretory mechanisms, although a few particles are released by lysis of dying cells. excess s and he gps which have not been incorporated into virions are also transported to the plasma membrane of the cell, where they may act as targets for the host's immune response (kienzle et al., ; payne et al., a) . the pathogenesis of bcv in the calf gastrointestinal tract and the associated pathological findings have been described in detail by several groups including mebus et al. ( b mebus et al. ( , , langpap et al. ( ), bridger et al ( b and. babiuk et al. ( ) . the accompanying physiological changes have been reported by lewis & phillips ( ) . these findings are briefly summarized below. calves may be infected with bcv by both the oral and respiratory routes. virus infection of the enteric tract starts in the proximal small intestine and spreads throughout the small and large intestines. virus replication occurs in the surface epithelial cells, particularly in those on the distal half of the villi in the lower small intestine. infected cells die, slough off and are replaced by immature cells. in the small intestine these changes result in stunting and fusion of adjacent villi, and in the large intestine they lead to atrophy of the colonic ridges. on histological examination it is seen that the tall columnar epithelial cells which normally line the small intestinal villi and colonic ridges are replaced by cuboidal and squamous epithelial cells, and in severe infections there may even be areas of complete desquamation. these changes are accompanied by a decrease in the number of goblet cells. scanning electron microscopy (sem) demonstrates that there are wide variations in the length and spacing of the microvilli on individual cells. the absorptive capacity of the gut is severely diminished by the loss in surface area and by the presence of immature cells. these cells retain some of their secretory activity which leads to a further increase in the volume of fluid in the gut lumen. at the same time the immature cells are unable to secrete the normal digestive enzymes, so the digestive capacity of the gut is reduced. undigested lactose accumulates in the gut lumen, leading to an increase in microbial activity and an osmotic imbalance which draws more water into the gut. the decrease in digestive and absorptive capacities leads to diarrhoea, with loss of water and electrolytes. in severe infections, diarrhoea may lead to dehydration, acidosis and hypoglycaemia, and death may occur due to acute shock and heart failure. more commonly the infection is serf-limiting, as the virus rarely attacks crypt epithelial cells. the mitotic activity of these cells increases, producing immature cells which are more resistant to virus infection and which migrate up the villi to replace the damaged cells. the severity of bcv enteritis varies with both the age and immunological status of the calf and the infective dose and strain of virus, diarrhoea developing more quickly and being more severe in very young or colostrum deprived calves. the clinical signs associated with bcv enteritis are indistinguishable from those associated with rotavirus infection. a yellow diarrhoea develops about h after experimental infection and continues for - days: the virus may be detected in the faeces throughout this period. calves are often dull and anorexic during the acute stage of infection, and if diarrhoea is severe they may also become pyrexic and dehydrated. the majority of calves recover, but a few may die if diarrhoea is particularly severe (mebus et al., b; bridger et al., b; reynolds et al., ; saif et al., ) . bovine coronavirus has been reported in many countries and is probably distributed world wide acres et al., ; zygraich et al., ; woode et al., ; de visser et al., ; tsunemitsu et al., ) . the virus is widespread in cattle populations, and consequently serum antibodies to bcv can be detected in the majority of adult cattle (hajer & storz, ; rodak et al., ) . the virus may be detected in both diarrhoeic and healthy calves, the reported incidence rates ranging from to % and to % for diarrhoeic and healthy calves respectively (marsolais et al., ; moon et al., ; woode et al., ; dea et al., ; langpap et al., ; reynolds et al., ; snodgrass et al., ) . the virus is frequently found in diarrhoeic faecal samples in conjunction with other enteropathogens, particularly rotavirus. bovine coronavirus causes enteritis in calves in both dairy and beef herds. affected animals range in age from day to about months old, but diarrhoea typically occurs at between and weeks of age (langpap et al., ; reynolds et al., ; mostl & burki, ) . disease is more prevalent during the winter months, and this may reflect the enhanced capacity of the virus to survive in a cool, moist environment. outbreaks of diarrhoea often occur in consecutive years on the same farm, and this may be because the virus remains viable in the environment from year to year. bovine coronavirus is, however, a labile virus and outbreaks of diarrhoea still occur if cows are transferred to clean ground at calving. it is therefore more likely that clinically normal adult cows which are persistently infected with the virus act as a source of infection for susceptible calves. bovine coronavirus has been detected in the faeces of a high proportion (over %) of clinically normal adult cows, despite the presence of specific antibodies in the serum and faeces (crouch & acres, ; crouch et al., ) . the rate of virus excretion increases during the winter months and at parturition, and although the infectivity of bcv particles in faeces from clinically normal adult cattle has so far not been demonstrated, calves born to carrier animals have a significantly higher risk of developing diarrhoea (collins et al., ; bulgin et al., ) . subclinical persistent or recurrent infections are also common in both neonatal and older calves and virus excretion from these animals may maintain a reservoir of infection for susceptible calves (heckert et al., (heckert et al., , c kapil et al, ) . enteric bcv infections are generally diagnosed by examination of faecal samples for the virus. initially negatively stained preparations were examined by electron microscopy, but accurate identification of the virus was often difficult (stair et al., ; durham et al., ) . virus recognition was facilitated by the use of specific antibodies and gold conjugated probes (langpap et al., ; saif et al., ; e -ghorr et al., ; heckert et al., ) . virus isolation is rarely used as a means of diagnosis as bcv is difficult to isolate, but some diagnostic tests are based on the haernagglutinating properties of the virus. the simplest of these methods is to use a haemagglutination (ha) test followed by a haemagglutination inhibition (hal) test to check for bcv specificity (sharpee et al., ; sato et al, ) . faecal samples cause problems when tested in haemagglutination assays as they contain non-specific haemagglutinins, so modifications have been made to the basic ha test in an attempt to overcome this problem (van balken et al., ; sato et al., ) . enzyme linked immunosorbent assays (elisas) are probably the most widely used diagnostic test for bcv. early assays were based on the use of polyclonal anti-. sera (reynolds et al., ) , but more recently mabs have been incorporated to improve the specificity of these tests (crouch et al., ; crouch & acres, ; czerny & eichhorn, ) . recently dot blot hybridization assays have also been described which use a cdna probe labelled with either phosphorus- (p ) or biotin to detect bcv rna (shockley et al., ; verbeek & tijssen, . calves suffering from bcv enteritis should be treated by the standard methods used to treat other forms of calf diarrhoea. the aim of treatment is to replace the loss of fluids and electrolytes which can otherwise lead to dehydration and acidosis, and this is achieved by fluid replacement therapy which may also be accompanied by discontinuing the feeding of milk. the fluids used should be balanced electrolyte solutions and these may be given via the oral or intravenous routes. oral administration of kaolin mixtures may be used to lessen the severity of diarrhoea. affected animals should be segregated from healthy animals and kept in a warm area with fresh bedding. protection against bcv diarrhoea is dependent on the presence of adequate levels of specific antibodies in the gut lumen. in neonatal calves this local immunity is passively acquired from the dam in the form of antibodies ingested in the colostrum and milk. the predominant isotype involved is igg , and this is largely derived from serum by a selective transport mechanism operating in the bovine mammary gland. the level of bcv specific antibodies in the lacteal secretions is very high at parturition but then declines rapidly (rodak et al., ; crouch & raybould, ) . duration of passively acquired immunity in the calf is prolonged by resecretion of absorbed antibodies back into the gut lumen and by adherence of immunoglobulins to the surface of the intestinal mucosa. following natural exposure to infection, calves develop active immunity to the virus and it is probably iga antibodies at the mucosal surface which protect against reinfection (saif, ; heckert et al., a, c) . diarrhoea is most likely to occur if the passively acquired immunity declines before an adequate level of active immunity has developed. the offspring of cows with low serum antibody titres and therefore low levels of antibody in their colostrum and milk are especially susceptible to infection, calves born to primiparous cows being particularly vulnerable (woode & bridger, ; moon et al., ; crouch, ; saif, ) . bcv diarrhoea can be prevented either by decreasing the challenge dose of virus to susceptible animals or by increasing their levels of specific immunity. the identification and segregation of carrier cows and calves should in theory decrease the challenge dose of virus, but in practice this approach may be impossible as bcv infections may be widespread even in a closed herd (radostits & acres, ; crouch & acres, ; bulgin et al., ; heckert et al., ) . the immune status of susceptible calves may be raised either by parenteral vaccination of pregnant cows to increase the level of passively acquired immunity or by oral vaccination of neonatal calves to stimulate active immunity. at present there are no bcv vaccines available in the uk, although several vaccines are available in other countries. parenteral vaccination of pregnant cows has proved successful for controlling rotavirus diarrhoea in neonatal calves (snodgrass et al., (snodgrass et al., , . vaccination of pregnant mice has protected their offspring against bcv infection and the same approach should be possible in cattle (bengelsdorff, ) . most adult cows have measurable serum antibody titres to bcv as a result of natural infection (rodak et al., ) , and the aim of vaccination is therefore to stimulate a secondary immune response which raises the level of protective antibody which is then ingested by the sucking calf in the colostrum and milk. the resulting level of passively acquired immunity in the calf should both prevent disease whilst at the same time permit subclinical infection to stimulate the development of active immunity. it has already been demonstrated that colostrum containing high levels of bcv specific antibodies will protect calves against clinical bcv infections, although it has also been found that high levels of passive immunity depress the active antibody response to whole bcv and the s and he gps (heckert et al., b, c) . in contrast to these findings, several groups have found that vaccination of cows with either experimental or commercially available vaccines has little "or no effect on the levels of bcv specific antibodies in the serum, colostrum and milk, and that adequate protection of calves is not achieved (myers & snodgrass, ; rodak et al., ; waltner-toews et al., ; collins et al., ; mostl & burki, ) . it has, however, been proposed that vaccination may prevent the increase in bcv shedding which occurs from carrier cows at parturition (collins et al., ) . active immunization of calves by oral inoculation with live, attenuated bcv vaccines has protected colostrum deprived calves in experimental trials but has not proved effective in field trials (thurber et al., ) . this is probably because the vaccine virus is neutralized in the gut by passively acquired maternal antibodies. vaccine administration by the respiratory route has been proposed as an alternative method of stimulating active intestinal immunity without the need for primary infection of the gut, but there is still a danger that the virus is neutralized by maternal antibodies which have been absorbed systemically (reynolds et al., ; saif et al., ) . there is also a danger that the neonate may fail to respond adequately to vaccines given by either the oral or respiratory routes due to immaturity of the immune system. in utero vaccination of bovine foetuses resulted in protective levels of immunity in -day-old calves, but the frequency of abortions and premature births precluded its practical application (mullaney et al, ) . in addition to being an enteric pathogen, bcv can also cause respiratory tract infections in a wide age range of calves. infection is generally subclinical, but when clinical signs are present they are most commonly seen in calves between and weeks of age (thomas et al., ; mcnulty et al., ; reynolds et al., ; singh et al., ; saif et al., ; saif, ; mostl & burki, ; heckert et al., heckert et al., , a tsunemitsu et al., ) . within the respiratory tract the primary sites of infection are the epithelial cells of the nasal cavity and trachea, where infection may lead to mild upper respiratory signs such as rhinitis, sneezing and coughing. immunofluorescent staining of nasal epithelial ceils using bcv specific antibodies is a valuable method for diagnosing these infections (reynolds et al., ) . the virus may also infect the lower respiratory tract and cause minor lung lesions, but clinical signs are generally absexlt. a more severe lower respiratory tract involvement has, however, also been reported (kapil et al., ) . bovine coronavirus respiratory tract infections are generally not sufficiently severe as to require treatment, but they may predispose calves to more severe secondary lower respiratory tract infections. current data suggest that bcvs originating from the enteric and respiratory tracts are antigenically identical (thomas et al., ; vautherot & laporte, ; mcnulty et al, ; reynolds et al., ; tsunemitsu et al., ) . experimental investigations have demonstrated that the outcome of infection is largely unaffected by both the origin of the virus (enteric or respiratory) and the route of inoculation (nasal or oral) (saif et al., ) . infected calves frequently harbour bcv in both the enteric and respiratory tracts simultaneously (reynolds et al., ; saif et a/., ; heckert et al., d) . the primary importance of bcv respiratory tract infections may be that they allow virus transmission by the aerosol-nasal route, in addition to the faecal-oral route generally used by enteric pathogens. spread of virus by aerosol infection is assisted by prolonged and recurrent shedding of virus from the upper respiratory tract (saif, ; heckert et al., heckert et al., , d . in a newly infected animal, initial virus replication in the upper respiratory tract may provide a large number of infective particles protected by mucus which are then transferred to the gut where a secondary infection occurs. the precise cause of winter dysentery is still unclear, but in recent years bcv has been widely implicated as the aetiological agent. for a more detailed account, readers should refer to the review by saif ( ) . the disease occurs durng the winter months in housed adult dairy and beef cattle, and is characterized by an acute onset of dark, bloody diarrhoea accompanied by a dramatic fall in milk production. affected animals may also develop a nasolacrimal discharge and cough, and become depressed and anorexic. the disease spreads rapidly within an affected herd leading to a very high morbidity ( - %), but the mortality rate is very low ( - %). economic losses due to the drop in milk production can, however, be very high, as production may not return to normal for several months. the clinical signs and pathological changes associated with winter dysentery are consistent with bcv being the causative agent (van kruiningen et al., ) . seroconversion to bcv has been demonstrated in affected cattle, and the virus has frequently been both detected in and isolated from diarrhoeic faecal samples. it has yet to be proven whether this virus is a causative agent of winter dysentery, an opportunistic invader or merely part of the normal microflora of the adult bovine gut (horner et al., ; durham et al., durham et al., , takahashi et al., takahashi et al., , espinasse et al., ; broes et al., ; saif et al., saif et al., , benfield & saif, ) . the epidemiology of winter dysentery is also consistent with bcv being a causative agent. herds with a previous history of winter dysentery are more likely to suffer further outbreaks of disease, possibly due to the presence of carrier animals. coronaviruses survive best at low temperatures and at low intensities of ultraviolet light, leading to higher levels of environmental contamination in winter (pensaert & callebaut, ) . since bcv may be transmitted by both the oral and respiratory routes, spread of infection is facilitated by the close confinement of large numbers of cattle during the winter months. the bcv associated with winter dysentery in adult cattle is closely related to the virus which causes diarrhoea in neonatal calves (akashi et al., ) . slightly different strains of the virus may, however, be involved in the two diseases, as benfield & saif ( ) demonstrated that two out of three winter dysentery isolates failed to agglutinate rat and mouse red blood cells, and that all three isolates failed to show strong cross-reactivity with m strain bcv in serum neutralization tests. whilst present data strongly suggest an association between bcv and winter dysentery, it is not yet possible to induce diarrhoea consistently in adult cattle by oral inoculation with faeces collected from natural cases of the disease, although diarrhoea has been reproduced in gnotobiotic calves (saif, ) . failure to reproduce the disease consistently in adult cattle may be because other risk factors are involved, and these may include both environmental stress factors such as changes in diet and low temperatures and also the presence of other microorganisms. research on bcv is currently at an exciting stage, as not only has our knowledge of the virus advanced rapidly in recent years but a number of important questions are likely to be resolved in the near future. the precise functions of the s and he gps in the initiation of infection remains to be elucidated, and the regions responsible for in vivo protection must be more fully mapped. the occurrence of infections in older animals, whether due to reinfection or the reactivation of subclinical persistent infections, should be further investigated, as should the possible role of bcv in winter dysentery. finally, and most importandy, effective vaccines must be developed which protect calves against bcv diarrhoea and which may also protect adult animals against winter dysentery. these vaccines may be either conventional whole virus or subunit vaccines, but in either case the protective levels of antibody should be defined and the effect of passive immunity on the development of active immunity further examined. deduced sequence of the bovine coronavirus spike protein and identification of the internal proteolytic cleavage site kda encoded between the spike and membrane protein genes of the bovine coronavirus acute undifferentiated neonatal diarrhoea in beef calves. . occurrence and distribution of infectious agents properties of a coronavirus isolated fi-om a cow with epizootic diarrhoea propagation of the kakegawa strain of bovine coronavirus in suckling mice, rats and hamsters rotavirus and coronavirus infections in animals susceptibility of laboratory mice to intranasal and contact infection with coronaviruses of other species cell culture propagation of a coronavirus isolated fiom cows with winter dysentery vaccination of cows against coronavirus-infection in their ofl~ spring: the mouse as a laborato o, animal model nucleotide sequence of tile glycoprotein s gene of bovine enteric coronavirus and comparison with the s proteins of two mouse hepatitis virus strains comparative structure of coronaviruses replication of an enteric bovine coronavirus in intestinal organ cultures isolation of coronaviruses from neonatal calf diarrhoea in great britain and denmark isolement d'un coronavirus chez des bovins atteints d'enterite homorragique hivernale (winter dysentery) en belgique detection ot" rotavirus and coronavirus shedding in two beef cow herds in idaho a comparison of bovine coronavirus strains using monoclonal antibodies shedding of enteric coronavirus in adult cattle the sequence of cdna of bovine coronavirus k nonstructural gene vaccination against enteric rota and coronaviruses in cattle and pigs: enhancement of lactogenic immunity prevalence ot" rotavirus and coronavil-us antigens in the feces of normal cows comparison of different antigen preparations as substrates for use in passive hemagglutination and enzyme-linked immunosorbent assays for detection of antibody against bovine enteric coronavirus monoclonal antibody capture enzyme-linked immunosorbent assay for detection of bovine enteric coronavirus chronic shedding of bovine enteric coronavirus antigen-antibody complexes by clinically normal cows sequence and analysis of bovine enteritic coronavirus (f ) genome characterization of monoclonal and polyclonal antibodies to bovine enteric coronavirus: establishment of an efficient elisa for antigen detection in feces counterimmunoelectroosmophoresis for detection of neonatal calf diarrhea coronavirus: methodology and comparison with electron microscopy physicochemical and biological properties of neonatal calf diarrhea coronaviruses isolated in quebec and comparison with the nebraska calf coronavirus bovine coronavirus isolation and cultivation in continuous cell lines antigenic variations among calf diarrhea coronaviruses by immunodiffusion and counterimmunoelectrophoresis monoclonal antibodies to bovine coronavirus: characteristics and topographical mapping of neutralizing epitopes on the e and e glycoproteins preliminary studies of a bovine coronavirus (bcv) antigen responsible for neutralization structural proteins of bovine coronavirus and their intracellular processing.g, gen. virol mapping of neutralizing epitopes to fragments of the bovine coronavirus e protein by proteolysis of antigen-antibody complexes monoclonal antibodies to bovine coronavirus glycoproteins e and e : demonstration of in vivo virus-neutralizing activity morphology and morphogenesis of a coronavirus infecting intestinal epithelial cells of newborn calves rotavirus and coronavirus associated diarrhoea in domestic animals coronavirusassociated diarrhea (winter dysentery) in adult cattle evaluation of an immunogold electron microscopy technique for detecting bovine coronavirus a serological comparison of bovine coronavirus strains winter dysentery: a coronavirus-like agent in the faeces of beef and dairy cattle with diarrhoea antigenic and biological relationships between human coronavirus oc and neonatal calf diarrhoea coronavirus bovine coronavirus genome antigens of bovine coronavirus strain ly- and their diagnostic properties development of protein a-gold immunoelectron microscopy for detection of bovine coronavirus in calves: comparison with elisa and direct immunofluorescence of nasal epithelial cells a longitudinal study of bovine coronavirus enteric and respiratory infections in dairy calves in two herds in ohio isotype-specific antibody responses to bovine coronavirus structural proteins in serum, feces and mucosal secretion from experimentally challenge-exposed colostrum deprived calves mucosal and systemic antibody responses to bovine coronavirus structural proteins in experimentally challengeexposed calves fed low or high amounts of colostral antibodies epidemiologic factors and isotype-specific antibody responses in serum and mucosal secretions of dairy calves with bovine coronavirus respiratory tract and enteric tract infections mucosal and systemic isotype-specific antibody responses to bovine coronavirus structural proteins in naturally infected dairy calves plaque assay of bovine coronavirus in bek- cells bovine coronavirus mrna replication continues throughout persistent infection in cell culture synthesis and processing of the bovine enteric coronavirus haemagglutinin protein coronaviridae and their replication coronavirus-like agent present in faeces of cows with diarrhoea comparison of bovine coronavirus (bcv) antigens: monoclonal antibodies to the spike glycoprotein distinguish between vaccine and wild-type strains excretion and persistence of bovine coronavirus in neonatal calves experimental infection with a virulent pneumoenteric isolate of bovine coronavirus calf diarrhoea coronavirus temporal regulation of bovine coronavirus rna synthesis structure and orientation of expressed bovine coronavirus hemagglutinin-esterase protein bovine coronavirus structural proteins bovine coronavirus hemagglutinin protein coronavirus: organization, replication and expression of genome coronaviral enteritis of young calves: virologic and pathologic findings in naturally occurring infections in vitro culture of bovine enteric coronavirus (bec). colloq. de i'inserm sequence analysis of the bovine coronavirus nucleocapsid and matrix protein genes pathophysiologic changes due to coronavirus-indtlced diarrhea in the calf sequence of mouse hepatitis virus a mrna : indications for rna recombination between coronaviruses and influenza c virus diagnosis of viral agents associated with neonatal calf diarrhoea coronavirus infection of the bovine respiratory tract neonatal calf diarrhea: results of a field trial using a reo-like virus vaccine neonatal calf diarrhea: propagation, attenuation and characteristics of a coronavirus-like agent pathology of neonatal calf diarrhea induced by a coronavirus-like agent scanning electron, light and immunofluorescent microscopy of intestine of gnotobiotic calf infected with calf diarrheal coronavirus. a m pathogenic relationships of rotavirus, escherichia coli, and other agents in mixed infections in calves incidence of diarrhoea and of rotavirus and coronavirus shedding in calves, whose dams had been vaccinated with an experimental oiladjuvanted vaccine containing bovine rotavirus and bovine coronavirus bovine coronavirus is also a cause of respiratory disease in calves humoral immune response of the bovine fetus to in utero vaccination with attenuated bovine coronavirus colostral and milk antibody titers in cows vaccinated with a modified live-rotavirus-coronavirus vaccine cloning and in vitro expression of the gene for the e haemagglutinin glycoprotein of bovine coronavirus expression and secretion of the bovine coronavirus hemagglutinin-esterase glycoprotein by insect cells infected with recombinant baculoviruses primary structure of the s peplomer gene of bovine coronavirus and surface expression in insect cells analysis of cell fusion induced by bovine coronavirus infection scanning electron microscopic characterization of bovine coronavirus plaques in hrt cells bovine coronavirus antigen in the host cell plasmalemma initial events in bovine coronavirus infection: analysis through immunogold probes and lysosomotropic inhibitors the coronaviruses: clinical and structural aspects with some practical implications. a. med. vet. the prevention and control of epidemics of acute undifferentiated diarrhea of beef calves in western canada evaluation of elisa and electron microscopy for the detection of coronavirus and rotavirus in bovine faeces studies on the relationship between coronaviruses from the intestinal and respiratory tracts of calves microbiology of calf diarrhoea in southern britain detection by radioimmunoassay and enzymelinked immunosorbent assay of coronavirus antibodies in bovine serum and lacteal secretions bovine enteric coronavirus structure as studied by a freeze-drying technique passive immunity to coronavirus and rotavirus infections in swine and cattle: enhancement by maternal vaccination development of nasal, fecal and serum isotype-specific antibodies in calves challenged with bovine coronavirus or rotavirus a review of evidence implicating bovine coronavirus in the etiology of winter dysentery in cows: an enigma resolved? cornell vet experimentally induced coronavirus infections in calves: viral replication in the respiratory and intestinal tracts winter dysentery in dairy herds: electron microscopic and serological evidence for an association with coronavirus infection hemagglutination by calf diarrhea coronavirus detection of bovine coronavirus in feces by reversed passive hemagglutination hemagglutinating encephalomyelitis virus attaches to n-acetyl- -o-acetylneuroaminic acid-containing receptors on erythrocytes: comparison with bovine coronavirus and influenza c virus the s protein of bovine coronavirus is a hemagglutinin recognizing -o-acetylated sialic acid as a receptor determinant isolated he-protein from hemagglutinating encephalomyelitis virus and bovine coronavirus has receptor destroying and receptor-binding activity characterization of a calf diarrheal coronavirus diagnosis of porcine and bovine enteric coronavirus infections using cloned cdna probes the organization and expression of coronavirus genomes pneumoenteric syndrome in bovine neonates by bovine coronavirus passive immunity in calf rotavirus infections: maternal vaccination increases and prolongs immunoglobulin g antibody secretion in milk diarrhoea in dairy calves reduced by feeding colostrum from cows vaccinated with rotavirus aetiology of diarrhoea in young calves coronaviruses: structure and genome expression coronaviruses bovine coronavirus-induced cytopathic expression and plaque formation: host cell and virus strain determine trypsin dependence structural proteins of bovine coronavirus strain l : effects of the host cell and trypsin treatment neonatal calf diarrhea: purification and electron microscopy ofa coronavirus-like agent reactivity of antibodies in human serum with antigens of an enteropathogenic bovine coronavirus enhancement of plaque formation and cell fusion of an enteropathogenic coronavirus by trypsin treatment monoclonal antibodies differentiate between the hemagglutinating and the receptor-destroying activities of bovine coronavirus replication of a bovine coronavirus in organ cultures of foetal trachea epizootic diarrhoea of adult cattle associated with a coronavirus-like agent bovine epizootic diarrhoea resembling winter dysentery caused by bovine coronavirus dat'verc propagation of bovine enteritic coronavirus in three cell systems: electron microscopic studies a search for new microorganisms in calf pneumonia by the inoculation of gnotobiotic calves field trial evaluation of a reocoronavirus calf diarrhea vaccine trypsin-enhanced replication of neonatal calf diarrhea coronavirus in bovine embryonic hmg cells isolation of bovine coronavirus from feces and nasal swabs of calves with diarrhoea detection of coronavirus in calf faeces with a haemadsorption-elution-haemagglutination assay (heha) calfhood coronavirus enterocolitis: a clue to the etiology of winter dysentery plaque assay for titration of bovine enteric coronavirus utilization of monoclonal antibodies for antigenic characterization of coronaviruses antigenic and polypeptide structure of bovine enteric coronavirus as defined by monoclonal antibodies topological and functional analysis of epitopes on the s (e ) and he (e ) glycoproteins of bovine enteric coronavirus biotinylated and radioactive cdna probes in the detection by hybridization of bovine enteric coronavirus polymerase chain reaction for probe synthesis and for direct amplification in detection of bovine coronavirus detection of bovine enteric coronavirus in clinical specimens by hybridization with cdna probes enteric infections in veal calves: a longitudinal study on four veal calf units the e protein of bovine coronavirus is a receptor-destroying enzyme with acetylesterase activity human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza c viruses a field trial to test the efficacy of a combined rotavirus-coronavirus/e, coli vaccine in dairy cattle viral enteritis of calves significance of bovine coronavirus infection analysis of the s spike (peplomer) glycoprotein of bovine coronavirus synthesised in insect cells the $ subunit of the spike glycoprotein of bovine coronavirus mediates membrane fusion in insect cells structural analysis of the conformational domains involved in neutralization of bovine coronavirus using deletion mutants of the spike glycoprotein s subunit expressed by recombinant baculoviruses comparison of the nucleotide and deduced amino acid sequences of the s genes specific by virulent and avirulent strains of bovine coronaviruses etiologie des diarrhtes ntonatales du veau. rtsultats d'une enquete strologique relative aux virus reo-like et corona dans la population bovine beige the author wishes to thank dr f. m. m. scott of the moredun research institute, edinburgh, for his helpful comments made during the preparation of this manuscript. this review is dedicated to my father,john bryan clark, who died suddenly during the completion of this manuscript: i hope there are hills and snow in heaven. key: cord- - fmul c authors: vabret, nicolas; britton, graham j.; gruber, conor; hegde, samarth; kim, joel; kuksin, maria; levantovsky, rachel; malle, louise; moreira, alvaro; park, matthew d.; pia, luisanna; risson, emma; saffern, miriam; salomé, bérengère; selvan, myvizhi esai; spindler, matthew p.; tan, jessica; van der heide, verena; gregory, jill k.; alexandropoulos, konstantina; bhardwaj, nina; brown, brian d.; greenbaum, benjamin; gümüş, zeynep h.; homann, dirk; horowitz, amir; kamphorst, alice o.; curotto de lafaille, maria a.; mehandru, saurabh; merad, miriam; samstein, robert m. title: immunology of covid- : current state of the science date: - - journal: immunity doi: . /j.immuni. . . sha: doc_id: cord_uid: fmul c abstract the coronavirus disease (covid- ) pandemic, caused by severe acute respiratory syndrome coronavirus (sars-cov- ) has affected millions of people worldwide, igniting an unprecedented effort from the scientific community to understand the biological underpinning of covid pathophysiology. in this review, we summarize the current state of knowledge of innate and adaptive immune responses elicited by sars-cov- infection and the immunological pathways that likely contribute to disease severity and death. we also discuss the rationale and clinical outcome of current therapeutic strategies as well as prospective clinical trials to prevent or treat sars-cov- infection. the recent emergence and rapid global spread of severe acute respiratory syndrome coronavirus (sars-cov- ) and the resulting coronavirus disease (covid- ) poses an unprecedented health crisis that was declared a pandemic by the world health organization (who) on march , . the origin of sars-cov- was traced to the city of wuhan in hubei province, china, where a cluster of viral pneumonia cases was first detected, many in connection with the huanan seafood wholesale market. china reported this outbreak to the who on december st , and soon after identified the causative pathogen as a betacoronavirus with high sequence homology to bat coronaviruses using angiotensin-converting enzyme (ace ) receptor as the dominant mechanism of cell entry wan et al., b) . following a likely zoonotic spillover, human-to-human transmission events were confirmed with clinical presentations ranging from no symptoms; to mild fever, cough, and dyspnea; to cytokine storm, respiratory failure, and death. sars-cov- is also closely related to sars (retrospectively named sars-cov- ) and mers (middle eastern respiratory syndrome) coronaviruses, causing local outbreaks and zoonotic epidemics in , respectively (de wit et al., . while sars-cov- is not as lethal as sars-cov- or mers-cov (fauci et al., ) , the considerable spread of the current pandemic has brought tremendous pressure and disastrous consequences for public health and medical systems worldwide. the scientific response to the crisis has been extraordinary with a plethora of covid- studies posted in preprint servers, in an attempt to rapidly unravel the pathogenesis of covid- and potential therapeutic strategies. in response, trainees and faculty members of the precision immunology institute at the icahn school of medicine at mount sinai (priism) have initiated an institutional effort to critically review the preprint literature (vabret et al., ) , together with peer-reviewed articles published in traditional journals, and summarize the current state of science on the fast evolving field of covid- immunology. we thematically focus on the innate and adaptive immune responses to sars-cov- and related coronaviruses, clinical studies and prognostic laboratory correlates, current therapeutic strategies, prospective clinical trials, and vaccine approaches. (bouvet et al., ; chen et al., ; ivanov et al., ) , thereby resembling host mrna to promote translation, prevent degradation, and evade rlr sensing. finally, covs also encode an endoribonuclease, nsp , that cleaves ' polyuridines formed during viral replication, which would otherwise be detected by mda (deng et al., ; hackbart et al., ) . coronaviruses have evolved additional strategies to impede activation of prrs. sars-cov- n-protein prevents trim activation of rig-i . likewise, mers-cov ns a, which itself binds dsrna, impedes pkr activation (comar et al., ; rabouw et al., ) and inhibits pact, an activator of rlrs (niemeyer et al., ; siu et al., ) . additionally, mers-cov ns b antagonizes rnasel, another activator of rlrs (thornbrough et al., ) . the role of other prrs remains unclear. for example, sars-cov- papain-like-protease (plp) antagonizes sting, suggesting that self-dna may also represent an important trigger (sun et al., ) . the extent to which sars-cov- homologs overlap in these functions is currently unknown. following activation, rlr and tlrs induce signaling cascades leading to the phosphorylation of transcription factors, such as nf-kb and the interferon-regulatory factor family (irf), ultimately leading to transcription of ifn and proinflammatory cytokines. although no experimental studies have delineated the precise functions of sars-cov- proteins, proteomic studies have demonstrated interactions between viral proteins and prr signaling cascades. sars-cov- orf b indirectly interacts with the signaling adaptor mavs via its association with tom (gordon et al., ) , consistent with prior reports that sars-cov- orf b suppresses mavs signaling (shi et al., ) . furthermore, sars-cov- nsp interacts with signaling intermediate tbk , and nsp is associated with rnf /nrdp , an activator of tbk and irf (gordon et al., ) . similarly, sars-cov- m protein is known to inhibit the tbk signaling complex (siu et al., ) , as does mers-cov orf b (yang et al., ) . other proteins, including sars-cov- plp, n, orf b and orf , block irf phosphorylation and nuclear translocation (devaraj et al., ; . nf-kb is also inhibited by covs proteins. these include sars-cov- plp (frieman et al., ) and mers-cov orf b and orf (canton et al., ; menachery et al., ) . finally, sars-cov- nsp (huang et al., a; kamitani et al., ) and mers-cov nsp (lokugamage et al., ) initiate general inhibition of host transcription and translation, thus limiting antiviral defenses nonspecifically. to prevent signaling downstream of ifn release, cov proteins inhibit several steps of the signal transduction pathway that bridge the receptor subunits (ifnar and ifnar ) to the stat proteins that activate transcription. for sars-cov- , these mechanisms include ifnar degradation by orf a (minakshi et al., ) , decreased stat phosphorylation by nsp (wathelet et al., ) , and antagonism of stat nuclear translocation by orf kopecky-bromberg et al., ) . however, sars-cov- orf shares only % sequence homology with sars-cov- , suggesting this function may not be conserved. in support of this notion, sars-cov- infection fails to limit stat phosphorylation, unlike in sars-cov- infection (lokugamage et al., ) . mucosal immune responses to infectious agents are orchestrated and regulated by myeloid cells with specialized functions, which include conventional dcs (cdcs), monocyte-derived dcs (modcs), plasmacytoid dcs (pdcs), and macrophages (guilliams et al., ) . a growing body of evidence points to dysregulated myeloid responses that potentially drive the covid- hallmark syndromes such as acute respiratory distress syndrome (ards), cytokine release syndrome (crs) and lymphopenia (mehta et al., ) . flow cytometric analyses of pbmcs from symptomatic covid- patients have shown a significant influx of gm-csf-producing, activated cd + t cells and cd + hla-dr lo inflammatory monocytes (im) (giamarellos-bourboulis et al., ; zhou et al., b) . this matches single-cell transcriptomic (scrnaseq) data demonstrating cd + il- β + monocytic expansion wen et al., ) , interferon-mapk driven adaptive immune responses , and il- βassociated inflammasome signatures (ong et al., ) in peripheral blood of covid- patients, although systemic levels of il- β detected are conspicuously low (gnjatic et al., unpublished) . importantly, these immune signatures track with progression of clinical disease. scrnaseq studies performed on pulmonary tissues of patients with severe covid- disease have revealed an expansion of ims and ficolin- + monocyte-derived macrophages, at the expense of tissue-resident reparative alveolar macrophages (am) . the aforementioned study also observed signatures of ifn-signaling and monocyte recruitment that likely contribute to the rapid decline in alveolar patency and promote ards. although most of the clinical focus has been on pulmonary damage and mononuclear phagocyte (mnp) dysfunction therein, it is increasingly clear that covid- likely presents systemic challenges in other organ sites such as the ileum and kidneys. understanding the role of non-pulmonary myeloid cells in tissue-specific pathology associated with covid- will be important. while data on covid- patients continues to rapidly emerge, studies of myeloid cell dysfunction in sars-cov- and mers-cov can provide an important roadmap to understanding covid- pathogenesis ( figure ). sars-cov- infection in mouse models results in an aberrant am phenotype that limits dc trafficking and t cell activation (zhao et al., ) . additionally, ym + fizz + alternative macrophages can increase airway hypersensitivity, thus exacerbating sars-associated fibrosis (page et al., ) . further, as described above, murine sars-cov- studies have demonstrated that delayed ifn-i signaling and inflammatory monocytes-macrophages promote lung cytokine and chemokine levels, vascular leakage, and impaired antigenspecific t cell responses, culminating in lethal disease (channappanavar et al., ) . the role played by prominent ifn-producing pdcs in sars-cov- control or pathogenesis warrants investigation, as they have been shown to be critical in murine coronavirus (mhv) control (cervantes-barragan et al., ) . longitudinal studies in sars-cov- models are awaited, but initial phenotypic studies in humanized hace mice have shown the characteristic alveolar interstitial pneumonia, with infiltration of lymphocytes and monocytes and accumulation of macrophages in the alveolar lumen (bao et al., a) , which recapitulates patient findings . lastly, nonhuman primate (nhp) studies and patient data on sars-cov- have also shown that virus spike-specific igg responses can exacerbate acute lung injury due to repolarization of alveolar macrophages into pro-inflammatory phenotypes and enhanced recruitment of inflammatory monocyte via ccl and il- (clay et al., ; liu et al., ) . however, the extent to which the antibody response contributes to disease pathophysiology remains to be confirmed. the initial mode of viral pathogen-associated signal (pamp) recognition by innate cells has a major impact on downstream myeloid signaling and cytokine secretion (de marcken et al., ) . while macrophages are somewhat susceptible to mers-cov and sars-cov- infection (perlman and dandekar, ; zhou et al., ) , data do not suggest that they are infected by sars-cov- , although one study reported ace and sars-cov- nucleocapsid protein is expressed in lymph nodes and spleenassociated cd + macrophages of covid- patients producing il- . significantly elevated systemic levels of pro-inflammatory cytokine il- have been reported in several covid- patient cohorts and shown to correlate with disease severity (mehta et al., ) . increased il- can also be associated with higher levels of il- , il- , ifn-ɣ and gm-csf as seen in secondary hemophagocytic lymphohistiocytosis. in response to viral infections, mnps drive interleukin, and ifn-i and ifn-iii production, resulting in inflammasome activation, induction of pathogenic th and th cell responses, recruitment of effector immune cells and crs pathology (prokunina-olsson et al., ; tanaka et al., ) . independently, in vitro studies have demonstrated sars-cov- infection can induce intracellular stress pathways resulting in nlrp -dependent inflammasome activation and macrophage pyroptosis shi et al., ) . functional studies are required to implicate these myeloid inflammasome pathways in covid- lung pathology and to assess other immunogenic pathways such as ripk / -dependent necroptosis (nailwal and chan, ) . in conclusion, the strength and duration of myeloid interferon-stimulated gene (isg) signaling potentially dictate covid- disease severity, but rigorous studies are warranted to confirm this. lastly, more work is needed to ascertain the mechanistic role played by lung-resident and recruited granulocytes in sars-cov- control and pathogenesis (camp and jonsson, ; flores-torres et al., ) . in contrast to their early protective role, neutrophil netosis and macrophage crosstalk can drive later-stage inflammatory cascades (barnes et al., ) , underscoring the overall pathogenic nature of damagesensing host responses ( figure ) . collectively, the current knowledge of coronaviruses and sars-cov- infection, in particular, points to an inadvertent collusion involving myeloid cells in covid- pathogenesis, despite their critical role in early sensing and antiviral responses. innate lymphoid cells (ilcs) are innate immune effector cells that lack the expression of rearranged antigen receptors (tcr, bcr). the ilc family is divided into two main groups: the cytotoxic natural killer (nk) cells and the non-cytotoxic helper ilcs, which include ilc , ilc and ilc (vivier et al., ) . conventional nk cells include cd bright cd -nk cells and cd dim cd + cells, that are specialized in cytokine production or cytotoxicity, respectively. multiple studies have reported reduced numbers of nk cells in the peripheral blood of covid- patients, which is associated with severity of the disease wang et al., f; yu et al., ; zheng et al., b) . a recent scrnaseq analysis revealed a transcriptomic signature for nk cells that was equally represented in lungs from patients and healthy donors . the majority of lung nk cells are non-resident (gasteiger et al., ; marquardt et al., ) , and cxcr has been shown to mediate nk cell infiltration upon influenza infection (carlin et al., ) . in vitro, cxcr ligands (cxcl - ) are increased in sars-cov- -infected human lung tissue (chu et al., ) , and cxcr ligand-producing monocytes are expanded in the lungs of covid- patients . this suggests that the cxcr pathway might facilitate nk cell recruitment from the peripheral blood to the lungs in covid- patients ( figure ). nk cells express inhibitory and activating receptors that regulate their cytotoxicity. they are therefore able to induce the lysis of virus-infected cells that upregulate virus-derived proteins, as well as stress-inducible ligands, which are then recognized by nk cellactivating receptors, such as nkp (cerwenka and lanier, ; draghi et al., ; duev-cohen et al., ; glasner et al., ) . future studies should investigate the expression of nk receptor ligands on sars-cov- -infected cells, in order to better understand the mechanisms underlying nk cell activation in covid- disease. further, secretion of igg and igg antibodies during sars-cov- infection (amanat et al., ) may induce cd dim cd + nk cell activation through fc receptor recognition of antibodies, either bound to surface antigens expressed on infected cells or to extracellular virions as immune complexes ( figure ). this interaction might trigger both cytokine production by nk cells and lysis of infected cells through antibodymediated cellular cytotoxicity (adcc), as shown in influenza infection (von holle and moody, ) . emerging data highlight the capacity for nk-mediated adcc in response to naturally isolated sars-cov- anti-s igg that cross-reacts with sars-cov- s glycoprotein when transfected into chinese hamster ovary (cho) cells (pinto et al., ) . these findings suggest that triggering nk cell activation may not only contribute to the resolution of infection, but also contribute to the cytokine storm in ards. ex vivo nk cells from peripheral blood of covid- patients have reduced intracellular expression of cd a, ksp , granzyme b and granulysin, suggesting an impaired cytotoxicity, as well as an impaired production of chemokines, ifn-ɣ and tnf-α (wilk et al., ; zheng et al., b) . several pathways may contribute to the dysregulation of nk cells. while influenza virus infects nk cells and induces apoptosis (mao et al., ) , lung nk cells do not express the entry receptor for sars-cov- , ace , and are therefore unlikely to be directly infected by sars-cov- (travaglini et al., ) . the majority of nk cells found in human lung display a mature cd + kir + cd dim phenotype and are able to induce cell cytotoxicity in response to loss of hla class i or through fc receptor signaling, although to a lower extent than their peripheral blood counterpart (marquardt et al., ) . killer-immunoglobulin receptors (kirs) are acquired during nk cell development alongside cd (fcrγiiia) and are essential for nk cell licensing and subsequent capacity for cytolytic function (sivori et al., ) . frequencies of nk cells expressing cd and/or kir are decreased in the blood following sars-cov- and sars-cov- infection, respectively (xia et al., ; wang et al., d) . collectively, the data suggest either an impaired maturation of the nk compartment or migration of the mature, circulating nk cells into the lungs or other peripheral tissues of sars-cov- -infected patients. the immune checkpoint nkg a is increased on nk cells and cd t cells from covid- patients . nkg a inhibits cell cytotoxicity by binding the nonclassical hla-e molecule (braud et al., ; brooks et al., ) , and this interaction is strongly correlated with poor control of hiv- infection (ramsuran et al., ) . genes encoding the inhibitory receptors lag and tim are also upregulated in nk cells from covid- patients (wilk et al., ; hadjadj et al., ) . thus, increased immune checkpoints on nk cells might contribute to viral escape. additionally, covid- patients have higher plasma concentrations of il- , which significantly correlate with lower nk cell numbers . in vitro stimulation by il- and soluble il- receptor has previously revealed impaired cytolytic functions (perforin and granzyme b production) by healthy donor nk cells, which can be restored following addition of tocilizumab (il- r-blockade) (cifaldi et al., ) . tnf-α is also upregulated in the plasma of covid- patients , and ligand-receptor interaction analysis of peripheral blood scrnaseq data suggests that monocyte-secreted tnf-α might bind to its receptors on nk cells . tnf-α is known to contribute to nk cell differentiation (lee et al., ) , which includes downregulation of nkp (ivagnes et al., ) , though no effect of tnf-α or il- on nk cell-mediated adcc has been reported so far. collectively, these data suggest that cross-talk with monocytes might impair nk cell recognition and killing of sars-cov- infected cells, and antibodies targeting il- and tnf-signaling may benefit enhanced nk cell functions in covid- patients ( figure ). no studies, to date, have reported ilc , ilc , or ilc functions in sars-cov- infection. all three subsets are present in healthy lung (de grove et al., ; yudanin et al., ) . ilc s are essential for the improvement of lung function following influenza infection in mice, through amphiregulin-mediated restoration of the airway epithelium and oxygen saturation (monticelli et al., ) . however, ilc s also produce il- , contributing to the recruitment of macrophages to the lung and influenza-induced airway hyperreactivity (chang et al., ) . indeed, ilcs are involved in the polarization of alveolar macrophages, either towards a m -like phenotype (ilc and ilc ) or a m like phenotype (ilc ) (kim et al., ) . given the increased il- concentrations and the dysregulation of the macrophage compartment observed in covid- patients, the role played by ilcs in sars-cov- infection warrants further investigation. t cells play a fundamental role in viral infections: cd t cells provide b cell-help for antibody production and orchestrate the response of other immune cells, whereas cd t cells kill infected cells to reduce the viral burden. however, dysregulated t cell responses can result in immunopathology. to better understand the role of t cell responses in sars-cov- infection, the pursuit of two major questions is imperative: ( ) what is the contribution of t cells to initial virus control and tissue damage in the context of covid- , and ( ) how do memory t cells established thereafter contribute to protective immunity upon re-infection? some tentative answers are beginning to emerge. similar to earlier observations about sars-cov- infection , several current reports emphasize the occurrence of lymphopenia with drastically reduced numbers of both cd and cd t cells in moderate and severe covid- cases ( figure ) nie et al., b; wang et al., d; zeng et al., ; zheng et al., b) . the extent of lymphopenia -most striking for cd t cells in patients admitted to icu -seemingly correlates with covid- -associated disease severity and mortality diao et al., ; liu et al., b liu et al., , c tan et al., a; wang et al., d zeng et al., ; zhou et al., c) . patients with mild symptoms, however, typically present with normal or slightly higher t cell counts thevarajan et al., ) . the cause of peripheral t cell loss in moderate to severe covid- , though a phenomenon also observed in other viral infections, remains elusive, and direct viral infection of t cells, in contrast to mers-cov (chu et al., ) , has not been reported. several mechanisms likely contribute to the reduced number of t cells in the blood, including effects from the inflammatory cytokine milieu. indeed, lymphopenia seems to correlate with serum il- , il- , and tnf-α (diao et al., ; wan et al., a) , while convalescent patients were found to have restored bulk t cell frequencies paired with overall lower pro-inflammatory cytokine levels diao et al., ; liu et al., a liu et al., , b zheng et al., b) . cytokines such as ifn-i and tnf-α may inhibit t cell recirculation in blood by promoting retention in lymphoid organs and attachment to endothelium (kamphuis et al., ; shiow et al., ) . however, in an autopsy study examining the spleens and hilar lymph nodes of six patients who succumbed to covid- , chen et al. observed extensive cell death of lymphocytes and suggested potential roles for il- as well as fas-fasl interactions . in support of this hypothesis, the il- receptor antagonist tocilizumab was found to increase the number of circulating lymphocytes (giamarellos-bourboulis et al., ) . t cell recruitment to sites of infection may also reduce their presence in the peripheral blood compartment. scrnaseq analysis of bronchoalveolar lavage (bal) fluid of covid- patients revealed an increase in cd t cell infiltrate with clonal expansion . likewise, post-mortem examination of a patient who succumbed to ards following sars-cov- infection showed extensive lymphocyte infiltration in the lungs . however, another study that examined post-mortem biopsies from four covid- patients only found neutrophilic infiltration (tian et al., a) . further studies are therefore needed to better determine the cause and impact of the commonly observed lymphopenia in covid- patients. available information about sars-cov- -specific t cell immunity may serve as an orientation for further understanding of sars-cov- infection. immunogenic t cell epitopes are distributed across several sars-cov- proteins (s, n, m as well as orf ), although cd t cell responses were more restricted to the s protein (li et al., ) . in sars-cov- survivors, the magnitude and frequency of specific cd memory t cells exceeded that of cd memory t cells and virus-specific t cells persisted for at least - years suggesting that t cells may confer long-term immunity (ng et al., ; tang et al., ) . limited data from viremic sars patients further indicated that virusspecific cd t cell populations might be associated with a more severe disease course, since lethal outcomes correlated with elevated th cell (il- , il- , il- ) serum cytokines (li et al., ) . however, the quality of cd t cell responses needs to be further characterized to understand associations with disease severity. few studies have thus far characterized specific t cell immunity in sars-cov- infection. in patients recovering from mild covid- , robust t cell responses specific for viral n, m and s proteins were detected by ifn-γ elispot, weakly correlated with neutralizing antibody concentrations (similar to convalescent sars-cov- patients (li et al., ) , and subsequently contracted with only n-specific t cells detectable in about one third of the cases post recovery . in a second study, pbmcs from covid- patients with moderate to severe ards were analyzed by flow cytometry, approximately weeks after icu admission (weiskopf et al., ) . both virus-specific cd and cd t cells were detected in all patients at average frequencies of . % and . %, respectively, and very limited phenotyping according to cd ra and ccr expression status characterized these cells predominantly as either cd tcm (central memory) or cd tem (effector memory) and temra (effector memory ra) cells. this study is notable for the use of large complementary peptide pools comprising , sars-cov- epitopes (overlapping -mers for s protein as well as computationally predicted hla-i-and -ii-restricted epitopes for all other viral proteins) as antigenspecific stimuli that revealed a preferential specificity of both cd and cd t cells for s protein epitopes, with the former population modestly increasing over ~ - days after initial onset of symptoms. a caveat, however, pertains to the identification of specific t cells by induced cd and cd co-expression, since upregulation of cd by cd t cells, in contrast to cd , may preferentially capture regulatory t cells (treg) (bacher et al., ) . further analyses of s protein-specific t cells by elisa demonstrated robust induction of ifn-γ, tnf-α and il- concomitant with lower levels of il- , il- , il- , il- and il- . a third report focused on s-specific cd t cell responses in patients with mild, severe or critical covid- using overlapping peptide pools and induced cd and cd co-expression as a readout for antiviral cd t cells. such cells were present in % of cases and presented with enhanced cd , hla-dr and ki- expression indicative of recent in vivo activation (braun et al., ) . of note, the authors also detected low frequencies of s-reactive cd t cells in % of sars-cov- seronegative healthy control donors. however, these cd t cells lacked phenotypic markers of activation and were specific for c-terminal s protein epitopes that are highly similar to endemic human coronaviruses, suggesting that crossreactive cd memory t cells in some populations (e.g., children and younger patients that experience a higher incidence of hcov infections) may be recruited into an amplified primary sars-cov- -specific response (braun et al., ) . similarly, endemic cov-specific cd t cells were previously shown to recognize sars-cov determinants (gioia et al., ) . how previous infections with endemic coronavirus may affect immune responses to sars-cov- will need to be further investigated. finally, in general accordance with the above findings on the induction of sars-cov- specific t cells, using tcrseq, huang et al. and liao et al. reported greater tcr clonality of peripheral blood as well as bal t cells in patients with mild vs. severe covid- . moving forward, a comprehensive identification of immunogenic sars-cov- epitopes recognized by t cells (campbell et al., ) , as well as further studies on convalescent patients who recovered from mild and severe disease, will be particularly important. while the induction of robust t cell immunity is likely essential for efficient virus control, dysregulated t cell responses may cause immunopathology and contribute to disease severity in covid- patients (figure ). this is suggested in a study by zhou et al. which reported a significantly increased pbmc frequency of polyclonal gm-csf + cd t cells capable of prodigious ex vivo il- and ifn-γ production only in critically ill covid- patients . of note, gm-csf + cd t cells have been previously implicated in inflammatory autoimmune diseases such as multiple sclerosis or juvenile rheumatoid arthritis, and high levels of circulating gm-csf + cd t cells were found to be associated with poor outcomes in sepsis . additionally, two studies observed reduced frequencies of treg cells in severe covid- cases qin et al., ) . since treg cells have been shown to help resolve ards inflammation in mouse models (walter et al., ) , a loss of tregs might facilitate the development of covid- lung immunopathology. similarly, a reduction of γδ-t cells, a subset of t cells with apparent protective antiviral function in influenza pneumonia (dong et al., ; zheng et al., ) , has been reported in severely sick covid- patients lei et al., b) . currently, little is known about specific phenotypical and/or functional t cell changes associated with covid- . in the majority of preprints and peer-reviewed studies, there are reports of increased presence of activated t cells ( figure ) characterized by expression of hla-dr, cd , cd , cd , cd and ki- (braun et al., ; dong et al., ; guo et al., ; liao et al., ; thevarajan et al., ; yang et al., a; zheng et al., a) . generally, independent of covid- disease severity, cd t cells seem to be more activated than cd t cells thevarajan et al., ; yang et al., a) , a finding that echoes stronger cd , than cd , t cell responses during sars-cov- (li et al., ) . furthermore, in a case study of covid- patients, diao et al. showed that levels of pd- increased from prodromal to symptomatic stages of the disease (diao et al., ) . pd- expression is commonly associated with t cell exhaustion, but it is important to emphasize that pd- is primarily induced by tcr signaling; it is thus also expressed by activated effector t cells (ahn et al., ) . in addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as ox- and cd , ctla- and tigit (zheng et al., a) , and nkg a . reduced numbers of cd + cd t cells as well as larger frequencies of pd- + /tim + cd t cells in icu patients were also reported . expression of most of these markers was found to be higher in cd than in cd t cells, and levels tended to increase in severe vs. non-severe cases, which may be due to differences in viral load. cellular functionality was shown to be impaired in cd and cd t cells of critically ill patients, with reduced frequencies of polyfunctional t cells (producing more than one cytokine) as well as generally lower ifn-γ and tnf-α production following re-stimulation with pma and ionomycin zheng et al., a zheng et al., , b . similarly, zheng et al. reported that cd t cells in severe covid- appear less cytotoxic and effector-like with reduced cd a degranulation and granzyme b (gzmb) production . in contrast, a different study found that both gzmb and perforin were increased in cd t cells of severely sick patients (zheng et al., a) . in accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe sars-cov- infection had significantly higher frequencies of polyfunctional t cells, with cd t cells producing more ifn-γ, tnf-α and il- , and cd t cells producing more ifn-γ, tnf-α and cd a, respectively (li et al., ) . however, given the vigorous dynamics of acute t cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive. accordingly, rnaseq data by liao et al. showed that cd t cells in the bal fluid of severe covid- patients express cytotoxic genes such as gzma, gzmb, and gzmk at higher levels, while klrc and xcl are enriched in mild cases . in summary, t cells in severe covid- seem to be more activated and may exhibit a trend towards exhaustion, based on continuous expression of inhibitory markers such as pd- and tim- as well as overall reduced polyfunctionality and cytotoxicity. conversely, recovering patients were shown to have an increase in follicular helper cd t cells (t fh ) as well as decreasing levels of inhibitory markers along with enhanced levels of effector molecules such as gzm a, gzmb and perforin (thevarajan et al., yang et al., a; zheng et al., b) . collectively, these studies provide a first glimpse into t cell dynamics in acute sars-cov- infection, but any conclusions have to be tempered at this stage on account of significant limitations in many of the current investigations. the humoral immune response is critical for the clearance of cytopathic viruses and is a major part of the memory response that prevents reinfection. sars-cov- elicits a robust b cell response, as evidenced by the rapid and near-universal detection of virusspecific igm, igg and iga, and neutralizing igg antibodies (nabs) in the days following infection. the kinetics of the antibody response to sars-cov- are now reasonably well described . similar to sars-cov- infection (hsueh et al., ) , seroconversion occurs in most covid- patients between and days after the onset of symptoms, and antibody titers persist in the weeks following virus clearance (figure ) , (haveri et al., ; lou et al., ; okba et al., ; wölfel et al., ; wu et al., b; zhao et al., a) . antibodies binding the sars-cov- internal n protein and the external s glycoprotein are commonly detected (amanat et al., ; ju et al., ; . the receptor binding domain (rbd) of the s protein is highly immunogenic and antibodies binding this domain can be potently neutralizing, blocking virus interactions with the host entry receptor, ace (ju et al., ; wu et al., b) . anti-rbd nabs are detected in most tested patients (ju et al., ; . although cross-reactivity to sars-cov- s and n proteins and to mers-cov s protein was detected in plasma from covid- patients, no cross-reactivity was found to the rbd from sars-cov- or mers-cov. in addition, plasma from covid- patients did not neutralize sars-cov- or mers-cov (ju et al., ) . rbd-specific cd + igg + memory b cells were single-cell sorted from a cohort of covid- donors between days - after the onset of symptoms (ju et al., ) . from their antibody gene sequences, sars-cov- specific monoclonal antibodies were produced. the monoclonal antibodies had a diverse repertoire, relatively low or no somatic mutations, and variable binding reactivity, with dissociation constants reaching - to - , similar to antibodies isolated during acute infections. two potent neutralizing sars-cov- rbd-specific monoclonal antibodies were characterized that did not cross-react with the rbd of sars-cov- or mers-cov (ju et al., ) . together, these results demonstrate that antibody mediated neutralization is virusspecific and likely driven by binding of epitopes within the rbd. the b cell response to a virus serves not only to protect from the initial challenge, but also to offer extended immunity against reinfection. following resolution of an infection, plasma cells formed during the acute and convalescent phases continue to secrete antibodies, giving rise to serological memory. memory b cells that are also formed during the primary infection constitute the second arm of b cell memory. memory b cells can quickly respond to a reinfection by generating new high affinity plasma cells. longterm protection is achieved through the induction of long-lived plasma cells and memory b cells. there is great interest in understanding the life-span of b cell memory responses to sars-cov- . protection from reinfection has direct medical and social consequences as the world works to develop vaccination strategies and resume normal activities. in covid- patients, evidence of near universal seroconversion and the lack of substantial descriptions of reinfection point to a robust antibody response, which, along with the t cell memory response, would offer protection to reinfection. indeed, a case study of a single patient described induction of cd hi cd hi antibody secreting cells (ascs), concomitant with an increase in circulating follicular t helper cells (tfh) cells (thevarajan et al., ) , and a scrnaseq study of pbmc from critically ill and recently recovered individuals revealed a plasma cell population . in addition, igg memory cells specific to the rbd have been identified in the blood of covid- patients (ju et al., ) . consistent with the development of immunity after covid- infection, a recent study of sars-cov- infection in rhesus macaques found that two macaques that had resolved the primary infection were resistant to reinfection days later (bao et al., b) . due to the timing of this outbreak, it is not yet possible to know the nature and extent of long-term memory responses, but lessons may again be learned from other human coronaviruses. in the case of the human coronavirus e, specific igg and nabs are rapidly induced but wane in some individuals around a year after infection with some residual protection to reinfection (callow et al., ; reed, ) . the life span of the humoral response following sars-cov- infection is also relatively short, with the initial specific igg and nab response to sars-cov- diminishing - years after infection and nearly undetectable in up to % of individuals (cao et al., ; liu et al., ) . a long-term study following sars-cov- infected healthcare workers over a years period also found that virus-specific igg declined after several years, but the authors observed detectable virus-specific igg years after infection . in the case of mers-cov, antibodies were detected in of volunteers tested years after infection (payne et al., ) . igg specific to sars-cov- trimeric spike protein was detectable in serum up to days after symptom onset, but igg titers began decreasing by weeks post-symptom onset (adams et al., ) . long term protection from reinfection may also be mediated by reactive memory b cells. a study that analyzed sars-cov- s protein-specific igg memory cells at , , and months post-infection found that s-specific igg memory b cells decreased progressively about % from to months after infection (traggiai et al., ) . a further retrospective study of individuals found no evidence of circulating sars-cov- -specific igg + memory b cells years after infection (tang et al., ) . this is in contrast to the memory t cell response, which was robustly detected based on induced ifn-γ production (tang et al., ) . studies of common coronaviruses, sars-cov- and mers-cov indicate that virus specific antibody responses wane over time, and, in the case of common coronaviruses, result in only partial protection from reinfection. these data suggest that immunity to sars-cov- may diminish following a primary infection and further studies will be required to determine the degree of long-term protection (figure ) . several studies have demonstrated that high virus-specific antibody titers to sars-cov- are correlated with greater neutralization of virus in vitro and are inversely correlated with viral load in patients ( figure ) wölfel et al., ; zhao et al., a) . despite these indications of a successful neutralizing response in the majority of individuals, higher titers are also associated with more severe clinical cases okba et al., ; zhao et al., a; zhou et al., a) , suggesting that a robust antibody response alone is insufficient to avoid severe disease ( figure ). this was also observed in the previous sars-cov- epidemic, where neutralizing titers were found to be significantly higher in deceased patients compared to patients who had recovered . this has led to concerns that antibody responses to these viruses may contribute to pulmonary pathology, via antibody-dependent enhancement (ade) (figure ). this phenomenon is observed, when non-neutralizing virus-specific igg facilitate entry of virus particles into fc-receptor (fcr) expressing cells, particularly macrophages and monocytes, leading to inflammatory activation of these cells (taylor et al., ) . a study in sars-cov- -infected rhesus macaques found that anti-s-igg contributed to severe acute lung injury (ali) and massive accumulation of monocytes/macrophages in the lung . furthermore, serum containing anti-s ig from sars-cov- patients enhanced the infection of sars-cov- in human monocyte-derived macrophages in vitro (yip et al., ) . ade was also reported with a monoclonal antibody isolated from a patient with mers-cov . somewhat reassuringly, there was no evidence of ade mediated by sera from rats vaccinated with sars-cov- rbd in vitro (quinlan et al., ) , nor in macaque immunized with an inactivated sars-cov- vaccine candidate (gao et al. ) . as of now, there is no evidence that naturally developed antibodies towards sars-cov- contribute to the pathological features observed in covid- . however, this possibility should be considered when it comes to experimental design and development of therapeutic strategies. importantly, in all of the descriptions of ade as it relates to coronavirus, the fcr was necessary to trigger the antibody-mediated pathology. high-dose intravenous immunoglobulin (ivig), which may blunt ade, has been trialed in covid- patients shao et al., ) , but further studies are needed to determine the extent to which ivig is safe or beneficial in sars-cov- infection. vaccine trials will need to consider the possibility of antibody-driven pathology upon antigen re-challenge; strategies using f(ab) fragments or engineered fc monoclonal antibodies may prove particularly beneficial in this setting (amanat and krammer, ) . with the rapidly growing number of cases in the first few months, numerous reports on predictors of covid- severity with small cohorts were released. these offered clinicians and immunologists the first understanding of the clinical course and pathological processes that are associated with the novel sars-cov- infection. this section highlights key findings from those studies, with a major focus on the immune factors associated with disease risk or severity. there are currently limited known risk factors for susceptibility to covid- , although this has been evaluated in several studies. zhao et al. compared the abo blood group distribution in a cohort of covid- patients to that of healthy controls from the corresponding regions . they found blood group a to be associated with a higher risk for acquiring covid- , when compared to non-a blood groups; blood group o had the lowest risk for the infection. another study demonstrated an identical association (zietz and tatonetti, ) , and similar results have been previously described for other viruses (lindesmith et al., ) , including for sars-cov- (cheng et al., a) . several large collaborative efforts are currently underway to generate, share and analyze genetic data to understand the links between human genetic variation and covid- susceptibility and severity, the most prominent of which is the covid- host genetics initiative (covid hg.org). these studies are supported by previous observations on sars-cov- that followed the outbreak, which have identified significant associations between genetic variants and immune phenotypes (chan et al., ; wang et al., ; zhao et al., ) . although identifying such polymorphisms and their associated genes and pathways for sars-cov- will require large cohorts, several studies have already highlighted genetic polymorphisms that may potentially impact susceptibility, which remain to be tested in clinical trials. these studies have focused on genetic variants that may impact the expression or function of genes important in viral entry, namely ace (sars-cov- receptor) and tmprss (spike protein activator) (asselta et al., ; cao et al., c; renieri et al., ; stawiski et al., ) . cao et al. identified variants that are potentially expression quantitative trait loci (eqtl) of ace (i.e. they may potentially alter ace gene expression) and analyzed their frequencies in different populations (cao et al., c) . stawiski et al. listed variants that may be critical in ace binding and thereby its function, and compared the frequencies of these variants within different populations (stawiski et al., ) . while there are several limitations to these studies, the major question is whether the utility of these biomarkers is replicable in large populations with covid- clinical outcomes data and in targeted or large-scale genomic analyses that are currently underway. in addition, these studies will reveal the potential associations between genetic variants and susceptibility in a gene or loci agnostic fashion. several routine blood and serological parameters have been suggested to stratify patients who might be at higher risk for complications to aid in allocation of healthcare resources in the pandemic (table ). serologic markers from routine blood work were reported, by comparing patients with mild/moderate symptoms to those with severe symptoms. this includes different acute phase proteins, such as saa (serum amyloid protein) and c-reactive protein (crp) . interestingly, elevations in crp appear to be unique to covid- patients, when compared to other viral infections. other consistently reported markers in non-survivors are increased procalcitonin (pct) and il- levels , as well as increased serum urea, creatinine, cystatin c, direct bilirubin, and cholinesterase . overall, inflammatory markers are common in severe cases of covid- and appear to correlate with the severity of the symptoms and clinical outcome. moreover, the extensive damage that occurs in specific organs of severe covid- patients is possibly related to differences in the expression of ace ( figure ) . lymphopenia is the most frequently described prognostic marker in covid- (table ) , and it appears to predict morbidity and mortality even at early stages (fei et al., ) . tan et al. proposed a prognostic model based on lymphocyte counts at two time points: patients with less than % lymphocytes at days - from the onset of symptoms and less than % at days - had the worst outcomes in this study (tan et al., a) . wynants et al. compared predictors of disease severity across studies (> patients), highlighting crp, neutrophil-to-lymphocyte ratio (n/l) and lactate dehydrogenase (ldh) as the most significant predictive biomarkers . furthermore, a meta-analysis of covid- studies with a total of patients also attempted to identify early-stage patients with poor prognosis . the most consistent findings across the different studies were elevated levels of crp, ldh and d-dimer, as well as decreased blood platelet and lymphocyte counts zhou et al., d) . systemic and pulmonary thrombi have been reported with activation of the extrinsic coagulation cascade, involving dysfunctional endothelium and monocytic infiltration (poor et al., ; varga et al., ) ; thrombocytopenia and elevated d-dimer levels may be indicative of these coagulopathies in covid- patients with important therapeutic implications (fogarty et al., ; poor et al., ) . immunological biomarkers are particularly important, as immunopathology has been suggested as a primary driver of morbidity and mortality with covid- . several cytokines and other immunologic parameters have been correlated with covid- severity (table ) . most notably, elevated il- levels were detected in hospitalized patients, especially critically ill patients, in several studies, and are associated with icu admission, respiratory failure, and poor prognosis (chen et al., f; huang et al., b; liu et al., f) . increased il- r, il- , il- , and gm-csf have been associated with disease severity as well, but studies are limited and further studies with larger cohorts of patients are needed to indicate predictive power zhou et al., b) . conflicting results regarding il- β and il- have been reported gong et al., ; wen et al., ) . although elevated cytokine concentrations have been widely described in covid- patients, the vast majority (including il- , il- , il- , ctack, ifn-γ) do not seem to have prognostic value, because they do not always differentiate moderate cases from severe cases (yang et al., b) . this stratification was possible with ip- , mcp- , and il- ra. while there are reports that levels of il- at first assessment might predict respiratory failure (herold et al., ) , other publications with longitudinal analyses demonstrated that il- increases fairly late during the disease's course, consequently compromising its prognostic value at earlier stages . liu et al. developed a web-based tool using k-means clustering to predict prognosis in terms of death or hospital discharge of covid- patients using age, comorbidities (binary), and baseline log helper t cell count (th), log suppressor t cell count (ts), and log th/ts ratio . total t cell, helper t cell, and suppressor t cell counts were significantly lower, and the th/ts ratio was significantly higher in patients who died from infection, as compared to patients who were discharged. importantly, most serological and immunological changes observed in severe cases are associated with disease severity, but can not necessarily serve as predictive factors, as they may not have utility in early identification of patients at higher risk. discovery of truly predictive biomarkers and potential drivers of hyper-inflammatory processes requires comprehensive profiling of asymptomatic and mild cases and longitudinal studies which are limited to date. confounding variables including age, gender, comorbidities may dramatically affect associations observed. in addition, direct correlation with patient viral load will be important to provide a greater understanding of underlying causes of morbidity and mortality in covid- and the contribution of viral infectivity, hyperinflammation and host tolerance (medzhitov et al., ) . in summary, lymphopenia, increases in proinflammatory markers and cytokines and potential blood hypercoagulability characterize severe covid- cases with features reminiscent of cytokine release syndromes. this correlates with a diverse clinical spectrum ranging from asymptomatic to severe and critical cases. during the incubation period and early phase of the disease, leukocyte and lymphocyte counts are normal or slightly reduced. after sars-cov- binds to ace overexpressing organs, such as the gastrointestinal tracts and kidneys, increases in non-specific inflammation markers are observed. in more severe cases, a marked systemic release of inflammatory mediators and cytokines occurs, with corresponding worsening of lymphopenia and potential atrophy of lymphoid organs, impairing lymphocyte turnover (terpos et al., ). antivirals are a class of small molecules that function as inhibitors of one or more stages of a virus life cycle. because of similarities between different virus replication mechanisms, some antivirals can be repurposed against various viral infections. currently, most of the available antiviral drugs tested against sars-cov- are smallmolecules previously developed against sars-cov- , mers-cov, or other rna and dna viruses. a number of small molecules with known antiviral activity against other human rna viruses are being evaluated for efficacy in treating sars-cov- . the ribonucleoside analog β-d-n -hydroxycytidine (nhc) reduced viral titers and lung injury in mice infected with sars-cov- via introduction of mutations in viral rna (sheahan et al., ) . further, an inhibitor of host dhodh, a rate-limiting enzyme in pyrimidine synthesis, was able to inhibit sars-cov- growth in vitro with greater efficacy than remdesivir or chloroquine xiong et al., ) . merimepodib, a non-competitive inhibitor of the enzyme inosine- ′-monophosphate dehydrogenase (impdh), involved in host guanosine biosynthesis, is able to suppress sars-cov- replication in vitro . finally, n-( -hydroxypropyl)- -trimethylammonium chitosan chloride (htcc), which was previously shown to efficiently reduce infection by the less pathogenic human coronavirus hcov-nl , was also found to inhibit mers-cov and pseudotyped sars-cov- in human airway epithelial cells (milewska et al., ) . much of the antiviral computational and experimental data currently available for sars-cov- focus on targeting the cl or main protease (mpro). two prominent drug candidates targeting the sars-cov- mpro were designed and synthesized, by analyzing the substrate binding pocket of mpro (dai et al., ) . the x-ray crystal structures of the novel inhibitors in complex with sars-cov- mpro were resolved at . Å. both compounds showed good pharmacokinetic activity in vitro, and one exhibited limited toxicity in vivo (dai et al., ) . multiple studies also aimed to repurpose protease inhibitors to reduce sars-cov- titers. nine existing hiv protease inhibitors (nelfinavir, lopinavir, ritonavir, saquinavir, atazanavir, tipranavir, amprenavir, darunavir, and indinavir) were evaluated for their antiviral activity in vero cells infected with sars-cov- (yamamoto et al., ) and nelfinavir was the most potent at inhibiting viral replication. the coronavirus rna-dependent rna polymerase (rdrp) catalyzes the synthesis of viral rna making it essential for viral replication and a prime target for antiviral inhibitors. remdesivir, an adenosine triphosphate analog, inhibits rdrp by binding to rna strands and preventing additional nucleotides from being added, thereby terminating viral rna transcription ( figure a ) (agostini et al., ) . remdesivir has been previously shown to be effective against mers-cov and sars-cov- infections in animal models (sheahan et al., ; de wit et al., ) . similarly, a study investigated the efficacy of remdesivir treatments on rhesus macaques with sars-cov- infections (williamson et al., ) . macaques treated with remdesivir showed a reduction in lung viral loads and pneumonia symptoms, but no reduction in virus shedding. this study does provide evidence that if administered early enough, remdesivir may be effective at treating sars-cov- infections. a large number of clinical trials using experimental antiviral drugs are currently underway. a small proportion of them are aimed at repurposing existing antivirals including: arbidol (umifenovir), a broad-spectrum antiviral that blocks viral fusion; lopinavir/ritonavir (lpv/r), a combination of anti-hiv protease inhibitors; favipiravir, an rdrp inhibitor used to treat severe influenza infections (hayden and shindo, ) ; and remdesivir ( figure a ). chen et al. conducted a multicenter, randomized priority trial on patients with confirmed covid- infection to test favipiravir or arbidol . favipiravir was suggested to significantly improve symptom relief. however, the interpretation of this study is limited by a short clinical recovery window of days, only of patients with confirmed covid- , and the lack of a control group. lpv/r has previously shown efficacy in treating sars-cov- (chu et al., ) , prompting an early sars-cov- clinical trial . patients were enrolled in a trial investigating the efficacy and safety of lpv/r (n= patients), arbidol (n= ), or control (n= ) as treatment for mild-to-moderate covid- . at day of treatment, . %, . % and . % of patients had a positive to negative conversion in the lpv/r, arbidol, and control groups, respectively, with no statistical significance between groups. a randomized controlled trial (rct) with severe covid- patients did not observe a significant benefit of lpv/r either (cao et al., a) . however, a study that looked at the impact of earlier administration of (lpv/r) treatment showed that when treatment of lpv/r was started within days of symptom onset, a shorter duration of virus shedding was observed. thus, timing of lpv/r administration may be critical to its efficacy . in a multicenter clinical study assessing the compassionate use of remdesivir in severe covid- patients, patients across several countries were treated with remdesivir for days (grein et al., ) . % of the patients who received remdesivir showed clinical improvement assessed through improved oxygen-support/extubations. without a proper control group, limited conclusions can be drawn with regards to the efficacy of remdesivir from this study. the measured % clinical improvement may be in line with average clinical improvement across patients treated with standard of care . a small rct in china with severe covid- patients randomized : to remdesivir vs. placebo demonstrated no significant benefit in time to clinical improvement . almost simultaneously, preliminary results from a larger niaid rct with more than patients were announced with remdesevir to be associated with quicker time to recovery: days compared with days (ledford, ) . a non-significant benefit in mortality was also noted and the trial was stopped early to allow access to remdesivir in the placebo arm. complete safety data and full publication are awaited but this study offers encouraging results and have resulted in an fda emergency use authorization for remdesivir in hospitalized covid- patients. chloroquine (cq) and its derivative hydroxychloroquine (hcq) have gained traction as possible therapeutics for covid- . both drugs are used as antimalarial agents and as immunomodulatory therapies for rheumatologic diseases. however, the application of cq and hcq to covid- stems for their past use as antivirals (savarino et al., ) , including for sars-cov- (keyaerts et al., ; vincent et al., ) . cq and hcq interfere with lysosomal activity and have been reported to have immuno-modulatory effects. cq augments antigen processing for mhc class i and ii presentation, directly inhibits endosomal tlr and tlr , and enhances the activity of regulatory t cells (garulli et al., ; lo et al., ; schrezenmeier and dörner, ; thomé et al., a thomé et al., , b . early studies involving in vitro infection of host cells with sars-cov- demonstrated that both cq and hcq significantly impact endosomal maturation, resulting in increased sequestration of virion particles within endolysosomes. however, there has been conflicting evidence whether cq is more potent than hcq in reducing viral load yao et al., a) . notably, one group reported that treatment of infected cells with hcq before and during infection significantly reduced viral load, suggesting that combined prophylactic and therapeutic hcq use yields maximum efficacy (clementi et al., ) . to better understand host immune responses to treatment, one group compared bulk transcriptomic changes in primary pbmcs treated with hcq for hours to pbmcs from confirmed sars-cov- positive patients and controls, followed by a comparison of hcq treated primary macrophages to bal and postmortem lung biopsies from covid- patients (corley et al., ) . across all comparisons, there was minimal overlap between host differential gene expression and genes altered by in vitro hcq treatment. thus, the potential mechanistic action of hcq in the context of sars-cov- remains poorly defined. despite the apparent widespread use of hcq and cq to treat covid- ( figure b ), few controlled clinical trials have been performed so far and thus the potential benefits of these drugs for covid- remains controversial. one of the earliest trials ( - - ) was a single-arm, open label trial of mg daily hcq in covid- patients. they reported that hcq alone, or in combination with the antibiotic azithromycin (az), reduced viral load by day (gautret et al., a) . a follow up trial in patients treated with hcq + az reported that % of patients had a negative pcr result on day of treatment, and . % were discharged within days of treatment. however, it is important to note that both trials had no control arms (gautret et al., b) . rigorous statistical analyses by others that accounted for the patients excluded from the original analysis found limited evidence for hcq monotherapy (hulme et al., ; lover, ) . a double blind rrct assessed hcq monotherapy in the treatment of mild covid- (chictr ) . a total of patients were enrolled; the treatment arm received mg hcq daily over days. by day , patients who received hcq had clinical resolution on average one day earlier than controls; no patients progressed to severe disease compared to patients in the control arm. in a smaller rct treated patients with mild covid- (nct ) with mg hcq for days, there were no significant differences in the number of patients with negative pcr results on day (all but one positive), median duration of hospitalization, time to fever resolution, or progression of disease on chest ct . the largest rct to date enrolled patients with mild covid- across centers in an open label trial of hcq + standard of care (chictr ). there were no significant differences between groups in conversion to negative sars-cov- rt-pcr result on day or rate of symptom resolution; there were significantly more adverse events in the hcq arm, though largely non-serious; they reported some evidence for faster normalization of c-reactive protein in the patients who received hcq plus standard of care, but this finding was not significant (tang et al., b) . a metaanalysis including most of the studies described here found no clinical benefits to patients receiving standard of care plus an hcq regimen (shamshirian et al., ) . two studies have assessed hcq efficacy in severe covid- . in a prospective study of patients who had received mg hcq over days with az on days - , there were several patients with worsening clinical status and one death; / patients had a positive pcr result on day ( molina et al., ) . an ongoing double blind rct of patients with severe covid- (nct ) randomized patients into high dose hcq ( mg x/d for days) or low dose ( mg/day for days) treatment groups (borba et al., ) . recruitment into the high dose arm was halted prematurely due to poor safety outcomes. there was no significant difference in negative pcr results on day or need for mechanical ventilation on day . taken together, the clinical trials performed thus far to evaluate the efficacy of hcq ± az for covid- have not demonstrated clear evidence of clinical benefit in patients with severe disease. a search of clinicaltrials.gov on april , found clinical trials investigating hcq. this number is rapidly growing, indicating the heightened interest in this therapeutic and pressing need for evidence-based recommendations. because of their anti-inflammatory activity, corticosteroids (cs) are an adjuvant therapy for ards and cytokine storm. however, the broad immunosuppression mediated by cs does raise the possibility that treatment could interfere with the development of a proper immune response against the virus. a meta-analysis of , patients with mers-cov, sars-cov- , or sars-cov- infection found that cs treatment was associated with higher mortality . a more recent meta-analysis of only sars-cov- infection assessed , patients and found no mortality difference associated with cs treatment, including in a subset of patients with ards (gangopadhyay et al., ) . other studies have reported associations with delayed viral clearance and increased complications in sars and mers patients (sanders et al., ) . in fact, the interim guidelines updated by the who on march , advise against giving systemic corticosteroids for covid- (world health organization, a) . yet, new data from covid- are conflicting. one group reported no significant difference in time to viral clearance between patients who received methylprednisolone orally (mild disease) or iv (severe) and those who did not . retrospective studies from groups in china report that patients who were transferred to the icu were less likely to have received cs and that patients with ards who received methylprednisolone had reduced mortality risk . in contrast, another retrospective analysis found that patients who received cs were more likely to have either been admitted to the icu or perished, although the cs treated group also had significantly more comorbidities . a smaller observational study of patients found no association between corticosteroid treatment and time to viral clearance, length of hospital stay, or symptom duration (zha et al., ) . a larger study of adjuvant cs in patients with critical covid- found no association with -day mortality; subgroup analysis of patients with ards found no association between treatment with cs and clinical outcomes . they also found that increased dosage was significantly associated with increased mortality risk. a retrospective review of patients, of whom received iv methylprednisolone, found that early, low-dose administration significantly improved spo and chest ct, time to fever resolution, and time on supplemental oxygen therapy (wang et al., h) . others have published perspectives in support of early and short-term, low dose administration based on anecdotal evidence, but not clinical trials. most of the current data on cs use in covid- are from observational studies, and support either modest clinical benefit or no meaningful effects. larger rcts are necessary to understand the risks and benefits of cs for these patients; there are trials evaluating various corticosteroids registered on clinicaltrials.gov as of april , . one of the first defenses of the human body against rna viruses like sars-cov- is the release of type i and iii ifns. it is important to note that type i ifn (ifnα/β) receptors are ubiquitously expressed, so ifnα/β signaling can result in not only antiviral effects, but also in the activation of immune cells that potentially exacerbate pathogenesis. in contrast, type iii ifn (also known as ifnλ) signals mainly in epithelial cells, as well as in a restricted pool of immune cells. because type iii ifns have immunomodulatory functions, subsequent signaling could induce a potent antiviral effect without enhancing pathogenic inflammation (andreakos et al., ; prokunina-olsson et al., ) . recently, there has been a growing interest in the potential therapeutic impact of modulating the ifn response to disable covid- pathogenesis. before the current pandemic, groups have studied the role of ifns in other betacoronavirus infections. one study of patients with sars-cov- infection described unresolved elevated type i ifns and ifn-stimulated genes (isgs) in those with poor outcomes (cameron et al., ) . others report that exogenous type i ifn does not improve outcomes when given with ribavirin in patients with mers-cov infection (arabi et al., ) , suggesting that the role of ifn as a therapeutic or prophylactic option may be strain-or species-specific (sheahan et al., ) . interestingly, a recent study by mount sinai virology groups revealed that type i ifn signaling is impaired in the early response to sars-cov- ; in vitro, sars-cov- may be more susceptible to type i ifn than sars-cov- (blanco-melo et al., ) . based on additional evidence that ifn responses to betacoronaviruses are altered as compared to other respiratory viruses (blanco-melo et al., ; channappanavar et al., ; okabayashi et al., ) , trials of ifn-i/iii administration have been initiated (nct , nct ). hyperinflammatory responses and elevated levels of inflammatory cytokines, including interleukins (il)- , , and , have been shown to correlate with covid- severity diao et al., ; gong et al., ; moore and june, ; wan et al., a; xu et al., b) . the drivers of this cytokine storm remain to be established, but they are likely triggered initially by a combination of viral pamps and host danger signals. the heterogeneous response between patients suggests other factors are involved, possibly including the sars-cov- receptor, ace (hirano and murakami, ) . several studies have begun to report the cellular programs that may contribute to the cytokine storm detected in covid- patients. one group reported that in the context of generalized lymphopenia, certain subsets of cd t cells that express gm-csf and il- are more abundant in severe covid- patients than in covid- patients who do not require intensive care . reports that other major proinflammatory cytokines (tnf-α, ifn-ɣ, il- ) and chemokines (ccl , ccl , ccl ) are elevated underscore a potentially pathogenic t h / program in covid- (diao et al., ; giamarellos-bourboulis et al., ) . histological and single-cell analyses identified monocytes/macrophages as other potent sources of inflammatory cytokines in covid- cytokine storm giamarellos-bourboulis et al., ; law et al., ; moore and june, ; zhou et al., b) . studies of other betacoronavirus infections, including sars-cov- and mers-cov, have also identified similar hyperactivation of monocytes, macrophages, and dendritic cells as a driver of cytokinemediated immunopathology in humans chien et al., ; huang et al., c; konig et al., ; wang et al., ; wong et al., ; xu et al., b; zhou et al., b) . following preliminary reports of il- as a critical cytokine in covid- -associated cytokine release syndrome (crs), monoclonal antibodies that target the il- signaling pathway have been proposed as therapeutic candidates (moore and june, ) ( figure c ). the commercial anti-il- r antibodies tocilizumab (actemra) and sarilumab (kevzara), and the anti-il- antibody siltuximab (sylvant), are now being tested for efficacy in managing covid- crs and pneumonia in ongoing clinical trials (table ). to date, only one group has reported preliminary results from a cohort of covid- patients treated with a single administration of tocilizumab ( mg, iv), along with lopinavir, methylprednisolone, and oxygen therapy (chictr ) . the single observation study found recuperated lymphocyte counts in / patients and resolution of lung opacities in / patients on chest ct; / patients were discharged. all patients experienced an improvement in symptoms, and no subsequent pulmonary infections were reported. a second report described an association between use of tocilizumab and reduced likelihood of icu admission and mechanical ventilation. still, in declining patients with severe covid- pneumonia, this retrospective study did not report significant improvement in mortality on weighted analysis (roumier et al., ) . nevertheless, these studies are encouraging but like other treatment approaches, larger rcts are needed. in addition to the il- signaling pathway, other cytokine-/chemokine-associated elements, including il- r, gm-csf and the chemokine receptor ccr , have been proposed as potential targets for blockade to manage covid- crs ( figure c ). finally, complement activation was shown to be over-activated in lungs of covid- patients. although results from the randomized trial are not yet published, anti-c a monoclonal antibody therapy showed benefits in two critically-ill covid- patients . while vaccines are being developed to educate a person's immune system to make their own nab against sars-cov- , there is interest in using adoptive transfer of nab as a therapeutic approach ( figure d ). this strategy has already proven to be effective against sars-cov- (cao et al., ; ho et al., ; ter meulen et al., ; sui et al., ; zhu et al., ) and mers-cov (forni et al., ; jia et al., ; ying et al., ) . in the case of sars-cov- , these efforts are primarily centered on identifying nab made during natural infections or generating nab through animal vaccination approaches. patients who have recovered from sars-cov- infection are one potential source of nabs (ju et al., ; walls et al., ; wölfel et al., ; ye et al., ; yuan et al., ) . in an effort to obtain these nabs, scientists sorted rbd specific memory b cells and cloned their heavy and light variable region to express recombinant forms of the corresponding antibodies (ju et al., ; ye et al., ) . four of the antibodies produced in these studies ( b , d , p c- f p c- f ) showed high neutralizing potential in vitro, and all inhibited ace /rbd binding. successful antibody-mediated neutralization of sars-cov- seems to be dependent on the inhibition of ace /rbd binding. however, ye et al. showed that nearly all antibodies derived from serum of recovered patients bound to s and rbd, with only actually inhibiting ace /rbd binding . of note, a sars-cov- derived neutralizing antibody ( d ) and a single chain antibody against sars-cov- (n ) have also been shown to neutralize sars-cov- without inhibiting ace /rbd binding. thus, blocking this interaction may not be a prerequisite for an effective sars-cov- nab. the generation of a hybridoma producing a monoclonal nab against sars-cov- provides the potential for a therapeutic ab that can be directly administered to patients to block ongoing infection and potentially even as a prophylactic ( figure d ). sars-cov- and sars-cov- consensus sequences share about % identity (tai et al., ) . thus, a wide range of sars-cov- nabs have been tested for crossreactivity with sars-cov- , as they could help speed up the development of potential covid- treatments. in a recent study, antibodies were isolated from the memory b cells of an individual who recovered from sars-cov- infection. while out of isolated antibodies could bind sars-cov- s protein, one of them (s , see table ) also neutralizes sars-cov- (pinto et al., ) . the combination of s with a weakly neutralizing antibody that could bind another rbd epitope led to enhanced neutralization potency. in addition, cr (table ) was found to bind sars-cov- rbd , but this antibody did not neutralize sars-cov- . computational simulations identified amino-acids that could be modified on cr to enhance its binding affinity with sars-cov- rbd (corrêa giron et al., ) , potentially augmenting its neutralization potential. animal models represent another tool to generate nabs against sars-cov- (table ) . in one study, the authors developed a protocol to synthetize human nanobodies, smaller antibodies that only contain a heavy variable (vh) chain as first described in camelids (figure d ). another antibody isolated from camelids immunized with sars-cov- and mers-cov s proteins then fused to a human fc fragment showed neutralization potential against sars-cov- (vhh- -fc) (wrapp et al., ) . genetically modified mice with humanized antibody genes can also be used to generate therapeutic monoclonal antibodies, as successfully experimented against ebola virus (levine, ) . similar studies are now focused on the use of sars-cov- or derivatives to generate highly effective nab in animal models, which can be directly given to infected patients, and efforts are already underway with estimates of clinical trials of pooled antibody cocktails beginning in early summer by regeneron. finally, another approach to nab development is to fuse ace protein and the fc part of antibodies as they would bind rbd and potentially be cross reactive among other coronaviruses ( figure d ). indeed, an ace -fc as well as an rbd-fc have been shown to neutralize both sars-cov- and sars-cov- in vitro. although recombinant nabs could provide an effective treatment, they will require a significant time investment to develop, test, and bring production to scale before becoming widely available to patients. a faster strategy consists of transferring convalescent plasma (cp) from previously infected individuals that have developed high titer nabs that target sars-cov- ( figure d ). despite the current lack of appropriately controlled trials, cp therapy has been previously used and shown to be beneficial in several infectious diseases such as the influenza pandemic (luke et al., ) , h n influenza (hung et al., ) , and sars-cov- (arabi et al., ) . thanks to the development of serological tests (amanat et al., ; cai et al., ; xiang et al., b; zhang et al., d) , recovered covid- patients can be screened to select plasma with high antibody titers. some studies and case reports on cp therapy for covid- have evaluated the safety and the potential effectiveness of cp therapy in patients with severe disease (ahn et al., ; duan et al., ; pei et al., ; shen et al., ; zhang et al., b) (table ). these studies were neither controlled nor randomized, but they suggest that cp therapy is safe and can have a beneficial effect on the clinical course of disease. further controlled trials are needed to determine the optimal timing and indication for cp therapy. cp therapy has also been proposed for prophylactic use in at-risk individuals, such as those with underlying health conditions or health care workers exposed to covid- patients. the fda has approved the use of cp to treat critically ill patients (tanne, ) . determining when to administer the cp is also of great importance, as a study in sars-cov- patients showed that cp was much more efficient when given to patients before day day of illness (cheng et al., b) , as previously shown in influenza (luke et al., ) . this study also showed that cp therapy was more efficient in pcr positive, seronegative patients. the amount of plasma and number of transfusions needed requires further investigation (table ) . overall, cp therapy seems to be associated with improved outcomes, and appears to be safe, but randomized clinical trials are needed to confirm this. several clinical trials are currently in progress worldwide (belhadi et al., ) the devastating effects of the pandemic spread of sars-cov- in a globally naïve population has resulted in unprecedented efforts to rapidly develop, test, and disseminate a vaccine to protect against covid- or to mitigate the effects of sars-cov- infection. although vaccination has a long and successful history as an effective global health strategy, there are currently no approved vaccines to protect humans against coronaviruses (andré, ) . previous work after the sars-cov- and mers-cov epidemics has provided a foundation on which many current efforts are currently building upon, including the importance of the s protein as a potential vaccine. diverse vaccine platforms and preclinical animal models have been adapted to sars-cov- , facilitating fast-moving and robust progress in creating and testing sars-cov- vaccine candidates. a number of vaccine candidates are already being tested in clinical trials and more are continuing to progress towards clinical testing. since sars-cov- first emerged, the s protein has been favored as the most promising target for vaccine development to protect against coronavirus infection. this particular viral protein has important roles in viral entry and in stimulating the immune response during natural infection and in vaccination studies of both sars-cov- and mers-cov (du et al., ; song et al., ; zhou et al., ) , which has also been confirmed for sars-cov- . the s protein has been found to induce robust and protective humoral and cellular immunity, including the development of nabs and t cell-mediated immunity (du et al., ) . in animal models, correlates of protection against sars-cov- infection appear to be induction of nabs against the s protein, although antibodies to other proteins have been detected such as those against nucleoprotein (n) and orf a (qiu et al., ; sui et al., ) . nabs are also believed to protect against infection by blocking receptor binding and viral entry, which has been shown with pseudovirus-based neutralization assays nie et al., a) . studies of sars-cov- indicate that t cell responses, which were targeted to the s protein after natural infection, included cd + t cell responses against the membrane (m) and n proteins, may also be a correlate of protection and that memory t cell responses can persist even years after infection (li et al., ; ng et al., ) . rbd-specific antiviral t cell responses have also been detected in people who have recovered from covid- , further validating its promise as a vaccine target (braun et al., ; dong et al., ) . although the antibodies targeting the rbd of the s protein have greater potential for providing cross-protective immunity, other fragments of the s protein and additional viral proteins have been investigated as target epitopes, especially for t cells. researchers have taken advantage of the genetic similarity between sars-cov- and sars-cov- and mers-cov and bioinformatics approaches to rapidly identify b and t cell potential epitopes in the s and other proteins, with many studies providing data regarding antigen presentation and antibody binding properties and one study looking into the predicted evolution of epitopes (ahmed et al., ; baruah and bose, ; bhattacharya et al., ; fast et al., ; grifoni et al., ; lon et al., ; zheng and song, ) . while the s protein has been found to be the most immunodominant protein in sars-cov- , the m and n proteins also contain b and t cell epitopes, including some with high conservation with sars-cov- epitopes . for sars-cov- and mers-cov, animal studies and phase i clinical trials of potential vaccines targeting the s protein had encouraging results, with evidence of nab induction and induction of cellular immunity martin et al., ; modjarrad et al., ) . these findings are being translated into sars-cov- vaccine development efforts, hastening the progress drastically. the who provided a report earlier in april that reported sixty-three vaccine candidates in preclinical testing and three in clinical testing (world health organization, b) . a recent search on may , , on clinicaltrials.gov revealed ten registered vaccine candidates (table ). the university of pittsburgh is also looking to move their microneedle array vaccine candidate containing a codon-optimized s subunit protein into clinical trials . sanofi and glaxosmithkline (gsk) have recently reported their intent to collaborate and bring together sanofi's baculovirus expression system, which is used to produce the influenza virus vaccine, flublok, to create an s protein vaccine adjuvanted with gsk's as . the purified inactivated sars-cov- virus vaccine candidate (picovacc) of sinovac biotech ltd. will also be starting a clinical trial in china after finding that their candidate protected rhesus macaques from viral challenge without signs of detectable immunopathology . although some of these vaccine candidates are based on platforms that have been used or tested for other purposes, there remain questions regarding their safety and immunogenicity, including the longevity of any induced responses, that will require continual evaluation. although the development of a vaccine to protect against sars-cov- infection has progressed at an unprecedented rate and produced an impressive volume of candidates for testing, many challenges lie ahead. the prior knowledge gained after sars-cov- was first discovered in and the subsequent emergence of mers-cov in provided a significant jumpstart, but the progress of sars-cov- vaccine development has already far outstripped the point of the blueprint created before covid- became a pandemic. while a variety of platforms are simultaneously being innovated or adapted, they each have strengths and limitations, many of which relate to the delicate balance between safety and immunogenicity. many shortcuts have been taken and will continue to be taken due to the urgency of the ongoing covid- pandemic, but significant concerns need to be addressed. one such concern involves the accumulating data supporting the initial assessment that covid- is disproportionately severe in older adults. in conjunction with the large body of work related to immune-senescence, these findings indicate that vaccine design should take into consideration the impact of aging on vaccine efficacy (nikolich-Žugich, ). furthermore, questions remain regarding the possibility of antibody-dependent enhancement of covid- , with in vitro experiments, animal studies, and two studies of covid- patients supporting this possibility (cao, ; tetro, ; zhao et al., a) . assuming vaccine candidates are identified that can safely induce protective immune responses, additional major hurdles will be the production and dissemination of a vaccine. for some types of vaccines, large-scale production will not be as much of an issue and infrastructure already in place to produce current good manufacturing practice (cgmp)-quality biologics can be repurposed, but this will only be applicable to a subset of the candidates (thanh le et al., ) . in order to address the urgent need and stem the covid- pandemic, regulatory agencies need to continue to support rapid testing and progression of vaccine candidates, companies need to disseminate important findings directly and openly, and researchers need to investigate correlates of protection using in-depth immune monitoring of patients with a broad range of clinical presentations and clinical trial participants. the newly announced accelerating covid- therapeutic interventions and vaccines (activ) is designed to bring together numerous governmental and industry entities to help address this need. the rapid spread of sars-cov- and the unprecedented nature of covid- has demanded an urgency in both basic science and clinical research, and the scientific community has met that call with remarkable productivity. within months, there has been a significant generation of scientific knowledge that has shed some light on the immunology of sars-cov- infections. studies of past coronavirus outbreaks, involving sars-cov- and mers-cov, have provided a foundation for our understanding. the pathology of severe cases of covid- do indeed resemble certain immunopathologies seen in sars-cov- and mers-cov infections, like crs. however, in many other ways, immune responses to sars-cov- are distinct from those seen with other coronavirus infections. the emerging epidemiological observation that significant proportions of individuals are asymptomatic despite infection, not only reflects our current understanding that sars-cov- has a longer incubation period and higher rate of transmission than other coronaviruses, but also speaks to significant differences in the host immune response. therefore, it is imperative that immune responses against sars-cov- and mechanisms of hyperinflammation-driven pathology are further elucidated to better define therapeutic strategies for covid- . here, we reviewed the recent literature and highlighted hypotheses that interrogate mechanisms for viral escape from innate sensing; for hyper-inflammation associated with crs and inflammatory myeloid subpopulations; for lymphopenia marked by t cell and nk cell dysfunction; and for correlates of protection and their duration, among others. still, additional studies are needed to address how these immune differences across patients or between different types of coronavirus infections dictate who succumbs to disease and who remains asymptomatic. existing studies of sars-cov- and mers-cov and ongoing studies of sars-cov- will likely provide a robust framework to fulfill that unmet need. overview of innate immune sensing (left) and interferon signaling (right), annotated with the known mechanisms by which sars-cov- and mers-cov antagonize the pathways (red). [based on data from preliminary covid- studies and earlier studies in related coronaviruses] il- , il- β and ifn-i/iii from infected pulmonary epithelia can induce inflammatory programs in resident (alternate) macrophages while recruiting inflammatory monocytes as well as granulocytes and lymphocytes from circulation. sustained il- , and tnf-ɑ by incoming monocytes can drive several hyperinflammation cascades. inflammatory monocyte-derived macrophages can amplify dysfunctional responses in various ways (listed in top left corner) . the systemic crs-and shlh-like inflammatory response can induce neutrophilic netosis and microthrombosis, aggravating covid- severity. other myeloid cells such as pdcs are purported to have an ifn-dependent role in viral control. monocyte-derived cxcl / / might recruit nk cells from blood. preliminary data suggest that the antiviral function of these nk cells might be regulated through cross-talk with sars-infected cells and inflammatory monocytes. a decrease in peripheral blood t cells associated with disease severity and inflammation is now well documented in covid- . several studies report increased numbers of activated cd and cd t cells which display a trend towards an exhausted phenotype in persistent covid- , based on continuous and upregulated expression of inhibitory markers as well as potential reduced polyfunctionality and cytotoxicity. in severe disease, production of specific inflammatory cytokines by cd t cells has also been reported. this working model needs to be confirmed and expanded on in future studies to assess virus-specific t cell responses both in peripheral blood and in tissues. in addition, larger and more defined patient cohorts with longitudinal data are required to define the relationship between disease severity and t cell phenotype. abbreviations: il, interleukin; ifn, interferon; tnf, tumor necrosis factor; gm-csf, granulocyte-macrophage colony-stimulating factor; gzma/b, granzyme a/granzyme b; prf , perforin. virus-specific igm and igg are detectable in serum between and days after the onset of symptoms. viral rna is inversely correlated with neutralizing antibody titers. higher titers have been observed in critically ill patients, but it is unknown whether antibody responses somehow contribute to pulmonary pathology. the sars-cov- humoral response is relatively short lived, and memory b cells may disappear altogether, suggesting that immunity with sars-cov- may wane - years after primary infection. the gastrointestinal tract, kidneys and testis have the highest ace expressions. in some organs, different cell types have remarkably distinct expressions, e.g. in the lungs, alveolar epithelial cells have higher ace expression levels than bronchial epithelial cells; in the liver, ace is not expressed in hepatocytes, kupffer cells nor endothelial cells, but is detected in cholangiocytes, which can explain liver injury to some extent. furthermore, ace expression is enriched on enterocytes of the small intestine compared to the colon. ace , angiotensin-converting enzyme ; bnp, b-type natriuretic peptide; crp, creactive protein; il, interleukin; n/l, neutrophil-to-lymphocyte ratio; pt, prothrombin time; aptt, activated partial thromboplastin time. a. rdrp inhibitors (remdesivir, favipiravir), protease inhibitors (lopinavir/ritonavir), and anti-fusion inhibitors (arbidol) are currently being investigated in their efficacy in controlling sars-cov- infections. b. cq and hcq increase the ph within lysosomes, impairing viral transit through the endolysosomal pathway. reduced proteolytic function within lysosomes augments antigen processing for presentation on mhc complexes and increases ctla expression on tregs. c. antagonism of il- signaling pathway and of other cytokine-/chemokine-associated targets has been proposed to control covid- crs. these include secreted factors like gm-csf that contribute to the recruitment of inflammatory monocytes and macrophages. d. several potential sources of sars-cov- neutralizing antibodies are currently under investigation, including monoclonal antibodies, polyclonal antibodies, and convalescent plasma from recovered covid- patients. abbreviations: gm-csf, granulocyte-macrophage colony-stimulating factor; cq, chloroquine; hcq, hydroxychloroquine; rdrp, rna-dependent rna polymerase. tai, w., he, l., zhang, x., pu, j., voronin, d., jiang, s., zhou, y., and du, l. ( ) . characterization of the receptor-binding domain (rbd) of novel coronavirus: implication for development of rbd protein as a viral attachment inhibitor and vaccine. cell. mol. immunol. tan, l., wang, q., zhang, d., ding, j., huang, q., tang, y.-q., wang, q., and miao, h. ( a) . lymphopenia predicts disease severity of covid- : a descriptive and predictive study. signal transduct target ther , . tan, w., lu, y., zhang, j., wang, j., dan, y., tan, z., he, x., qian, c., sun, q., hu, q., et al. ( b) . viral kinetics and antibody responses in patients with covid- . medrxiv . . . . tanaka, t., narazaki, m., and kishimoto, t. ( ) . immunotherapeutic implications of il- blockade for cytokine storm. immunotherapy , - . tian, x., li, c., huang, a., xia, s., lu, s., shi, z., lu, l., jiang, s., yang, z., wu, y., et al. ( b) . potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody. emerg. microbes infect. , - . evaluation of antibody testing for sars-cov- using elisa and lateral flow immunoassays coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease preliminary identification of potential vaccine targets for the covid- coronavirus (sars-cov- ) based on sars-cov immunological studies role of pd- during effector cd t cell differentiation use of convalescent plasma therapy in two covid- patients with acute respiratory distress syndrome in korea chadox and mva based vaccine candidates against mers-cov elicit neutralising antibodies and cellular immune responses in mice sars-cov- vaccines: status report. immunity a serological assay to detect sars-cov- seroconversion in humans vaccinology: past achievements, present roadblocks and future promises interferon-λs: front-line guardians of immunity and homeostasis in the respiratory tract clinical assessment of a novel recombinant simian adenovirus chadox as a vectored vaccine expressing conserved influenza a antigens feasibility of a randomized controlled trial to assess treatment of middle east respiratory syndrome coronavirus (mers-cov) infection in saudi arabia: a survey of physicians ribavirin and interferon therapy for critically ill patients with middle east respiratory syndrome: a multicenter observational study ace and tmprss variants and expression as candidates to sex and country differences in covid- severity in italy regulatory t cell specificity directs tolerance versus allergy against aeroantigens in humans. cell the pathogenicity of sars-cov- in hace transgenic mice reinfection could not occur in sars-cov- infected rhesus macaques targeting potential drivers of covid- : neutrophil extracellular traps immunoinformatics-aided identification of t cell and b cell epitopes in the surface glycoprotein of -ncov a brief review of antiviral drugs evaluated in registered clinical trials for covid- development of epitope-based peptide vaccine against novel coronavirus (sars-cov- ): immunoinformatics approach chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (sars-cov- ) infection: preliminary safety results of a randomized, doubleblinded in vitro reconstitution of sars-coronavirus mrna cap methylation hla-e binds to natural killer cell receptors cd /nkg a, b and c presence of sars-cov- reactive t cells in covid- patients and healthy donors nkg a complexed with cd defines a novel inhibitory natural killer cell receptor the impdh inhibitor merimepodib suppresses sars-cov- replication in vitro a peptide-based magnetic chemiluminescence enzyme immunoassay for serological diagnosis of corona virus disease the time course of the immune response to experimental coronavirus infection of man interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome lack of innate interferon responses during sars coronavirus infection in a vaccination and reinfection ferret model a role for neutrophils in viral respiratory disease prediction of sars-cov- epitopes across hla class i alleles mers-cov b protein interferes with the nf-κb-dependent innate immune response during infection covid- : immunopathology and its implications for therapy a trial of lopinavir-ritonavir in adults hospitalized with severe covid- high-dose intravenous immunoglobulin as a therapeutic option for deteriorating patients with coronavirus disease disappearance of antibodies to sars-associated coronavirus after recovery comparative genetic analysis of the novel coronavirus ( -ncov/sars-cov- ) receptor ace in different populations potent and persistent antibody responses against the receptor-binding domain of sars-cov spike protein in recovered patients natural killer cell recruitment to the lung during influenza a virus infection is dependent on cxcr , ccr , and virus exposure dose control of coronavirus infection through plasmacytoid dendritic-cell-derived type i interferon natural killer cells, viruses and cancer association of icam genetic variant with severe acute respiratory syndrome innate lymphoid cells mediate influenza-induced airway hyper-reactivity independently of adaptive immunity dysregulated type i interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in sars-cov-infected mice ifn-i response timing relative to virus replication determines mers coronavirus infection outcomes developing a new class of engineered live bacterial therapeutics to treat human diseases favipiravir versus arbidol for covid- : a randomized clinical trial clinical and immunological features of severe and moderate coronavirus disease severe acute respiratory syndrome coronavirus viroporin a activates the nlrp inflammasome a pilot study of hydroxychloroquine in treatment of patients restoration of leukomonocyte counts is associated with viral clearance in covid- hospitalized patients detectable serum sars-cov- viral load (rnaaemia) is closely associated with drastically elevated interleukin (il- ) functional screen reveals sars coronavirus nonstructural protein nsp as a novel cap n methyltransferase the novel severe acute respiratory syndrome coronavirus (sars-cov- ) directly decimates human spleens and lymph nodes (medrxiv) efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical trial abo blood group and susceptibility to severe acute respiratory syndrome use of convalescent plasma therapy in sars patients in hong kong cytokine responses in severe acute respiratory syndrome coronavirus-infected macrophages in vitro: possible relevance to pathogenesis temporal changes in cytokine/chemokine profiles and pulmonary involvement in severe acute respiratory syndrome role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings middle east respiratory syndrome coronavirus efficiently infects human primary t lymphocytes and activates the extrinsic and intrinsic apoptosis pathways comparative replication and immune activation profiles of sars-cov- and sars-cov in human lungs: an ex vivo study with implications for the pathogenesis of covid- inhibition of natural killer cell cytotoxicity by interleukin- : implications for the pathogenesis of macrophage activation syndrome primary severe acute respiratory syndrome coronavirus infection limits replication but not lung inflammation upon homologous rechallenge combined prophylactic and therapeutic use maximizes hydroxychloroquine anti-sars-cov- effects in vitro antagonism of dsrna-induced innate immune pathways by ns a and ns b accessory proteins during mers coronavirus infection comparative in vitro transcriptomic analyses of covid- candidate therapy hydroxychloroquine suggest limited immunomodulatory evidence of sars-cov- host response genes on the interactions of the receptorbinding domain of sars-cov- and sars-cov- spike proteins with monoclonal antibodies and the receptor structure-based design, synthesis and biological evaluation of peptidomimetic aldehydes as a novel series of antiviral drug candidates targeting the sars-cov characterization and quantification of innate lymphoid cell subsets in human lung coronavirus nonstructural protein mediates evasion of dsrna sensors and limits apoptosis in macrophages regulation of irf- -dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus reduction and functional exhaustion of t cells in patients with coronavirus disease currently available intravenous immunoglobulin (gamunex ® -c and flebogamma ® dif) contains antibodies reacting against sars-cov- antigens characterization of anti-viral immunity in recovered individuals infected by sars-cov- gammadelta t cells provide protective function in highly pathogenic avian h n influenza a virus infection. front. immunol. nkp and nkg d recognition of infected dendritic cells is necessary for nk cell activation in the human response to influenza infection the spike protein of sars-cov -a target for vaccine and therapeutic development multi-omics evaluation of gastrointestinal and other clinical characteristics of sars-cov- and covid- the feasibility of convalescent plasma therapy in severe covid- patients: a pilot study the human b and ntb-a receptors bind the influenza viral hemagglutinin and co-stimulate nk cell cytotoxicity low-dose corticosteroid therapy does not delay viral clearance in patients with covid- potential t-cell and b-cell epitopes of covid- -navigating the uncharted reduction of lymphocyte at early stage elevates severity and death risk of covid- patients: a hospitalbased case-cohort study early prediction of disease progression in novel coronavirus pneumonia patients outside wuhan with ct and clinical characteristics eosinophils and respiratory viruses covid- coagulopathy in caucasian patients the heptad repeat region is a major selection target in mers-cov and related coronaviruses severe acute respiratory syndrome coronavirus orf antagonizes stat function by sequestering nuclear import factors on the rough endoplasmic reticulum/golgi membrane severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of irf and nf-b signaling virologic and clinical characteristics for prognosis of severe covid- : a retrospective observational study in wuhan, china. medrxiv the role of corticosteroids in the management of critically ill patients with coronavirus disease (covid- ): a meta-analysis machine intelligence design of -ncov drugs prognostic value of nt highly pathogenic coronavirus n protein aggravates lung injury by masp- -mediated complement overactivation primary cd + t-cell response to soluble ovalbumin is improved by chloroquine treatment in vivo tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in covid- patients with at least a six-day follow up: a pilot observational study complex immune dysregulation in covid- patients with severe respiratory failure t-cell response profiling to biological threat agents including the sars coronavirus elucidating the mechanisms of influenza virus recognition by ncr correlation analysis between disease severity and inflammation-related parameters in patients with covid- pneumonia (medrxiv) a sars-cov- protein interaction map reveals targets for drug repurposing compassionate use of remdesivir for patients with severe covid- a sequence homology and bioinformatic approach can predict candidate targets for immune responses to sars-cov- division of labor between lung dendritic cells and macrophages in the defense against pulmonary infections tocilizumab treatment in severe covid- patients attenuates the inflammatory storm incited by monocyte centric immune interactions revealed by single-cell analysis coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors impaired type i interferon activity and exacerbated inflammatory responses in severe covid- patients serological and molecular findings during sars-cov- infection: the first case study in finland influenza virus polymerase inhibitors in clinical development effects of severe acute respiratory syndrome (sars) coronavirus infection on peripheral blood lymphocytes and their subsets level of il- predicts respiratory failure in hospitalized symptomatic covid- patients covid- : a new virus, but an old cytokine release syndrome neutralizing antibody response and sars severity chronological evolution of igm, iga, igg and neutralisation antibodies after infection with sars-associated coronavirus the severe acute respiratory syndrome coronavirus nucleocapsid inhibits type i interferon production by interfering with trim -mediated rig-i ubiquitination a systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease sars coronavirus nsp protein induces template-dependent endonucleolytic cleavage of mrnas: viral mrnas are resistant to nsp -induced rna cleavage clinical features of patients infected with novel coronavirus in wuhan high levels of circulating gm-csf(+)cd (+) t cells are predictive of poor outcomes in sepsis patients: a prospective cohort study distinct patterns of ifitm-mediated restriction of filoviruses, sars coronavirus, and influenza a virus blood single cell immune profiling reveals the interferon-mapk pathway mediated adaptive immune response for clinical characteristics of non-survivors with covid- in wuhan convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (h n ) virus infection tnfr /birc -traf signaling pathway as a novel nk cell immune checkpoint in cancer multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase analysis clinical features of covid- infection in secondary epidemic area and report potential biomarkers in evaluation single intranasal immunization with chimpanzee adenovirus-based vaccine induces sustained and protective immunity against mers-cov infection multi-antigenic human cytomegalovirus mrna vaccines that elicit potent humoral and cell-mediated immunity potent human neutralizing antibodies elicited by sars-cov- infection a two-pronged strategy to suppress host protein synthesis by sars coronavirus nsp protein type i interferons directly regulate lymphocyte recirculation and cause transient blood lymphopenia in vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine microneedle array delivered recombinant coronavirus vaccines: immunogenicity and rapid translational development. ebiomedicine innate immune crosstalk in asthmatic airways: innate lymphoid cells coordinate polarization of lung macrophages sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum targeting the catecholamine-cytokine axis to prevent sars-cov- cytokine storm syndrome severe acute respiratory syndrome coronavirus open reading frame (orf) b, orf , and nucleocapsid proteins function as interferon antagonists chemokine up-regulation in sars-coronavirus-infected, monocyte-derived human dendritic cells hopes rise on coronavirus drug remdesivir tumor necrosis factor-alpha enhances il- -induced natural killer cell differentiation early preemptive immunomodulators (corticosteroids) for severe pneumonia patients infected with sars-cov- potent neutralization of novel coronavirus by recombinant ace -ig the phenotypic changes of γδ t cells in covid- patients monoclonal antibody therapy for ebola virus disease t cell responses to whole sars coronavirus in humans virushost interactome and proteomic survey of pmbcs from covid- patients reveal potential virulence factors influencing sars-cov- pathogenesis radiographic findings and other predictors in adults with covid- . medrxiv an exploratory randomized controlled study on the efficacy and safety of lopinavir/ritonavir or arbidol treating adult patients hospitalized with mild/moderate covid- (elacoi) potential host range of multiple sars-like coronaviruses and an improved ace -fc variant that is potent against both sars-cov- and sars the landscape of lung bronchoalveolar immune cells in covid- revealed by single-cell rna sequencing safety and immunogenicity from a phase i trial of inactivated severe acute respiratory syndrome coronavirus vaccine human susceptibility and resistance to norwalk virus infection persistent sars-cov- presence is companied with defects in adaptive immune system in nonsevere covid- patients longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of sars-cov- neutrophil-to-lymphocyte ratio predicts severe illness patients with novel coronavirus in the early stage. medrxiv hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection prediction of the clinical outcome of covid- patients using t lymphocyte subsets with cases from wuhan the potential role of il- in monitoring severe case of coronavirus disease two-year prospective study of the humoral immune response of patients with severe acute respiratory syndrome clinical features and outcomes of novel coronavirus-infected patients with cardiac injury association between platelet parameters and mortality in coronavirus disease : retrospective cohort study patients with lrba deficiency show ctla loss and immune dysregulation responsive to abatacept therapy middle east respiratory syndrome coronavirus nsp inhibits host gene expression by selectively targeting mrnas transcribed in the nucleus while sparing mrnas of cytoplasmic origin sars-cov- is sensitive to type i interferon pretreatment prediction and evolution of b cell epitopes of surface protein in sars-cov- serology characteristics of sars-cov- infection since the exposure and post symptoms onset quantifying treatment effects of hydroxychloroquine and azithromycin for covid- : a secondary analysis of an open label non-randomized clinical trial genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding adjuvant corticosteroid therapy for critically ill patients with covid- (medrxiv) meta-analysis: convalescent blood products for spanish influenza pneumonia: a future h n treatment? potent antiviral activities of type i interferons to sars-cov- infection influenza virus directly infects human natural killer cells and induces cell apoptosis tlr and tlr activate distinct pathways in monocytes during rna virus infection human lung natural killer cells are predominantly comprised of highly differentiated hypofunctional cd (-)cd (dim) cells a sars dna vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a phase i clinical trial disease tolerance as a defense strategy covid- : consider cytokine storm syndromes and immunosuppression mers-cov accessory orfs play key role for infection and pathogenesis human monoclonal antibody as prophylaxis for sars coronavirus infection in ferrets htcc as a highly effective polymeric inhibitor of sars-cov- and mers-cov the sars coronavirus a protein causes endoplasmic reticulum stress and induces ligand-independent downregulation of the type interferon receptor safety and immunogenicity of an anti-middle east respiratory syndrome coronavirus dna vaccine: a phase , open-label, single-arm, dose-escalation trial no evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe covid- infection innate lymphoid cells promote lung-tissue homeostasis after infection with influenza virus cytokine release syndrome in severe covid- necroptosis in anti-viral inflammation memory t cell responses targeting the sars coronavirus persist up to years post-infection establishment and validation of a pseudovirus neutralization assay for sars-cov- metabolic disturbances and inflammatory dysfunction predict severity of coronavirus disease (covid- ): a retrospective study middle east respiratory syndrome coronavirus accessory protein a is a type i interferon antagonist severe acute respiratory syndrome coronavirus e protein transports calcium ions and activates the nlrp inflammasome the twilight of immunity: emerging concepts in aging of the immune system review-article cytokine regulation in sars coronavirus infection compared to other respiratory virus infections severe acute respiratory syndrome coronavirus -specific antibody responses in coronavirus disease a dynamic immune response shapes covid- progression induction of alternatively activated macrophages enhances pathogenesis during severe acute respiratory syndrome coronavirus infection immunoglobulin fragment f(ab') against rbd potently neutralizes sars-cov- in vitro zika virus protection by a single low-dose nucleosidemodified mrna vaccination spike protein binding prediction with neutralizing antibodies of sars-cov- persistence of antibodies against middle east respiratory syndrome coronavirus convalescent plasma to treat covid- : chinese strategy and experiences immunopathogenesis of coronavirus infections: implications for sars ly e impairs coronavirus fusion and confers immune control of viral disease structural and functional analysis of a potent sarbecovirus neutralizing antibody covid- critical illness pathophysiology driven by diffuse pulmonary thrombi and covid- and emerging viral infections: the case for interferon lambda dysregulation of immune response in patients with covid- in wuhan, china antibody responses to individual proteins of sars coronavirus and their neutralization activities platelet-to-lymphocyte ratio is associated with prognosis in patients with coronavirus disease- the sars-cov- receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement middle east respiratory coronavirus accessory protein a inhibits pkr-mediated antiviral stress responses elevated hla-a expression impairs hiv control through inhibition of nkg a-expressing cells the behaviour of recent isolates of human respiratory coronavirus in vitro and in volunteers: evidence of heterogeneity among e-related strains ace variants underlie interindividual variability and susceptibility to covid- in italian population. medrxiv interleukin- blockade for severe covid- pharmacologic treatments for coronavirus disease (covid- ): a review effects of chloroquine on viral infections: an old drug against today's diseases? mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology hydroxychloroquine versus covid- : a rapid systematic review and meta-analysis on the use of corticosteroids for -ncov pneumonia clinical efficacy of intravenous immunoglobulin therapy in critical patients with covid- : a multicenter retrospective cohort study broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov treatment of critically ill patients with covid- with convalescent plasma open reading frame- b suppresses innate immunity by targeting mitochondria and the mavs/traf /traf signalosome sars-coronavirus open reading frame- b triggers intracellular stress pathways and activates nlrp inflammasomes association of cardiac injury with mortality in hospitalized patients with covid- in wuhan, china cd acts downstream of interferon-alpha/beta to inhibit s p and lymphocyte egress from lymphoid organs severe acute respiratory syndrome coronavirus m protein inhibits type i interferon production by impeding the formation of traf ·tank·tbk /ikkε complex middle east respiratory syndrome coronavirus a protein is a double-stranded rna-binding protein that suppresses pact-induced activation of rig-i and mda in the innate antiviral response severe acute respiratory syndrome coronavirus orf a protein activates the nlrp inflammasome by promoting traf -dependent ubiquitination of asc human nk cells: surface receptors, inhibitory checkpoints, and translational applications covid- early warning score: a multi-parameter screening tool to identify highly suspected patients critical role of type iii interferon in controlling sars-cov- infection, replication and spread in primary human intestinal epithelial cells human ace receptor polymorphisms predict sars-cov- susceptibility. biorxiv potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s protein that blocks receptor association evaluation of human monoclonal antibody r for immunoprophylaxis of severe acute respiratory syndrome by an animal study, epitope mapping, and analysis of spike variants sars-cov- and sars-cov spike-rbd structure and receptor binding comparison and potential implications on neutralizing antibody and vaccine development coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of sting-mediated signaling temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study an efficient method to make human monoclonal antibodies from memory b cells: potent neutralization of sars coronavirus a molecular cell atlas of the human lung from single cell rna sequencing safety, efficacy, and immunogenicity of vgx- , a therapeutic synthetic dna vaccine targeting human papillomavirus and e and e proteins for cervical intraepithelial neoplasia / : a randomised, double-blind, placebo-controlled phase b trial advancing scientific knowledge in times of pandemics endothelial cell infection and endotheliitis in covid- chloroquine is a potent inhibitor of sars coronavirus infection and spread innate lymphoid cells: years on influenza and antibody-dependent cellular cytotoxicity structure, function, and antigenicity of the sars-cov- spike glycoprotein multidimensional assessment of alveolar t cells in critically ill patients characteristics of lymphocyte subsets and cytokines in peripheral blood of hospitalized patients with receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus molecular mechanism for antibody-dependent enhancement of coronavirus entry c-reactive protein levels in the early stage of covid- a human monoclonal antibody blocking sars-cov- infection persistence of lung inflammation and lung cytokines with high-resolution ct abnormalities during recovery from sars clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in no clear benefit to the use of corticosteroid as treatment in adult patients with coronavirus disease : a retrospective cohort study characteristics of peripheral lymphocyte subset alteration in covid- pneumonia remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro human-leukocyte antigen class i cw and class ii dr genotypes are associated with resistance to severe acute respiratory syndrome (sars) infection the definition and risks of cytokine release syndrome-like in covid- -infected pneumonia critically ill patients: disease characteristics and retrospective analysis remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial early, lowdose and short-term application of corticosteroid treatment in patients with severe covid- pneumonia: single-center experience from wuhan severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp and rational design of an attenuated strain phenotype of sars-cov- -specific t-cells in covid- patients with acute respiratory distress syndrome immune cell profiling of covid- patients in the recovery stage by single-cell sequencing clinical benefit of remdesivir in rhesus macaques infected with sars-cov- sars and mers: recent insights into emerging coronaviruses prophylactic and therapeutic remdesivir (gs- ) treatment in the rhesus macaque model of mers-cov infection virological assessment of hospitalized patients with covid- plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome clinical management of severe acute respiratory infection (sari) when covid- disease is suspected: interim guidance (world health organization) draft of the landscape of covid- candidate vaccines structural basis for potent neutralization of betacoronaviruses by single-domain camelid antibodies risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease neutralizing antibody responses to sars-cov- in a covid- recovered patient cohort and their implications fully human single-domain antibodies against systematic review and critical appraisal of prediction models for diagnosis and prognosis of covid- infection the involvement of natural killer cells in the pathogenesis of severe acute respiratory syndrome potential biochemical markers to identify severe cases among covid- patients evaluation of enzyme-linked immunoassay and colloidal gold-immunochromatographic assay kit for detection of novel coronavirus (sars-cov- ) causing an outbreak of pneumonia novel and potent inhibitors targeting dhodh, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against rna viruses including newly emerged coronavirus sars-cov- acute myocardial injury of patients with coronavirus disease effective treatment of severe covid- patients with tocilizumab pathological findings of covid- associated with acute respiratory distress syndrome nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus in vitro factors associated with prolonged viral shedding and impact of lopinavir/ritonavir treatment in patients with sars-cov- infection prediction of criticality in patients with severe covid- infection using three clinical features: a machine learning-based prognostic model with clinical data in wuhan analysis of adaptive immune cell populations and phenotypes in the patients infected by sars-cov- middle east respiratory syndrome coronavirus orf b protein inhibits type i interferon production through both cytoplasmic and nuclear targets exuberant elevation of ip- , mcp- and il- ra during sars-cov- infection is associated with disease severity and fatal outcome the effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) human monoclonal antibodies block the binding of sars-cov- spike protein to angiotensin converting enzyme receptor development of human neutralizing monoclonal antibodies for prevention and therapy of mers-cov infections antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus immunodepletion with hypoxemia: a potential high risk subtype of coronavirus disease a highly conserved cryptic epitope in the receptor-binding domains of sars-cov- and sars-cov spatial and temporal mapping of human innate lymphoid cells reveals elements of tissue specificity mortality of covid- is associated with cellular immune function compared to immune function in chinese han population corticosteroid treatment of patients with coronavirus disease (covid- ) immune phenotyping based on neutrophil-to-lymphocyte ratio and igg predicts disease severity and outcome for patients with treatment with convalescent plasma for critically ill patients with sars-cov- infection covid- infection induces readily detectable morphological and inflammation-related phenotypic changes in peripheral blood monocytes, the severity of which correlate with patient outcome. medrxiv serological detection of -ncov respond to the epidemic: a useful complement to nucleic acid testing antibody responses against sars coronavirus are correlated with disease outcome of infected individuals evasion by stealth: inefficient immune activation underlies poor t cell response and severe disease in sars-cov-infected mice antibody responses to sars-cov- in patients of novel coronavirus disease relationship between the abo blood group and the covid- susceptibility. medrxiv the immune responses of hla-a* restricted sars-cov s peptide-specific cd (+) t cells are augmented in varying degrees by cpg odn, polyi:c and r interferon induction of ifitm proteins promotes infection by human coronavirus oc identification of residues controlling restriction versus enhancing activities of ifitm proteins on entry of human coronaviruses ly e restricts the entry of human coronaviruses, including the currently pandemic sars-cov incidence, clinical characteristics and prognostic factor of patients with covid- : a systematic review and metaanalysis novel antibody epitopes dominate the antigenicity of spike glycoprotein in sars-cov- compared to sars-cov elevated exhaustion levels and reduced functional diversity of t cells in peripheral blood may predict severe progression in covid- patients gammadelta-t cells: an unpolished sword in human antiinfection immunity functional exhaustion of antiviral lymphocytes in covid- patients clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study active replication of middle east respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis prospects for a mers-cov spike vaccine hhs public access aberrant pathogenic gm-csf+ t cells and inflammatory cd +cd + pathogenic t cells and inflammatory monocytes incite inflammatory storm in severe covid- patients a new predictor of disease severity in patients with covid- in wuhan safety and immunogenicity of a novel recombinant adenovirus type- vector-based ebola vaccine in healthy adults in china: preliminary report of a randomised, double-blind safety and immunogenicity of a recombinant adenovirus type- vector-based ebola vaccine in healthy adults in sierra leone: a single-centre, randomised, double-blind potent cross-reactive neutralization of sars coronavirus isolates by human monoclonal antibodies sars-cov- receptor ace is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues testing the association between blood type and covid- infection, intubation, and death. medrxiv. lymphocyte count predicted the disease severity and the outcomes of hospitalized patients prognostic value was confirmed in numerous studies decreased continuously in non-surviving patients were reported to be more likely to develop severe illness and to require intensive care unit (icu) admission on admission a risk factor for short-term progression of patients with moderate pneumonia to severe pneumonia confirmed to be of prognostic value in covid- in several studies even in early stages, crp levels were positively correlated with lung lesions and reflected disease severity confirmed in numerous studies predicted the risk of acute myocardial injury ldh (lactate dehydrogenase) higher in severe cases than in mild cases we apologize to all authors whose work we could not cite due to space limitations. trainee (phd and md/phd or postdocs) and faculty contributing authors are listed in alphabetical order. illustrations by jill k gregory and used with permission of ©mount sinai health system. we would like to acknowledge funding sources including fastgrant (mm), nci cancer center support grant supplement (mm, rms) burroughs wellcome fund (rms), nih director's early independence award (rms) and nih r ai (nv, nb, bdg) purpose ro uti ne bl oo dw or k predicted severity independently of other variables . elevated levels and disseminated intravascular coagulation are found in non-survivors . identified patients at risk for acute cardiac injury . other coagulation parameters such as fibrin degradation product levels, longer prothrombin time and activated partial thromboplastin time, were also associated with poor prognosis (tang et al., a) . saa (serum amyloid protein) saa was proposed to be used as an auxiliary index for diagnosis as it was elevated in % of the patients in a small cohort . nt-probnp (n terminal pro b type natriuretic peptide) nt-probnp was an independent risk factor of in-hospital death in patients with severe covid- . high platelet-to-lymphocyte ratio is associated with worse outcome (qu et al., ) . thrombocytopenia is associated with poor outcome and with incidence of myocardial injury in covid- (liu et al., h; shi et al., ) . im mu nol ogi cal cd +, cd + and nk cell counts lower cd +, cd + and nk cells in pbmc correlated with severity of covid- (nie et al., b) . validated by several studies zheng et al., b) . pd- and tim- expression on t cells increasing pd- and tim- expression on t cells could be detected as patients progressed from prodromal to overtly symptomatic stages (diao et al., ) .expression was higher in infected patients versus healthy controls and in icu versus non-icu patients in both cd and cd t cells . phenotypic changes in peripheral blood monocytes the presence of a distinct population of monocytes with high forward scatter (cd b+, cd +, cd +, cd +, cd +, cd +, cd + which secrete il- , il- and tnf-alpha) was identified in patients requiring prolonged hospitalization and icu admission . cd +cd +il- + monocytes are increased in icu patients . ip- , mcp- , and il- ra ip- , mcp- , and il- ra were, among examined cytokines, the only ones that closely associated with disease severity and outcome of covid- in a study by yang et al. (yang et al., b) . associated with disease severity (hospitalization and icu admission) and poor prognosis (chen et al., f; huang et al., b; liu et al., b . increase levels were associated with higher risk of respiratory failure (yao et al., b) . il- positively correlated with disease severity (chen et al., d; gong et al., ) , with severe cases showing the highest il- levels. increased in severe or critical patients as compared to mild patients zhou et al., d ) without a statistically significant difference between severe and critical cases . associated with disease severity in a study that, amongst other cytokines, also associated ferroprotein levels, pct levels, and eosinophil counts with covid- severity . il- β cd +il- β+ monocytes are abundant in early recovery patients as shown in a single-cell rna-seq analysis and thought to be associated with cytokine storm . il- β did not correlate with disease severity in a cross-sectional study with mild, severe and critical patients . il- il- was associated with impaired lung lesions , but some reports point to a potential mediator effect . in modeling immune cell interaction between dc and b cells in late recovery covid- patients, il- was found to be important in b cell production of antibodies, which suggests its importance in recovery . gm-csf (granulocytemacrophage colony-stimulating factor) gm-csf+ifn-γ+ t cells are higher in icu than non-icu patients, cd +cd +gm-csf+ monocytes are higher in covid- patients as compared to healthy controls .il- and ifn-γ il- and ifn-γ levels were shown to be increased in severe cases . anti-sars-cov- antibody levels prolonged sars-cov- igm positivity could be utilized as a predictive factor for poor recovery . higher anti-sars-cov- igg levels and higher n/l were more commonly found in severe cases . between and days after hospital admission.-body temperature normalized within days in of patients -clinical improvement -viral loads became negative within d after the transfusion -neutralizing antibody titers increased severe patients ( - yo)median . dpo.-disappearance of clinical symptoms after d -chest ct improved -elevation of lymphocyte counts in patients with lymphocytopenia.-increase in sao in all patients -resolution of sars-cov- viremia in patients increase in neutralizing antibody titers in patients (ahn et al., ) key: cord- -j qperwz authors: lallie, harjinder singh; shepherd, lynsay a.; nurse, jason r. c.; erola, arnau; epiphaniou, gregory; maple, carsten; bellekens, xavier title: cyber security in the age of covid- : a timeline and analysis of cyber-crime and cyber-attacks during the pandemic date: - - journal: nan doi: nan sha: doc_id: cord_uid: j qperwz the covid- pandemic was a remarkable unprecedented event which altered the lives of billions of citizens globally resulting in what became commonly referred to as the new-normal in terms of societal norms and the way we live and work. aside from the extraordinary impact on society and business as a whole, the pandemic generated a set of unique cyber-crime related circumstances which also affected society and business. the increased anxiety caused by the pandemic heightened the likelihood of cyber-attacks succeeding corresponding with an increase in the number and range of cyber-attacks. this paper analyses the covid- pandemic from a cyber-crime perspective and highlights the range of cyber-attacks experienced globally during the pandemic. cyber-attacks are analysed and considered within the context of key global events to reveal the modus-operandi of cyber-attack campaigns. the analysis shows how following what appeared to be large gaps between the initial outbreak of the pandemic in china and the first covid- related cyber-attack, attacks steadily became much more prevalent to the point that on some days, or unique cyber-attacks were being reported. the analysis proceeds to utilise the uk as a case study to demonstrate how cyber-criminals leveraged key events and governmental announcements to carefully craft and design cyber-crime campaigns. the coronavirus pandemic which started in quickly became a global crisis event, resulting in the mass quarantine of s of millions of citizens across numerous countries around the world. at the time of writing, the world health organisation (who) coronavirus disease (covid- ) dashboard reported over . million confirmed cases and in excess of , deaths[ ] globally. as covid- spread across the globe, it also led to a secondary significant threat to a technology-driven society; i.e., a series of indiscriminate, and also a set of targeted, cyber-attacks and cyber-crime campaigns. since the outbreak, there have been reports of scams impersonating public authorities (e.g., who) and organisations (e.g., supermarkets, airlines)[ , ], targeting support platforms [ , ] , conducting personal protection equipment (ppe) fraud [ ] and offering covid- cures [ , ] . these scams target members of the public generally, as well as the millions of individuals working from home. working at home en-masse has realised a level of cyber security concerns and challenges never faced before by industry and citizenry. cybercriminals have used this opportunity to expand upon their attacks, using traditional trickery (e.g., [ ] ) which also prays on the heightened stress, anxiety and worry facing individuals. in addition, the experiences of working at home revealed the general level of unpreparedness by software vendors, particularly as far as the security of their products was concerned. cyber-attacks have also targeted critical infrastructure such as healthcare services [ ] . in response to this, on april th , the united kingdom's national cyber security centre (ncsc) and the united states department of homeland security (dhs) cybersecurity and infrastructure security agency (cisa) published a joint advisory on how cyber-criminal and advanced persistent threat (apt) groups were exploiting the current covid- pandemic [ ] . this advisory discussed issues such as phishing, malware and communications platform (e.g., zoom, microsoft teams) compromise. what is arguably lacking here and in research, however, is a broader assessment of the wide range of attacks related to the pandemic. the current state of the art is extremely dispersed, with attacks being reported from governments, the media, security organisations and incident teams. it is therefore extremely challenging for organisations to develop appropriate protection and response measures given the dynamic environment. in this paper we aim to support ongoing research by proposing a novel timeline of attacks related to the covid- pandemic. this timeline and the subsequent analysis can assist in understanding those attacks and how they are crafted, and as a result, to better prepare to confront them if ever seen again. our timeline maps key cyber-attacks across the world against the spread of the virus, and also measures such as when lockdowns were put in place. the timeline reveals a pattern which highlights cyber-attacks and campaigns which typically follow events such as announcements of policy. this allows us to track how quickly cyber-attacks and crimes were witnessed as compared to when the first pandemic cases were reported in the area; or, indeed, if attacks preempted any of these events. we expand the timeline to focus on how specific attacks unfolded, how they were crafted and their impact on the uk. to complement these analyses, we reflect more broadly on the range of attacks reported, how they have impacted the workforce and how the workforce may still be at risk. in many ways this timeline analysis also forms a key contribution of our work both in terms of the chronological sequencing of attacks and the representation of campaigns using an accepted attack taxonomy. this therefore provides a platform which aligns with current literature and also provides the foundation which other research can easily build on. this paper is structured as follows. section ii reflects on relevant cyber-attack and cyber-crime literature, and considers how opportunistic attacks have emerged in the past due to real-life crises/incidents. we then present our covid- -related cyber-attack timeline in section iii as well as a dedicated focus on the united kingdom as a case study of key-cyber-criminal activity. this is followed by a broader reflection on the attacks (those within and outside of the timeline). in section iv we discuss the impact of attacks on those working from home and wider technology risk. section v concludes the paper and outlines directions for future work. with the broad adoption of digital technologies many facets of society have moved online, from shopping and social interactions to business, industry, and unfortunately, also crime. the latest reports establish that cybercrime is growing in frequency and severity [ ] , with a prediction to reach $ trillion by (up from $ trillion in ) [ ] and even take on traditional crime in number and cost [ , ] . due to its lucrative nature [ ] and low risk level (as cyber-criminals can launch attacks from anywhere across the globe), it is clear that cybercrime is here to stay. cyber-crime, as traditional crime, is often described by the crime triangle [ ] , which specifies that for a cybercrime to occur, three factors have to exist: a victim, a motive and an opportunity. the victim is the target of the attack, the motive is the aspect driving the criminal to commit the attack, and the opportunity is a chance for the crime to be committed (e.g., it can be an innate vulnerability in the system or an unprotected device). other models in criminology, such as routine activity theory (rat) [ ] and the fraud triangle [ ] use similar factors to describe crimes, with some replacing the victim by the means of the attacker, which it can be considered otherwise as part of the opportunity. while attacks today have become more sophisticated and targeted to specific victims depending on attacker's motivation, for example for financial gain, espionage, coercion or revenge; opportunistic untargeted attacks are also very prevalent. we define "opportunistic attacks" as attacks that select the victims based on their susceptibility to be attacked [ ] . opportunistic attackers pick-up victims that have specific vulnerabilities or use hooks, usually in the form of social engineering, to create those vulnerabilities. thus, we define as hook any mechanism used to mislead a victim into falling prey of an attack. these hooks take advantage of distraction, time constraints, panic and other human factors to make them work [ , ] . when victims are distracted by what grabs their interest/attention or when they are panicked, they are more susceptible to be deceived. similarly, time constraints put victims under more pressure which can lead to mistakes and an increased likelihood to fall victim to scams and attacks. other examples include work pressure, personal change of situation, medical issues, or events that cause deep and traumatic impact in the whole society in general such as fatalities and catastrophes. opportunistic attackers always seek to maximise their gain, and therefore, will wait for the best time to launch an attack where conditions fit those mentioned above. a natural disaster, ongoing crisis or significant public event are perfect cases of these conditions [ ] . in the past, several opportunistic attacks have been observed that took advantage of specific incidents; below, we provide few examples: • natural disasters: in hurricane katrina caused massive destruction in the city of new orleans and surrounding areas in the usa [ ] . not long after, thousands of fraudulent websites appeared appealing for humanitarian donations, and local citizens received scam emails soliciting personal information to receive possible payouts or government relief efforts. similar scams and attacks have been witnessed in countless natural disasters since, such as the earthquakes in japan and ecuador in [ ] , hurricane harvey in [ ] , or the bush fires in australia in [ ] . • notable incidents or events: on th june , the tragic death of michael jackson dominated news around the world. only hours after his demise, spam emails claiming knowing the details of the incident were circulating online [ ] . waves of illegitimate emails echoing the fatality appeared soon after, containing links promising access to unpublished videos and pictures or jackson's merchandise, that in reality were linked to malicious websites, or emails with malware infected attachments [ ] . noteworthy public events also attract a range of cyber-crime activities. during the fifa world cup in for instance, there were various attempts to lure individuals with free tickets and giveaways [ ] . these were, in fact, scams leading to fraud. • security incidents: in , million of email addresses and passwords were exposed in a linkedin data breach [ ] . this data was not disclosed until years later, , when it appeared for sale in the dark market. soon after that, opportunistic attackers began to launch a series of attacks. many users experienced scams, such as blackmail and phishing, and some compromised accounts that had not changed their passwords since the breach, were used to send phishing links via private message and inmail [ ] . considering the variety of scams and cyber-attacks occurring around the events above, it is unsurprising that similar attacks have emerged during the ongoing covid- pandemic. the outbreak has caused mass disruption worldwide, with people having to adapt their daily routines to a new reality: working from home, lack of social interactions and physical activity, and fear of not being prepared [ , ] . these situations can overwhelm many, and cause stress and anxiety that can increase the chances to be victim of an attack. also, the sudden change of working contexts, has meant that companies have had to improvise new working structures, potentially leaving corporate assets less protected than before for the sake of interoperability. since the covid- started, the numbers of scams and malware attacks have significantly risen [ ] , with phishing being reported to have increased by % in march [ ] . during april , google reportedly blocked million malware and phishing emails related to the virus daily [ ] . to increase likelihood of success, these attacks target sale of goods in high demand (e.g., personal protection equipment (ppe) and coronavirus testing kits and drugs), potentially highly profitable in-vestments in stocks related to covid- , and impersonations of representatives of public authorities like who and aid scams [ , ] . brute force attacks on the microsoft remote desktop protocol (rdp) systems have increased as well [ ] , signaling attacks also on technology, not only on human aspects. it is clear then that attackers are trying the make the most of the disruption caused by pandemic, particularly given it continues to persist. as a consequence, several guidelines and recommendations have also been published to protect against attacks [ , , ] . these guidelines are imperative for mitigating the increasing threat, but to strengthen their basis, there first needs to be a core understanding of the cyber-attacks being launched. this paper seeks to address this gap in research and practice by defining a timeline of cyber-attacks and consideration of how they impact citizens and the workforce. the cyber-crime incidents erupting from the covid- pandemic pose serious threats to the safety and global economy of the world-wide population, hence understanding their mechanisms, as well as the propagation and reach of these threats is essential. numerous solutions have been proposed in the literature to analyse how such events unfold ranging from formal definitions to systemic approaches reviewing the nature of threats [ , , ] . while these approaches enable the categorisation of the attack, they often lack the ability to map larger, distributed events such as the ones presented in this manuscript, where numerous events stem from the pandemic are, however, unrelated. to this end, we opted for temporal visualisation, enabling us to map events without compromising the narrative [ ] . furthermore, this type of visualisation is used across the cyber-security domain to represent consequent cyberattacks [ , , ] . in this section, we outline the methodology used to create the timeline. we explain the search terms used to gather relevant covid- cyber-attack data, the data sources (search engines) utilised, the sources of information we chose to focus on, and types of attack. we also acknowledge the potential limitations of the work. ) nomenclature: we explore a range of cyberattacks which have occurred during the covid- pandemic. the novel coronavirus has been referred to by several different terms in the english-speaking world, including coronavirus, covid , covid- , -ncov, and sars-cov- . we use the term covid- to refer to the virus, which falls in line with terminology used by the world health organization [ ] . ) construction of the timeline: to aid in the construction of the timeline, we initially conducted a number of searches to identify cyber-attacks associated with the pandemic. these cyber-attacks were categorised by attack type, delivery method, and were ordered by date. the information gathered has been collated and is presented in figure which serves as a baseline for the construction of table i . information presented in the timeline includes the date china alerted the who about the virus, the date the pandemic was officially declared, and cyber-attacks which specifically relate to hospitals or medicine. additionally, key countries involved in the pandemic were identified, and for those, we present the first identified case, the date lockdown was implemented, and the first cyber-attack they suffered. the table seeks to examine a sub-set of the information from the timeline. furthermore, we have chosen to include a number of sources offering reports of attacks. the sources are a mixture of reputable news outlets (such as reuters, and the bbc), blog articles, security company reports, and social media posts. though blog articles and social media posts are not considered to be an academic source, in the context of this research where we are examining an emerging threat, they offer important insights into trends of cyber-attacks. it is also important to note that cyber-attacks may first be presented in these domains, before being highlighted by mainstream media outlets. with regards to the inclusion of news reports in the table of attacks and subsequent timeline, it should be acknowledged that these attacks are being presented through a journalistic lens, and as such may be written in an attempt to grab headlines. nevertheless, these reported cyber-attacks still pose a tangible threat to the general public during the covid- pandemic. the timeline seeks to provide an overview of attacks which have occurred. the state-of-the-art review of reports was performed from mid-march to mid-may . the timeline limits cyber-attacks to those experienced by st march. this is because we reached what we believed to be a saturation point comprising a sufficient number of cyber-attacks to be representative. following the conclusion of the search, the earliest reported attack was on th january [ ] , whilst the most recently listed attack in the timeline was st march [ ] . the most recently listed attack in the table was th may [ ] . the table progresses the time period a bit further as it intends to provide more detail in regards to cyber-attacks experienced during this time. sources were gathered from a number of locations. the criteria used to locate reports have been defined below and are presented in a similar way to existing reviews in cyber security literature [ , ] . the structure of the timeline is described in further detail in section iii-b. search engines: several search engines were used in the creation of the table and timeline. these were-google (us-based and dominates the search engine market share), baidu (chinese-based search provider), qwant (french-based search engine with a focus on privacy), and duckduckgo (us-based search engine with a focus on privacy). keywords used: a variety of keywords were used when collating reports of cyber-attacks. non-english terms were translated using the google translate service [ ] and additional independent sources were used as a means of validating the translation. when focussing on the virus itself, the following key words were used: sarscov- , covid, covid , coronavirus, 冠状病毒(chinese translation for coronavirus, confirmed by the world health organization [ ] ), コ ロ ナ ウ イ ル ス(japanese translation for coronavirus, confirmed by the japanese ministry of health, labour and welfare [ ] ). when searching for cyber-attacks, the following key phrases were used: 网络攻击(chinese translation means network attack [ ] or cyber attack [ ] ), サ イ バ 攻 (japanese translation for cyber attack or hacking attack [ ] ), attaque informatique (french translation for computer attack [ ] ), attacco informatico (italian translation for cyber attack [ ] ). time range: we attempted to find the earliest reported cyber-attack which was associated with the covid- pandemic. to allow for development of the timeline, and analysis of findings, mid-may was defined as a cutoff point, with the most recent news article being dated th may [ ] . exclusion criteria: although we have created a comprehensive table and timeline, a number of results were excluded from the research. these included results which a) were behind a paywall, b) required account creation before full article was displayed, c) were duplicates of existing news reports, and d) could not be translated. ) types of cyber-attacks : to guide our analysis and the creation of a timeline of covid- -related cyberattacks, we decided to define attacks based on their types. this allowed us to examine the prominence in certain types of attacks. although there exist numerous taxonomies relating to attacks and cyber-crimes (e.g., [ , , , ] ), there exists no universally accepted model [ ] . in this work therefore, we relied on the uk's crown prosecution service (cps) categorisation of fig. . cyber-dependent and cyber-enabled crimes [ ] cyber-crime. this definition includes cyber security by default and has inspired many international definitions of cyber-crime. the cps guidelines categorise cyber-crime into two broad categories: cyber-dependent and cyber-enabled crimes [ ] . a cyber-dependent crime is an offence, "that can only be committed using a computer, computer networks or other form of information communications technology (ict)" [ ] . cyber-enabled crimes are, "traditional crimes, which can be increased in their scale or reach by use of computers, computer networks or other forms of information communications technology (ict)" [ ] . these categories as well as examples of their subcategories can be seen in figure . some of the elements described by cps are often interlinked in a cyber-attack. for instance, a phishing email or text message (e.g., sms or whatsapp) might be used to lure a victim to a fraudulent website. the website then may gather personal data which is used to commit financial fraud, or it may install malware (more specifically, ransomware) which is then used to commit extortion. this notion of cyber-attack sequences is explained in further detail in section iii-b. similarly denial of service (dos) attacks are increasingly used by cyber-criminals to distract (or, act as 'smokescreens' for) businesses during hacking attempts [ , ] . in what follows, we consider the types of these attacks and reflect on how they have been launched, including any human factors or technical aspects (e.g., vulnerabilities) they attempt to exploit. phishing, or social engineering more broadly, includes attempts by illegitimate parties to convince individuals to perform an action (e.g., share information or visit a website) under the pretence that they are engaging with a legitimate party. quite often email messages are used, occasionally sms or whatsapp messages are used (referred to as smishing). pharming is similar to phishing but instead of deceiving users into visiting malicious sites, attackers rely on compromising systems (e.g., the user's device or dns servers) to redirect individuals to illegitimate sites. this type of attack is less common in general, as it requires more access or technical capabilities. financial fraud generally involves deceiving individuals or organisations using technology for some financial gain to the attacker or criminal. extortion refers to actions that force, threaten or coerce individuals to perform some actions, most commonly, releasing finances. hacking, malware and denial of service (dos) attacks are forms of crime that are often favoured by more technical attackers. hacking involves compromising the confidentiality or integrity of a system, and requires a reasonable about of skill; its techniques can involve exploiting system vulnerabilities to break into systems. malware refers to malicious software and can be used for disrupting services, extracting data and a range of other attacks. ransomware is one of the most common type of malware today [ , ] , and combines malware with extortion attempts. dos attacks target system availability and work by flooding key services with illegitimate requests. the goal here is to consume the bandwidth used for legitimate server requests, and eventually force the server offline. these types of attack provide the foundation for our analysis in the timeline and how we approach our discussion in later part of this research. ) limitations of the table: within table i , two columns referring to dates are provided. the first column "article date" refers to the date the reference was initially published. we acknowledge that in some cases, the web pages linked to the references continued to be updated with information following its inclusion with the paper. the table has been ordered by "article date" to provide a consistent chronological representation of events. we have also provided a second column,"attack date". when examining each reference, if a specific date was provided as to when the attack was executed, it was included. the rational behind including the attack date and report date is that an attack may not surface until several days after it has been carried out. ) limitations of the timeline: two types of cyberattack reports are considered within this manuscript, those which describe cyber-attacks without providing the date of the attack and those which describe cyberattacks and include the date of the perpetration. when the date of the attack is not included, the date provided in the timeline refers to the date of the publication. the rationale behind the inclusion of both types of reports is based on providing a chronological representation of events. furthermore, while the table provides an extensive overview of the threat landscape, it is by no means an exhaustive list of all the attacks carried out in relation to the pandemic, as gathering such information would not be possible in this context due to the lack and quality of reporting, the number of targeted incidents, the number of incidents targeted at the general public, the global coverage of the pandemic and the number of malicious actors carrying out these attacks. however, despite these limitations we have explored all resources available to depict the threat landscape as accurately as possible. in this section, we examine the cyber-attacks in further detail. figure provides a detailed temporal representation of the chain of key cyber-attacks induced by the covid- pandemic. the timeline includes the first reported cases in china, japan, germany, singapore, spain, uk, france, italy, and portugal and then the subsequent lockdown announcements. the timeline presents cyber-attacks categorised using the cps taxonomy described in section iii-a and abbreviated as: p:phishing (or smishing), m:malware. ph:pharming, e:extortion, h:hacking, d:denial of service and f:financial fraud. the events related to the crisis were validated against who timeline of events to ensure an accurate temporal reproduction. table i describes a number of cyber-attacks in further detail. within the table, cyber-attacks have been organised by attack date. if the attack date was not available within the reference, then the article date has been used. the target-country of each cyber-attack has been listed, alongside a brief description of the methods involved. finally, the attack type has also been classified in accordance with the cps taxonomy described earlier where it has been mentioned within the reference. both the figure and the table present specific cyberattacks and incidents and exclude: general advisories (e.g. from governmental departments), general discussions and summaries of attacks, and detailed explanations of techniques and approaches utilised by the attackers. the extent of the cyber-security related problems faced in the uk was quite exceptional, and in this section we use the uk as a case study to analyse covid- related cyber-crime. the discussion herein demonstrates that as expected and outlined above, there was a loose correlation between policy/news announcements and associated cyber-crime campaigns. the analysis presented herein focuses only on cyber-crime events specific to the uk. so for example, although many of the incidents identified in the previous section and particularly in [ ] are global cyber-attacks, the discussion herein ignores these. consequently, numerous announcements purportedly coming from reputed organisations such as who and a plethora of malware which reached uk citizens is ignored as these were not uk specific issues. indications of the extent of the uk cyber-crime incident problem experienced during the pandemic are provided by the reported level of suspect emails and fraud reported. by early may ( - - ), more than , 'suspect' emails had been reported to the national cyber security centre [ ] and by the end of may ( - - ), £ . m had been lost to covid- related scams with around , victims of phishing and / or smishing campaigns [ ] . in response, the national cyber security centre (ncsc) took down fake online shops [ ] and hmrc (her majesty's revenue and customs) took down fake websites [ ] . the timeline in figure shows a series of uk specific events and cyber-crime incidents. the timeline indicates a direct and inverse correlation between announcements and incidents. direct correlations are instances where perpetrators appear to follow announcements or events, they may have drawn on these events and carefully configured cyber-attacks around policy context. these are shown in the figure with a solid coloured connecting arrow. inverse correlations are instances where an incident has no clear correlation with an event or announcement. although inverse correlations do not appear to have a direct correlation, these may exist because a number of events were being actively highlighted in the media. for example, the issue of personal protective equipment (ppe) was in active discussion well before the uk government gave this priority consideration. similarly, the likelihood of a tax rebate scheme was in active consideration in early march before the budget announcement on - - . the first tax rebate phishing campaigns were in active circulation before the budget announcement. in both cases, we should emphasise that these are loose correlations and more work needs to be done in terms of whether a predictive model can be built using this data and data around the world as examples. on th march , the uk government made a number of important budgetary announcements [ ] which included: a £ bn emergency response fund to support the nhs and other public services in england; an entitlement to statutory sick pay for individuals advised to self-isolate; a contributory employment support allowance for self-employed workers; a £ m hardship fund for councils to help the most vulnerable in their areas; a covid- business interruption loan scheme for small firms; and the abolishment of business rates for certain companies. soon after, the government continued to make an-nouncements to support the citizenry and economy. these announcements included: a scheme to support children entitled to receive free school meals ( - - ) ; a hardship fund ( - - ) ; help for supermarkets to target vulnerable people ( - - ) ; the potential availability of home test kits ( - - ); a job retention scheme ( - - ) ; and the launch of the much awaited track and trace app ( - - ). events such as these increase the likelihood of a ) , and a charitable donation to the recipient. none of these events have associated governmental announcements or even general public speculation. examples supporting our notion of a correlation between events and cyber-security campaigns are provided in table ii and illustrated in figure . these examples indicate a loose correlation between events and cybercriminal campaigns. many of the cases outlined in table ii and figure , were very simple. potential victims were provided urls through email, sms, or whatsapp. an example of this is provided in figure . in this case, the url pointed to a fake institutional website which requests credit/debit card details. although there are elements of this process which are obviously suspicious to a more experienced computer user, for example, spelling errors (relieve instead of relief in the covid- relief scam), suspect reply email addresses and clearly incorrect urls, these are not immediately obvious to many users. the timeline shown in figure and the uk case study above creates an ideal platform through which to analyse the cyber-attacks that have occurred in light of the pandemic. from the point that the first case was announced in china ( - [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] , the first reported covid- inspired cyber-attack took days. the next reported cyber-attack was days ( - - ) . from this point onwards, it is clear that the timeframe between events and cyber-attacks reduces dramatically. the cyber-attacks presented in the timeline can be further categorised as follows: • ( %) involved phishing and / or smishing • ( %) involved hacking • ( %) involved denial of service • ( %) involved malware fig. . the covid- -relieve scam [ ] • ( %) involved financial fraud • ( %) involved pharming • ( %) involved extortion whilst this analysis is useful, the sequence of events in the complete attack can also provide key attack insights. the timeline reveals these sequences and shows the complete campaign comprising of, for instance, the distribution of malware (m) through phishing (p) which steals payment credentials which are used for financial fraud (f ). we can describe this cyber-attack sequence as p,m,f. analysing cyber-attacks in this way is important because this indicates multiple points in a cyber-attack where protections could be applied. the timeline reveals the following cyber-attack sequences: this analysis does not include the sequence of events that took place in the two hacking and two denial of service incidents. it should be noted that although financial fraud is the most likely goal in most of the cyber-attacks described in the timeline, financial fraud was only recorded in the timeline where reports have clearly indicated that this was the outcome of a cyberattack. in reality, the p,m,f and p,ph,f cases are likely to be higher. figure provides a summary of the countries that were the target of early cyber-attacks during the pandemic, organised by attack date. as shown, china and the usa account for % of the attacks reported. it is also clear from table i that both of these countries were primary target from the start of the pandemic. the attacks then spread to the united kingdom and more other countries. by march however, a vast majority of the attacks are targeted at the whole world, with a reminder of attacks specifically focused at events in a single country, such as tax rebates due to covid- , or contact tracing phishing messages. it is useful to consider this in the context of uk specific cyber-attacks. this examination reveals that phishing was a component of all (n= ) the cyberattacks analysed. involved extortion as the final goal, the remaining involved financial fraud. cyberattacks comprised the sequence: p,ph,f, comprised the sequence p,f, the remaining comprised of p,e. it is notable that although an nhs malware distribution website was discovered and removed on - , none of the cyber-attacks we analysed appeared to involve malware in the same way that the global analysis reveals. there may be a number of reasons for this. launching a malware connected campaign requires more sophistication and time. there may be less opportunity to directly connect it to a specific event or announcement. the time delay between some of the announcements and the associated campaigns was remarkably short. for instance, the time delay between the lockdown announcement ( - - ) and the 'lockdown contravention fine' ( - - ) was days, and the time delay between the job retention scheme announcement ( - - ) and the job retention scam ( - - ) was also days. to reflect more generally on the cyber-attacks discovered, we can see that phishing (including smishing) were, by far, the most common based on our analysis. in total, it was involved in % of the global attacks. this is however, unsurprising, as phishing attempts are low in cost and have reasonable success rates. in the case of covid- , these included attempts at impersonating government organisations, the who, the uk's national health service (nhs), airlines, supermarkets and communication technology providers. the specific context of the attacks can be slightly different however the underlying techniques, and the end goal is identical. for instance, in one email impersonating the who, attackers attach a zip file which they claim contains an ebook that provides, "the complete research/origin of the corona-virus and the recommended guide to follow to protect yourselves and others" [ ] [ ]. moreover, they state: "you are now receiving this email because your life count as everyone lives count". here, attackers are using the branding of who, posing as helpful (the fig. . cyber-attack distribution across countries examined remainder of the email contains legitimate guidance), and appealing to people's emotions in crafting their attack email [ , ] . similar techniques can be seen in a fake nhs website created by criminals detected online, which possesses identical branding but is riddled with malware [ ] , and a malicious website containing malware which also presents the legitimate johns hopkins university covid- dashboard[ ]. it is notable that the fake who email contains spelling/grammatical errors. the discussion in section iii-c provides further specific examples of this. to further increase the likely success of phishing attacks cyber-criminals have been identified registering large numbers of website domains containing the words 'covid' and 'coronavirus' [ ] . such domains are likely to be believable, and therefore accessed, especially if paired with reputable wording such as who or centers for disease control and prevention (cdc) or key words (e.g., corona-virusapps.com, anticovid -pharmacy.com, which have been highlighted as in use [ ] ). communications platforms, such as zoom, microsoft and google, have also been impersonated, both through emails and domain names [ ] . this is noteworthy given the fact that these are the primary technologies used by millions across the world to communicate, both for work and pleasure. these facts, in combination with convincing social engineering emails, text messages and links, provide several notable avenues for criminals to attack. pharming attacks were much less common but did occur in % of cases. as can be seen table i, these often occur alongside other attacks. covid- -inspired fraud has leveraged governmental/scientific announcements to exploit the anxieties of users and seek financial benefit. from our analysis, fraud was typically committed through phishing and email attacks-we also can see this in our sequencing above. in one case, criminals posed as the cdc in an email and politely requested donations to develop a vaccine, and also that any payments be made in bitcoin [ ] . typical phishing techniques were used, but on this occasion these included requests for money: "funding of the above project is quite a huge cost and we plead for your good will donation, nothing is too small". a notable point about this particular attack is that it also ask recipients to share the message with as many people as possible. this is concerning given that people are more likely to trust emails they believe have been vetted by close ones [ ] . there were a range of other fraud attempts, largely based on threats or appeals. for instance, our analysis identified offers of investment in companies claiming to prevent, detect or cure covid- , and investment in schemes/trading options which enable users to take advantage of a possible covid- driven economic downturn [ ] . there were offers of cures, vaccines, and advice on effective treatments for the virus. the food and drugs administration (fda) issued warning letters between th march and st april to companies "for selling fraudulent products with claims to prevent, treat, mitigate, diagnose or cure" covid- [ , ] . the european anti-fraud office (olaf) has responded to the flood of fake products online by opening an enquiry concerning imports of fake products due to covid- pandemic [ ] , and in the uk, the medical and healthcare products regulatory agency (mhra) has began investigating bogus or unlicensed medical devices currently being traded through unauthorised and unregulated websites [ ] . extortion attacks were witnessed in our analysis but were less prevalent (appearing in only % of cases) compared to the others above. the most prominent case of this attack was an extortion email threatening to infect the recipient and their family members with covid- unless a bitcoin payment is made [ ] . to increase the believability of the message, it included the name of the individual and one of their passwords (likely gathered from a previous password breach). after demanding money, the message goes on to state: "if i do not get the payment, i will infect every member of your family with coronavirus". this attempts to use fear to motivate individuals to pay, and uses passwords (i.e., items that are personal) to build confidence in the criminal's message. malware related to covid- increased in prominence during the pandemic and impacted individuals and organisations across the world. as shown above, it was the second largest cyber-attack type, appearing in % of cases. vicious panda and mbr loader were the only new malware discovered in this period. the remaining malware attacks were variants of existing malware and included metaljack, rem-cos, emotet, lokibot, cxk-nmsl, dharma-crysis, netwalker, mespinoza/pysa, spymax (disguised as the corona live . app) guloader, hawkeye, formbook, trickbot and ginp. ransomware, in particular, was a notable threat and an example of such was covidlock, an android app disguised as a heat map which acted as ransomware; essentially locking the user's screen unless a ransom was paid [ ] . at the organisational level, ransomware has significantly impacted healthcare services-arguably the most fragile component of a country's critical national infrastructure at this time. attacks have been reported in the united states, france, spain and the czech republic [ , ] , and using ransomware such as netwalker. such attacks fit a criminal modus operandi if we assume that malicious actors will target areas where they believe they stand to capitalise on their attacks; i.e., health organisations may be more likely to pay ransoms to avoid loss of patient lives. interestingly there have since been promises from leading cyber-crime gangs that they will not (or stop) targeting healthcare services. in one report, operators behind clop ransomware, dop-pelpaymer ransomware, maze ransomware and nefilim ransomware stressed that they did not (normally) target hospitals, or that they would pause all activity against healthcare services until the virus stabilises [ ] . other notable malware examples during the pandemic include: trickbot, a trojan that is typically used as a platform to install other malware on victims' devicesaccording to microsoft, trickbot is the most prolific malware operation that makes use of covid- themed lures for its attacks [ ] ; a master boot record (mbr) rewriter malware that wipes a device's disks and overwrites the mbr to make them no longer usable [ ] ; and corona live . , an app that leveraged a legitimate covid- tracker released by john hopkins university and accessed device photos, videos, location data and the camera [ ] . as the pandemic continues, there are likely to be more strains of malware, targeting various types of harm, e.g., physical, financial, psychological, reputational (for businesses) and societal [ ] . during the covid- pandemic our analysis only identified a very small amount ( %) of dos attacks, but there were several reports of hacking. these reports suggested that hacking was not indiscriminate but instead, targeted towards institutions involved in research on coronavirus. in one report, fbi deputy assistant director stated, "we certainly have seen reconnaissance activity, and some intrusions, into some of those institutions, especially those that have publicly identified themselves as working on covid-related research" [ ] . this was further supported by a joint security advisory a month later from the uk's ncsc and usa's cisa [ ] . in this advisory, advanced persistent threat (apt) groupssome of which may align with nation states-were identified as targeting pharmaceutical companies, medical research organisations, and universities involved in covid- response. the goal was not necessarily to disrupt their activities (as with the ransomware case), but instead to steal sensitive research data or intellectual property (e.g., on vaccines, treatments). while a detailed analysis of these attacks has not yet surfaced, password spraying (a brute-force attack which applying commonly-used passwords in attempting to login to accounts) and exploiting vulnerabilities in virtual private network (vpn) have been flagged [ ] . attribution is another important consideration during such attacks. determining the true origin of cyber-attacks has always been difficult, however, in response to these covid- -related threats, the us openly named the people's republic of china (prc) as a perpetrator in a joint fbi/cisa announcement [ ] . the effects of the pandemic, the mass quarantine of staff and the measures put in place to facilitate remote working and resilience of existing cyber-infrastructures, against the attacks and timelines previously described, had a profound effect on the workforce -the people engaged in or available for work. the pandemic also had an effect on the resilience of technology, socio-economic structures and threatened, to a certain degree, the way people live and communicate. figure illustrates the covid- impact on the workforce across eight different categories. all categories seemingly integrate with cyber-enabled assets and tools and different categories may be impacted differently. the pandemic created risk conflicts, for example, strict compliance with security standards which discourage data sharing, could be more harmful than sharing the data. so, whilst there may be strict requirements for patient data not to be accessed at home by gps (general practitioners), this causes a greater harm during quarantine than enabling gps to access patient data. also, the way confidential patient information is processed requires a data protection impact assessment (dpia) to enable further nhs support where needed. this can have an impact in terms of the timely delivery of medical interventions in response to covid- . in traditional risk classification, elements like asset registration and valuation, threat frequency and vulnerability probability are at greater risk of cyber threat. we, therefore, anticipate changes on the way the workforce accesses those information assets and how strategic, tactical and operational tasks are executed to generate socio-economical outputs. these changes can be captured by the development and testing of risk statements capturing ) threat agents, ) vulnerabilities, ) policy/process violation and ) overall asset exposure on all emerging threat landscapes as illustrated in figure . these changes unavoidably cascade further changes to the threat landscapes associated with remote workforce activities and the increasing frequency of weaponised attack vectors related to the coronavirus spreading. given the current climate, it is difficult to predict whether these changes will have a long-lasting effect on the workforce, but their significance is already recorded [ ] . therefore, it is increasingly important that the control of information (storage, processing, transmission) has an elevated importance given the increase of cyber-attacks on important infrastructures. governments, private and public sectors throughout europe currently consider measures to contain and mitigate covid- impact on existing data structures and information governance frameworks (for example, fig. . covid- impact on workforce [ ] ). particular emphasis is placed upon the implications of the pandemic in the processing of personal data. the general data protection regulation (gdpr) legislation in the uk dictates that personal data must be processed only for the specific and explicit purposes for which it has been obtained [ ] . in addition, data subjects should always receive explicit and transparent information with regard to the processing activities undertaken, including that of features and nature of the activity, retention period and purpose of processing. there are challenges related to the governance legal and regulatory compliance landscape in terms of conformance versus rapid access and processing of data by different entities. this is quite apparent in cases where public authorities seek to obtain pii to reduce the spread of covid- . typical examples also include contact tracing applications and platforms in which the data is aggregated online for post-processing [ ] . specific legislative measures have to be re-deployed or introduced to safeguard public security while maintaining privacy at scale, while legal and regulatory principles continue to upheld [ ] . with the rapid increase of covid- symptoms, governments had to derive a plan that would enable them to understand epidemiological data further and identify positive interventions to contain and mitigate the impact of the pandemic. research shows a high correlation between the use of big data that includes private identifiable information in the effectiveness of these epidemiological investigations [ ] . that meant that in most cases, citizens had to provide this information voluntarily and that quickly resulted in discussions and debates on the tradeoffs between public safety versus personal privacy [ ] . the information has also been obtained through internet communication technology. medical testing equipment and coronavirus testing at a large-scale were used as instruments for data collection in the fight to reduce mortality rates. the legal and regulatory compliance frameworks differ between countries; thus, managing personal information was subject to different privacy protection measures. the de-identification of personal information was another component that governments had to exercise to satisfy personal privacy requirements and increase the trust of human participants during the epidemiological investigations. the process of collecting and process-ing personal information by applying de-identification technologies raised technical challenges with regards to accuracy and consent, safe and legally defensive data disposal and robustness of associated policies of data processing and management for epidemiological research. the urgency of the situation and the speed at which the data had to be acquired and processed, created a sense of distrust amongst citizens and challenged the efficacy of the existing processes in place [ ] . the extensive lockdown periods introduced in many countries (described in section iii) have also tested their ability to deploy strategies for business recovery after these periods. these strategies had to ensure smooth and phased out recovery within an ongoing pandemic, which has proved to be a challenging task. however, there is an unprecedented speed and scale on the r&d activities in response to the covid- outbreak forcing crossorganizational multilateral collaborations [ , ] . there is currently a challenge across europe to orchestrate information sharing in a timely and accurate manner as even mainstream media sources seem to have propagated false information [ ] . the increase on both frequency and impact of these attacks will test further our existing monitoring and auditing capabilities, logical and physical access controls, authentication and verification schemes currently deployed. also, as part of the current enterprise risk management approaches the way organisations sanitise incident reporting, media disposal and data destruction and sharing processes will also be tested alongside to traditional defence-in-depth principles currently established as de-facto. the finance sector is also affected as the predicted financial recession will leverage the sophistication and scale of targeted attacks as threat actors grow their capabilities [ ] . the covid- pandemic has generated remarkable and unique societal and economic circumstances leveraged by cyber-criminals. our analysis of events such as announcements and media stories has shown what appears to be a loose correlation between the announcement and a corresponding cyber-attack campaign which utilises the event as a hook thereby increasing the likelihood of success. the covid- pandemic, and the increased rate of cyber-attacks it has invoked have wider implications, which stretch beyond the targets of such attacks. changes to working practises and socialization, mean people are now spending increased periods of time online. in addition to this, rates of unemployment have also increased, meaning more people are sitting at home online-it is likely that some of these people will turn to cyber-crime to support themselves. the combination of increased levels of cyber-attacks and cyber-crime means there may be implications for policing around the worldlaw enforcement must ensure it has the capacity to deal with cyber-crime [ ] . the analysis presented in this paper has highlighted a common modus-operandi of many cyber-attacks during this period. many cyber-attacks begin with a phishing campaign which directs victims to download a file or access a url. the file or the url act as the carrier of malware which, when installed, acts as the vehicle for financial fraud. the analysis has also shown that to increase the likelihood of success, the phishing campaign leverages media and governmental announcements. although this analysis is not necessarily novel, we believe this is the first time that this has been supported with a context of actual live events. this analysis gives rise to the recommendation that governments, the media and other institutions should be aware that announcements and the publication of stories are likely to give rise to the perpetration of associated cyber-attack campaigns which leverage these events. the events should be accompanied by a note / disclaimer outlining how information relating to the announcement will be relayed. our research presents opportunity for further research. this research has shown what can best be described as a loose direct and inverse correlation between events and cyber-attacks. further research should investigate this phenomenon and outline whether a predictive model can be used to confirm this relationship. there is an abundant supply of cyber-attack case studies relating to countries around the world and a wider analysis of the problem can help in affirming this phenomenon. malware," , https://krebsonsecurity.com/ / /live-coronavirusmap-used-to-spread-malware/ (accessed june ). [ ] r. smithers, "fraudsters use bogus nhs contact-tracing app in phishing scam," , https://www.theguardian.com/world/ /may/ / fraudsters-use-bogus-nhs-contact-tracing-app-inphishing-scam (accessed may ). deals could have been avoided," , https://www.bloomberg.com/opinion/articles/ - - /coronavirus-trillions-in-aid-draws-scams-anddodgy-deals (accessed may ). [ ] d. galov, "remote spring: the rise of rdp bruteforce attacks," , https://securelist.com/remote-spring-therise-of-rdp-bruteforce-attacks/ (accessed may ). [ ] ncsc, "home working: preparing your organisation and staff," , https://www.ncsc.gov.uk/guidance/home-working (accessed may ). [ ] nist, "security for enterprise telework, remote access, and bring your own device (byod) solutions," , https://csrc.nist.gov/csrc/media/publications/shared/ documents/itl-bulletin/itlbul - .pdf (accessed may ). [ ] ftc, "online security tips for working from home," pandemic profiteering: how criminals exploit coronavirus phishing emails: how to protect against covid- scams us authorities battle surge in coronavirus scams, from phishing to fake treatments cybercrime and you: how criminals attack and the human factors that they seek to exploit hackers are targeting hospitals crippled by coronavirus uk's national cyber security centre (ncsc) and the us' department of homeland security (dhs) cybersecurity and infrastructure security agency (cisa) the hiscox cyber readiness report official annual cybercrime report less traditional crime, more cybercrime measuring the changing cost of cybercrime understanding the growth of cybercrime economy scene of the cybercrime the novelty of 'cybercrime' an assessment in light of routine activity theory other people's money; a study of the social psychology of embezzlement hacking: the next generation: the next generation understanding scam victims: seven principles for systems security how cybercriminals prey on victims of natural disasters hurricane katrina fraud how to help the earthquake victims in ecuador and japan watch out for hurricane harvey phishing scams hundreds of bushfire donation scams circulating michael jackson's death sparks off spam michael jackson's death spurs spam, malware campaigns you have not won! a look at fake fifa world cup-themed lotteries and giveaways blackmailing and passwords leaks compromised linkedin accounts used to send phishing links via private message and inmail tips to help if you are worried about coronavirus facing down the myriad threats tied to covid- threat spotlight: coronavirus-related phishing protecting businesses against cyber threats during covid- and beyond covid aid scams and dodgy a systematic approach toward description and classification of cybercrime incidents a cyber attack modeling and impact assessment framework a taxonomy and survey of intrusion detection system design techniques, network threats and datasets extracting narrative timelines as temporal dependency structures classification of cyber attacks in south africa sony's nightmare before christmas: the north korean cyber attack on sony and lessons for us government actions in cyberspace naming the coronavirus disease (covid- ) and the virus that causes it cybercrime -prosecution guidance vietnamese threat actors apt targeting wuhan government and chinese ministry of emergency management in latest example of covid- related espionage skype phishing attack targets remote workers' passwords fake coronavirus tracking apps are really malware that stalks you how to design browser security and privacy alerts bayesian network models in cyber security: a systematic review google translate coronavirus disease (covid- ) pandemic latest information on coronavirus disease (covid- ) research on computer network attack modeling based on attack graph who reports fivefold increase in cyber attacks, urges vigilance search (accessed municipal:"massive" computer attack at the town hall of marseille cyber attack on easyjet, compromised the data of nine million customers an extended model of cybercrime investigations a taxonomy of operational cyber security risks a taxonomy of technical attribution techniques for cyber attacks a taxonomy of network threats and the effect of current datasets on intrusion detection systems chapter : cyberdependent crimes cyber-enabled crimes -fraud and theft research reveals hacker tactics: cybercriminals use ddos as smokescreen for other attacks on business from cybersecurity deception to manipulation and gratification through gamification recent ransomware attacks define the malware's new age state of malware report social engineering attacks and covid- chinese hackers 'weaponize' coronavirus data for new cyber attack: here's what they did coronavirus email attacks evolving as outbreak spreads coronavirus phishing threat intel:cyber attacks leveraging the covid- /coronavirus pandemic hackers are using the "coronavirus" fear for phishing, please pay attention to prevention take advantage of the fire! "the epidemic is a bait" cyber attack global shipping industry attacked by coronavirus-themed malware fighting the spread of coronaviruses who faces severe cybersecurity threats indian hackers targeting chinese medical institutes amid coronavirus outbreak, says report analysis and suggestions on several types of network security threats during the epidemic prevention and control period coronavirus and ransomware infection -what's the connection? fresh virus misery for illinois: public health agency taken down by... web ransomware. great timing, scumbags coronavirus test results delayed by cyber-attack on czech hospital cyber-attack hits u.s. health agency amid covid- outbreak new threat discovery shows commercial surveillanceware operators latest to exploit covid- new android app offers coronavirus safety mask but delivers sms trojan scams, lies, and coronavirus cyber-attack threatens spanish hospital computer systems covid sms phishing attempt our @glospolice fcr have had calls asking if covid- texts like the below are genuine the school meals coronavirus text scam which could trick parents out of thousands android malware takes payment for 'coronavirus finder' map warning over coronavirus netflix scam cyber criminals create a spoof copy of the nhs website in the midst of the coronavirus pandemic to trick users into downloading dangerous malware that can steal their passwords and credit card data hackers exploit hmrc coronavirus job retention scheme with phishing email scam new coronavirus screenlocker malware is extremely annoying docusign phishing campaign uses covid- as bait new threat intelligence report: days of coronavirus ncsc shines light on scams being foiled via pioneering new reporting service coronavirus: fraud victims have lost more than £ . m to virus-related scams coronavirus: israel enables emergency spy powers hmrc shuts down almost covid phishing scam sites budget : what you need to know coronavirus scams pervasive ehealth services a security and privacy risk awareness survey baiting the hook: factors impacting susceptibility to phishing attacks cyber criminals create a spoof copy of the nhs website in the midst of the coronavirus pandemic to trick users into downloading dangerous malware that can steal their passwords and credit card data check point there are now more than , 'high-risk' covid- threats on the web covid- fraud a study on situational awareness security and privacy of wearable health monitoring devices food and drugs administration (fda) olaf launches enquiry into fake covid- related products uk medicines and medical devices regulator investigating cases of fake or unlicensed covid- medical products dirty little secret extortion email threatens to give your family coronavirus covidlock update: deeper analysis of coronavirus android ransomware spanish hospitals targeted with coronavirus-themed phishing lures in netwalker ransomware attacks ransomware gangs to stop attacking health orgs during pandemic trickbot named most prolific #covid malware coronavirus trojan overwriting the mbr a taxonomy of cyber-harms: defining the impacts of cyber-attacks and understanding how they propagate fbi official says foreign hackers have targeted covid- research uk's national cyber security centre (ncsc) and the us' department of homeland security (dhs) cybersecurity and infrastructure security agency (cisa) people's republic of china (prc) targeting of covid- research organizations why cybersecurity matters more than ever during the coronavirus pandemic data protection and covid- general data protection regulation (gdpr): principle (b): purpose limitation nhs contact-tracing app 'falls short of data protection law covid- information governance advice for ig professionals privacy in the age of medical big data balancing personal privacy and public safety in covid- : case of korea and france astrazeneca advances response to global covid- challenge as it receives first commitments for oxford's potential new vaccine covid- : collaboration is the engine of global science -especially for developing countries the danger of mainstream media infections with viral and fake information covid- : companies and verticals at risk for cyber attacks the implications of the covid- pandemic for cybercrime policing in scotland: a rapid review of the evidence and future considerations, ser. research evidence in policing: pandemics. scottish institute for policing research key: cord- -l f hg authors: amor, sandra; fernández blanco, laura; baker, david title: innate immunity during sars‐cov‐ : evasion strategies and activation trigger hypoxia and vascular damage date: - - journal: clin exp immunol doi: . /cei. sha: doc_id: cord_uid: l f hg innate immune sensing of viral molecular patterns is essential for development of antiviral responses. like many viruses, sars‐cov‐ has evolved strategies to circumvent innate immune detection including low cpg levels in the genome, glycosylation to shield essential elements including the receptor binding domain, rna shielding and generation of viral proteins that actively impede anti‐viral interferon responses. together these strategies allow widespread infection and increased viral load. despite the efforts of immune subversion, sars‐cov‐ infection activates innate immune pathways inducing a robust type i/iii interferon response, production of proinflammatory cytokines, and recruitment of neutrophils and myeloid cells. this may induce hyperinflammation or alternatively, effectively recruit adaptive immune responses that help clear the infection and prevent reinfection. the dysregulation of the renin‐angiotensin system due to downregulation of angiotensin converting enzyme , the receptor for sars‐cov‐ , together with the activation of type i/iii interferon response, and inflammasome response converge to promote free radical production and oxidative stress. this exacerbates tissue damage in the respiratory system but also leads to widespread activation of coagulation pathways leading to thrombosis. here, we review the current knowledge of the role of the innate immune response following sars‐cov‐ infection, much of which is based on the knowledge from sars‐cov and other coronaviruses. understanding how the virus subverts the initial immune response and how an aberrant innate immune response contributes to the respiratory and vascular damage in covid‐ may help explain factors that contribute to the variety of clinical manifestations and outcome of sars‐cov‐ infection. the emergence in wuhan china of a novel severe acute respiratory syndrome coronavirus (sars-cov- ) triggered an epidemic of the coronavirus disease (covid- ) . as of september th , the confirmed , , cases including , deaths have been reported worldwide (worldometers.info/coronavirus). at the end of january , the who declared covid- a pandemic and a global health emergency. the family coronaviridae is subdivided into torovirinae and coronavirinae that contains the genera alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus. the human coronaviruses (hcov) belong to the αlpha-cov (hcov- e and hcov-nl ) and beta-cov (middle east respiratory syndrome coronavirus-mers-cov, sars-cov, hcov-oc and hcov-hku ) [ table ; ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ]. in comparison with most hcovs that cause mild upper respiratory tract infections, sars-cov, mers-cov and sars-cov- induce severe pneumonia ( ) . the clinical presentation of covid- ranges from mild 'flu-like' symptoms to severe respiratory failure and death although between . - % of sars-cov- infections are asymptomatic depending on the population ( ) . common symptoms include fever, cough, fatigue, shortness of breath, headache and pneumonia. in addition, some patients develop gastrointestinal problems ( ) , and neurological manifestations, including headache, dizziness, hyposmia and hypogeusia. age and comorbidities i.e., hypertension, chronic obstructive pulmonary disease, diabetes, obesity and cardiovascular disease predispose to more severe manifestations, including severe respiratory failure, septic shock, coagulation dysfunction, strokes, cardiovascular problems ( ) and neurological manifestations ( ) . although the origin and transmission of sars-cov- is unclear, genome sequencing reveals marked similarities with sars-cov ( ) . however, in comparison, sars-cov- spreads more quickly than sars-cov, likely due to the - % fold higher in infectivity and transmissibility during the initial non-symptomatic period ( - days) . in some cases, transmission has been reported after development of initial symptoms despite the presence of antibodies, ( ) indicating that both, neutralising antibodies and t cell responses, are necessary to prevent reinfection and for protection ( ) . this is further supported by studies showing pd + cd + t cell exhaustion, depletion or inactivation is associated with viral persistence in severe cases ( ) . sars-cov- is a positive-sense rna ( , nucleotides) enveloped virus of to nm diameter ( ) . the envelope is studded with homotrimers spike proteins of - nm length that are heavily decorated with n-glycans [figure ( , ) ]. similar to other hcovs, sars- this article is protected by copyright. all rights reserved non-structural proteins (nsp) while orfs - encode the viral structural proteins -spike, envelope, membrane and nucleocapsid, and the accessory proteins [figure b]. differences between the structural, non-structural and accessory proteins of sars-cov- and other coronaviruses help to explain the high infectivity rate and the range of pathologies observed ( , , ) . while knowledge of sars-cov is rapidly emerging, parallels with sars-cov, as well as ongoing sequencing data and antigenic typing will be crucial to understand the dynamics of the pandemic. sars-cov- cell entry is similar to sars-cov being mediated by the binding of the receptor-binding domain (rbd) of the s protein, to the angiotensinconverting enzyme- (ace- ), although other receptors such as cd and cd-sign have been reported [ table ]. docking of the rbd to the receptor and the action of furin, a serine protease that separates the s and s proteins exposes a second binding domain on s allowing membrane fusion. binding of the s protein to ace- requires priming by cell proteases -primarily tmprss , however, tmprss is expressed by a subset of ace + cells supporting the notion that the virus likely uses other host enzymes such as tmprss , lysosomal cathepsins and neuropilin- ( ) to augment the impact of furin and expose the rdb thus promoting sars-cov- entry ( ) . the structural proteins m, e and n are crucial for stability of the viral genome and viral replication. the nsp and accessory proteins ( ) encoded by open reading frames (orfs) have differing functions during viral replication [table and many also act to deviate the innate immune response thus augmenting viral replication and spread. the degree to which the innate immune system is suppressed and evaded clearly determines the viral load and the host's outcome to infection, the clinical symptoms and the severity of the disease. following infection, viral rna is sensed by several classes of pattern recognition receptors (pprs). the retinoic acid-like receptors (rlrs) include retinoid inducible gene i (rig-i) and melanoma differentiation-associated gene (mda ), toll-like receptors (tlr) -classically , and that trigger ifn pathways and cytokines production [ figure ]. once engaged these pprs act downstream via the kinases tank-binding kinase- (tbk ) and inhibitor-b kinases (ikks). such triggering leads to the activation of the transcription factors interferonregulatory factor- (irf ) and (irf ) and nuclear factor kappa-light-chain-enhancer of activated b cells (nfb). these subsequently induce expression of type i ifns (ifnα/β) and interferon stimulated genes (isgs) [figure ] many of which have potent antiviral activities, as well as other proinflammatory mediators e.g. cytokines, chemokines and antimicrobial peptides that are essential to initiate the host innate and adaptive immune response. in addition, the absent in melanoma (aim )-like receptors and nod-like receptors (nlrs) this article is protected by copyright. all rights reserved trigger the inflammasome and il-  and il- production leading to pyroptosis [ figure ]. immune responses include c-type lectins and the stimulator of interferon genes (sting). while the cgas/sting pathway is commonly associated with sensing cytosolic dna, it is also activated following binding of enveloped viruses to host cells and cytosolic viral rna ( , ) . similar to tlrs and rlr, downstream, sting engages tbk to active irf and/or nfb inducing type i ifn and/or proinflammatory cytokines [ figure ]. coronaviruses have evolved several strategies to escape such innate immune recognition allowing widespread replication. such evasion includes evolution of low genomic cpg, rna shielding, masking of potential key antigenic epitopes as well as inhibition of steps in the interferon type i/iii pathways. generally, the zinc finger antiviral protein (zap) specifically binds to and degrades cpg motifs in genomes of rna viruses. in comparison with other viruses, sars-cov- has evolved the most extreme cpg deficiency of all betacoronavirus [ ( ) . another strategy to protect mrna used by the host and many viruses is the processing of capping the ′ end. for both host and virus rna, capping limits degradation and importantly blocks recognition by cytosolic pprs. like many rna viruses sars-cov- has exploited several mechanisms to protect the ′ ends by a cap structure of rna generated during replication. while some viruses snatch the caps from host rna, sars-cov- , like other coronaviruses uses its own capping machinery composed of nsp , nsp and the this article is protected by copyright. all rights reserved proteins of - nm length that are heavily decorated with glycans. each spike protein comprises of two subunits (s and s ) that each bear glycan groups ( ) . cell entry of the highly glycosylated s protein of sars-cov is promoted by dc-sign possibly augmenting virus uptake or aiding capture and transmission of sars-cov by dcs and macrophages ( ) ( ) ( ) . similar to the spike protein, the other structural, non-structural and accessory proteins are also modified by glycosylation, palmitoylation, phosphorylation, sumoylation and adpribosylation ( ) . conversely, some viral proteins e.g. nsp , possess deubiquitinating (dub) and deisgylation activity thereby interfering with host functions targetting those that are critical for signalling transduction of innate immunity ( ) . insertion of the spike protein into cell membranes during replication is a key step for virus budding. whilst this takes place in the rtc [suppl figure ], receptor-bound spike proteins interact with tmprss expressed on the uninfected cell surface, mediates fusion between infected and uninfected cells promoting the formation of syncytia allowing the virus to spread to adjacent uninfected cells while evading detection by the immune response ( ) . in addition to strategies to evade ppr recognition, sars-cov- has also evolved strategies to inhibit steps in the pathway leading to type i/iii ifn production. this may be especially relevant in the lungs where type ifn iii (lambda) is considered to be more effective in controlling viral infections and critically affected in covid- . knowledge arising from the study of other coronaviruses, especially sars-cov and mers, has shown that many of the non-structural, structural and accessory proteins interfere with elements of the ifn pathway [ table , figure ], essential for the development of effective immunity. ifn antagonism has been attributed to several of the structural, non-structural and accessory proteins that interfere with stimulator of interferon genes (sting)-traf -tbk complex, thereby blocking sting/tbk /ikkε-induced type i ifn production, stat- / translocation to the nucleus, irf , nfb signalling as well as interfering with the actions of the isg products including ifits [ table ]. as examples, nsp , and , and orf interfere with stat- / signalling while nsp , and cap the viral rna [ table ] preventing recognition by rig-i, mda and ifits. nsp also acts by dub proteins thereby preventing their activity such as rig-i and other steps in the ifn pathways for which ubiquitination is essential. cov plpro (nsp ) also interrupts the stimulator of interferon genes sting.traf . tbk complex thereby blocking sting/tbk /ikkε-type i ifn production ( , ) . as well as subversion of the ifn pathway, sars-cov orf a (also present in sars-cov- ) blocks the activity of tetherin also known as bone marrow stromal antigen (bst- ) ( ). bst acts by tethering budding viruses to the this article is protected by copyright. all rights reserved cell membrane thus preventing its release from the cells. orf a removes this inhibition aiding the release of mature virions. in summary, emerging evidence from sars-cov- , and comparison with other sars-cov and mers, reveals many strategies used to evade the innate immune response and subvert the interferon pathway. while this facilitates widespread viral replication increasing the viral load also promotes the viral cytopathic effects leading to tissue damage described below, likely leads to exacerbation and hyperinflammation of the innate immune response once triggered. despite immune evasion and subverting innate immune responses during early infection, sars-cov- effectively initiates immune signalling pathways. this is likely due to the increased viral load that exponentially produces viral rna and viral proteins (pathogen associated molecular patterns -pamps), also induces cell damage that release damage associated molecular patterns (damps) both of which trigger innate immune pathways. like sars-cov and nl , sars-cov- uses the angiotensin (ang)-converting enzyme- (ace ) as a cell receptor [ table ], expressed on epithelia in renal, cardiovascular and gastrointestinal tract tissues, testes and on pneumocytes and vascular endothelia ( ) . ace regulates the renin-angiotensin system (ras) by balancing the conversion of angiotensin i to angiotensin - and angiotensin ii to angiotensin - . binding of sars-cov- to ace leads to endosome formation, reducing ace expression on the cell surface [figures and ] and pushing the ras system to a pro-inflammatory mode triggering production of reactive oxygen species, fibrosis, collagen deposition and a proinflammatory environment including il- and a balanced response to infection via tlr pathway is essential to trigger a protective response to sars-cov ( ) . this study also supports the idea that in addition, pamps, this article is protected by copyright. all rights reserved immune pathways triggered by damps such as oxidised phospholipids, high mobility group box (hmgb ), histones, heat shock proteins and adenosine triphosphate released by damaged cells may contribute to covid- outcome [figures and ] . in addition to rig-i, mda and mavs, rna viruses are also sensed by the stimulator of interferon genes (sting) that is activated by cgamp when enveloped rna viruses interact with the host membranes ( ) . downstream, sting engages tbk that actives irf and/or nfb inducing type ifn and/or proinflammatory cytokines. that hyperactivation of sting contributes to severe covid- as has been hypothesised by berthelot and lioté ( ) . these authors present several lines of evidence, the strongest being that gain of function mutations of sting associated with hyperactivation of type i ifn induces the disease savi (sting-associated vasculopathy with onset in infancy). affected children with savi present with pulmonary inflammation, vasculitis and endothelial-cell dysfunction that mimics many aspects of covid- ( ) . furthermore, sting polymorphisms are associated with ageing-related diseases such as obesity and cardiovascular disease, possibility explaining the impact of comorbidities and development of severe covid- ( ) . also, in bats in which sars-cov- may have arisen, sting activation and thus consequently ifn is blunted ( ), likely aiding viral replication and spread as observed in early sars-cov- infection in humans. that damps released due to viral cytotoxicity may contribute to severe covid- which is best exemplified by hmbg released by damaged and dying cells as well as activated innate immune cells especially in sepsis ( ) . depending on its conformation hmgb triggers tlr , tlr and tlr , the receptor for advanced glycation end-products (rage) and triggering receptor expressed in myeloid cells (trem- ) [ figure ]. in mice, intratracheal administration of hmgb activates mitogen-activated protein kinase (mapk) and nfκb, inducing proinflammatory cytokines, activating the endothelium and recruiting neutrophils in the lung -key pathological features of severe covid- ( , ) . hmgb , and especially the platelet-derived source may play a crucial role in sars-cov- vascular damage since hmgb -/mice display delayed coagulation, reduced thrombus formation and platelet aggregation ( ) . furthermore, blocking hmgb is beneficial in experimental lung injury and sepsis, suggesting therapies targeting hmgb might also be beneficial in severe covid- ( ) . studies of peripheral blood and post-mortem tissues from severe covid- cases reveal high levels of il- β and il- and increased numbers of cd +il- β monocytes, suggesting activation of the nod-like receptor family, pyrin domain-containing (nlrp ) inflammasome pathway ( ) . activation of the nlrp inflammasome, essential for effective antiviral immune responses, is elicited by several factors associated with sars-cov infection including ras this article is protected by copyright. all rights reserved disbalance, engagement of ppr, tnfr and ifnar, mitochondrial ros production, complement components including mac, as well as sars-cov viral proteins such as orf a, n and e [figure , table ]. as a consequence, nlrp interaction with adaptor apoptosis specklike protein (asc) recruits and activates procaspase- , processing pro-il- β and pro-il- to the activate forms [ figure ]. this drives the propyroptotic factor gasdermin d (gsdmd) formation of pores in the cell membrane, i.e. pyroptosis that facilitates the release of proinflammatory cytokines. the pores also aid the release of cellular damps such as hmgb , and viral pamps that further exacerbate inflammation suggesting that targeting the nlrp pathway might be beneficial in severe covid- cases. the delayed interferon response, increased viral load and virus dissemination, coupled with the release of damps and pamps lead to activation of several innate immune pathways. following infection, pneumocytes, epithelial and alveolar cells, and infiltrating monocytemacrophages and neutrophils likely produce the first wave of tnfα, il- , ip- , mcp- , mip-  and rantes production ( , ) . hyperinflammation is likely promoted by comorbidities due to increased ace expression, concurrent bacterial infections and ageing as well as a direct effect of sars-cov- replication since virus-host interactome studies reveal that sars-cov- nsp regulates the nfb repressor factor nkrf, facilitating il- production ( ). this is followed by a second wave of cell recruitment including nk cells that produce ifn and further recruitment of (alternatively activated) monocytes/macrophages and neutrophils sars-cov- exploits many strategies to subvert innate immune responses allowing the virus to replicate and disseminate within the host. the extent to which the virus replicates within this article is protected by copyright. all rights reserved the host, and the efficacy of the host innate immune response to eradicate the infection and trigger effective adaptive immune responses, but not hyper-responsiveness of innate immunity, strongly determines the disease outcome [ table ]. the severity of infection has been linked to age, smoking, comorbidities such as cancer, immune suppression, autoimmune diseases, inflammatory disease, neurodegenerative diseases, obesity, gender and race ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . for example, in a large cohort of , cases the case fatality ratio for over years was . % versus . % in the total cohort ( ) . this is likely higher due to inflamm-ageing, an aberrant innate immune response such as lower production of ifnβ ( ), increased oxidative stress ( ) and sensence of macrophages that become less effective in their reparative functions with age ( ). likewise, viral load, obesity, gender, race, blood groups and comorbidities have all been reported to influence the response to sars-cov- infection, [ table ; ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ] although few studies have fully examined the extent to which subversion and activation of innate immune components contribute to susceptibility in these cases. understanding the innate immune factors that exacerbate the vascular complications will be crucial to control severe disease following sars-cov- infection. rapidly emerging studies reveal the extent to which therapeutic approaches for other viral infections and inflammatory diseases can be repurposed to target innate immunity to treat covid- patients ( , ) . likewise, novel approaches have been put forward to target the susceptible ageing population or those with comorbidities. one approach under investigation is to re-establish the youthful function of macrophages and repair mechanisms using metformin, a drug used in type diabetes that has been shown to attenuate hallmarks of ageing ( ) . in a retrospective study of , subjects tested for covid- while diabetes was reported to be an independent risk factor for covid- -related mortality ( ) this article is protected by copyright. all rights reserved upr -unfolded protein response; zap -zinc finger antiviral protein. this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved (b) and hyperinflammation with influx of macrophages, nk cells and neutrophils (c). this self-augmenting cycle triggers further cell damage and damps and pamps release as well as ros production. d) activation of neutrophils induces neutrophil extracellular traps (net) aided by the n protein and generated in response to ros-induced endothelial cell damage. disruption of the vascular barrier and endothelial cell exposure to proinflammatory cytokine and ros increases expression of p-selectin, von willebrand factor (vwf) and fibrinogen, that attract platelets triggering expression of tissue factor. together this sequence activates the complement system, one of many pathways that crucially activates the coagulation cascade leading to thrombi formation. human aminopeptidase n is a receptor for human coronavirus e tmprss activates the human coronavirus e for cathepsin-independent host cell entry and is expressed in viral target cells in the respiratory epithelium infection of primary cultures of human neural cells by human coronaviruses e and oc hla class i antigen serves as a receptor for human coronavirus oc human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza c viruses dc-sign and dc-signr interact with the glycoprotein of marburg virus and the s protein of severe acute respiratory syndrome coronavirus cd l (l-sign) is a receptor for severe acute respiratory syndrome coronavirus human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry identification of major histocompatibility complex class i c molecule as an attachment factor that facilitates coronavirus hku spike-mediated infection host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein a multibasic cleavage site in the spike protein of sars-cov- is essential for infection of human lung cells clinical and immunologic features in severe and moderate coronavirus disease asymptomatic carriage and transmission of sars-cov- : what do we know? gastrointestinal involvement in covid- : a systematic review and meta-analysis description and proposed management of accepted article this article is protected by copyright. all rights reserved the acute covid- cardiovascular syndrome neurological associations of covid- the proteins of severe acute respiratory syndrome coronavirus- (sars cov- or n-cov ), the cause of covid- breadth of concomitant immune responses prior to patient recovery: a case report of non-severe covid- targets of t cell responses to sars-cov- coronavirus in humans with covid- disease and unexposed individuals marked t cell activation, senescence, exhaustion and skewing towards th in patients with covid- pneumonia genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding d models of glycosylated sars-cov- spike protein suggest challenges and opportunities for vaccine development glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy neuropilin- is a host factor for sars-cov- infection accessory proteins of sars-cov and other coronaviruses extreme genomic cpg deficiency in sars-cov- and evasion of host antiviral defense identification of residues of sars-cov nsp that differentially affect inhibition of gene expression and antiviral signaling severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp and rational design of an attenuated strain severe acute respiratory syndrome coronavirus nsp protein suppresses host gene expression by promoting host mrna degradation the nsp replicase proteins of accepted article this article is protected by copyright murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication severe acute respiratory syndrome coronavirus nonstructural protein interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling the sars-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds severe acute respiratory syndrome coronavirus nonstructural proteins , , and induce double-membrane vesicles sars coronavirus papain-like protease inhibits the type i interferon signaling pathway through interaction with the sting-traf -tbk complex severe acute respiratory syndrome coronavirus c-like protease-induced apoptosis structure of the sars-cov nsp polymerase bound to nsp and nsp co-factors the nsp replicase protein of sars-coronavirus, structure and functional insights the severe acute respiratory syndrome-coronavirus replicative protein nsp is a single-stranded rna-binding subunit unique in the rna virus world structural basis and functional analysis of the sars coronavirus nsp -nsp complex the interaction of the sars coronavirus non-structural protein with the cellular oxido-reductase system causes an extensive cytopathic effect crystal structure and functional analysis of the sars-coronavirus rna cap ′-o-methyltransferase nsp /nsp complex multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase discovery of an rna virus '-> ' exoribonuclease that is critically involved in coronavirus rna synthesis coronavirus nonstructural protein mediates evasion of dsrna sensors and limits apoptosis in macrophages attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking '-o-methyltransferase activity coronavirus non-structural protein : evasion, attenuation, and possible treatments structure, function, and antigenicity of the sars-cov- spike glycoprotein the discovery of angiotensin-converting enzyme and its role in acute lung injury in mice site-specific glycan analysis of the sars-cov- spike severe acute respiratory syndrome coronavirus orf a protein interacts with caveolin this article is protected by copyright severe acute respiratory syndrome coronavirus orf a inhibits bone marrow stromal antigen virion tethering through a novel mechanism of glycosylation interference sars coronavirus a protein blocks cell cycle progression at g /g phase via the cyclin d /prb pathway the orf b protein of severe acute respiratory syndrome coronavirus (sars-cov) is expressed in virus-infected cells and incorporated into sars-cov particles the orf protein of sars-cov- mediates immune evasion through potently downregulating mhc-i. biorxiv the severe acute respiratory syndrome coronavirus nucleocapsid inhibits type i interferon production by interfering with trim -mediated rig-i ubiquitination sars-coronavirus open reading frame- b suppresses innate immunity by targeting mitochondria and the mavs/traf /traf signalosome the cgas-sting defense pathway and its counteraction by viruses the cgas-cgamp-sting pathway: a molecular link between immunity and metabolism nidovirus rna polymerases: complex enzymes handling exceptional rna genomes post-translational modifications of coronavirus proteins: roles and function inhibition of sars-cov- (previously -ncov) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion cell entry mechanisms of sars-cov- complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases identification of immune complement function as a determinant of adverse sars-cov- infection outcome. medrxiv mannose-binding lectin in severe acute respiratory syndrome coronavirus infection complement proteins c b- induce secretion of high molecular weight multimers of endothelial von willebrand factor and translocation of granule membrane protein gmp- to the cell surface netosis, complement, and coagulation: a triangular relationship complement activation contributes to severe acute respiratory syndrome coronavirus pathogenesis in silico studies on the comparative characterization of the interactions of sars-cov- spike glycoprotein with ace- receptor homologs and human tlrs sars coronavirus spike protein-induced innate immune response occurs via activation of the nf-κb pathway in human monocyte macrophages in vitro toll-like receptor signaling via trif contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection covid- as a sting disorder with delayed over-secretion of interferon-beta activated sting in a vascular and pulmonary syndrome dampened sting-dependent interferon activation in bats pathogenic role of hmgb in sars? med hypotheses complexity of danger: the diverse nature of damage-associated molecular patterns platelet-derived hmgb is a critical mediator of thrombosis extracellular hmgb : a therapeutic target in severe pulmonary inflammation including covid- severe acute respiratory syndrome coronavirus e protein transports calcium ions and activates the nlrp inflammasome accepted article this article is protected by copyright. all rights reserved transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in covid- patients host-viral infection maps reveal signatures of severe covid- patients virus-host interactome and proteomic survey of pbmcs from covid- patients reveal potential virulence factors influencing sars-cov- pathogenesis chemokine up-regulation in sars-coronavirus-infected, monocyte-derived human dendritic cells the cytokine storm in covid- : an overview of the involvement of the chemokine/chemokine-receptor system imbalanced host response to sars-cov- drives development of covid- devilishly radical network in covid- : oxidative stress, neutrophil extracellular traps (nets), and t cell suppression endothelial cell infection and endotheliitis in covid- pericyte-specific vascular expression of sars-cov- receptor ace -implications for microvascular inflammation and hypercoagulopathy in covid- patients. biorxiv pericyte alteration sheds light on micro-vasculopathy in covid- infection characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china reduced dynamic range of antiviral innate immune responses in aging oxidative stress, inflamm-aging and immunosenescence genomewide association study of severe covid- with respiratory failure metabolic alterations in aging macrophages: ingredients for inflammaging? harnessing the natural anti-glycan immune response to limit the transmission of enveloped viruses such as sars-cov- abo blood group is a determinant of von willebrand factor protein levels in human pulmonary endothelial cells covid- and the cardiovascular system: implications for risk assessment, diagnosis, and treatment options covid- and cancer: what we know so far covid- and diabetes mellitus: an unholy interaction of two pandemics impact of sex and gender on covid- outcomes in europe inflamm-aging: why older men are the most susceptible to sars-cov- complicated outcomes ethnic and socioeconomic differences in sars-cov- infection: prospective cohort study using uk biobank increased expression of toll-like receptors (tlrs) and and other cytokines in systemic lupus erythematosus (sle) patients: ethnic differences and potential new targets for therapeutic drugs obesity and covid- severity in a designated hospital in shenzhen dysregulation of natural killer cells in obesity prevention and treatment of coivid- by control of innate immunity potential drugs targeting early innate immune evasion of sars-coronavirus via '-o-methylation of viral rna benefits of metformin in attenuating the hallmarks of aging metformin use is associated with reduced mortality in a diverse population with covid- and diabetes. medrxiv the antidiabetic drug metformin blunts netosis in this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved accepted article key: cord- -l b mw d authors: prashantha, c.n.; gouthami, k.; lavanya, l.; bhavanam, sivaramireddy; jain, ajay; shakthiraju, r.g.; suraj, v.; sahana, k.v.; sujana, h.s.; guruprasad, n.m.; ramachandra, r. title: molecular screening of antimalarial, antiviral, anti-inflammatory and hiv protease inhibitors against spike glycoprotein of coronavirus date: - - journal: j mol graph model doi: . /j.jmgm. . sha: doc_id: cord_uid: l b mw d the target spike protein docking with antimalarial, antimicrobial, anti-inflammatory and hiv-protease inhibitors. the docking processed using autodock vina and the binding affinity score is noted based on kcal/mol and estimated inhibitory constant (ki). [figure: see text] by coronavirus (cov) it belongs to the family of coronaviridae [ , ] . initially most of the infected people reported in china, wuhan city in with a large extent of seafood and animal meat market [ , ] . many researchers have reported that the disease is distributed among humans, mammals and birds with the large implications on respiratory, gastrointestinal and neurological infections [ ] . in the beginning of january , the disease is increasing in china and distributed throughout world with quantifiable speed [ ] . [ ] [ ] [ ] . in april , , the disease infected patients , , ; deaths , and recovered , cases were reported globally [ ] . the most common symptoms observed with the patients are fever, runny nose, sore throat, diarrhea, tiredness, dry cough and some patients have observed aches and pains in the body [ ] . some people become infected but have not develop any symptoms; about % of population was recovered from the disease without needing special treatment [ ] . till date, there are no approved drugs and therapeutic protocols recommended to prevent the disease. it is the greatest challenge of both pharmaceutical companies and research organizations to develop novel anticorona viral drug. understanding the molecular structure of the virus is important to researchers to develop targeted therapies to the disease. based on the taxonomy of corona virus, sars-cov is causing disease in [ ] . sars-cov belongs to the group of single stranded rna (++ssrna) virus associated with nucleoprotein within the capsid comprised of matrix protein. the virus has spherical or pleomorphic enveloped proteins surrounded by a fatty outer layer covered with a thin layer of crown like structure (spike protein) made of glycoprotein projections. it also associated with membrane glycoprotein, hemagglutinin-acetylesterase glycoprotein, and small envelope glycoprotein [ ] [ ] [ ] . the target spike glycoprotein has two importance functions ( ) receptor binding domain (rbd), ( ) cleavage site. the rbd grapping hook that grip onto host receptor such as zinc peptidase angiotensin-converting enzyme (ace ) [ ] [ ] , j o u r n a l p r e -p r o o f aminopeptidase n (apn) [ ] [ ] , and dipeptidyl peptidase (dpp ) [ ] [ ] and the cleave site that can opens host receptor that allows the virus to enter host cells. the envelop (e) is small, integral membrane structural protein involved in virus' life cycle and pathogenesis, but still the complete structural and functional information remains unknown [ ] . the membrane (m) protein is most abundant structural protein involved in viral envelop and integrate in pathogenesis. the integration of s with m proteins in necessary for viral envelope and cause pathogenesis [ ] [ ] . the nucleocapsid protein relating to viral genome involved in cov replication cycle and the host cellular response to viral infection [ ] . although, the interaction between viral and human proteins is suggested as potential targets for identification of therapeutic protocols. the solidarity trails of world health organization (who) and indian council of medical research (icmr) proposed the fda approved drugs, trails with the combination of antimalarial drugs chloroquine and hydroxychloroquine can helps to prevent the disease. chloroquine prevents the viral attachment itself to the ace receptors but it causes several side effects in this regard the current trail made with the less toxic derivative hydroxychloroquine [ ] [ ] [ ] . the effect of these two drugs is still being studied to understand the inhibition of sars-cov . another set of trails include antihiv drug combination such as lipinovir-ritonavir regulates inflammation in the body that can split hiv proteins [ ] , these combinations also recommended to inhibit sars-cov . the another trailed drug remdesivir is a nucleotide analog originally created to inhibit ebola virus, but this drug also recommended to inhibit the novel coronavirus by targeting the action of a key enzyme that facilitates its replication [ ] . some studies are looking at the investigation of viral protein structure and its behavior as a potential target for future drugs. in recent study suggested that the recommended drugs might help patients with mild cased of covid , but that study has limitations. researchers also evaluating the results of the disease in severe condition go into overdrive with inflammation that can damage the lungs and other organs, but so far there is no proof that it has that effect. based on these limitations, the current research is designed to evaluate the drugs with target proteins. the major objective is to design the target proteins of both structural and non-structural proteins. second objective is to j o u r n a l p r e -p r o o f study the modeling and evaluating the target proteins to predict active site amino acids. third objective is focused o screening of recommended drugs based on pharmacophore and pharmacokinetic analysis. fourth objective is to predict the protein-ligand interaction and virtual screening to understand how strong the drug can interact with target proteins to predict the potential effect against sars-cov . the insilico analyses were performed using hp z workstation with next-generation hp intel xeon e - v . hz processor. the antimalarial, antibiotic, anti-inflammatory and hiv-protease inhibitor drugs were retrieved from drug bank database [ ] and the conformational structures were observed in chemsketch v . [ ] . pharmacophore properties are analyzed using molinspiration [ ] . absorption, distribution, metabolism, excretion and toxicity (admet) properties of chemical structure were analyzed using admetsar tool [ ] . further, the docking studies were carried out using autodock . [ ] and virtual screening using autodock vina [ ] . the intermolecular interactions were analyzed using pymol [ ] and biovia discovery studio (ds) r [ ] . based on data mining approaches and clinical practicing antimalarial drugs such as chloroquine the experimental spike protein sequence was retrieved from genbank database translated as a large polypeptide that is subsequently cleaved to s and s domains [ ] [ ] . using c-itasser pipeline to create three dimensional protein models based on deep convolutional neural-network guide to the i-tasser (https://zhanglab.ccmb.med.umich.edu/i-tasser/) fragment assembly simulations [ ] . the d protein structure is evaluated using structure analysis and verification server (saves v . ) (https://servicesn.mbi.ucla.edu/saves/) and ramapage . saves is used to understand the complexity of protein structure based on atom-to-atom interaction of Ψ versus Φ conformational angels of d macromolecule measures the torsion angels of cα (ideal) -n-cβ (obs) and the results were represented in ramachandran plot. active site amino acids were predicted using the castp calculation server based on the delineating measures of surface regions such as surface area and surface volume of d protein structure. molecular docking studies used to find the binding affinity of the ligand molecule with target protein. the homology modeled protein structure docked with selected chemical structures using autodock . and virtual screening by autodock vina. the protein structure is selected to add gasteiger chargers and hydrogen atoms to the polar group of amino acids the macromolecule, whereas ligand structure by adding torsion counts of amide bonds rotatable and all active bonds non-rotatable and generated the pdbqt file for both protein and ligand structures. grid space was set in autogrid by selecting important residues with the grid box size x= Å, y= Å and z= Å and grid spacing of . Å that provides search space, the grid centre was selected at dimensions x=− . , y=- . , z= . used to calculate grid parameters that help to understand the grid energy with equilibrated energy distribution. autodock was used to dock protein and ligand structures by adding lamarckian genetic algorithm (lga) with default parameters. the best docking conformation of protein-ligand interactions is predicted with the energy value in kcal/mol and followed by the analysis of hydrogen bonding interaction and the hydrophobic interaction. the best docking complex of protein-ligand was screened based on clustering analysis and visualized using pymol and biovia discovery studio ( v). pharmacophore analysis is performed to understand the drug-like character of the chemicals based on lipinski and veber's rule with selected parameters such as logp, tpsa, j o u r n a l p r e -p r o o f molecular weight, hydrogen bond donor, hydrogen bond acceptor, volume, number of rotatable bonds and total number of atoms, bioactive properties such as gpcr, ion channel, kinase inhibitor, nuclear receptor, protease inhibitor and enzyme inhibitor properties are predicted using molinspiration. admet analysis is performed to the selected compounds using admetsar tool to screen the compounds based on absorption, distribution, metabolism, excretion and toxicity prediction. the most important parameters such as blood-brain barrier, acute toxicity, carcinogenicity, ld , maximum recommended daily dose and mutagenicity are predicted by lazar toxicity predictions server. prediction of protein structure is important in molecular docking, using i-tasser to build three dimensional protein structure and used for homology modeling using swisspdbviewer (spdbv) software. ramachandran plot were predicted to understand the complexity of amino acids within allowed region, energy is minimized to the protein structure with e-value=- . . using saves to predict the errat value of . % and verify d of . %. castp is used to predict ligand binding sites with fmoc-amino acids lys , arg , arg , lys , ile , asp , pro , asp , phe , tyr , leu , asn , leu , lys , pro , phe , ser , gln , tyr , gly , phe , leu amino acids ( fig. ). spike protein structure predicted using i-tasser, the red label represents ( ) spike receptor binding domain ( - ) which corresponds to immunogenic ace receptor binding domain. ( ) coronavirus s glycoprotein ( - ) is translated as a large polypeptide that is subsequently cleaved to s and s domains from molecular docking plays vital role in computer-aided drug discovery to predict best active molecules to the target protein. using autodock . and autodock vina to predict the best drug binding sites towards the affinity of active site amino acids are screened based on binding energy and number of hydrogen bonds formed to the target amino acids. the antimalarial drugs such as chloroquine, hydroxychloroquine, artemisinin, gly amino acids ( fig. ; table ). j o u r n a l p r e -p r o o f (fig. , table ). the antibiotic drugs is also docked with target receptors by forming - hydrogen bonds and the interaction energy ranges from - . to - . kcal/mol. the azithromycin is strong interaction with target receptor by forming hydrogen bonds within active site amino acids and leu amino acids ( fig. ; table ). table: ). the outbreak of research is to finding multiple treatment plans for coronavirus infection perspectives for repurposing drugs for the coronavirus disease chapter -coronaviruses, fenner and white's medical virology a novel coronavirus from patients with pneumonia in china who statement regarding cluster of pneumonia cases in wuhan first case of novel coronavirus in the united states a novel coronavirus emerging in china -key questions for impact assessment clinical features of patients infected with novel coronavirus in wuhan novel wuhan ( -ncov) coronavirus korean society of epidemiology -ncov task force team. an interim review of the epidemiological characteristics of novel coronavirus host factors in coronavirus replication incubation period of novel coronavirus ( -ncov) infections among travellers from wuhan, china report : estimating the potential total number of novel coronavirus cases in wuhan city structure, function, and evolution of coronavirus spike proteins sars-associated coronavirus understanding the coronavirus novel coronavirus disease (covid- ): the importance of recognising possible early ocular manifestation and using protective eyewear angiotensin-converting enzyme is a functional receptor for the sars coronavirus human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry aminopeptidase-n is a major receptor for the enteropathogenic coronavirus tgev further characterization of aminopeptidase-n as a receptor for coronaviruses dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc receptor usage and cell entry of bat coronavirus hku provide insight into bat-to-human transmission of mers coronavirus coronavirus envelope protein: current knowledge coronavirus envelope (e) protein remains at the site of assembly a structural analysis of m protein in coronavirus assembly and morphology assembly of severe acute respiratory syndrome coronavirus rna packaging signal into virus-like particles is nucleocapsid dependent chloroquine and hydroxychloroquine in the treatment of covid- with or without diabetes: a systematic search and a narrative review with a special reference to india and other developing countries chloroquine and hydroxychloroquine as available weapons to fight covid- breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies a trial of lopinavir-ritonavir in adults hospitalized with severe covid- remdesivir is a direct-acting antiviral that inhibits rna-dependent rna polymerase from severe acute respiratory syndrome coronavirus with high potency drugbank: a comprehensive resource for in silico drug discovery and exploration acd/chemsketch . (freeware) acd/chemsketch . and its tautomers, dictionary, and d plug-ins application of pharmaceutical profiling assays for optimization of drug-like properties admet in silico modelling: towards prediction paradise? autodock and autodocktools : automated docking with selective receptor flexiblity autodock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading the pymol-molecular graphics system discovery studio modeling environment the structure of a rigorously conserved rna element within the sars virus genome cloning and sequencing of the gene encoding the spike protein of the coronavirus ibv protein structure and sequence re-analysis of -ncov genome refutes snakes as its intermediate host and the unique similarity between its spike protein insertions and hiv- • corona virus infection is a pandemic disease caused from coronaviridae. • the spike protein is the major target to attached to the host-receptor ace • computational approaches to build the d structure of protein • drug selection for preclinical trials to study the efficacy and disease treatment • molecular docking approaches to screen the compounds based on binding energy we thank dr.c.n.prashantha, assistant professor, department of biotechnology, school of applied sciences, reva university for providing overall guidance towards the docking studies. the authors declare no conflict of interest. the authors declare no conflict of interest. key: cord- - nwaxy authors: sato, kunihiko; inaba, yuji; miura, yasuo; tokuhisa, shuichi; akashi, hiroomi; shinozaki, tatsuhiko; matumoto, minoru title: neutralizing antibody to calf diarrhea coronavirus in various animal species in japan date: - - journal: microbiol immunol doi: . /j. - . .tb .x sha: doc_id: cord_uid: nwaxy nan coronavirus infections associated with respiratory, intestinal or other diseases have been reported in a number of animal species, including man, cattle, pig, dog, cat, mouse, rat, turkey, and chicken ( ) ( ) ( ) , , , , , ) . recently coronaviruses have been divided by immunofluorescence into two distinct groups on the basis of antigenic cross-reactivity ( ) , although coronaviruses, as a group, display complex serologic variability ( ) . in this paper we report on the presence of neutralizing antibodies against calf diarrhea coronavirus ( , ) in serum specimens from various animal species. calf diarrhea coronavirus passaged in bovine embryonic kidney cells ( ) was kindly supplied by dr. c.a. mebus, university of nebraska, u.s.a. in our laboratory the virus was shown to replicate readily and induce a cytopathic effect in cultures of a continuous cell line, bek-l, derived from bovine embryonic kidney ( ) . in the present study the virus was used at the th passage level in bek-l cells. the neutralization test was carried out by the serum dilution method in ii x -mm tube cultures of bek-l cells. the growth medium was eagle's minimum essential medium (mem) containing % tryptose phosphate broth (tpb) and % inactivated calf serum, and the maintenance medium was mem containing % tpb, . % yeast extract, . % sodium glutamate and . % glucose. serial fourfold dilutions of the serum inactivated at c for min were made in maintenance medium and mixed with equal volumes of maintenance medium containing tcid so of virus per . ml. the serum-virus mixtures were incubated at c for hr before inoculation ofo.l-ml volumes into two tube cultures per serum dilution. the tests were read after incubation in a roller drum at c for days. the antibody titer was expressed as the reciprocal of the highest serum dilution which showed complete neutralization in at least one of the two tubes. titers of or higher were taken as positive. a total of serum samples were collected from animal species in various parts of japan during the period from to (table ) . these samples were stored at - c and inactivated at c for min before being tested. the results of neutralization tests on these serum samples are summarized table i . neutralizing antibody to calf diarrhea coronavirus was detected in serum samples from all species except goat, hamster, and chicken. the incidence of antibody in titers of or higher ranged from to %, and high incidences, exceeding %, were obtained in cattle, horses, sheep, pigs, rats, and human beings. high titers were detected especially in cattle, pigs, and rats, some animals having titers of even , or higher. similar high incidences of neutralizing and hemagglutination-inhibiting antibodies to calf diarrhea coronavirus have been reported in normal adult cattle and pigs (ii) . these serological results suggest that calf diarrhea coronavirus or antigenically related virus(es) occur commonly in these animal species in japan. the present observation that swine and rat sera, like bovine sera, showed not only high antibody incidence but also frequent high antibody titers for calf diarrhea coronavirus may suggest close antigenic relationships between calf diarrhea coronavirus and coronaviruses occurring in pigs and rats. however, our recent study (ii) showed that there is a marked antigenic difference between calf diarrhea coronavirus and hemagglutinating encephalomyelitis virus of swine ( ), although there is some cross reaction. there is an urgent need to conduct a systematic comparative study on the antigenic composition of coronaviruses. these results seem to provide serological evidence for the occurrence of coronavirus infection in horses, sheep, rabbits, and guinea pigs, in which no report on the occurrence of coronavirus is available. coronavirus and gastroenteritis in foals recovery and characterization of a coronavirus from military dogs with diarrhea feline infectious peritonitis virus replication of bovine coronavirus in cell line bek-i culture coronaviruses: a comparative review neonatal calf diarrhea: propagation, attenuation and characteristics of a coronavirus-like agent characteristics of a coronavirus (strain n) of pigs morphologic and physical characteristics of feline infectious peritonitis virus and its growth in autochthonous peritoneal cell cultures antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species electron microscopy of coronavirus-like particles characteristic of turkey bluecomb disease serological relation between calf diarrhea coronavirus and hemagglutinating encephalomyelitis virus characterization of a calf diarrheal coronavirus key: cord- -da ypiy authors: mônica vitalino de almeida, sinara; cleberson santos soares, josé; lima dos santos, keriolaine; emanuel ferreira alves, josival; galdino ribeiro, amélia; trindade tenório jacob, Íris; juliane da silva ferreira, cindy; celerino dos santos, jéssica; ferreira de oliveira, jamerson; bezerra de carvalho junior, luiz; do carmo alves de lima, maria title: covid- therapy: what weapons do we bring into battle? date: - - journal: bioorg med chem doi: . /j.bmc. . sha: doc_id: cord_uid: da ypiy urgent treatments, in any modality, to fight sars-cov- infections are desired by society in general, by health professionals, by estate-leaders and, mainly, by the scientific community, because one thing is certain amidst the numerous uncertainties regarding covid- : knowledge is the means to discover or to produce an effective treatment against this global disease. scientists from several areas in the world are still committed to this mission, as shown by the accelerated scientific production in the first half of with over , published articles related to the new coronavirus. three great lines of publications related to covid- were identified for building this article: the first refers to knowledge production concerning the virus and pathophysiology of covid- ; the second regards efforts to produce vaccines against sars-cov- at a speed without precedent in the history of science; the third comprehends the attempts to find a marketed drug that can be used to treat covid- by drug repurposing. in this review, the drugs that have been repurposed so far are grouped according to their chemical class. their structures will be presented to provide better understanding of their structural similarities and possible correlations with mechanisms of actions. this can help identifying anti-sars-cov- promising therapeutic agents. the world is facing a huge challenge in the coronavirus disease (covid- ) pandemic: how to fight an enemy without weapons in terms of therapy? unfortunately, even before the severe acute respiratory syndrome coronavirus (sars-cov- ) worldwide spread, there were no clinical treatments nor prevention strategies available for any human coronavirus. it is understandable that both society and researchers urge the discovery of new compounds or even of a drug that is commercially available that can be employed by physicians mainly for patients with the extreme presentation of covid- . there is also urgency in the discovery of medicine with prophylactic action to prevent the entry of the virus in host cells after exposure. vaccine research experts already indicate that rescue from sars-cov- will come from a long but effective journey to produce a vaccine. while this is not a reality, the scientific community, including medicinal chemists and doctors who accompany patients, are trying to identify therapeutic alternatives. this is a meritorious attitude: the commitment with the protection of humanity. nevertheless, the rigorous feature of science in the discovery of a new drug cannot be disregarded, even during a pandemic and in the face of the urgent demand for a treatment, to avoid eventual mistakes and spurious hope. the increase in studies related to sars-cov- during the first semester in has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. it is noteworthy the increase in outbreaks of sars-cov ( ) and mers-cov ( ), with accelerated production of knowledge on these hcovs, which has been very useful for ongoing investigations on sars-cov- . one example is the availability of technological devices that allowed the fast sequencing of sars-cov- genome and the elucidation of a promising antigen target, the s glycoprotein. nonetheless, the development of a human vaccine can take years, especially because employing emergent technologies requires extensive safety tests and expansion to large scale production in order to assist the world population, as demanded in the case of the covid- pandemic. the development of new medicine also demands many years of research that involve stages of reasonable planning, synthesis, structural characterization, formulation of prototypes, preclinical and clinical trials. therefore, the literature highlights, as alternative treatments for covid- , the repurposing of drugs, which is fast and useful in emergencies such as the one experienced today. the repurposing of drugs means the use of broad-spectrum medicine for a new disease, once its metabolic characteristics, doses, potential efficacy and adverse effects are pre-established due to drug studies extracellular liquid volume and arterial pressure of the human body. it is largely expressed in fifteen human tissues, including ciliated bronchial epithelial cells and type ii pneumocytes form pulmonary alveoli, the main location of lesions caused by sars-cov- . , after ace receptor-binding, a conformational alteration occurs in protein s allowing the fusion between the viral envelope and the host cell membrane via endosomal. then, sars-cov- releases the rna into the cytoplasm to be translated into viral replicase polyproteins pp a and pp ab, which are processed by cl pro and pl pro proteases, respectively. the cleavage products are nsps that form the transcription and replication complex. next, the positive rna strand is translated into a template of negative strand that allows the synthesis of new genomics and sub genomics mrnas. these mrnas are translated and transcribed producing structural and accessory proteins. viral proteins and rna genomic are put together in virions at endoplasmic reticulum and golgi complex, finally transported through vesicles and released from the cell host for infecting new cells. , the covid- symptomatology starts after the virus is installed in host cells. in general, the symptoms include lasting and high fever, dry cough, shortness of breath, muscles aches or tiredness, sputum production, headaches, and a small percentage of individuals presented gastrointestinal symptoms such as diarrhoea and vomit. the incubation period of sars-cov- , from exposure to first symptoms, lasts to days. the pre-symptomatic stage lasts from - days (possibly more) before the beginning of symptoms. the post-symptomatic stage lasts at least days after the beginning of symptoms and days after lowering of fever and improvement of respiratory symptoms. there are many unanswered questions such as the duration of potential immunity of both symptomatic and asymptomatic individuals when infected with sars-cov- . it is noteworthy that efficient strategies to fight the disease should not depend on the symptoms of patients, once asymptomatic or pre-symptomatic subjects can play an important role in the direct and indirect transmission to others, as demonstrated by arons et al. this investigation reports that half the residents in a nursing facility, who tested positive, were asymptomatic when tested and probably contributed to the transmission to other residents. thus, control strategies focused on symptomatic residents were not sufficient to prevent transmission once sars-cov- had been introduced in the facility. laboratory exams of infected patients showed alterations in haematology and biochemistry. it was verified the increase of leukocytes and the reduction of lymphocytes; increased d-dimer and erythrocyte sedimentation rate (esr), prolongation in prothrombin times (pt), followed by increase in bilirubin levels, aspartate transaminase (ast), alanine transaminase (alt), creatinine, lactate dehydrogenase (ldh), protein c reactive (pcr), hypoalbuminemia (low albumin), microcytosis and thrombocytopenia. in addition, inflammatory factors that indicate the immune condition of patients, such as interleukins (il) il- , il- , il- , and il- and the tumoral necrosis factor-α (tnf-α) become elevated. plasma levels of granulocyte-colony stimulating factor (gcsf), protein induced by interferon gamma, monocyte chemoattractant protein- (mcp- ), macrophages inflammatory protein α and tnf-α also display significant increase. potential risk factors or comorbidities that can lead to complications of covid- include elderly individuals (specially above years of age), cardiovascular issues, cerebrovascular, chronic pulmonary diseases, immunocompromising, renal problems, hepatic disease, hypertension, diabetes and obesity. [ ] [ ] [ ] [ ] [ ] [ ] there is a notorious concern regard the medicine administered to fight these comorbidities because some of them can lead to greater expression of ace , such as treatments for diabetes or hypertension. this may favour or even aggravate covid- infection. these facts justify the urgency of research that contemplate alternative therapeutic targets such as calcium channels blockers for hypertensive individuals as suggested by fang et al. however, there is little clinical evidence on the risk of treating covid- patients with therapies that induce greater expression of ace . further investigation is necessary to explore whether these medicines inhibit or trigger the viral entry into the cells of an infected host. a frequent report in epidemiological data regarding the mortality of covid- concerns the sex of individuals, as men are the predominant fatal victims of the disease. therefore, being of the male sex is considered a bad prognostic factor for infection. , a possible explanation lies in the relation between gonadal hormones and the expression of ace enzymes or even an alleged vitamin d deficiency, according to vignera et al. the latter suggest monitoring of serum levels of testosterone and vitamin d in infected patients for a better understanding of the different fatality rates between sexes, including the hypothesis that women's hygiene justify a lesser rate of infection. understanding the pathogenic effects of sars-cov- for the different organs affected by the disease has also been object of investigation, such as gut-lung crosstalk. data from research conducted thus far indicate that the infection caused by sars-cov- is not only capable of causing pneumonia, but it can also damage other organs such as the heart, the liver, the kidneys and organic systems such as the blood and the immune system. , , patients with the extreme form of the disease frequently manifest lymphopenia, , hepatic insufficiency and viral sepsis diagnostic, whose complications can be related to the severity of the cases and the mortality of patients. , there are reports that the eventual death of such patients is due to multiple organ insufficiency, acute respiratory distress syndrome (ards), cardiac insufficiency, arrhythmia and renal insufficiency. , therefore, great attention is necessary to the disease's potential damage to multiple organs and to therapeutic alternatives to fight covid- , given that some of these alternatives can have side effects on organs initially unrelated to the respiratory system, but that may be susceptible to a systemic compromise prompted by the virus once the treatment has begun. hence, it is possible to observe the existence of different forms of aggravating the disease. in this regard, wang et al. recommend the creation of a system to categorize patients with the severe form of covid- . several investigations report that all hcovs, sars-cov, mers-cov and sars-cov- induce exaggerated immune responses in the host, which are associated to the severity of pulmonary pathology and might lead to the development of acute respiratory distress syndrome (ards) or death. the incidence of the extreme form of the infection is associated with cytokine storm syndrome, characterized by high plasma concentration of several interleukin, inflammatory cytokine, inflammatory chemokines, among other factors that cause infiltrated inflammatory in the organs. , , survivors of this excessive response by the immune system can develop long-term fibrosis and pulmonary damages that might culminate in functional injuries to these organs, thus reducing the patient's quality of life. during the development of drugs to fight microorganisms, the adoption of strategies that allow the design of molecules to act against specific biological targets of bacteria, parasites or viruses is preferred. therapies for covs can be divided into several categories, based on specific paths: ( ) covs proteins or functional enzymes that are essential for viral replication; ( ) structural proteins of the virus that prevent its binding to the respective receptors in human cells or its assembly process; ( ) some viral factor that restores the host's inherent immunity and; ( ) host-specific enzymes or receptors, that prevent the entry of the virus in the host cells. , so far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-covs therapies (fig. ) . investigations by wu et al. through bioinformatics, analysed possible sars-cov- therapeutic targets. the proteins coded by this virus were verified and compared to proteins coded by other covs. the results enabled the detection of structural similarities to sars-cov, from which it was possible to conduct homology modelling to build proteins for sars-cov- . among the targets were spike (s) glycoprotein, nsp (rna-dependent rna polymerase -rdrp), enzyme helicase ( cl pro and pl pro ), tmprss, orf a factor and ace presents in the host cells. these targets have pivotal roles in the development of the virus and have great influence on its pathogenicity, hence, some details are provided next. molecular modelling showed that spike (s) glycoprotein is a transmembrane protein of approximately to kda type i whose n-terminal turns to the exterior of the virus and its cterminal segment turns to the interior of the virus. the typical structure of covs is given by the assemble of a bulbous projection of a corolla as trimers of protein s and it is cleaved into two important subunits from the pathogenic perspective: s and s . sars-cov and sars-cov- (s) glycoprotein share about % of amino acid identity and enable the entry of the virus in the host cells. therefore, s glycoprotein present in covs has been considered a promising biological target for antiviral mechanisms. , the moment when the virus approximates the target cell prompts the recognition by the receptor-binding domain (rbd) in the s glycoprotein of its receptor, which leads to the binding to subunit s . next, the subunit s allows fusion of viral and cellular membranes, which enables entry in the cell and the release of viral rna genome. , , some investigations suggest that the strong binding affinity between s protein and ace is essential for viral entry, hence, ace is also relevant for the development of drugs. , molecules that bind to the surface of the virus can destabilize the formation of s glycoproteins and interfere both with the trimerization of the protein and with the continuity of the life cycle of covs. several studies have been conducted on s protein to clarify its sars-cov- structure and its binding process as well as to evaluate its relevance as target for in-silico and in-vitro assays on molecules for anti-sars-cov- therapies. one study conducted by hoffman et al. investigated how the sars-cov- s protein facilitates viral entry in the target cells and how this process could be blocked. results showed that ace is used as receptor for the entry of sars-cov- in host cells and that the spread of this cov in the infected host depends on the activity of tmprss (a cellular serine protease responsible for initiating the binding process between s protein and ace ). this process can be blocked with clinically approved tmprss inhibitor. prior to this, the relevance of tmprss was highlighted in the dissemination of several types of viruses such as influenza a and other covs, which also makes it a relevant target for covid- therapeutic intervention. [ ] [ ] [ ] [ ] [ ] [ ] [ ] binding between s proteins and ace receptors was corroborated through x-ray crystallography conducted by lan et al. to elucidate the interaction between the sars-cov- rbd and ace at a higher resolution. in spite of different interactions with ace , the sars-cov- rbd /ace and sars-cov rbd /ace interfaces share a substantial similarity regarding the surface area, the number of interacting residues and the networks of hydrophilic interactions. such similarity strongly points to a convergent evolution of both sars-cov- and sars-cov rbd structure which improves the binding affinity for the same receptor, the ace . the non-conserved rbd regions in s protein, such as subunit s , could be potential targets for cross-reactive antibodies. considering rbd as a critical region for receptor binding, antibodies that target the conserved epitopes in the rbd are also good candidates for the development of highly potent cross-reactive therapeutic agents against several species of covs, including sars-cov- . investigations on ligands obtained from drugbank . used molecular docking to identify target regions in the pockets of the quaternary structure of sars-cov- s glycoprotein (from protein data bank-pdb). six pockets present in s glycoprotein deserve further investigation in medicinal chemistry due to suitable features for small molecule binding. among the six pockets, the eight best ligand candidates from drugbank were all binding pocket # , which contained residues of amino acids proline, leucine, lysine, asparagine, phenylalanine, glycine, threonine, glutamine, alanine, methionine and tyrosine. one of the best ligands was the drug saquinavir, an antiviral from the class of protease inhibitors, used in anti-hiv therapy. nsps are involved in the rna transcription, translation, protein synthesis, processing and modification, viral replication and infection of the host. significant functional proteins, cl pro , pl pro , helicases and rdrp are important targets for the development of small-molecule inhibitors, due to their biological function and vital enzyme active site. factors nsp , nsp c and orf a are related to assistance to the immune evasion of sars-cov- . interaction between nsp and the host ribosomal subunit induce the degradation of mrna, allowing the virus to develop resistance to the host innate immunity. binding between orf a and bone marrow matrix antigen (bst- ) inhibits activity and blocks bst- glycosylation. these results suggest that all three structures are potential targets for antiviral medicine. proteases pl pro and cl pro mediate the proteolytic cleavage of polypeptides produced by βcoronavirus sars after genome transcription, thus generating other proteins. the cl pro , known as nsp , cleavages several non-structural proteins of importance for viral replication and the maturation of nsps, which is essential in the life cycle of the virus. therefore, it is an attractive biological target for that has been inhibited in-silico by several antiviral, anti-inflammatory and anti-hypertensive drugs from the database zinc (fda). in addition, docking and molecular dynamic studies conducted by qamar et al. showed that non-toxic natural products formed strong bonds with sars-cov- catalytic dyad cis -his of cl pro . moreover, the proteinase pl pro is responsible for cleavages of n-terminus in the replicase polyprotein to release nsp , nsp and nsp , which are essential for correcting virus replication significant to antagonize the host's innate immunity. analysis of the docking model showed that ribavirin formed hydrogen bonds with residues gly , gln , tyr , asp as well as hydrophobic interactions between tyr and the pl pro residue. these results indicate ribavirin as a powerful pl pro enzyme inhibitor, which means it has promising features for anti-covid- therapy given the inhibition of a likely pl pro therapeutic target. helicase (nsp ) has been identified as a promising target for antiviral drug discovery, particularly against sars-cov- . it is a multifunctional protein necessary for a wide range of biological processes, such as genome replication, recombination and dislocation of proteins related to chromatin and nucleic acid remodelling. for covs, helicase is indispensable for viral replication. in studies on molecular modelling, several antibacterial, antifungal and antiviral drugs were analysed and presented elevated affinity to helicase, suggesting it as a good target for sars-cov- therapy. rna-dependent rna polymerase (rdrp -also nominated nsp ) catalyses the viral rna, which performs a key role in the replication/transcription complex of sars-cov- , possibly aided by nsp and nsp complex as cofactor. , nsp has been studied as potential target for several sars-cov and mers-cov inhibitors, due to its importance for viral control. satisfactory results of rdrp inhibition by several ligands were presented in the modelling studies by gao et al. yin et al. those ligands included antiviral analogous to nucleotides, such as remdesivir, which already shows great potential in the treatment of covid- infections. in addition, some nonstructural proteins, including nsp b, nsp e, nsp , nsp , nsp , nsp , nsp , nsp and nsp , also stood out as useful targets due to their significant role in the synthesis and replication of viral rna. cl pro is key enzyme for covs, also called main protease (m pro ), that plays a pivotal role in mediating viral replication and transcription, making it an attractive target for anti-sars-cov- drugs. such claim is reinforced by studies by jin et al. after the virtual screening of n inhibitor. results show that n ( ) is a time-dependent irreversible inhibitor of this enzyme and that a stable covalent bond is formed between n and cl pro . high-throughput screening (hts) was applied to , drugs and drug candidates, demonstrating that ebselen ( ), px- ( ) and carmofur ( ) are all able to covalently bind to cl pro do sars-cov- , with ic that varied from . to . µm (fig. ) . it is likely that a part of the hits identified by hts are bonded to the catalytic cysteine of cl pro through their sulfhydryl groups. in-vitro studies on antiviral activity were performed to corroborate the results. real time quantitative pcr (qrt-pcr) demonstrated that ebselen and n had the strongest antiviral effects at a concentration of μm treatment in sars-cov- infected vero cells. after plaque-reduction assay, the dose-response curves suggested that both could penetrate cellular membrane to access their targets. this result strongly supports the hypothesis that developing a single antiviral agent targeting cl pro or in combination with other therapies could provide an effective first line of defence against all covs related diseases. in relation to sars-cov- therapy, some of the aforementioned targets have been explored for both new drug proposition as well as for sars-cov- drug repurposing. our focus is on this last type, and for each medicine, the putative mechanism of action and viral target will be described trying to find an understandable rational therapy even for an immediate illness situation like covid- pandemic. carmofur ( ). as previously mentioned, sars-cov- is an enveloped virus, whose nucleocapsid consists of a positive rna genome surrounded by multiple copies of nucleocapsid protein. this virus, after entry in the host cell, replicates fast the viral genome with new virion production. the rna replication into the cell host depends on enzymes and substrates for rna synthesis, such as ribonucleotides (adenine, guanine, cytosine or uracil) that have nitrogenous bases in the purine or pyrimidine classes. compounds can mimic these chemical structures and interfere with the formation or use of one of these essential normal organism metabolites. the interference is generally prompted by enzyme inhibition in the biosynthetic pathway of the metabolite or by incorporation, as a false building block, into vital macromolecules such as proteins and polynucleotides. so, this class of therapeutic agents is called antimetabolites. , diverse antimetabolites have been indicated as promising anti-sars-cov- . they are described next. pyrimidine derivatives are aromatic organic compounds necessary for all life forms. examples of pyrimidine derivatives are nitrogenous bases cytosine ( ), uracil ( ) and thymine ( ) (fig. ) . they are found in dna and rna and participate in the metabolic process that involves carbohydrate and lipids. , these heterocyclic rings share two nitrogen atoms at and positions, but display variations between themselves, such as an amine group at -position in the cytosine and a methyl at -position in the thymine. from the pharmacologic perspective, nitrogenous bases are investigated as pharmacophores and are found in the structure of many drugs and experimental substances with various activities, such as antitumoral, antibacterial, antiparasitic, and antiviral. , regarding antiviral activity, there are several approved drugs that are classified as pyrimidine nucleotide biosynthesis inhibitors (pnbi) because, after phosphorylation, they are incorporated either into the dna or into the rna and inhibit hosts or pathogenic enzymes, such as polymerases. therefore, the likely mechanism of action of some pyrimidine derivative drugs has been considered for repurposing. some pyrimidine derivatives with antiviral activity are often formulated as prodrugs. this format solves issues of high polarity in its final structure prompted by the phosphonic acid, which interferes with pharmacological properties and causes low cellular permeability and low oral bioavailability. one compound appointed as potential anti-sars-cov- is the -fluorouracil ( ) ( -fu) (fig. ) , a heterocyclic aromatic amine similar to uracil (u) that presents a fluorine-carbon bond at -position. this compound is used in the treatment of oesophageal cancer, stomach cancer, breast and colon cancer. the similarity between -fu and uracil allows the direct action on nuclei acid as it is incorporated into the genetic material and inhibits replication. tests with -fu as monotherapy confirmed its failure against any coronaviruses. the reason proposed to such failure relied on the fact that coronaviruses rna proofreading activities involve a ' → ' exoribonuclease in the nsp , which removes -fu during replication and metabolism. hence, the combination between -fu and deoxyribonucleoside and deoxyribose was suggested so that, after its insertion in the rna, it escapes rna proofreading and prompt lethality and/or lethal mutagenesis in the virus. despite the proposition of using a widely marketed drug to treat several types of cancer, which means it has well-established efficiency and safety, no other type of test has been made to confirm its efficacy against sars-cov- . therefore, further experiments are necessary to explore -fu potentialities. another antitumoral drug considered for its anti-sars-cov- potential is gemcitabine (gct) ( ) (fig. ) , an analogue of deoxycytidine whose pharmacological action is triggered after the intracellular transformation into triphosphate gemcitabine. the latter competes with endogenous nucleoside triphosphates by incorporation into the genetic material, thus inhibiting dna synthesis. initially, gct was developed for antiviral activity, however, initial results caused it to be redirected for anticancer therapy. it became, then, widely used against non-small cell lung cancer, pancreas, bladder and breast cancers as well. [ ] [ ] [ ] in-vitro analyses of gemcitabine hydrochloride inhibited mers-cov and sars-cov, with a ce of . μm and . μm, respectively, in addition to low cell toxicity for vero e cells. , these data are indicative of a possible activity against sars-cov- , but complementary preclinical investigations are necessary before clinical trials. albeit considered a safe drug under predetermined doses, gct adverse effects are noteworthy and include myelosuppression and disruption of liver functions. in february , the european union (eu) approved baricitinib ( ) as second-line oral treatment for mild to severe active rheumatoid arthritis in adults. a differential feature of baricitinib structure is the azetidine ring bearing an ethylsulfonyl, beyond an acetonitrile group at -position. the same ring binds to the n atom at -position in the pyrazole, which, in its turn, binds to the pyrimidine conjugated to a pyrrole ring. this medicine can modulate human innate and adaptive immune system. based on this property, presumably, one of the important mechanisms of action of baricitinib in the treatment of rheumatoid arthritis is the inhibition of the il- / jak / jak pathway. the promising nature of baricitinib and other small molecule inhibitors against sars-cov- was pointed by richardson et al. through in-silico tests using benevolent ai. the authors evaluated compounds to show that sunitinib ( ) and erlotinib ( ) inhibit ap -associated protein kinase (aak ) interrupting the virus entry to the cells and the intracellular assembly of new viral particles (fig. ) . regarding these two antitumor drugs, it is known that sunitinib is an oral oxindole multitargeted kinase inhibitor that inhibits certain tyrosine kinases including vascular endothelial growth factor receptors (vegfr types and ), platelet-derived growth factor receptors (pdgfr-α and pdgfr-β), stem cell factor receptor (kit), fms-like tyrosine kinase- (flt ), glial cell-line derived neurotrophic factor receptor (ret) and the receptor of macrophage-colony stimulating factor (csf r). concerning erlotinib, it was developed as reversible and highly specific small-molecule tyrosine kinase inhibitor that competitively blocks the binding of adenosine triphosphate to its binding site in the tyrosine kinase domain of epidermal growth factor receptor (egfr), thereby inhibiting autophosphorylation and blocking downstream signalling. however, these oncological drugs have serious adverse effects such as diarrhoea, loss of appetite and skin rashes. in addition, high doses of these medications can aggravate those effects. in relation to baricitinib, its anti-sars-cov- potential was explained in three ways: aak inhibition like sunitinib and erlotinib; the kinase associated to cyclin g, which is another endocytosis regulator; and the janus kinase, that inhibits the action of cytosines that triggers the inflammatory process. because baricitinib can inhibit aak at the therapeutic dose ( or mg/day), the drug is indicated for clinical trials. it is highlighted that baricitinib is not indicated for patients with neutropenia or lymphopenia, once it lowers rates of neutrocytes and lymphocytes, which can lead the disease to progress and increase anaemia. furthermore, treatment with baricitinib can reactivate varicella-zoster, herpes simplex and epstein-barr viruses. this implicates in a conflict between the potential effect and the adverse effects of baricitinib against covid- to prevent aggravating the disease and the mortality of patients. an analogue of adenosine, galidesivir (gsv) ( ) is a broad-spectrum antiviral drug that blocks viral rna polymerase by replacing a natural nucleotide with galidesivir triphosphate. this alteration prompts changes in electrostatic interactions and prevents the formation of the rna elongated strand. , adenosine and gsv differ in that galidesivir has one carbon at -position in the pyrimidine ring and nitrogen in the ribose ring, whereas adenosine has one nitrogen in the former and oxygen in the latter (fig. ) . it is noteworthy that gsv has not been approved for clinical trial and is an experimental drug in advanced stages of development. gsv was first developed against hepatitis c (hcv) but first clinical trials were conducted to ensure its safety (in healthy individuals) and efficacy against yellow fever. furthermore, gsv displayed in-vitro and in-vivo antiviral activity against filoviridae, alphavirus, bunyavirus, arenavirus, paramyxovirus, flavivirus, orthomyxovirus, picornavirus and sars and mers coronaviruses. , , recent in-silico studies have shown the existence of a strong bond between gsv and sars-cov-rdrp to demonstrate the capacity of alterations in rna polymerase, which can eradicate the virus. although, preclinical and clinical trials are necessary to either confirm or deny this hypothesis. it is noteworthy that investigations have pointed the inactivity of gsv against sars-cov- at concentrations lower than mΜ. the existence of antiviral activity against other coronaviruses indicates that more investigations on gsv against sars-cov- are required to elucidate its potential activity in advanced testing. next, sofosbuvir (sbv) ( ) is an example of successful nucleotide prodrug, approved by the food drug administration (fda) since , against chronic hepatitis c infections. sbv is also combined with other antiviral drugs, such as ledipasvir, velpatasvir and voxilaprevir. , the structural similarity between sbv (fig. ) and uridine allows that drug to act on hcv rdrp, incorporate itself into the viral rna and terminate the synthesis of the nucleotide sequence. structural analysis of sbv revealed that its elevated potential is partly due to the presence of the 'phosphate, which terminates the primary enzyme transformation monophosphate inhibitor. the antiviral activity has been explored against other viruses through in-vitro and in-silico studies and shown potential for inhibiting the dengue virus, yellow fever, telbivudine (tbv) ( ) (fig. ) is a thymidine nucleoside analogue used with specific activity against the hepatitis b virus (hbv). it starts acting after phosphorylation by cellular kinases, which results in the active metabolite, telbivudine '-triphosphate, enabling dna polymerase and inhibiting viral replication. the hydroxyl at -position in the sugar β-l- '-desoxirribose provides specificity to hbv polymerase. suggesting repurposing tbv to fight covid- was prompted by virtual screening to find drugs that act on viral m pro . among other results were ribavirin, tbv and two vitamins, cyanocobalamin (b ) and nicotinamide (b ). researchers suggest that these four drugs can be combined and used against covid- , once they are safe, marketed and approved by the authorities. notwithstanding, the suggestion of repurposing these drugs requires more information, including on drug interaction parameters. in spite of well-tolerated and safe for monotherapy, associating tbv and ribavirin, another antiviral drug, can increase hepatotoxic activities of tbv. , it is also important to consider the elevated risk of resistance to tbv, which and pyrimidine derivatives drugs: -fluorouracil ( ); gemcitabine ( ); baricitinib ( ); sunitinib ( ); erlotinib ( ); galidesivir ( ); sofosbuvir ( ) ; telbivudine ( ). purine is a and -membered bicyclic ring. similar to pyrimidines, purine derivatives are essential to life. they are basic constituents of nitrogenous bases adenine (a) ( ) and guanine (g) ( ) (fig. ) . the safety of rdv for humans infected with ebov was evaluated in the democratic republic of congo. results confirmed its safety but did not point rdv as the best therapeutic option, once its mortality rate reached % of treated group. it has been proved that gs- inhibits epidemic and zoonotic hcov. of viral loads and weight loss in murine. therefore, rdv is a potential drug to treat mers-cov infections. regarding covid- , rdv was used to treat the first us case. the patient was years old, had slight cough, low fever and no evidence of pneumonia at day of the disease. when the clinical symptoms became worse, the patient was given vancomycin and cefepime. as the symptoms worsened, intravenous treatment with rdv was administered at day , and vancomycin and cefepime were no longer administered. at day , the patient displayed clinical improvement, unfortunately details on the doses and duration of treatment were not provided. after this first case, a clinical trial with a larger number of covid- patients was conducted. this study of efficacy involved patients infected with sars-cov- who displayed saturation equal or inferior to % while they were breathing ambient air or receiving oxygen support. the treatment lasted days, patients were given mg intravenously on day , followed by mg daily for the remaining days of treatment. follow up of patients treated for days indicated that, after the first dose of rdv, % improved oxygen support whereas % of patients got sicker, % were discharged and mortality rate was %. the most common adverse events ( % of patients) were increased hepatic enzymes, diarrhoea, rash, renal impairment, and hypotension. some limitations were noted in the study, such as the small size of the cohort, the short duration of follow-up and the lack of information on the patients. hence, the efficacy of rdv requires validation by the ongoing randomized, placebo-controlled trials. one advantage of repurposing rdv is the availability of data on safety and pharmacokinetics, which were obtained previously at phase clinical trial. in addition to the promising results shown by rdv, other purine analogues have been investigated for sars-cov . ganciclovir (gcv) ( ) also named, according to its chemical structure, -( , -dihydroxy- -propoxymethyl) guanine (fig. ) , is a guanine analogue, similar to acyclovir, except for the bond between the methyl group and one hydroxyl. gcv inhibits the human herpesvirus and is also indicated in the treatment of cytomegalovirus infections related to acquired immunodeficiency syndrome (aids). gcv is converted into ganciclovir triphosphate by cellular kinase, which inhibits dgtp and disrupts viral dna synthesis due to substitution of various adenosine bases in the dna chain. recently, gcv was used to treat covid- patients in china. the drug was administered with other antivirals, such as oseltamivir and kaletra. as a descriptive study, the relation between gcv as key factor in clinical outcome of the patients ( % of which were discharges) was not possible. therefore, gcv efficacy as monotherapy or part of combined therapy is yet necessary for more robust investigations. valganciclovir ( ) (fig. ) is the antiviral prodrug of gcv taken by mouth. it is indicated for the same treatments as gcv (cytomegalovirus in people who have acquired immunodeficiency syndrome, gastrointestinal disorders related to aids). the drug has great bioavailability and is converted by hydrolysis into ganciclovir. using valganciclovir in its oral form enables clinical treatment and makes patients more comfortable. [ ] [ ] [ ] the mechanism of action is the same of gcv. valganciclovir was computationally evaluated for covid- . the assay with the main proteins coded for sars-cov- allowed the determination of possible binding targets, of which were proteins and host targets. valganciclovir, one of the drugs used in the study, was presented as a possible anti-sars-cov- therapeutic drug due to its high binding affinity to two wellestablished viral targets. the first target was pl pro , indispensable enzyme in viral replication; the second, rdrp, conserved nsp in coronavirus, which is vital for its replication/transcription. therefore, valganciclovir could be a significant antiviral drug to treat sars-cov- . but there are no clinical reports on valganciclovir used to treat covid- in addition to what has been reported about gcv. hence, its efficacy is yet to be confirmed as anti-sars-cov- therapeutic. tenofovir (tfv) ( ) is another adenine analogue pointed as promising covid- therapeutic (fig. ) , it is also called tenofovir disoproxil fumarate or alafenamide tenofovir (taf). approved by the fda in , tfv is a prodrug used to treat hiv and cases of nucleoside resistance. tfv is an analogue reverse-transcriptase inhibitor (ntrti). inside cells, tfv is phosphorylated and competes with deoxyadenosine '-monophosphate (d-amp), thus preventing the formation of dna. once incorporated into a growing dna strand, it causes premature termination of dna transcription and prevents viral replication. , modelling and docking studies evaluated the antiviral effects of tfv and verified a strong bond to sars-cov-rdrp, which can disrupt this polymerase and terminate the viral infection. however, in-vitro tests showed that tfv lacks apparent antiviral effect at concentrations inferior to μm for sars-cov- . in spite of lukewarm in-vitro and in-silico outcomes, an ongoing clinical study on tfv (chictr ), expected to end in june , aims at assessing the effect of the combination tenofovir + emtricitabine (cytidine analogue) related to lpv/r in covid- patients. in addition to the efficacy of treatment, clinical trials can validate the prevalence of adverse effects related to the toxicity of tfv in patients. tfv is also a powerful nephrotoxic drug causing damage to proximal tubular cells. in spite of that, interrupting the treatment is sufficient to improve adverse effects, which makes monitoring of patients essential. heterocyclic compounds with different heteroatoms such as nitrogen, sulphur and oxygen can present different pharmacological properties. one such property is to serve as analogue of nitrogenous bases of nucleic acids, such as triazoles, which have a five-membered ring of two carbon atoms and three nitrogen atoms. this aromatic ring can assume two isometric forms, , , -triazole and , , -triazole. the former is stable under acid and basic conditions and becomes more reactive when binding to electronegative elements. , triazoles are important and stand out for their various biological activities, such as anticancer, antituberculosis, anti-inflammatory, antimicrobial, and antiviral. specifically for the latter action, triazole-based derivatives have shown promising invitro activity against coronavirus, probably by cl pro inhibition. ribavirin ( ) (fig. ) is a powerful triazole-based antiviral analogue to guanosine. it presents a wide range of pharmacological activities related to several viruses, for instance: herpes simplex virus, human immunodeficiency (hvi- ), influenza, respiratory syncytial (rsv) and hepatitis c. , the drug was initially used in to treat syncytial virus in children, generally combined with interferon (inf). however, ribavirin treatment presents undesirable adverse effects, like lowering of haemoglobin, which limit clinical use. its action mechanism relies on the inhibition of enzyme inosine monophosphate dehydrogenase, necessary in the synthesis of guanosine triphosphate, which prevents viral dna and, mainly, rna replication. the necessary concentration for in-vitro inhibition of rsv and influenza ranges from - μg/ml. site similar to other sars-pl pro inhibitors. the formation of hydrogen bonds and π-π stacking were also predicted. these findings suggest that ribavirin as a powerful pl pro inhibitor. nonetheless, investigation on triazole derivatives for anti-sars-cov- therapy are still preliminary. on the other hand, favipiravir (fpv) ( ) (fig. ) is a prodrug, approved in in japan, to treat cases of influenza a and b that displayed resistance to first line drugs. it has provided results that indicate a promising character and is currently undergoing clinical trials against covid- . its antiviral efficacy has also been investigated in different countries to fight ebola and lassa, for example. the molecular structure of the drug consists of a pyrazine heterocyclic ring with fluorine at -position, carboxamide at -position and a double bond between oxygen and carbon , which renders its analogue to guanine ( ). , the metabolization of the prodrug into its active form, favipiravir-ribofuranosyl- '-triphosphate, requires intracellular ribosylation and phosphorylation. fpv therapeutic targets are rdrp enzymes, necessary in viral transcription and replication, and its inhibition blocks synthesis of viral rna for a spectrum of viruses, including human coronavirus. a different investigation compared patients treated with fpv plus interferon inhalation to lpv/rtv. patients under fpv therapy responded better to the progression of the disease with accentuated viral depuration. also, the incidence of nausea and vomit was higher for lpv/rtv. in addition to these clinical trials, the antiviral activity of fpv against sars-cov- was also evaluated but no clear antiviral effect was noted for doses lower than μm. an in-vitro study using molecular docking focused on the binding properties of sars-cov- protein structures to antiviral agents, including oseltamivir. the study showed that molecules form bonds to sars-cov- crystal proteins. however, data did not show oseltamivir as the best structure because lopinavir, asunaprevir and remdesivir interacted with more than two protein structures in the virus. hence, they are likely more promising than oseltamivir. notwithstanding, we suggest further look into oseltamivir against other enzyme targets since different studies achieved positive results regarding its use as anti-sars-cov- . nelfinavir ( ) (fig. ) is a safe anti-retroviral drug largely used for hiv- protease inhibition with strong in-vivo activity. generally, nelfinavir is combined with other anti-retroviral medication as part of a highly active antiretroviral therapy (haart) that reduces significantly the viral load by increasing cell number to mm - cd (+) lymphocytes. the drug is prescribed for children, young individuals, adults and pregnant women. , nelfinavir and its active metabolite m strongly bind to serum proteins, displaying optimal tissue distribution. a frequent adverse effect is light to moderate diarrhoea, reported for to % of patients. the sars-cov outbreak in several countries triggered the search for antiviral drugs active against the disease. among the drugs likely to inhibit sars-cov, nelfinavir stands out in all assays. the mechanism of action suggested for nelfinavir involves preventing sars-cov replication after its entry in the host cell and disrupting virion production. based on results from previous studies as well, nelfinavir was considered a likely therapy for covid- after its indication for clinical trials as a promising anti-sars drug. recently, , drugs were evaluated for their binding affinity to sars-cov- m pro . among the compounds, drugs were selected based on the docking score and three-dimensional atazanavir ( ) (fig. ) is an antiretroviral drug protease inhibitor used to treat hiv infections with in-vitro inhibitory concentration of , - , nmol. compared to other protease inhibitors, atazanavir has the advantage of allowing a daily posology regimen with a favourable metabolic profile and low frequency of adverse effects. , several hiv- resistant to protease inhibitors are still sensitive to in-vitro atazanavir, which is considered safe and well tolerated. the atazanavir acts to inhibit hiv- protease, which is indispensable in the processing of polyproteins precursors of viral structures and prevents the formation of infectious and mature viral particles. the good activities reported for this drug as well as the search for safe and fast therapy for captopril ( ) (fig. ) is an angiotensin-converting enzyme inhibitor (acei). it is a zinc metallopeptidases inhibitor that converts angiotensin-i into angiotensin-ii, an essential function that regulates arterial pressure. it is predominantly indicated as vasodilator in patients with cardiac insufficiency. this drug was suggested as potential antibiotic capable of inhibiting zinc succinyls/dipeptidase by blocking its zinc catalytic center. , tolerance to captopril has been largely investigated; its single dose by mouth is well-established and confirms the pharmacological activity in the short term ( - minutes) at the cellular level. this capacity is related to captopril transport mainly through plasma proteins such as albumins with absorption rate between - %. reported adverse effects are neutropenia, proteinuria, dysgeusia and cough, but less frequent for low doses. , some investigations have suggested captopril as possible covid- treatment. serafin et al. indicated captopril as potential for inhibiting the bond between human sars-cov- and ace- and reduce severe pneumonia symptoms. in-silico studies using molecular docking were conducted with fda-approved drugs capable of binding to the main active site in proteinase cl pro . two drugs were identified as ligands for the enzyme active site: captopril and disulfiram. the former binds to the active site at the same position of n inhibitor (a standard inhibitor that reacts irreversibly in the same site with cl pro cys ). it is, thus, suggested that captopril binds to the same site of n , obstructing the function of cys -his catalytic dyad. captopril probably inhibits the enzyme in two stages. initially, it establishes non-covalent bonds to sites in the enzyme targets, then, a reaction takes place between the critic groups, which results in a more stable inhibitor complex. the hypothesis is that captopril can bind covalently to cl pro cys . although the potential of captopril on the enzyme has been demonstrated, therapeutic use against covid- is controversial, once the drug induces overexpression of ace- -the main receptor used by sars-cov- to entry the cells. therefore, combination with other drugs, such as angiotensin-ii receptor blockers, needs analysis to clarify the effects of captopril in covid- treatment. the cyclosporin a (csa) ( ) (fig. ) is isolated from the fungus beauveria nivea and was approved for use by the fda in . this drug has been used for decades to prevent organ rejection and to treat t cell-associated autoimmune diseases such as behcet's disease, psoriatic arthritis, lupus nephritis, rheumatoid arthritis, systemic lupus erythematosus or interstitial lung disease. such drug exerts its immunosuppressive function and anti-inflammatory effects by inhibiting the transcription of genes required for t cell proliferation, notably interleukin- . [ ] [ ] [ ] due to the severity of covid- , csa can be potential to prevent hyperinflammation-induced lung injury. in this regard, it is known sars-cov nps induces the expression of interleukin- via nuclear factor of activated t cell (nf-at) activation, which can trigger the cytokine storm seen in patients with severe covid- status. another advantage presented by csa in relation to other antiinflammatory drugs is its already known anti-cov action against all genus, including sars-cov, [ ] [ ] [ ] at low and non-cytotoxic micromolar concentrations verified in cell culture assays. this antiviral property is thought to be mediated by the inhibition of cyclophilin-a-dependent viral assembly as well as inhibition of the nf-at pathway or even by genetic or pharmacological specific inhibition of cyclophilin-d, hindering the viral replication. , as already reported, sars-cov and sars-cov- are very similar ( . % sequence identity). teicoplanin ( ) (fig. ) is an antibiotic used against gram-positive bacteria with major compounds at different side chains. it prevents polymerization of peptidoglycans and inhibits the development of the cell-wall, thus prompting cell death. it is a big molecule that has displayed antiviral activity on an early stage of the viral life cycle by inhibiting the low-ph cleavage of the viral spike protein by cathepsin l in the late endosomes thereby preventing release of viral rna and replication. this compound has already shown inhibitory activity against ebola virus, mers-cov and sars-cov. recent investigations have suggested teicoplanin as alternative treatment for covid- after an in-vitro assay achieved ic value of . µm, thus proving its efficacy against sars-cov- . these results need to be confirmed through randomized clinical trials, which are still to be conducted. , , using antibiotics to fight viruses, albeit completely ignored, can become useful to treat covid- . , some studies report the possibility of repurposing drugs like terconazole, which displayed good in-vitro results against mers-cov and sars-cov, dasabuvir ( ) (fig. ) is a drug from the naphthalene class and phenyl-naphthalene subclass due to the bond between its naphthalene ring and a phenyl group. dasabuvir is a first line drug used as combined therapy for chronic hepatitis c. dasabuvir is a non-nucleoside inhibitor that binds to nps b (non-structural protein b -rdrp) and induces conformational change that makes rdrp incapable of elongating the viral rna. repurposing of this drug can be useful as sars-cov- therapy due to its antiviral activity. dasabuvir was subjected to docking studies against sars briefly, dasabuvir forms π-cation interactions with lys a (present in the ace ), π-π interactions with phe b (s protein residue) and hydrogen bonds to ace residues glu a and asp a and gly b and ser b (s protein residue). the authors highlight the importance of repurposing drugs as new therapeutic alternatives not only for the new coronavirus but for the next viral outbreaks. darunavir ( ) (fig. ) is a benzene derivative that has been evaluated for repurposing against covid- . this drug is an antiviral used in the treatment of hiv- infections. it provides a great genetic barrier to resistance and is highly active against resistant strains of hiv- that are not susceptible to other protease inhibitors. darunavir is administered orally as pills or suspension and is often used with low doses of ritonavir as part of a combined art protocol. its mechanism of actions works by protease inhibition. darunavir establishes high affinity bonds to hiv- protease forming a stable complex, thereby selectively inhibiting polyprotein gag-pol coded by the virus. this prevents the formation of mature viral particles. fda-approved drugs against cl pro , rdrp, helicase, exonuclease ′ a ′, endornase e ′-o-ribose methyltransferase. among the best drugs in the assay, darunavir was a surprise because, despite inhibiting viral proteinase, the study showed that it binds to the replication complex components of sars-cov- with inhibitory potency kd < nm. one example is rdrp, whose kd value was . nm and exonuclease ′ to ′ with k d value of . nm. a docking study was conducted by sang et al. as in-silico evaluation of anti-hiv drugs in their interaction capacity to proteinase cl pro . results suggest that all drugs have higher binding affinity to sars-cov- cl pro than to the homolog sars-cov proteinase. among the evaluated drugs, indinavir and darunavir displayed the highest docking scores, therefore, they were subjected to molecular dynamic (md) simulations, free binding energy calculations and molecular mechanics poisson-boltzmann surface area (mm-pbsa) to detail molecular interactions between inhibitors and proteinase. the data suggest darunavir had better binding affinity to sars-cov- cl pro with binding affinity of - , kj / mol. in addition, darunavir bind to sars-cov- cl pro via contact residues and to sars-cov cl pro via residues. this difference explains the lower binding energy values between darunavir and sars-cov cl pro . it was also noted hydrogen bonds between darunavir and sars-cov- cl pro but none for indinavir and this proteinase. because hydrogen bonds are important in the stability of the inhibitor-enzyme complex, darunavir is probably more promising against covid- . finally, a different in-silico assay was conducted by pant at al. to assess a large variety of compounds ( ) from several data banks and potential compounds from fda-approved drugs. the compounds were tested against sars-cov- cl pro . darunavir was among the best fda-approved drugs, with a score of - . . all data collected from in-silico studies still require experimental studies to validate the anti-sars-cov- activity of darunavir. a research conducted by dyall et al. performed a robust in-vitro assay and showed that the drug dasatinib ( ) (fig. ) , a kinase signalling inhibitor developed to treat human cancers, inhibited mers-cov and sars-cov, exhibiting ec values . and . , respectively. this study also revealed that kinase signalling may also be important for replication of this hcovs. nevertheless, the authors reported that dasatinib may be valuable against coronaviruses infections if a dosing regimen that minimizes immunotoxicity while still blocking viral replication can be defined. results indicated this drug as a likely therapeutic alternative against sars-cov- infection. an in-silico study carried out by qiao et al. showed that dasatinib, among others, is one of the most promising drugs for the inhibition of sars-cov- cl pro . more preclinical and clinical studies are required to prove whether dasatinib is really promising for covid- patient treatment. imatinib ( ) (fig. ) is an oral anticancer agent that inhibits the activity of some tyrosine kinases, most prominently the bcr-abl fusion oncoprotein (whose overactivation can lead to chronic myeloid leukaemia, cml), c-kit (involved in gastrointestinal stromal tumours development), platelet-derived growth factor receptor (pdgfr), and the native abl kinase, which has a ubiquitous expression and plays important roles in several biological processes. in addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during cov infection), by interfering with virus-cell fusion, and other rna viruses including coxsackie virus, hepatitis c virus, ebola, among others, mainly by blocking viral entry or egress from the host cell. besides, this drug showed activity against sars-cov and mers-cov, both phylogenetically related to sars-cov- . in this regard, it is reported that imatinib has anti-cov activity in two points of the virus life cycle. in the early phases of infection, it inhibits virion fusion with the endosome and subsequent release into the cytoplasm, thus preventing viral entry and viral replication via abl-mediated cytoskeletal rearrangement. in a later phase of the infection, abl protein expression, which is inhibited by this drug, enables sars-cov and mers-cov replication, which suggests that abl is a new host cell protein required for viral growth. furthermore, evidences suggest that imatinib can modulate the immune response by sundry mechanisms, [ ] [ ] [ ] for several diseases, such as rheumatoid arthritis, asthma, and crohn's disease. this information insinuates that such drug might perform its potentially beneficial immunomodulatory role as a treatment alternative for covid- pneumonia. in addition, the use of imatinib as treatment appears to be reasonable from an economic point of view and its high availability in hospitals, since this drug is well tolerated and the risk of severe adverse effects is relatively low, especially in short-term administration. it is also recognized that adverse effects, mostly mild to moderate in intensity, will be easily controlled by dose reduction or discontinuation. in light of this information, tatar and turhan used the docking methodology to better understand the mechanism of inhibition of the sars-cov- n protein with antiviral compounds. based on this study results, imatinib was one of the highly binding affinities performed against the aforementioned target, with the lowest micromolar ki values among the compounds evaluated. in line with this study, an in-vitro research carried out by weston et al. found fda approved drugs that inhibited sars-cov- at non-cytotoxic concentrations. the authors indicate imatinib as one of the hits, since it exhibited ic value of . μm. they subsequently determined the mechanism of action, demonstrating this drug inhibits fusion of covs with cellular membranes, precluding their entry. this result indicates imatinib use against sars-cov- . however, its efficacy and safety need to be better confirmed in further preclinical and clinical trials in order of elect him as candidate drug in the treatment of covid- . synthesized for the first time by jean francois rossignol in the beginning of the s, the acetyloxy-n-( -nitro- -thiazolyl) benzamide, sold under the name nitazoxanide (ntz) ( ) (fig. ) , is the result of a structural modification in the antiparasitic niclosamide when a benzene ring is replaced with a nitrothiazole. , developed and sold as antiparasitic, ntz is also a first line broad spectrum antiviral with good results against parainfluenza, coronavirus, rotavirus, hepatitis and other respiratory infections. [ ] [ ] [ ] [ ] following oral administration, ntz is absorbed in the intestine, where it is rapidly hydrolysed by plasma esterase into the active metabolite tizoxanide. the mechanism of action of ntz varies according to the pathogen. in relation to antiviral activity, ntz blocks the maturation of the viral hemagglutinin at the post-translation stage in treatments against influenza. in treatments against hcv (hepatitis c), it activates protein kinase r (pkr), which leads to phosphorylation of the eukaryotic initiation factor- α thereby preventing translation. cao et al. conducted an in-vitro evaluation of ntz against recombinant murine coronavirus expressing the firefly luciferase (mhv- afls). the strand was pivotal to triage the drugs with likely anti-cov activity. the first assay resulted in molecules among which was ntz. the antiviral effect of ntz verified for mouse astrocytoma (dbt) and fibroblasts ( cl- ). the dbt cells infected with mhv- afls were treated with ntz at µm for hours, after which the viral titer (tcid ) was determined and viral n protein was subjected to western blot. results show the strong inhibitory effect of ntz on the viral titer. in-vitro studies on ntz or its metabolite tizoxanide were also conducted to verify efficacy against different coronaviruses. the replication of canine coronavirus (strain k ) in a cells, for instance, was blocked by the tizoxanide with ic of µg/ml. on the other hand, ntz inhibited the viral n protein in bovine coronavirus l (βcov-l ) and human enteric coronavirus (hecov- ) with approximate values of . µg/ml. , ntz is also responsible for inhibiting pro-inflammatory cytokines, such as tnf-α, il- , il- nitazoxanide ( ) drugs. more recently, molecules with a quinoline group have been widely investigated as treatment for the new coronavirus (sars-cov- ), such as chloroquine (cq) ( ) and hydroxychloroquine (hcq) ( ) (fig. ) that belong to the quinoline class and aminoquinoline subclass. both are quickabsorption synthetic drugs approved to treat malaria (plasmodium falciparum) by several regulating agencies in the world. cq and hcq are water soluble; the latter is more soluble due to presence of hydroxyl group. they are currently used to treat autoimmune diseases such as lupus erythematosus, antiphospholipid syndrome, rheumatoid arthritis as they have immunomodulatory and antithrombosis properties. [ ] [ ] [ ] therefore, these drugs could be useful against covid- due to the elevated levels of cytokine caused by cov infections in humans. the mechanism of action of cq for anti-malarial treatment is not entirely clear, but the interference with the digestion of haemoglobin by the parasite has been suggested. hcq has a similar mechanism, however, in regard to sars-cov- , clinical trials showed it to be safer. [ ] [ ] [ ] therefore, hcq, rather than cq, is used against sars-cov- . recent studies report antiviral activity of cq and hcq as they impair viral entry and release in different in-vitro and in-vivo models. , a factor that can also justify viral mechanisms is the aminoquinoline bioaccumulation in the tissues, as defended by patil, singhal & masand. a factor that facilitates viral replication is the acidic ph of endosomes, lysosomes and golgi complex of the host. thus, cq is promising because it increases the ph of intracellular vacuoles, binds to the cellular receptors, changes the glycosylation and because of its selective and reversible immunomodulator effect on human cd + t cells. hcq exerts similar mechanism of action: a) increases the ph; b) modulation of activated immune cells; c) reduces the number of proinflammatory cytokine and other mediators to control inflammation. it has also been suggested by roldan et al. a likely involvement of hcq in iron homeostasis during sars-cov- infection, which is a similar mechanism to other viral infections in humans. [ ] [ ] [ ] the little difference between the therapeutic and the toxic dose of cq is also known, and poisoning is related to cardiovascular complications that can be fatal. using either cq or hcq, then, requires strict prescription and self-medication is not advised. based on the recovery data, it was concluded that hcq is not effective in patients admitted with covid- . this highlights the importance of randomized clinical trials and the collection of clear data on the efficacy and safety of medications. ivermectin ( ) (fig. ) is an fda-approved broad-spectrum antiparasitic agent used in the treatment of tropical diseases, such as onchocerciasis, lymphatic filariasis, strongyloidiasis and lice. there is also evidence of its effectiveness in the management of myiasis, trichinosis, malaria, leishmaniasis, trypanosomiasis, chagas disease and schistosomiasis as well as bed bugs, inflammatory skin lesions, epilepsy, neurological diseases, tuberculosis and some cancers. it is known that ivermectin is capable of inhibiting the bond between a virus and the nuclear transport mediated by the superfamily of importin proteins (imp α/β ) based on the fact that sars-cov- is a rna virus deeply related to sars-cov, studies on sars-cov proteins have revealed a potential role for imp α/β during infection in signal-dependent nucleocytoplasmic shutting of the sars-cov nucleocapsid protein. furthermore, the sars-cov accessory protein orf has been shown to antagonize the antiviral activity of the stat transcription factor by sequestering imp α/β on the rough er/golgi membrane. considering the ivermectin nuclear transport inhibitory activity, such drug is widely believed as a promising therapeutic approach against sars-cov- . recently, caly et al. a different mechanism of action that consolidates the use of ivermectin against covid- is its immunomodulatory property. the inflammatory response (proinflammatory cytokine) is exaggerated in patients with the extreme case of the disease, which is likely explained by the hypoxiainducible factor (hif- α) that is activated by the virus when no inhibitory medication is administered. this understanding can be explained by the study conducted by kosyna et al. , whose lab tests with and without ivermectin aimed to examine whether the properties of the bond between hif- α and imp α/β and between hif- and nuclear localization signals were affected by the hypoxia mechanism on the cellular level. the authors concluded that ivermectin inhibited both imp α/β and hif- α. regarding this hinders its indication and clinical decisions. thus far, data indicate ivermectin is useful at the early stages of the disease, even the epidemiologic profile of covid- shows significant differences regarding the age of patients for the affected countries and patients with comorbidity. therefore, large scale randomized clinical trials are necessary to standardize clinical, laboratory and image evaluations, as well as combined drug therapy with vitamins and zinc, for example. financially, ivermectin is inexpensive and its doses and protocols are well established for different purposes. in addition, this drug has little side effects. indole, also named benzo [b] pyrrole, is a planar bicyclic heteroaromatic, whose ten π electrons move across its structure making this chemical group behave as a weak base. , the indole ring is the most abundant heterocyclic in nature and is commonly found in biologically active natural products, such as vegetables and seafood. it is also present in the structure of the essential amino acid tryptophan, which interferes with protein synthesis and with the regulation of physiological mechanisms such as precursors for serotonin and vitamin b . and adding the indole ring to spirothiazolidinones conducted to better influenza a/h n inhibition. now, the antiviral activity of indole and its derivatives for covid- therapy is supposed. arbidol ( ) is also a promising drug to fight covid- (fig. ) . this drug is classified as antiviral and has been used for there is high expression of eca , identified as human receptor for virus entry. notwithstanding, a different clinic trial concluded that arbidol monotherapy is best for the patient than lpv/rtv. despite the results, both investigations recognize their own limitations due to small cohort size and lack of placebo-control group. according to the authors, these limitations are inherent to pandemic times when placebo-control groups are difficult to conduct due to life-threatening conditions. most studies with arbidol use mg/ *day , , following the chinese guidelines. previous investigations on the pharmacokinetics of arbidol in healthy chinese patients showed that a single mg oral dose is sufficient for cmax de ~ , μm. this value was obtained through invitro assays that pointed the drug as effective and promising against sars-cov- . hence, clinical trials are still necessary to confirm the efficacy of arbidol at elevated doses to treat covid- . rizatriptan (rzt) ( ) (fig. ) is used to treat migraine and is a selective receptor of serotonin ( -ht) type b and d, structurally and pharmacologically related to other selective antagonists at these receptors. its structure is based on an indole ring replaced with methyltriazole at -position and unsubstituted ethanamine replaced with methyl at -position, the substitution sites are the same of melatonin (mlt). after virtual triage through molecular dock at spike-ace interface, ligations π-cation, interactions π-π and hydrogen bonds were identified between rzt and the sars-cov- protein complex. as one of the outstanding compounds in the analysis, in-vitro tests are still necessary. it is noteworthy that overdosing of the drug can trigger dizziness, fainting, cardiac issues, hypertension, bradycardia and vomiting. despite the safety of the drug in regular doses, there are no reports on either in-vitro or in-vivo tests to support the theoretical data and the antiviral action thus far. one last indole derivative that could be repurposed to treat covid- is melatonin (mlt) ( ) (fig. ) . mlt is classified as a hormone and nutraceutical, as it is naturally produced by the pineal gland and released into the bloodstream. it regulates the sleep-wake cycle as well as our mood, learning and memory, fertility, reproduction and the immune system. from a chemical perspective, it is an indole derivative with a methoxy group at -position and one ethylacetamide at -position. regarding its antiviral potential, mlt acts indirectly through anti-inflammatory, antioxidant and immune modulating activities. an investigation with murine infected with semliki forest virus (sfv) and west nile virus (wnv) showed the efficiency of mlt in reducing mortality rates for these viruses as well as in reducing the levels of pro-inflammatory cytokines. the anti-inflammatory and antioxidant properties of mlt point to its antiviral effects in humans. based on computational data, zhou et al. suggested using combined medication to fight sars-cov- . one such combination involves mlt plus mercaptopurine in synergic action against the following targets: pl pro , ace , c-jun signal and anti-inflammatory vias. therefore, experimental studies on modifications of ace pathways caused by mlt are useful to understand this drug. on the other hand, it has been suggested that using this neuro-hormone can mitigate the extreme form of the disease, the acute respiratory syndrome that has caused most deaths by sars-cov- cases. despite its safety for humans, the lack of data on the relevance of its use for covid- patients emetine ( ) is an approved anti-protozoal drug used against amebae with reported inhibitory activity for enterovirus infections, zika virus and ebola by interfering with the process of viral replication and entry in host cells. emetine is an isoquinoline alkaloid that presents methoxy groups in its structure (fig. ) . studies also confirm emetine has in-vitro activity against coronaviruses, including sars-cov and mers-cov. assays to clarify the activity of these drugs and the mechanism involved in the antiviral action of emetine both in isolation and combined to other drugs. another alkaloid candidate to repurpose against covid- is homoharringtonine (hht) ( ) (fig. ) . hht is an fda-approved drug in semi-synthetic form known as omacetaxine. this drug displays antitumoral activity in the treatment of myeloid chronic leukaemia. the mechanism of action implicates the ribosomal bond to prevent protein translation. in addition to antitumor activity, there are data in the literature that describe antiviral activity of hht against several types of viruses including covs. , a recent in-vitro evaluation of anti-sars-cov- activity displayed ec of . µm. however, the mechanism of action is not yet clear, which demands further investigation on ideal doses of hht to achieve the clinical results expected of a covid- therapeutic drug. the first reports on tetraethylthiuram disulfide, disulfiram (dsf) ( ) (fig. ) , date back to . however, only in the s that dsf would become popular when it was discovered that it could form copper chelates which favoured the death of micro-organisms and enabled treatment of intestinal parasites. [ ] [ ] [ ] in , dsf alcohol sensitivity was discovered accidentally and it was soon used in the clinical treatment of alcohol dependence. , dsf is used to treat alcohol dependence because it irreversibly inhibits the acetaldehyde dehydrogenase enzyme and modifies cysteine residues in its active site. this change prompts the formation of a disulphide bond between two cysteine residues in the active site. dsf effectiveness is based on its similarly to several proteins yielding a range of biological activities, such as antitumoral, , antimicrobial, and anti-sars and mers-cov. adding to the list of drugs to be repurposed against sars-cov- , recent studies indicate that dsf is able to inhibit other enzymes, such as methyltransferase, urease and kinase, all by reacting with important cysteine residues that suppress the natural cycle of the enzymes, suggesting broad-spectrum characteristics. , covs have two viral enzymes, m pro and pl pro , that are cysteine protease involved in the formation of structural and non-structural proteins that constitute the viruses and favour control of host cells. different assays, such as proteolytic and binding synergy assays, were also conducted and described. although outcomes indicate dsf for anti-mers-cov and anti-sars-cov therapy, to the present date ( th june ), no other article was published claiming the availability of the compound as promising anti-sars-cov- . recently, an announcement was published on the oxford university website on the results of one randomized evaluation of covid- therapy. more specifically, the study focused on dexamethasone ( ), a corticosteroid with fluorine at -position (fig. ) . the drug is mostly used as anti-inflammatory, which works by inhibiting vasodilation, reducing leukocyte migration to the inflammation site and increasing vascular permeability. immunotherapy is an effective intervention in viral infections. most attempts at immunotherapy were successful in fighting viruses similar to sars-cov- . the principal methods include vaccine, neutralizing antibodies (nabs) candidates and convalescent plasma. , , , , , , in addition, according to the evidences from viral infections (ebola, influenza, sars and mers), immunotherapeutic interventions can reduce viral load and mortality rate of patients. , development of either monoclonal (mabs) or polyclonal (pabs) neutralizing antibodies is a commonly adopted immunotherapeutic alternative due to its specificity, purity, low contamination by blood-transmitted pathogens and relative safety. however, there are limitations to the use of nabs once its development and large-scale production for clinical use are a complex, expensive and slow process. promising scientific investigations have suggested using mabs or pabs as prophylactic and therapeutic measures against influenza and hcovs, such as mers-cov and sars-cov. targets reported as promising for hcovs immunotherapy were cytokine, s -receptor-binding domain (s -rbd), s n-terminal domain (s -ntd) and some other region of subunit s in order to block the rbds bonds to their respective receptors and to interfere either with s -mediated membrane fusion or with the entry in the host cells, thus inhibiting infection. these researchers have encouraged the development of nabs with cross reactivity potential and/or cross neutralization effect on sars-cov- infections, as shown by tian et al. data suggest that mab cr can be developed as therapeutic candidate, either isolated or combined with neutralizing antibodies to prevent and treat covid- , given that it could potently form bonds with sars-cov- rbd (kd of . nm). a different study by wang et al. reported the discovery of a human mab ( d ) that promoted cross neutralization of sars-cov and sars-cov- in a culture of cells through an independent receptor-binding inhibition mechanism that targets a conserved epitope on the spike hcovs rbd mentioned above. it is also reported the on-going investigation of convalescent plasma or immunoglobulin as last resource to improve the survival rate of patients with several viral infections such as h n avian influenza, a possible explanation for the efficacy of convalescent plasma is that immunoglobulin antibodies in the plasma of recovered patients can suppress viremia. shen et al. reported that five patients with extreme symptoms of covid- received blood transfusion containing convalescent plasma with specific sars-cov- antibodies. after a series of blood transfusions, the improvement in clinical status of patients was observed. viral loads also decreased and became negative within days after the transfusion, and sars-cov- -specific elisa and nabs titers increased following the transfusion. in spite of the limited sample, the authors concluded that convalescent plasma transfusion benefited patients infected with sars-cov- . therefore, testing safety and efficacy of transfusing convalescent plasma in patients infected with sars-cov- can be of value. , among the modalities of immunotherapy, vaccines are expected to be more promising, hence the global engagement in their production. over the last decade, the scientific community and the vaccine industry had to answer urgently to the epidemics of h n , ebola, zika and, more recently, sars-cov- . vaccine development is an expensive and slow process with high risks of failure, which often motivate developers to follow a linear sequence of steps with several breaks for data analysis and fabrication processes. therefore, it is fundamental that vaccines be developed through faithful methods even if it takes longer to move them onto clinical trials or to make a large number of doses available, a challenge during a pandemic. developing efficient vaccines for sars-cov- will be essential to reduce the severity of the disease, viral shedding and transmission to control future outbreaks. prior to the covid- pandemic, multiple strategies were used to generate vaccines for the first hcovs (sars-cov and mers-cov). several studies related to sars-cov vaccine production targeting the protein s, due to its function in the receptor binding and fusion to the host membrane, were successful in animal tests against that coronavirus. - these vaccines employed live-attenuated virus vaccines, killed virus, dna vaccines and viral vector vaccines. theoretically, these techniques could be applied to develop sars-cov- vaccines given their similarities from both the genomic perspective and the mechanisms employed in the invasion and infection of host cells. gao et al. promoted the pilotscale production of a purified inactivated sars-cov- virus vaccine candidate (picovacc), which induced sars-cov- -specific nabs in mice, rats and non-human primates. in addition, three immunizations using two different doses ( μg or μg per dose) in macaques provided partial or complete protection against the sars-cov- challenge, respectively, without observable antibodydependent enhancement of infection. these data reinforce the use of picovacc in the next steps of clinical trials targeting sars-cov- still for the present year. given the magnitude of the covid- pandemic, it has become indispensable to work as fast as possible to develop vaccines for global distribution. however, protocols are necessary to safekeep the population's health. hence, before allowing human testing of covid- vaccines, regulatory organizations must evaluate their safety against a series of virus strains and more than one animal model. they also must demand preclinical evidences that experimental vaccines prevent infectioneven if it means waiting weeks or months for models to become available. this is time well-spent, once testing vaccines without investing the due amount of time to completely understand the risks can lead to setbacks for current and future pandemics. repurposing potential relies on the mechanism for other viruses, such as hepatitis c, by inducing conformational changes that compromise rdrp activity. it was also possible to identify benzene derivatives used to treat cancer (dasatinib and imatinib) and one antiviral (darunavir), but predominant in-silico and some in-vitro outcomes demand more conclusive studies. representative of benzoic derivatives, ntz displayed significant inhibitory activity against pro-inflammatory cytokines, which can benefit control of ards, in spite of an unclear mechanism against sars-cov- . quinoline derivatives, hcq and cq, were some of the first drugs investigated. after several in-silico, in-vitro and in-vivo assays, based on results presented by recovery to the present date, unfortunately, these drugs were proven ineffective in hospitalized covid- patients. ivermectin represents macrolide derivatives and is suggested as promising due to both immunostimulatory activity and inhibitory activity on nuclear transport when administered at the early stages of the disease. among indole derivatives, arbidol was pointed out as useful for reducing viral binding and releasing of intracellular vacuoles that contain the virus. nonetheless, clinical trials are still necessary after dose adjustment for better outcomes. both indole derivatives (emetine and hht), in spite of promising results, were only submitted to in-silico and in-vitro tests, thus demanding further investigation on their toxicity and mechanism of control. hence, the currently available data on the classes of drugs investigated here revealed that drugs were considered promising mainly after in-silico tests only. in fact, the inefficacy of some of these drugs became evident after in-vitro or in-vitro tests, as cq and hcq, whose clinical trials failed to confirm the so-expected anti-sars-cov- activity. it is necessary to highlight the importance of clinical trials with drugs considered promising in theoretical studies, with due calm and openness to question and refute hypotheses, in the absence of scientific evidence to support their use to treat covid- . similarly, the careful analysis of practices involving patients with the extreme form of the disease is also important to identify new alternatives, such as the results recently published by recovery on dexamethasone. it is also expected that detailed clinical trials are conducted with some of the drugs described in this article as potential anti-sars-cov- , for instance sofosbuvir, origin and evolution of pathogenic coronaviruses the covid- vaccine development landscape sars-cov- vaccines: status report recent discovery and development of inhibitors targeting coronaviruses analysis of therapeutic targets for sars-cov- and discovery of potential drugs by computational methods drug repurposing for viral infectious diseases: how far are we? tenofovir against sars-cov- rna dependent rna polymerase (rdrp): a molecular docking study virtual screening and repurposing of fda approved drugs against covid- main protease baricitinib as potential treatment for -ncov acute respiratory disease remdesivir and sars-cov- : structural requirements at both nsp rdrp and nsp exonuclease active-sites coronaviruses -drug discovery and therapeutic options development of one-step, real-time, quantitative reverse transcriptase pcr assays for absolute quantitation of human coronaviruses oc and e coronavirus as a possible cause of severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia a review of coronavirus disease- (covid- ) emergence of novel coronavirus -ncov: need for rapid vaccine and biologics development a pneumonia outbreak associated with a new coronavirus of probable bat origin world health organization. coronavirus disease (covid- ) pandemic advances in virus research covid- : a promising cure for the global panic genotype and phenotype of covid- : their roles in pathogenesis molecular evolution of human coronavirus genomes recent progress and challenges in drug development against covid- coronavirus (sars-cov- ) -an update on the status genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding structure analysis of the receptor binding of -ncov mechanistic insights into the effect of humidity on airborne influenza virus survival, transmission and incidence visualizing speech-generated oral fluid droplets with laser light scattering pitfalls of judgment during the covid- pandemic a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study origin of viruses: primordial replicators recruiting capsids from hosts the coronavirus spike protein is a class i virus fusion protein: structural and functional characterization of the fusion core complex sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor renin-angiotensin-aldosterone system inhibitors in patients with covid- renin-angiotensin-aldosterone system and covid- infection covid- infection: origin, transmission, and characteristics of human coronaviruses review of the clinical characteristics of coronavirus disease (covid- ) mild or moderate covid- the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreakan update on the status clinical features of patients infected with novel coronavirus in wuhan, china clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study clinical characteristics of coronavirus disease in china clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study are patients with hypertension and diabetes mellitus at increased risk for covid- infection? comorbidities and multi-organ injuries in the treatment of covid- the vasoprotective axes of the renin-angiotensin system: physiological relevance and therapeutic implications in cardiovascular, hypertensive and kidney diseases sars-cov- and viral sepsis: observations and hypotheses novel coronavirus infection (covid- ) in humans: a scoping review and meta-analysis sex-specific sars-cov- mortality: among hormone-modulated ace expression, risk of venous thromboembolism and hypovitaminosis d probiotics and covid- : one size does not fit all clinical characteristics of deceased patients with coronavirus disease : retrospective study pathological findings of covid- associated with acute respiratory distress syndrome liver injury in covid- : management and challenges endothelial cell infection and endotheliitis in covid- comorbidities and multi-organ injuries in the treatment of covid- coronavirus infections and immune responses longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of sars-cov- infected patients reducing mortality from -ncov: host-directed therapies should be an option ribavirin and interferon alfa- a for severe middle east respiratory syndrome coronavirus infection: a retrospective cohort study coronavirus membrane fusion mechanism offers a potential target for antiviral development pharmacological therapeutics targeting rna-dependent rna polymerase, proteinase and spike protein: from mechanistic studies to clinical trials for covid- structure of the sars-cov- spike receptor-binding domain bound to the ace receptor structural basis of receptor recognition by sars-cov- a possible strategy to fight covid- : interfering with spike glycoprotein trimerization the spike protein of the emerging betacoronavirus emc uses a novel coronavirus receptor for entry, can be activated by tmprss , and is targeted by neutralizing antibodies evidence that tmprss activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response contributes to virus spread and immunopathology in the airways of murine models after coronavirus infection simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry efficient activation of the severe acute respiratory syndrome coronavirus spike protein by the transmembrane protease tmprss transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry protease inhibitors targeting coronavirus and filovirus entry structural basis of sars-cov- clpro and anti-covid- drug discovery from medicinal plants structure of the rna-dependent rna polymerase from covid- virus structural basis for inhibition of the rna-dependent rna polymerase from sars-cov- by remdesivir structure of mpro from sars-cov- and discovery of its inhibitors efficiency of incorporation and chain termination determines the inhibition potency of ′-modified nucleotide analogs against hepatitis c virus polymerase protective effect and potential mechanisms of wei-chang-an pill on high-dose -fluorouracil-induced intestinal mucositis in mice higher order structures in purine and pyrimidine metabolism human pyrimidine nucleotide biosynthesis as a target for antiviral chemotherapy pyrrolopyrimidines: an update on recent advancements in their medicinal attributes synthesis and evaluation of anti-tumor activity of novel triazolo[ , -a] pyrimidine on cancer cells by induction of cellular apoptosis and inhibition of epithelial-to-mesenchymal transition process a facile one pot synthesis of novel pyrimidine derivatives of , -benzodiazepines via domino reaction and their antibacterial evaluation high antiparasitic activity of silver complexes of , -dimethyl- , , -triazolo[ , a]pyrimidine new carbocyclic n -substituted adenine and pyrimidine nucleoside analogues with a bicyclo[ . . ]heptane fragment as sugar moiety; synthesis, antiviral, anticancer activity and x-ray crystallography new prodrugs of two pyrimidine acyclic nucleoside phosphonates: synthesis and antiviral activity -fluorouracil upregulates cell surface b -h (pd-l ) expression in gastrointestinal cancers a new animal model of intestinal mucositis induced by the combination of irinotecan and -fluorouracil in mice -fluorouracil in combination with deoxyribonucleosides and deoxyribose as possible therapeutic options for the coronavirus, covid- infection the safety and efficacy of gemcitabine for the treatment of bladder cancer depletion of sirt sensitizes human non-small cell lung cancer cells to gemcitabine therapy by inhibiting autophagy gemcitabine for recurrent ovarian cancer -a systematic review and meta-analysis repurposing of clinically developed drugs for treatment of middle east respiratory syndrome coronavirus infection drug repositioning is an alternative for the treatment of coronavirus covid- an efficient synthesis of baricitinib janus kinase inhibitor baricitinib modulates human innate and adaptive immune system in vivo antitumor activity of su , a novel tyrosine kinase inhibitor targeting vascular endothelial growth factor and platelet-derived growth factor receptors: determination of a pharmacokinetic/pharmacodynamic relationship the egf receptor family as targets for cancer therapy janus kinase inhibitor baricitinib is not an ideal option for management of covid- protection against filovirus diseases by a novel broad-spectrum nucleoside analogue bcx galidesivir limits rift valley fever virus infection and disease in syrian golden hamsters therapeutic options for the novel coronavirus ( -ncov) new nucleoside analogues for the treatment of hemorrhagic fever virus infections remdesivir, lopinavir, emetine, and homoharringtonine inhibit sars-cov- replication in vitro genotype and subtype profiling of psi- as a nucleotide inhibitor of hepatitis c virus selected nucleos(t)ide-based prescribed drugs and their multi-target activity mechanism of activation of psi- and its diastereoisomer psi- evaluation of sofosbuvir (β-d- ′-deoxy- ′-α-fluoro- ′-β-cmethyluridine) as an inhibitor of dengue virus replication yellow fever virus is susceptible to sofosbuvir both in vitro and in vivo the fda-approved drug sofosbuvir inhibits zika virus infection beyond members of the flaviviridae family, sofosbuvir also inhibits chikungunya virus replication sofosbuvir as repurposed antiviral drug against covid- : why were we convinced to evaluate the drug in a registered/approved clinical trial antiviral β-l-nucleosides specific for hepatitis b virus infection. in: frontiers in viral hepatitis treatment of chronic hepatitis b: focus on telbivudine safety and efficacy of telbivudine for the treatment of chronic hepatitis b. ther clin risk manag -trisubstituted- h-purine)- -chalcone derivatives as potent anti-gastric cancer agents: design, synthesis and structural optimization novel phosphodiesterases inhibitors from the group of purine- , -dione derivatives as potent modulators of airway smooth muscle cell remodelling novel butanehydrazide derivatives of purine- , -dione as dual pde / inhibitors with potential anti-inflammatory activity: design, synthesis and biological evaluation the purines: potent and versatile small molecule inhibitors and modulators of key biological targets synthesis and biological evaluation of novel hiv- protease inhibitors with pentacyclic triterpenoids as p -ligands seley-radtke, design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity remdesivir in covid- : a critical review of pharmacology, pre-clinical and clinical studies the epidemiology, diagnosis and treatment of covid- therapeutic efficacy of the small molecule gs- against ebola virus in rhesus monkeys a randomized, controlled trial of ebola virus disease therapeutics broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov first case of novel coronavirus in the united states compassionate use of remdesivir for patients with severe covid- pharmacologic treatments for coronavirus disease (covid- ) oral ganciclovir for patients with cytomegalovirus retinitis treated with a ganciclovir implant drugbank . : a major update to the drugbank database epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study incidence, risk factors, and outcome of cytomegalovirus infection and disease in patients receiving prophylaxis with oral valganciclovir or intravenous ganciclovir after umbilical cord blood transplantation pharmacokinetics of ganciclovir after oral valganciclovir versus intravenous ganciclovir in allogeneic stem cell transplant patients with graft-versus-host disease of the gastrointestinal tract the first days of novel coronavirus (sars-cov- ) outbreak: recent advances, prevention, and treatment tenofovir disoproxil fumarate -triazole-containing hybrids as leads in medicinal chemistry: a recent overview medicinal attributes of , , -triazoles: current developments synthesis and anticancer activity of long chain substituted , , -oxadiazol- -thione, , , -triazol- -thione and , , -triazolo[ , -b]- , , -thiadiazine derivatives chemical synthesis and biological evaluation of triazole derivatives as inhibitors of inha and antituberculosis agents synthesis, antiinflammatory and analgesic activity of -[ -(substituted benzylideneamino)- -(substituted phenoxymethyl)- h- , , -triazol- -yl thio] acetic acid derivatives synthesis and biological evaluation of some novel triazol- -ones as antimicrobial agents design, synthesis, antiviral and cytostatic activity of ω-( h- , , -triazol- -yl)(polyhydroxy)alkylphosphonates as acyclic nucleotide analogues synthesis, biological evaluation and molecular modeling of a novel series of fused , , -triazoles as potential anti-coronavirus agents treatment options for covid- : the reality and challenges compounds with therapeutic potential against novel respiratory ribavirin in the treatment of sars: a new trick for an old drug? inhibition of novel β coronavirus replication by a combination of interferon-α b and ribavirin remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro anti-hcv, nucleotide inhibitors, repurposing against covid- ebola virus dynamics in mice treated with favipiravir favipiravir (t- ), a broad-spectrum inhibitor of viral rna polymerase favipiravir versus arbidol for covid- : a randomized clinical trial. medrxiv [epub ahead of print a possible pharmaceutical treatment for covid- experimental treatment with favipiravir for covid- : an open-label control study. engineering an antiviral for covid- ? covid- -the search for effective therapy coronavirus disease (covid- ): current status and future perspectives role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings improves outcome of mers-cov infection in a nonhuman primate model of common marmoset combination therapy with lopinavir/ritonavir, ribavirin and interferon-alpha for middle east respiratory syndrome: a case report a trial of lopinavir-ritonavir in adults hospitalized with severe covid- triple combination of interferon beta- b, lopinavirritonavir, and ribavirin in the treatment of patients admitted to hospital with covid- : an openlabel, randomised, phase trial molecular modeling evaluation of the binding abilities of ritonavir and lopinavir to wuhan pneumonia coronavirus proteases oseltamivir treatment of influenza in children therapeutic management of covid- patients: a systematic review in silico studies on therapeutic agents for covid- : drug repurposing approach synergistic antiviral effect of galanthus nivalis agglutinin and nelfinavir against feline coronavirus hiv protease inhibitor nelfinavir inhibits replication of sars-associated coronavirus nelfinavir was predicted to be a potential inhibitor of -ncov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation atazanavir for the treatment of human immunodeficiency virus infection influence of atazanavir on the pharmacodynamics and pharmacokinetics of gliclazide in animal models therapy with atazanavir plus saquinavir in patients failing highly active antiretroviral therapy: a randomized comparative pilot trial predicting commercially available antiviral drugs that may act on the novel coronavirus (sars-cov- ) through a drug-target interaction deep learning model déjà vu: stimulating open drug discovery for sars-cov- state-of-the-art tools unveil potent drug targets amongst clinically approved drugs to inhibit helicase in sars-cov- fda-approved thiolreacting drugs that potentially bind into the sars-cov- main protease, essential for viral replication cyclosporin a and cardioprotection: from investigative tool to therapeutic agent modulation of innate immunity by cyclosporine a the use of cyclosporine a in rheumatology: a comprehensive review cyclosporine a: a valid candidate to treat covid- patients with acute respiratory failure? the sars-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors cyclosporin a inhibits the replication of diverse coronaviruses human coronavirus nl replication is cyclophilin a-dependent and inhibited by non-immunosuppressive cyclosporine a-derivatives including alisporivir cyclophilins and cyclophilin inhibitors in nidovirus replication identification of antiviral drug candidates against sars-cov- from fda-approved drugs cyclosporin a is a potential inhibitor of sars-cov- . researchgate (preprint) cyclosporine therapy in cytokine storm due to coronavirus disease (covid- ) clinically significant drug interactions with cyclosporin glycopeptide antibiotics potently inhibit cathepsin l in the late endosome/lysosome and block the entry of ebola virus, middle east respiratory syndrome coronavirus (mers-cov), and severe acute respiratory syndrome coronavirus (sars-cov) discovery and development of safe-in-man broadspectrum antiviral agents teicoplanin: an alternative drug for the treatment of covid- ? fighting viruses with antibiotics: an overlooked path current epidemiological and clinical features of covid- ; a global perspective from china pharmacokinetics and safety of co-administered paritaprevir plus ritonavir, ombitasvir, and dasabuvir in hepatic impairment dasabuvir: a non-nucleoside inhibitor of ns b for the treatment of hepatitis c virus infection in silico studies on therapeutic agents for covid- : drug repurposing approach darunavir: a review in pediatric hiv- infection darunavir: a review of its use in the management of hiv- infection discovering drugs to treat coronavirus disease (covid- ) therapeutic options and critical care strategies in covid- patients; where do we stand in this battle? majallahi danishkadahi pizishkii isfahan insight derived from molecular docking and molecular dynamics simulations into the binding interactions between hiv- protease inhibitors and sars-cov- clpro peptide-like and small-molecule inhibitors against covid- computational view toward the inhibition of sars-cov imatinib: a breakthrough of targeted therapy in cancer coronavirus s protein-induced fusion is blocked prior to hemifusion by abl kinase inhibitors virus-induced abl and fyn kinase signals permit coxsackievirus entry through epithelial tight junctions abl tyrosine kinase regulates hepatitis c virus entry productive replication of ebola virus is regulated by the c-abl tyrosine kinase abelson kinase inhibitors are potent inhibitors of severe acute respiratory syndrome coronavirus and middle east respiratory syndrome coronavirus fusion sars coronavirus spike protein-induced innate immune response occurs via activation of the nf-κb pathway in human monocyte macrophages in vitro imatinib attenuates inflammation and vascular leak in a clinically relevant two-hit model of acute lung injury imatinib stimulates prostaglandin e and attenuates cytokine release via ep receptor activation imatinib mesylate induces clinical remission in rheumatoid arthritis kit inhibition by imatinib in patients with severe refractory asthma long-standing remission of crohnʼs disease under imatinib therapy in a patient with crohnʼs disease imatinib might constitute a treatment option for lung involvement in covid- european leukemianet recommendations for the management and avoidance of adverse events of treatment in chronic myeloid leukaemia principal long-term adverse effects of imatinib in patients with chronic myeloid leukemia in chronic phase investigation of n terminal domain of sars cov nucleocapsid protein with antiviral compounds based on broad anti-coronaviral activity of fda approved drugs against sars-cov- in vitro and sars-cov in vivo nitazoxanide: a first-in-class broad-spectrum antiviral agent nitazoxanide: a new thiazolide antiparasitic agent nitazoxanide/azithromycin combination for covid- : a suggested new protocol for early management therapeutic potential of nitazoxanide against newcastle disease virus: a possible modulation of host cytokines nitazoxanide, a new drug candidate for the treatment of middle east respiratory syndrome coronavirus the anti-hepatitis c agent nitazoxanide induces phosphorylation of eukaryotic initiation factor α via protein kinase activated by double-stranded rna activation a screen of the nih clinical collection small molecule library identifies potential anti-coronavirus drugs nitazoxanide suppresses il- production in lpsstimulated mouse macrophages and tg-injected mice a systematic review on use of aminoquinolines for the therapeutic management of covid- : efficacy, safety and clinical trials the possible mechanisms of action of -aminoquinolines (chloroquine/hydroxychloroquine) against sars-cov- infection (covid- ): a role for iron homeostasis? chloroquine: modes of action of an undervalued drug cardiovascular risks of hydroxychloroquine in treatment and prophylaxis of covid- patients: a scientific statement from the indian heart rhythm society chloroquine and hydroxychloroquine as available weapons to fight covid- hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro of chloroquine and covid- viral infection and iron metabolism hepcidin and the iron-infection axis iron and infection comparison of the antiviral activity in vitro of some non-steroidal antiinflammatory drugs antihistaminics, local anesthetics, and other amines as antiviral agents effect of chloroquine on the growth of animal viruses in vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine a systematic review on the efficacy and safety of chloroquine for the treatment of covid- chloroquine and hydroxychloroquine in the treatment of covid- with or without diabetes: a systematic search and a narrative review with a special reference to india and other developing countries structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against sars-cov- infection hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial hydroxychloroquine in the management of critically ill patients with covid- : the need for an evidence base association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in new york state observational study of hydroxychloroquine in hospitalized patients with covid- this national clinical trial aims to identify treatments that may be beneficial for people hospitalised with suspected or confirmed covid- ivermectin: enigmatic multifaceted 'wonder' drug continues to surprise and exceed expectations ivermectin is a specific inhibitor of importin α/β-mediated nuclear import able to inhibit replication of hiv- and dengue virus ivermectin is a potent inhibitor of flavivirus replication specifically targeting ns helicase activity: new prospects for an old drug repurposing ivermectin to inhibit the activity of sars cov helicase: possible implications for covid therapeutics influenza a viruses escape from mxa restriction at the expense of efficient nuclear vrnp import nuclear localization of dengue virus (denv) - non-structural protein ; protection against all denv serotypes by the inhibitor ivermectin the broad spectrum antiviral ivermectin targets the host nuclear transport importin α/β heterodimer nucleocytoplasmic transport of nucleocapsid proteins of enveloped rna viruses severe acute respiratory syndrome coronavirus orf antagonizes stat function by sequestering nuclear import factors on the rough endoplasmic reticulum/golgi membrane the fda-approved drug ivermectin inhibits the replication of sars-cov- in vitro the importin α/β-specific inhibitor ivermectin affects hif-dependent hypoxia response pathways antiviral treatment of covid- hydroxychloroquine and ivermectin: a synergistic combination for covid- chemoprophylaxis and treatment? therapeutic potential of ivermectin for covid enhancing immunity in viral infections, with special emphasis on covid- : a review safety of high-dose ivermectin: a systematic review and meta-analysis five-membered heterocycles: indole and related systems. modern heterocyclic chemistry a review on recent developments of indole-containing antiviral agents discovery of novel multi-target indole-based derivatives as potent and selective inhibitors of chikungunya virus replication medicinal applications of (benz)imidazole-and indole-based macrocycles medicinal chemistry of indole derivatives: current to future therapeutic prospectives synthesis and antiviral activity of some novel indole- -carboxylate derivatives superior inhibition of influenza virus hemagglutinin-mediated fusion by indole-substituted spirothiazolidinones arbidol combined with lpv/r versus lpv/r alone against corona virus disease : a retrospective cohort study arbidol monotherapy is superior to lopinavir/ritonavir in treating covid- the anti-influenza virus drug, arbidol is an efficient inhibitor of sars-cov- in vitro pharmacokinetics of single and multiple oral doses of arbidol in healthy chinese volunteers rizatriptan vs sumatriptan in the acute treatment of migraine ação da melatonina no tecido cartilaginoso covid- : melatonin as a potential adjuvant treatment protective effects of melatonin in mice infected with encephalitis viruses melatonin: its possible role in the management of viral infections-a brief review network-based drug repurposing for novel coronavirus -ncov/sars-cov- lungs as target of covid- infection: protective common molecular mechanisms of vitamin d and melatonin as a new potential synergistic treatment emetine protects mice from enterovirus infection by inhibiting viral translation emetine inhibits zika and ebola virus infections through two molecular mechanisms: inhibiting viral replication and decreasing viral entry high-throughput screening and identification of potent broad-spectrum inhibitors of coronaviruses the natural compound homoharringtonine presents broad antiviral activity in vitro and in vivo novel antiviral activities of obatoclax, emetine, niclosamide, brequinar, and homoharringtonine tracing the journey of disulfiram: from an unintended discovery to a treatment option for alcoholism supervised disulfiram as adjunct to psychotherapy in alcoholism treatment the clinical use of disulfiram (antabuse®): a review disulfiram inhibits the in vitro growth of methicillin-resistant staphylococcus aureus disulfiram, an alcohol dependence therapy, can inhibit the in vitro growth of francisella tularensis structural basis for inactivation of giardia lamblia carbamate kinase by disulfiram disulfiram/copper markedly induced myeloma cell apoptosis through activation of jnk and intrinsic and extrinsic apoptosis pathways disulfiram is a direct and potent inhibitor of human o -methylguanine-dna methyltransferase (mgmt) in brain tumor cells and mouse brain and markedly increases the alkylating dna damage disulfiram can inhibit mers and sars coronavirus papain-like proteases via different modes coronaviruses -drug discovery and therapeutic options inhibition of urease by disulfiram, an fda-approved thiol reagent used in humans the microcirculation and inflammation: site of action for glucocorticoids the convalescent sera option for containing covid- the possible of immunotherapy for covid- : a systematic review perspectives on monoclonal antibody therapy as potential therapeutic intervention for coronavirus disease- (covid- ) potential rapid diagnostics, vaccine and therapeutics for novel coronavirus ( -ncov): a systematic review advances in respiratory virus therapeutics -a meeting report from the th isirv antiviral group conference a mouse model for mers coronavirus-induced acute respiratory distress syndrome neutralizing human monoclonal antibodies to severe acute respiratory syndrome coronavirus: target, mechanism of action, and therapeutic potential effective treatment of severe covid- patients with tocilizumab neutralizing antibodies against sars-cov- and other human coronaviruses potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody a human monoclonal antibody blocking sars-cov- infection treatment with convalescent plasma for influenza a (h n ) infection convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (h n ) virus infection evaluation of convalescent plasma for ebola virus disease in guinea the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with middle east respiratory syndrome coronavirus infection: a study protocol treatment of critically ill patients with covid- with convalescent plasma convalescent plasma as a potential therapy for covid- developing covid- vaccines at pandemic speed a decade after sars: strategies for controlling emerging coronaviruses severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus sars coronavirus: a new challenge for prevention and therapy coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus development of an inactivated vaccine candidate for sars-cov- don't rush to deploy covid- vaccines and drugs without sufficient safety guarantees the authors would like to thank facepe (fundação de amparo à ciência e tecnologia none. all authors researched data for the article, contributed substantially to discussion of the content, wrote the article and reviewed and edited the manuscript before submission. key: cord- -ewcv m authors: xiao, shu‐yuan; wu, yingjie; liu, huan title: evolving status of the novel coronavirus infection: proposal of conventional serologic assays for disease diagnosis and infection monitoring date: - - journal: j med virol doi: . /jmv. sha: doc_id: cord_uid: ewcv m the novel coronavirus (ncov- ) outbreak in wuhan, china has spread rapidly nationwide, with some cases occurring in other parts of the world. although most patients present with mild febrile illness with patchy pulmonary inflammation, a significant portion develop severe acute respiratory distress syndrome (ards), with a current case fatality of . - %. diagnosis is based on clinical history and laboratory and chest radiographic findings, but confirmation currently relies on nucleic acid-based assays. the latter are playing an important role in facilitating patient isolation, treatment and assessment of infectious activities. however, due to their limited capacity to handle an epidemic of the current scale and insufficient supply of assay kits, only a portion of suspected cases can be tested, leading to incompleteness and inaccuracy in updating new cases, as well as delayed diagnosis. furthermore, there has not been enough time to assess specificity and sensitivity. conventional serological assays, such as enzyme-linked immunoassay (elisa) for specific igm and igg antibodies, should offer a high-throughput alternative, which allows for uniform tests for all suspected patients, and can facilitate more complete identification of infected cases and avoidance of unnecessary cross infection among unselected patients. this article is protected by copyright. all rights reserved. the diagnosis needs to be differentiated from influenza, parainfluenza, adenovirus, respiratory syncytial virus, rhinovirus, sars coronavirus, mycoplasma, chlamydia, and bacterial pneumonia, as well as noninfectious diseases such as vasculitis. , | diagnosis using the rna-based assays currently, the diagnosis of suspected cases is confirmed by rna tests with real-time rt-pcr or next-generation sequencing. it had been shown that viral rna can be detected from the nasal and pharyngeal swab, bronchoalveolar lavage, and blood plasma using rt -pcr targeting the np gene of the virus. , , before the wuhan citywide shutdown, specimens for confirmatory tests had to be sent to china cdc, with a long turnaround time. subsequently, several main tertiary care hospitals in wuhan were authorized to perform the tests. therefore, in the earlier stages of the outbreak, a very limited number of patients were tested and confirmed for the diagnosis. since january tests have become increasingly available for clinically suspected patients, with a history of exposure, fever, and positive findings on chest ct. however, since only a limited number of tests can be offered each day due to limited supplies and lab facilities, only a portion of the targeted population received tests. for example, during the month of january , only specimens were tested (media report by the hospital on wechat, / / ), compared with the vast number of clinic patients during that period (between january and january alone, there were over visits to one of the designated fever clinic). this created a significant backlog, as many patients had to wait for days to receive a confirmation or exclusion of diagnosis. it also led to problems in realtime reporting, causing artificial fluctuation in daily updates of new cases ( figure b ). for example, as shown in table , using data collected from the national health commission's daily updates, on some dates, the change in the number of newly confirmed cases varies drastically. this cannot be explained by realistic changes in the speed of infection spread. needless to say, the recorded figures of daily confirmed cases are likely underestimated. f i g u r e ct images of patients with novel coronavirus pneumonia. a, patchy ground-glass-like density change from a -year-old woman who developed a mild illness after exposure at work. b, bilateral diffuse thickening of interlobular septa with network-like densities, bronchiolar thickening, and consolidation of the left lower lobe from an -year-old woman. she presented with fever, chills, and sore throat; she had dry cough, chest tightness, and shortness of breath for a week. her body temperature at presentation was . °c, cbc showed wbc . × /l, neutrophilic differential . %, and lymphocytic differential . % (reduced). (courtesy of prof haibo xu). cbc, complete blood count; ct, computed tomography; wbc, white blood cells another concern related to the nucleic acid tests is that there has not been sufficient time to assess their sensitivity and specificity. a fast-performing serologic assay is acutely needed for the current and future outbreaks. the authors would like to thank dr haibo xu for graciously providing the computed tomography images and dr jingyi fan for sharing her personal observations. a familial cluster of pneumonia associated with the novel coronavirus indicating person-toperson transmission: a study of a family cluster clinical features of patients infected with novel coronavirus in wuhan a novel coronavirus from patients with pneumonia in china a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus genome identified in a cluster of pneumonia cases-wuhan office of state administration of traditional chinese medicine. notice on the issuance of strategic guidelines for diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia health emergency office of national health commission of the prc. update on the epidemic of novel coronavirus ( -ncov) sars and common viral infections detection of specific antibodies to severe acute respiratory syndrome (sars) coronavirus nucleocapsid protein for serodiagnosis of sars coronavirus pneumonia a sequential study of serum specific igm antibody responses in ehf and their relationship to the severity of illness effect of ribavirin on the specific humoral immune responses of patients with hemorrhagic fever with renal syndrome the authors declare that there are no conflict of interests. key: cord- -yy abob authors: chavez, summer; long, brit; koyfman, alex; liang, stephen y. title: coronavirus disease (covid- ): a primer for emergency physicians date: - - journal: am j emerg med doi: . /j.ajem. . . sha: doc_id: cord_uid: yy abob introduction: rapid worldwide spread of coronavirus disease (covid- ) has resulted in a global pandemic. objective: this review article provides emergency physicians with an overview of the most current understanding of covid- and recommendations on the evaluation and management of patients with suspected covid- . discussion: severe acute respiratory syndrome coronavirus (sars-cov- ), the virus responsible for causing covid- , is primarily transmitted from person-to-person through close contact (approximately ft) by respiratory droplets. symptoms of covid- are similar to other viral upper respiratory illnesses. three major trajectories include mild disease with upper respiratory symptoms, non-severe pneumonia, and severe pneumonia complicated by acute respiratory distress syndrome (ards). emergency physicians should focus on identifying patients at risk, isolating suspected patients, and informing hospital infection prevention and public health authorities. patients with suspected covid- should be asked to wear a facemask. respiratory etiquette, hand washing, and personal protective equipment are recommended for all healthcare personnel caring for suspected cases. disposition depends on patient symptoms, hemodynamic status, and patient ability to self-quarantine. conclusion: this narrative review provides clinicians with an updated approach to the evaluation and management of patients presenting to the emergency department with suspected covid- . on january , , the world health organization (who) designated an outbreak of a novel coronavirus not seen before in humans to be a "public health emergency of international concern" (pheic); this was followed by the declaration of a pandemic on march , [ , ] . severe acute respiratory syndrome coronavirus (sars-cov- ), previously referred to as -ncov, is the virus responsible for causing coronavirus disease (covid- ) [ ] [ ] [ ] [ ] [ ] . the pandemic traces its early beginnings to the report of a cluster of unexplained pneumonia cases in late december originating from a seafood and live animal market in wuhan, hubei province, china [ ] [ ] [ ] [ ] . from the outset, the causative agent was thought to be viral, with most patients reporting fever or dyspnea [ , ] . with unprecedented numbers of individuals under travel restrictions or quarantine, worldwide spread, and no known cure or vaccine yet available, covid- has proven a formidable adversary [ , [ ] [ ] [ ] . the ebola virus disease (evd) outbreak of in west africa provided valuable lessons with regards to emergency preparedness, personal protective equipment use, and triage processes and underscored the important role that emergency physicians play on the frontlines of emerging infectious diseases [ ] [ ] [ ] . we describe the virology, epidemiology, clinical presentation, radiographic and laboratory findings, current testing protocols, and management of patients presenting with covid- to the emergency department (ed). in this review article, we provide emergency physicians with best practices based on the rapidly evolving body of literature surrounding covid- . sars-cov- is a member of the coronavirus family, named for the crown-like appearance of spikes on the virus surface [ , ] . other members of the coronavirus family include middle east respiratory syndrome coronavirus (mers-cov) and sars-cov- , as well as coronaviruses responsible for the common cold (figs. and ) [ , , , ] . like mers-cov and sars-cov- , sars-cov- is a betacoronavirus and is likely associated with an animal reservoir (e.g., bats) [ , , ] . while an exact animal source has not been confirmed for covid- , many of the early cases in china were linked to a live animal and seafood market [ , , , ] . american journal of emergency medicine xxx (xxxx) xxx the majority of initial covid- cases were associated with travel to hubei province, china; however, a growing number of cases due to person-to-person transmission have been reported both in and outside of china (fig. ) [ , , , ] . up to % of covid- cases were reported to originate from hubei province in december ; as of march , the greatest number of new cases are now being reported in italy, spain, germany, and the united states (u.s.) (figs. and ) [ ] [ ] [ ] . based on what is known about other coronaviruses, experts believe covid- primarily spreads from person-to-person through close contact (approximately ft) by respiratory droplets [ , , , , ] . transmission of the virus through contaminated surfaces or fomites with subsequent contact with the eyes, nose, or mouth may also occur [ , , ] . patients are felt to be at highest risk of spreading the illness when they are most symptomatic [ , ] . limited data support viral shedding in asymptomatic patients while increased levels of viral shedding may be more pronounced in those critically ill [ ] [ ] [ ] . current epidemiologic patterns of covid- in china indicate that it is highly contagious with sustained spread; the extent of person-to-person transmission within the u.s. was initially limited but has progressed now to community transmission in many parts of the country [ ] . the current r or basic reproduction number is estimated to be n . ; for every case of covid- identified in the population, n additional cases are possible in the absence of adequate isolation. [ , [ ] [ ] [ ] in an early epidemiologic analysis of covid- cases in wuhan, china, the median patient age was years, and % were male [ ] . in the largest study to date of covid- , comprising over , patient records (up to february , ) from china, . % of patients were - years of age [ ] . while . % of these cases were reported to be mild, the overall case fatality rate was . % [ ] . few pediatric cases of covid- have been reported, with patients aged - years representing just . % of all cases [ , ] . approximately . % of laboratory confirmed cases of covid- occurred in healthcare personnel, and . % of these cases were either severe or critical [ ] . to be classified as severe, the following characteristics were required: pao /fio b , oxygen saturation ≤ %, presence of n % lung infiltrates within - h, respirations ≥ breaths/min, or dyspnea [ ] . critical patients, defined as those with septic shock, multiple organ dysfunction/failure, and/or respiratory failure, accounted for approximately % of the study population with a case fatality rate of . % [ , ] . the highest case fatality rate was observed in those older than years ( . %) [ ] . patients without comorbidities had a case fatality rate of just . %, in contrast to those with comorbid conditions such as cardiovascular disease ( . %) [ ] . caution should be exercised in interpreting early findings, as underreporting and variable testing practices have been a concern with covid- [ , ] . case fatality rates in hubei province have been reported to be % ( % confidence interval [ci] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] , while those outside mainland china range from . - . % [ ] . mortality rates have been calculated to be as high as - % [ , ] . when compared to other recent epidemics such as sars ( . ) or evd ( . ), the average case fatality rate ( . %) for covid- is much lower (table ) [ , ] . in comparison, the h n influenza pandemic and influenza season were responsible for approximately times more cases [ , ] . based on what is known about similar coronaviruses, the longest potential incubation period for covid- is thought to be days from initial exposure [ , ] . the mean incubation period is . days ( % ci . - . ) but can range from to days [ , , ] . co-infections occur in - % of patients and may be higher in critical patients [ , ] . risk factors for severe covid- disease include advanced age, chronic medical conditions, immunocompromise, and cancer [ ] . data regarding pregnancy and covid- are limited [ ] . pregnant women and fetuses may be more vulnerable to covid- infection compared to the general population [ ] . there are case reports of pregnant women diagnosed with covid- complicated by adverse outcomes including preterm birth [ ] . historically, infants born to mothers with other coronaviruses such as mers-cov or sars-cov- have been small for gestational age or preterm [ ] . newborn infants are also an at-risk population [ ] . occupational exposure to pathogens is an inherent risk of working in healthcare settings [ ] . during the sars outbreak, % of healthcare professionals (hcps) in toronto, canada participating in endotracheal intubation of infected patients became infected themselves [ ] . in another study, % of sars patients in toronto had ties to the hospital setting, and % of cases were hcps [ ] . during the h n influenza pandemic, hcps were significantly more likely to develop infection (odds ratio [or] . , % ci . - . ) with a pooled prevalence of . % [ ] . as covid- has disproportionately affected hcps, emergency physicians must be vigilant about potential exposure risks and adhere to appropriate infection prevention precautions [ , ] . in italy, anywhere from to % of hcps have been infected with sars-cov- [ , ] . the symptoms of covid- are similar to other viral upper respiratory illnesses and include fever, cough, fatigue, and dyspnea [ , , ] . the differential diagnosis for covid- should be tailored to the patient and their presenting symptoms and comorbidities. influenza, respiratory syncytial virus (rsv), other viral illnesses, and bacterial pneumonia should be considered, as well as other pulmonary diseases (ie, pulmonary embolism). completing a thorough yet focused history and physical examination and obtaining collateral history from family members are vital. aside from pulmonary symptoms, patients with covid- may initially present with more vague complaints including diarrhea, lethargy, myalgias, and nausea [ , ] . patients may also experience headache, confusion, vomiting, pleurisy, sore throat, sneezing, rhinorrhea, and nasal congestion [ , ] . a case series of patients (median age . years) with covid- from wuhan, china found the most commonly reported symptoms were cough ( %), fever ( %), or dyspnea ( %) [ ] . in the same case series, patients also reported myalgias/fatigue ( %), productive cough ( %), headache ( %), hemoptysis ( %), and diarrhea ( %) [ ] . in a nationwide study of covid- cases from across china, the most common presenting symptoms included cough ( %), fever ( %), fatigue ( %), sputum production ( %), and shortness of breath ( %) [ ] . fever was not a predominant symptom at the time of initial presentation. in patients with more severe disease, dyspnea may be present in % of patients and progress to acute lung injury in % of patients [ ] . one study of patients with confirmed covid- suggests . % of patients have gastrointestinal (gi) symptoms [ ] . these symptoms may include anorexia ( . %), diarrhea ( . %), vomiting ( . %), and abdominal pain ( . %). seven of the patients had only gi symptoms with no respiratory symptoms [ ] . atypical presentations of infection in general may be more likely in the elderly and immunocompromised, who may not mount a febrile response [ , ] . to increase sensitivity and identify potential covid- patients sooner, the u.s. centers for disease control and prevention (cdc) recommends using a temperature cutoff of . f o [ ] . patients older than years of age and those with comorbidities may also present with more severe disease compared to other populations [ ] . three major trajectories for covid- have been described: mild disease with upper respiratory symptoms, non-severe pneumonia, and severe pneumonia complicated by acute respiratory distress syndrome (ards) necessitating aggressive resuscitative measures [ ] . anywhere from to % of patients may develop ards [ , ] . other complications of covid- include secondary bacterial infection, acute kidney injury, septic shock, ventilator-associated pneumonia, and cardiac injury [ , ] . an emergency medicine approach to covid- should focus on identifying and isolating patients at risk for infection, informing hospital infection prevention and local public health authorities, and engaging infectious disease and other specialists early in care. the world health organization (who) has established case and contact definitions for covid- to standardize global surveillance ( table ). most patients with confirmed covid- have had a subjective or confirmed fever and/or symptoms of acute respiratory illness (e.g., cough, difficulty breathing) [ ] . in concert with clinician judgment regarding patient presentations compatible with covid- , cdc guidelines prioritize patients from defined populations for further evaluation and testing as persons under investigation (pui) ( table ). these criteria are not exhaustive, and patients with an unestablished etiology or equivocal history of exposure may be considered for further testing on an individual basis [ ] . confirmed local covid- cases in the setting of known community transmission should reduce the threshold for further covid- evaluation in the ed. collaboration with local and state public health departments is strongly recommended [ , ] . a pui should be asked to wear a facemask to reduce risk of transmission to others in the immediate vicinity. fig. details cdc recommendations for identifying and assessing suspected covid- . emergency medical services (ems) directors and public health authorities working in conjunction with the cdc will need to modify emergency preparedness strategies to address covid- [ ] . emergency medical dispatchers should consider whether callers describing risk factors and symptoms concerning for covid- should be a contact is a person who experienced any one of the following exposures during the days before and the days after the onset of symptoms of a probable or confirmed case: • face-to-face contact with a probable or confirmed case within m and for n min; • direct physical contact with a probable or confirmed case; • direct care for a patient with probable or confirmed covid- disease without using proper personal protective equipment; or • other situations as indicated by local risk assessments. note: for confirmed asymptomatic cases, the period of contact is measured as the days before through the days after the date on which the sample was taken which led to confirmation. identified as a potential pui [ , ] . if so, ems personnel arriving onscene as well as hcps at the receiving hospital should be notified immediately to ensure proper personal protective equipment (ppe) use and confirm that appropriate isolation facilities are available [ , ] . once contact is made with the patient, initial triage and assessment should be done at least ft or meters away and minimized until the pui dons a facemask [ ] . in addition to limiting the number of ems personnel in the patient compartment, those providing any direct patient care should follow standard, droplet (surgical mask), and contact precautions (gown and gloves) while wearing eye protection (face shield or goggles) [ ] . airborne precautions (n respirator) should be employed if the patient is critically ill and/or if an aerosol-generating procedure is anticipated during transport. ideally, transport vehicles with isolated compartments or high efficiency particulate air (hepa) filtration should be used, and the patient should be transferred directly to a treatment room on arrival at the receiving healthcare facility [ ] . after the patient has been transported and ems documentation is being completed, patient compartment doors should be left open to allow proper ventilation [ ] . when cleaning the vehicle, disposable gown, gloves, surgical mask, and face shield should be worn [ ] . routine cleaning should be followed by application of a hospital-grade disinfectant, preferably one approved by the u.s. environmental protection agency (epa) for use against emerging viral pathogens including sars-cov- [ ] . patients presenting with symptoms concerning for covid- to the ed should be separated from other patients by at least ft or m and asked to wear a facemask [ , ] . ideally, stable covid- puis would be identified at time of check-in or triage and then placed in a private room with the door closed [ , ] . critically ill patients and those requiring aerosol-generating procedures should be placed in an airborne infection isolation room (aiir), also known as a negative pressure isolation room, with hepa filtration of the recirculated air [ , ] . once a pui is identified, the appropriate health department or agency and institutional personnel should be notified in an expeditious manner [ , ] . movement into and out of the patient's treatment room should be limited to only essential hcps involved in patient care [ ] . while in the room, the pui may remove their facemask [ ] . however, it is reasonable to ask the patient to wear a facemask during interactions with hcps (e.g., performing a physical examination) in the room as tolerated to contain respiratory droplets generated from coughing. hcps should either use alcohol-based hand sanitizer or wash their hands with soap and water before and after contact with a covid- pui [ , ] . they should be trained in the appropriate use of ppe per hospital guidelines, including techniques to safely doff equipment protecting mucous membranes [ ] . when caring for a stable pui, hcps should adhere to droplet (surgical mask), contact (gown and gloves), and standard precautions with the addition of eye protection (face shield or goggles) [ , , , , ] . if a pui is critically ill or an aerosol-generating procedure (e.g., endotracheal intubation, suctioning of the airway, sputum induction) is necessary, hcps should escalate to airborne precautions with the use of a fitted n respirator in place of a surgical mask [ , , ] . reusable respirators such as powered air purifying respirators (paprs) may also be used, but should be disinfected and maintained appropriately [ ] . patients with a history of covid- exposure presenting with non-infectious symptoms may be evaluated and treated in adherence to standard precautions alone [ ] . if portable studies (e.g., plain radiography) cannot be completed within the patient's room or the patient requires transport elsewhere within the ed or hospital by wheelchair or stretcher, hcps should don appropriate ppe [ , ] . healthcare professionals at the destination or receiving location should be made aware of the patient's arrival and likewise don appropriate ppe [ , ] . patients leaving their treatment room should wear a facemask, be dressed in a clean hospital gown (when possible), perform hand hygiene, and be educated in proper respiratory hygiene [ ] . personnel cleaning empty pui rooms should follow droplet, contact, and standard precautions with eye protection as infectious particles may be present [ ] . it is unclear how long sars-cov- remains in the air, but drawing parallels from other airborne disease such as tuberculosis can be helpful, particularly if an aerosol-generating procedure has been performed [ ] . frequently used surfaces should be cleaned at least twice daily with implementation of standard institutional cleaning procedures [ ] . intubation is a high-risk procedure due to the aerosolization of respiratory droplets [ , ] . rescue intubations should be avoided whenever possible as complete adherence to ppe may be inadequate in a timesensitive critical scenario [ ] . society of critical care medicine (sccm) surviving sepsis covid- guidelines recommend performing endotracheal intubation under airborne precautions, including use of a fitted n respirator and placement of the patient in an aiir [ ] . based on prior cases of hcps infected with sars-cov- while using n respirators, some experts recommend using a papr [ ] . the most experienced provider should intubate [ , ] . to reduce inadvertent contamination by touching one's face or hair, a full face shield and head cover is recommended if a papr is not used [ , ] . wrist exposure can be minimized by using longer-sleeved gloves or vertically taping gloves to the gown [ ] . applying tape circumferentially makes removing ppe more difficult and does not have added benefit [ ] . shoe covers should be avoided, as they can lead to accidental selfcontamination. instead, impermeable shoes that can be appropriately decontaminated should be worn [ ] . if available, coveralls with or without a hood may be used, but processes and training in safe doffing should be established beforehand as hcps may be less experienced in using these ppe ensembles [ ] . in order to inform decisions related to infection control. . other symptomatic individuals such as, older adults and individuals with chronic medical conditions and/or an immunocompromised state that may put them at higher risk for poor outcomes (e.g., diabetes, heart disease, receiving immunosuppressive medications, chronic lung disease, chronic kidney disease). . any persons including healthcare personnel a , who within days of symptom onset had close contact b with a suspect or laboratory-confirmed c covid- patient, or who have a history of travel from affected geographic areas d within days of their symptom onset. notes: a for healthcare personnel, testing may be considered if there has been exposure to a person with suspected covid- without laboratory confirmation. because of their often extensive and close contact with vulnerable patients in healthcare settings, even mild signs and symptoms (e.g., sore throat) of covid- should be evaluated among potentially exposed healthcare personnel. hcps may consider double gloving and positioning waste and other transport receptacles close by to limit droplet and/or contact transmission when securing contaminated equipment for disposal or reprocessing [ ] . preoxygenation should be optimized with nonaerosol generating strategies including head of bed elevation, jaw thrust, and use of positive end expiratory pressure valves. fiberoptic laryngoscopy should be avoided unless absolutely necessary as atomization of anesthetic will cause the virus to become aerosolized [ ] . preoxygenation for at least min with % oxygen before performing rapid sequence intubation (rsi) may be used with nasal cannula, though this may increase the risk of contamination [ , ] . to reduce this risk, a surgical mask can be placed on the patient over the device. non-invasive positive pressure ventilation (nippv) may increase risk of aerosolization and is not recommended for preoxygenation [ , ] . a high efficiency hydrophobic filter should be used between the facemask and the rest of the respiratory circuit [ ] . video laryngoscopy is preferred to direct laryngoscopy to increase distance between the intubator and the patient [ , ] . a closed system should be utilized for suctioning. once the intubation is complete, the emergency physician should immediately place the laryngoscope in their outer glove along with all other equipment used for intubation in a double ziplocked plastic bag [ ] . the presence of a high-efficiency particulate air (hepa) filter should be verified in the expiratory limb of the mechanical ventilator prior to patient use. the cdc has developed a real time reverse transcription polymerase chain reaction (rt-pcr) assay for detecting sars-cov- in upper and lower respiratory specimens obtained from covid- puis [ ] . [ ] a nasopharyngeal swab specimen should be collected for testing [ ] . for lower respiratory tract specimens, sputum can be obtained from patients with productive cough, otherwise bronchoalveolar lavage or tracheal aspirate can be substituted [ ] . serum samples are not necessary [ , ] . there are few data available regarding sensitivity and specificity for the test, but false negatives may be seen in asymptomatic individuals or those early in the course of their disease who may not have high viral burden [ ] . patients who test negative for covid- using a sample taken while they were symptomatic likely do not have the disease [ ] . however, the sensitivity of rt-pcr has been reported to range from % to % [ ] . a single negative rt-pcr should not be used to exclude the diagnosis, especially if the patient is in the early stages of the disease with no severe symptoms. a patient with negative rt-pcr with continued suspicion of covid- should be isolated and rechecked several days later. molecular testing (e.g., respiratory virus panel) for alternative diagnoses such as influenza should be considered for all puis [ ] . however, co-infection with other viruses may occur. anemia, lymphopenia, hypoxemia, abnormal kidney and liver function, elevated creatine kinase and d-dimer, thrombocytopenia, and increased lactate dehydrogenase can be present [ , , ] . lymphocytopenia can occur in up to % of patients [ ] . interestingly, one study found procalcitonin was elevated in just % of patients, while other inflammatory markers like serum ferritin and c-reactive protein were elevated [ ] . troponin and brain natriuretic peptide may be elevated in those with cardiac involvement and should be obtained in patients with suspected myocardial infarction or heart failure [ ] . advanced imaging such as computed tomography (ct) is not required for diagnosis and may create additional infection prevention challenges in the ed. however, if obtained, ct may demonstrate several findings. lung findings may be present on imaging before patients develop clinical manifestations. in a case series of patients from wuhan, china admitted with covid- , % had chest ct findings consistent with pneumonia [ ] . patients may also have radiographic groundglass opacities [ ] . another study of covid- patients found % of patients had bilateral pneumonia, % had unilateral pneumonia, and % had mottling and ground-glass opacities on chest x-ray and ct imaging [ ] . ultrasound can be utilized as well, as it is repeatable and reliable, has no radiation, and is inexpensive. ultrasound findings depend on the stage and severity of the disease, and it cannot detect lesions deeper in the lung. patients with covid- typically demonstrate an irregular/thickened pleural line, scattered/confluent b lines, consolidations of various sizes, and both non-translobar and translobar consolidations on lung ultrasound [ ] . pleural effusions are typically small and localized if they are present, and abnormalities are typically found in multiple lung zones. currently, no specific treatments exist nor are recommended for patients with covid- [ , , ] . several vaccines are under study, including dna-based, vector-based, and protein based vaccines [ ] . supportive care is the mainstay of treatment, preferably with acetaminophen [ , ] . if pneumonia is present on imaging or the patient is critically ill, antibiotics are recommended. patients presenting with respiratory insufficiency in the setting of potential covid- infection should be given supplementary oxygen to maintain an oxygenation saturation ≥ % but no higher than % [ , ] . up to % of patients require oxygen therapy [ ] . for those with acute hypoxemic respiratory failure who require intubation, endotracheal intubation should be performed. for those with hypoxemic respiratory failure who do not require intubation but who do not improve with conventional oxygen therapies, high flow nasal cannula (hfnc) is recommended over noninvasive positive pressure ventilation (nippv) [ ] . if hfnc is not available and there is no urgent need for intubation, a trial of nippv ventilation is recommended with frequent reassessment, though nippv increases the risk of aerosolization [ ] . nippv may result in patient improvement. the sccm does not make a clear recommendation for helmet nippv compared to mask nippv [ ] . while most recommend avoiding nippv due to the risk of aerosolization, it can be utilized safely if high risk patients are cohorted and clinicians use appropriate ppe [ ] . patients who decline despite use of hfnc or nippv should be intubated [ ] . if intubation is indicated, airborne precautions should be used with the patient ventilated using tidal volumes of - ml/kg of predicted body weight and plateau pressures b cm h o [ ] . if available, patients with severe ards may benefit from prone ventilation n h per day [ , ] . over-resuscitation with intravenous fluids should be avoided, which can potentially worsen oxygenation [ ] . even when covid- is suspected as the cause of the patient's symptoms, the who recommends administering empiric antibiotics and a neuraminidase inhibitor within h of identifying sepsis [ ] . early recognition of septic shock is critical, with management of sepsis focusing on intravenous fluid resuscitation and antibiotics [ ] . a conservative resuscitation strategy with buffered/balanced crystalloids is recommended for those in shock, and hypotonic crystalloids should be avoided [ , ] . vasopressors, preferentially norepinephrine, are indicated for persistent shock with a goal map of - mmhg [ , ] . for those with continued shock despite norepinephrine, vasopressin should be added, rather than increasing norepinephrine dose [ ] . if cardiac dysfunction is present and there is persistent hypoperfusion, dobutamine is recommended [ ] . systemic steroids (hydrocortisone mg per day) should be considered in those with vasopressor-refractory shock or for those with another indication for steroids such as chronic obstructive pulmonary disease exacerbation [ , , ] . without delaying antibiotic administration, bacterial blood cultures should be obtained [ ] . clinical trials of investigational drugs and antivirals are underway, although none are currently approved by the u.s. food and drug administration (fda) ( table ) [ , ] . remdesivir has demonstrated activity against mers-cov and sars-cov in vitro and animal models [ , ] . an in vitro study found that remdesivir and chloroquine inhibit viral infection, but further study is required [ , ] . results from a single study of over covid- patients found chloroquine was superior to control in reducing pneumonia exacerbation, improving imaging findings and virus-negative conversion, and shortening the course of the disease [ ] . a study evaluating lopinavir-ritonavir found no improvement in patient survival or differences in detectable viral rna [ ] . hydroxychloroquine and azithromycin are also under study [ ] . in a single prospective, observational study of patients with covid- , those receiving hydroxychloroquine demonstrated higher rates of viral load reduction/disappearance, though no patient centered outcomes were assessed [ ] . other medications under study include tocilizumab and favipiravir [ , ] . there are no clear data supporting harm or benefit with angiotensin converting enzyme inhibitors or ace receptor blockers (arbs) [ , ] . unless authorized through a clinically approved trial or monitored emergency use of unregistered interventions framework (meuri), unlicensed treatments should not be administered [ ] . continuous renal replacement therapy (crrt), extracorporeal membrane oxygenation (ecmo), and immunoglobulin have been utilized for management, but have not been definitively shown to be beneficial [ ] . patients with severe symptoms, hypoxemia requiring oxygen supplementation, or high risk for clinical deterioration (i.e. pneumonia on radiograph, severe comorbidities) may require admission for further management and monitoring. patients with mild symptoms and no significant comorbidities without concern for deterioration of clinical condition may be candidates for discharge, self-quarantine for two weeks, and home monitoring [ ] . these patients must have the ability to be safely isolated at home to prevent transmission to others and be carefully monitored [ ] . social distancing is a vital component of reducing the spread of the virus, comprised of limiting events, mass gatherings, and even small group meeting [ ] . individuals should remain ft or meters apart from other individuals. health departments should be involved early in the care of these patients and can assist with decisions regarding disposition, further surveillance, and testing, especially until confirmatory test results are available [ , ] . emergency physicians should counsel these patients to return for worrisome symptoms including new or worsening pulmonary complaints and fever [ , ] . development of a clinical pathway among emergency physicians, infectious disease specialists, and health departments is critical to safely evaluate covid- puis in the community. covid- is a novel coronavirus that has affected an unprecedented number of people to date. patients typically present with a combination of fever or cough and have a history of exposure to either a close contact with covid- or travel to an affected geographic area. while most patients will have mild disease, some may develop severe complications including ards and multi-organ failure, with some succumbing to the disease. special consideration should be given to those at the extremes of age, the immunocompromised, or pregnant women. no curative treatment is currently approved. emergency physicians should obtain a detailed travel history from all patients and suspect covid- in patients presenting with symptoms of an acute upper respiratory illness and fever. early recognition and isolation of a patient with covid- in the ed may help decrease exposure to other patients and healthcare personnel. future research is necessary to expand our collective knowledge of covid- and optimize patient outcomes. none. author contributions sc, sl, ak, and bl conceived the idea for this manuscript and contributed substantially to the writing and editing of the review. none. statement on the second meeting of the international health regulations ( ) emergency committee regarding the outbreak of novel coronavirus world health organization. who director-general's opening remarks at the media briefing on covid- - world health organization. who director-general's remarks at the media briefing on -ncov on q&a on coronaviruses new images of novel coronavirus sars-cov- now available|nih: national institute of allergy and infectious diseases ovel coronavirus ( -ncov) frequently asked questions and answers naming the coronavirus disease (covid- ) and the virus that causes it a timeline of the coronavirus. the new york times chp closely monitors cluster of pneumonia cases on mainland coronavirus travel restrictions, across the globe. the new york times million people in china face travel restrictions over coronavirus outbreak novel coronavirus ( -ncov) situation summary novel coronavirus ( -ncov) prevention & treatment. centers for disease control and prevention the impact of a case of ebola virus disease on emergency department visits in metropolitan dallas-fort worth ebola virus disease: preparedness and infection control lessons learned from two biocontainment units inform: emergency department evaluation and management for patients under investigation (puis) for ebola virus disease (evd)|emergency services|clinicians|ebola (ebola virus disease early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia covid- ) covid- ). date novel coronavirus ( -ncov) transmission. centers for disease control and prevention general's remarks at the media briefing on covid- outbreak on february world health organization novel coronavirus ( -ncov) cases in the u.s. centers for disease control and prevention transcript for cdc media telebriefing sars-cov- viral load in upper eespiratory specimens of infected patients presumed asymptomatic carrier transmission of covid- practical recommendations for critical care and anesthesiology teams caring for novel coronavirus ( -ncov) patients. can j anesth can anesth covid- -new insights on a rapidly changing epidemic pattern of early human-to-human transmission of wuhan how does the new coronavirus compare with the flu? livescience the epidemiological characteristics of an outbreak of novel coronavirus diseases (covid- ) -china more outbreak details emerge as covid- cases top , facts vs. fears: five things to help weigh your coronavirus risk report : estimating the potential total number of novel coronavirus cases in wuhan city report : severity of -novel coronavirus (ncov) clinical features of patients infected with novel coronavirus in wuhan epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study mortality, morbidity, and hospitalisations due to influenza lower respiratory tract infections, : an analysis for the global burden of disease study novel coronavirus ( -ncov) symptoms clinical diagnosis of samples with -novel coronavirus in wuhan higher co-infection rates in covid novel coronavirus ( -ncov) clinical care novel coronavirus ( -ncov) pregnant women what are the risks of covid- infection in pregnant women? infectious agents -niosh workplace safety and health topic intubation of sars patients: infection and perspectives of healthcare workers clinical features and short-term outcomes of patients with sars in the greater toronto area the occupational risk of influenza a (h n ) infection among healthcare personnel during the pandemic: a systematic review and meta-analysis of observational studies american college of emergency physicians. two emergency physicians in critical condition er doctors at rush oak park hospital test positive for coronavirus. nbc chic italy has a world-class health system. the coronavirus has pushed it to the breaking point doctors: covid- pushing italian icus toward collapse novel coronavirus ( -ncov) flowchart for healthcare professionals a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster clinical characteristics of coronavirus disease in china clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical characteristics of covid- patients with digestive symptoms in hubei, china: a descriptive, cross-sectional, multicenter study clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected covid- ) interim infection prevention and control recommendations novel coronavirus ( -ncov) healthcare infection prevention and control faqs for covid- covid- : what is next for public health? covid- ): evaluating and testing persons for coronavirus disease (covid- ) novel coronavirus ( -ncov) evaluating and reporting pui covid- ) interim guidance for emergency medical services (ems) systems and public safety answering points (psaps) for covid- in the united states novel coronavirus ( -ncov) infection control surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease infection prevention and control for coronavirus disease (covid- ): interim guidance for acute healthcare settings anesthesia patient safety foundation novel coronavirus ( -ncov) testing novel coronavirus ( -ncov) information for laboratories covid- requests for diagnostic panels and virus covid- ) interim guidelines for collecting, handling, and testing clinical specimens from persons under investigation (puis) for coronavirus disease (covid- ) detection of sars-cov- in different types of clinical specimens correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases. radiology troponin and bnp use in covid- . latest in cardiology. http% a% f% fwww.acc.org% flatest-in-cardiology% farticles% f % f % f % f % f % ftroponin-and-bnp-use-in-covid findings of lung ultrasonography of novel corona virus pneumonia during the - epidemic. intensive care med world health organization. draft landscape of covid- candidate vaccines episode -covid- update. an interview with andrea duca, md. ebmedicine the antiviral compound remdesivir potently inhibits rna-dependent rna polymerase from middle east respiratory syndrome coronavirus compounds with therapeutic potential against novel respiratory coronavirus remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro drug treatment options for the -new coronavirus ( -ncov) breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies a trial of lopinavir-ritonavir in adults hospitalized with severe covid- hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial tocilizumab vs crrt in management of cytokine release syndrome (crs) in covid- (tacos) favipiravir combined with tocilizumab in the treatment of corona virus disease angiotensin-converting enzyme (ace ) as a sars-cov- receptor: molecular mechanisms and potential therapeutic target are patients with hypertension and diabetes mellitus at increased risk for covid- infection? home care for patients with suspected novel coronavirus (ncov) infection presenting with mild symptoms and management of contacts covid- ): interim us guidance for risk assessment and public health management of persons with potential coronavirus disease (covid- ) exposures: geographic risk and contacts of laboratory-confirmed cases this manuscript did not utilize any grants, and it has not been presented in abstract form. this clinical review has not been published, it is not under consideration for publication elsewhere, its publication is approved by all authors and tacitly or explicitly by the responsible authorities where the work was carried out, and that, if accepted, it will not be published elsewhere in the same form, in english or in any other language, including electronically without the written consent of the copyright-holder. this review does not reflect the views or opinions of the u.s. government, department of defense, u.s. army, u.s. air force, brooke army medical center, or saushec em residency program. key: cord- -yxqbe dj authors: ren, yunzhao r.; golding, amit; sorbello, alfred; ji, ping; chen, jianmeng; bhawana, saluja; witzmann, kimberly; arya, vikram; reynolds, kellie s.; choi, su‐young; nikolov, nikolay; sahajwalla, chandrahas title: a comprehensive updated review on sars‐cov‐ and covid‐ date: - - journal: j clin pharmacol doi: . /jcph. sha: doc_id: cord_uid: yxqbe dj this literature review aims to provide a comprehensive current summary of the pathogenesis, clinical features, disease course, host immune responses, and current investigational antiviral and immunomodulatory pharmacotherapies, in order to facilitate the development of future therapies and measures for prevention and control. this article is protected by copyright. all rights reserved the disease name -covid- ‖ and the associated virus name -sars-cov- ‖ were coined by the world health organization (who) and the coronavirus study group of the international committee on virus taxonomy, respectively, on february , . currently no specific drug has been approved by the fda for treating covid- , and the current management of patients is mainly supportive. fda has issued only emergency use authorizations (eua) to permit the emergency use of chloroquine phosphate, hydroxychloroquine sulfate, and remdesivir. therapeutic development for covid- includes repurposing existing medications and developing investigational candidates. the first reported confirmed covid- case was presented as atypical pneumonia on december , in wuhan, china. the patient was among a cluster of cases reported to who on january , . as of may , , sars-cov- has infected over . million people worldwide . covid- had resulted in a global death toll of more than , . an epidemiology study noted that of , confirmed covid- cases in china through february , . % and . % of patients were in severe and critical condition, respectively . the reported median incubation period of covid- is days , and the median period from symptom onset to hospital admission ranges from to days , . median time from onset of the first symptom to dyspnea is - days , ; to pneumonia, days ; to icu admission, days ; and to acute respiratory distress syndrome (ards), days . the median duration of hospitalization is days to days ; median length of icu stay, days ; median time from admission to invasive mechanical ventilation, . days ; and median time from admission to death was . days . the currently estimated reproductive number (r ) of sars-cov- , the average number of people to which one infected individual will pass the virus, ranges from . to . [ ] [ ] [ ] , whereas the reported r for sars-cov is approximately . sars-cov- is an airborne virus which can be transmitted by aerosol . a hospital survey detected the maximum transmission distance of sars-cov- aerosol might be meters from the covid- patients . in the contaminated area of the hospital, the viral nucleic acid positive rate was % for computer mice, % for floor swabs, % for trash cans, % for sickbed handrails, and % for doorknobs. in a virus viability test, authors used a nebulizer to generate artificial aerosols with small particle size (< μm) containing sars-cov- . the results showed that sars-cov- remained viable in the artificial aerosols for at least hours. the virus is most stable on plastic and stainless steel surfaces, on which viable virus had been detected for up to hours. no viable virus was detected after hours on copper and after hours on cardboard. the who, therefore, advises the public not to touch their eyes, nose, or mouth with their hands to limit self-contamination . in addition, the centers for disease control and prevention (cdc) recommends wearing cloth face coverings in public settings where other social distancing measures ( feet) are difficult to maintain . a case study reported that of passengers on a coach bus contracted the virus from an infected patient who did not wear a protective face mask. however, the same patient bought a mask and wore it before transferring to a mini-bus, and none of the passengers on the mini-bus contracted the virus . live sars-cov- was isolated from nasal/pharyngeal swabs and sputum, but not from stool, in patients with covid- . the live viral copies peaked during the early stage of symptom onset (≤ days); and could not be detected after day in samples from mild cases of infection. this discovery suggests that the viral transmission occurs primarily through the airborne route rather than the fecal-oral route during early stages of the disease. indeed, there have been sporadic case reports on the human-to-human transmission from asymptomatic or pre-symptomatic subjects [ ] [ ] [ ] . one study estimated that the transmissibility of the asymptomatic cases is comparable to that of symptomatic cases . an epidemiology report from china indicated that . % ( ) of , tested/suspected/diagnosed cases were asymptomatic . identification and isolation of asymptomatic subjects has helped reduce the pandemic in an italian village . these reports suggest that a panpopulation screening for viral exposure is an effective way to critically contain the spread of the disease. two meteorology models consistently found that higher relative humidity favored sars-cov- transmission , . the two models differed regarding the trend of temperature effect on viral transmission, probably due to the different ranges of temperature studied in china (winter) and brazil (autumn). an epidemiology study from china found that although the proportion of male patients ( . %) was comparable to that of females ( . %), male patients ( . %) comprised almost two-thirds of the total deaths . data from the cdc website as of may , showed that among approximately , covid- cases in the u.s., % were in children (< years old); % were in the elderly (≥ years old), and most ( %) were in patients between and years old . of hospitalized patients in u.s. states from march - , ( %) were non-hispanic white; ( . %) were non-hispanic black; ( . %) were hispanic; ( . %) were asian, two ( . %) were american indian/alaskan native, and ( . %) were of other ethnic origins or unknown . culture of bronchoalveolar lavage fluid collected from early wuhan cases identified the etiology of the virus to date, the virus phylogenetically closest to sars-cov- by genetic homogeneity is a coronavirus isolated from the horseshoe bat (bat cov ratg ) with an overall genome sequence identity of . %, which is higher than that of sars-cov (< %) . angiotensinconverting enzyme (ace ) was identified as a shared receptor required for cell entry both for sars-cov and sars-cov- , with higher binding affinity for sars-cov- . sequence comparison of spike (s) protein, the viral ligand of ace , identified three short insertions located at the n-terminus region that are conserved in sars-cov- and bat cov ratg , but not in sars-cov . examination of the receptor-binding domain (rbd) of s protein surprisingly identified that a malayan pangolin coronavirus had a higher degree of similarity ( . %) than bat cov ratg ( . %), indicating that recombination may have occurred during the evolution of sars-cov- . variation analysis based on sequences of sars-cov- up to february revealed very high homology (> . %) among different strains . another group estimated that the evolution rate of sars-cov- is approximately . × - per base per year , which indicates that sars-cov- transmission in humans is a recent event. the sars-cov- genome sequence can be found at https://www.ncbi.nlm.nih.gov/genbank/sars-cov- -seqs/. the direct diagnosis of covid- requires detection of sars-cov- -specific rna from patients' samples. reverse transcription-polymerase chain reaction (rt-pcr) is the most widely used technique for diagnosis. a commercial rt-pcr test kit usually uses to pairs of primers detecting the different regions of sars-cov- genomic rna to increase the test specificity. the sensitivity of this method is not optimal. one paper noted that the sensitivity of rt-pcr ( %), even after % of patients had multiple tests, was lower than that of a ct scan ( %) . a test report of , wuhan cases with typical covid- symptoms and history of close patient contact demonstrated that the positive rate was about % for nasal and pharyngeal swabs, % for sputum samples, and % to % for bronchoalveolar lavage fluid . another study screened subjects in wuhan and found that the positive rate from nasopharyngeal swabs was . -fold higher than that of oropharyngeal swabs . interestingly, pharyngeal swab viral nucleic acid screening results of , patients between january and february from a hospital fever clinic in hunan province (a neighboring province of hubei) demonstrated that the positive rate of sars-cov- ( . %) was lower than that of influenza a ( . %) and influenza b ( . %) . it is unclear whether the lockdown status of hubei province or the sensitivity of the detection methods between different viruses contributed to the result. the disease course also affects viral nucleic acid detection results. one study closely followed throat swab samples or deep nasal cavity swab samples from hospitalized covid- patients and found that the positive rate was the highest ( %) within week since the symptom onset . however, the positive rate reduced to about one-third at week . similar results were obtained from another study, in which the positive rate of throat swabs from patients was > % when tested within - days since symptom onset, but decreased to < % on day , and < % after day . other than the traditional rt-pcr, other viral rna detecting methods such as loop-mediated isothermal amplification (lamp) were expeditiously developed and approved by the fda . the apparent advantage of lamp is the much shorter waiting time for the results (< minutes) compared to the traditional rt-pcr ( hours). crispr, the powerful gene editing technique, premiered in this pandemic and was also approved by fda, though the commercial kit requires an isothermal amplification step . reports on the relationship between viral load in respiratory tracts and disease severity showed conflicting results. one study (n= ) reported that the high viral load from a patient's respiratory tracts is moderately associated with a high murray score for acute lung injury and low pao /fio . the same study also reported that the high viral load is associated with high plasma angiotensin ii concentration. however, two other studies (n= and n= ) did not find significant differences in viral load between mild and severe cases , . one study demonstrated that the speed of viral clearance differs significantly in mild and severe cases . the average time of viral nucleic acid turning positive to negative was about days in mild cases and days in severe cases. in non-survivors, persistent viral rna was detected until death . however, another study with intensive testing was able to detect viral nucleic acid in throat/deep nasal cavity swab samples from of hospitalized patients with mild-to-moderate confirmed covid- weeks after symptom onset . sars-cov- was detected in the whole blood and serum , . more studies are needed to investigate the correlation between viremia with blood viral load and disease severity. patients on admission, and discovered that the cutoff of . µg/ml had a sensitivity of % and a specificity of % in predicting in-hospital mortality . higher levels of hypersensitive troponin i in patients with severe covid- (table ) indicates an association of sars-cov- infection and cardiomyopathy , . a review summarized that cardiovascular complications associated with covid- include myocardial injury, myocarditis, acute myocardial infarction, heart failure, dysrhythmias, and thromboembolic events two covid- -associated kawasaki disease cases were reported in a -month-old girl and a -year-old boy, respectively il- , il- , tnf-α and ifn-γ were found between the two groups. whether the age differences between the two groups also contributed to these observed differences is unclear. two rsv-infected children ( . %) and one sars-cov- -infected child ( . %) developed severe pneumonia. all children survived. various case reports, case series, retrospective and case-controlled studies of pregnant women with covid- presented clinical and laboratory data on maternal and neonatal manifestations and outcomes [ ] [ ] [ ] [ ] [ ] . reviews and analyses of published reports provided additional insights [ ] [ ] [ ] [ ] . most of the pregnant women in these studies and reports were in their third trimester, and many of their babies were delivered by caesarean section. in general, they experienced signs and symptoms of covid- much like those in non-pregnant women. no maternal deaths were reported. fetal distress, premature births, premature rupture of membranes, respiratory difficulties, and low birth weight were observed among some babies born to mothers with covid- , , . no definitive cases of vertical transmission of the sars coronavirus (sars-cov- ) from mother to fetus have been identified, although two highly suspect cases have been reported. wang and colleagues described a male infant delivered by emergency cesarean section to a -year-old woman with covid- confirmed by pharyngeal swab . the infant had a viral nucleic acid detected from pharyngeal swab approximately hours after birth. tests of the cord blood, placenta, and the mother's breast milk were negative for sars-cov- . both mother and infant recovered. alzamora and colleagues reported on a -year-old diabetic woman with covid- -induced respiratory failure whose neonate was positive for sars-cov- nucleic acid from nasopharyngeal swab hours after a cesarean section delivery . serologies for sars-cov- were negative for the mother and the baby at the time of delivery. the mother converted to seropositive status on postpartum day ; whereas the neonate, who had not been breastfed, remained seronegative at that time. in relation to neonatal survival, zhu and colleagues reported one neonatal death in which a male baby born to a mother with confirmed covid- developed refractory shock, gastric bleeding, multi-organ failure, and disseminated intravascular coagulation approximately days after birth three publications reported findings with inconsistent results from systematic reviews or meta-analyses. a systematic review by vardavas and nikitara found an association between smoking and covid- illness progression . emami and colleagues in a meta-analysis reported a high prevalence of smoking ( . %) in hospitalized patients with covid- . however, a meta-analysis by lippi and henry found no association between smoking and covid- , although they acknowledged the findings reported by liu above . the inconsistent results on smoking may be attributed to lack of data on smoking quantity and duration, small population size and/or few smokers in certain studies, and the presence of other concurrent comorbid conditions. future research should consider including documentation of nicotine exposures through vaping and ecigarettes. the scientific community recently has debated a possible therapeutic role for nicotine in treating covid- . some epidemiologic data has shown lower numbers of smokers among patients with covid- , indicating that nicotine may mediate the viral transmission by lowering ace levels , . a randomized clinical study is being planned in france to more formally assess if nicotine could reduce the risk of contracting the disease . an analysis of deceased patients with covid- revealed that deaths were due to complications directly related to the viral infection . among them, ards was most prevalent ( %), followed by myocardial injury ( %), liver injury ( %), and renal insufficiency ( %). multiple organ dysfunction syndrome occurred in % of cases. autopsy and biopsy of covid- cases have been sporadically reported. a report of complete autopsy in consecutive covid- -positive deaths ( males and females with median age of years) in germany found that half of the cases had coronary heart disease and a quarter of the cases had respiratory diseases (asthma/copd) . the cause of death was found within the lungs or the pulmonary vascular system in all cases. deep venous thrombosis was identified in of patients ( %) in whom venous thromboembolism was not suspected before death. pulmonary embolism was the direct cause of death in patients. the histopathology examination of lungs found diffuse alveolar damage in cases. the lesions included hyaline membranes, activated pneumocytes, microvascular thromboemboli, capillary congestion, and protein-enriched interstitial edema, which were consistent with ards diagnosis. however, another immunohistology investigation of lung tissues from covid- patients who died with respiratory failure found that the pattern of covid- pneumonitis was predominantly a pauci-inflammatory septal capillary injury with significant septal capillary mural and luminal fibrin deposition and permeation of the inter-alveolar septa by neutrophils without hallmarks of classic ards three clinical studies recorded the baseline cytokine plasma concentrations in , , and patients with covid- on admission or from initial tests. the median time from symptom onset to admission in these three papers was - days , days , and - days , respectively. however, the cytokine examination date from a fourth study may be even later , since the median time for blood sample collection in this paper was days since subjects were transferred to a designated hospital. one study reported that ifn-γ, tnf-α, il- β, and il- plasma concentrations in covid- patients were significantly higher compared to results from four healthy in addition to the consistent trend of lower lymphocyte counts observed in severe cases of covid- (table ) from different studies, total t cells, cd + t cells, and cd + t cells also were significantly lower in severe/critical covid- cases than in non-severe cases , , . subgroups of cd + t cells did not show significant proportion changes of cd ra + naïve t cells and cd ro + memory t cells between severe cases and moderate cases . however, the proportion of cd ra + regulatory t cells in severe cases ( . %) was only half the value of that in moderate cases ( . %). one study noted a slight improvement of mean t cell counts (including cd + or cd + subpopulations) in comparison to baseline values after - days of in-hospital treatment . the count improvement appears baselineproportional, regardless of disease severity. several published studies have observed features of cellular exhaustion in t cells analogous to that described for nk cells . in two related studies, the authors showed that healthy individuals could be distinguished from mild and severe covid- t cells; specifically, the severe group had much lower levels of non-exhausted (pd- -ctla- -tigit -) cd + t cells , . they also found that cd + t cells in covid- patients exhibit many aspects of exhaustion and reduced function, such as once in the cell, the virus is not killed or neutralized; instead, it may continue to replicate, and/or stimulate or kill the target cells, causing more inflammation and damage. of note is that ade is not necessarily associated with past humoral response to a related pathogen, such as dengue virus , and can occur during the primary humoral response when the neutralizing antibody is at a suboptimal level. this was documented in some severe cases following sars-cov infection , . in a study reporting patients with sars, the lung radiographic worsening of some severe cases was correlated with the time of igg seroconversion . the pattern is consistent with that of covid- , in which the disease in some severe cases suddenly worsened around one to two weeks , , when seroconversion of anti-sars-cov- occurred (around to days after the onset of the first symptom) . in addition, the recovered sars patients had higher and sustainable or steadily increasing levels of both anti-n antibody and anti-s neutralizing antibody since the seroconversion . however, the titer of anti-n antibody in the sras non-survivors was low, and the titer of anti-s antibody decreased rapidly approximately days after the peak, an observation much like that in some patients with severe cases of covid- . in vitro studies demonstrated that human anti-s serum enhanced sars-cov infection in human monocyte-derived macrophages (mdm) . the infection mechanism is very different from that of the ace -mediated, endosomal/lysosomaldependent pathway, and can be blocked by anti-fcγr ii antibody on april , the national institutes of health (nih) issued general treatment guidelines for covid- , with the recommendations based on scientific evidence and expert opinion. we do not intend to repeat the previously well-documented work in our review, but prefer to focus on two important topics: antiviral and immunomodulatory pharmacotherapies. because results from clinical trials currently are being generated at such a blazing pace, this review was up to date at the time it was written. siddiqi hk et al. many viral cellular adherence/endocytosis blocking reagents were proposed. the cellular infection mechanism of sars-cov- is believed to be the same as sars-cov, which is an ace -mediated, endosomal-dependent pathway. chloroquine and hydroxychloroquine were first identified through in vitro drug screening to reduce viral titers from the supernatant of infected cell cultures. the mechanism probably is through interference with viral entry/endocytosis by increasing the ph of the endosome . two series of open-label, non-randomized studies in france reported only one death in patients with relatively mild disease treated with hydroxychloroquine sulfate ( mg tid for days) and azithromycin ( mg on day followed by mg qd) , . the authors justified the use of azithromycin because it had been shown to be effective against zika and ebola viruses in vitro. of note is that azithromycin also prolongs the qt interval. based on limited scientific information, it is reasonable to believe that hcq may be an effective treatment. fda issued an eua on march to permit the emergency use of chloroquine phosphate and hydroxychloroquine sulfate supplied from the strategic national stockpile to treat adults and adolescents who weigh kg or more and are hospitalized with covid- for whom a clinical trial is not available, or participation is not feasible . it should be noted that the fda's typical process for eua is to review its circumstances and appropriateness periodically. the review would include regular assessments, based on additional information from the sponsor, regarding progress on the unapproved product's -or unapproved use of an approved product's-approval, licensure, or clearance. an observational study in patients from new york city did not find a significant difference in the rate of intubation or mortality between patients who received hydroxychloroquine and those did not o intravenous immunoglobulin (ivig) has been used to treat sars patients [ ] [ ] [ ] the covid- pandemic is still ongoing, and a long time may pass before we can fully grasp the complete picture of the pathogen's characteristics; including its vulnerabilities, which can be used to inform development of effective and efficient treatments. development of antiviral therapeutics, led by dna/rna polymerase and protease inhibitors, has been streamlined since their invention in combatting hiv. given worldwide extensive efforts, we are hopeful that anti-sars-cov- replication drugs will be discovered. it is unclear whether overreactive immune response and/or css play important roles in patients with severe covid- . however, some case reports suggest the efficacy of immunomodulatory agents in treating patients with severe covid- , which could pave the way for large-scale randomized, blinded, and controlled clinical trials. last, but not least, the antibody profiles and timelines in recovered covid- patients are encouraging. these should inform and guide the development of the ultimate antiviral weapon, the vaccine, for preventing covid- in the st century. symptom wang d et al. deng y et al. zhou f et al. wu j et al. deng y et al. zhou f et al. wu j et al. p≤ . counted as endocrine system disease counted as heart disease counted as coronary heart disease patients experienced severe acute respiratory syndrome the degree of severity at the time of admission using the american thoracic society guidelines for communityacquired pneumonia wang d et al. deng y et al. zhou f et al. wu j et al. parameter huang c et al. chen g et al. wang z et.al chen t et al. xu b et al. who. who director-general's remarks at the media briefing on -ncov on coronaviridae study group of the international committee on taxonomy of v. the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- who. novel coronavirus -china. available at clinical features of patients infected with novel coronavirus in wuhan novel coronavirus pneumonia emergency response epidemiology t clinical characteristics of coronavirus disease in china clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan clinical characteristics of fatal and recovered cases of coronavirus disease (covid- ) in wuhan, china: a retrospective study early antiviral treatment contributes to alleviate the severity and improve the prognosis of patients with novel coronavirus disease (covid- ) clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study pattern of early human-to-human transmission of wuhan preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a data-driven analysis in the early phase of the outbreak high contagiousness and rapid spread of severe acute respiratory syndrome coronavirus consensus document on theepidemiology of severe acuterespiratory syndrome (sars) transmission of covid- to health care personnel during exposures to a hospitalized patient aerosol and surface distribution of severe acute respiratory syndrome coronavirus in hospital wards aerosol and surface stability of sars-cov- as compared with sars-cov- use of cloth face coverings to help slow the spread of covid- covid- : face masks and human-to-human transmission. influenza other respir viruses virological assessment of hospitalized patients with covid- familial cluster of covid- infection from an asymptomatic asymptomatic and human-to-human transmission of sars-cov- in a -family cluster transmission of -ncov infection from an asymptomatic contact in germany the relative transmissibility of asymptomatic cases among close contacts characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention covid- : identifying and isolating asymptomatic people helped eliminate virus in italian village covid- transmission in mainland china is associated with temperature and humidity: a time-series analysis evidence that high temperatures and intermediate relative humidity might favor the spread of covid- in tropical climate: a case study for the most affected brazilian cities hospitalization rates and characteristics of patients hospitalized with laboratory-confirmed coronavirus disease -covid-net, states a novel coronavirus from patients with pneumonia in china a pneumonia outbreak associated with a new coronavirus of probable bat origin structure, function, and antigenicity of the sars-cov- spike glycoprotein identifying sars-cov- related coronaviruses in malayan pangolins the establishment of reference sequence for sars-cov- and variation analysis transmission dynamics and evolutionary history of -ncov correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases positive rate of rt-pcr detection of sars-cov- infection in cases from one hospital in comparison of nasopharyngeal and oropharyngeal swabs for sars-cov- detection in patients received tests with both specimens simultaneously laboratory data analysis of novel coronavirus (covid- ) screening in patients profile of rt-pcr for sars-cov- : a preliminary study from covid- patients profiling early humoral response to diagnose novel coronavirus disease (covid- ) assay techniques and test development for covid- diagnosis first crispr test for the coronavirus approved in the united states clinical and biochemical indexes from -ncov infected patients linked to viral loads and lung injury temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study viral dynamics of sars-cov- across a spectrum of disease severity in covid- molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes comparisons of viral shedding time of sars-cov- of different samples in icu and non-icu patients lack of dyspnea in patients with covid- : another neurological conundrum? the neuroinvasive potential of sars -cov may play a role in the respiratory failure of covid- patients olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (covid- ): a multicenter european study conjunctivitis can be the only presenting sign and symptom of covid- corona virus disease- (covid- ) presenting as conjunctivitis: atypically high-risk during a pandemic chilblains in children in the setting of covid- pandemic clustered cases of acral perniosis: clinical features, histopathology and relationship to covid- covid- in critically ill patients in the seattle region -case series central nervous system manifestations of covid- : a systematic review the use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease (covid- ): the perspectives of clinical immunologists from china complex immune dysregulation in covid- patients with severe respiratory failure cardiovascular disease, drug therapy, and mortality in covid- abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia incidence of thrombotic complications in critically ill icu patients with covid- prominent changes in blood coagulation of patients with sars-cov- infection analysis of coagulation parameters in patients with covid- in d-dimer levels on admission to predict in-hospital mortality in patients with covid- cardiovascular complications in covid- elevated troponin in patients with coronavirus disease : possible mechanisms a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury patients of covid- may benefit from sustained lopinavircombined regimen and the increase of eosinophil may predict the outcome of covid- progression clinical features of fatal cases of covid- from wuhan: a retrospective observational study abnormalities of peripheral blood system in patients with covid- in wenzhou, china chest ct findings in patients with corona virus disease and its relationship with clinical features chest ct findings in coronavirus disease- (covid- ): relationship to duration of infection novel coronavirus ( -ncov) pneumonia initial ct findings and temporal changes in patients with the novel coronavirus pneumonia ( -ncov): a study of patients in wuhan, china time course of lung changes on chest ct during recovery from novel coronavirus (covid- ) pneumonia epidemiology of covid- among children in china clinical characteristics of children with coronavirus disease clinical and epidemiological features of children with coronavirus disease (covid- ) in zhejiang, china: an observational cohort study covid- and kawasaki disease: novel virus and novel case. hosp pediatr incomplete kawasaki disease in a child with covid- . indian pediatr hyperinflammatory shock in children during covid- pandemic. lancet. . . department nh. health alert # :pediatric multi-system inflammatory syndromepotentially associated with covid- the profile of peripheral blood lymphocyte subsets and serum cytokines in children with novel coronavirus pneumonia clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records clinical features and obstetric and neonatal outcomes of pregnant patients with covid- in wuhan, china: a retrospective, single-centre, descriptive study infants born to mothers with a new coronavirus (covid- ). front pediatr clinical features and outcomes of pregnant women suspected of coronavirus disease maternal and neonatal outcomes of pregnant women with covid- pneumonia: a case-control study risks of novel coronavirus disease (covid- ) in pregnancy; a narrative review an analysis of pregnant women with covid- , their newborn infants, and maternal-fetal transmission of sars-cov- : maternal coronavirus infections and pregnancy outcomes vertical transmission of coronavirus disease (covid- ) from infected pregnant mothers to neonates: a review maternal and perinatal outcomes with covid- : a systematic review of pregnancies clinical analysis of neonates born to mothers with -ncov pneumonia a case report of neonatal covid- infection in china severe covid- during pregnancy and possible vertical transmission coronaviruses and immunosuppressed patients. the facts during the third epidemic clinical course of covid- in a series of patients with chronic arthritis treated with immunosuppressive targeted therapies successful recovery of covid- pneumonia in a renal transplant recipient with long-term immunosuppression case report of covid- in a kidney transplant recipient: does immunosuppression alter the clinical presentation? covid- in post-transplantation patients-report of two cases successful treatment of severe covid- pneumonia in a liver transplant recipient covid- clinical guidance for adult patients with rheumatic diseases guidance for patients covid- outbreak nicotine and the renin-angiotensin system smoking upregulates angiotensin-converting enzyme- receptor: a potential adhesion site for novel coronavirus sars-cov- (covid- ) analysis of factors associated with disease outcomes in hospitalized patients with novel coronavirus disease comorbidity and its impact on patients with covid- in china: a nationwide analysis clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical characteristics of patients infected with sars-cov- in wuhan covid- and smoking: a systematic review of the evidence prevalence of underlying diseases in hospitalized patients with covid- : a systematic review and meta-analysis active smoking is not associated with severity of coronavirus disease (covid- ) low rate of daily active tobacco smoking in patients with symptomatic covid- prevalence of current smoking and association with adverse outcome in hospitalized covid- patients: a systematic review and meta-analysis. preprints beyond smoking cessation: investigating medicinal nicotine to prevent and treat covid- analysis of deceased patients with covid- autopsy findings and venous thromboembolism in patients with covid- : a prospective cohort study complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases clinical and immunologic features in severe and moderate coronavirus disease clinical features of cases with coronavirus disease clinical characteristics of deceased patients with coronavirus disease : retrospective study functional exhaustion of antiviral lymphocytes in covid- patients suppressed t cell-mediated immunity in patients with covid- : a clinical retrospective study in wuhan the nkg a immune checkpoint -a new direction in cancer immunotherapy nkg a is a nk cell exhaustion checkpoint for hcv persistence elevated exhaustion levels and reduced functional diversity of t cells in peripheral blood may predict severe progression in covid- patients reduction and functional exhaustion of t cells in patients with coronavirus disease (covid- ) antibody responses to sars-cov- in patients of novel coronavirus disease interleukin- use in covid- pneumonia related macrophage activation syndrome on the alert for cytokine storm: immunopathology in covid- . arthritis rheumatol hemophagocytic syndromes--an update ifn-gamma and cd drive distinct pathologic features during hemophagocytic lymphohistiocytosis interleukin- in biology and medicine immunotherapeutic implications of il- blockade for cytokine storm il- : a multifunctional cytokine in viral infections the roles of interleukin- and interleukin- in b cell hyperactivity in systemic lupus erythematosus interleukin- (il- ) and monocyte chemotactic and activating factor (mcaf/mcp- ), chemokines essentially involved in inflammatory and immune reactions plasma ip- and mcp- levels are highly associated with disease severity and predict the progression of covid- invited commentary: dengue lessons from cuba clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study antibody responses against sars coronavirus are correlated with disease outcome of infected individuals antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus anti-severe acute respiratory syndrome coronavirus spike antibodies trigger infection of human immune cells via a ph-and cysteine proteaseindependent fcgammar pathway anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection covid- ) treatment guidelines covid- : ibuprofen should not be used for managing symptoms, say doctors and scientists covid- : european drugs agency to review safety of ibuprofen renin-angiotensin-aldosterone system inhibitors and risk of covid- risks of ace inhibitor and arb usage in covid- : evaluating the evidence updated approaches against sars-cov- controversial treatments: an updated understanding of the coronavirus disease review of emerging pharmacotherapy for the treatment of coronavirus disease sars cov- : recent reports on antiviral therapies based on lopinavir/ritonavir, darunavir/umifenovir, hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirus covid- illnessin native and immunosuppressed states: a clinical-therapeutic staging proposal. the journal of heart and lung transplantation remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro insights from nanomedicine into chloroquine efficacy against covid- hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in covid- patients with at least a six-day follow up: a pilot observational study eua) of hydroxychloroquine sulfate supplied from the strategic national stockpile for treatment of covid- in certain hospitalized patients observational study of hydroxychloroquine in hospitalized patients with covid- effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus (sars-cov- ) infection: a randomized clinical trial assessment of qt intervals in a case series of patients with coronavirus disease (covid- ) infection treated with hydroxychloroquine alone or in combination with azithromycin in an intensive care unit risk of qt interval prolongation associated with use of hydroxychloroquine with or without concomitant azithromycin among hospitalized patients testing positive for coronavirus disease american heart association tacocathrs. caution recommended on covid- treatment with hydroxychloroquine and azithromycin for patients with cardiovascular disease detection of severe acute respiratory syndrome coronavirus in blood of infected patients therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in wuhan, china inhibition of sars-cov- (previously -ncov) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion a trial of lopinavir-ritonavir in adults hospitalized with severe covid- coronaviruses -drug discovery and therapeutic options crystal structure of sars-cov- main protease provides a basis for design of improved alpha-ketoamide inhibitors clinical trial shows remdesivir accelerates recovery from advanced covid- triple combination of interferon beta- b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with covid- : an open-label, randomised, phase trial asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus (sars-cov- ): facts and myths impact of corticosteroid therapy on outcomes of persons with sars-cov- , sars-cov, or mers-cov infection: a systematic review and meta-analysis covid- , cytokines and immunosuppression: what can we learn from severe acute respiratory syndrome? covid- : the new challenge for rheumatologists covid- : consider cytokine storm syndromes and immunosuppression first case of covid- in a patient with multiple myeloma successfully treated with tocilizumab tocilizumab, an anti-il receptor antibody, to treat covid- -related respiratory failure: a case report acute respiratory distress syndrome in critically ill patients with severe acute respiratory syndrome management of hospital-acquired severe acute respiratory syndrome with different disease spectrum effect of regular intravenous immunoglobulin therapy on prognosis of severe pneumonia in patients with covid- recent developments in the management of haemophagocytic lymphohistiocytosis high-dose intravenous immunoglobulin as a therapeutic option for deteriorating patients with coronavirus disease continuous intravenous anakinra infusion to calm the cytokine storm in macrophage activation syndrome. acr open rheumatol interleukin- blockade with high-dose anakinra in patients with covid- , acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study emapalumab for the treatment of relapsed/refractory hemophagocytic lymphohistiocytosis direct antiviral mechanisms of interferon-gamma plasma therapy against infectious pathogens, as of yesterday, today and tomorrow the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis treatment of critically ill patients with covid- with convalescent plasma guidance for industry: investigational covid- convalescent plasma we would like to thank joanne berger, fda library, and karen valentine, fda center for devices and radiological health, for editing the manuscript. procalcitonin (ng/ml) % vs. % , n/a % vs % key: cord- -d pb kik authors: cheval, sorin; mihai adamescu, cristian; georgiadis, teodoro; herrnegger, mathew; piticar, adrian; legates, david r. title: observed and potential impacts of the covid- pandemic on the environment date: - - journal: int j environ res public health doi: . /ijerph sha: doc_id: cord_uid: d pb kik various environmental factors influence the outbreak and spread of epidemic or even pandemic events which, in turn, may cause feedbacks on the environment. the novel coronavirus disease (covid- ) was declared a pandemic on march and its rapid onset, spatial extent and complex consequences make it a once-in-a-century global disaster. most countries responded by social distancing measures and severely diminished economic and other activities. consequently, by the end of april , the covid- pandemic has led to numerous environmental impacts, both positive such as enhanced air and water quality in urban areas, and negative, such as shoreline pollution due to the disposal of sanitary consumables. this study presents an early overview of the observed and potential impacts of the covid- on the environment. we argue that the effects of covid- are determined mainly by anthropogenic factors which are becoming obvious as human activity diminishes across the planet, and the impacts on cities and public health will be continued in the coming years. the earth is a dynamically changing planet, permanently shaped by socio-ecological interactions. variations and changes are common in a nonlinear and dynamic system such as our planet but passing certain thresholds may push the stability of the systems into a new regime which can have significant consequences at different spatial and temporal scales. understanding and early prediction of the impacts of such dramatic changes is a challenge for all sciences (including economics, social or medical sciences) but also for our society as a whole [ , ] . extreme variations in natural processes and phenomena, in many cases enhanced or even caused by human actions, generate hazards that lead to risks for both communities and the environment, and as a result, sometimes disasters occur. the concept of disaster has evolved over time, and here we use an adapted intergovernmental panel on climate change (ipcc) definition: a disaster is an event, which severely alters the functioning of a community due to hazardous physical, biological or human related impacts leading to widespread adverse effects on multiple scales and systems (environment, economic, social). immediate emergency the main cause of pandemic events and epidemic diseases is the close interaction between human populations with both domesticated and wildlife pathogens [ ] . most pathogens pass from wildlife reservoirs and enter into human populations through hunting and consumption of wild species, wild animal trade and other contact with wildlife. urban areas are especially vulnerable through the high population density and mobility. the covid- dwarfs the six previous large scale epidemics of the st century in terms of spatial extent and societal consequences [ ] , and it is the only pandemic with widespread and complex environmental impacts. we briefly present a few characteristics of the other large-scale epidemic events of the st century. a. the severe acute respiratory syndrome (sars) occurred in , leading to more than infections with a mortality rate of approximately % and an impact limited only to local and regional economies [ ] . the epidemic ended abruptly in july and no human cases of the sars coronavirus have been detected since. b. the h n influenza virus (swine flu) was a pandemic which first appeared in mexico and the united states in march and april of . it became a global pandemic as a result of global mobility and airline travel and led to an estimated . % case fatality [ ] . c. middle east respiratory syndrome (mers) was first identified in humans in saudi arabia and jordan in [ ] . mers is considered a zoonotic pathogen, with infected dromedary camels being the animal source of infection to humans [ , ] . by contrast to sars, which was contained within a year of emerging, mers continues to have a limited circulation and causes human disease with intermittent sporadic cases, community clusters and nosocomial outbreaks in the middle east region with a high risk of spreading globally [ ] . d. the ebola virus was first detected in in zaire (presently the democratic republic of congo). since the virus was first detected, over known outbreaks of ebola have been identified in sub-saharan africa, mostly in sudan, uganda, democratic republic of congo and gabon [ ] . at present, no vaccine or efficient antiviral management strategy exists for ebola [ ] . although the ebola virus has substantial epidemic and pandemic potential (due to the ease of international travel), as shown by the - west-african ebola virus epidemic with approximately , confirmed cases and , deaths [ , ] , ebola outbreaks have been geographically limited [ ] . e. the zika fever ( - ) was first isolated in from a febrile rhesus macaque monkey in the zika forest of uganda. since , when the first cases in humans were reported, the zika virus had only limited sporadic infections in africa and asia. however, a large outbreak with approximately , to , , cases spread from brazil to countries in the americas in [ ] . in november , who announced the end of the zika outbreak. f. avian flu (bird flu) was first reported in in hong kong with only infections and human deaths. more than cases of the avian flu have been reported from over countries [ ] of the reported outbreaks occurred in in china [ ] . in the absence of any effective treatments, sars-cov, mers-cov and sars coronaviruses are of very high societal concern since they could unexpectedly become a global pandemic at any time [ ] . as a result, coronaviruses in general have been studied to anticipate their societal and environmental impact. this has immediate application to the covid- virus. furthermore, [ ] summarizes relevant knowledge on the causative agent, pathogenesis and immune responses, epidemiology, diagnosis, treatment and management of the disease, control and prevention strategies of the covid- . a calendar of the covid- events potentially related to the environmental impacts is presented as list s . the development and spread of covid- under the control of environmental factors justify the scientific interest for the combined studies of coronaviruses on one side and socio-ecological systems (including the interplay between climate, water, soil) on the other side. the number of scientific publications examining such topics has constantly increased in recent decades, and the covid- pandemic strongly motivates the record ( figure ). saharan africa, mostly in sudan, uganda, democratic republic of congo and gabon [ ] . at present, no vaccine or efficient antiviral management strategy exists for ebola [ ] . although the ebola virus has substantial epidemic and pandemic potential (due to the ease of international travel), as shown by the - west-african ebola virus epidemic with approximately , confirmed cases and , deaths [ , ] , ebola outbreaks have been geographically limited [ ] . e. the zika fever ( - ) was first isolated in from a febrile rhesus macaque monkey in the zika forest of uganda. since , when the first cases in humans were reported, the zika virus had only limited sporadic infections in africa and asia. however, a large outbreak with approximately , to , , cases spread from brazil to countries in the americas in [ ] . in november , who announced the end of the zika outbreak. f. avian flu (bird flu) was first reported in in hong kong with only infections and human deaths. more than cases of the avian flu have been reported from over countries [ ] of the reported outbreaks occurred in in china [ ] . in the absence of any effective treatments, sars-cov, mers-cov and sars coronaviruses are of very high societal concern since they could unexpectedly become a global pandemic at any time [ ] . as a result, coronaviruses in general have been studied to anticipate their societal and environmental impact. this has immediate application to the covid- virus. furthermore, [ ] summarizes relevant knowledge on the causative agent, pathogenesis and immune responses, epidemiology, diagnosis, treatment and management of the disease, control and prevention strategies of the covid- . a calendar of the covid- events potentially related to the environmental impacts is presented as list s . the development and spread of covid- under the control of environmental factors justify the scientific interest for the combined studies of coronaviruses on one side and socio-ecological systems (including the interplay between climate, water, soil) on the other side. the number of scientific publications examining such topics has constantly increased in recent decades, and the covid- pandemic strongly motivates the record ( figure ). in general, temperature, humidity, wind and precipitation may favour either the spread or the inhibition of epidemic episodes. however, while some research found that local weather conditions of lowered temperature, mild diurnal temperature range and low humidity may favour the transmission [ ] , other studies claim there is no evidence that warmer weather can determine the decline of the case counts of covid- [ ] . increased ultraviolet light, as occurs particularly during the summer months, leads to inactivation of the coronaviruses and [ , ] analyse the subject comprehensively and find that warming weather is unlikely to stop the spread of the pandemic. to understand the relative importance between physical and social parameters that favour the spread of the virus, an area in which different health and social policies have been equally in general, temperature, humidity, wind and precipitation may favour either the spread or the inhibition of epidemic episodes. however, while some research found that local weather conditions of lowered temperature, mild diurnal temperature range and low humidity may favour the transmission [ ] , other studies claim there is no evidence that warmer weather can determine the decline of the case counts of covid- [ ] . increased ultraviolet light, as occurs particularly during the summer months, leads to inactivation of the coronaviruses and [ , ] analyse the subject comprehensively and find that warming weather is unlikely to stop the spread of the pandemic. to understand the relative importance between physical and social parameters that favour the spread of the virus, an area in which different health and social policies have been equally implemented on a variety of environmental and climatic conditions must be examined. italy is a viable experimental model to examine the impact of different health policies, as stated by the government authorities themselves [ , ] . in italy, the regionalization of public health has addressed the pandemic following completely different schemes from one region to another and represents an important test to verify the scientific hypotheses on the behaviour of sars-cov- . given that coronaviruses tend to spread in lowered temperatures and drier conditions during the winter months (i.e., during a period of reduced solar radiation), it is surprising that italy was the first european country severely affected by the pandemic and its hospitals were suddenly overrun. northern italy experienced a very dry and mild winter caused by the presence of a strong polar vortex. the winter of - was one of the driest winters in years (https://www.arpae.it/dettaglio_n otizia.asp?idlivello= &id= ). the impact on the social and economic structure of the country immediately gave rise to concerns about the potential transmission pathways of the virus and the spread at european scale. the impact of the covid- pandemic on the environment raised attention from the very beginning of the crisis, consisting of (a) observations and analysis of the immediate effects and (b) estimations related to long-term changes. qualitative assumptions prevail, while consistent quantitative research must wait for relevant data sets and additional knowledge. most facets of the environmental impact of the covid- pandemic have not directly resulted from the virus itself. the consequence of abruptly limiting or closing economic sectors, such as heavy industry, transport, or hospitality businesses, has affected the environment directly. moreover, the impact of the covid- pandemic on socio-ecological systems may be highly variable, from radical changes in individual lifestyle, society and international affairs [ ] , to simply facilitating a faster change than would normally have emerged [ ] . from an anthropocentric perspective, the pandemic may lead to a more sustainable future, including increased resilience of the socio-ecological systems or shorter supply chains, which is a positive development. however, it is still possible that some nations will opt for less sustainability by pursuing rapid economic growth and focusing less concern on the environment. while negative impacts on the economy and society in general are probably huge, it is very likely that the global-scale reduction of economic activities due to the covid- crisis triggers a lot of sensible improvements in environmental quality and climatic systems. however, not all the environmental consequences of the crisis have been or will be positive. this includes an increased volume of nonrecyclable waste, the generation of large quantities of organic waste due to diminish agricultural and fishery export levels and difficulties in maintenance and monitoring of natural ecosystems [ ] . the temporal resolution of the coronavirus impact ranges from immediate (days to weeks), short-term (months) and long-term (years), and different examples are provided in a matrix ( figure ). while the first impacts are divided between rapid environmental improvements, such as urban air and water quality, and pollution episodes, such as the ones caused by the sanitary disposals, the estimated short-and long-term impacts are mainly positive. impacts are rarely limited to a single physical system. however, for the sake of better inventory and understanding, the impact of the covid- on the physical systems focuses on the air, water and soil individually, with an emphasis on urban areas. large cities or megacities are often very centralized structures providing a certain degree of comfort and protection for the citizen, but they increase the exposure to specific threats. for example, the higher population densities favour higher exposure to hazards. in contrast to rural areas, where the population tends to have gardens, the effects of the lockdown conditions in cities showed more severe effects on the mental health of individuals living in close quarters. the covid- crisis is driving towards a new paradigm that brings urban policies closer to present and strengthens the future needs of urban population and public health. one of the key characteristics of the pandemic event in focus in this study is the spatial extent but also versatility of the scale of the impact. no other disaster has covered the whole planet with comparable intensities over so many urban areas with multifaceted threats that are challenging our cities during the crisis. air quality is highly sensitive to anthropogenic emissions. in the european economic area countries (eu, norway, liechtenstein and iceland), the energy used by industrial processes and the road transportation sector is responsible for about % of the nonmethane volatile organic compounds (nmvoc), % of the nox, % of pm . and % of sox emissions [ ] . the covid- crisis has caused severe impacts to the energy and resources, high-tech and communications, retail, manufacturing and transportation sectors, in terms of personnel, operations, supply chain and revenue [ ] . by mid-april, a % to % decline in economic activity was estimated as a result of the draconian disease-suppression policies, and severe multiquarter economic impacts in multiple markets became imminent [ ] . consequently, the impact on air quality was rapidly visible at various spatial scales. even as early as the end of march , reductions in air pollution were reported in china, italy and new york city, and sharp declines in global greenhouse-gas emissions have been predicted for the rest of the year [ ] . moreover, an overview focused on several european countries impacts are rarely limited to a single physical system. however, for the sake of better inventory and understanding, the impact of the covid- on the physical systems focuses on the air, water and soil individually, with an emphasis on urban areas. large cities or megacities are often very centralized structures providing a certain degree of comfort and protection for the citizen, but they increase the exposure to specific threats. for example, the higher population densities favour higher exposure to hazards. in contrast to rural areas, where the population tends to have gardens, the effects of the lockdown conditions in cities showed more severe effects on the mental health of individuals living in close quarters. the covid- crisis is driving towards a new paradigm that brings urban policies closer to present and strengthens the future needs of urban population and public health. one of the key characteristics of the pandemic event in focus in this study is the spatial extent but also versatility of the scale of the impact. no other disaster has covered the whole planet with comparable intensities over so many urban areas with multifaceted threats that are challenging our cities during the crisis. air quality is highly sensitive to anthropogenic emissions. in the european economic area countries (eu, norway, liechtenstein and iceland), the energy used by industrial processes and the road transportation sector is responsible for about % of the nonmethane volatile organic compounds (nmvoc), % of the no x , % of pm . and % of so x emissions [ ] . the covid- crisis has caused severe impacts to the energy and resources, high-tech and communications, retail, manufacturing and transportation sectors, in terms of personnel, operations, supply chain and revenue [ ] . by mid-april, a % to % decline in economic activity was estimated as a result of the draconian disease-suppression policies, and severe multiquarter economic impacts in multiple markets became imminent [ ] . consequently, the impact on air quality was rapidly visible at various spatial scales. even as early as the end of march , reductions in air pollution were reported in china, italy and new york city, and sharp declines in global greenhouse-gas emissions have been predicted for the rest of the year [ ] . moreover, an overview focused on several european countries reveals that the reduction of the weekly no , pm and pm . concentrations during march and april is quasigeneral ( figure s ). one possible cause of the impact of the pandemic in northern italy is that a high concentration of particulate matter (pm, including pm and pm . ) makes the respiratory system more susceptible to infection and complications of the coronavirus disease. higher and consistent exposure to pm (particularly for the elderly) leads to a higher probability that the respiratory system is compromised before the onset of the virus. this was a serious concern right after the publication of a position paper by sima (italian environmental medical society), where correlations were found between pollution levels and the spread of the virus [ ] . strong evidence exists on the greater predisposition of the respiratory system to serious diseases [ ] , but the hypothesis that pollutants can be a carrier for the virus in the free atmosphere seems very unlikely. the spread of droplets produced by sneezing or coughing is necessary so that high viral concentration and a lack of air circulation and exchange can be potentially very dangerous [ ] [ ] [ ] [ ] . the analysis of the demographic and economic characteristics of the two italian regions most affected by the pandemic help to understand that the spread of the virus is dependent on parameters other than simply air transport [ ] . the most affected regions are quite similar demographically; lombardy has a population density of per km while veneto has a density of per km and the average age of the populations is practically identical. economic indicators also reveal a gross domestic product of lombardy of , €/capita and veneto of , €/capita. the number of beds in the healthcare facilities for intensive care are nearly identical in the two regions, while there is a public health laboratory for every , , inhabitants in lombardy and for every , people in veneto. the healthcare structure is a very important aspect that explains the notable difference between the two regions, as the home care service for the elderly and disabled is more than double in veneto than in lombardy [ ] . for neighbouring regions with similar pollution levels, the infection rate is extremely uneven. thus, it appears unlikely that pm is a viable vector for the virus, but it does illustrate the concern over disparate regional healthcare systems. this also has an important impact on future exit strategies from the pandemic and on the use of personal protective equipment (ppe) as the virus may vector using healthcare workers [ ] . it is very likely that the italian case provides lessons for other european countries and validates the measures taken to limit the effects of the pandemic. as for the environmental impacts, physical and ecological systems have been affected in many places, as addressed and detailed in the next sections. the massive lockdowns of entire cities, economies, schools and social life for weeks led to unknown large-scale and extensive restrictions in mobility as a response to social distancing guidance related to covid- ( figure ). globally, largest reductions in mobility are visible for western and southern europe (e.g., spain- %, italy- %, france- %) and south america (e.g., bolivia- % or columbia- %). in south america, mobility in the period april to april showed a mean decrease of % compared to the -week period january- february . other continents showed a mean decrease of around %. south korea was the only country that showed a slight positive trend of + . % for the analysed period. the reason here is that the mobility trends for places like national parks, public beaches, marinas, dog parks, plazas, and public gardens increased significantly, although other mobility categories (e.g., workplaces, transit stations) showed a decrease. even if general mobility characteristics may vary by country and the period of strongest reductions in mobility may not be evident in april, figure shows the global picture of the effects of the covid- pandemic. in particular, one of the most hit sectors was the aviation that contributes about - % of global greenhouse gas emissions [ ] and about - % of global co emissions [ ] . between january and april , travel restrictions caused air traffic to decline by around % in the total number of flights and about % in the number of commercial flights ( figure ). the latest scenario of the international air transport association (iata) suggests that air traffic will fall by % for [ ] . even if the aviation sector returns to its pre-pandemic levels, % of the passengers indicate they will wait at least six months before returning to air travel. specifically, % indicate they will wait for their financial situation to stabilize [ ] . the strong decrease in both short-term and mid-term aviation travel will lead to a reduction in greenhouse gas emissions, particularly co . additionally, the reduction in contrails may increase the daily temperature range [ ] . the reduction of contrails will probably lead to a decrease in air temperature due to the decreasing greenhouse effect [ ] . in particular, one of the most hit sectors was the aviation that contributes about - % of global greenhouse gas emissions [ ] and about - % of global co emissions [ ] . between january and april , travel restrictions caused air traffic to decline by around % in the total number of flights and about % in the number of commercial flights ( figure ). the latest scenario of the international air transport association (iata) suggests that air traffic will fall by % for [ ] . even if the aviation sector returns to its pre-pandemic levels, % of the passengers indicate they will wait at least six months before returning to air travel. specifically, % indicate they will wait for their financial situation to stabilize [ ] . the strong decrease in both short-term and mid-term aviation travel will lead to a reduction in greenhouse gas emissions, particularly co . additionally, the reduction in contrails may increase the daily temperature range [ ] . the reduction of contrails will probably lead to a decrease in air temperature due to the decreasing greenhouse effect [ ] . in particular, one of the most hit sectors was the aviation that contributes about - % of global greenhouse gas emissions [ ] and about - % of global co emissions [ ] . between january and april , travel restrictions caused air traffic to decline by around % in the total number of flights and about % in the number of commercial flights ( figure ). the latest scenario of the international air transport association (iata) suggests that air traffic will fall by % for [ ] . even if the aviation sector returns to its pre-pandemic levels, % of the passengers indicate they will wait at least six months before returning to air travel. specifically, % indicate they will wait for their financial situation to stabilize [ ] . the strong decrease in both short-term and mid-term aviation travel will lead to a reduction in greenhouse gas emissions, particularly co . additionally, the reduction in contrails may increase the daily temperature range [ ] . the reduction of contrails will probably lead to a decrease in air temperature due to the decreasing greenhouse effect [ ] . regarding the transport sector, motor vehicles were responsible for % of the greenhouse gases emissions in austria, for example. this was the second largest source of greenhouse gas emissions in austria, behind the energy and industry sectors, which together contributed % [ ] . regarding the transport sector, motor vehicles were responsible for % of the greenhouse gases emissions in austria, for example. this was the second largest source of greenhouse gas emissions in austria, behind the energy and industry sectors, which together contributed % [ ] . regarding the transport sector, motor vehicles were responsible for % of the greenhouse gases emissions in austria, for example. this was the second largest source of greenhouse gas emissions in austria, behind the energy and industry sectors, which together contributed % [ ] . the covid- crisis has led to a substantial reduction in motor vehicle traffic with not only a reduction in greenhouse gas emissions and particulate pollution but also a major reduction in traffic noise and tire wear on road surfaces. in vienna, with a population of . million, car and truck traffic were reduced by % and %, respectively, between march and the first week of april [ ] . these reductions, extrapolated to similar urban areas in europe, have led to significantly improved air quality. in milan, average concentrations of no for the - march period was % lower than for the same week in . in bergamo, average concentrations of no in were % lower than in for the same week, and similar reduction of average no concentrations have been observed in other major cities (e.g., barcelona, %; madrid, %; lisbon, %) [ ] . data also show a reduction in the urban pm concentration. reduced concentrations of pm . in seoul (south korea) were % lower from february to march when compared to the same period in . los angeles (united states) observed its longest continuous period of clean air on record, lasting over days from march to . pm . concentration levels were lower by % from the same time last year and down % from the average of the previous four years (https://www.iqair. com/blog/air-quality/report-impact-of-covid- -on-global-air-quality-earth-day). for barcelona, [ ] reported approximately % reduction of no and black carbon, % decrease of pm and - % increase of o concentrations, very likely due to the lockdown of the city. however, the favourable role of meteorological conditions was also granted. well-known for its high level of pollution, milan is considering a shift from car traffic to pedestrian and bicycle over km of streets, as a result of the coronavirus crisis (https://www.theguardian.com/ world/ /apr/ /milan-seeks-to-prevent-post-crisis-return-of-traffic-pollution). milan launched on april a new strategy for adaptation asking for an open contribution from the population [ ] where it is clearly stated that the mission is to elaborate a new strategy to exit from pandemic, called phase . the objectives are to remake the city by accounting for problems faced during the pandemic. public transportation is one of the main foci along with the protections of elderly people. the immediate impact of the covid- pandemic on aquatic systems and water resources is very limited, but water quality and resources may be affected on monthly and annual perspectives. due to less boat traffic and tourist activities, venice waters cleared during the coronavirus lockdown of the city in march and april (figure ) . reference [ ] first detected the presence of the sars-cov- in sewage and indicated it as a sensitive tool to monitor the circulation of the virus. although the viral rna has been detected in wastewater, this does not necessarily imply a risk [ ], either to the public or to the environment. reference [ ] showed that coronaviruses die off rapidly in wastewater and are inactivated faster in warmer water (i.e., days in water at • c and > days in water at • c). disposal of sanitary consumables, such as ppe, is already creating concern about the impact of the pandemic event on water bodies. by may , many reports have claimed significant harm on the aquatic environment especially along the shorelines (e.g., in hong kong and canada) due to sanitary disposal resulting from medical activities or personal protection. the covid- crisis has and probably will exhibit longer-term impacts on water resources usage and management. the economic effects of the covid- pandemic, changes in national budgets and changes in funding priorities may lead to lack of funding for water related infrastructure and water utilities. the impacts of underfunding (e.g., increased forthcoming losses or lack of investments to improve efficiency) may only manifest after a few years. reference [ ] first detected the presence of the sars-cov- in sewage and indicated it as a sensitive tool to monitor the circulation of the virus. although the viral rna has been detected in wastewater, this does not necessarily imply a risk [ ], either to the public or to the environment. reference [ ] showed that coronaviruses die off rapidly in wastewater and are inactivated faster in warmer water (i.e., days in water at °c and > days in water at °c). disposal of sanitary consumables, such as ppe, is already creating concern about the impact of the pandemic event on water bodies. by may , many reports have claimed significant harm on the aquatic environment especially along the shorelines (e.g., in hong kong and canada) due to sanitary disposal resulting from medical activities or personal protection. the covid- crisis has and probably will exhibit longer-term impacts on water resources usage and management. the economic effects of the covid- pandemic, changes in national budgets and changes in funding priorities may lead to lack of funding for water related infrastructure and water utilities. the impacts of underfunding (e.g., increased forthcoming losses or lack of investments to improve efficiency) may only manifest after a few years. during lockdown conditions, water utilities from germany and austria report that the daily peak in water consumption in the morning is shifted by around . to h. generally, a dampening effect and a more even distribution in water consumption during the day is observed. regarding the amount of water consumed, increases as well as decreases of around % are reported. increases are explained by higher demands due to watering of gardens-surprisingly, not due to increased hand washing-and decreases by fewer commuters, students and pupils in supply areas [ ] [ ] [ ] [ ] [ ] . by contrast, municipalities with high touristic activity-a leading cause of water demand [ , ]-will exhibit important reduction in water consumption. reports from the strong tourism heritage of tirol, austria, suggest reductions in water consumption of up to % in municipalities where tourism plays an important role [ ] . depending on the return of tourism following the end of the pandemic, a noteworthy reduction of water demand and pressures on water resources can be expected. during lockdown conditions, water utilities from germany and austria report that the daily peak in water consumption in the morning is shifted by around . to h. generally, a dampening effect and a more even distribution in water consumption during the day is observed. regarding the amount of water consumed, increases as well as decreases of around % are reported. increases are explained by higher demands due to watering of gardens-surprisingly, not due to increased hand washing-and decreases by fewer commuters, students and pupils in supply areas [ ] [ ] [ ] [ ] [ ] . by contrast, municipalities with high touristic activity-a leading cause of water demand [ , ] -will exhibit important reduction in water consumption. reports from the strong tourism heritage of tirol, austria, suggest reductions in water consumption of up to % in municipalities where tourism plays an important role [ ] . depending on the return of tourism following the end of the pandemic, a noteworthy reduction of water demand and pressures on water resources can be expected. industrial water consumption, a generally poorly measured quantity, has certainly decreased. the longer-term impacts on water resources will depend on economic developments following the crisis. in comparison to domestic and industrial water demand, the highest pressures on water resources come from the agricultural sector. here, long-term forecasts will depend on the return of agriculture following the crisis, although short-term effects are probably visible in reduced irrigation demand. soil provides essential ecosystem services for human society, ranging from agricultural production to carbon sequestration, which are fundamental for several sustainable development goals (sdgs), such as "zero hunger" or "life on land" [ ] . the immediate impact of the pandemic or other similar disasters on the soil environment is linked with the increasing risks of food insecurity and disruption of the food supply chain. the persistence of sars-cov- on different surfaces is a key issue for successfully controlling its spread. reference [ ] found the viruses can remain viable on surfaces for several days. other studies investigated the survival of different viruses in soils and sediments [ ] . at present, there is no clear evidence about the role of the soil environment in hosting and transmission of the sars-cov- nor about the impact of this coronavirus on the soil surface, and calls for collecting eventual results have been issued [ ] . from an ecological perspective, the covid- crisis is fundamentally related to the relationships between society and ecosphere. while the origin in a wuhan wet market or industrial livestock or other source is not yet fully clarified [ ] , it is well known that mers-cov, sars-cov and sars-cov- are all animal coronaviruses which infected people and then succeeded to spread in different communities at large scale. around the globe more than . million people are dying from zoonosis in a year [ ] , but the impact is even greater as the zoonosis are also affecting human health, livestock sector and agriculture and usually the poorer human populations are more affected. the coronavirus crisis is most probably one of the many challenges our society will have to face in the forthcoming decades as an indirect consequence of the impact of climate change on the ecosphere through many mechanisms, including diminishing species habitats [ ] , changing species distributions [ ] and an increasing influx of alien invasive species [ ] . currently, economic development focuses on continuous growth without considering the conservation of natural systems. in a letter sent to the who (world health organisation) in april , more than animal welfare and conservation organisations stressed the need to recognise the link between wildlife markets and pandemics (https://lioncoalition.org/ / / /open-letter-to-world-health-organisation/). however, this is related with the need to act on existing international conventions, such as cites (the convention on international trade in endangered species of wild fauna and flora, also known as the washington convention) to protect endangered plants and animals from trafficking. as this is not the first time such outbreaks have occurred (see the sars event between and ), conventions like cites should be reinforced. forest landscape fragmentation also may facilitate more often human contact with wild animals, increasing the likelihood of transmission risk of animal-to-human viruses [ , ] . the pandemic has also had an impact on ecological research, field work and experiments. in many cases, this research activity has been diminished or halted, with important consequences on conservation of species and habitats. there is also a possible economic impact on conservation programs around the globe as a result of pandemic and different programs are assessing their long-term viability (such as the global environmental fund) [ ] . even after the pandemic ends, a danger exists that both research and conservation programs will be diminished mainly due to miscommunication between decision makers and scientists. however, perhaps the most important impact of the pandemic on the ecological transition focuses on sustainability and the still possible choices that the society could make to ensure its long-term survivability. as explained in figure , the coupled natural-human system is on a path of transitioning from an unsustainable development towards sustainability being under pressure from different drivers. the instability caused by the pandemic is characterized by variables that have sudden and multiple impacts on both the natural environment and on society and could push the system into three different potential states. the fast variables are characterizing the instability phase and the slow variables act as controlling variables [ ] [ ] [ ] . only one of these potential states is the desirable one, moving away from unwanted events and ensuring that the pandemic was a painful but still a "learning event" that drove towards a "better future". the main characteristic of the pandemic is that it is acting like a shock that pushes the system towards a regime shift with difficult to predict consequences. system into three different potential states. the fast variables are characterizing the instability phase and the slow variables act as controlling variables [ ] [ ] [ ] . only one of these potential states is the desirable one, moving away from unwanted events and ensuring that the pandemic was a painful but still a "learning event" that drove towards a "better future". the main characteristic of the pandemic is that it is acting like a shock that pushes the system towards a regime shift with difficult to predict consequences. reference [ ] advocates that nature is part of the solution for recovery and sustainable reconstruction. nevertheless, the effect of the covid- pandemic on ecological systems has not yet been fully realized, and further monitoring will bring new findings and perspectives. it is very likely that the covid- pandemic will reshape the economic and environmental policies at an international scale. the strength of some bilateral agreements and international partnerships has been tested by this pandemic. whereas china persistently invested in africa's natural resources and infrastructure projects, the treatment of african citizens living in china and the frustration at beijing's opposition on granting debt relief could deteriorate the chinese economic and political supremacy in africa [ ] . reference [ ] also discusses the impact of the crisis on african economies with unpredictable environmental consequences. the roles that china and the usa currently play for mitigating risk include an ecological emphasis to the pandemic strategy preparedness in order to better protect the global community from zoonotic disease [ ] . the coronavirus epidemic could significantly impact the italians' relationship with the eu, as indicated by the widely spread perception that the eu was not efficient in supporting the fight against coronavirus [ ] , at least in february-march (i.e., % of italians believed so in march ). such changes are expected to generate indirect long-term environmental impacts. climate changes are often perceived as a risk driver at the global scale and covid- has offered an excellent example of how a single underestimated threat can challenge the foundations of global security, economic stability and democratic governance [ ] . according to analyses before the reference [ ] advocates that nature is part of the solution for recovery and sustainable reconstruction. nevertheless, the effect of the covid- pandemic on ecological systems has not yet been fully realized, and further monitoring will bring new findings and perspectives. it is very likely that the covid- pandemic will reshape the economic and environmental policies at an international scale. the strength of some bilateral agreements and international partnerships has been tested by this pandemic. whereas china persistently invested in africa's natural resources and infrastructure projects, the treatment of african citizens living in china and the frustration at beijing's opposition on granting debt relief could deteriorate the chinese economic and political supremacy in africa [ ] . reference [ ] also discusses the impact of the crisis on african economies with unpredictable environmental consequences. the roles that china and the usa currently play for mitigating risk include an ecological emphasis to the pandemic strategy preparedness in order to better protect the global community from zoonotic disease [ ] . the coronavirus epidemic could significantly impact the italians' relationship with the eu, as indicated by the widely spread perception that the eu was not efficient in supporting the fight against coronavirus [ ] , at least in february-march (i.e., % of italians believed so in march ). such changes are expected to generate indirect long-term environmental impacts. climate changes are often perceived as a risk driver at the global scale and covid- has offered an excellent example of how a single underestimated threat can challenge the foundations of global security, economic stability and democratic governance [ ] . according to analyses before the covid- pandemic, if countries are unable to implement the nationally determined contributions as ratified through the paris agreement, the emissions reduction efforts would cost the whole world about . - . trillion dollars until [ ] . plans prepared for reinforcing the emission reduction goals established under the paris agreement are not only postponed until , but they will probably suffer consistent adjustments in the new economic circumstances. in the short term, it is hard to assume that climate change and environmental sustainability will be priorities for the world governments or local authorities, while the long-term cost for emission reduction could be raised. the coronavirus crisis also threatens local commitments to implement climate change adaptation and mitigation measures that have been initiated in the recent period [ ] . both national and international governance will be affected. the impact of coronavirus on the eu climate plan was already the subject of discussions in several meetings in brussels and there are concerns that the targets set for now will be difficult to reach especially due to the necessity for a rapid economic recovery. poland, in particular, expressed doubts on reaching the targets set for (http://www.caneurope.org/publications/press-releases/ -eu-aims-f or-net-zero-emissions-by- -now-it-needs-to-work-on-raising-the- -target). big industries such as car manufacturers also have expressed concerns of not being able to meet the targets set (https://ww w.carbonbrief.org/daily-brief/eu-leaders-agree-to-consider-climate-in-coronavirus-recovery-plan). during the s, environmental efforts have intensively addressed the generous framework of the "transforming our world: the agenda for sustainable development" [ ] . this agenda includes sustainable development goals (sdgs) designed to eradicate poverty and achieve sustainable development by . we argue that most of these goals were immediately impacted by the covid- pandemic, while longer-term effects are also expected ( table ) , most of them directly connected to urban areas and population health. it is very likely that the concept and implementation of the agenda must be reconsidered according to the new findings related to our exposure, vulnerabilities and resilience to global disaster risks. the discovery of the permanence of the virus on surfaces and in aquifers requires a revision of the purification and sanitation systems. days to years [ ] : affordable and clean energy alternative energy sources and backup storage and transport systems should be developed to secure societal needs during crises. years to decades [ ] : decent work and economic growth the pandemic has shown that there are groups of workers most exposed to risk to health and life by requiring a revision of the working methods in industry, commerce and health. months to decades [ , ] : industry, innovation and infrastructure technological innovation and a close link with the research invention, also to the advantage of a change in production methods, has proved to be an unavoidable condition for the solution of global problems months to decades [ , ] : reduced inequality improvements in access to information technologies to reduce inequalities in poor and large families who have to use remote school systems and access to other resources. days to months [ , ] : sustainable cities and communities revisions of adaptation plans are foreseen for major cities to increase health resilience in citizens and to better protect elderly population. months to decades [ , , ] revision of production systems from the global to the local scale to ensure access and distribution of strategic resources with consequent enhancement of territorial activities. months to decades [ ] months to decades [ , ] : peace and justice strong institutions the importance of strong coordination between institutions has been markedly indicated for national ones but, above all, for international ones where the exchange of exact and punctual information can indicate safe ways for solving problems on a global level. months to decades [ , ] : partnerships to achieve the goal the efficiency of international agreements have been dramatically challenged, and the need for rethinking regional and global partnerships emerged. days to decades [ ] the covid- crisis has challenged environmental monitoring and climate services, creating both adversities in observations as well as challenges to create better preparedness. lack of reliable data on the spread of covid- could lead to not only a once-in-a-century pandemic but also a once-in-a-century decision fiasco [ ] . the crisis has revealed the crucial need to access long-term, real-time data for supporting policy makers and reaction at different scales, and it has motivated environmental scientists to reinforce our monitoring capacity to address sustainability issues the pandemic has raised [ ] . challenges like the dearth of airborne meteorological measurements or the maintenance of environmental monitoring in protected areas will gradually be resolved once previous levels of social and economic activity resume [ ] . however, actions are needed now to build reliable responses to future threats. the covid- crisis has strongly biased the production and delivery of both weather forecasting (https://news.un.org/en/story/ / / ) and climate services (i.e., climate-based information and products tailored for various end-users related to the present climate and adaptation to different scenarios) as well as the observation of oceans and remote locations (https://www.theguardian.com/sc ience/ /apr/ /climate-monitoring-research-coronavirus-scientists#maincontent). the pandemic has dramatically lowered the quantity and quality of aircraft weather observations, thereby adversely impacting weather forecasts and modelling efforts. the european centre for medium-range weather forecasts (ecmwf) has noted a reduction of % in aircraft reports received between march and march (figure ). on april, the world meteorological organization (wmo) issued its concern about the impact of the crisis on the global observing system [ ] . however, the exceptional slowdown of societal activities that began in march of has generated opportunities to capture environmental information of a novel event. for example, the "noise" associated with human activities that adversely affect seismographic records dropped sharply around the world, improving the ability to detect seismic waves and the locations of number of daily aircraft reports over europe received and used at ecmwf. source: https://www.ecmwf.int/en/about/media-centre/news/ /drop-aircraft-observations-could-h ave-impact-weather-forecasts. however, the exceptional slowdown of societal activities that began in march of has generated opportunities to capture environmental information of a novel event. for example, the "noise" associated with human activities that adversely affect seismographic records dropped sharply around the world, improving the ability to detect seismic waves and the locations of earthquake aftershocks [ ] . transmission of diseases by population mobility within the context of climate change received scientists' attention before the current pandemic [ , ] . the examination of the relationship between climate and coronavirus focuses on two queries: (a) how the climate can modulate the spread and persistence of the virus, and (b) the extent of the impact of the virus on economic policies taken to offset climate impacts. the first aspect is inherently scientific and mainly involves the atmospheric and epidemiological disciplines. the second is much more complex as the economic, political and social dynamics will affect processes that will alter our worldview. climatic effects on the coronavirus are currently difficult to estimate given that this pandemic is still under development. these effects, therefore, can only be speculated by comparing them to the characteristics of other coronaviruses. reference [ ] investigated the observed growth rate of coronavirus worldwide and related it to the climate, making a prediction for forthcoming seasons. they argue a specific climate exists in which the coronavirus spreads optimally. outbreak dynamics also were investigated in terms of climate and environmental conditions [ ] to link directly daily growth rates to the local climate. the correlation found was significant leading them to conclude that such a link was valid, but their study also highlighted the fact that population density could be a confounding variable. these results, although very speculative, have led to initial hypotheses on the transmission conditions of sars-cov- under different combinations of atmospheric parameters [ ] and to forecast conditions for the summer of [ , ] . an analogy with the other coronaviruses becomes fundamental to validate such hypotheses but it is not currently possible to establish whether the virologic characteristics of the new pathogen can be assumed to be like other coronaviruses. analysing the direct and indirect effects of the pandemic on the climate is more complicated as forecasts must resolve not just the contagion dynamics but also incorporate economic, social, and political aspects of the virus propagation. direct effects on climate change could result mainly from the global slowdown of production activities and transportation. at this stage, the overall effects are not easily determined but, for example, emissions in china-the country with the longest period of closure-have decreased by % [ ] , corresponding to a decrease of about million tons of co in february alone [ ] . nevertheless, the possible decrease in global co emissions is likely to be around % worldwide [ ] (reuters, ). for the representative concentration pathway (rcp) climate change scenario, scripps research institute [ ] suggests a possible trend in emissions ( figure ) which shows an immediate drop followed by a recovery when activities resume. this projection leads to fundamental speculations as to what indirect effects coronavirus will have on the earth's climate. we note that following the - economic crisis, co emissions exhibited rapid growth [ ] and we suggest that a similar response will follow this pandemic. experts suggest one of two sharply divergent paths will arise from the demise of the pandemic [ ] . on the one hand, a feeling exists that the coronavirus will support the government, science, and business infrastructure in addressing environmental issues, including climate change [ ] . although the coronavirus and climate change operate on different time scales, they represent similar phenomena in terms of the evolution and impacts of the problem. thus, lessons from the pandemic provide lessons to be learned in environmental protection. recovery from the pandemic, therefore, may lead the focus away from environmental concerns [ ] . surely something has already changed. covid- has undermined the basic tenets of global manufacturing. companies must now reconsider the multistep, multi-country supply chains that dominated production and derivative production [ ] . individuals too must reconsider life choices as profound changes also await us [ , ] . scripps research institute [ ] suggests a possible trend in emissions ( figure ) which shows an immediate drop followed by a recovery when activities resume. this projection leads to fundamental speculations as to what indirect effects coronavirus will have on the earth's climate. we note that following the - economic crisis, co emissions exhibited rapid growth [ ] and we suggest that a similar response will follow this pandemic. experts suggest one of two sharply divergent paths will arise from the demise of the pandemic [ ] . on the one hand, a feeling exists that the coronavirus will support the government, science, and business infrastructure in addressing environmental issues, including climate change [ ] . although the coronavirus and climate change operate on different time scales, they represent similar phenomena in terms of the evolution and impacts of the problem. thus, lessons from the pandemic provide lessons to be learned in environmental protection. recovery from the pandemic, therefore, may lead the focus away from environmental concerns [ ] . surely something has already changed. covid- has undermined the basic tenets of global manufacturing. companies must now reconsider the multistep, multi-country supply chains that dominated production and derivative production [ ] . individuals too must reconsider life choices as profound changes also await us [ , ] . the covid- pandemic has triggered unprecedented environmental impacts in terms of spatial extent, complexity and even uniqueness. it is the first time in history that the metabolism of all the urban agglomerations with more than million inhabitants from europe was virtually stopped regarding movement, traffic and economic exchanges. the societal and economic measures adopted to contain the pandemic led to local, regional and global impacts, both negative and positive, spanning from immediate to long-term consequences. the full evaluation of the impacts is far from being possible with an ongoing disaster of epic proportion and tremendous complexity, and this paper pledges for several directions to be pursued by further research. the covid- pandemic provides a clear demonstration that human and planetary health are intimately interconnected [ ] , and the role of interdisciplinary approaches in finding solutions has been clearly highlighted [ ] . the disaster reached the planetary scale within only two months (i.e., february through march ). despite six other pandemic outbreaks having occurred during the st century, humankind was still not prepared to deal with a global event. most countries adopted a strict lockdown of economies and societal activities, triggering immediate impacts on many physical and ecological systems. longer-term consequences are also assumed, and a systemic approach is required to support the prevention, early warning, and similar impacts of environmental degradation. the covid- pandemic has triggered unprecedented environmental impacts in terms of spatial extent, complexity and even uniqueness. it is the first time in history that the metabolism of all the urban agglomerations with more than million inhabitants from europe was virtually stopped regarding movement, traffic and economic exchanges. the societal and economic measures adopted to contain the pandemic led to local, regional and global impacts, both negative and positive, spanning from immediate to long-term consequences. the full evaluation of the impacts is far from being possible with an ongoing disaster of epic proportion and tremendous complexity, and this paper pledges for several directions to be pursued by further research. the covid- pandemic provides a clear demonstration that human and planetary health are intimately interconnected [ ] , and the role of interdisciplinary approaches in finding solutions has been clearly highlighted [ ] . the disaster reached the planetary scale within only two months (i.e., february through march ). despite six other pandemic outbreaks having occurred during the st century, humankind was still not prepared to deal with a global event. most countries adopted a strict lockdown of economies and societal activities, triggering immediate impacts on many physical and ecological systems. longer-term consequences are also assumed, and a systemic approach is required to support the prevention, early warning, and similar impacts of environmental degradation. the coronavirus pandemic has generated an active involvement of the research community and has garnered an early response from international, national, and local authorities. since the events are ongoing and the end is still difficult to predict, we shall refer only to preliminary results and possible lessons to be learned. the reaction of the scientific community to the crisis was prompt and led to rapid accumulation of knowledge and operational decisions. faced with an unprecedented interruption of data from aeronautical meteorological service providers (amsps) and other observational platforms, the wmo has enumerated preliminary guidelines to assist the amsps [ ] at the beginning of april . eventually, problems associated with environmental monitoring have reinforced the need to secure backup systems to collect information, as such data are crucial for operational forecasting of ecological, weather and hydrological conditions. of note, relationships between weather conditions and the spread of the virus are still unclear and more research is needed to derive relevant conclusions. the advancements of new specific techniques would be of great interest for controlling the environmental dissemination of coronaviruses [ ] , and more precise and extended monitoring would favour the collection of more relevant information. early developments with this crisis have revealed that monitoring of socio-ecological conditions is crucial for an early intervention to limit the scale of the epidemic and the pandemic hazard. reference [ ] argues that better monitoring of immigrant tracks and travel volumes could have helped countries be better prepared to contain the spread of the novel coronavirus. data, tools and lessons learned may provide significant improvements in preparation to fight potential pandemics in the future [ ] . this global crisis has convincingly demonstrated that the disaster research, climate change diplomacy and ecosystem services must reconsider their strategic and integrated development considering even the most unlikely events. eventually, the covid- pandemic will determine profound changes of the social and economic behaviour at the planetary scale, and this study highlights the environmental dimension of the consequent impacts resulting from the emerging pandemic. supplementary materials: the following are available online at http://www.mdpi.com/ - / / / /s , list s : calendar of events relevant for covid- impact on environment ( december - april ), figure s : average weekly no concentration between january and april in urban areas from spain, france, united kingdom, italy, austria and poland. source: https://www.eea.europa.eu/themes/air/air-quality-a nd-covid /monitoring-covid- -impacts-on. predicting population responses to environmental change from individual-level mechanisms: towards a standardized mechanistic approach ten principles to integrate the water-energy-land nexus with climate services for co-producing local and regional integrated assessments managing the risks of extreme events and disasters to advance climate change adaptation: special report of the intergovernmental panel on climate change defining disaster: the emergency department perspective defining disaster: an evolving concept medium-and long-term health effects of earthquakes in high-income countries: a systematic review and meta-analysis pandemics: risks, impacts, and mitigation who declares covid- a pandemic who director-general's opening remarks at the media briefing on covid- - quantifying sars-cov- transmission suggests epidemic control with digital contact tracing united nations development programme can you put a price on covid- options? experts weigh lives versus economics transition from democracy-loss of quality, hybridisation and breakdown of democracy long-term memory for the terrorist attack of september : flashbulb memories, event memories, and the factors that influence their retention the / attacks-a study of al qaeda's use of intelligence and counterintelligence the deterioration of democratic political culture: consequences of the perception of inequality polarization and the global crisis of democracy: common patterns, dynamics, and pernicious consequences for democratic polities the socio-economic implications of the coronavirus and covid- pandemic: a review nuclear war as a global catastrophic risk the academic analysis of the financial crisis: round rapidly expanding nuclear arsenals in pakistan and india portend regional and global catastrophe stability of democracies: a complex systems perspective covid- : disease, management, treatment, and social impact coronavirus disease (covid- ): a literature review detection and attribution of observed impacts host range and emerging and reemerging pathogens the first pandemic of the st century the first influenza pandemic of the st century middle east respiratory syndrome enzootic patterns of middle east respiratory syndrome coronavirus in imported african and local arabian dromedary camels: a prospective genomic study a case-crossover analysis of the impact of weather on primary cases of middle east respiratory syndrome middle east respiratory syndrome ebola virus: a global public health menace: a narrative review heterogeneities in the case fatality ratio in the west african ebola outbreak - anatomy of an epidemic a literature review of zika virus history of highly pathogenic avian influenza global avian influenza outbreaks - : a systematic review of their distribution, avian species and virus subtype impact of meteorological factors on the covid- transmission: a multi-city study in china association between ambient temperature and covid- infection in cities from china inactivation of influenza virus by solar radiation the relationship between coronavirus (covid- ) spread and the weather pandemic's new epicenter the recovery from the covid- crisis must lead to a different economy the pandemic will accelerate history rather than reshape it ratios, benchmarks, and research advisories for it management tracking the global impact of the coronavirus outbreak climate vs coronavirus: why massive stimulus plans could represent missed opportunities position paper relazione circa l'effetto dell'inquinamento da particolato atmosferico e la diffusione di virus nella popolazione home | state of global air does air pollution influence covid- outbreaks? atmosphere is the coronavirus airborne? experts can't agree droplets and aerosols in the transmission of sars-cov- lack of covid- transmission on an international flight inquinamento atmosferico e covid- mascherine per tutti? available online civil aviation, air pollution and human health a post-carbon aviation future: airports and the transition to a cleaner aviation sector remarks of alexandre de juniac at the iata media briefing on covid- contrails reduce daily temperature range contrail cirrus radiative forcing for future air traffic verkehr in wien halbiert air pollution goes down as europe takes hard measures to combat coronavirus changes in air quality during the lockdown in barcelona (spain) one month into the sars-cov- epidemic presence of sars-coronavirus- in sewage survival of coronaviruses in water and wastewater how covid- impacts water consumption | aquatech wie sich unser wasserverbrauch in corona-zeiten verändert - - _artikel_orf_-_cov_fuenf_prozent_mehr_wasserverbrauch.pdf mitigating vulnerability of water resources under climate change. wp -vulnerability of water resources in see.-report version vulnerability of water resources to climate change in south-east europe united nations official document aerosol and surface stability of sars-cov- as compared with sars-cov- ranking hazards pertaining to human health concerns from land application of anaerobic digestate what do we know about the sars-cov- coronavirus in the environment? the proximal origin of sars-cov- mapping of poverty and likely zoonoses hotspots impacts of the coronavirus pandemic on biodiversity conservation using species distribution model to predict the impact of climate change on the potential distribution of japanese whiting sillago japonica does global change increase the success of biological invaders? habitat fragmentation, livelihood behaviors, and contact between people and nonhuman primates in covid- and nature are linked. so should be the recovery special feature: interactions of fast and slow variables in ecosystems using fast and slow processes to manage resources with thresholds resilience of ecosystems: local surprise and global change coronavirus ends china's honeymoon in africa covid- pandemic, a war to be won: understanding its economic implications for africa. appl health econ synergistic china-us ecological research is essential for global emerging infectious disease preparedness coronavirus shows we are not at all prepared for the security threat of climate change self-preservation strategy for approaching global warming targets in the post-paris agreement era floor | new; t . . . , n. - u.| how covid- could impact the climate crisis united nations | peace, dignity and equality <br> on a healthy planet available online the impact of covid- on gender equality united nations. policy brief: the impact of covid- on women water sector preparation, vigilance crucial impact of covid on customers and society recommendations from the european power sector. union of the electricity industry-eurelectric aisbl boulevard de l'impératrice, -bte - brussels covid- ) outbreak: rights, roles and responsibilities of health workers, including key considerations for occupational safety and health the innovation ecosystem, united against coronavirus how novel coronavirus could change the map on global manufacturing covid- , school closures, and child poverty: a social crisis in the making covid- could affect cities for years. here are ways they're coping now planners and pandemics: identifying problems and providing solutions covid- may be delivering a local manufacturing renaissance spread of sars-cov- coronavirus likely to be constrained by climate covid- at sea: impacts on the blue economy, ocean health, and ocean security could coronavirus lead to a "positive peace the role of environmental ris in the context of the current covid- crisis: a position by elter-lter in europe impacts on the global observing system coronavirus lockdowns have changed the way earth moves the impact of climate change and population mobility on neglected tropical disease elimination climate change and infectious disease: is the future here? environ. health perspect climate affects global patterns of covid- early outbreak dynamics high temperature and high humidity reduce the transmission of covid- will coronavirus pandemic diminish by summer? causal empirical estimates suggest covid- transmission rates are highly seasonal economic slowdown as a result of covid is no substitute for climate action analysis: coronavirus temporarily reduced china's co emissions by a quarter coronavirus could trigger biggest fall in carbon emissions since world war two correspondence: rapid growth in co emissions after the - global financial crisis. nat after the coronavirus, two sharply divergent paths on climate how the world will look after the coronavirus pandemic. foreign policy the real impact on the climate-geographical magazine covid- and air pollution: a deadly connection. available online covid- : epidemiology, evolution, and cross-disciplinary perspectives coronavirus and migration: analysis of human mobility and the spread of covid- a data ecosystem to defeat covid- this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license we thank very much the four reviewers for their valuable comments and suggestions. the authors declare no conflict of interest. key: cord- -iy h pyf authors: nasrallah, ali a.; farran, sarah h.; nasrallah, zainab a.; chahrour, mohamad a.; salhab, hamza a.; fares, mohammad y.; khachfe, hussein h.; akl, elie a. title: a large number of covid- interventional clinical trials were registered soon after the pandemic onset: a descriptive analysis date: - - journal: j clin epidemiol doi: . /j.jclinepi. . . sha: doc_id: cord_uid: iy h pyf abstract background there is a pressing need for evidence-based interventions to address the devastating clinical and public health effects of the coronavirus disease (covid- ) pandemic. the number of registered trials related to covid- is increasing by the day. objectives to describe the characteristics of the currently registered clinical trials related to covid- . methods we searched the world health organization (who)’s international clinical trials registry platform (ictrp) on may , . we included any entry that is related to covid- . we abstracted then descriptively analyzed the following characteristics of the registered trials: study design, status, phase, primary endpoints, experimental interventions, and geographic location among other qualifiers. results we identified , eligible registered trials. the majority of trials were initially registered with clinicaltrials.gov (n= ; . %) and the chinese clinical trial registry (chictr) (n= ; . %). the number of participants to be enrolled across these trials was , , with a median of participants per trial. the most-commonly studied intervention category was pharmacologic (n= ; . %), with antiparasitic medications being the most common subcategory. while over half of trials were already recruiting, we identified published peer-reviewed results for only of those trials. conclusion there is a relatively large number of registered trials but very few results published so far. while our findings suggest an appropriate initial response by the research community, the real challenge will be to get these trials completed, published, and translated into practice and policy. in december , the chinese city of wuhan witnessed the outbreak of a pneumonia of unknown origin [ ] . the outbreak was traced back to wuhan's seafood market [ ] , and characterized by a strong person-to-person transmission [ ] . subsequently, scientists identified a new strain of coronavirus, the severe acute respiratory syndrome coronavirus (sars-cov- ), as the source of the outbreak [ ] . sars-cov- is a novel member of the beta coronavirus family, which includes sars-cov, source of an outbreak in , and mers-cov, the origin of an outbreak in saudi arabia in [ ] . on th of february , the world health organization (who) announced coronavirus disease (covid- ) as the name of this new disease [ ] . within three months, covid- outbreak had already affected six continents [ ] , and the who upgraded its status from epidemic to pandemic on march , [ ] . as of may th , there have been , , confirmed cases and , deaths [ ] . patients infected with covid- present with a wide spectrum of clinical presentations [ ] , ranging from no symptoms to acute respiratory distress syndrome (ards) and death [ ] . in parallel, with the high infectivity rates of the virus have led to the overstraining of healthcare systems [ ] [ ] [ ] . supportive management remain the pivot of treatment protocols in the absence of evidence on efficacious antiviral or anti-inflammatory medications [ ] . to date, most recommendations on preventing disease transmission and treating infected patients are based on anecdotal evidence and experts' opinions. randomized control trials (rcts) are needed to provide unbiased evidence to guide the clinical care and public health practices aimed to control covid- outbreak [ ] . analyzing the status of clinical trials is a way of describing the current status of research in a scientific field, assessing the direction and magnitude of progress, and identifying potential gaps in interventional research [ ] . thus, this study aimed to describe the characteristics of the currently registered clinical trials related to covid- . we used the who international clinical trials registry platform (ictrp) database [ ] to identify on all covid- clinical trials and retrieve related information. the ictrp is a network of international clinical trial registers which ensures single-point access and unambiguous identification of trials [ ] we included all records retrieved on may th , from the ictrp that were labeled as one of the following study types: interventional, screening, prevention, treatment. we excluded the following: trials not directly related to treating or preventing covid- disease, noninterventional trials, and the following types of trials; basic science, diagnostic test, epidemiological research, expanded access, health-services, observational, and prognosis. we exported for each record all the variables reported by ictrp (see appendix a). we included the following variables for our analysis: study id, source register unique identifier, original registry, public title, primary sponsor, location (country and region), recruitment status, age range, gender, target size, study design, phase, publication (yes/no, count, and url), intervention (category, subcategory, and name), primary outcomes, registration date, enrollment date, retrospective label, and trial url. using the source register unique identifier numbers, we verified the data exported from the ictrp datafile and collected any missing data. then, two investigators (aan and hhk) categorized in duplicate and independently the intervention variables into detailed subcategories, as shown in appendix b. similarly, they categorized outcomes into the following types: mortality, morbidity, patient-reported, surrogate, composite, and other. in addition, we searched for publications related to the eligible trials. we used the source register unique identifier to search for peer-reviewed publications related to the eligible trials (on pubmed, medline, embase, and scopus), and for pre-print articles (on medrxiv and osf) [ , ] . two investigators (hhk and zan) reviewed potentially relevant peer-reviewed publications and pre-print articles independently to confirm their relatedness to the eligible trials. the complete covid- file retrieved from ictrp database included a total of , records. we excluded , records for the following reasons: non-interventional trials (n= , ); cancelled/withdrawn/suspended/terminated/retracted trials (n= ), not directly related to covid- (n= ), duplicate records (n= ), not found in source registry (n= ). as a result, , records met our eligibility criteria. figure shows the time distributions of the cumulative number of registered trials with the cumulative number of confirmed cases of covid- [ ] . while the former follows an exponential growth pattern, the latter follows an arithmetic growth pattern. case [ ] . it is worth mentioning that seven trials started between the years of and , respectively, and adjusted their protocols and eligibility criteria to include covid- patients. table : characteristics of registered trials stratfitied by phase, and across phases (n= ) table : characteristics of assessed interventions stratified across phases (n= ) table provide a re-categorization of the types of primay outcomes assessed in the eligible trials. overall, the majority of trials planned to include morbidity outcomes as primary outcomes (n= ; . %). the next types by order of frequency were surrogate outcomes (n= ; . %), mortality (n= ; . %), and composite outcomes (n= ; . %). of these trials, ( . %) had surrogate only outcomes, ( . %) had morbidity-only outcomes, while trials ( . %) had both. only one study did not report any primary outcomes. table : types of primay outcomes in the eligible trials stratified by phase male < female < we have described the characteristics of currently registered clinical trials related to covid- . the trials were planned in countries, with the majority in china. the median number of participants per trial was , with only % of trials being phase . % of the trials were recruiting or ongoing, and . % were completed. we only found peer-reviewed original articles reporting results for the eligible trials. we also found preprints of trial results. pharmacologic interventions were the most-studied category, with antiparasitic drugs, alone or in combination, being the most studied subcategory. the majority of trials included morbidity outcomes as primary outcomes. our study was based on trials registered in the who international clinical trials registry platform (ictrp), which allows single-point access and unambiguous identification of trials [ ] . also, we used duplicate and independently approach to categorizing interventions and outcomes. a major limitation of our study is that the pool of covid- registered trials is rapidly growing, hence the data would need to be periodically updated. moreover, some registered trials may have incorrect, missing or outdated information [ ] . this shift in geographical location reflects the change of the geographical focus of the pandemic itself to europe and united states. the number of trials also remarkably increased in iran, which is now the third largest country of origin for registered trials ( . %). the previous focus of trials was on traditional chinese medicine, which is somehow expected given that the pandemic started in china. the current focus is on antiparasitic drugs, immunomodulators, and antivirals. during the covid- pandemic, breakthrough news from chinese hospitals regarding the effectiveness of hydroxychloroquine in covid- patients drew significant attention to the drug [ ] . it was especially made the subject of public attention after a cohort study in france found the use of hydroxychloroquine with azithromycin effective and free of side-effects in patients if used early after diagnosis [ ] . chloroquine and its reportedly less toxic derivative, hydroxychloroquine [ ] , used alone or in combination with azithromycin, are now part of clinical practice for the management of covid- in more than countries including china, iran, and italy [ ]. on march , , the us food and drug administration also approved hydroxychloroquine for emergency use authorization in treating covid- patients [ ] . the increasingly widespread use of the drug brings important considerations regarding evidence supporting its use. as of may , , the results of four clinical trials and one prospective observational study on the use of hydroxychloroquine in covid- were published. three found it superior to conventional treatment [ , , ] , while the others did not observe significant difference between groups [ , ] . one target trial emulation of patients did not find evidence supporting the use of hydroxychloroquine for covid- related hypoxic pneumonia [ ] . with no long-term follow-up, small sample sizes, multiple methodological flaws, and conflicting results, these published trials do not offer enough high-quality evidence to adequately support guideline recommendatios [ ] . we found registered trials investigating the use of hydroxychloroquine in covid- patients for either treatment or prophylaxis. the majority are either in phase (n= ), or phase (n= ), and most are conducted in europe (n= ). only three of these trials had published results [ , , ] . with the known side effect profile of the drug, including cardiomyopathy and arrhythmias [ ] and its suggested ability to induce renal and liver impairment [ ] , the inclusion of hydroxychloroquine in clinical practice remains questionable until strong and convincing evidence can be generated. other therapeutic agents under study included anti-virals, immunomodulators, and biological agents. these include many drugs previoulsy used for the treatment of other infectious pathogens. one example is umifenovir (brand name arbidol), an antiviral agent used in russia and china for treating influenza infection, but not approved by the u.s. food and drug administration (fda) [ ] . another example is oseltamivir, an fda-approved drug for the treatment of influenza a and b [ ] . remdesivir is an anti-viral agent that has recently received considerable attention. the adaptive covid- treatment trial (actt), a phase trial involving participants lead by the national institute of allergy and infectious diseases , found that patients treated with remdesivir had significantly faster recovery and lower mortality compared to placebo [ ] . in light of the optimistic results, remdesivir was announced as the new standard of care for covid- patients in the us on april , [ ] . available results by another, although smaller, clinical trial lead by gilead sciences did not a significant difference in outcomes between and days of treatment with remdesivir [ ] . ongoing trials investigating vaccines for covid- are very important, as vaccination is the sustainable solution for counteracting this public health threat [ ] . traditionally, vaccine development is a lengthy process faced by multiple challenges including unknown virus immunogenic profile, vaccine safety, and participants recruitment/adherence [ ] . in times of pandemics, additional challenges appear, such as difficulty randomizing populations in high mortality situations, overburdening ethics and regulatory authorities, as well as the absence of large-scale manufacturing for any novel platform technology [ ] . although promising results are available for one trial investigating the adenovirus type (ad ) vectored covid- vaccine [ ] , and most of the identified trials on covid- vaccines are in phase and/or , the much-awaited vaccine is not expected to be available before at least year to months [ ] . the selection of primary outcomes reflects how researchers define meaningful evidence for the success of an intervention. however, the selection of outcomes has to insure adequate validity of their measurments and their generalizability for translation in clinical practice or health policies [ ] . we found that pharmacologic and biological interventional trials addressed mainly morbidity and surrogate outcomes more frequently than composite, mortality or patient-reported outcomes. trials targeting psychological interventions or physical therapy measured patientrelated outcomes, an expected finding. we found that % of registered trials addressed surrogate outcomes exclusively. in general, it is unclear to what degree surrogate outcome correlates with clinically meaningful effects, like those targeted by clinical outcomes [ ] . however, surrogate outcomes are used in accelerated approval pathways during epidemics or increases in life-threatening diseases, as they allow measurement of intervention effects with smaller sample sizes and shorter trial durations [ ] . we identified no completed trials, and only peer-reviewed articles were available. the most likely cause is the recency of the events that triggered the trials of interest. while peer review can be a lengthy process, peer-review platforms are making changes to optimize their assessments, for example by directly posting their reviews to preprint servers [ ] . there is no available evidence to date that appropriately guides recommendations for the prevention and treatment of covid- . those guiding health policies and clinical practice may therefore have to rely on a limited number of trial results, or indirect evidence derived from other diseases. there is a need for evidence-based interventions to mitigate the global humanitarian and economic sequelae of the pandemic. registration of ongoing trials is essential for researchers to coordinate efforts, but more importantly to optimize the methods of those trials and ensure the transparency of their methods. the case of hydroxychloroquine illustrates very well how the medical community adopted a promising but still unproven intervention, in spite of the supporting evidence being inadequate, and that trials are still ongoing. this could be explained by the lack of effective medications in the face of high mortality rate. still, the medication comes with a significant side effects and harms. therefore, it is imperative to have a living process to keep the evidence uptodate as the results of trials start coming out [ ] , and then feeding them into living recommendations [ ] . tracking registered trials would improve the efficiency of those living processes. future research can focus on improving trial recruitment process, and generating results in the most expeditious way possible. in the face of ongoing challenges, collaborative international efforts may be the key to success. there is also need to explore how to make trial outcomes available to decision makers, including guideline developers in a timely fashion. future research on trial registration in this field will need to explore its dynamics over the time given the large number of trials being registered. for example, it would be interesting to explore whether and how the country where the trial is being conducted changes with the change of the countries most badly affected. similarly, it will be important to explore how the categories of interventions and outcomes change over time. none to declare. epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study a new emerging zoonotic virus of concern: the novel coronavirus (covid- ) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia <em>severe acute respiratory syndrome-related coronavirus</em>: the species and its viruses -a statement of the coronavirus study group journal of experimental stroke & translational medicine naming the coronavirus disease (covid- ) and the virus that causes it a bibliometric analysis of covid- research activity: a call for increased output coronavirus disease (covid- ) situation report - , in coronavirus disease (covid- ) situation reports. , world health organization: world health organization an interactive web-based dashboard to track covid- in real time clinical characteristics of coronavirus disease in china clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study. the lancet respiratory medicine the response of milan's emergency medical system to the covid- outbreak in italy critical care utilization for the covid- outbreak in lombardy, italy: early experience and forecast during an emergency response how will country-based mitigation measures influence the course of the covid- epidemic? the lancet the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak -an update on the status randomized controlled trials: part of a series on evaluation of scientific publications status of the pediatric clinical trials enterprise: an analysis of the us clinicaltrials.gov registry international clinical trials registry platform (ictrp) our world in data exploring qualitative methods reported in registered trials and their yields (equity): systematic review traditional chinese medicine in the treatment of patients infected with -new coronavirus (sars-cov- ): a review and perspective breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro coronavirus (covid- ) update: daily roundup efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical trial. medrxiv preliminary evidence from a multicenter prospective observational study of the safety and efficacy of chloroquine for the treatment of covid- a pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease- (covid- ) hydroxychloroquine in patients mainly with mild to moderate covid- : an open-label, randomized no evidence of clinical efficacy of hydroxychloroquine in patients hospitalized for covid- infection with oxygen requirement: results of a study using routinely collected data to emulate a target trial should chloroquine and hydroxychloroquine be used to treat covid- ? a rapid review liver and kidney injuries in covid- and their effects on drug therapy; a letter to editor. archives of academic emergency medicine arbidol as a broad-spectrum antiviral: an update oseltamivir for influenza infection in children: risks and benefits remdesivir for the treatment of covid- -preliminary report emory helps lead research on drug to treat covid- patients remdesivir for or days in patients with severe covid- the effect of control strategies to reduce social mixing on outcomes of the covid- epidemic in wuhan, china: a modelling study the current challenges for vaccine development developing covid- vaccines at pandemic speed safety, tolerability, and immunogenicity of a recombinant adenovirus type- vectored covid- vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. the lancet how will country-based mitigation measures influence the course of the covid- epidemic? choosing primary endpoints for clinical trials of health care interventions time to review the role of surrogate end points in health policy: state of the art and the way forward living systematic review: . introduction-the why, what, when, and how living systematic reviews: . living guideline recommendations ( ) ( key findings:• , eligible trials related to covid- were registered up to may th , • trials were planned in countries, with the majority in europe• while more than half of the trials were already recruiting, eight had peer-reviewed publications what this adds to what is known • the research community has shown a good response to the pandemic in terms of initiating trials. • the ultimate test will be whether the research community will be able to generate the needed evidence to guide the management of the pandemic.• efforts should focus on completing the trials and publishing them in a timely fashion. none to declare. key: cord- - tu ng authors: zhang, lei; liu, yunhui title: potential interventions for novel coronavirus in china: a systematic review date: - - journal: j med virol doi: . /jmv. sha: doc_id: cord_uid: tu ng an outbreak of a novel coronavirus (covid‐ or ‐cov) infection has posed significant threats to international health and the economy. in the absence of treatment for this virus, there is an urgent need to find alternative methods to control the spread of disease. here, we have conducted an online search for all treatment options related to coronavirus infections as well as some rna‐virus infection and we have found that general treatments, coronavirus‐specific treatments, and antiviral treatments should be useful in fighting covid‐ . we suggest that the nutritional status of each infected patient should be evaluated before the administration of general treatments and the current children's rna‐virus vaccines including influenza vaccine should be immunized for uninfected people and health care workers. in addition, convalescent plasma should be given to covid‐ patients if it is available. in conclusion, we suggest that all the potential interventions be implemented to control the emerging covid‐ if the infection is uncontrollable. coronaviruses (covs) belong to the subfamily orthocoronavirinae in the family of coronaviridae in the order nidovirales, and this subfamily including α-coronavirus, β-coronavirus, γ-coronavirus, and deltacoronavirus. coronaviruses primarily cause enzootic infections in birds and mammals and, in the last decades, have shown to be capable of infecting humans as well. the outbreak of severe acute respiratory syndrome (sars) in and middle east respiratory syndrome (mers) in has demonstrated the lethality of coronaviruses when they cross the species barrier and infect humans. belong to the β-coronavirus family. recently, a novel flu-like coronavirus related to the mers and sars coronaviruses was found at the end of in china , and the evidence of human-to-human transmission was confirmed among close contacts. the genome of covid- is a single-stranded positive-sense rna. the sequence analysis showed that the covid- possessed a typical genome structure of coronavirus and belonged to the cluster of β-coronaviruses including sars-cov and mers-cov. covid- was more than % identical to those of sars-cov. vitamin a is the first fat-soluble vitamin to be recognized and β-carotene is its plant-derived precursor (table ). there are three active forms of vitamin a in the body, retinol, retinal, and retinoic acid. vitamin a is also called "anti-infective" vitamin and many of the body's defenses against infection depend on an adequate supply. researchers have believed that an impaired immune response is due to the deficiency of a particular nutritional element. vitamin a deficiency is strongly involved in measles and diarrhea and measles can become severe in vitamin a-deficient children. in addition, semba et al had reported that vitamin a supplementation reduced morbidity and mortality in different infectious diseases, such as measles, diarrheal disease, measles-related pneumonia, human immunodeficiency virus (hiv) infection, and malaria. vitamin a supplementation also offers some protection against the complications of other life-threatening infections, including malaria, lung diseases, and hiv. jee et al had reported that low vitamin a diets might compromise the effectiveness of inactivated bovine coronavirus vaccines and render calves more susceptible to infectious disease. the effect of infection with infectious bronchitis virus (ibv), a kind of coronaviruses, was more pronounced in chickens fed a diet marginally deficient in vitamin a than in those fed a diet adequate in vitamin a. the mechanism by which vitamin a and retinoids inhibit measles replication is upregulating elements of the innate immune response in uninfected bystander cells, making them refractory to productive infection during subsequent rounds of viral replication. therefore, vitamin a could be a promising option for the treatment of this novel coronavirus and the prevention of lung infection. b vitamins are water-soluble vitamins and work as part of coenzymes. each b vitamin has its special functions. for example, vitamin b (riboflavin) plays a role in the energy metabolism of all cells. vitamin b deficiency had been suspected to occur among us elderly. keil et al had reported that vitamin b and uv light effectively reduced the titer of mers-cov in human plasma products. vitamin b , also called nicotinamide, could enhance the killing of staphylococcus aureus through a myeloid-specific transcription factor and vitamin b was efficacious in both prophylactic and therapeutic settings. moreover, vitamin b treatment significantly inhibited neutrophil infiltration into the lungs with a strong anti-inflammatory effect during ventilatorinduced lung injury. however, it also paradoxically led to the development of significant hypoxemia. vitamin b is also needed in protein metabolism and it participates in over reactions in body tissues. in addition, it also plays important role in body immune function as well. as shortage of b vitamins may weaken host immune response, they should be supplemented to the virus-infected patients to enhance their immune system. therefore, b vitamins could be chosen as a basic option for the treatment of covid- . vitamin c is another water-soluble vitamin and it is also called ascorbic acid, which means "no-scurvy acid." vitamin c is best known for its role in the synthesis of collagen in connective tissues and acts as an antioxidant. vitamin c also supports immune functions and protects against infection caused by a coronavirus. infection. vitamin c may also function as a weak antihistamine agent to provide relief from flu-like symptoms such as sneezing, a running or stuffy nose, and swollen sinuses. three human controlled trials had reported that there was significantly lower incidence of pneumonia in vitamin c-supplemented groups, suggesting that vitamin c might prevent the susceptibility to lower respiratory tract infections under certain conditions. the covid- had been reported to cause lower respiratory tract infection, so vitamin c could be one of the effective choices for the treatment of covid- . vitamin d is not only a nutrient but also a hormone, which can be synthesized in our body with the help of sunlight. in addition to its role in maintaining bone integrity, it also stimulates the maturation of and omega- pufas predominantly promote anti-inflammatory and pro-inflammatory effects. they are precursors of resolvins/protectins and prostaglandins/leukotrienes, respectively. begin et al had studied plasma lipids levels in patients with aids and had found that a selective and specific lack of the long-chain pufas of omega- series, which are found in high concentrations in fish oils. in addition, protectin d , the omega- pufa-derived lipid mediator, could markedly attenuate influenza virus replication via rna export machinery. in addition, treatment of protectin d with peramivir could completely rescue mice from flu mortality. leu et al had found that several pufas also had anti-hepatitis c virus (hcv) activities. therefore, omega- including protectin d , which served as a novel antiviral drug, could be considered for one of the potential interventions of this novel virus, covid- . selenium is an essential trace element for mammalian redox biology. the nutritional status of the host plays a very important role in the defense against infectious diseases. nutritional deficiency impacts not only the immune response but also the viral pathogen itself. dietary selenium deficiency that causes oxidative stress in the host can alter a viral genome so that a normally benign or mildly pathogenic virus can become highly virulent in the deficient host under oxidative stress. deficiency in selenium also induces not only impairment of host immune system, but also rapid mutation of benign variants of rna viruses to virulence. beck et al had reported that selenium deficiency could not only increase the pathology of an influenza virus infection but also drive changes in genome of coxsackievirus, permitting an avirulent virus to acquire virulence due to genetic mutation. it is because that selenium could assist a group of enzymes that, in concert with vitamin e, work to prevent the formation of free radicals and prevent oxidative damage to cells and tissues. it was reported that synergistic effect of selenium with ginseng stem-leaf saponins could induce immune response to a live bivalent infectious bronchitis coronavirus vaccine in chickens. therefore, selenium supplementation could be an effective choice for the treatment of this novel virus of covid- . zinc is a dietary trace mineral and is important for the maintenance and development of immune cells of both the innate and adaptive immune system. zinc deficiency results in dysfunction of both humoral and cell-mediated immunity and increases susceptibility to infectious diseases. zinc supplement given to zinc-deficient children could reduce measles-related morbidity and mortality caused by lower respiratory tract infections. increasing the concentration of intracellular zinc with zinc-ionophores like pyrithione can efficiently impair the replication of a variety of rna viruses. in addition, the combination of zinc and pyrithione at low concentrations inhibits the replication of sars coronavirus (sars-cov). in addition, interferons have also been found to be potent inhibitors of mers-cov replication. moreover, the combination of interferon-α- a with ribavirin was administered to patients with severe mers-cov infection and the survival of these patients was improved. these findings suggest that these approved ifn's could be also used for the treatment of this novel coronavirus. intravenous gammaglobulin (ivig) was first developed in the late s and is probably the safest immunomodulating drug available for long-term use in all ages. however, it does have adverse reactions. during the sars outbreak in , ivig was used extensively in singapore. however, one-third of critically ill patients developed venous thromboembolism including pulmonary embolism despite the use of lowmolecular weight heparin prophylactic. it was due to the ivig-induced increase of viscosity in hypercoagulable states of sars patients. thymosin α- (ta ) is a thymic peptide hormone and it has a peculiar ability to restore the homeostasis of the immune system. it is was first isolated from thymic tissue in the mid-sixties and it had gained much attention for its immunostimulatory activity. it was chemically synthesized and used in diseases where the immune system was hindered or impaired. besides its role in thymocyte development, thymosin α- could also increase resistance to glucocorticoid-induced death of the thymocyte. thymosin α- could also be used as immune enhancer to sars patients and it was effective in controlling the spread of the disease. , methylprednisolone was often used during the current treatment of covid- and the side effect of corticoid-induced death of thymocytes should be considered. so, it is wise to use thymosin α before the administration of methylprednisolone. thymopentin (tp , munox), a synthetic pentapeptide corresponding to the active site of thymopoietin, had been shown to restore antibody production in old mice. additionally, it could enhance the antibody response in humans when it was applied subcutaneously three times a week at doses of mg. moreover, thymopentin could also be used as an adjuvant treatment for non-responders or hyporesponders to hepatitis b vaccination. levamisole, a synthetic low-molecular-weight compound, is the first member of a new class of drugs that can increase the functions of cellular immunity in normal, healthy laboratory animals. medicine could also be considered as a choice to enhance host immunity against the infection of covid- . in summary, the general treatment for viral infection including nutritional interventions and all kinds of immunoenhancers has been used to enhance host immunity against rna viral infections. therefore, they may also be used to fight covid- infection by correcting the lymphopenia of patients. chymotrypsin-like ( c-like) and papain-like protease (plp) are coronavirus encoded proteins (table ) . they have an essential function for coronaviral replication and also have additional function for inhibition of host innate immune responses. targeting c-like protease ( clpro) and papain-like protease (plpro) are more attractive for the treatment of coronavirus. cinanserin cinanserin, an old drug, is well-known for serotonin receptor antagonist. it could inhibit the chymotrypsin-like ( c-like) protease and was a promising inhibitor of replication of sars-cov. the clpro was also been found to be encoded in covid- . therefore, cinanserin may be a better choice for the treatment of covid- infection. papain-like protease (plp) of human coronavirus is a novel viralencoded deubiquitinase and is an ifn antagonist for inhibition of host innate antiviral immune response. diarylheptanoids is a natural product and is extracted from the stem bark of alnus japonica. it had been found to be able to inhibit papainlike protease of sars-cov. therefore, cinanserin together with flavonoids and other natural compounds could be chosen as alternative choices to fight covid- infection through targeting coronaviral proteases. angiotensin-converting enzyme- (ace ) is a type i integral membrane protein which functions as a carboxypeptidase and is the first human homolog of ace. ace efficiently hydrolyzes the potent vasoconstrictor angiotensin ii to angiotensin ( - ) and it has been implicated in hypertension, cardiac function, heart function, and diabetes. in addition, ace is also a functional receptor of sars-cov and it mediates virus entry into the cell through binding with spike (s) protein. chloroquine is a -aminoquinoline known since . apart from its well-known antimalarial effects, the drug also has many interesting biochemical properties including antiviral effect. in addition, it had been used against viral infection. moreover, chloroquine was also found to be a potent inhibitor of sars coronavirus infection through interfering with ace , one of cell surface binding sites for s protein of sars-cov. emodin is an anthraquinone compound derived from genus rheum and polygonum and it is also a virucidal agent. emodin could significantly block the interaction between the s protein of sars-cov and ace . therefore, emodin might abolish sars-cov infection by competing for the binding site of s protein with ace . promazine, anti-psychotic drug, shares a similar structure with emodin. it has been found to exhibit a significant effect in inhibiting the replication of sars-cov. as compared to emodin, promazine exhibited potent inhibition of the binding of s protein to ace . these findings suggested that emodin and promazine might be able to inhibit sars-cov infectivity through blocking the interaction of s protein and ace . therefore, the monoclonal antibody (scfv r), chloroquine, emodin, and promazine could be used as alternative choices for the treatment of covid- . nicotianamine is an important metal ligand in plants and it is found a novel angiotensin-converting enzyme- inhibitor in soybean. so, it is another potential option to be used to reduce the infection of covid- . ribavirin, a broad-spectrum antiviral agent, is routinely used to treat hepatitis c (table ). during the outbreak of sars, ribavirin was used extensively for most cases with or without concomitant use of steroids in hong kong. however, there was considerable skepticism from overseas and local experts on the efficacy of ribavirin. because there was a report mentioned that ribavirin had no significant activity against sars-cov in vitro and the use of ribavirin was found to be associated with significant toxicity, including hemolysis (in %) and decrease in hemoglobin (in %). remdesivir (rdv), a nucleoside analog gs- , had been reported to inhibit human and zoonotic coronavirus in vitro and to restrain severe acute respiratory syndrome coronavirus (sars-cov) in vivo. recently, the antiviral activity of rdv and ifn-β was found to be superior to that of lpv/rtv-ifn-β against mers-cov in vitro and in vivo. in addition, rdv could improve pulmonary function and reduce lung viral loads and severe lung pathology in mice, which was impossible for lpv/rtv-ifn-β. recently, a first covid- - nelfinavir is a selective inhibitor of hiv protease, which is responsible for posttranslational processing of hiv propeptides. yamamoto et al had found that nelfinavir could strongly inhibit the replication of sars-cov. therefore, nelfinavir could also be an option for the treatment of covid- . arbidol (arb) is a russian-made small indole-derivative molecule and is licensed in russia and china for prophylaxis and treatment of influenza and other respiratory viral infections. arbidol had been found to be able to block viral fusion against influenza a and b viruses as well as hepatitis c virus. arbidol could also inhibit hepatitis c virus by blocking hepatitis c virus entry and replication in vitro. in addition, arbidol and its derivatives, arbidol mesylate, had been reported to have antiviral activity against the pathogen of sars in the cell cultures and arbidol mesylate was nearly times as effective as arbidol in reducing the reproduction of sars virus in the cultured cells. nitric oxide (no) is a gas with diverse biological activities and is produced from arginine by no synthases. no is able to interact with superoxide, forming peroxynitrite, which, in turn, can mediate bactericidal or cytotoxic reactions. in addition, no had played an important role in regulating airway function and in treating inflammatory airway diseases. rossaint et al reported that the beneficial effects of no inhalation could be observed in most patients with severe acute respiratory distress syndrome. no was also found to inhibit the synthesis of viral protein and rna. (table ). ala, as an antioxidant, has played a pivotal role in scavenging free radicals to protect against oxidative damage in several diseases. in addition, ala also had its capability to enhance intracellular glutathione (gsh) levels and to normalize the oxidative stress induced by dexamethasone in chicken. wu et al also reported that the oxidative stress in host cells was an important factor in the infectivity of human coronavirus e and the glucose- -phosphate dehydrogenase (g pd) deficiency was another factor that enhanced human coronavirus e infection. the addition of α-lipoic acid to g pd-knockdown cells could attenuate the increased susceptibility to human coronavirus e infection. interestingly, baur et al also found that α-lipoic acid was effective to inhibit the replication of hiv- . in summary, we speculate that ala could be also used as an optional therapy for this new virus. females, generally, mount more robust immune responses to viral challenges than males, which can result in more efficient virus clearance. epidemiological studies showed that males experiencing a higher rate of incidence and case fatality compared with females after sars-cov infection. , during the mers outbreak, the disease occurrence rate in men was almost twice as much as in women and the case fatality rate was the same as the occurrence rate among men and women. in addition, channappanavar et al had reported that male mice were more susceptible to sars-cov infection compared with age-matched female mice. however, the mortality was increased in female mice when the ovariectomy was done or the estrogen receptor antagonist was given. wei et al also found that serum levels of prolactin, follicle-stimulating hormone, and luteinizing hormone of zhang and liu | sars patients were significantly higher than those of control groups, while estradiol (e ), pregnancy hormone, and thyroid-stimulating hormone were considerably lower than those of normal controls. interestingly, estrogenic compounds had been found to reduce influenza a virus replication in primary human nasal epithelial cells derived from female, but not male, donors. in addition, resveratrol, a phytoestrogen from grape seeds and red wine, had been reported to be a potent anti-mers agent in vitro. therefore, β-estradiol or phytoestrogen could also be an alternative option to be considered for the treatment of covid- . mucroporin-m is a scorpion venom-derived peptide and has broadspectrum virucidal activity against many viruses including measles, influenza h n viruses, and sars-cov. therefore, this peptide could also be used for the treatment of covid- infection as well as the new drug design to target covid- . in this review, we summarize all the potential interventions for regarding short-term protection and prevention of viral infection, passive immunotherapy should not be neglected. monoclonal antibody therapy is one of the best forms of passive immunotherapy. a human igg mab, cr , had been generated and it had been found to be reactive with whole inactivated sars coronavirus. in addition, cr could be used as prophylaxis for sars coronavirus infection in ferrets. however, cr was found to be able to block the interaction in parent sars-cov strain, but not in escape variants. this led to the ineffectiveness of cr to prevent infection in humans. cr was another monoclonal antibody and it had been found to neutralize cr escape viruses. the combination of cr and cr had also been reported to have the potential to control immune escape. however, the clinical trial of cr with cr had never been tried due to the high cost of manufacturing. convalescent plasma can also be called passive immunotherapy. it is usually chosen when there are no specific vaccines or drugs available for emerging infection-related diseases. arabi et al had tested the feasibility of convalescent plasma therapy as well as its safety and clinical efficacy in critically ill mers patients. they found that convalescent plasma had an immunotherapeutic potential for the treatment of mers-cov infection. in addition, convalescent plasma from recovered sars patients had also been reported to be useful clinically for treating other sars patients. , importantly, the use of convalescent plasma or serum was also suggested by the world health organization under blood regulators network when vaccines and antiviral drugs were unavailable for an emerging virus. in summary, these findings suggest that the current children's rna-virus-related vaccines are the best alternative methods to be used to vaccinate the uninfected people and health care workers. convalescent plasma should be routinely used for the treatment of covid- infected critically sick patients if it is available. the avian ibv vaccine is also another choice for clinical trials if its safety has been approved in monkeys. therefore, we suggest that all the potential interventions be implemented to control the emerging covid- if the infection is uncontrollable. the authors declare that there are no conflict of interests. yunhui liu http://orcid.org/ - - - bats and coronaviruses coronavirus envelope protein: current knowledge middle east respiratory syndrome new sars-like virus in china triggers alarm a novel coronavirus from patients with pneumonia in china early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia coronaviruses: genome structure, replication, and pathogenesis recent advances in the detection of respiratory virus infection in humans genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan selenium, selenoproteins and viral infection importance of vitamin a deficiency in pathology and immunology of viral infections vitamin a and immunity to viral, bacterial and protozoan infections vitamin a supplements ameliorate the adverse effect of hiv- , malaria, and diarrheal infections on child growth effects of dietary vitamin a content on antibody responses of feedlot calves inoculated intramuscularly with an inactivated bovine coronavirus vaccine epithelia-damaging virus infections affect vitamin a status in chickens retinoids inhibit measles virus through a type i ifn-dependent bystander effect riboflavin (vitamin b- ) and health inactivation of middle east respiratory syndrome coronavirus (mers-cov) in plasma products using a riboflavin-based and ultraviolet light-based photochemical treatment c/ebpepsilon mediates nicotinamide-enhanced clearance of staphylococcus aureus in mice nicotinamide exacerbates hypoxemia in ventilator-induced lung injury independent of neutrophil infiltration the effect of ascorbic acid on infection chick-embryo ciliated tracheal organ cultures by coronavirus nutrients and their role in host resistance to infection vitamin c intake and susceptibility to pneumonia vitamin d insufficiency among free-living healthy young adults sunlight and vitamin d for bone health and prevention of autoimmune diseases, cancers, and cardiovascular disease acute phase response elicited by experimental bovine diarrhea virus (bvdv) infection is associated with decreased vitamin d and e status of vitamin-replete preruminant calves vitamin e metabolic effects and genetic variants: a challenge for precision nutrition in obesity and associated disturbances vitamin e deficiency intensifies the myocardial injury of coxsackievirus b infection of mice increased virulence of coxsackievirus b in mice due to vitamin e or selenium deficiency macrophage-derived extracellular vesicles induce long-lasting immunity against hepatitis c virus which is blunted by polyunsaturated fatty acids plasma fatty acid levels in patients with acquired immune deficiency syndrome and in controls the lipid mediator protectin d inhibits influenza virus replication and improves severe influenza anti-hcv activities of selective polyunsaturated fatty acids selenium and human health micronutrients and host resistance to viral infection review: micronutrient selenium deficiency influences evolution of some viral infectious diseases selenium deficiency increases the pathology of an influenza virus infection rapid genomic evolution of a non-virulent coxsackievirus b in selenium-deficient mice results in selection of identical virulent isolates combined adjuvant effect of ginseng stem-leaf saponins and selenium on immune responses to a live bivalent vaccine of newcastle disease virus and infectious bronchitis virus in chickens zinc and immunity: an essential interrelation zinc deficiency zinc supplementation for the treatment of measles in children zn( +) inhibits coronavirus and arterivirus rna polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture crossing the iron gate: why and how transferrin receptors mediate viral entry childhood iron deficiency anemia leads to recurrent respiratory tract infections and gastroenteritis chicken interferon type i inhibits infectious bronchitis virus replication and associated respiratory illness prevention of experimental coronavirus colds with intranasal alpha- b interferon ribavirin and interferon-beta synergistically inhibit sars-associated coronavirus replication in animal and human cell lines in vitro susceptibility of clinical isolates of sars coronavirus to selected antiviral compounds interferon priming enables cells to partially overturn the sars coronavirus-induced block in innate immune activation inhibition of sars coronavirus infection in vitro with clinically approved antiviral drugs peginterferon alfa- b plus ribavirin compared with interferon alfa- b plus ribavirin for initial treatment of chronic hepatitis c: a randomised trial pegylated interferon-alpha protects type pneumocytes against sars coronavirus infection in macaques proposal for vaccination against sars coronavirus using avian infectious bronchitis virus strain h from the netherlands interferon alfacon- plus corticosteroids in severe acute respiratory syndrome: a preliminary study current treatment options and the role of peptides as potential therapeutic components for middle east respiratory syndrome (mers): a review uses of intravenous gammaglobulin in immune hematologic disease acute respiratory distress syndrome in critically ill patients with severe acute respiratory syndrome strokes, thromboembolic events, and ivig: rare incidents blemish an excellent safety record thymosin alpha and hiv- : recent advances and future perspectives a reappraisal of thymosin alpha in cancer therapy serum thymosin alpha levels in normal and pathological conditions thymosin alpha antagonizes dexamethasone and cd -induced apoptosis of cd + cd + thymocytes through the activation of camp and protein kinase c dependent second messenger pathways clinical investigation of outbreak of nosocomial severe acute respiratory syndrome anti-sars coronavirus agents: a patent review ( -present) modulation of immune response in aged humans through different administration modes of thymopentin phase variation in the modulation of the human immune response thymopentin as adjuvant in non-responders or hyporesponders to hepatitis b vaccination the general immunopharmacology of levamisole lymphocyte subsets in measles. depressed helper/inducer subpopulation reversed by in vitro treatment with levamisole and ascorbic acid systemic cyclosporine and corneal transplantation nucleocapsid protein of sars coronavirus tightly binds to human cyclophilin a factor in virus replication and potential target for anti-viral therapy the sars-coronavirus-host interactome: identification of cyclophilins as target for pancoronavirus inhibitors glycyrrhizin, an active component of liquorice roots, and replication of sars-associated coronavirus diarylheptanoids from alnus japonica inhibit papain-like protease of severe acute respiratory syndrome coronavirus cinanserin is an inhibitor of the c-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro flavonoids: an overview flavonoids from pterogyne nitens inhibit hepatitis c virus entry inhibition of sars-cov cl protease by flavonoids characteristics of flavonoids as potent mers-cov c-like protease inhibitors biflavonoids from torreya nucifera displaying sars-cov cl(pro) inhibition angiotensin-converting enzyme- : a molecular and cellular perspective angiotensin-converting enzyme is a functional receptor for the sars coronavirus the secret life of ace as a receptor for the sars virus characterization of severe acute respiratory syndromeassociated coronavirus (sars-cov) spike glycoprotein-mediated viral entry severe acute respiratory syndrome coronavirus entry into host cells: opportunities for therapeutic intervention potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s protein that blocks receptor association effects of chloroquine on viral infections: an old drug against today's diseases? chloroquine is a potent inhibitor of sars coronavirus infection and spread membrane-related effects underlying the biological activity of the anthraquinones emodin and barbaloin emodin blocks the sars coronavirus spike protein and angiotensin-converting enzyme interaction old drugs as lead compounds for a new disease? binding analysis of sars coronavirus main proteinase with hiv, psychotic and parasite drugs the transition metal chelator nicotianamine is synthesized by filamentous fungi nicotianamine is a novel angiotensin-converting enzyme inhibitor in soybean managing sars amidst uncertainty critics slam treatment for sars as ineffective and perhaps dangerous clinical features and short-term outcomes of patients with sars in the greater toronto area comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings combination therapy with lopinavir/ritonavir, ribavirin and interferon-alpha for middle east respiratory syndrome coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease. mbio first case of novel coronavirus in the united states a review of its therapeutic efficacy in hiv infection hiv protease inhibitor nelfinavir inhibits replication of sars-associated coronavirus arbidol as a broad-spectrum antiviral: an update arbidol: a broadspectrum antiviral compound that blocks viral fusion the synthetic antiviral drug arbidol inhibits globally prevalent pathogenic viruses nitric oxide nitric oxide and airway disease efficacy of inhaled nitric oxide in patients with severe an overview on severe acute respiratory syndrome (sars) nitric oxide inhibits the replication cycle of severe acute respiratory syndrome coronavirus efficacy of thioctic acid in the therapy of peripheral diabetic neuropathy biochemical and clinical relevance of alpha lipoic acid: antioxidant and anti-inflammatory activity, molecular pathways and therapeutic potential effects of dietary vitamin c, vitamin e, and alpha-lipoic acid supplementation on the antioxidant defense system and immune-related gene expression in broilers exposed to oxidative stress by dexamethasone glucose- -phosphate dehydrogenase deficiency enhances human coronavirus e infection alphalipoic acid is an effective inhibitor of human immuno-deficiency virus (hiv- ) replication sexual dimorphism in innate immune responses to infectious organisms do men have a higher case fatality rate of severe acute respiratory syndrome than women do? sars in singapore--predictors of disease severity the pattern of middle east respiratory syndrome coronavirus in saudi arabia: a descriptive epidemiological analysis of data from the saudi ministry of health sex-based differences in susceptibility to severe acute respiratory syndrome coronavirus infection endocrine cells of the adenohypophysis in severe acute respiratory syndrome (sars) estrogenic compounds reduce influenza a virus replication in primary human nasal epithelial cells derived from female, but not male, donors effective inhibition of mers-cov infection by resveratrol virucidal activity of a scorpion venom peptide variant mucroporin-m against measles, sars-cov and influenza h n viruses severe acute respiratory syndrome vaccine development: experiences of vaccination against avian infectious bronchitis coronavirus protection from sars coronavirus conferred by live measles vaccine expressing the spike glycoprotein live-attenuated bivalent measles virus-derived vaccines targeting middle east respiratory syndrome coronavirus induce robust and multifunctional t cell responses against both viruses in an appropriate mouse model measles-derived vaccines to prevent emerging viral diseases human monoclonal antibody combination against sars coronavirus: synergy and coverage of escape mutants human monoclonal antibody as prophylaxis for sars coronavirus infection in ferrets convalescent plasma: new evidence for an old therapeutic tool? feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with middle east respiratory syndrome coronavirus infection: a study protocol use of convalescent plasma therapy in sars patients in hong kong retrospective comparison of convalescent plasma with continuing high-dose methylprednisolone treatment in sars patients key: cord- -m vlv q authors: ogundokun, r. o.; awotunde, j. b. title: machine learning prediction for covid pandemic in india date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: m vlv q background: coronavirus was detected in december in a bulk seafood shop in wuhan, china. the original incident of covid- pandemic in india was conveyed on th january instigating from the nation called china. as of th april , the ministry of health and family welfare has established a total of , incidents, , recuperation including relocation, and demises in the republic. objective: the objective of the paper is to formulate a simple average aggregated machine learning method to predict the number, size, and length of covid- cases extent and wind-up period crosswise india. method: this study examined the datasets via the autoregressive integrated moving average model (arima). the study also built a simple mean aggregated method established on the performance of regression techniques such as support vector regression (svr, nn, and lr), neural network, and linear regression. result: the results showed that covid- disease can correctly be predicted. the result of the prediction shows that covid- ailment could be conveyed through water and air ecological variables and so preventives measures such as social distancing, wearing of mask and hand gloves, staying at home can help to avert the circulation of the sickness thereby resulting in reduced active cases and even mortality. conclusion: it was established that the projected method outperformed when likened to previously obtainable practical models on the bases of prediction precision. hence, putting in place the preventive measures can effectively manage the spread of covid- , and also the death rate will be reduced and eventually be over in india and other nations. coronaviruses are a wide intimate of diseases, few of which lead to disease in humans and the remaining which mingle between animals and natures. animal coronaviruses will occasionally transmit to individuals and only transmit to humans [ ] . in recent years, zoonotic coronaviruses have formed triggering humanoid outbursts for instance coronavirus ailment (covid- ) , severe acute respiratory syndrome (sars), as well as a respiratory syndrome in the middle east (mers). the human disease occurs often as a lung infection, or occasionally as a stomach infection. the clinical range of disease ranges from no signs or moderate breathing problems to extreme, increasingly progressing pneumonia, severe breathing suffering condition, infected tremor, or death-induced multiple-body part catastrophe [ ] . as of april , india registered more than , established crisis of . around , individuals are now in good health from these, whereas crises have led to death. the sum of individuals afflicted with the disease was increasing in the south asian nation which led to the government swinging into action to further curb the outbreak's spread. as of mid-april , more than two million cases of coronavirus have been identified worldwide. a sikh preacher who, bearing the virus, returned from traveling to italy and germany, became a "mega propagator". he was present at a sikh commemoration in anandpur sahib from th to th of march [ , ] . cases of covid- were backtracked in the direction of him [ ] . on march more than , residents were quarantined in villages in punjab to control the circulation of the disease [ , ] . on st of march, an occasion of a spiritual assembled group of people in tablighi jamaat that happened in delhi at the beginning of march arose as a novel disease asperity next multiple crisis around the world were backtracked toward the occasion [ ] . more than thousand proselytizers might have joined the service, accompanying the bulk arriving from different nations in india [ , ] including nine hundred and sixty from forty republics abroad [ ] . as reported by the office of health and family wellbeing, this incident was related to , out of , confirmed cases in twenty-three indian cities including unified terrains before the th of april [ ] . on the th of april , nurses and physicians were found to have been diagnosed with the virus in mumbai's wockhardt hospital. hospitals were locked down immediately, and a safety region was professed. health treatment incompetence was responsible for the infections [ ] . in india, covid- infection rates are estimated towards . , slightly lesser than in the worst-pretentious nations [ ] . the outburst had proclaimed a widespread in over nations as well as unification terrains, where requirements of the infectious ailments act were applied, and public institutions and other business enterprises were on standstill. indian had revoked entirely every traveler entry permit since most reported cases have been related to other countries [ ] . on march , at prime minister narendra modi's say, india implemented a -aera community restriction. the government responded with movement restriction in areas wherever covid- events and all major cities had taken place [ , ] . also, the prime minister ordered a -day national shutdown on march, affecting india's entire . billion population [ , ] . the prime minister extended the current national lockout until may on april [ ] . michael ryan, chief executive officer of the healthiness emergencies program of the world health organization, said that india has "great potential" to cope with covid- epidemic as per the next most populated nation, would possess a significant effect proceeding the ability of the globe to cope with the disease [ ] . many analysts were apprehensive concerning the financial destruction instigated via the lockout, having immense consequences on migrant employees, large as well as trivial initiatives, agriculturalists, and entrepreneurial individuals, who were abandoned without an income in the nonappearance of transport and consumer contact [ , ] . spectators noted the lockout reduced the pandemic's progress frequency by april to double every six days [ ] and by april to double every eight days [ ] . founded on statistics from seventy-three nations, the oxford covid- régime response tracker (oxcgrt) states that the indian government has reacted to the pandemic more rigorously than other nations. this acknowledged the fast intervention of the government, emergency policymaking emergency healthcare spending, budgetary initiatives, expenditure in vaccine development and successful reaction towards the crisis, and rated india with a " " aimed at her firmness [ , ] . india registered the first covid- case in kerala on january, which grew to incidences by rd february ; altogether were undergraduates who came back from wuhan, china [ , ] . the remainder of february showed no noticeable increase in events. on the th of march , twenty-two fresh incidence was discovered together with those groups of visitors from italy involving of the participants contaminated [ ] . the spread intensified in mid-march, amid news of multiple cases around the world, several of which were related to individuals with itinerant antiquity to pretentious nations. on the th of march, an individual of age who had come back from saudi arabia turned out to be the country's primary survivor of the covid- disease [ ] . confirmed deaths reached a hundred on th march , [ ] thousand by th march , [ ] thousand by th of april , [ ] thousand by th april [ ] . demise toll passed by st april [ ] then by th april [ ] . with covid- no additional antiviral therapy is recommended. infected patients should provide medical medication to help in pain relief. in extreme cases, the function of vital organs should be protected. [ ] sars-cov- is currently not available as a vaccine. evitement is the primary form of deterrence. numerous international projects have quickly arisen to identify and evaluate the efficacy of antivirals, immunotherapies, monoclonal antibodies, and vaccines. pharmacotherapy protocols and reviews for covid- have been written. [ , [ ] [ ] [ ] . transmission of infectious disease is a dynamic mechanism of transmission that happens within the crowd. frameworks can be developed for this method to potentially examine and test the propagation mechanism of infectious diseases [ ] so that we can forecast correctly the future pattern of infectious diseases [ ] . therefore, to monitor or reduce the damage of infectious diseases, the study and review of predictive models for infectious diseases have been a hot topic of science [ ] . therefore, the study projected a simple average aggregated scheme, and the aggregated system has been established by aggregating three regression methods which include support vector regression, linear regression as well as artificial neural network. the variables utilized for the formulation of an aggregated method are the figures of covid- cases. the dataset was gathered and collated from statistica.com from january to april gathered monthly. the study predicted the values from the previous covid- incidents and values of environment variables such as water and air. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the authentic datasets of covid- have been gathered from https://www.mygov.in/ and https://www.pharmaceutical-technology.com/ the dataset is publicly available on cases from india from the first case index on january . the datasets gathered were in a monthly form that is january to april . table displays the scenario of covid- incidents in india from january to april . as at th april covid- dataset includes accumulated , total samples, confirmed cases of , , recovered cases of , ; death cases and migration. is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may , . . https://doi.org/ . / . . . doi: medrxiv preprint there are numerous diverse methods utilized to perform machine learning tasks. machine learning approaches require certain types of algorithmic approaches. according to dataquest, , there are three types of machine learning algorithms and they are: i. supervised learning algorithms such as classification, regression, and ensemble ii. unsupervised learning algorithm such as association, clustering, dimensionality reduction iii. reinforcement learning the utmost extensively anns utilized in the estimation problem is multi-layer perceptions (mlps), which employs the solitary tiers feed-forward network [ ] . this method is categorized by a system of layers. the nodes in several tiers are as well identified as altering fundamentals. the outcome of the method is calculated employing the subsequent mathematical expression in statistics, linear regression is the scheme for demonstrating the association amid the scalar or reliant variables and solitary or additional self-determining variables [ , , , , ] . the circumstance of the descriptive variables is termed a simple linear regression while in the circumstance of greater than single descriptive variables the procedure is referred to as multiple linear regressions. the mathematical formulation of the linear regression is as specified beneath. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may , . . support vector machines (svm) are a supervised learning scheme which could be employed for the classification as well as regression glitches (adikari et al., ; shanthi et al., ) . the core impression of svm once employed to dual categorization difficulties is to discover an established manic level that excellently splits the assumed clusters of tutoring models. in circumstances where data points are not linearly divisible, a lenient border manic level classifier is created as below to employ svmr, as in the categorization difficulty this belongs to a few clusters, for instance, a and a in the circumstance of regression and support vector machine at this point is the actual figure and additional variables are equivalent as for the categorization glitches [ ] . regression techniques are one of the prevailing methods for the prediction of specific datasets. in this study, the authors formulated a simple mean aggregated method by combining popular regression models and predicted the sum of covid- in india. authors such as [ ] and [ ] have employed the regression method predominantly to communicable datasets and as well hypotheses an ensemble model typically with estimation approaches. there is a key challenge in the study of prediction predominantly in the relation of predicting an occurrence of a specific illness as it had been stated earlier. . employing the independent variables, this revert them to discover the estimation by employing svr, lr, and ann . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may , . ܰ is the overall scope of crises. this section describes the objective of finding the equivalence between the figures of covid- cases with environmental variables such as water (sewage overflow) and air (air streams or wind). in this study, ecological variables play an important role in the spread of covid- diseases. to accomplish this objective the authors have applied a statistical p-value test to determine the equivalence between the figure of covid- cases. after examination by the pvalue test, it was concluded that water is a protuberant ecological variable for the incidence of covid- incident in india. many authors have found the equivalence between infectious diseases and ecological variables by p-value test [ , ] . the application of the p-value test accomplishes that ecological variables like water and air had a positive equivalence with the occurrence of several cases for the period since this disease started. the statistical implication was measured p< . . the study discards the null hypothesis. the equivalence of covid- cases with water and air is substantial table . tables - displays the evaluation of the prediction precision in terms of root mean square error, mean scaled error and mean absolute error. for the confirmation of our postulated aggregated system, one instantaneous series dataset was utilized in this research. these are the numeral of covid- crises in india and these datasets were gathered on statistica.com. the explanation of period series datasets is obtainable in table . . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may , . . the figures of all these errors are anticipated is to be as low as probable for improved prediction accuracy. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may , . . figure of recorded covid- crises as of january to april as a substitute for epidemiologic spread procedure, the study employed aggregated methods svr, nn, and lr to predict the instantaneous movement of the conveyance dynamics and generate the real-time predictions of covid- disease transversely the metropolises of india. the finding presented that the precision of estimation and succeeding multiple-process prediction was extreme. it was revealed that predicting enhanced when aggregating regression models together compared to when used individually. the postulated system appraised the possible period when there will be decreasing evolution of fresh established cases crosswise the metropolises and the extent of covid- disease across india and the minute the figure of the accrued established incident of covid- would spread to the upland of their accrued crises. the core intention of this investigation is to formulate a simple mean aggregated method for the estimation of covid- disease in india. to formulate this, the study first computed the revert figures of the covid- disease from the whole separate regression procedure followed by their amalgamation in an aggregated method. in the second stage of formulating the method, the study intention is to decrease the prediction errors of covid- in india and these errors include rmse, mae, and mape. each time a certain method gives a greater prediction error compared to alternative methods its weightiness in the aggregate is diminished and vice versa. this study has joined the employed methods and presented the data for covid- disease in india as stated below. in this study, the formulation of aggregated methods illustrates a substantial enhancement in the prediction of the covid- disease in india. the postulated aggregated method is likened with the separate prediction of these methods. the attained covid- prediction precision attained for the entire approach is represented in the table - . the obtainable outcome of covid- disease is shown in table which demonstrates that our postulated aggregated system delivered the least prediction error amid the entire separate fitted methods. the study delivered a substantial enhancement in prediction precisions for covid- disease in india when the postulated aggregated system was employed. if the datasets are dependable and there exist no subsequent outbreak, the aggregated methods predicted that covid- outburst in india could end by may ending. the aggregated methods permit entering the interferences information as well as examining the influence of interferences on the extent of the disease outburst and the ending period if the covid- epidemic. employing the assumed original extents of the covid- outburst, the study utilized the aggregated methods (svr, nn, and lr) with identified framework and model to evaluate the extent of the outburst in time to come and excite the influence of the interferences on the magnitude and asperity of the pandemic. approbatory to the individually used methods for the conveyance of the covid- diseases, the aggregated methods (svr, nn, and lr) provide real-time predicting instruments used for shaping and tracking covid- disease in india, . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted may , . . https://doi.org/ . / . . . doi: medrxiv preprint reckoning the covid- disease, obtaining covid- disease asperity, predicting the extent of the pandemic together with supporting government and health staffs to constitute strategy and competent verdicts towards the eradication of the covid- diseases in india. the integration of the prediction from diverse methods substantially decreases prediction errors and consequently makes available advanced precision. a few decades back, several researchers' studies have suggested several statistical methods. the study postulated a simple-mean aggregated method for the prediction of covid- disease in india. the projected aggregated approach investigated separate predictions and therefore the prediction of covid- disease in india is formulated with very recognized methods: neural network, support vector regression, and linear regression. the result indicates that the postulated method outperformed based on prediction precision of the covid- disease in india when likened to currently existing applicable methods. in the future the competence of the postulated method could be as well as be investigated and some other regression models or algorithms can be used and evaluated. the authentic datasets of covid- have been gathered from https://www.mygov.in/ and https://www.pharmaceutical-technology.com/ the dataset is publicly available on cases from india from the first case index on january , . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may , . . is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted may , . . https://doi.org/ . / . . . doi: medrxiv preprint effectiveness of n respirators versus surgical masks in protecting health care workers from acute respiratory infection: a systematic review and meta-analysis effectiveness of surgical and cotton masks in blocking sars-cov- : a controlled comparison in patients coronavirus disease (covid- ) situation report - . world health organization novel coronavirus ( -ncov) in the u.s. centers for disease control and prevention (cdc) wuhan virus: what clinicians need to know us now has more coronavirus cases than either china or italy mmwr morb mortal wkly rep northern california coronavirus patient wasn't tested for days. the washington post early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster covid- ): covid- situation summary impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand cdc: first person-to-person spread of novel coronavirus in us reports its first case of person-to-person transmission. the new york times covid- ): people at higher risk novel coronavirus the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention lost sense of smell may be peculiar clue to coronavirus infection. the new york times epidemiological characteristics of pediatric patients with coronavirus disease in china clinical and epidemiological features of children with coronavirus disease (covid- ) in zhejiang, china: an observational cohort study interim healthcare infection prevention and control recommendations for patients under investigation for novel coronavirus novel coronavirus covid- treatment: a review of early and emerging options. open forum infectious diseases (ofid) novel coronavirus aerosol and surface stability of sars-cov- as compared with sars-cov- stability of sars-cov- in different environmental conditions. the lancet microbe virological assessment of hospitalized patients with covid- clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study viral dynamics in mild and severe cases of covid- presumed asymptomatic carrier transmission of covid- a familial cluster of infection associated with the novel coronavirus indicating potential person-to-person transmission during the incubation period sars-cov- viral load in upper respiratory specimens of infected patients respiratory virus shedding in exhaled breath and efficacy of face masks infectious diseases society of america guidelines on the treatment and management of patients with covid- pharmacologic treatments for coronavirus disease (covid- ): a review review of emerging pharmacotherapy for the treatment of coronavirus disease analysis and projections of transmission dynamics of ncov in wuhan reporting, epidemic growth, and reproduction numbers for the novel coronavirus ( -ncov) epidemic real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model retrieved on th forecasting strong seasonal time series with artificial neural networks dimensionality reduction for indexing time series based on the minimum distance work watermarking mpeg- d mesh animation with time-series analysis an evaluation of neural network ensembles and model selection for time series prediction prediction of blood glucose concentration ahead of time with feature based neural network an empirical application of linear regression method and fir individual versus super ensemble forecasts of seasonal influenza outbreaks in the united states ensemble method for dengue prediction classification of dengue illness based on readily available laboratory data predicting the severity of dengue fever in children on admission based on clinical features and laboratory indicators: application of classification tree analysis the author declared that they didn't receive any funds from any organization. authors declared that there is no conflict of interest key: cord- - v grqa authors: kasilingam, dharun; prabhakaran, s.p sathiya; dinesh kumar, r; rajagopal, varthini; santhosh kumar, t; soundararaj, ajitha title: exploring the growth of covid‐ cases using exponential modelling across countries and predicting signs of early containment using machine learning date: - - journal: transbound emerg dis doi: . /tbed. sha: doc_id: cord_uid: v grqa covid‐ pandemic disease spread by the sars‐cov‐ single‐strand structure rna virus, belongs to the (th) generation of the coronavirus family. following an unusual replication mechanism, it’s extreme ease of transmissivity has put many counties under lockdown. with uncertainty of developing a cure/vaccine for the infection in the near future, the onus currently lies on healthcare infrastructure, policies, government activities, and behaviour of the people to contain the virus. this research uses exponential growth modelling studies to understand the spreading patterns of the covid‐ virus and identifies countries that have shown early signs of containment until (th) march . predictive supervised machine learning models are built using infrastructure, environment, policies, and infection‐related independent variables to predict early containment. covid‐ infection data across countries are used. logistic regression results show a positive significant relationship between healthcare infrastructure and lockdown policies, and signs of early containment. machine learning models based on logistic regression, decision tree, random forest, and support vector machines are developed and show accuracies between . % to . % to predict early signs of infection containment. other policies and the decisions taken by countries to contain the infection are also discussed. coronaviruses, though uncommon, are serious pathogens responsible for infections that posit flu-like symptoms in infected individuals. these symptoms sometimes resemble the cold and cough symptoms caused by the rhinovirus. recently, the family has added its seventh generation coronavirus -sars-cov- (chengxin et al., ) . the virus shares % identity to severe acute respiratory syndrome (sars) and % identity to middle east respiratory syndrome (mers) epidemic outbreak in and (salute, ) . sarc-cov- that causes covid- mutated to transmit from animal to human. this virus is believed to have transferred to humans through bats from a meat market in wuhan, china (rajendran et al., ; shereen et al., ) . in march , who declared the covid- to be a pandemic; a pandemic being described as an infection that has spread across countries and international borders rather than within a local region or neighbouring countries. the sarc-cov- is a deadly corona virus that is transmitted readily between humans and already infected more than , people all over the world in countries as on th march which led global shutdowns (who, ) . the fatality rate has varied among countries and age groups. until june , the fatality rate averaged . % with italy recording the highest of . %. the fatality rate of us, germany, and india were . %, . %, and . % respectively until june (our world in data, ) . of the total deaths, less than % belonged to the age group of less than years thereby indicating that the younger population is much more resilient to the covid- (worldmeters, ) . while these fatality rates are significantly less than those of mers ( . %) and sars ( . %) (petrosillo et al., ) , covid- has severe transmissivity because of the possibility of asymptomatic people being carriers and spreaders of the virus (daw et al., ) . the reproduction number r for sarc-cov- has been found to be between . to . (sheng et al., ) . a value of r greater than indicates that the disease can invade the human population and higher the value, the easier is it's spread. sarc-cov- is the largest single-strand rna virus known to the humankind; while other viruses have a single protein spike for attachment to the human cell, this coronavirus family has to spike proteins, which makes it easier for the virus to attach itself to the ace- protein in humans (paraskevis et al., ) . the virus follows an unusual double step replication mechanism, which leads to high rates of proliferation (luan et al., ) . the this article is protected by copyright. all rights reserved incubation period is typically to days, and the infected person often does not have serious symptoms, rather showing common symptoms associated with flu and pneumonia (rodeny, ) . general symptoms of pneumonia include fever, cough, chest pain, shortness of pain, fatigue, headache, myalgia, and arthralgia (sattar sba, ) . in addition to symptoms of pneumonia, covid- infected individuals may experience a loss of taste or smell, nausea, congestion, and diarrhoea (cdc, ) . there are a few drugs that are being recommended and used to manage the symptoms of covid- , but there has, as yet, been no vaccines that are proven to be effective against the coronavirus family, including covid- (sexton et al., ; gautret et al., ) . in the absence of vaccines, it is imperative to check transmission of the virus by alternative ways (dey et al., ) . policy changes in pandemic and epidemic situations involve social distancing, lockdowns, travel restrictions, awareness campaigns etc. it has been speculated in past research that environmental conditions of countries like temperature and humidity also sometimes play a significant role in controlling pandemics (lin et al., ) . quantitative covid- impact analyses are scarce in literature, given the recency of the pandemic and more studies in this area are necessary, given the seriousness of the infection. epidemics are assumed to have an exponential growth at an early stage and the number of infections reduces over time, due to interventions like lockdowns, travel restrictions, awareness programs, etc. mathematical modelling studies using exponential growth analysis coupled with machine learning could provide a better prediction model for covid- transmission (keeling and danon, ; siettos and russo, ; victor, ) . such models must incorporate the various precautionary measures taken during the viral outbreak. the objective of the research is to develop a mathematical model using exponential growth analysis coupled with machine learning, to predict worldwide covid- early containment signs. models have been developed based on data collected from countries. the objectives of this work are twofold. first, it seeks to identify countries that were successful in early containment of the covid- virus. secondly, the research aims at building supervised machine learning models with high accuracies for predicting signs of early containment with infrastructure availability, environmental factors, infection severity factors, and government policies of countries as independent variables. in the process of modelling, the significance of the above variables in containing the infection at early stages is this article is protected by copyright. all rights reserved also studied. this report also includes a discussion on other activities undertaken by the governments of various nations to flatten the infections curve and their corresponding effectiveness. covid- is believed to have originated in an animal meat market in wuhan, china and it is thought to have been transmitted from bats (shereen et al., ) . within few months, the virus has rapidly spread across the world, through transmissions of fluids and aerosol particles between humans. initially, all diagnosed cases outside china had a travel history to the wuhan market. soon, community transfer caused exponential increases in infections in countries like italy, us, uk, korea, japan, etc. the ability of the sars-cov- virus to double replicate with the spike protein, has posed significant challenges to the development of vaccines (shereen et al., ) . while hydroxychloroquine and azithromycin have been recommended by some researchers, to treat covid- -infected people, there haven't been too many clinical trials to validate the claim (gautret et al., ) . thus, until a scientifically validate cure or vaccine is developed, countries have to rely on preventive measures to contain the spread. this, in turn, depends on epidemiological studies that can predict spreading patterns so that policymakers can take appropriate protective measures. several viruses including sars have been reported to be vulnerable to hot temperatures, which results in differences in spreading patterns across geographic locations (zhang et al., ) . however, such geographic variations have not yet been analysed for covid- . other factors like government policies and interventions, infrastructure availability, and the severity of the infection itself can affect the ability of a country to contain epidemics and pandemics. this research seeks to explore all the above factors. the climatic conditions such as temperature and humidity play an important role in both airborne and aerosol virus transmissions. the -year human relationship with the influenza virus has proven that the mortality rate is directly related to temperature and humidity (lowen and steel, ) . hence, in order to minimize transmission of diseases, isolation wards in hospitals generally tend to have optimized pressure, temperature, and humidity (who, ) . research on the virus in the diamond cruise ship off the coast of japan showed that a one-degree rise in temperature and a one percent increase in pressure this article is protected by copyright. all rights reserved could reduce the reproduction number r down by . - . . it must be mentioned that the generalizability of the study is questionable because the ship was a contained environment and the results may not apply to the real world (sheng et al., ) . certain studies in china and indonesia have investigated the relationship between the temperature and the spread of infection and resultant deaths and have reported a low to medium level of correlation (tosepu et al., ; yueling ma et al., ) . relative humidity was found to have low to no correlation with infection spread or deaths. global warming has also been a reason for recent temperature increases and certain studies indicate that this can reduce flu based viral infections (national research council, ; actuaries, ; dincer et al., ) . however, these statements need to be further validated. while the spread of virus may be affected by climatic conditions, once the virus enters the human body, it is independent of the outside environment. however, since the virus lives outside the human body for a period of at least hours under normal conditions (richard, ) , it is necessary to study the effects of the environmental on the spreading patterns itself. social distancing, although a new terminology for the st century, is not a new approach to epidemic control. it was used by the united kingdom in to control the influenza virus outbreak that caused about million deaths. social distancing involves the avoidance of mass gatherings and distancing of at least six feet between people. such measures are combined with enhanced personal hygiene through regular hand wash, and wearing a protective mask for flu-like outbreaks (yu et al., ; leung et al., ) . this is done primarily because flu causing viruses are spread through aerosols generated from saliva and nasal fluid, which can be transmitted across distances as much as three feet. the average lifetime of covid- viruses in the outer environment is believed to be about hours, which increases transmissivity because aerosols from infected people can settle on doorknobs, lifts, transports, hotels, malls etc. and stay active for a long time, thus increasing the window of transmission. direct physical contacts, such as hand-shaking, are also avenues of transmission of the virus. the reduction of social contact has been proven to significantly reduce flu-like diseases (maharaj and kleczkowski, ) . the closure of schools and malls flattened the this article is protected by copyright. all rights reserved spread curve during the influenza pandemic in (rashid et al., n.d.; moh, ) . thus, governments worldwide have stressed on social distancing and quarantining measures for at least daysthe typical incubation period of covid- virus -to contain its spread (prem et al., ) . lockdown is a preventive strategy taken by local, central or global administration during the spread of epidemic or pandemic diseases and involves stopping transportation between cities, provinces or counties. the world has so far seen four major pandemics, viz., plague in the th century, influenza in , sars in , and the current covid- in as reported by who (porta, ; east et al., ; pi, ) . in all these cases, lockdowns were implemented by various countries to control the outbreaks. china announced lockdown as early as january , to flatten the curve of the covid- infections over time. in march, most countries around the globe announced lockdowns of local transport, office, industries, city and national borders to contain the virus (callaway et al., ) . although quarantine centres for the infected are available in hospitals, large-scale infections necessitate self-quarantines and lockdown measures, in addition to the hospital-based quarantines (wuhan, ) . during epidemic and pandemic viral outbreaks, the availability of and access to health care infrastructure such as hospitals, beds, healthcare workers, clinical equipment, first aid kits, ventilators, and protective equipment are vital to pandemic management (bambas and drayton, ; persoff et al., ) . during the massive influenza outbreak of , even developed countries had inadequate health care infrastructure, which further expanded the outbreak (george, ). the ebola outbreak in west africa became uncontrollable due to lack of infrastructure facilities (paweska et al., ) . after the outbreak, who in south africa had asked the hospitals to report their available facilities to plan for future infections optimally (murrin, ) . innovative measures have been recommended, to create necessary healthcare infrastructure during pandemic and epidemic situations by converting schools, colleges, theatres, and stadiums into hospitals and quarantine centres (wimberly, ; nuzzo et al., ) . health care workers supported by ngos, youth, and volunteers also play a significant role in containing outbreaks (itzwerth, ) . hence studying health care this article is protected by copyright. all rights reserved infrastructure availability across countries can predict covid- containment at an early stage. predictive modelling using machine learning and growth models can provide actionable insights to policy makers and governments to contain epidemic and pandemic infections (thompson et al., ) . during the onset of an epidemic, it is crucial to use exponential growth models to understand the infection rates and with proper policy implementations and behavioural changes among the susceptible group of the population, the slope reduces and the curve flattens over time (keeling and danon, ). for other outbreaks like smallpox, ebola, sars, and influenza, various studies have used mathematical and statistical modelling to understand the growth of infections (dietz, ; nishiura, ; kerkhove and ferguson, ) . in fact, the centres for disease control and prevention has an exclusive book with established procedures for analysing disease outbreaks, stressing on the importance of the such modelling studies. (dicker, ) in outbreaks, epidemiologists generally use the exponential growth model at the onset of an outbreak and proceed with prediction and classification techniques like regression, decision trees, neural networks deep learning, etc. to forecast outbreaks. (sameni, ; victor, ) . there are few studies on modelling and predicting containment of covid- so far (lin et al., ; prem et al., ) . the research work reported in this paper, sought to integrate crucial variables concerning infrastructure, environment, policies, and severity of the disease to predict initial signs of containment. the study used a machine learning and exponential growth model. the variables used as part of the predictive mode were, doctors per population, beds per population, average temperature, average humidity, days since official lockdown, percentage of lockdown days, total cases per million population, deaths per million population, days since the first contact, and percentage of serious cases of infected. data associated with the variables were collected from different official sources for a total of counties with respect to covid- infections as on th march . this accounts for , covid- cases comprising of . % of the total infections this article is protected by copyright. all rights reserved worldwide. the daily number of infections, recovery, and deaths were collected from the website of the who. the data for infrastructure-centred variables like the number of hospitals and the number of doctors were taken form (world bank, ) . environmentbased variables like average temperature and humidity since the onset of covid- was taken from (weather underground, ). day-wise covid- case distributions extracted from who were used to identify countries that showed sign of containment of the virus based on a novel exponential growth modelling approach. raw data from the sources were also consolidated and the variables physicians per thousand individuals, hospitals per thousand individuals, percentage of lockdown days since the first contact, cases per million population, deaths per million population, days since the first case, serious cases per thousand infections, average temperature since the first infection, and average humidity since the first infection were calculated to train the machine learning models. most epidemic and pandemic diseases grow exponentially in the initial stages of the outset in a country (ma, ) . a popular modelling technique that demonstrates this is the susceptible-infectious-recovered (sir) model (kermack et al., ) . if s denotes the fraction of susceptible individuals to a pandemic, i indicates the fraction of infectious people, r is the fraction of recovered patients, β indicates the transmission rate per infectious individual, and the recovery rate is denoted by γ, the infectious period is exponentially distributed with a mean of / γ as shown below. linearizing this about the disease-free equilibrium, we get the following. hence from the above expression, if − > , then the infection function i(t) grows exponentially about the disease-free equilibrium point. in addition to this, at the onset of the infection, ≈ and hence the incidence rate = also grows exponentially. hence, modelling the initial stages on a pandemic like covid- is both relevant and crucial in understanding the growth of the infection. although sub-exponential and polynomial modelling have worked in cases of outbreaks like ebola, hiv, and foot and mouth diseases (chowell et al., ) , they generally work well with proceeding generations. for pandemics like covid- , the exponential growth model is relevant and the use of least-squares at the initial stages can afford precise insights. figure shows the analysis plan to achieve the objectives of the research. this article is protected by copyright. all rights reserved the exponential growth model assumes that the onset of any outbreak follows an exponential distribution. however, due to government interventions, medical innovations, behavioural changes etc, at a later stage, the growth curve flattens and rate of infections gradually reduces (kermack et al., ) . to identify such signs, we looked at the infections in the last seven-day period and the deviation of the data points from the modelled exponential curve was captured using the mean absolute percentage error metric. based on the errors and the direction in which the actual data points were to the modelled growth curve, the countries were classified according to whether they showed initial sign of containment or not. in line with the objectives of the study, classifiers were built based on a set of independent variables to predict if a country that has covid- infections showed early signs of infection containment as a reflection of policy implementations and behaviour changes. logistic regression was used to understand the list of independent variables significantly affecting the infection containment and their corresponding importance in the model. then, to predict signs of early containment, machine learning algorithms like logistic regression, decision trees, random forest and support vector machines were used and their corresponding accuracies are compared. for all models, cross-validation was done in folds to address overfitting. logistic regression by le cessie and van houwelingen, ( ) is a generalized linear model (glm) and is one of the most widely used classifiers. according to (kondofersky and theis, ) , when there is binary response, as in this research, by using logistic regression one typically aims at estimating the conditional probability . as with simple linear regression, bearing equation = + , estimating the dependent variable y directly, the logistic regression estimates p( = ) using the following equation. this article is protected by copyright. all rights reserved as with multiple linear regression, logistic regression can also handle multiple independent variables and its probability estimate can be represented as follows. = + −( + + ……+ the conditional probability ( = | = ) can be calculated using the odds ratio /( − ). the significance of the beta coefficient values ( , , , … , ) in the above equation can be tested to see if their corresponding independent variables ( , , , … , ) are influencers of the dependent variable. a wald test is generally conducted to evaluate the statistical significance of the coefficients in the model. since logistic regression falls under the category of glm, the significance of each independent variable in predicting the outcome of the dependent variable, sign of early containment, can be studied. a decision tree is a decision support model that illustrates the consequences, chance, and event outcomes of certain decisions. decision trees are used as a predictive model to make statistical conclusions about an item's target value, based on observations. in this tree structure, leaves represent class labels and branches represent conjunctions of features that lead to those class labels. there are both classification trees where the response variable takes on a set of categorical values and regression trees where the response variable takes on a set of continuous values. the collective name for such trees is classification and regression trees (cart), first introduced and developed by (breiman et al., ) in classification and regression trees. decision trees use two metrics namely entropy and information gain to arrive at the final tree. entropy is the measure of the total amount of uncertainity in the dataset and is given as follows: s -the data set for which entropy is to be calculated cset of classes in the data set s p(c)ratio of number of elements in class c to the number of elements in set s this article is protected by copyright. all rights reserved when the entropy value is equal to zero, the dataset s is perfectly classified. the information gain metric is defined as the measure of the difference in the entropy from before to after the dataset s is split based on an atribute a and is given as follows. step : compute entropy for the dataset step : for every feature in the dataset, compute the following i. calculate the entropy for all the categorical values ii. find the average information entropy for current attributes iii. calculate the gain for curret attributes step : select the attribute with the highest gain step : repeat from step till the desired tree is achieved introduced by (breiman, ) , random forest is a statistical supervised machine learning technique that we used for both regression and classification. this is an ensemble learning technique that uses an averaged combination of many decision trees for the final prediction. the technique of averaging a statistical machine learning model is called bagging and it improves stability and avoids overfitting (hastie et al., ) . normally, decision trees are not competitive to the best-supervised learning approaches in terms of prediction accuracy since they tend to have high variance and low bias. this is because building two different decision trees can yield in two different trees. bagging is therefore well suited for this article is protected by copyright. all rights reserved decision tress since it reduces the variance. the idea behind random forests is to draw bootstrap samples from the training data set and then build several different decision trees on the different training samples. this method is called random forest because it chooses random input variables before every split when building each tree. by doing this, each tree would have reduced covariance, which, in turn, would lower the overall variance even further (hastie et al., ) . the random forest algorithm has two stagesrandom forest creation followed by random forest prediction. the steps involved in the stages are as follows. step : randomly select 'k' features from the total 'm' features available in the dataset where k << m step : using the best split point, calculate the node 'd', among the selected 'k' step : split the node into daughter nodes using the best split step : repeat steps to until 'l' nodes are reached step : repeat steps to for 'n' number times to create a forest of 'n' number of trees stage ii: random forest prediction step : using the features and applying the rules of randomly selected decision tree, predict the outcome and store it as a predicted target step : calculate the votes for each predicted target step : the highest voted predicted target will be the prediction of the random forest algorithm the objective of support vector machine (svm) is to find a line that best separates the data into multiple groups. this is achieved by an optimization process supported by the data in the training set. these instances are called support vectors and they form a crucial role in the classification process (flake and lawrence, ) . finally, few datasets can be separated with just a straight line. sometimes a line with curves or even polygonal regions must be marked. this is achieved with svm by projecting the data into a higher-dimensional space to draw the lines and make predictions. svms calculate a maximum margin around the boundary that ultimately results in a homogenous partition. the ultimate goal is to establish a this article is protected by copyright. all rights reserved margin as wide as possible. in order to so, a lagrange multiplier has to be constructed as follows and maximized. ( , ) = + table shows the result for logistic regression with early containment as the dependent variable. of all the independent variables, the availability of beds in hospitals and the percentage of lockdown days significantly and positively affected the signs of early this article is protected by copyright. all rights reserved containment. other variables did not significantly influence the dependent variables. the model had an accuracy of . % in the classification. the true positive and false negative rates were found to be . % and . % respectively. precision and recall values were . and . . the f score and roc values were found to be . and . respectively. a j decision tree was constructed for predicting early infection containment with the independent variables listed in figure . the batch size was set to and a confidence factor was selected as . . the minimum number of objects on the tree was set as . the accuracy of the tree was found to be . %. the variables in the decision tree were percentage lockdown days, days since official lockdown, and death rate per million population. the decision tree is shown in figure . the true positive and false negative rates were found to be % and . % respectively. precision and recall values were . and . . the f score and roc values were found to be . and . respectively. a random forest ensemble algorithm was created with combined trees. the batch size was selected as and the depth of the trees was set to unlimited. other metrics for the random forest algorithm are given in table . this model reported a high accuracy figure of . % in correctly classifying countries that showed signs of early containment. the true positive and false negative rates were found to be . % and . % respectively. precision and recall values were . and . . the f score and roc values were found to be . and . respectively. in order to make predictions for signs of early containment, an svm was modelled this article is protected by copyright. all rights reserved on -fold cross-validation with the data for all the algorithms and models, it can be inferred that the random forest design produces the minimum error and maximum accuracy as reported in table . it outshines all the other machine learning algorithms constructed in the study. j decision tree, logistic regression and svm produce almost similar levels of accuracy in predicting the sign of containment of covid- . this research is one of the first of its kind to integrate exponential growth modelling with machine learning techniques for predicting the spread of covid- . the research presents machine learning models based on variables such as infrastructure, environment, policies, and the infection itself, to predict early signs of containment in the country. for the purpose, disease data from leading countries in covid- infections were taken and exponential growth modelling was used to see if the countries showed signs of containment. then with the sign of the early containment of the infection as a dependent variable, supervised machine learning predictive models including logistic regression, decision tree, random forest, and support vector machine were developed. this research can directly be of use to countries and policymakers to understand if their proposed interventions are effective in containing infections even during early stages. (tosepu et al., ; yueling ma et al., ) . however, the long-term effect of environmental factors on the infection rates may prove to be significant. decision tree analysis also shows that early signs of containment are possible if the number of lockdown days is at least . % of the days since the first contact to contain the infection. if that is not the case, countries show recovery signs if the lockdown is at least days or more. for countries with a lockdown period less than days, variable depicting the number of deaths per million population plays a significant role in containing the infection. this variable is indirectly related to the health care infrastructure of countries like beds, physician, ventilators, icus etc. hence in any pandemic situation, governments must be proactive and frame policies even at the onset, thereby reducing the risk of spread, which would ultimately lead to early containment. this also emphasises on the need for resilient health care infrastructure to contain infections at an early stage. the machine learning models random forest and support vector machines were able to classify the countries with respect to their signs of early containment with an accuracy of . and . percentages, respectively, proving random forest to be the best machine learning algorithm for the problem studied. although this research applies data from only countries, the proposed models with their corresponding hyper parameters can be extended to predict early containment for the other countries as well. similarly, although these models were built only for the covid- pandemic, they can serve as a base for other future pandemics that have similar characteristics and reproduction numbers thereby giving governments the necessary information to take timely actions to protect both people and the economy. this article is protected by copyright. all rights reserved act called covid- act which has proven to be effective to contain the infection (library of congress, ). the number of hospital beds per population of austria was also high, which facilitated early recovery. chile has implemented sanitary barriers and intense screening mechanisms to track and quarantine the infected (us embassy, ). in addition to tough quarantine measures, denmark closed down schools and also announced lockdown in march. employers were also instructed to not cut salaries of the employees on quarantine thereby encouraging social distancing and hence containing the infection (carstensen, a) . japan, south korea, and singapore did not announce any lockdowns. south korea used processes that led to early detection of the covid- and quarantining the infected, thus stopping spread. they also predicted the movement of viruses and tactical interventions were taken to minimize spread (npr, ). singapore had a ready infrastructure with isolation wards in place during the sars outbreak and was readily equipped, which led to early containment of covid- . strong community engagement messages and communications from the government also led to better pandemic management in singapore (fisher, a) . most other countries that showed early signs of recovery rigorously followed lockdowns, social distancing, travel restrictions, and testing to contain infections. another reason for the countries like japan, korea and austria to contain the infection was the presence of availability of strong health care infrastructures in these countries to address the infections. the various actions taken by the government to control the transmission of covid- are shown in table . countries like italy, brazil, india, malaysia, pakistan, united kingdom etc. do not have the necessary health care infrastructure to support mass admission of covid- patients and hence need to rely on intense lockdowns to contain the infections. the increase in the number of covid- cases in the us and the inability to contain it is also due to late lockdown decision of the government post-outbreak. the percentage of lockdown days since the first infection continues to be low for these countries to be on a recovery path against the infection. with time, there is a high probability that the infection will be contained. however, in the long run, these countries must invest in improving health care facilities to reduce causalities during pandemics. countries must be prepared for epidemics and pandemics and proactive policies and infrastructure as in the case of singapore can save more lives than reactive measures. it is evident that covid- , unlike sars, will not be controlled by environmental factors and any future outbreaks will still rely on healthcare infrastructures, timely lockdowns, and social distancing for containment. this article is protected by copyright. all rights reserved there is no conflict of interest with the authors. no funding received. the data is openly available in world health organisation report. the research confined to the highest level of ethics. this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved gesley, ) brazil employees at the airport were asked to wear a mask. borders were closed for flights from affected countries (cdcp, ) canada all travellers were forced to self-isolate for days upon entry to control the outbreak (gc, ) chile screening in the airport was enhanced and people with symptoms were iran followed strict social distancing and lockdown (duddu, ) ireland invested in massive testing facilities. treated all patients equally irrespective of their income strata. all hospitals operated on a not for profit basis (bbc, this article is protected by copyright. all rights reserved ) used technology to track the movement of infected individuals with their mobiles and quarantined the people who came in contact with the individual (lomas, ) italy though italy closed borders during the onset, lack of proper testing facilities caused a massive outbreak. this was followed by a strict lockdown (gary, ) japan managed the outbreak with rules and excellent medical infrastructure. (japan, ) luxembourg quarantined people over years to reduce casualties (piscitelli, ) malaysia the banned entry of people from infected countries followed with additional screening measures in the airport. promoted personal hygiene and eventually ended with a lockdown. (world, a) netherlands travellers returning from affected countries were advised to visit doctors and medical facilities if symptoms were felt. post outbreak, the country went under lockdown. (world, b) norway travel bans and closure of schools, public services like gums, malls, theatres etc. (norway panorama, ) formed a team to monitor situations and take necessary actions on a daily basis. (pakistan, ) portugal employed strict lockdown (ivo oliveira, ) qatar proper tracking, and strict screening and testing of travellers (health, ) republic of korea proactively built a centralized testing and quarantine facility before an outbreak in the country. china's reports triggered this action (beaubien, ) romania lockdown and border closing (gherasim, ) singapore with previous experience from sars pandemic, the country had a proper infrastructure facility with negative pressure room for pandemic control. the testing was done rigorously and the infected were not let back into society. migrants from other countries were not allowed to work until the pandemic is controlled. (fisher, b) slovenia used innovative ways to spread covid- control messages before going into lockdown. (slovenija, ) south africa immediately implemented entry and exit to affected countries. declared as a this article is protected by copyright. all rights reserved national disaster and went for the lockdown to prevent a major outbreak (fihlani, ) spain local movement controlled by social distancing. travel to an affected country completely banned. enhanced medical attention at arrival to control the spread. (kate mayberry, ) after closing school, colleges and non-essential business, the country used their military and civilian support to enhance infrastructure and healthcare needs to contain the infection (keystone, ) the united kingdom people with symptoms were asked to self-quarantine. cancelled overseas travels and only tested people who were admitted. followed social distancing, lookdown, isolation and house quarantined. the country did not force people for testing. (yong, ) united states of america enforce travel restriction and implemented mandatory quarantine in new york. a level of screening and lockdown was implemented. (brittany potential impact of pandemic influenza on the u . s . health insurance industry sponsored by committee on life insurance research health section joint risk management section society of actuaries prepared by health & human development in the new global economy : the contributions and perspectives of civil society in the americas editors bbc, : bbc, coronavirus: republic of ireland introduces stronger measures : goats and soda, how south korea reined in the outbreak without shutting everything down random forests classification and regression trees the washington post, trump says quarantine for new york area 'will accepted article this article is protected by copyright. all rights reserved not be necessary coronavirus-related deaths double in two days the world, denmark takes swift action against coronavirus the world, denmark takes swift action against coronavirus: 'you can't do enough to contain this epidemic : cdcp, travel health notices covid- : france calls unemployed to work in fields as borders stay closed : protein structure and sequence re-analysis of -ncov genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and hiv- . - characterizing the reproduction number of epidemics with early subexponential growth dynamics : preliminary epidemiological analysis of suspected cases of corona virus infection in libya analyzing the epidemiological outbreak of covid- : a visual exploratory data analysis (eda) approach preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a data-driven analysis in the early phase of the outbreak principles of epidemiology in public health practice daniel bernoulli ' s epidemiological model revisited global warming: engineering solutions : focus, covid- in iran: coronavirus outbreak, measures and impact eclinicalmedicine emerging zoonoses : a one health challenge greece on total lockdown all new arrivals will be quarantined : bbc, coronavirus: african states impose strict restrictions why singapore isn't in a coronavirus lockdown -as told by a doctor of the country b: the print, why singapore isn't in a coronaviruslockdown -as told by a doctor of the country accepted article this article is protected by copyright. all rights reserved efficient svm regression training with smo : hbr, lessons from italy's response to coronavirus : hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial prime minister announces new actions under canada's covid- response responding to simulated pandemic influenza : euobserver, romania's orban sworn in again amid corona emergency the elements of statistical learning: data mining, inference, and prediction : state of qatar, coronavirus disease critical infrastructure and preparedness perspectives on pandemic influenza : pololitico, portugal shuts down to tackle coronavirus accepted article this article is protected by copyright. all rights reserved emergency management, epidemics, government, infectious and parasitic diseases, public health test every suspected case" of covid- -live updates mathematical modelling of infectious diseases : cnn, why is covid- death rate so low in germany epidemic and intervention modelling -a of the royal society of london. s.a. mckendrick containing papers of a mathematical, and physical character, : a contribution to the mathematical theory of epidemics : swissinfo, coronavirus: the situation in switzerland statistical learning with sparsity: the lasso and generalizations : iceland review, steps taken to prevent spread of covid- in iceland ridge estimators in logistic regression individual preventive social distancing during an epidemic may have negative population-level outcomes austria: government tightens rules to contain spread of coronavirus : international journal of infectious diseases a conceptual model for the coronavirus disease ( covid- ) outbreak in wuhan , china with individual reaction and governmental action : the reproductive number of covid- is higher compared to sars coronavirus : tech crunch, israel passes emergency law to use mobile data for covid- contact tracing roles of humidity and temperature in shaping influenza seasonality : spike protein recognition of mammalian ace predicts the host range and an optimized ace for sars-cov- infection estimating epidemic exponential growth rate and basic reproduction number controlling epidemic spread by social distancing : do it well or not at all moh pandemic readiness and response plan for influenza and other acute respiratory diseases office of inspector general hospitals reported improved preparedness for emerging infectious diseases after the ebola outbreak linkages between climate, ecosystems, and infectious accepted article this article is protected by copyright. all rights reserved disease real-time forecasting of an epidemic using a discrete time stochastic model : a case study of pandemic influenza : the nordic page, norway government takes radical decisions against spread of coronavirus: first time since ww how south korea reined in the outbreak without shutting everything down what makes health systems resilient against infectious disease outbreaks and natural hazards ? results from a scoping review channel news asia, covid- self-isolation is punishing the poor in indonesia gulf news, steps pakistan is taking to contain coronavirus : full-genome evolutionary analysis of the novel corona virus ( -ncov ) rejects the hypothesis of emergence as a result of a recent recombination event a modular high biosafety field laboratory the role of hospital medicine in emergency preparedness: a framework for hospitalist leadership in disaster preparedness, response, and recovery elsevier has created a covid- resource centre with free information in english and mandarin on the novel coronavirus covid- . the covid- resource centre is hosted on elsevier connect , the company ' s public news and information life lessons from the history of lockdowns : msan, measures taken by the government council on march in response to the coronavirus dictionary of epidemiology : articles the effect of control strategies to reduce social mixing on outcomes of the covid- epidemic in wuhan , china : a modelling study systematic literature review on novel corona virus sars-cov- : a threat to human era. virusdisease - social distancing evidence summary coronavirus epidemic , humidity and temperature novel coronavirus ( -ncov) update: uncoating the virus nuovo coronavirus covid- . minist. della salut : mathematical modeling of epidemic diseases ; a case study of the covid- coronavirus : statistica, precautionary measures to prevent spread of covid- india : bacterial pneumonia homology-based identification of a mutation in the coronavirus rna-dependent rna polymerase that confers resistance to multiple mutagens : estimation of the reproductive number of novel coronavirus ( covid- ) and the probable outbreak size on the diamond princess cruise ship : a data-driven analysis covid- infection: origin, transmission, and characteristics of human coronaviruses mathematical modeling of infectious disease dynamics : statnews, ecuador becomes the latest country to eye compulsory licensing for covid- products gov of slovenija accepted article this article is protected by copyright. all rights reserved : detection , forecasting and control of infectious disease epidemics : modelling outbreaks in humans , animals and plants : correlation between weather and covid- pandemic in jakarta : u.s embassy in chile, global level health advisory : mathematical predictions for covid- as a global pandemic : wunderground infection prevention and control of epidemic-and pandemic-prone acute respiratory infections in health care covid- ) outbreak situation report of the who-china joint mission on coronavirus disease (covid- ). world health organization who, c: report of the who-china joint mission on coronavirus disease : digitalcommons @ unmc pandemic planning : estimating disease burden of pandemic influenza to guide preparedness planning decisions for nebraska medicine physicians (per , people) [online] available at accepted article this article is protected by copyright a: garda world, malaysia: new travel restrictions introduced february /update b: garda world, netherlands: government confirms first case of covid- nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study : locked down wuhan and why we always overplay the threat of the new kenan malik china ' s reaction to the coronavirus outbreak may have the opposite effect to what ' s needed : tthe atlantic, the u.k.'s coronavirus 'herd immunity' debacle effects of reactive social distancing on the influenza pandemic effects of temperature variation and humidity on the death of covid- in sars-cov- turned positive in a discharged patient with covid- arouses concern regarding the present standard for discharge : estimating the effective reproduction number of the -ncov in china this article is protected by copyright. all rights reserved key: cord- -zp aqpm authors: harrison, andrew g.; lin, tao; wang, penghua title: mechanisms of sars-cov- transmission and pathogenesis date: - - journal: trends immunol doi: . /j.it. . . sha: doc_id: cord_uid: zp aqpm the emergence of sars-coronavirus (sars-cov- ) marks the third highly pathogenic coronavirus to spill over into the human population. sars-cov- is highly transmissible with a broad tissue tropism that is likely perpetuating the pandemic. however, important questions remain regarding its transmissibility and pathogenesis. in this review, we summarize current sars-cov- research, with an emphasis on transmission, tissue tropism, viral pathogenesis, and immune antagonism. we further present advances in animal models that are important for understanding the pathogenesis of sars-cov- , vaccine development, and therapeutic testing. when necessary, comparisons are made from studies with sars to provide further perspectives on covid- , as well as draw inferences for future investigations. infection. first, viral entry may heavily depend on the expression of tmprss , as nearly undetectable amounts of ace still support sars-cov entry, so long as tmprss is present [ ] . second, the mrna expression of cellular genes such as escrt (endosomal sorting complex required for transport) machinery gene members (including chmp , chmp , chmp a, and vps b) related to pro-sars-cov- lifecycle is higher in a small population of human type ii alveolar cells with abundant ace , relative to ace -deficient cells [ ] . this suggests that sars-cov- hijacks a small population of type ii alveolar cells with high expression of ace and other pro-viral genes for its productive replication. third, the lungas the main tropism of sars-covs-may be contingent on the regulation of ace at the transcriptional and protein levels [ , , ] [ , ] . for example, in human airway epithelial cells, ace gene expression is upregulated by type i and ii interferons [ , ] during viral infection. lastly, compared to other sars-covs, sars-cov- spike contains a unique insertion of rrar at the s /s cleavage site [ ] [ ] . this site can be pre-cleaved by furin, thus reducing the dependence of sars-cov- on target cell proteases (tmprss /cathepsin l) for entry [ ] [ ] and potentially extending its cellular tropism, given that proteolytically active furin is abundantly expressed in human bronchial epithelial cells [ , ] . one of the distinctions between sars-cov and sars-cov- is the latter's ability to efficiently infect the upper respiratory tract (urt), such as nasopharyngeal (np) and/or oropharyngeal (op) tissues, possibly due to its higher affinity for ace , which is expressed in human nasal and oral tissues [ ] [ ] [ , , ] . the readily detectable titers of sars-cov- in the urt mucus of covid- patients during prodromal periods might contribute to explaining the more rapid and effective transmissibility of sars-cov- relative to sars-cov [ ] . human covs often cause enteric infections, with variable degrees of pathogenicity [ ] . indeed, ace and tmprss are abundantly expressed within the human and many other mammalian intestinal tracts, specifically the brush border of intestinal enterocytes [ , , , ] . accordingly, gastrointestinal illness has been frequently reported in covid- patients [ , ] , consistent with the recovery of sars-cov from sars patients' stool samples [ ] , suggesting a potential fecal-oral route of transmission for these two covs. of note, ~ % of covid- patients examined have had detectable sars-cov- rna in feces, even after respiratory symptoms subsided, suggesting that sars-cov- titers might be prolonged in the intestinal tract [ ] . although further testing is warranted, these data suggest the possibility that fecal-oral transmission of sars-cov- might occur. evidently, robust epidemiological studies are needed to conclusively demonstrate if covid- patients recovering from respiratory illness are able to spread sars-cov- . human covs are transmitted primarily through respiratory droplets, but aerosol, direct contact with contaminated surfaces, and fecal-oral transmission were also reported during the sars epidemic [ ] [ ] [ ] . early reports of patients with cough, lung ground glass opacities, and symptom progression to severe pneumonia, suggested communicability of sars-cov- via the respiratory route (figure ) [ ] [ ] [ ] . direct transmission by respiratory droplets is reinforced by productive sars-cov- replication in both the urt and lrt, and the increasing number of reports indicating human-to-human spread among close contacts exhibiting active coughing ( figure ) [ , [ ] [ ] [ ] . so far, the basic reproduction number (r ) is ~ . , based on early case j o u r n a l p r e -p r o o f journal pre-proof tracking in the beginning of the pandemic, with a doubling time of days [ ] [ ] . furthermore, there is now evidence for non-symptomatic/pre-symptomatic spread of sars-cov- , which is in contrast to the transmission dynamics of sars-cov [ ] . this finding underscores the ability of sars-cov- to colonize and replicate in the throat during early infection [ , , ] . based on these apparent disparities in virus transmission, one study modeled the transmission dynamics of sars-cov- in pre-symptomatic individuals, and indicated that the pre-symptomatic r has approached the threshold for sustaining an outbreak on its own (r > ); by contrast, the corresponding estimates for sars-cov were approximately zero [ ] . similarly, asymptomatic spread of sars-cov- has been documented throughout the course of the pandemic [ ] [ , [ ] [ ] [ ] [ ] . understanding the relative importance of cryptic transmission to the current covid- pandemic is essential for public health authorities to make the most comprehensive and effective disease control measures that include mask-wearing, contact tracing, and physical isolation. for sars-cov- , various modes of transmission have been proposed, including aerosol, surface contamination, fecal-oral route, representing confounding factors in the current covid- pandemic; thus, their relative importance is still being investigated (figure ) [ ] . aerosol transmission (spread > m) was implicated in the amoy gardens outbreak during the sars epidemic, but the inconsistency of these findings in other settings suggested that sars-cov was likely an opportunistic airborne infection [ , ] . similarly, no infectious sars-cov- virions have been isolated, though viral rna was detectable in the air of covid- hospital wards [ ] . generation of experimental aerosols carrying sars-cov- (comparable to those that might be generated by humans) have offered the plausibility of airborne transmission, but the aerodynamic characteristics of sars-cov- during a natural course of infection is still an area of intense inquiry [ ] . nonetheless, deposition of virus-laden aerosols might contaminate j o u r n a l p r e -p r o o f objects (e.g. fomites) and contribute to human transmission events [ , ] . finally, fecal-oral transmission has also been considered as a potential route of human spread, but this route remains an enigma despite evidence of rna-laden aerosols being found nearby toilet bowls, along with detectable sars-cov- rna in rectal swabs during the precursor epidemic of covid- in china [ , , ] . in general, common cold covs tend to cause mild urt symptoms and occasional gastrointestinal involvement (figure ) . on the contrary, infection with the highly pathogenic covs, including sars-cov- , causes severe 'flu'-like symptoms that can progress to acute respiratory distress (ards), pneumonia, renal failure, and death [ , , , ] . the most common symptoms are fever, cough and dyspnea, accounting for %, % and % of covid- patients (n= ), respectively in one epidemiological study [ ] . the incubation period in covid- is rapid, ~ - days, versus - days in sars-cov infections [ , , ] . as the pandemic is progressing, it has become increasingly clear that covid- encompasses not only rapid respiratory/gastrointestinal illnesses, but can have long-term ramifications such as myocardial inflammation [ ] . furthermore, severe covid- is not restricted to the aged population as initially reported; children and young adults are also at risk [ ] . from a diagnostic perspective, covid- presents with certain 'hallmark' laboratory and radiological indices, which can be helpful in assessing disease progression ( table ) it is widely accepted that the aging process predisposes individuals to certain infectious diseases [ ] . in the case of covid- , older age is associated with greater covid- morbidity, admittance to the icu, progressing to ards, higher fevers and greater mortality rates [ ] [ , ] . moreover, lymphocytopenia, neutrophilia, elevated inflammation-related indices, and coagulation-related indicators have been consistently reported in older (≥ years old) relative to young and middle-aged covid- patients [ table ;( [ , ] ) [ , , , , ] . at the cellular level, a lower capacity of cd + and cd + t-cells to produce ifn-γ and il- , as well as an impairment in t-cell activation from dendritic cells (dcs) in acute covid- patients (≥ years old), might potentially compromise an optimal adaptive immune response [ ] . based on examples from mice, a productive cd + t-cell response relies heavily on lung resident dcs (rdcs) and abates sars-cov infection [ , ] . however, whether a reduction in the dc population in the lungs of older, more severe patients causes sub-optimal t-cell activation during sars-cov- infection remains to be robustly investigated. higher proportions of proinflammatory macrophages and neutrophils have also been observed in the bronchoalveolar lavage fluid (balf) of covid- patients with severe symptoms compared with those exhibiting mild symptoms (key figure, figure ) [ ] . accordingly, proinflammatory cytokines (e.g. il- , il- ) are elevated in the balf of severe j o u r n a l p r e -p r o o f journal pre-proof covid- patients, along with higher expression of inflammatory chemokines (e.g. ccl ) in macrophages relative to non-severe covid- patients [ ] [ ] [ ] [ ] . indeed, similar inflammatory milieux have been associated with severe lung pathology in sars patients, along with the notable 'cytokine storm' that can present in critically ill covid- patients [ , ] [ , [ ] [ ] [ ] . these proinflammatory mediators can, in turn, perpetuate lung disease by elevating creactive protein (crp) from the liver ( table ) products [ ] . specifically, covs can avoid immune sensing via i) the formation of dmvs that sequester viral nucleic acid from being recognized by prrs and ii) direct ablation of the functionality of immune signaling molecules by viral proteins [ , ] . the structural and functional conservation of these proteins across the betacoronavirus genus and in nsps between sars-cov and sars-cov- , suggests that some of these suppressive mechanisms might be employed by sars-cov- (see below) [ ] . indeed, patients with severe covid- have reported an imbalanced immune response with high concentrations of inflammatory cytokines/chemokines, but little circulating ifn-β or ifn-λ, resulting in persistent viremia [ ] . of note, among several respiratory viruses tested, sars-cov- has demonstrated to most potently suppress type i and type iii ifn expression in both human bronchial epithelial cells and ferrets [ ] . thus, evasion of ifn signaling by sars-cov- and impaired ifn production in j o u r n a l p r e -p r o o f human peripheral blood immune cells might contribute to the productive viral replication, transmission, and severe pathogenesis during covid- , although further testing is warranted to fully dissect these putative evasion pathways [ ] . with regard to functional conservation of viral proteins, sars-cov and mers-cov nsps and accessory proteins circumvent viral rna-sensing pathways at multiple stages (e.g. rig-i, mda- ) through proteasomal degradation and/or prevention of protein activation ( figure ) [ ] . functional conservation between sars-cov and mers-cov pl pro (encoded by nsp ) proteins has been reported, where these proteins target the initial prr signaling cascade at multiple levels of the pathway includingbut not limited to-rig-i, mavs, tbk , irf and nf-k b ( figure ) [ ] [ ] [ ] . the sars-cov pl pro also targets the dna-sensing pathway at sting ( figure ) ; antagonizing this pathway might be important as mitochondrial stress during dengue virus infection triggers ifn-β production that is dependent on sting activation [ , ] . recent evidence suggests the sars-cov- pl pro might also inhibits ifn-i expression in human kidney epithelial cells, yet the mechanisms remain to be defined [ ] . moreover, nsp of highly pathogenic hcovs, including sars-cov and mers-cov displays a pleiotropic effect, targeting several components of ifn-i signaling ( figure ) [ , ] . this potent suppressive function of nsp also appears to be maintained in sars-cov- , primarily through shutdown of translational machinery and prevention of immune gene expression [ , , ] . furthermore, because there are only five accessory genes in the mers-cov genome compared to eight and seven in the sars-cov and sars-cov- genomes, respectively, similar immunosuppressive mechanisms may exist but appear to be mediated via different proteins [ , ] . for example, sars-covs orf can inhibit irf activation and stat nuclear translocation, whereas this same effect is obtained by orf a/b and orf of mers-cov j o u r n a l p r e -p r o o f ( figure ) [ , ] . coincidently, the apparent loss of these proteins may provide evidence for why mers-cov is more sensitive to ifn treatment than sars-covs in primary and continuous cells of the human airways [ ] . the sars-cov- proteins appear to have stronger inhibitory effects than their counterparts of highly pathogenic sars-and mers-cov [ ] . in light of these findings, sars-cov- has replicated more efficiently than sars-cov in ex vivo human lung explants, possibly through the greater suppression of ifn-i/iii cytokines [ ] ; further work given that sars-cov- uses the same ace entry receptor as sars-cov, rapidly deploying mouse models for pathogenesis studies were well underway within weeks of the pandemic's inception. however, various impediments remain for sars-cov- in productively infecting mice in these models, as it is unable to bind mouse ace (mace ) [ ] . to overcome these prerequisites, several mouse models have been developed that recapitulate certain components of j o u r n a l p r e -p r o o f human covid- . one of these strategies is to genetically modify mice to express human ace (hace ) (humanized mice) under the epithelial cell-specific cytokeratin- (krt ) promoter [ ] , a universal chicken beta-actin promoter [ ] , or the endogenous mace promoter [ ] . all these mice are susceptible to sars-cov- infection, but phenotypic disease varies because of differential hace tissue expression [ ] [ ] [ ] . for instance, krt -hace and betaactin-hace -transgenic mice rapidly succumb to sars-cov- infection with lung infiltration of inflammatory immune cells inducing severe pulmonary disease, accompanied by evident thrombosis and anosmia, which partially recapitulate human covid- [ ] [ ] . as the onset of severe histopathological changes occurs days after peak virus infection, these models recapture the delayed morbidity seen in covid- patients as a result of inflammatory cell infiltration [ ] . therefore, employing humanized mouse models of severe sars-cov- infection might be useful for testing the efficacy of antiviral drugs, vaccines, and immune therapeutics that ablate hyperinflammation [ ] . however, the broad expression of hace in these models significantly expands sars-cov- tissue tropisms and might alter its pathogenic mechanisms [ ] [ ] . for example, both sars-cov and sars-cov- infection lead to encephalitis in these mouse models, which is not common in covid- patients [ , , ] . considering the fact that the majority of human sars-cov- infections are asymptomatic or mild, mice originally bearing mace that is replaced by hace may be more appropriate for assessing pathogenesis and tissue tropism [ ] . this model develops mild lung pathology, with sars-cov- infection being restricted to the lung and intestine [ ] . in addition to the transgenic modification, mice can also be sensitized to sars-cov- infection via transient transduction of adenovirus (ad )-or adeno-associated virus (aav)-expressing hace in respiratory tissues, akin to the approach previously used for mers-cov infection [ ] [ ] [ ] . these mice develop viral pneumonia, weight loss, severe pulmonary pathology, and a high viral load in the lung, consistent with human covid- [ ] . this approach might be quickly adapted to many genetically modified mouse strains that might provide mechanisms of sars-cov- pathogenesis and protective immune responses. this model is limited, however, by the transient ectopic expression of hace from the ad /aav vector that can induce mild bronchial inflammation and expand cell tropism of sars-cov- and thus, presumably alter disease pathogenesis [ ] . rather than genetic modification in host animals, viruses can also be genetically modified and be used in model animals [ , ] . for instance, in one study, serial passaging of sars-cov- in mice led to enrichment of a n y viral mutant that elicited interstitial pneumonia and inflammatory responses in both aged and young wild-type balb/c mice [ ] . another mouseadapted sars-cov- strain (ma ) carrying three mutations in the rbd of spike protein caused severe lung pathology and ards in mice, characteristic of severe covid- [ ] . despite the three mutations in the rbd of the mouse-adapted spike, vaccination with full length sars-cov- spike elicited robust neutralizing antibody titers and complete protection against a secondary challenge with ma [ ] ; these findings suggest that this strain may be applicable to pathogenesis studies, as well as antiviral drug and vaccine testing in rodents. the role of non-human primates (nhp) in evaluating coronavirus pathogenesis cannot be understated. depending on the nhp model utilized, clinical signs/symptoms may be mild or absent entirely [ ] [ ] [ ] . in rhesus macaques, several studies have noted reduced appetite, j o u r n a l p r e -p r o o f transient fevers ( day post infection: dpi) and mild weight loss without overt signs of respiratory distress or mortality [ ] [ ] [ ] . by contrast, cynomolgus macaques did not display any observational signs of disease in another study [ ] . although certain nhps appear to only mimic mild disease (if any), rhesus macaques have exhibited high viral loads in nasal swabs, throat samples, and balf early post inoculation, and viral rna was still measurable by qpcr in the trachea and lung on day p.i., highlighting the apparent tropism of sars-cov- for the urt and lingering viral nucleic acid in respiratory tissues after resolution of disease [ , ] . sars-cov- has also been detected in nasal swabs at dpi in nhps, consistent with the prolonged urt shedding of virus in covid- patients at ~ dpi [ , , , ] . the tropism of sars-cov- for the lrt in nhps has also been recapitulated by the development of multifocal lesions and interstitial pneumonia, supporting the hypothesis that lung injury is driven by increased infiltration of neutrophils and macrophages into the lung following viral infection such as thickened alveolar septum and diffuse severe interstitial pneumonia when compared to young macaques ( - years old) [ ] . therefore, these studies highlight the importance of also considering the age factor, as an additional variable, when selecting animal models that might closely, or accurately, recapitulate human disease. evaluating efficacious vaccine candidates in nhps will also be important for understanding correlates of protection against sars-cov- . accordingly, reports of antibodydependent enhancement, as well as of non-neutralizing humoral responses to the conserved regions of sars-cov- , raise concerns on our future ability to effectively administer an immunogen without inducing immunopathology [ , ] . furthermore, upon viral challenge, lymphocytes have expanded in rhesus macaque models around dpi with complementary b-cell responses against sars-cov- spike appearing - dpi in blood samples [ ] ; expansion of these adaptive immune compartments was analogous to those observed in covid- patients [ , , [ ] [ ] [ ] . subsequent re-challenged rhesus macaque have presented a rapid anamnestic immune response characterized by significantly higher neutralizing antibody (nab) titers than the primary infection macaques [ ] . thus, protective efficacy seems to depend primarily on nab titers, at least in nhps, and so far, t-cell numbers have not substantially increased following re-challenge in the serum of these animals, and in a secondary study, cd + and cd + cytokine (e.g. ifn-γ) responses did not correlate with immune protection from dna vaccines with different components of the sars-cov- spike protein [ ] [ ] . although these animals have failed to manifest overt signs of infection and respiratory compromise, nhps still represent the 'gold standard' for evaluating the protective efficacy of human-bound sars-cov- vaccines based on parallels to humans in terms of viral tropism, immunopathology, and correlates of protection [ ] . further research is urgently needed to j o u r n a l p r e -p r o o f explore the durability of immune responses to sars-cov- , considering reports of waning immunity to other covs and the detection of pre-existing cross-reactive 'common-cold' cov tcells with sars-cov- in naïve humans (see outstanding questions) [ , ] . the emergence of sars-cov- as the most recent example of zoonotic virus spillovers into in the last hours leading up to death, all patients which were included for this metric had a prothrombin time of > . s. aerosol: suspension of fine solid or liquid droplets in the air (or a gas medium), such as dusts, mists, or fumes. anamnestic immune response: memory immune response to a previously encountered antigen. angiotensin-converting enzyme (ace ): cell surface enzyme of endothelial, epithelial, and other cells, with a well-defined function in maintaining normal blood pressure. anosmia: partial or complete loss of the sense of smell. antibody-dependent enhancement: phenomenon by which antibodies against a virus are suboptimal to the virus and enhance its entry into host cells. convalescence period: the time of gradual recovery after an illness or injury. correlates of protection: quantifiable parameters such as antibodies, indicating that a host is protected against microbial infection. cytokine storm: severe immune reaction in which the body releases too many cytokines into the blood too quickly. d-dimer: fibrin degradation product in the blood after a clot is degraded by fibrinolysis. disseminated intravascular coagulation (dic): condition in which blood clots form throughout the body and block small blood vessels, leading to multiorgan failure. fecal-oral transmission: route of disease transmission by which an infectious agent in fecal materials is passed to the mouth of another. fomite: inanimate object (clothes, utensil, and furniture etc.) that, when contaminated with an infectious agent, can transfer the infectious agent to a new host. furin: proprotein convertase that cleaves a precursor protein into a biologically active state. incubation period: timeframe elapsed between when a host is first exposed to an infectious agent and when signs or symptoms begin to appear. lung ground glass opacity: nonspecific radiological description of an area of increased opacity in the lung through which vessels and bronchial structures are still visible. neutralizing antibody (nab): an antibody that binds a pathogen with high affinity and prevents the latter from exerting its biological effect. neutrophil extracellular traps (nets): networks of extracellular fibers, primarily composed of dna from neutrophils due to chromatin decondensation, which can 'trap' extracellular pathogens. pattern recognition receptor: germline-encoded host sensor that recognizes a signature pattern in microbial molecules. prodromal period: the time immediately following the incubation period of a microbial infection in which a host begins to experience symptoms or changes in behavior/functioning. prothrombin time: measurement of the extrinsic pathway of coagulation. r (reproductive number): the expected number of new disease cases generated by one case. an r > indicates the outbreak will expand; r < the outbreak will die out. respiratory droplet: small aqueous droplet produced by exhalation, consisting of saliva or mucus and other matter derived from respiratory tract surfaces. zoonotic disease: infectious disease caused by a pathogen that has crossed a species barrier from animals to humans. the ongoing covid- pandemic has resulted in numerous accounts of different transmission routes between humans. droplet transmission (> μm) is the most pronounced and heavily implicated mode of transmission reported during the pandemic. direct contact spread from one infected individual to a second, naïve person has also been considered a driver of human-to-human transmission, especially in households with close interactions between family members. the contagiousness of sars-cov- after disposition on fomites (e.g. door handle) is still under investigation, but is likely a compounding factor for transmission events, albeit less frequently than droplet or contact-driven transmission. both airborne and fecal-oral human-to-human transmission events were reported in j o u r n a l p r e -p r o o f the precursor sars-cov epidemic but have yet to be observed in the current crises. solid arrows show confirmed viral transfer from one infected person to another with a declining gradient in arrow width denoting the relative contributions of each transmission route. dashed lines show the plausibility of that transmission type but have yet to be confirmed. sars-cov- symbol in "infected patient" indicate where rna/infectious virus has been detected [ , , - , , ] a pneumonia outbreak associated with a new coronavirus of probable bat origin coronavirus as a possible cause of severe acute respiratory syndrome clinical features of patients infected with novel coronavirus in wuhan coronavirus disease (covid- ) pandemic the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding a genomic perspective on the origin and emergence of sars-cov- coronaviruses post-sars: update on replication and pathogenesis a new coronavirus associated with human respiratory disease in china sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex subgenomic messenger rna amplification in coronaviruses clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study cryo-em structure of the -ncov spike in the prefusion conformation angiotensin-converting enzyme is a functional receptor for the sars coronavirus structural basis for the recognition of sars-cov- by full-length human ace cell entry mechanisms of sars-cov- a multibasic cleavage site in the spike protein of sars-cov- is essential for infection of human lung cells structural and functional analysis of the d g sars-cov spike protein variant the impact of mutations in sars-cov- spike on viral infectivity and antigenicity tracking changes in sars-cov- spike: evidence that d g increases infectivity of the covid- virus ace receptor expression and severe acute respiratory syndrome coronavirus infection depend on differentiation of human airway epithelia tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury sars-cov- receptor ace is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues atlas of ace gene expression in mammals reveals novel insights in transmission of sars-cov- a transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry single-cell rna expression profiling of ace , the receptor of sars-cov- angiotensin-converting enzyme protects from severe acute lung failure endocytosis of the receptor-binding domain of sars-cov spike protein together with virus receptor ace cigarette smoke exposure and inflammatory signaling increase the expression of the sars-cov- receptor ace in the respiratory tract furin cleavage of the sars coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry sars-cov- receptor ace and tmprss are primarily expressed in bronchial transient secretory cells tropism, replication competence, and innate immune responses of the coronavirus sars-cov- in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures clinical and virologic characteristics of the first patients with coronavirus disease (covid- ) in the united states high expression of ace receptor of -ncov on the epithelial cells of oral mucosa virological assessment of hospitalized patients with covid- epidemiology, genetic recombination, and pathogenesis of coronaviruses the digestive system is a potential route of -ncov infection: a bioinformatics analysis based on single-cell transcriptomes high prevalence of concurrent gastrointestinal manifestations in patients with sars-cov- : early experience from california evidence for gastrointestinal infection of sars-cov- enteric involvement of severe acute respiratory syndromeassociated coronavirus infection evidence of airborne transmission of the severe acute respiratory syndrome virus transmission of sars and mers coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination role of air distribution in sars transmission during the largest nosocomial outbreak in hong kong clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster quantifying sars-cov- transmission suggests epidemic control with digital contact tracing presymptomatic sars-cov- infections and transmission in a skilled nursing facility sars-cov- viral load in upper respiratory specimens of infected patients viral load of sars-cov- in clinical samples estimating the asymptomatic proportion of coronavirus disease (covid- ) cases on board the diamond princess cruise ship ct imaging and clinical course of asymptomatic cases with covid- pneumonia at admission in wuhan transmission of -ncov infection from an asymptomatic contact in germany the clinical feature of silent infections of novel coronavirus infection (covid- ) in wenzhou possible modes of transmission of novel coronavirus sars-cov- : a review sars: experience at prince of wales hospital, hong kong aerodynamic analysis of sars-cov- in two wuhan hospitals aerosol and surface stability of sars-cov- as compared with sars-cov- air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding a novel coronavirus associated with severe acute respiratory syndrome clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: a report of nosocomial transmission epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study outcomes of cardiovascular magnetic resonance imaging in patients recently recovered from coronavirus disease (covid- ) clinical characteristics and outcomes of hospitalized and critically ill children and adolescents with coronavirus disease (covid- ) at a tertiary care medical center the twilight of immunity: emerging concepts in aging of the immune system estimating clinical severity of covid- from the transmission dynamics in wuhan, china the aging transcriptome and cellular landscape of the human lung in relation to sars-cov- clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study clinical characteristics of covid- in people with sars-cov- infection on the diamond princess cruise ship: a retrospective analysis clinical characteristics of cases of death from covid- risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease clinical features of covid- in elderly patients: a comparison with young and middle-aged patients acute sars-cov- infection impairs dendritic cell and t cell responses cellular immune responses to severe acute respiratory syndrome coronavirus (sars-cov) infection in senescent balb/c mice: cd + t cells are important in control of sars-cov infection evasion by stealth: inefficient immune activation underlies poor t cell response and severe disease in sars-cov-infected mice single-cell landscape of bronchoalveolar immune cells in patients with covid- dysregulation of immune response in patients with covid- in wuhan, china imbalanced host response to sars-cov- drives development of covid- sars-cov- activates lung epithelia cell proinflammatory signaling and leads to immune dysregulation in covid- patients by single-cell sequencing the clinical pathology of severe acute respiratory syndrome (sars): a report from china lung pathology of fatal severe acute respiratory syndrome clinical predictors of mortality due to covid- based on an analysis of data of patients from wuhan, china cytokine release syndrome in severe covid- pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology c-reactive protein: ligands, receptors and role in inflammation neutrophil extracellular traps in covid- endothelial cell infection and endotheliitis in covid- clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia sars coronavirus pathogenesis: host innate immune responses and viral antagonism of interferon interaction of sars and mers coronaviruses with the antiviral interferon response impaired type i interferon activity and inflammatory responses in severe covid- patients regulation of irf- dependent innate immunity by the papainlike protease domain of the sars coronavirus severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of irf and nf-κb signaling crystal structure of the middle east respiratory syndrome coronavirus (mers-cov) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression interleukin- β induces mtdna release to activate innate immune signaling via cgas-sting coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of sting-mediated signaling activation and evasion of type i interferon responses by sars-cov- severe acute respiratory syndrome coronavirus protein nsp is a novel eukaryotic translation inhibitor that represses multiple steps of translation initiation middle east respiratory syndrome coronavirus nsp inhibits host gene expression by selectively targeting mrnas transcribed in the nucleus while sparing mrnas of cytoplasmic origin structural basis for translational shutdown and immune evasion by the nsp protein of sars-cov- evasion of type-i interferon by sars-cov- the structural and accessory proteins m, orf a, orf b, and orf of middle east respiratory syndrome coronavirus (mers-cov) are potent interferon antagonists severe acute respiratory syndrome coronavirus open reading frame (orf) b, orf , and nucleocapsid proteins function as interferon antagonists human cell tropism and innate immune system interactions of human respiratory coronavirus emc compared to those of severe acute respiratory syndrome coronavirus comparative replication and immune activation profiles of sars-cov- and sars-cov in human lungs: an ex vivo study with implications for the pathogenesis of covid- ribose ′-o-methylation provides a molecular signature for the distinction of self and non-self mrna dependent on the rna sensor mda the pathogenicity of sars-cov- in hace transgenic mice lethal infection of k -hace mice infected with severe acute respiratory syndrome coronavirus severe acute respiratory syndrome coronavirus infection of mice transgenic for the human angiotensin-converting enzyme virus receptor k -hace mice for studies of covid- treatments and pathogenesis including anosmia sars-cov- infection of human ace -transgenic mice causes severe lung inflammation and impaired function severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ace a sars-cov- infection model in mice demonstrates protection by neutralizing antibodies rapid generation of a mouse model for middle east respiratory syndrome generation of a broadly useful model for covid- pathogenesis vaccination, and treatment adenovirus vectors for gene therapy, vaccination and cancer gene therapy a mouse-adapted sars-coronavirus causes disease and mortality in balb/c mice a mouse-adapted sars-cov- model for the evaluation of covid- medical countermeasures a sars-cov- protein interaction map reveals targets for drug repurposing a mouse-adapted sars-cov- induces acute lung injury (ali) and mortality in standard laboratory mice respiratory disease in rhesus macaques inoculated with sars-cov- comparative pathogenesis of covid- , mers, and sars in a nonhuman primate model sars-cov- infection protects against rechallenge in rhesus macaques cynomolgus macaque as an animal model for severe acute respiratory syndrome age-related rhesus macaque models of covid- immunization with sars coronavirus vaccines leads to pulmonary immunopathology on challenge with the sars virus anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection antibody responses to sars-cov- in patients of novel coronavirus disease antibody responses to sars-cov- in patients with covid- deep immune profiling of covid- patients reveals distinct immunotypes with therapeutic implications dna vaccine protection against sars-cov- in rhesus macaques seasonal coronavirus protective immunity is short-lasting targets of t cell responses to sars-cov- coronavirus in humans with covid- disease and unexposed individuals type-i, type-iii ifns then signal in an autocrine or paracrine manner through the janus kinase (jak )/signal transducer and activator of transcription and (stat / ) pathway, culminating in antiviral interferon-stimulated gene (isg) transcription. listed here are sars-cov (abbreviated cov), sars-cov- (abbreviated cov- ) and mers-cov (abbreviated m-cov) ifn-i antagonists, which make these viruses resistant to interferon responses. ifn-iii is also implicated in exhibiting potent antiviral effects in lung/intestinal tissues, but the underlying evasion strategies of this pathway for these viruses are currently unknown. sars-cov proteins are highlighted in blue, while functions of sars-cov- and mers-cov proteins are highlighted in red and green, respectively. question mark symbol (?) denotes sars-cov- protein bound a member of that signaling pathway in [ ], but further work is necessary to confirm its immunological mechanism. sars-cov- proteins with * denotes functional conservation with sars-cov which animal(s) serves as the natural reservoir of sars-cov- ?  does active replication of sars-cov- in the upper respiratory tract contribute to enhanced transmissibility in humans?  is intestinal sars-cov- infection a source of virus transmission?  which sars-cov- proteins antagonize innate and adaptive immune responses? do the sars-cov- proteins with more potent antagonistic immune functions increase virulence in humans compared to other hcovs?  why do some recovered patients fail to develop neutralizing antibodies?  what are the host and/or viral factors driving  what are the underlying mechanisms contributing to an inadequate ifn response to sars-cov- ?  what are the correlates of immune protection for sars-cov and will they provide sterilizing immunity?  will candidate vaccines against sars-cov also be effective in elderly subpopulations this work was supported by a national institutes of health grant r ai to p.w.the authors declare no competing financial/non-financial interest.j o u r n a l p r e -p r o o f journal pre-proof j o u r n a l p r e -p r o o f key: cord- - yqc zcx authors: hozhabri, hossein; piceci sparascio, francesca; sohrabi, hamidreza; mousavifar, leila; roy, rené; scribano, daniela; de luca, alessandro; ambrosi, cecilia; sarshar, meysam title: the global emergency of novel coronavirus (sars-cov- ): an update of the current status and forecasting date: - - journal: int j environ res public health doi: . /ijerph sha: doc_id: cord_uid: yqc zcx over the past two decades, there have been two major outbreaks where the crossover of animal betacoronaviruses to humans has resulted in severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov). in december , a global public health concern started with the emergence of a new strain of coronavirus (sars-cov- or novel coronavirus, -ncov) which has rapidly spread all over the world from its origin in wuhan, china. sars-cov- belongs to the betacoronavirus genus, which includes human sars-cov, mers and two other human coronaviruses (hcovs), hcov-oc and hcov-hku . the fatality rate of sars-cov- is lower than the two previous coronavirus epidemics, but it is faster spreading and the large number of infected people with severe viral pneumonia and respiratory illness, showed sars-cov- to be highly contagious. based on the current published evidence, herein we summarize the origin, genetics, epidemiology, clinical manifestations, preventions, diagnosis and up to date treatments of sars-cov- infections in comparison with those caused by sars-cov and mers-cov. moreover, the possible impact of weather conditions on the transmission of sars-cov- is also discussed. therefore, the aim of the present review is to reconsider the two previous pandemics and provide a reference for future studies as well as therapeutic approaches. coronaviruses (covs) are a group of highly enveloped viruses that are diversely found in humans and wildlife. with their high mutation rate and infectivity, covs are important zoonotic pathogens that can infect animals [ , ] and humans, leading to - % of acute respiratory syndromes [ ] . apart from infecting a variety of economically important vertebrates (such as pigs and chickens), six species have been identified to cause disease in humans [ ] . they are known to infect respiratory, gastrointestinal, hepatic and neurologic systems with a wide range of clinical features from asymptomatic course to severe disease that require hospitalization in the intensive care unit [ , ] . the first human coronaviruses (hcovs), hcov- e and oc , shown to be significant respiratory pathogens, were identified in the s [ , ] . however, it is assumed that the first recorded coronavirus-related disease was feline infectious peritonitis (fip) in [ ] . the "corona"-like or crown-like morphology of these viruses leads to choose the name "coronavirus," in [ ] . coronaviruses were not considered as highly pathogenic for humans before the beginning of the st century. afterward, two highly pathogenic hcovs, including severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov), emerging from animal reservoirs, have led to global epidemics of deadly pneumonia in humans with high morbidity and mortality [ , ] . in december , seven years after mers outbreak, the third pathogenic hcov emerged in wuhan, the capital city of hubei province in china, causing severe pneumonia [ , ] . considered as agents that are a great public health threat, an epidemiological alert was placed by the world health organization (who) and this new coronavirus was named sars-cov- and the related respiratory disease covid- (https://www.who.int). compared with sars-cov, sars-cov- appears to be more readily transmitted from human-to-human, spreading to multiple continents and the outbreak of sars-cov- was declared on january , [ ] (https://www.who.int). in this review, we will introduce the current knowledge on the origin and evolution of sars-cov- , emphasizing its characteristics and its genetic diversity from previous coronaviruses, with a brief comment on its epidemiology and pathogenesis. we also highlight the environmental factors involved in virus transmission. knowledge about this novel coronavirus is rapidly evolving, and efforts must be implemented in order to protect the populations by reducing transmission and controlling the spread of this fatal disease. according to the international committee on taxonomy of viruses, covs are classified under the order of nidovirales, a family of coronaviridae and subfamily of coronavirinae [ ] . based on previous serologic and recent genomic evidences, the family of coronaviridae encompasses two subfamilies: subfamily orthocoronavirinae and subfamily torovirinae ( figure ) [ , ] . the subfamily of orthocoronavirinae consists of four genera: alphacoronavirus, betacoronavirus, gammacoronavirus and deltacoronavirus [ , , ] . covs can be isolated from different animal species, including birds, livestock and mammals such as camels, bats, masked palm civets, mice, dogs and cats [ , ] . animal covs are known to cause acute diseases in several animals and could be responsible for economic losses in domestic animals or birds [ , ] . domestic animals may play an important role as intermediate hosts that enable virus transmission from one species to humans [ ] . the genera gamma-and deltacoronavirus infect birds, but some of them can also infect mammals [ ] . these animal covs include transmissible gastroenteritis virus (tgev), porcine epidemic diarrhea virus (pedv), avian infectious bronchitis virus (ibv)-and more recently-swine acute diarrhea syndrome coronavirus (sads-cov). however, animal covs can also infect humans that can spread the infection through human-tohuman transmission [ , ] . on the other hand, alpha-and betacoronavirus infect only mammals and usually cause respiratory illness in humans; among these, strains e, oc , hku and nl are the most widespread infecting young children, infants as well as elderly individuals [ ] [ ] [ ] . the high rates of mutation characterizing all rna viruses [ , ] , the evolving nature of covs and the simplicity of transmission from one species to another are the most relevant features learned from sars-cov and mers-cov previous outbreaks [ , , ] . importantly, most of alpha-and betacoronavirus were found only in bats, and many genetically diverse coronaviruses phylogenetically related to sars-cov and mers-cov have been discovered in diverse bat species worldwide [ ] . therefore, hcovs such as sars-and mers-covs seem to have originated in bats by sequential mutations and recombination, including those occurring in the intermediate hosts, civets and raccoon dogs for sars-cov and camels in the case of mers-cov, finally acquiring the ability to infect humans [ , ] . comparative genome studies published in recent papers strongly support the hypothesis that sars-cov- originated in bats and that pangolins (manis javanica) acted as intermediate mammalian hosts [ , ] (figure ) . indeed, the genetic sequence of the sars-cov- showed more than % nucleotide identity with the sequence of sars-cov and % with mers-cov [ , ] . the high degree of homology of the angiotensin-converting enzyme (ace ) receptor in several animal species can be considered as an additional evidence to support that sars-cov- originated from bats [ ] . based on findings from molecular studies, the ace proteins of non-human primates, pigs, cats and ferrets closely resemble the human ace receptor. therefore, these species covs can be isolated from different animal species, including birds, livestock and mammals such as camels, bats, masked palm civets, mice, dogs and cats [ , ] . animal covs are known to cause acute diseases in several animals and could be responsible for economic losses in domestic animals or birds [ , ] . domestic animals may play an important role as intermediate hosts that enable virus transmission from one species to humans [ ] . the genera gammaand deltacoronavirus infect birds, but some of them can also infect mammals [ ] . these animal covs include transmissible gastroenteritis virus (tgev), porcine epidemic diarrhea virus (pedv), avian infectious bronchitis virus (ibv)-and more recently-swine acute diarrhea syndrome coronavirus (sads-cov). however, animal covs can also infect humans that can spread the infection through human-to-human transmission [ , ] . on the other hand, alphaand betacoronavirus infect only mammals and usually cause respiratory illness in humans; among these, strains e, oc , hku and nl are the most widespread infecting young children, infants as well as elderly individuals [ ] [ ] [ ] . the high rates of mutation characterizing all rna viruses [ , ] , the evolving nature of covs and the simplicity of transmission from one species to another are the most relevant features learned from sars-cov and mers-cov previous outbreaks [ , , ] . importantly, most of alphaand betacoronavirus were found only in bats, and many genetically diverse coronaviruses phylogenetically related to sars-cov and mers-cov have been discovered in diverse bat species worldwide [ ] . therefore, hcovs such as sars-and mers-covs seem to have originated in bats by sequential mutations and recombination, including those occurring in the intermediate hosts, civets and raccoon dogs for sars-cov and camels in the case of mers-cov, finally acquiring the ability to infect humans [ , ] . comparative genome studies published in recent papers strongly support the hypothesis that sars-cov- originated in bats and that pangolins (manis javanica) acted as intermediate mammalian hosts [ , ] (figure ) . indeed, the genetic sequence of the sars-cov- showed more than % nucleotide identity with the sequence of sars-cov and % with mers-cov [ , ] . the high degree of homology of the angiotensin-converting enzyme (ace ) receptor in several animal species can be considered as an additional evidence to support that sars-cov- originated from bats [ ] . based on findings from molecular studies, the ace proteins of non-human primates, pigs, cats and ferrets closely resemble the human ace receptor. therefore, these species may be susceptible to sars-cov- infection, as has been shown for sars-cov. although a recent study showed that neither pigs nor chickens are susceptible to sars-cov- by intranasal or oculo-oronasal infections, more evidences are needed to exclude pigs as intermediate host of sars-cov- [ ] . [ ] . based on the genetic sequence identity and the phylogenetic reports, sars-cov- is sufficiently different from sars-cov; thus, who has classified it as a new betacoronavirus that infects humans [ ] . the genome of hcovs is a single-stranded positive-sense rna (+ssrna) (~ - kb) with ′cap structure and ′-poly a tail, which is among the largest known rna genomes [ ] [ ] [ ] . the typical hcovs gene order is ′-replicase-s-e-m-n- ′, with numerous ( to ) open reading frames (orfs) encoding accessory proteins scattered among the structural genes [ , ] . the first orfs (orf a and b) comprise two-thirds (approximately %) of the genome length and encode nonstructural polyproteins (nsps [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] and are directly translated from the genomic rna [ ] . there is a − ribosomal frameshift between orf a and orf b, leading to the production of two large replicase polypeptides (pp): pp a and pp ab. these polypeptides are further processed by two virally encoded cysteine proteases, the papain-like protease (plpro) and a -chymotrypsin-like protease ( clpro) into nsps [ , , ] . there are at least four structural proteins encoded by the coronaviral genome: a spike glycoprotein (s), an envelope protein (e), a membrane protein (m) and nucleocapsid protein (n) with short untranslated regions at both termini, required to produce a structurally complete viral particle [ ] . the typical coronavirus virion structure and proteins are shown in figure . the m protein is in higher quantities in comparison to any other proteins in the virus particle; with its three transmembrane domains, it shapes virions, promotes membrane curvature and binds to the nucleocapsid [ , ] . the n protein contains two domains, both of which can bind to nsp protein to help tether the genome to replication-transcription complex (rtc) and package viral rna into the viral particle during viral assembly [ , ] . the e protein is involved in virus assembly and virion release from host cells, while the s protein plays a vital role in attachment to host receptors, viral entry and determines host tropism [ , ] . additionally, some coronaviruses, such as hcov-oc and hcov-hku , have a hemagglutinin-esterase (he) gene between orf b and s [ ] [ ] [ ] [ ] . this based on the genetic sequence identity and the phylogenetic reports, sars-cov- is sufficiently different from sars-cov; thus, who has classified it as a new betacoronavirus that infects humans [ ] . the genome of hcovs is a single-stranded positive-sense rna (+ssrna) (~ - kb) with -cap structure and -poly a tail, which is among the largest known rna genomes [ ] [ ] [ ] . the typical hcovs gene order is -replicase-s-e-m-n- , with numerous ( to ) open reading frames (orfs) encoding accessory proteins scattered among the structural genes [ , ] . the first orfs (orf a and b) comprise two-thirds (approximately %) of the genome length and encode nonstructural polyproteins (nsps - ) and are directly translated from the genomic rna [ ] . there is a − ribosomal frameshift between orf a and orf b, leading to the production of two large replicase polypeptides (pp): pp a and pp ab. these polypeptides are further processed by two virally encoded cysteine proteases, the papain-like protease (plpro) and a -chymotrypsin-like protease ( clpro) into nsps [ , , ] . there are at least four structural proteins encoded by the coronaviral genome: a spike glycoprotein (s), an envelope protein (e), a membrane protein (m) and nucleocapsid protein (n) with short untranslated regions at both termini, required to produce a structurally complete viral particle [ ] . the typical coronavirus virion structure and proteins are shown in figure . the m protein is in higher quantities in comparison to any other proteins in the virus particle; with its three transmembrane domains, it shapes virions, promotes membrane curvature and binds to the nucleocapsid [ , ] . the n protein contains two domains, both of which can bind to nsp protein to help tether the genome to replication-transcription complex (rtc) and package viral rna into the viral particle during viral assembly [ , ] . the e protein is involved in virus assembly and virion release from host cells, while the s protein plays a vital role in attachment to host receptors, viral entry and determines host tropism [ , ] . additionally, some coronaviruses, such as hcov-oc and hcov-hku , have a hemagglutinin-esterase (he) gene between orf b and s [ ] [ ] [ ] [ ] . this hemagglutinin, like the influenza homolog enzyme, binds to sialic acid on host cell-surface glycoproteins and possesses acetyl-esterase activity [ ] . besides coronavirus-conserved genes, the sars-cov, sars-cov- and mers-cov genomes contain several specific accessory genes including orf a/b, a/b, orf , orf , orf a/b, orf a/b and b ( figure ) [ , , ] . all the structural and accessory proteins are translated from subgenomic rnas (sgrnas) generated during genome transcription/replication of covs [ ] . hemagglutinin, like the influenza homolog enzyme, binds to sialic acid on host cell-surface glycoproteins and possesses acetyl-esterase activity [ ] . besides coronavirus-conserved genes, the sars-cov, sars-cov- and mers-cov genomes contain several specific accessory genes including orf a/b, a/b, orf , orf , orf a/b, orf a/b and b ( figure ) [ , , ] . all the structural and accessory proteins are translated from subgenomic rnas (sgrnas) generated during genome transcription/replication of covs [ ] . attachment, cell entry, translation of viral replicase, genome replication, translation of structural proteins and virion assembly and release are the phases of coronavirus replication cycle [ , ] . sars-cov, mers-cov and sars-cov- bind to different host receptors to gain entry into host cells [ , , ] . viral entry is mediated by the transmembrane s glycoprotein that comprises two functional subunits (s and s subunits) responsible for receptor recognition and viral-host cell membranes fusion, respectively [ , ] . s receptor-binding domain (rbd) mediates binding to the cognate host cell receptor; however, the s domain mediates the fusion events, between viral envelope and host cell membrane [ , , ] . as recently found, sars-cov- uses the same ace receptor [ ] , as sars-cov, whereas mers-cov uses dipeptidyl peptidase (dpp , also known as cd ) receptor (table ) [ ] . the fusion of the s protein to the plasma membrane of host cell generates a double membrane vesicle in the host cell, thereby allowing release of the nucleocapsid into the cytoplasm, followed by genome transcription [ , ] . upon entry into the cell, virus-specific rna and proteins are synthesized, probably entirely in the cytoplasm. translation starts with the expression of two polyproteins, pp a and pp ab, which undergo co-translational proteolytic processing into the proteins that form the replicase complex. this complex is used to transcribe a ′-coterminal set of nested subgenomic mrnas, as well as genomic rna that have a common ′ "leader" sequence derived from the ′ end of the genome. new virions are assembled by budding into intracellular membranes of the pre-golgi compartment and released through the cell secretory mechanisms [ , , , ] . attachment, cell entry, translation of viral replicase, genome replication, translation of structural proteins and virion assembly and release are the phases of coronavirus replication cycle [ , ] . sars-cov, mers-cov and sars-cov- bind to different host receptors to gain entry into host cells [ , , ] . viral entry is mediated by the transmembrane s glycoprotein that comprises two functional subunits (s and s subunits) responsible for receptor recognition and viral-host cell membranes fusion, respectively [ , ] . s receptor-binding domain (rbd) mediates binding to the cognate host cell receptor; however, the s domain mediates the fusion events, between viral envelope and host cell membrane [ , , ] . as recently found, sars-cov- uses the same ace receptor [ ] , as sars-cov, whereas mers-cov uses dipeptidyl peptidase (dpp , also known as cd ) receptor (table ) [ ] . the fusion of the s protein to the plasma membrane of host cell generates a double membrane vesicle in the host cell, thereby allowing release of the nucleocapsid into the cytoplasm, followed by genome transcription [ , ] . upon entry into the cell, virus-specific rna and proteins are synthesized, probably entirely in the cytoplasm. translation starts with the expression of two polyproteins, pp a and pp ab, which undergo co-translational proteolytic processing into the proteins that form the replicase complex. this complex is used to transcribe a -coterminal set of nested subgenomic mrnas, as well as genomic rna that have a common "leader" sequence derived from the end of the genome. new virions are assembled by budding into intracellular membranes of the pre-golgi compartment and released through the cell secretory mechanisms [ , , , ] . , the ′-terminus of the sars-cov- and sars-cov genomes contain eight accessory proteins ( a, b, p , a, b, b, b and orf and a, b, p , a, b, a, b and b, respectively) while mers-cov genome contains only five ( , a, b, and b). the genes encoding accessory proteins are unique in different coronaviruses in terms of number, genomic organization, sequence and functions (data extracted from [ , , ] the coronavirus genomes encode two replicase polypeptides pp a and pp ab translated from orf a and orf b; four structural genes encoding for four structural proteins including (s) spike, (m) membrane, (e) envelope and (n) nucleocapsid proteins. the single-stranded rna genomes of sars-cov- (~ . kb), sars-cov (~ . kb) and mers-cov (~ . kb) harbor two large genes, the orf a (red) and b (blue) genes encoding accessory genes (nsps - , shades of red and blue). encoded nonstructural proteins: nsps (nsp -nsp ) in sars-cov- , sars-cov and mers-cov. along with structural proteins (s, e, m and n), the -terminus of the sars-cov- and sars-cov genomes contain eight accessory proteins ( a, b, p , a, b, b, b and orf and a, b, p , a, b, a, b and b, respectively) while mers-cov genome contains only five ( , a, b, and b). the genes encoding accessory proteins are unique in different coronaviruses in terms of number, genomic organization, sequence and functions (data extracted from [ , , ] virologic as well as genetic studies have demonstrated that bats are reservoir hosts of both sars-cov and mers-cov, but also that they can use other species as intermediate hosts before spreading to humans [ , ] . the detection of two genomes distinct from known swine in ill piglets were reported by two independent groups [ , ] . the phylogenetic analyses showed that these novel swine enteric alphacoronaviruses (seacovs) were strongly related to the rhinolophus bat coronavirus hku isolated in guangdong province, in southern china [ , ] . this suggests that coronaviruses of bat origin may have 'jumped' the barrier of the species to infect pigs as intermediate hosts. the cd receptor sequence alignment between humans and pigs demonstrates a . % overlap, which is sufficient for the possible cross-species transmission [ ] . it has also been documented that pigs are susceptible to human sars-cov [ ] and mers-cov infections [ ] . the large number of mutations within the rbd enabled viruses to infect new hosts, representing a potential threat for both animal and human health. in southern china, the unique climate, the high density of domestic as well as wild pigs, along with the extensive bat distribution and carriage of tremendous quantities of recombinant novel coronaviruses may result in the appearance of more novel coronaviruses in the future [ ] . it is generally acknowledged that numerous viruses have existed and were restricted to their natural reservoirs for lengthy times [ ] . the consistent spillover of viruses from natural hosts to humans and other species is essentially related to human activities, including urbanization and modern agricultural practices, leading to the constant human exposure to the ever-changing mutant covs from their reservoirs [ , ] . the close contact between humans and animals and the practice of eating raw meat are both risk factors for causing a new human cov outbreak [ ] . hence, covid- should be considered as a zoonotic disease that spread from animals to humans. following the first sars-cov- outbreak in seafood and wildlife market in wuhan, secondary cases started to be identified after ten days. although these new patients did not have any contact with the market, they had a history of contact with people who attended the market [ ] . therefore, similarly to sars-cov and unlikely to mers-cov, human-to-human transmission for sars-cov- has been reported and is currently considered as the main type of transmission worldwide [ , ] . on january , , thailand announced the first non-chinese case of infection that spread from the chinese provinces, to the asian continent [ ] . this case was a chinese tourist who has traveled to thailand and did not have any epidemiological link to the market [ ] . more recently, forster et al., by using phylogenetic analysis based on nucleotide mutations of complete human sars-cov- genomes found that three variants of sars-cov- (a as the ancestral type, plus b and c) represent the bat outgroup coronaviruses. in particular, the a and c types were found mostly in european-american patients, whereas the b type was common in east asia suggesting that this kind of analysis could help in following the evolution of sars-cov- [ ] . it was demonstrated that sars-covs have adapted themselves to bind to human ace receptor and infect human cells effectively [ ] . this form of adaptation required a series of amino acid changes in the rbd within the s protein of sars viruses that circulated in bats [ , ] . therefore, the human-to-human transmission that was seen in the course of the sars-cov outbreaks is directly attributable to the ability of sars-covs to adapt their s protein to efficiently bind to human ace , thus infecting ciliated bronchial epithelial cells and type ii pneumocytes [ , ] . similar to sars-cov, ace is also used by sars-cov- as the entry receptor in the ace -expressing cells, suggesting that sars-cov- has a life cycle similar to sars-cov [ , ] . as outlined before, sars-cov s protein regulates the receptor binding and membrane fusion activities determining host tropism and transmission capacity. several evidences highlighted a higher binding affinity of sars-cov- rbd to the ace receptor. in particular, molecular and in silico analyses demonstrated that sars-cov- rbd conformation and amino acid composition enhance the bonding between the s protein and ace receptor [ , , ] . a recent biophysical and structural analysis of the sars-cov- s protein showed that it binds to ace receptor with about -to -fold higher affinity than the s protein of sars-cov [ , ] . this high affinity could account for its extreme infectivity among human populations. another feature of the powerful infectivity of sars-cov- is that the shedding pattern of viral particles in sars-cov- diagnosed patients is similar to that of influenza patients in which viral loads at the time of symptom onset are higher and gradually decrease within days; interestingly, this pattern seems to be different from that reported for sars-cov patients where the highest shedding is reported days after the onset of symptoms [ , , ] . these results indicate that sars-cov- can spread more easily than sars-cov in the community even in the absence of symptoms or when only initial mild symptoms are present [ ] . the human-to-human transmission of sars-cov- mainly occurs by inhalation of respiratory droplets spread by coughing or sneezing from an infected individual, but also by direct contact of contaminated surfaces and then touching the nose, mouth and eyes [ , [ ] [ ] [ ] . the virus was shown to remain stable in favorable atmospheric conditions on different surfaces for days [ ] . additionally, transmission in an unventilated environment or closed spaces due to high aerosol concentrations has been suggested [ , ] . in agreement, the presence of sars-cov- in the surfaces of the houses of confirmed patients was reported, further strengthening this mode of contact transmission. moreover, live viruses were also found in the stool of covid- patients, as previously found for both sars-cov and mers-cov [ ] . given its capacity for survival in feces and the expression of ace within intestine, it was demonstrated that sars-cov- can infect these tissues and can be released in feces; therefore, water supply contamination and fecal-oral route transmission is also hypothesized [ , ] . however, at present, there have not been reported cases of fecal-oral transmission of the virus. studies have also indicated that sars-cov- transmission via ocular surfaces should not be overlooked, as contaminated droplets and body fluids could easily infect the human conjunctival epithelium [ ] . sars-cov- is also responsible for cluster transmission, in particular within family clusters [ ] . in some cities, % to % of all reported cases of covid- accounted for cluster transmission [ ] . based on the current information, there is no evidence for transplacental transmission from infected pregnant women to their fetus, who underwent caesarean section [ , ] . therefore, whether transmission during vaginal birth can occur remains to be established, neonatal covid- disease as postnatal transmission was documented [ ] . although, sars-cov- may definitely infect infants, it has been reported that neonates, infants and children develop significantly milder forms of the disease than their adult counterparts [ , ] . coronaviruses are responsible for - % of acute respiratory illness while it has been estimated that % of the population is deemed as an asymptomatic carrier of these viruses. the first discovered hcov was ibv that causes respiratory disease in human whereas, hcov- e and hcov-oc , which cause the common cold in humans [ , , ] . they were not considered to be highly pathogenic for humans until the outbreak of sars in guangdong state of china in and . sars-cov infected more than people worldwide and caused deaths (table ) , representing a mortality rate by around % [ ] . ten years later in , mers-cov emerged in saudi arabia and infected over people with deaths, accounting for a mortality rate approximately of % [ , , ] . starting in china in december , there were reports of patients presenting severe viral pneumonia [ , , ] . this public health concern resulted in many unknown pneumonia cases who were admitted to local hospitals [ , ] (https://www.who.int). primary etiologic investigations performed in those patients showed that they were epidemiologically linked to a huanan wholesale seafood market that also traded live animals and wildlife [ , , ] . by january th, chinese authorities announced that a new type of coronavirus was isolated [ , ] . the epicenter of infection was probably linked to a zoonotic pathogen being present in the seafood and exotic animal wholesale market [ , ] . the rapid increasing numbers and rate of fatalities indicated a second mode of transmission, from human-to-human, that allowed viral spreading primarily in other asian countries such as south korea and iran followed by many countries such as italy, spain, germany, france, brazil and usa [ , ] . it is very intriguing to note that the sars epidemic in southern china in and the current outbreak of covid- had peaked in mid-february due to exposure to live animals sold in markets. furthermore, similar to the sars outbreak, this epidemic has occurred during the spring festival in china, as the most famous traditional countrywide festival in china, gathering nearly three billion people from different areas. these favorable conditions caused the wide transmission of this fatal pneumonia and severe difficulties for disease control and prevention of the epidemic [ ] . based on clinical data of diagnosed patients during the sars-cov- outbreak, the basic reproduction number (r ) is estimated to range between and . in various modeling studies [ , ] . the sars-cov- r is in line with the one estimated for sars-covs and mers-covs (from to ) [ , ] . currently, increasing countries are experiencing clusters of cases and community transmission following sars-cov- pandemic. since its emergence, the covid- has drawn well-deserved attention from authorities in order to protect their community and stop or slow down transmission of this disease. at the time of this review, according to the daily report of the world health organization, sars-cov- has affected over , , people with around , daily new cases and killed more than , people all over the world, by august rd, (the up to date fatality rate is reported from https://covid .who.int). we must take into consideration that these data are relative to laboratories and clinically confirmed cases while the actual number including asymptomatic cases, infected undiagnosed and death patients would be much higher than reported cases. the transmission of seasonal respiratory coronaviruses can be affected by several climate parameters such as temperature and humidity [ ] . therefore, understanding the relationship between weather and transmission of covid- is the key to forecast the intensity and end time of this pandemic. to this regard, emerging evidence suggests that whether climate conditions may influence the transmission of the sars-cov- by boosting the spread (much of the data have not been peer-reviewed yet). to date, covid- has had a significant expansion in the northern hemisphere (nh) belt, given that it covers cities and populated areas; conversely, in the belt of the southern hemisphere (sh), which covers very low population and landless areas, covid- has not been reported yet. based on climate and era-interim reanalysis dataset in nh belt from november to march , we compared the average rate of humidity and temperature between five cities in european countries with significant community transmission of covid- versus five cities of north africa which are expected to be less exposed to covid- . the information recorded by the meteorological stations has been used, since these are more accurate than satellite data [ ] . as shown in table , the average amount of humidity is very close between european and african selected sites. the main reason is the proximity of these cities to the mediterranean sea coastline. in addition, the north wind, which blows from northern europe to european cities (ecs), increases the humidity of these cities. conversely, there are temperature differences between considered ecs and north african cities (table ) . thus, temperature and humidity should be considered parameters involved in the transmission of covid- . up to know, few studies have investigated the association of temperature and humidity with covid- incidence and death rates. the first meteorological study was done in different chinese cities each having more than cases of covid- in a -day period during the end of january [ ] . this group showed that high temperature and humidity significantly reduces the transmission of covid- . their results indicate that the increases of • c in temperature and % in relative humidity lower r by . and . , respectively [ ] . a preprint study on confirmed covid- cases collected from cities showed that every • c increase in the minimum temperature of higher-temperature cities reduced the disease incidence and death rates by . [ ] . another preprint study suggested that the average increase of • c in temperature correlates negatively with the predicted number of cases worldwide [ ] . these results are in accordance with wu y et al. who showed that among all confirmed covid- new cases and new deaths from countries (excluding china), a • c increase in temperature is associated with a . % reduction in daily new cases and a . % reduction in daily new deaths, whereas a % increase in relative humidity was associated with a . % reduction in daily new cases and a . % reduction in daily new deaths [ ] . a recent study conducted in italy showed a positive correlation of sars-cov- spreading and weather conditions including temperatures ranging - • c and relative humidity of - % [ ] . in a geographic and population modeling study conducted in five largest cities in colombia, the transmission of sars-cov- seems to be comodulated by temperature and humidity. their observation revealed a strong reduction of transmission in climates with temperatures above • c and relative humidity below % which may comodulate the infectivity of sars-cov- within respiratory droplets [ ] . table . average humidity and temperature in different cities in europe and north africa between november to march . the first five cities represent significant communities where transmission of covid- was reported, whereas the second cities are expected to be less exposed to covid- due to different weather conditions. average humidity (%) temperature ( • c) rome paris madrid milan lisbon rabat algiers tunis tripoli cairo overall, these meteorological analyses support that the combination of temperature and humidity could represent a direct influence on the transmission of the covid- . it can be assumed that the arrival of summer and rainy season in the nh can effectively reduce the transmission of the covid- . the distribution of covid- across different longitudes and latitudes with a range of temperatures and humidity may help to predict the prevalence of this disease in terms of environmental characteristics. this could lead to a better understanding of how the virus spreads around the world ( figure ). it should be noted that apart from the capability of sars-cov- to persist on environmental surfaces under favorable atmospheric conditions, the duration of its persistence may be affected by temperature and humidity. however, caution is needed when considering the implications of these findings, which may be subject to confounding. although warmer climates may slow the spread of sars-cov- , relying on weather changes alone to slow the transmission of covid- are unlikely to be enough. however, using this type of dataset and climate analysis modeling is possible to identify areas that are most likely to be at risk of significant covid- cases in the future and serve as an alarm signal to various government departments and agencies to adopt the necessary measures to prevent virus spread [ ] . moreover, more data are gathering around the world due to the change of the season and all authors agree that the association between temperature/humidity and sars-cov- is an appreciable hypothesis, but not a certainty yet. cases in the future and serve as an alarm signal to various government departments and agencies to adopt the necessary measures to prevent virus spread [ ] . moreover, more data are gathering around the world due to the change of the season and all authors agree that the association between temperature/humidity and sars-cov- is an appreciable hypothesis, but not a certainty yet. the most common symptoms of patients at onset of covid- disease are defined as fever, dry cough, fatigue and less often, symptoms of sputum production, headache, sore throat, myalgia; hemoptysis, dyspnea, diarrhea and lymphopenia were also observed [ , , ] (figure ). the spectrum of clinical features of covid- has been found ranging from an asymptomatic state to severe respiratory failure and multiorgan dysfunction [ , ] . symptomatic people are considered to be more contagious, similar to most viral-related respiratory diseases. however, individuals who remain asymptomatic may also transmit the virus and cases infected by an asymptomatic individual in the prodrome period of covid- have also been reported [ ] . asymptomatic infections can occur because of weakened immune responses and subclinical manifestations or also because the the most common symptoms of patients at onset of covid- disease are defined as fever, dry cough, fatigue and less often, symptoms of sputum production, headache, sore throat, myalgia; hemoptysis, dyspnea, diarrhea and lymphopenia were also observed [ , , ] (figure ). the spectrum of clinical features of covid- has been found ranging from an asymptomatic state to severe respiratory failure and multiorgan dysfunction [ , ] . symptomatic people are considered to be more contagious, similar to most viral-related respiratory diseases. however, individuals who remain asymptomatic may also transmit the virus and cases infected by an asymptomatic individual in the prodrome period of covid- have also been reported [ ] . asymptomatic infections can occur because of weakened immune responses and subclinical manifestations or also because the virus is waiting for opportunities to invade and reproduce. a recent study has shown that a viral load detected in an asymptomatic patient was just like to the one observed in symptomatic patients, indicating the capability of transmission in asymptomatic patients [ ] . according to disease presentation, covid- can be classified as mild, moderate, severe and critical ( virus is waiting for opportunities to invade and reproduce. a recent study has shown that a viral load detected in an asymptomatic patient was just like to the one observed in symptomatic patients, indicating the capability of transmission in asymptomatic patients [ ] . according to disease presentation, covid- can be classified as mild, moderate, severe and critical (table ) [ , , ] . in % of all confirmed covid- cases. dry cough, mild fever, sore throat, nasal congestion, muscle pain, headache and malaise. absence of serious symptoms like dyspnea, also the absence of radiograph features. it may rapidly deteriorate into severe or critical cases, non-pneumonia or mild pneumonia. dry cough, tachypnea and shortness of breath. acute respiratory distress syndrome (ards), severe pneumonia, severe dyspnea, sepsis or septic shock, tachypnea (respiratory frequency) ≥ /min, blood oxygen saturation (spo ) ≤ %, partial pressure of arterial oxygen to fraction of inspired oxygen ratio (pao /fio ) < , and/or lung infiltrates > % within to h. fever can be absent or moderate. in % of all confirmed covid- cases. respiratory failure, septic shock, rnaemia, cardiac injury and/or multiple organ dysfunction or failure. case fatality rate is % (higher case fatality rate for patients with preexisting co-morbidities and lower-case fatality rate ( . %) for patients without co-morbidities). cardiovascular disease ( . %), diabetes ( . %), respiratory disease ( . %), hypertension ( %) and oncological complications ( . %). in % of all confirmed covid- cases. dry cough, mild fever, sore throat, nasal congestion, muscle pain, headache and malaise. absence of serious symptoms like dyspnea, also the absence of radiograph features. it may rapidly deteriorate into severe or critical cases, non-pneumonia or mild pneumonia. dry cough, tachypnea and shortness of breath. acute respiratory distress syndrome (ards), severe pneumonia, severe dyspnea, sepsis or septic shock, tachypnea (respiratory frequency) ≥ /min, blood oxygen saturation (spo ) ≤ %, partial pressure of arterial oxygen to fraction of inspired oxygen ratio (pao /fio ) < , and/or lung infiltrates > % within to h. fever can be absent or moderate. in % of all confirmed covid- cases. respiratory failure, septic shock, rnaemia, cardiac injury and/or multiple organ dysfunction or failure. case fatality rate is % (higher case fatality rate for patients with preexisting co-morbidities and lower-case fatality rate ( . %) for patients without co-morbidities). cardiovascular disease ( . %), diabetes ( . %), respiratory disease ( . %), hypertension ( %) and oncological complications ( . %). and % of patients are likely to experience symptoms within . days from contact [ , [ ] [ ] [ ] . however, in an asymptomatic carrier the incubation period was days, complicating the challenge to contain the outbreak [ ] . the median time between onset of symptoms and dyspnea is days, days for hospitalization and days for acute respiratory distress syndrome (ards) (figure ) [ ] (https://www.epicentro.iss.it/coronavirus/sars-cov- ). patients at this stage in intensive care unit (icu) with quarantine facilities may require mechanical ventilation. moreover, bacterial infections can cause a secondary pneumonia [ ] . in addition, the period from the beginning of covid- symptoms to death varied between and days with an average of days [ ] . this period depends on immune system status and the patient's age, being shorter in -year-old subjects compared with those younger [ , ] . in people with compromised immune systems and in elderly patients with underlying health problems, sars-cov- is able to infect the lower respiratory tract leading to severe pneumonia [ ] . in - % of patients presenting acute lung injury, shock, ards and acute kidney injury, icu admission was absolutely required [ ] . recovery started within the nd or rd weeks with the median duration of hospitalization of days. the virus appears to be more fatal in individuals with underlying co-morbidities ( - % of fatal cases) [ , ] . available dataset was obtained from italian istituto superiore di sanità (iss) on , patients dying in-hospitals ( figure ) . the mean number of diseases was . (median , sd . ). overall, . % of the reported cases has no co-morbidities, . % with a single comorbidity, . % with and . % with or more (https://www.epicentro.iss.it/coronavirus/sars-cov- ). sars-cov- infections revealed some unique clinical characteristics that include targeting the lower airway which is evident by symptoms of upper respiratory tract including rhinorrhoea, sneezing and sore throat [ ] . chest computed tomography (ct) scans revealed pneumonia in most sars-cov- infected patients and several cases showed an infiltrate in the upper lung lobe, which is related to increasing dyspnea with hypoxemia [ , , ] . table describes the full picture of covid- clinical manifestation. atypical symptoms include rnaemia, acute cardiac injury, ards and grand-glass opacities that lead to death [ ] . it should be noted that covid- manifestations such as fever, dyspnea, dry cough and bilateral ground-glass opacities in chest ct scans are similar to the previous betacoronavirus-related diseases [ , ] . although gastrointestinal symptoms such as diarrhea were reported in sars-cov- infected patients, the similar gastrointestinal distress occurred in only a small percentage of mers-cov or sars-cov patients ( figure ) [ ] . it was shown that severe cases were characterized by an increased inflammation due to both systemic and localized immune response activation [ , ] . higher leukocyte numbers, significantly high blood concentrations of cytokines and chemokines were noted in these cases [ , ] . hence, it is now accepted that high levels of proinflammatory cytokines could worsen the prognosis [ , ] . the symptoms of sars-cov- infection appear after an incubation period of to days, similar to those of sars-and mers-cov infections (median approximately . days in different studies) and % of patients are likely to experience symptoms within . days from contact [ , [ ] [ ] [ ] . however, in an asymptomatic carrier the incubation period was days, complicating the challenge to contain the outbreak [ ] . the median time between onset of symptoms and dyspnea is days, days for hospitalization and days for acute respiratory distress syndrome (ards) (figure ) [ ] (https://www.epicentro.iss.it/coronavirus/sars-cov- ). patients at this stage in intensive care unit (icu) with quarantine facilities may require mechanical ventilation. moreover, bacterial infections can cause a secondary pneumonia [ ] . in addition, the period from the beginning of covid- symptoms to death varied between and days with an average of days [ ] . this period depends on immune system status and the patient's age, being shorter in -year-old subjects compared with those younger [ , ] . in people with compromised immune systems and in elderly patients with underlying health problems, sars-cov- is able to infect the lower respiratory tract leading to severe pneumonia [ ] . in %- % of patients presenting acute lung injury, shock, ards and acute kidney injury, icu admission was absolutely required [ ] . recovery started within the nd or rd weeks with the median duration of hospitalization of days. the virus appears to be more fatal in individuals with underlying co-morbidities ( %- % of fatal cases) [ , ] . available dataset was obtained from italian istituto superiore di sanità (iss) on , patients dying inhospitals ( figure ) . the mean number of diseases was . (median , sd . ). overall, . % of the reported cases has no co-morbidities, . % with a single comorbidity, . % with and . % with or more (https://www.epicentro.iss.it/coronavirus/sars-cov- ). figure . median times, in days, from the onset of symptoms to death, to hospitalization, from hospitalization to death with and without intensive care unit (icu)-admittance (report based on available data on july th, collected from istituto superiore di sanità, iss). sars-cov- infections revealed some unique clinical characteristics that include targeting the lower airway which is evident by symptoms of upper respiratory tract including rhinorrhoea, sneezing and sore throat [ ] . chest computed tomography (ct) scans revealed pneumonia in most sars-cov- infected patients and several cases showed an infiltrate in the upper lung lobe, which is related to increasing dyspnea with hypoxemia [ , , ] . table describes the full picture of covid- clinical manifestation. atypical symptoms include rnaemia, acute cardiac injury, ards and grand-glass opacities that lead to death [ ] . it should be noted that covid- manifestations figure . median times, in days, from the onset of symptoms to death, to hospitalization, from hospitalization to death with and without intensive care unit (icu)-admittance (report based on available data on july th, collected from istituto superiore di sanità, iss). covid- clinical evaluation is focused mainly on epidemiological data, clinical symptoms and clinical and laboratory tests. although the scenario is continually changing, several approaches were selected as standard laboratory methods for covid- diagnosis. lab tests, differently from clinical-based analyses, immediately reveal sars-cov- infected patients. this was particularly important for diagnosis due to the difficulties in detecting specific clinical signs and symptoms in covid- patients. moreover, atypical manifestations revealed by pulmonary imaging [ ] and the huge number of different clinical signs and symptoms forced the development of molecular-based laboratory tests [ , ] . lastly, the analysis of personal history of each patient played a fundamental role in covid- diagnosis and up to now is considered one of the key information for detecting infected patients also in the early phases of infection. therefore, the epidemiological history together with clinical and laboratory tests are all required for the diagnosis of covid- . a detailed description focused on clinical diagnostic methods was reviewed by taisheng li [ ] . herein, we present an updated overview of the principal techniques used for covid- diagnosis. high-throughput sequencing and real time quantitative polymerase chain reaction (rt-qpcr) are the best nucleic acid detection techniques for sars-cov- . however, in clinical diagnosis, the application of high-throughput sequencing technology is limited due to high cost and its equipment dependency [ , , ] . moreover, to speed up the development of standardized analytic kits for diagnostic application, the quantification of viral load was not considered. therefore, the rt-pcr method was chosen as the gold standard for the detection of sars-cov- infections from the commonly used samples such as naso-and oropharyngeal swabs [ , , , ] . this molecular method relies on the amplification of up to three sars-cov- specific targets including the rna-dependent rna polymerase (rdrp), e and n genes [ ] . the who has released numerous rt-pcr protocols for the detection of sars-cov- rna at https://www.who.int/emergencies/diseases/novel-coronavirus- /technical-guidance/laboratory-guidance (accessed march , ). three of those protocols are mentioned below. the us centers for disease control and prevention (cdc) developed an rt-pcr that includes three sets of oligonucleotide primers and probes recognizing three regions of the virus n gene (named n , n and n ) and an additional primer/probe set to detect the human rnase p gene (rp) representing an internal control for rna extraction and retro-transcription. moreover, the positive control consisting in retro-transcribed viral rna is also available at cdc. to report the positivity for sars-cov- two out of three n regions must be positive. the chinese center for disease control and prevention (china cdc) recommends the use of specific primers and probes targeting the orf ab and n gene regions for sars-cov- detection by rt-pcr [ ] . the positivity is confirmed when both targets are detected. available online: http://ivdc.chinacdc.cn/kyjz/ /t _ .html (accessed on january ). overall, the who summarized all the primer pairs and probes that can be used to detect sars-cov- in clinical specimens with the description of rt-pcr settings and the specificity. apart from the possibility to perform the rt-pcr in house using the selected primer pairs and probes, several ready to use kits were developed for rt-pcr performing. one of the most used is the allplex -ncov (seegene, seoul, south korea) which includes three different viral targets and a positive control [ ] . another example is represented by the bgi's real-time fluorescent rt-pcr kit for detecting sars-cov- that includes one sars-cov- specific target and an internal control of the reaction (bgi, cambridge, ma, usa). both companies declared a sensibility of - viral copies per ml and a high specificity that excludes most respiratory tract viral and bacterial pathogens. the recommended samples for both in-house and ready-to-use rt-pcr kits include upper and lower respiratory specimens such as throat, nasal nasopharyngeal (np) and/or oropharyngeal (op) swabs, lower respiratory tract aspirates, sputum, bronchoalveolar lavage (bal) fluid and nasopharyngeal wash/aspirate or nasal aspirate. it was observed that samples of the lower respiratory tract provide the higher viral loads [ ] . on the other hand, it was shown that in the early stage of infection, the positive rate of rt-pcr was reported to be about % for throat swab samples [ ] . indeed, although being the gold standard, the rt-pcr presents some drawbacks. one of the most important is related to the sensibility because it was extensively reported that in the presence of low viral load this technique fails in detecting viral genome leading to false negative results [ ] . due to this problem, clinical governance as well as kit troubleshooting indicate to retest all the samples showing only single positive target along with patient resampling. to this respect, it should be underlined that operator skills or sampling sources can profoundly affect rt-pcr testing results [ ] . finally, during this pandemic several microbiologic labs worldwide are experiencing scarce availability of rna extraction as well as ready-to-use rt-pcr kits increasing the timing of diagnosis confirmation through molecular approaches. very recently, it was reported that the allplex -ncov and the realstar sars-cov- rt-pcr kits can amplify the target genes bypassing the rna extraction step for a faster diagnosis [ ] . although rt-pcr is specific for the diagnosis of covid- , its false-negative rate cannot be overlooked due to the severe consequences of missed diagnosis. clinicians have demonstrated the usefulness of ct and chest radiography for the diagnosis of covid- associated pneumonia [ ] . moreover, the ability of radiologists to diagnose covid- pneumonia from chest ct evaluations has been reported to be very high [ ] . then a combination between rt-pcr and ct imaging represents the best approach for the correct covid- diagnosis. in particular, for early detection and assessment of disease severity, the high-resolution ct (hrct) of the chest is considered necessary [ , ] . one study analyzed the consistency and diagnostic value of rt-pcr test compared with chest ct in patients with suspected sars-cov- infection. findings indicated that the chest ct sensitivity in suspected patients was % based on negative rt-pcr results and % based on positive rt-pcr results [ ] . moreover, salehi et al. confirmed the higher sensibility of pulmonary imaging with respect to rt-pcr for covid- diagnosis and showed a positive correlation between specific ct findings with the different stages of the disease and its severity [ ] . the collection of numerous ct images has opened the possibility to build a database of pulmonary images from covid- patients. interestingly, the recent progress in integrating artificial intelligence (ai) with computer-aided design (cad) software for diagnostic imaging revealed that ai could be used to support disease diagnosis [ , ] . ito et al. reviewed the literature on the use of ai for lung diagnostic imaging of covid- patients. among the selected studies, used ai for ct and used ai for chest radiography. the number of datasets ranged from to , with sensitivities ranging from - % and specificities ranging from - % for prediction of covid- pneumonia. this study revealed the usefulness of ai approach to support the diagnosis of covid- , but also for future emerging diseases [ ] . all the collected knowledge on lung lesions revealed some characteristic ct findings of covid- pneumonia: the pulmonary ground-glass opacities in a peripheral distribution and the consolidation referring to an increase in pulmonary parenchymal density [ ] [ ] [ ] . however, chest ct manifestations can vary in different patients and stages of infection, highlighting certain shortcomings of this approach. apart from atypical manifestation that cannot be recognized by radiologists, several lung images are common in viral pneumonia leading to misdiagnosis [ ] . soon after the beginning of sars-cov- spreading, infected patients underwent antibody research for both basic research and clinical applications. one of the first studies reported the seroconversion of % of infected patients (n = ) within days after symptom onset. seroconversion for igm and igg occurred simultaneously or sequentially and both immunoglobulins titers plateaued within days after seroconversion. importantly, the application of serology testing in surveillance in a cluster of close contacts of covid- patients identified . % of positive patients showing negative rt-pcr results [ ] . hence, several studies underlined the recommended usage of serology to promote the detection of sars-cov- infections where np swab specimens were improperly collected, molecular assays were unsatisfactorily carried out and for determining asymptomatic infections [ ] . based on these data, several companies developed kits for igm/igg testing showing a high detection rate of infected patients. basically, there are two different testing methods: the rapid igg-igm test and the classical enzyme-linked immunosorbent assay (elisa)-based test. the rapid test consists in a lateral flow qualitative immunoassay on a strip to detect the presence of both anti-sars-cov- -igm and anti-sars-cov- -igg in human specimens such as whole blood, serum and plasma. this igg-and igm-combined antibody test kit has a sensitivity of . % and specificity of . %. results are obtained in min leading to its useful application as point-of-care testing and in supporting rt-pcr-based diagnostic [ ] . on the other hand, several elisa-based kits are now commercially available, and their sensitivity and specificity were compared showing an overall high specificity, but a variable sensibility [ ] . differently from the rapid tests, the elisa-based test should be performed on serum or plasma samples collected from venous sampling. interestingly, the authors showed the neutralizing capacity of sars-cov- specific antibodies on caco- cells directly incubating the sera from patients with the cell monolayers [ ] . this assay is extremely important for the plasma-based therapies that are successfully used to treat seriously ill patients (see below). finally, recently published papers described the seroconversion of covid- patients including the evaluation of iga that seems high in the early stages of infection (about days' post symptom development) [ , ] . another interesting application of antibody detection is represented by the fluorescence immuno-chromatographic assay for the detection of sars-cov- nucleocapsid protein in human specimens such as np swab [ ] . it shows the fastness of rapid tests (results in min), the possibility to use the same type of sample that is commonly used for rt-pcr-based diagnosis and high sensibility (detection of the nucleoprotein in all positive samples tested). although these methods were suggested for covid- diagnosis, the extent of antibodies production by infected patients is greatly variable. moreover, the delay of antibodies production with respect to the onset of symptoms affects the use of this approach for diagnosis. vice versa, it is reported that several governments, included italy, are using serologic test for population screening to assess the proportion of people that have developed an immunological response against sars-cov- (http://www.salute.gov.it/portale/nuovocoronavirus). this screening will help also to detect asymptomatic and/or paucisymptomatic subjects. the rapid spread of sars-cov- raises an urgent requirement for effective therapeutic strategies against covid- . although many efforts have been intended to develop vaccines against hcovs infections in recent years, there is no official and effective treatment against sars-cov- . however, different considerable options have been applied for possible vaccine validity, efficacy and safety along with speeding up other ongoing searches to discover valuable modalities for dealing with the emerging covid- [ , [ ] [ ] [ ] [ ] . most of the drugs that are being used to cope with covid- epidemic are directed towards specific viral molecular targets and biologic processes through which the virus spreads damaging the host. in line, all available experimental therapies for covid- management are based on previous experiences in treating sars-cov and mers-cov infections, such as inhibitors of sars-cov- fusion/entry/replication, anti-viral agents against main viral proteases, regulators of sars-cov- induced host inflammatory response and direct administration of human monoclonal antibodies (mabs) (figure ) [ ] . apart from all these possible therapeutic approaches, it has been reported that the chinese medicine products, as lianhuaqingwen and shufeng jiedu capsules may be helpful for sars-cov- treatment [ , ] . indeed, this product is mainly used to treat upper respiratory tract infections such as the flu, swelling and pain in the throat, mumps and strep throat [ , ] . moreover, four covid- cases have been described to gain improvement after taking combined chinese and western medicine [ ] . notably, encouraging progress in deciphering sars-cov- genome will lead to new potential therapeutic targets. likewise, more prospective, rigorous population studies are urgently required to confirm the therapeutic effect as well as the safety of new potential therapeutic strategies in order to further implement robust preventive and control measures against sars-cov- spread. as outlined above, multiple strategies are aimed at developing covs vaccines, most of which are headed for the surface-exposed spike (s protein) glycoprotein as the major virus-host cell membrane interactor. to this aim, vaccines under study are based on full-length s protein, s -rbd, expression of virus-like particles (vlp), dna or viral vectors [ , [ ] [ ] [ ] [ ] [ ] . as outlined above, the s includes the rbd that interacts with its host cell receptor, ace , whereas the s mediates fusion between the virus and host cell membranes promoting the entry and subsequent replication of the viral rna into the cytoplasm [ ] . the ace receptor, as a specific biologic target for vaccine development, is under study in a controlled pilot clinical trial to investigate the effect of recombinant human ace (rhace ; gsk ) in patients with severe covid- (nct ) ( figure i ) [ , ] . vice versa, both recombinant proteins containing rbd and the recombinant vectors encoding rbd can be used to generate the effective sars-cov vaccines given the capability of this domain to induce neutralizing antibody [ ] . indeed, the first available sars-cov-specific human monoclonal antibody with neutralizing activity against sars-cov, named cr , was found to bind potently to sars-cov- rbd, in agreement with the high homology shared by this domain with sars-cov homolog [ ] . however, it must be taken into account that more than % of the rbd antibody epitopes in sars-cov- show implicit noticeable changes, indicating the necessity to develop more specific monoclonal antibodies for sars-cov- [ ] . angiotensin receptor blockers (arbs), such as losartan, valsartan, telmisartan, usually assumed for treating high blood pressure, heart and kidney failure in people with diabetes, have been recently proposed as a novel therapeutic approach to block sars-cov- rbd binding to ace -expressing cells binding, similarly to ace inhibitors [ ] . additional targetable epitopes that should be considered are the heptad repeat (hr ) and heptad repeat (hr ) in sars-cov- s protein. in fact, the hr -derived peptides (hr p) and ek (a modified oc -hr p peptide), exhibit effective fusion inhibitory activity towards sars-cov- , suggesting a promising strategy in treating sars-cov- infection, although further studies are required to strengthen these hypotheses ( figure i ) [ , ] . lately, immuno-informatics have been employed to identify significant cytotoxic t lymphocyte (ctl) and b-cell epitopes in sars-cov- s protein, such as the nucleocapsid (n) protein as well as the potential b cell epitopes of the e protein of mers-cov as likely immunoprotective targets [ , ] . reverse genetic strategies have been successfully used in live-attenuated vaccines to inactivate the exonuclease effects of non-structural protein (nsp ) or to wipe out the envelope protein in sars [ ] . a recent study also revealed that the invasion process requires the priming of the s protein which is facilitated by the host cell produced serine protease tmprss . the clinically demonstrated serine protease tmprss inhibitor camostat mesylate, which partially blocks sars-cov- entry into host cells, was shown to be a good target to significantly reduce pulmonary infection in covid- affected individuals ( figure i ) [ ] moreover, it has been suggested that coronavirus entry also involves ph and receptor-dependent endocytosis [ , ] ; thus, targeting endocytosis may be another assessable option for fighting sars-cov- ( figure i ). in this view, throughout ai technology, a group of approved drugs, such as the janus kinase (jak) inhibitor baricitinib [ ] targeting the ap- -associated protein kinase (aak ) regulating clathrin-mediated endocytosis, has been developed ( figure i ) [ ] . furthermore, other drugs such as arbidol (chictr ), a haemagglutinin inhibitor and chloroquine phosphate, a traditional antimalarial drug, have been added to the national health commission of the people's republic of china (nhc) guidelines for covid- treatment ( figure i ) (http://www.nhc.gov.cn). in particular, in vitro studies have demonstrated that chloroquine as well as hydroxychloroquine could impair the endosome-mediated viral entry or later stages of viral replication [ ] . combination of hydroxychloroquine and azithromycin has also been suggested as a valid approach since it showed more rapid resolution of infection than hydroxychloroquine alone [ ] ; however, the combined use of azithromycin and hydroxychloroquine seems to be associated with at increased risk of arrhythmias. available online: https://www.acc.org/latest-in-cardiology/articles/ / / / / /ventricular-arrhythmia-riskdue-to-hydroxychloroquine-azithromycin-treatment-for-covid- (accessed on march ). to date, several attempts have also been made in targeting viral main enzymes; in fact, many inhibitory drugs targeting the coronavirus main proteinase c-like protease ( clpro) have been validated in clinical trials (e.g., lopinavir/ritonavir; chictr , chictr , chictr ) ( figure ii ) [ ] . moreover, four additional molecules including prulifloxacin, tegobuvir, bictegravir and nelfinavir, detected by high-throughput screening, showed reasonable binding conformations with the viral main protease [ ] . moreover, a recent study by performing a virtual screening using a three-dimensional model of the sars-cov- c-like protease ( cl), identified biologic candidates that deserve further consideration. among these, the antivirals ledipasvir or velpatasvir proved to be particularly attracting as therapeutics to combat the new coronavirus showing optimal anti-viral activity and minimal side effects, such as fatigue and headache; also, epclusa (velpatasvir/sofosbuvir) and harvoni (ledipasvir/sofosbuvir) are promising antivirals, not only for their effective and synergic inhibitory activities against two viral enzymes, but also for their minimized possibilities to develop resistance [ ] . a certain number of clinical trials on antiviral drugs aimed to arrest sars-cov- replication are currently in progress, such as remdesivir (nct , nct ) favipiravir (chictr , chictr ) and asc (chictr ) ( figure iii ). among these, remdesivir was recently approved for medical use in america and european union and seems to be the most promising antiviral for fighting sars-cov- [ ] (http://www.who.int), as in vitro studies demonstrated that this molecule, a mono-phosphoramidate prodrug of an adenosine, effectively inhibited sars-cov- rna synthesis [ ] . targeting the sars-cov- rna genome could, therefore, be another potential strategy. in fact, a crispr/cas d technology, which is an rna-guided rna-targeting crispr system, has been employed to specifically chew up sars-cov- rna genome. in this system, a cas d protein and guide rnas-containing spacer sequences are used to specifically complement the virus rna genome ( figure iv ). furthermore, rna genome can be packaged into one adeno-associated virus (aav) vector, making the crispr/cas d system more efficient for virus elimination and resistance prevention, taking into account that aav has serotypes highly specific to the lung, the main organ infected by sars-cov- [ ] . in addition to antiviral therapy, a new treatment strategy having a significant impact on clinical outcomes is utmost required. immunomodulatory therapy to downregulate the cytokine storm may provide great benefit to the treatment of covid- . recently, researchers focused on targeting specific molecular markers involved in inflammatory cytokines-receptors interactions, their correlation in health and disease and drugs in use that can activate or block their actions. a higher concentration of cytokines has been found in the plasma from covid- patients in icu compared with the ones from non-icu covid- patients, suggesting that the cytokine storm could be linked to the severity of the disease [ ] . corticosteroids are among the most commonly used drugs for immunomodulatory therapy of infectious diseases. however, the use of corticosteroids in the treatment of covid- can cause host immune suppression and delay of viral clearance. a recent study on patients with ards showed that treatment with methylprednisolone decreased the risk of death (hazard ratio . , % confidence interval . - . ). these findings indicate that using corticosteroids does not influence viral clearance time, length of hospital stays or duration of symptoms in patients with mild covid- [ ] . thus, the use of corticosteroids is considered beneficial in severe cases of covid- (especially in patients with ards), but not in mild cases. accordingly, a recent retrospective study showed the potential benefits from low-dose corticosteroids treatment in a subset of critically sars-cov- patients [ ] ; these data are in contrast with nhc guidelines that highlight that systematic use of corticosteroids is not recommended for these cases, due to their immunosuppressive effects. however, administration of corticosteroids has been indicated for specific reasons such as exacerbation of asthma or chronic obstructive pulmonary disease (copd), septic shock or severe acute respiratory distress syndrome (ards). further studies are required to find out how and when it is appropriate the use of corticosteroids for covid- , as there are no available data on the benefits of corticosteroid treatment in sars-cov or mers infection [ ] . apart from corticosteroids, il- pathway inhibitors such as sarilumab, siltuximab and tocilizumab have been proposed as experimental approach considering the increased il- levels that have been observed in patients with severe covid- [ ] . tocilizumab is a recombinant, humanized monoclonal antibody commonly used for treating patients with rheumatoid arthritis, lupus and psoriasis that binds to il- receptors blocking fcr activation; in covid- patients, tocilizumab could reduce sars-cov- -induced inflammatory responses [ ] . accordingly, several case reports have referred positive outcomes regarding tocilizumab [ , [ ] [ ] [ ] [ ] [ ] , but clinical impact of tocilizumab on covid- patients as an approved clinical approach has not been evaluated yet. in line, to further investigate the efficacy and safety of tocilizumab in patients with covid- , a controlled clinical trial is now under way (chictr ) ( figure v ). overall, the combination of an immunomodulatory agent to reduce the cytokine storm with an antiviral agent may give physicians more time to provide supportive treatment for patients with covid- . at the time of writing this review, due to the lack of a specific available therapy, plasma from convalescent patients containing specific antibodies has been proposed as a principal treatment [ , ] , for patients in rapid disease progression, severe or critical conditions ( figure vi ). in a recent retrospective study, one dose ( ml) of convalescent plasma (cp) collected from severe adult cases has been reported to be tolerated; thus, increasing or maintaining high level of neutralizing antibodies broke down the viral load in seven days, improve clinical symptoms and paraclinical criteria within three days and lung lesions were found to be differently absorbed on radiological examination within seven days [ ] . therefore, being cp a promising rescue option for severe covid- , several clinical trials (chictr , chictr , and chictr ) are in progress to investigate the efficacy and safeness of cp direct infusion in covid- patients [ ] . in addition, combined therapy with mabs and remdesivir seems to be an ideal therapeutic option for covid- [ ] . pharmaceuticals companies are now focused on searching for specific and effective mabs against covid- . taking into account that technologies capable of making fully human antibodies such as human single-chain antibody variable fragments (hu-scfvs) or humanized-nanobodies (single-domain antibodies, sdab) able to overpass virus-infected cell membranes (trans bodies) and to interact or interpose with biologic processes required for virus replication are already available [ ] . a large number of clinical trials regarding cell-based therapies have been started in china during covid- outbreak. among these, mesenchymal stromal cells (mscs)-based therapy displayed strong safety profile and possible efficacy in patients with ards, according to covid- -related clinical studies listed on the who's international clinical trials registry platform (who ictrp) and national institutes of health's clinical trials.gov databases [ ] . nevertheless, further investigations are required to better understand if these therapies could be effective in treating respiratory virus-induced complications. mscs have been largely employed in basic research and clinical trials [ ] [ ] [ ] , and their safeness and effectiveness have been extensively documented especially in immune-mediated inflammatory disorders, such as graft-versus-host disease (gvhd) [ ] and systemic lupus erythematosus (sle) [ ] . mscs immunomodulatory and differentiation abilities [ ] as well as their competency to produce several cytokine types or to directly interact with immune cells have been already described [ ] . indeed, they are activated by pathogen-associated molecules (pamps) such as single or double-stranded rnas [ , ] , priming the immune response during infections. two clinical investigations of systemic msc administration in patients with either covid- or avian influenza a (h n ) have been recently published [ , ] . the first one, a single-center msc transplantation pilot study, was aimed at exploring mscs therapeutic potentiality in patients with covid- pneumonia and conducted at the you'an hospital in beijing, china, from jan to feb (chictr ). seven patients with covid- pneumonia, sars-cov- rna positive, with different degrees of severity, including one critically ill requiring icu care were enrolled and monitored for days after msc injection. a significant improvement of pulmonary function and symptoms were observed two days after msc transplantation characterized by an increase of peripheral lymphocytes and of the anti-inflammatory il- levels and a decrease of the c-reactive protein and tnf-α amounts [ ] . moreover, an increment of the cd + cd c + cd b mid regulatory dendritic cell (dc) population and a decrease of cytokine-secreting immune cells such as cxcr + cd + t cells, cxcr + cd + t cells, and cxcr + nk were detected within - days in the treated patients compared to the placebo control group [ ] . mscs play a role in attenuating cytokine storm, most importantly, because these cells do not express ace and tmprss viral receptors are insusceptible of sars-cov- infection. these observations are in agreement with the knowledge that mscs induce the maturation of dendritic cells into a novel jagged- -dependent regulatory dendritic cell population [ ] , shifting the th /th balance towards th . thus, from these preliminary results, it seems evident that mscs intravenous transplantation could represent a secure and effective treatment in patients with covid- pneumonia, especially those critical. indeed, it inhibits the over activation of the immune system and promotes endogenous repair by preventing pulmonary fibrosis and improving both pulmonary microenvironment and lung function [ ] . more than potential vaccine candidates for covid- are under development around the world, including inactivated, recombinant subunits, nucleic-acid-based, adenoviral vector, and recombinant influenza viral vector vaccines [ ] . moreover, taking into consideration the strong homologies existing among the various coronavirus strains, it was thought that vaccines acting on other coronaviruses, such the avian live ibv vaccine (strain h) directed towards the chicken cov ibv, could be a valuable alternative therapeutic strategy [ ] . the coalition for epidemic preparedness innovations (cepi) recently announced that three programs aimed to develop covid- vaccines, by utilizing established vaccine platforms, have started [ ] . in addition, cepi already financed the company moderna, inc. to compare mrna therapeutics and vaccines, allowing the release of the first batch of mrna- in february , which is an mrna vaccine against sars-cov- ready for phase i study in the united states. available online: https://investors.modernatx.com/news-releases/news-release-details/moderna-ships-mrnavaccine-against-novel-coronavirus-mrna- (accessed on february ). more recently, scientists from the university of pittsburgh have announced a potential vaccine against sars-cov- , delivered throughout a fingertip-sized patch, capable of producing sars-cov- specific igg antibodies, sufficient for virus neutralization in mice. this vaccine, called pittcovacc (acronym of pittsburgh coronavirus vaccine), is a trimeric recombinant sars-cov- -s subunit vaccine delivered intracutaneously by microneedle arrays (mnas) [ ] . delivering vaccine components to a defined skin microenvironment improves safety by reducing systemic exposure, allowing to reach high vaccine concentrations with a relatively low dose of antigen [ , ] . furthermore, the skin delivery strategy promotes strong and long-lasting antigen-specific antibody responses due to both the high immunogenicity [ ] [ ] [ ] [ ] [ ] and the redundant immunoregulatory circuits of the skin [ , , ] . given the urgent need for covid- vaccines, mnas strategy seems to be a promising immunization approach against coronavirus infection including sars, mers and other emerging infectious diseases. on april , the oxford chadox ncov- vaccine was the first in europe to start human trial stage, with healthy volunteers enrolled for the tests. oxford scientists have already employed chadox in the past to dispense vaccines against ebola, chikungunya, rift valley fever and, above all, mers. chadox , a chimpanzee-derived adenovirus vector, has been employed to deliver the full-length mers spike gene and shown to induce large amounts of neutralizing antibodies against mers in a mouse model [ , ] . therefore, the modified chadox vaccine, carrying the sars-cov- spike gene is under human trial stage. on april , the university of oxford has announced a collaboration with the uk-based global biopharmaceutical company astrazeneca for further development, large-scale production and potential delivery of the covid- vaccine candidate. available online: https://www. ovg.ox.ac.uk/news/landmark-partnership-announced-for-development-of-covid- -vaccine (accessed on april ). since chadox technology is already available and formerly tested in humans for other vaccines, phase iii will consist in administering vaccine to volunteers following them into their regular environments to ensure that these subjects actually become immune to the disease up to three years. if trials succeed, oxford researchers have proposed to complete testing throughout ring vaccination, namely delivering vaccine to members of the first circle of contacts of covid- positive people and then to evaluate if the virus spreads to the second circle, as was previously done during the ebola epidemic in the democratic republic of the congo. to be a promising immunization approach against coronavirus infection including sars, mers and other emerging infectious diseases. on april , the oxford chadox ncov- vaccine was the first in europe to start human trial stage, with healthy volunteers enrolled for the tests. oxford scientists have already employed chadox in the past to dispense vaccines against ebola, chikungunya, rift valley fever and, above all, mers. chadox , a chimpanzee-derived adenovirus vector, has been employed to deliver the full-length mers spike gene and shown to induce large amounts of neutralizing antibodies against mers in a mouse model [ , ] . therefore, the modified chadox vaccine, carrying the sars-cov- spike gene is under human trial stage. on april , the university of oxford has announced a collaboration with the uk-based global biopharmaceutical company astrazeneca for further development, large-scale production and potential delivery of the covid- vaccine candidate. available online: https://www.ovg.ox.ac.uk/news/landmark-partnership-announced-fordevelopment-of-covid- -vaccine (accessed on april ). since chadox technology is already available and formerly tested in humans for other vaccines, phase iii will consist in administering vaccine to volunteers following them into their regular environments to ensure that these subjects actually become immune to the disease up to three years. if trials succeed, oxford researchers have proposed to complete testing throughout ring vaccination, namely delivering vaccine to members of the first circle of contacts of covid- positive people and then to evaluate if the virus spreads to the second circle, as was previously done during the ebola epidemic in the democratic republic of the congo. figure . schematic representation of sars-cov- infection and virus-induced human immune system response. proposed drugs directed both towards specific sars-cov- molecular targets and biologic processes are highlighted: inhibitors of sars-cov- fusion/entry targeting ace receptor, spike protein, tmprss or hr and hr epitopes and clathrin-mediated endocytosis (i); molecules against sars-cov- main protease (ii); molecules against viral genome replication (iii); crispr figure . schematic representation of sars-cov- infection and virus-induced human immune system response. proposed drugs directed both towards specific sars-cov- molecular targets and biologic processes are highlighted: inhibitors of sars-cov- fusion/entry targeting ace receptor, spike protein, tmprss or hr and hr epitopes and clathrin-mediated endocytosis (i); molecules against sars-cov- main protease (ii); molecules against viral genome replication (iii); crispr technologies targeting sars-cov- rna genome (iv); modulators of sars-cov- induced inflammatory response (v) and human neutralizing antibodies (vi). ace , angiotensin-converting enzyme ; tmprss , type transmembrane serine proteases; rdrp, rna-dependent rna polymerase; hr , heptad repeat ; hr , heptad repeat ; hr p, heptad repeat -derived peptides; ek , a modified oc -hr p peptide. adapted from [ ] . overall, a joint effort headed to apply both already consolidate and innovative approaches, such as ai to facilitate drug discovery, will be required to develop a broad-spectrum antiviral drugs and vaccines towards existing and potential future coronavirus infections to prevent another highly pathogenic virus epidemic. moreover, continuous collaboration in basic and clinical studies will improve the discovery of new antiviral drugs with therapeutic potentials, decrease the time for drug release on the market and make them affordable for all countries. furthermore, vaccine delivery strategies and cell-based therapies benefit from the significant progresses made by recombinant dna technologies combined with emerging biotechnology and bioengineering methodologies. thus, these approaches can speed up the development and set up of new vaccines and clinical therapies to fight against novel pathogens to protect public health all over the world. this study represents a holistic picture of the current investigations in response to the outbreak of covid- . the current pandemic is obviously an international public health problem and it remains a challenging task to fight the sars-cov- of unknown origin and mysterious biologic features. lesson from the previous two pandemics, mers and sars outbreaks, provide valuable insights about how to manage the current pandemic and provide a reference for future studies to combat disease progression. despite sars-cov- rapid transmission, the scale up country readiness, speedy response teams and the capacity of all laboratories are reducing the spread of the virus as well as its mortality rate. as the pandemic is still ongoing and expanding, further studies on all aspects of the disease are needed to better understand the infection, beneficial treatments and development of vaccines. nevertheless, this pandemic, together with the previous ones, have taught us in the harshest possible way that the entire scientific community must be vigilant and ready to advice appropriate containment and screening measures to avoid the spread of any future emerging pathogen. we would like to acknowledge majidi nezhad for providing the meteorological data and climate analyses and gaia scoarughi and adeleh salehi for drawing figures. the authors declare no conflict of interest. the following abbreviations are used in this manuscript: nonstructural polyproteins (nsps - ); novel coronavirus ( -ncov); -chymotrypsin-like protease ( clpro); c-like protease ( cl); acute respiratory distress syndrome (ards); adeno-associated virus (aav); angiotensin receptor blockers (arbs); angiotensin-converting enzyme (ace ); ap- -associated protein kinase (aak ); artificial intelligence (ai); avian infectious bronchitis virus (ibv); basic reproduction number (r ); blood oxygen saturation (spo ); bronchoalveolar lavage (bal); centers for disease control and prevention (cdc); chinese center for disease control and prevention (china cdc); chronic obstructive pulmonary disease (copd); coalition for epidemic preparedness innovations (cepi); computed tomography (ct); computer-aided design (cad); convalescent plasma (cp); coronavirus (cov); cytotoxic t lymphocyte (ctl); dendritic cell (dc); dipeptidyl peptidase (dpp , also known as cd ); envelope glycoprotein (e); enzyme-linked immunosorbent assay (elisa); european center for medium-range weather forecasts (ecmwf); european cities (ecs); feline infectious peritonitis (fip); graft versus-host disease (gvhd); hemagglutinin-esterase glycoprotein (he); heptad repeat (hr ) and heptad repeat (hr ); high-resolution ct (hrct); hr -derived peptides (hr p); ek (a modified oc -hr p peptide); human coronaviruses (hcovs); human covs (hcovs); human single-chain antibody variable fragments (hu-scfvs); humanized-nanobodies (single-domain antibodies, sdab); intensive care unit (icu); istituto superiore di sanità (iss); janus kinase (jak); membrane glycoprotein (m); mesenchymal stromal cells (mscs); microneedle arrays (mnas); middle east respiratory syndrome coronavirus (mers-cov); monoclonal antibodies (mabs); naso-pharyngeal (np); national health commission of the people's republic of china (nhc); nonstructural protein (nsp ); northern hemisphere (nh); nucleocapsid phosphoprotein (n); open reading frames (orfs); oro-pharyngeal (op); papain-like protease (plpro); partial pressure of arterial oxygen to fraction of inspired oxygen ratio (pao /fio ); pathogen-associated molecules (pamps); pittsburgh coronavirus vaccine (pittcovacc); polypeptides (pps); porcine epidemic diarrhea virus (pedv); real time quantitative polymerase chain reaction (rt-qpcr); receptor-binding domain (rbd); recombinant human ace (rhace ); replication-transcription complex (rtc); rna-dependent rna polymerase (rdrp); rnase p gene (rp); severe acute respiratory syndrome coronavirus (sars-cov); single-stranded positive-sense rna (+ssrna); southern hemisphere (sh); spike glycoprotein (s); subgenomic rnas (sgrnas); swine acute diarrhea syndrome coronavirus (sads-cov); swine enteric alphacoronaviruses (seacovs); systemic lupus erythematosus (sle); transmissible gastroenteritis virus (tgev); virus-like particles (vlp); who's international clinical trials registry platform (who ictrp); world health organization (who). the emerging novel middle east respiratory syndrome coronavirus: the "knowns" and "unknowns coronaviruses-drug discovery and therapeutic options emerging coronaviruses: genome structure, replication, and pathogenesis human coronavirus: host-pathogen interaction covid- ): a review of clinical features, diagnosis, and treatment cultivation of a novel type of common-cold virus in organ cultures coronavirus genomics and bioinformatics analysis evaluation of risks and benefits associated with vaccination against coronavirus infections in cats identification of a novel coronavirus in patients with severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle coronaviridae study group of the international committee on taxonomy of viruses. the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- an overview of their replication and pathogenesis insights into the recent novel coronavirus (sars-cov- ) in light of past human coronavirus outbreaks discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus origin and evolution of pathogenic coronaviruses genomic characterization of severe acute respiratory syndrome-related coronavirus in european bats and classification of coronaviruses based on partial rna-dependent rna polymerase gene sequences genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding coronavirus as a possible cause of severe acute respiratory syndrome sars and other coronaviruses as causes of pneumonia estimating the potential total number of novel coronavirus cases in wuhan city molecular evolution of human coronavirus genomes a review of coronavirus disease- (covid- ) genetic recombination, and pathogenesis of coronaviruses coronaviruses in avian species-review with focus on epidemiology and diagnosis in wild birds probable pangolin origin of sars-cov- associated with the covid- outbreak coronavirus disease : what we know? sars-cov- in fruit bats, ferrets, pigs, and chickens: an experimental transmission study the continuing -ncov epidemic threat of novel coronaviruses to global health-the latest novel coronavirus outbreak in wuhan identification of a new human coronavirus identification of new human coronaviruses a structural view of sars-cov- rna replication machinery: rna synthesis, proofreading and final capping accessory proteins of sars-cov and other coronaviruses from sars to mers, thrusting coronaviruses into the spotlight the sars-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins the molecular biology of coronaviruses identification of in vivo-interacting domains of the murine coronavirus nucleocapsid protein the m, e, and n structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles the spike protein of sars-cov-a target for vaccine and therapeutic development the genome sequence of the sars-associated coronavirus characterization of a novel coronavirus associated with severe acute respiratory syndrome unique and conserved features of genome and proteome of sars-coronavirus, an early split-off from the coronavirus group lineage structure, function and evolution of the hemagglutinin-esterase proteins of corona-and toroviruses identification of a coronavirus hemagglutinin-esterase with a substrate specificity different from those of influenza c virus and bovine coronavirus coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. microbiol genome composition and divergence of the novel coronavirus ( -ncov) originating in china covid- infection: origin, transmission, and characteristics of human coronaviruses receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus cryo-em structure of the -ncov spike in the prefusion conformation structural and functional basis of sars-cov- entry by using human ace structure, function, and antigenicity of the sars-cov- spike glycoprotein characterization of severe acute respiratory syndrome-associated coronavirus (sars-cov) spike glycoprotein-mediated viral entry identification and characterization of novel neutralizing epitopes in the receptor-binding domain of sars-cov spike protein: revealing the critical antigenic determinants in inactivated sars-cov vaccine characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of , cases from the chinese center for disease control and prevention dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc interaction of sars and mers coronaviruses with the antiviral interferon response novel coronavirus (covid- ) outbreak: a review of the current literature a new bat-hku -like coronavirus in swine discovery of a novel swine enteric alphacoronavirus (seacov) in southern china bat-to-human: spike features determining 'host jump' of coronaviruses sars-cov, mers-cov, and beyond sars-associated coronavirus transmitted from human to pig a bat-derived putative cross-family recombinant coronavirus with a reovirus gene phylogenetic network analysis of sars-cov- genomes receptor and viral determinants of sars-coronavirus adaptation to human ace ace receptor expression and severe acute respiratory syndrome coronavirus infection depend on differentiation of human airway epithelia role of changes in sars-cov- spike protein in the interaction with the human ace receptor: an in silico analysis structural basis of receptor recognition by sars-cov- covid- infection and circulating ace levels: protective role in women and children. front contact tracing: a game of big numbers in the time of covid- sars-cov- viral load in upper respiratory specimens of infected patients covid- , sars and mers: are they closely related? evaluation and treatment coronavirus (covid- ) the transmission and diagnosis of novel coronavirus infection disease (covid- ): a chinese perspective the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents enteric involvement of coronaviruses: is faecal-oral transmission of sars-cov- possible? -ncov transmission through the ocular surface must not be ignored special expert group for control of the epidemic of novel coronavirus pneumonia of the chinese preventive medicine association. an update on the epidemiological characteristics of novel coronavirus pneumonia (covid- ) clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records novel coronavirus infection in hospitalized infants under year of age in china human coronaviruses: a review of virus-host interactions animal models for sars and mers coronaviruses crossref] . national health commission of the people's republic of china. pneumonia epidemic situation of new coronavirus infection on pneumonia of unknown aetiology in wuhan, china: potential for international spread via commercial air travel review of early and emerging options. open forum infect. dis. epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study novel coronavirus: where we are and what we know modeling the spread of middle east respiratory syndrome coronavirus in saudi arabia transmission dynamics and control of severe acute respiratory syndrome seasonality of respiratory viral infections assessment of china's offshore wind resources based on the integration of multiple satellite data and meteorological data high temperature and high humidity reduce the transmission of covid- temperature significant change covid- transmission in cities preliminary evidence that higher temperatures are associated with lower incidence of covid- , for cases reported globally up to effects of temperature and humidity on the daily new cases and new deaths of covid- in countries distribution of the sars-cov- pandemic and its monthly forecast based on seasonal climate patterns the transmission of sars-cov- is likely comodulated by temperature and by relative humidity wind energy potential analysis using sentinel- satellite: a review and a case study on mediterranean islands unique epidemiological and clinical features of the emerging novel coronavirus pneumonia (covid- ) implicate special control measures early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in covid- (novel coronavirus ) -recent trends presumed asymptomatic carrier transmission of covid- updated understanding of the outbreak of novel coronavirus ( -ncov) in wuhan return of the coronavirus: -ncov. viruses importation and human-to-human transmission of a novel coronavirus in vietnam clinical features of patients infected with novel coronavirus in coronavirus disease : initial chest ct findings ct imaging of the novel coronavirus ( -ncov) pneumonia. radiology coronavirus disease (covid- ): a systematic review of imaging findings in patients abdominal and testicular pain: an atypical presentation of covid- atypical presentation of covid- in a frail older person diagnosis and clinical management of severe acute respiratory syndrome coronavirus (sars-cov- ) infection: an operatioal recommendation of peking union medical college hospital (v . ) a pneumonia outbreak associated with a new coronavirus of probable bat origin molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes molecular diagnosis of a novel coronavirus ( -ncov) causing an outbreak of pneumonia sars-cov- foch hospital study group. the allplex -ncov (seegene) assay: which performances are for sars-cov- infection diagnosis? evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of -ncov infections emergence of a novel coronavirus disease (covid- ) and the importance of diagnostic testing: why partnership between clinical laboratories, public health agencies, and industry is essential to control the outbreak sas-cov- detection by direct rrt-pcr without rna extraction radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study imaging of coronavirus disease : a chinese expert consensus statement time course of lung changes at chest ct during recovery from coronavirus disease (covid- ) initial ct findings and temporal changes in patients with the novel coronavirus pneumonia ( -ncov): a study of patients in wuhan, china correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases artificial intelligence applications for thoracic imaging a review on the use of artificial intelligence for medical imaging of the lungs of patients with coronavirus disease radiological role in the detection, diagnosis and monitoring for the coronavirus disease (covid- ) ct imaging changes of corona virus disease (covid- ): a multi-center study in southwest china ct imaging features of novel coronavirus ( -ncov) ct differential diagnosis of covid- and non-covid- in symptomatic suspects: a practical scoring method antibody responses to sars-cov- in patients with covid- development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis brief clinical evaluation of six high-throughput sars-cov- igg antibody assays profiling early humoral response to diagnose novel coronavirus disease (covid- ) serum iga, igm, and igg responses in covid- diagnosis of acute respiratory syndrome coronavirus infection by detection of nucleocapsid protein recent discovery and development of inhibitors targeting coronaviruses this scientist hopes to test coronavirus drugs on animals in locked-down wuhan emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments design, synthesis and molecular docking of novel triazole derivatives as potential cov helicase inhibitors updated approaches against sars-cov- traditional chinese medicine for covid- treatment complementary and alternative medicine is expected to make greater contribution in controlling the prevalence of influenza application of in vitro bionic digestion and biomembrane extraction for metal speciation analysis, bioavailability and risk assessment in lianhua qingwen capsule clinical characteristics and therapeutic procedure for four cases with novel coronavirus pneumonia receiving combined chinese and western medicine treatment a decade after sars: strategies for controlling emerging coronaviruses a dna vaccine induces sars coronavirus neutralization and protective immunity in mice cross-species transmission of the newly identified coronavirus -ncov towards a solution to mers: protective human monoclonal antibodies targeting different domains and functions of the mers-coronavirus spike glycoprotein angiotensin-converting enzyme (ace ) as a sars-cov- receptor: molecular mechanisms and potential therapeutic target therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in wuhan, china potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody novel antibody epitopes dominate the antigenicity of spike glycoprotein in sars-cov- compared to sars-cov angiotensin receptor blockers as tentative sars-cov- therapeutics fusion mechanism of -ncov and fusion inhibitors targeting hr domain in spike protein inhibition of sars-cov- (previously -ncov) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion epitope-based vaccine target screening against highly pathogenic mers-cov: an in silico approach applied to emerging infectious diseases analysis of the genome sequence and prediction of b-cell epitopes of the envelope protein of middle east respiratory syndrome-coronavirus sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor clathrin-dependent entry of severe acute respiratory syndrome coronavirus into target cells expressing ace with the cytoplasmic tail deleted sars coronavirus entry into host cells through a novel clathrin-and caveolae-independent endocytic pathway baricitinib as potential treatment for -ncov acute respiratory disease ap- -associated protein kinase and cyclin g-associated kinase regulate hepatitis c virus entry and are potential drug targets effects of chloroquine on viral infections: an old drug against today's diseases? in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov therapeutic drugs targeting -ncov main protease by high-throughput screening prediction of the sars-cov- ( -ncov) c-like protease ( cl pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates compounds with therapeutic potential against novel respiratory remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro virus against virus: a potential treatment for -ncov (sars-cov- ) and other rna viruses corticosteroid treatment of patients with coronavirus disease (covid- ) potential benefits of precise corticosteroids therapy for severe -ncov pneumonia clinical evidence does not support corticosteroid treatment for -ncov lung injury a systematic review of anakinra, tocilizumab, sarilumab and siltuximab for coronavirus-related infections understanding sars-cov- -mediated inflammatory responses: from mechanisms to potential therapeutic tools hlh across speciality collaboration, uk. covid- : consider cytokine storm syndromes and immunosuppression tocilizumab treatment in covid- : a single center experience tocilizumab, an anti-il- receptor antibody, to treat covid- -related respiratory failure: a case report first case of covid- in a patient with multiple myeloma successfully treated with tocilizumab convalescent plasma: new evidence for an old therapeutic tool? convalescent plasma as a potential therapy for covid- effectiveness of convalescent plasma therapy in severe covid- patients remdesivir as a possible therapeutic option for the covid- human transbodies that interfere with the functions of ebola virus vp protein in genome replication and transcription and innate immune antagonism current status of cell-based therapies for respiratory virus infections: applicability to covid- autologous mesenchymal stem cells for the treatment of secondary progressive multiple sclerosis: an open-label phase a proof-of-concept study mesenchymal stem (stromal) cells for treatment of ards: a phase clinical trial mesenchymal stromal cell secretome for severe covid- infections: premises for the therapeutic use survival after mesenchymal stromal cell therapy in steroid-refractory acute graft-versus-host disease: systematic review and meta-analysis therapeutic applications of mesenchymal stem cells for systemic lupus erythematosus mesenchymal stromal cells: clinical challenges and therapeutic opportunities mesenchymal stromal cells: sensors and switchers of inflammation tumour viruses and innate immunity mesenchymal stem cells: a double-edged sword in regulating immune responses transplantation of ace -mesenchymal stem cells improves the outcome of patients clinical study of mesenchymal stem cell treating acute respiratory distress syndrome induced by epidemic influenza a (h n ) infection, a hint for covid- treatment mesenchymal stem cells induce mature dendritic cells into a novel jagged- -dependent regulatory dendritic cell population potential rapid diagnostics, vaccine and therapeutics for novel coronavirus ( -ncov): a systematic review potential interventions for novel coronavirus in china: a systematic review cepi. cepi to fund three programmes to develop vaccines against the novel coronavirus microneedle array delivered recombinant coronavirus vaccines: immunogenicity and rapid dissolving undercut microneedle arrays for multicomponent cutaneous vaccination microneedle delivery of autoantigen for immunotherapy in type diabetes the immunological anatomy of the skin professional antigen-presenting cells of the skin cd + t cell responses elicited by different subsets of human skin migratory dendritic cells cutaneous immune responses mediated by dendritic cells and mast cells microneedle patches for vaccination in developing countries organization of the skin immune system and compartmentalized immune responses in infectious diseases neuronal regulation of cutaneous immunity a novel chimpanzee adenovirus vector with low human seroprevalence: improved systems for vector derivation and comparative immunogenicity chadox and mva based vaccine candidates against mers-cov elicit neutralising antibodies and cellular immune responses in mice pharmacologic treatments for coronavirus disease (covid- ): a review key: cord- -s hc fxs authors: ostaszewski, marek; niarakis, anna; mazein, alexander; kuperstein, inna; phair, robert; orta-resendiz, aurelio; singh, vidisha; aghamiri, sara sadat; acencio, marcio luis; glaab, enrico; ruepp, andreas; fobo, gisela; montrone, corinna; brauner, barbara; frischman, goar; monraz gómez, luis cristóbal; somers, julia; hoch, matti; gupta, shailendra kumar; scheel, julia; borlinghaus, hanna; czauderna, tobias; schreiber, falk; montagud, arnau; de leon, miguel ponce; funahashi, akira; hiki, yusuke; hiroi, noriko; yamada, takahiro g.; dräger, andreas; renz, alina; naveez, muhammad; bocskei, zsolt; messina, francesco; börnigen, daniela; fergusson, liam; conti, marta; rameil, marius; nakonecnij, vanessa; vanhoefer, jakob; schmiester, leonard; wang, muying; ackerman, emily e.; shoemaker, jason; zucker, jeremy; oxford, kristie; teuton, jeremy; kocakaya, ebru; summak, gökçe yağmur; hanspers, kristina; kutmon, martina; coort, susan; eijssen, lars; ehrhart, friederike; rex, d. a. b.; slenter, denise; martens, marvin; haw, robin; jassal, bijay; matthews, lisa; orlic-milacic, marija; senff ribeiro, andrea; rothfels, karen; shamovsky, veronica; stephan, ralf; sevilla, cristoffer; varusai, thawfeek; ravel, jean-marie; fraser, rupsha; ortseifen, vera; marchesi, silvia; gawron, piotr; smula, ewa; heirendt, laurent; satagopam, venkata; wu, guanming; riutta, anders; golebiewski, martin; owen, stuart; goble, carole; hu, xiaoming; overall, rupert w.; maier, dieter; bauch, angela; gyori, benjamin m.; bachman, john a.; vega, carlos; grouès, valentin; vazquez, miguel; porras, pablo; licata, luana; iannuccelli, marta; sacco, francesca; nesterova, anastasia; yuryev, anton; de waard, anita; turei, denes; luna, augustin; babur, ozgun; soliman, sylvain; valdeolivas, alberto; esteban-medina, marina; peña-chilet, maria; helikar, tomáš; puniya, bhanwar lal; modos, dezso; treveil, agatha; olbei, marton; de meulder, bertrand; dugourd, aurélien; naldi, aurelien; noel, vincent; calzone, laurence; sander, chris; demir, emek; korcsmaros, tamas; freeman, tom c.; augé, franck; beckmann, jacques s.; hasenauer, jan; wolkenhauer, olaf; wilighagen, egon l.; pico, alexander r.; evelo, chris t.; gillespie, marc e.; stein, lincoln d.; hermjakob, henning; d’eustachio, peter; saez-rodriguez, julio; dopazo, joaquin; valencia, alfonso; kitano, hiroaki; barillot, emmanuel; auffray, charles; balling, rudi; schneider, reinhard title: covid- disease map, a computational knowledge repository of sars-cov- virus-host interaction mechanisms date: - - journal: biorxiv doi: . / . . . sha: doc_id: cord_uid: s hc fxs we hereby describe a large-scale community effort to build an open-access, interoperable, and computable repository of covid- molecular mechanisms - the covid- disease map. we discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. we highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. we describe the contents of the map and their relevance to the molecular pathophysiology of covid- and the analytical and computational modelling approaches that can be applied to the contents of the covid- disease map for mechanistic data interpretation and predictions. we conclude by demonstrating concrete applications of our work through several use cases. the coronavirus disease (covid- ) pandemic due to severe acute respiratory syndrome coronavirus (sars-cov- ) [ ] has already resulted in the infection of over million people worldwide, of whom one million have died . the molecular pathophysiology that links sars-cov- infection to the clinical manifestations and course of covid- is complex and spans multiple biological pathways, cell types and organs [ , ] . to gain the insights into this complex network, the biomedical research community needs to approach it from a systems perspective, collecting the mechanistic knowledge scattered across the scientific literature and bioinformatic databases, and integrating it using formal systems biology standards. with this goal in mind, we initiated a collaborative effort involving over biocurators, domain experts, modelers and data analysts from institutions in countries to develop the covid- disease map, an open-access collection of curated computational diagrams and models of molecular mechanisms implicated in the disease [ ] . to this end, we aligned the biocuration efforts of the disease maps community [ , ] , reactome [ ] , and wikipathways [ ] and developed common guidelines utilising standardised encoding and annotation schemes, based on community-developed systems biology standards [ ] [ ] [ ] , and persistent identifier repositories [ ] . moreover, we integrated relevant knowledge from public repositories [ ] [ ] [ ] [ ] and text mining resources, providing a means to update and refine contents of the map. the fruit of these efforts was a series of pathway diagrams describing key events in the covid- infectious cycle and host response. we ensured that this comprehensive diagrammatic description of disease mechanisms is machine-readable and computable. this allows us to develop novel bioinformatics workflows, creating executable networks for analysis and prediction. in this way, the map is both human and machine-readable, lowering the communication barrier between biocurators, domain experts, and computational biologists significantly. computational modelling, data analysis, and their informed interpretation using the contents of the map have the potential to identify molecular signatures of disease predisposition and development, and to suggest drug repositioning for improving current treatments. covid- disease map is a collection of diagrams containing interactions between elements, supported by publications and preprints. the summary of diagrams available in the covid- disease map can be found online in supplementary material . the map is a constantly evolving resource, refined and updated by ongoing efforts of biocuration, sharing and analysis. here, we report its current status. in section we explain the set up of our community effort to construct the interoperable content of the resource, involving biocurators, domain experts and data analysts. in section we demonstrate that the scope of the biological maps in the resource reflects the state-ofthe-art about the molecular biology of covid- . next, we outline analytical workflows that can be used on the contents of the map, including initial, preliminary outcomes of two such workflows, discussed in detail as use cases in section . we conclude in section with an outlook to further development of the covid- map and the utility of the entire resource in future efforts towards building and applying disease-relevant computational repositories. the covid- disease map project involves three main groups: (i) biocurators, (ii) domain experts, and (iii) analysts and modellers: i. biocurators develop a collection of systems biology diagrams focused on the molecular mechanisms of sars-cov- . ii. domain experts refine the contents of the diagrams, supported by interactive visualisation and annotations. iii. analysts and modellers develop computational workflows to generate hypotheses and predictions about the mechanisms encoded in the diagrams. all three groups have an important role in the process of building the map, by providing content, refining it, and defining the downstream computational use of the map. figure illustrates the ecosystem of the covid- disease map community, highlighting the roles of different participants, available format conversions, interoperable tools, and downstream uses. the information about the community members and their contributions are disseminated via the fairdomhub [ ] , so that content distributed across different collections can be uniformly referenced. the biocurators of the covid- disease map diagrams follow the guidelines developed by the community, and specific workflows of wikipathways [ ] and reactome [ ] . the biocurators build literature-based systems biology diagrams, representing the molecular processes implicated in the covid- pathophysiology, their complex regulation and the phenotypic outcomes. these diagrams are main building blocks of the map, and are composed of biochemical reactions and interactions (further called altogether interactions) taking place between different types of molecular entities in various cellular compartments. as there are multiple teams working on related topics, biocurators can provide an expert review across pathways and across platforms. this is possible, as all platforms offer intuitive visualisation, interpretation, and analysis of pathway knowledge to support basic and clinical research, genome analysis, modelling, systems biology, and education. table lists information about the created content. for more details see supplementary material . communicating to refine, interpret and apply covid- disease map diagrams. these diagrams are created and maintained by biocurators, following pathway database workflows or standalone diagram editors, and reviewed by domain experts. the content is shared via pathway databases or a gitlab repository; all can be enriched by integrated resources of text mining and interaction databases. the covid- disease map diagrams, available in layout-aware systems biology formats and integrated with external repositories, are available in several formats allowing a range of computational analyses, including network analysis and boolean, kinetic or multiscale simulations. both interactions and interacting entities are annotated following a uniform, persistent identification scheme, using either miriam or identifiers.org [ ] , and the guidelines for annotations of computational models [ ] . viral protein interactions are explicitly annotated with their taxonomy identifiers to highlight findings from strains other than sars-cov- . moreover, tools like modelpolisher [ ] , sbmlsqueezer [ ] or memote help to automatically complement the annotations in the sbml format and validate the model (see also supplementary material ). the knowledge on covid- mechanisms is rapidly evolving, as demonstrated by the rapid growth of the covid- open research dataset (cord- ) dataset, a source scientific manuscript text and metadata on covid- and related coronavirus research [ ] . cord- currently contains over , articles and preprints, over four times more than when it was introduced . in such a quickly evolving environment, biocuration efforts need to be supported by other repositories of structured knowledge about molecular mechanisms relevant for covid- , like molecular interaction databases, or text mining resources. contents of such repositories may suggest improvements in the existing covid- disease map diagrams, or establish a starting point for developing new pathways (see section "biocuration of database and text mining content"). interaction and pathway databases contain structured and annotated information on protein interactions or causal relationships. while interaction databases focus on pairs of molecules, offering broad coverage of literature-reported findings. pathway databases provide detailed description of biochemical processes and their regulations of related interactions, supported by diagrams. both types of resources can be a valuable input for covid- disease map biocurators, given the comparability of identifiers used for molecular annotations, and the reference to publications used for defining an interaction or building a pathway. table text-mining approaches can help to sieve through such rapidly expanding literature with natural language processing (nlp) algorithms based on semantic modelling, ontologies, and linguistic analysis to automatically extract and annotate relevant sentences, biomolecules, and their interactions. this scope was recently extended to pathway figure mining: decoding pathway figures into their computable representations [ ] . altogether, these automated workflows lead to the construction of knowledge graphs: semantic networks incorporating ontology concepts, unique biomolecule references, and their interactions extracted from abstracts or full-text documents [ ] . the covid- disease map project integrates open-access text mining resources, indra [ ] , biokb , ailani covid- , and pathwaystudio . all platforms offer keyword-based search allowing interactive exploration. additionally, the map benefits from an extensive protein-protein interaction network (ppi) generated with a custom text-mining pipeline using opennlp and gnormplus [ ] . this pipeline was applied to the cord- dataset and the collection of medline abstracts associated with the genes in the sars-cov- ppi network [ ] using the entrez gene reference-into-function (generif). for detailed descriptions of the resources, see supplementary material . molecular interactions from databases and knowledge graphs from text mining resources discussed above (from now on called altogether 'knowledge graphs') have a broad coverage at the cost of depth of mechanistic representation. this content can be used by the biocurators in the process of building and updating the systems biology focused diagrams. biocurators can use this content in three main ways: by visual exploration, by programmatic comparison, and by direct incorporation of the content. first, the biocurators can visually explore the contents of the knowledge graphs using available search interfaces to locate new knowledge and encode it in the diagrams. moreover, solutions like covidminer project , pathwaystudio and ailani offer a visual representation of a group of interactions for a better understanding of their biological context, allowing search by interactions, rather than just isolated keywords. finally, indra and ailani offer assistant bots that respond to natural language queries and return meaningful answers extracted from knowledge graphs. second, programmatic access and reproducible exploration of the knowledge graphs is possible via data endpoints: sparql for biokb and application programming interfaces for indra, ailani, and pathway studio. users can programmatically submit keyword queries and retrieve functions, interactions, pathways, or drugs associated with submitted gene lists. this way, otherwise time-consuming tasks like an assessment of completeness of a given diagram, or search for new literature evidence, can be automated to a large extent. finally, biocurators can directly incorporate the content of knowledge graphs into sbml format using biokc [ ] . additionally, the contents of the elsevier covid- pathway collection can be translated to sbgnml preserving the layout of the diagrams. the sbgnml content can then be converted into other diagram formats used by biocurators (see section . below). the biocuration of the covid- disease map is distributed across multiple teams, using varying tools and associated systems biology representations. this requires a common approach to annotations of evidence, biochemical reactions, molecular entities and their interactions. moreover, the interoperability of layout-aware formats is needed for comparison and integration of the diagrams in the map. the covid- disease map diagrams are encoded in one of three layout-aware formats for standardised representation of molecular interactions: sbml [ ] [ ] [ ] , sbgnml [ ] , and gpml [ ] . these xml-based formats focus to a varying degree on user-friendly graphical representation, standardised visualisation, and support of computational workflows. for the detailed description of the formats, see supplementary material . each of these three languages has a different focus: sbml emphasizes standardised representation of the data model underlying molecular interactions, sbgnml provides standardised graphical representation of molecular processes, while gpml allows for a partially standardised representation of uncertain biological knowledge. nevertheless, all three formats are centered around molecular interactions, provide a constrained vocabulary to encode element and interaction types, encode layout of their diagrams and support stable identifiers for diagram components. these shared properties, supported by a common ontology [ ] , allow cross-format mapping and enable translation of key properties between the formats. therefore, when developing the contents of the map, biocurators use the tools they are familiar with, facilitating this distributed task. the covid- disease map community ecosystem of tools and resources (see figure ) ensures interoperability between the three layout-aware formats for molecular mechanisms: sbml, sbgnml, and gpml. essential elements of this setup are tools capable of providing cross-format translation functionality [ , ] and supporting harmonised visualisation processing. another essential translation interface is a representation of reactome pathways in wikipathways gpml [ ] and sbml. the sbml export of reactome content has been optimised in the context of this project and facilitates integration with the other covid- disease map software components. the contents of the covid- disease map diagrams can be directly transformed into inputs of computational pipelines and data repositories. besides the direct use of sbml format in kinetic simulations, celldesigner sbml files can be transformed into sbml qual [ ] using casq [ ] , enabling boolean modelling-based simulations (see also supplementary material ). in parallel, casq converts the diagrams to the sif format , supporting pathway modelling workflows using simplified interaction networks. notably, the gitlab repository features an automated translation of stable versions of diagrams into sbml qual. finally, translation of the diagrams into xgmml format (the extensible graph markup and modelling language) using cytoscape [ ] or ginsim [ ] allows for network analysis and interoperability with molecular interaction repositories [ ] . thanks to the community effort discussed above supported by a rich bioinformatics framework, we constructed the covid- disease map, focussing on the mechanisms known from other coronaviruses [ ] and suggested by early experimental investigations [pmid: ]. then, we applied the analytical and modelling workflows to the contributed diagrams and associated interaction databases to propose initial map-based insights into covid- molecular mechanisms. the covid- disease map is an evolving repository of pathways affected by sars-cov- . figure . it is currently centred on molecular processes involved in sars-cov- entry, http://www.ebi.ac.uk/sbo/main/ http://www.cbmc.it/fastcent/doc/sifformat.htm replication, and host-pathogen interactions. as mechanisms of host susceptibility, immune response, cell and organ specificity emerge, these will be incorporated into the next versions of the map. the covid- map represents the mechanisms in a "host cell". this follows literature reports on cell specificity of sars-cov- [ , [ ] [ ] [ ] [ ] [ ] . some pathways included in the covid- map may be shared among different cell types, as for example the ifn- pathway found in cells such as dendritic, epithelial, and alveolar macrophages [ ] [ ] [ ] [ ] [ ] . while at this stage, we do not address cell specificity explicitly in our diagrams, extensive annotations may allow identification of pathways relevant to the cell type of interest. the sars-cov- infection process and covid- progression follow a sequence of steps ( figure ), starting from viral attachment and entry, which involve various dynamic processes on different time scales that are not captured in static representations of pathways. correlation of symptoms and potential drugs suggested to date helps downstream data exploration and drug target interpretation in the context of therapeutic interventions. human host ilc , ilc- , ilc natural killer renin-angiotensinaldosterone system (raas) granulocytes nasal mucosa disease map golgi er cd + cd + ace tmprss integrative stress response dendritic cells transmission of sars-cov- primarily occurs through contact with respiratory drops, airborne transmission, and through contact with contaminated surfaces [ ] [ ] [ ] . upon contact with the respiratory epithelium, the virus infects cells mostly by binding the spike surface glycoprotein (s) to angiotensin-converting enzyme (ace ) with the help of serine protease tmprss [ ] [ ] [ ] [ ] . importantly, recent results suggest viral entry using other receptors of lungs and the immune system [ , ] . once attached, sars-cov- can enter cells either by direct fusion of the virion and cell membranes in the presence of proteases • dendritic cells. • nk cells. • monocytes and macrophages. • t cells, th and th response. • b cells, antibody production. asymptomatic/pre -symptomatic. vaccine? pre-exposure prophylaxis? antivirals? sirs, shock. shortness of breath. anosmia, ageusia, cough, fever, diarrhea. multiple organ dysfunction ards, complications. host response • cellular stress. • apoptosis. systemic and ventilation support oxygen therapy host raas ards; acute respiratory distress syndrome. raas; renin-angiotensin-aldosterone system. sirs; systemic inflammatory response syndrome. pathophysiology virus-host cell interactions and host response disease map critical asymptomatic (lung, heart, kidney) (nasal and respiratory epithelium, alveoli, vascular endothelial) tmprss and furin or by endocytosis in their absence. regardless of the entry mechanism, the s protein has to be activated to initiate the plasma or endosome membrane fusion process. while in the cell membrane, s protein is activated by tmprss and furin, in the endosome s protein is activated by cathepsin b (ctsb) and cathepsin l (ctsl) [ , ] . activated s promotes the cell-or endosome-membrane fusion [ ] with the virion membrane, and then the nucleocapsid is injected into the cytoplasm. these mechanisms are represented in the corresponding diagrams of the map . within the host cell, sars-cov- hijacks the rough endoplasmic reticulum (rer)-linked host translational machinery. it then synthesises viral proteins replicase polyprotein a (pp a) and replicase polyprotein ab (pp ab) directly from the virus (+)genomic rna (grna) [ , ] . through a complex cascade of proteolytic cleavages, pp a and pp ab give rise to non-structural proteins (nsps) [ ] [ ] [ ] . most of these nsps collectively form the replication transcription complex (rtc) that is anchored to the membrane of the double-membrane vesicle [ , ] endoplasmic reticulum stress and unfolded protein response as discussed above, the virus hijacks the er to replicate. production of large amounts of viral proteins exceeds the protein folding capacity of the er, creating an overload of unfolded proteins. as a result, the unfolded protein response (upr) pathways are triggered to assure the er homeostasis, using three main signalling routes of upr via perk, ire , and atf [ ]. their role is to mitigate the misfolded protein load and reduce oxidative stress. the resulting protein degradation is coordinated with a decrease in protein synthesis via eif alpha phosphorylation and induction of protein folding genes via the transcription factor xbp [ ] . when the er is unable to restore its function, it can trigger cell apoptosis [ , ] . the results are er stress and activation of the upr. the expression of some human coronavirus (hcov) proteins during infection, in particular the s glycoprotein, may induce activation of the er stress in the host cells [ ] . based on sars-cov results, this may lead to activation of the perk [ ], ire and in an indirect manner, of the atf pathways [ ] . processes of degrading malfunctioning proteins and damaged organelles, including the ubiquitin-proteasome system (ups) and autophagy [ ] are essential to maintain energy homeostasis and prevent cellular stress [ , ] . autophagy is also involved in cell defence, including direct destruction of the viruses via virophagy, presentation of viral antigens, and inhibition of excessive inflammatory reactions [ , ] . sars-cov- directly affects the process of ups-based protein degradation, as indicated by the host-virus interactome dataset published recently [ ] . this mechanism may be a defence against viral protein degradation [ ] . the map describes in detail the nature of this interaction, namely the impact of orf virus protein on the cul ubiquitin ligase complex and its potential substrates. interactions between sars-cov- and host autophagy pathways are inferred based on results from other covs. a finding that covs use double-membrane vesicles and lc -i for replication [ ] may suggest that the virus induces autophagy, possibly in atg -dependent manner [ ] , although some evidence points to the contrary [ ] . also, the cov nsp restricts autophagosome expansion, compromising the degradation of viral components [ ] . recently revealed mutations in nsp [ ] indicate its importance, although the exact effect of the mutations remains unknown. based on the connection between autophagy and the endocytic pathway of the virus replication cycle [ ] , autophagy modulation was suggested as a potential therapy strategy, either pharmacologically [ , [ ] [ ] [ ] , or via fasting [ ] . apoptosis, a synonym for programmed cell death, is triggered by virus-host interaction upon infection, as the early death of the virus-infected cells may prevent viral replication. many viruses block or delay cell death by expressing anti-apoptotic proteins to maximize the production of viral progeny [ ] . in turn, apoptosis induction at the end of the viral replication cycle might assist in viral dissemination while reducing an inflammatory response. for instance, sars-cov- [ ] and mers [ ] are able to invoke apoptosis in lymphocytes, compromising the immune system. apoptosis follows two major pathways [ ] , called extrinsic and intrinsic. extrinsic signals are transmitted by death ligands and their receptors (e.g., fasl and tnf-alpha). activated death receptors recruit adaptors like fadd and tradd, and initiator procaspases like caspase- , leading to cell death with the help of effector caspases- and [ , ] . in turn, the intrinsic pathway involves mitochondria-related members of the bcl- protein family. cellular stress causes bcl- proteins-mediated release of cytochrome c from the mitochondria into the cytoplasm. cytochrome c then forms a complex with apaf and recruits initiator procaspase- to form the apoptosome, leading to the proteolytic activation of caspase- . activated caspase- can now initiate the caspase cascade by activating effector caspases and [ ] . the intrinsic pathway is modulated by sars-cov molecules [ , ] . as intrinsic apoptosis involves mitochondria, its activity may also be exacerbated by sars-cov- disruptions of the electron transport chain, mitochondrial translation, and transmembrane transport [ ] . the resulting mitochondrial dysfunction may lead to increased release of reactive oxygen species and pro-apoptotic factors. another vital crosstalk is that of the intrinsic pathway with the pi k-akt pro-survival pathway. activated akt can phosphorylate and inactivate various pro-apoptotic proteins, including bad and caspase- [ ] . sars-cov uses pi k-akt signalling cascade to enhance infection [ ] . moreover, sars-cov could affect apoptosis in a cell-type-specific manner [ , ] . sars-cov structural proteins s, e, m, n, and accessory proteins a, b, , a, a, and b have been shown to act as crucial effectors of apoptosis in vitro. structural proteins seem to affect mainly the intrinsic apoptotic pathway, with p mapk and pi k/akt pathways regulating cell death. accessory proteins can induce apoptosis via different cascades and in a cellspecific manner [ ] . sars-cov e and a protein were shown to activate the intrinsic pathway by blocking anti-apoptotic bcl-xl localized to the er [ ] . sars-cov m protein and the ion channel activity of e and a were shown to interfere with pro-survival signalling cascades [ , ] . the viral replication and the consequent immune and inflammatory responses cause damage to the epithelium and pulmonary capillary vascular endothelium and activate the main intracellular defence mechanisms, as well as the humoral and cellular immune responses. resulting cellular stress and tissue damage [ , ] impair respiratory capacity and lead to acute respiratory distress syndrome (ards) [ , , ] . hyperinflammation is a known complication, causing widespread damage, organ failure, and death, followed by a not yet completely understood rapid increase of cytokine levels (cytokine storm) [ ] [ ] [ ] , and acute ards [ ] . other reported complications, such as coagulation disturbances and thrombosis are associated with severe cases, but the specific mechanisms are still unknown [ , [ ] [ ] [ ] , although some reports suggest that covid- coagulopathy has a distinct profile [ ] . the sars-cov- infection disrupts the coagulation cascade and is frequently associated with hyperinflammation, renin-angiotensin system (ras) imbalance and intravascular coagulopathy [ , [ ] [ ] [ ] . hyperinflammation leads in turn to detrimental hypercoagulability and immunothrombosis, leading to microvascular thrombosis with further organ damage [ ] . importantly, ras is influenced by risk factors of developing severe forms of covid- [ ] [ ] [ ] . ace , used by sars-cov- for host cell entry, is a regulator of ras and is widely expressed in the affected organs [ ] . the main function of ace is the conversion of angii to angiotensin - (ang - ), and these two angiotensins trigger the counter-regulatory arms of ras [ ] . the signalling via angii and its receptor agtr , elevated in the infected [ , ] , induces the coagulation cascade leading to microvascular thrombosis [ ] , while ang - and its receptor mas attenuate these effects [ ] . the innate immune system detects specific pathogen-associated molecular patterns (pamps), through pattern recognition receptors (prrs). detection of sars-cov- is mediated through receptors that recognise double-stranded and single-stranded rna in the endosome during endocytosis of the virus particle, or in the cytoplasm during the viral replication. these receptors mediate the activation of transcription factors such as ap , nfkappab, irf , and irf , responsible for the transcription of antiviral proteins, in particular, interferon-alpha and beta [ , ] . sars-cov- reduces the production of type i interferons to evade the immune response [ ] . the detailed mechanism is not clear yet; however, sars-cov m protein inhibits the irf activation [ ] and suppresses nfkappab and cox transcription. at the same time, sars-cov n protein activates nfkappab [ ] , so the overall impact is unclear. these pathways are also negatively regulated by sars-cov nsp papain-like protease domain (plpro) [ ] . the map contains the initial recognition process of the viral particle by the innate immune system and the viral mechanisms to evade the immune response. it provides the connection between virus entry (detecting the viral endosomal patterns), its replication cycle (detection cytoplasmic viral patterns), and the effector pathways of pro-inflammatory cytokines, especially of the interferon type i class. the latter seems to play a crucial but complex role in covid- pathology: both negative [ , ] and positive effects [ , ] of interferons on virus replication have been reported. interferon type i signalling interferons (ifns) are central players in the antiviral immune response of the host cell [ ] , specifically affected by sars-cov- [ ] [ ] [ ] [ ] . type i ifns are induced upon viral recognition of pamps by various host prrs [ ] as discussed earlier. the ifn-i pathway diagram represents the activation of tlr and ifnar and the subsequent recruiting of adaptor proteins and the downstream signalling cascades regulating key transcription factors including irf / , nf-kappab, ap- , and isre [ , ] . further, the map shows irf mediated induction of ifn-i, affected by the sars-cov- proteins. sars-cov nsp and orf interfere with irf signalling [ , ] and sars-cov m, n, nsp and nsp act as interferon antagonists [ , , , , ] . moreover, coronaviruses orf a, orf and nsp proteins can repress interferon expression and stimulate the degradation of ifnar and stat during the unfolded protein response (upr) [ , ] . another mechanism of viral rna recognition is rig-like receptor signalling [ ] , leading to sting activation [ ] , and via the recruitment of traf , tbk and ikkepsilon to phosphorylation of irf [ ] . this in turn induces the transcription of ifns alpha, beta and lambda [ ] . sars-cov viral papain-like-proteases, contained within the nsp and nsp proteins, inhibit sting and the downstream ifn secretion [ ] . in line with this hypothesis, sars-cov- infection results in a unique inflammatory response defined by low levels of ifn-i and high expression of cytokines [ , ] . the ifnlambda diagram describes the ifnl receptor signaling cascade [ ] , including jak-stat signaling and the induction of interferon stimulated genes, which encode antiviral proteins [ ] . the interactions of sars-cov- proteins with the ifnl pathway are based on the literature [ ] or sars-cov homology [ ] . metabolic pathways govern the immune microenvironment by modulating the availability of nutrients and critical metabolites [ ] . infectious entities reprogram host metabolism to create favourable conditions for their reproduction [ ] . sars-cov- proteins interact with a variety of immunometabolic pathways, several of which are described below. heme catabolism is a well-known anti-inflammatory system in the context of infectious and autoimmune diseases [ , ] . the main effector of this pathway, heme oxygenase- (hmox ) was found to interact with sars-cov- orf a, although the nature of this interaction remains ambiguous [ , ] . hmox cleaves heme into carbon monoxide, biliverdin (then reduced to bilirubin), and ferrous iron [pmid: ]. biliverdin, bilirubin, and carbon monoxide possess cytoprotective properties, and have shown promise as immunomodulatory therapeutics [ , ] . importantly, activation of hmox also inhibits the nlrp inflammasome [ ] [ ] [ ] , which is a pro-inflammatory and prothrombotic multiprotein system [ ] highly active in covid- [ ] [ ] [ ] . it mediates production of the pro-inflammatory cytokines il- b and il- via caspase- [ ] . the sars-cov orf a, e, and orf a incite the nlrp inflammasome [ ] [ ] [ ] [ ] . still, the potential of the hmox pathway to fight covid- inflammation remains to be tested [ , , ] despite promising results in other models of inflammation [ , , [ ] [ ] [ ] . the tryptophan-kynurenine pathway is closely related to heme metabolism. the ratelimiting step of this pathway is catalysed by the indoleamine , dioxygenase enzymes (ido and ido ) in dendritic cells, macrophages, and epithelial cells in response to inflammatory cytokines like ifn-gamma, ifn- , tgf-beta, tnf-alpha, and il- [ ] [ ] [ ] . crosstalk with the hmox pathway also increases the expression of ido and hmox in a feed-forward manner. metabolomics analyses from severe covid- patients revealed enrichment of kynurenines and depletion of tryptophan, indicating robust activation of ido enzymes [ , ] . depletion of tryptophan [ , , ] and kynurenines and their derivatives affect the proliferation and immune response of a range of t cells [ , [ ] [ ] [ ] [ ] [ ] . however, despite high levels of kynurenines in covid- , cd + t-cells and th cells are enriched in lung tissue, and t-regulatory cells are diminished [ ] . this raises the question of whether and how the immune response elicited in covid- evades suppression by the kynurenine pathway. the sars-cov- protein nsp interacts with three human proteins: gla, sirt , and impdh [ ] . the galactose metabolism pathway, including the gla enzyme [ ] , is interconnected with amino sugar and nucleotide sugar metabolism. sirt is a naddependent desuccinylase and demalonylase regulating serine catabolism, oxidative metabolism and apoptosis initiation [ ] [ ] [ ] . moreover, nicotinamide metabolism regulated by sirt occurs downstream of the tryptophan metabolism, linking it to the pathways discussed above. finally, impdh is the rate-limiting enzyme in the de novo synthesis of gtp, allowing regulation of purine metabolism and downstream potential antiviral targets [ , ] . the pyrimidine synthesis pathway, tightly linked to purine metabolism, affects viral dna and rna synthesis. pyrimidine deprivation is a host targeted antiviral defence mechanism, which blocks viral replication in infected cells and can be regulated pharmacologically [ ] [ ] [ ] . it appears that components of the dna damage response connect the inhibition of pyrimidine biosynthesis to the interferon signalling pathway, probably via sting-induced tbk activation that amplifies interferon response to viral infection, discussed above. inhibition of de novo pyrimidine synthesis may have beneficial effects on the recovery from covid- [ ] ; however, this may happen only in a small group of patients. covid- pathways featured in the previous section cover mechanisms reported so far. still, certain aspects of the disease were not represented in detail because of their complexity, namely cell-type-specific immune response, and susceptibility features. their mechanistic description is of great importance, as suggested by clinical reports on the involvement of these pathways in the molecular pathophysiology of the disease. the mechanisms outlined below will be the next targets in our curation roadmap. cell type-specific immune response covid- causes serious disbalance in multiple populations of immune cells. some studies report that covid- patients have a significant decrease of peripheral cd + and cd + cytotoxic t lymphocytes (ctls), b cells, nk cells, as well as higher levels of a broad range of cytokines and chemokines [ , [ ] [ ] [ ] [ ] . the disease causes functional exhaustion of cd + ctls and nk cells, induced by sars-cov- s protein and by excessive pro-inflammatory cytokine response [ , ] . moreover, the ratio of naïve-to-memory helper t-cells, as well as the decrease of t regulatory cells, correlate with covid- severity [ ] . conversely, high levels of th and cytotoxic cd + t-cells have been found in the lung tissue [ ] . pulmonary recruitment of lymphocytes into the airways may explain the lymphopenia and the increased neutrophil-lymphocyte ratio in peripheral blood found in covid- patients [ , , ] . in this regard, an abnormal increase of the th :treg cell ratio may promote the release of pro-inflammatory cytokines and chemokines, increasing disease severity [ ] . sars-cov- infection is associated with increased morbidity and mortality in individuals with underlying chronic diseases or a compromised immune system [ ] [ ] [ ] [ ] . groups of increased risk are men, pregnant and postpartum women, and individuals with high occupational viral exposure [ ] [ ] [ ] . other susceptibility factors include the abo blood groups [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] and respiratory conditions [ ] [ ] [ ] [ ] [ ] [ ] . importantly, age is one of the key aspects contributing to the severity of the disease. the elderly are at high risk of developing severe or critical disease [ , ] . age-related elevated levels of pro-inflammatory cytokines (inflammation) [ ] [ ] [ ] [ ] , immunosenescence and cellular stress of ageing cells [ , , , , ] may contribute to the risk. in contrast, children are generally less likely to develop severe disease [ , ] , with the exception of infants [ , [ ] [ ] [ ] . however, some previously healthy children and adolescents can develop a multisystem inflammatory syndrome following sars-cov- infection [ ] [ ] [ ] [ ] [ ] . several genetic factors have been proposed and identified to influence susceptibility and severity, including the ace gene, hla locus, errors influencing type i ifn production, tlr pathways, myeloid compartments, as well as cytokine polymorphisms [ , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] . we aim to connect the susceptibility features to specific molecular mechanisms and better understand the contributing factors. this can lead to a series of testable hypotheses, including the role of vitamin d counteracting pro-inflammatory cytokine secretion [ ] [ ] [ ] in an age-dependent manner [ , ] , and modifying the severity of the disease. another example of a testable hypothesis may be that the immune phenotype associated with asthma inhibits pro-inflammatory cytokine production and modifies gene expression in the airway epithelium, protecting against severe covid- [ , , ] . in order to understand complex and often indirect dependencies between different pathways and molecules, we need to combine computational and data-driven analyses. standardised representation and programmatic access to the contents of the covid- disease map enable the development of reproducible analytical and modelling workflows. here, we discuss the range of possible approaches and demonstrate preliminary results, focusing on interoperability, reproducibility, and applicability of the methods and tools. our goal is to work on the computational challenges as a community, involving the biocurators and domain experts in the analysis of the covid- disease map and rely on their feedback to evaluate the outcomes. in this way, we aim to identify approaches to tackle the complexity and the size of the map, proposing a state-of-the-art framework for robust analysis, reliable models, and useful predictions. visualisation of omics data can help contextualise the map with experimental data creating data-specific blueprints. these blueprints could be used to highlight parts of the map that are active in one condition versus another (treatment versus control, patient versus healthy, normal versus infected cell, etc.). combining information contained in multiple omics platforms can make patient stratification more powerful, by reducing the number of samples needed or by augmenting the precision of the patient groups [ , ] . approaches that integrate multiple data types without the accompanying mechanistic diagrams [ ] [ ] [ ] produce patient groupings that are difficult to interpret. in turn, classical pathway analyses often produce long lists mixing generic and cell-specific pathways, making it challenging to pinpoint relevant information. using disease maps to interpret omics-based clusters addresses the issues related to contextualised visual data analytics. footprints are signatures of a molecular regulator determined by the expression levels of its targets [ ] . for example, a footprint can contain targets of a transcription factor (tf) or peptides phosphorylated by a kinase. combining multiple omics readouts and multiple measurements can increase the robustness of such signatures. nevertheless, an essential component is the mechanistic description of the targets of a given regulator, allowing computation of its footprint. with available sars-cov- related omics and interaction datasets [ ] , it is possible to infer which tfs and signalling pathways are affected upon infection [ ] . combining the covid- disease map regulatory interactions with curated collections of tf-target interactions like dorothea [ ] will provide a contextualised evaluation of the effect of sars-cov- infection at the tf level. the virus-host interactome is a network of virus-human protein-protein interactions (ppis) that can help understanding the mechanisms of disease [ , [ ] [ ] [ ] . it can be expanded by merging virus-host ppi data with human ppi and protein data [ ] to discover clusters of interactions indicating human mechanisms and pathways affected by the virus [ ] . these clusters first of all can be interpreted at the mechanistic level by visual exploration of covid- disease map diagrams. in addition, these clusters can potentially reveal additional pathways to add to the covid- disease map (e.g., e protein interactions or tgfbeta diagrams) or suggest new interactions to introduce into the existing diagrams. computational modelling is a powerful approach that enables in silico experiments, produces testable hypotheses, helps elucidate regulation and, finally, can suggest via predictions novel therapeutic targets and candidates for drug repurposing. mechanistic models of pathways allow bridging variations at the scale of molecular activity to variations at the level of cell behaviour. this can be achieved by coupling the molecular interactions of a given pathway with its endpoint and by contextualising the molecular activity using omics datasets. hipathia is such a method, processing transcriptomic or genomic data to estimate the functional profiles of a pathway conditioned by the data studied and linkable to phenotypes such as disease symptoms or other endpoints of interest [ , ] . moreover, such mechanistic modelling can be used to predict the effect of interventions as, for example, the effect of targeted drugs [ ] . hipathia integrates directly with the diagrams of the covid- map using the sif format provided by casq (see section . ), as well as with the associated interaction databases (see section . ). the drawback of approaches like hipathia is their computational complexity, limiting the size of the diagrams they can process. an approach to large-scale mechanistic pathway modelling is to transform them into causal networks. carnival [ ] combines the causal representation of networks [ ] with transcriptomics, phosphoproteomics, or metabolomics data [ ] to contextualise cellular networks and extract mechanistic hypotheses. the algorithm identifies a set of coherent causal links connecting upstream drivers such as stimulations or mutations to downstream changes in transcription factor activities. analysis of the dynamics of molecular networks is necessary to understand their dynamics and deepen our understanding of crucial regulators behind disease-related pathophysiology. discrete modelling framework provides this possibility. covid- disease map diagrams, translated to sbml qual (see section . ), can be directly imported by tools like cell collective [ ] or ginsim [ ] for analysis. preserving annotations and layout information ensures transparency and reusability of the models. importantly, cell collective is an online user-friendly modelling platform that provides features for real-time in silico simulations and analysis of complex signalling networks. the platform allows users without computational background to simulate or analyse models to generate and prioritise new hypotheses. references and layout are used for model visualisation, supporting the interpretation of the results. the mathematics and code behind each model, however, remain accessible to all users. in turn, ginsim is a tool providing a wide range of analysis methods, including efficient identification of the states of convergence of a given model (attractors). model reduction functionality can also be employed to facilitate the analysis of large-scale models. viral infection and immune response are complex processes that span many different scales, from molecular interactions to multicellular behaviour. the modelling and simulation of such complex scenarios require a dedicated multiscale computational architecture, where multiple models run in parallel and communicate among them to capture cellular behaviour and intercellular communications. multiscale agent-based models simulate processes taking place at different time scales, e.g., diffusion, cell mechanics, cell cycle, or signal transduction [ ] , proposed also for covid- [ ] . physiboss [ ] allows such simulation of intracellular processes by combining the computational framework of physicell [ ] with maboss [ ] tool for stochastic simulation of logical models to study of transient effects and perturbations [ ] . implementation of detailed covid- signalling models in the pysiboss framework may help to better understand complex dynamics of multi-scale processes as interactions and crosstalk between immune system components and the host cell in covid- . in this case study, we combine computational approaches discussed above and present results derived from omics data analysis on the covid- disease maps diagrams. we measured the effect of covid- at the transcription factor (tf) activity level by applying viper [ ] combined with dorothea regulons [ ] on rna-seq datasets of the sars-cov- infected cell line [ ] . then, we mapped the tfs normalised enrichment score (nes) on the interferon type i signalling pathway diagram of the covid- disease map using the sif files generated by casq (see section . ). as highlighted in figure , our manually curated pathway included some of the most active tfs after sars-cov- infection, such as stat , stat , irf and nfkb . these genes are well known to be involved in cytokine signalling and first antiviral response [ , ] . interestingly, they are located downstream of various viral proteins (e, s, nsp , orf a and orf a) and members of the mapk pathway (mapk , mapk and map k ). sars-cov- infection is known to promote mapk activation, which mediates the cellular response to pathogenic infection and promotes the production of proinflammatory cytokines [ ] . altogether, we identified signaling events that may capture the mechanistic response of the human cells to the viral infection. in this use case, the hipathia [ ] algorithm was used to calculate the level of activity of the subpathways from the covid- apoptosis diagram, with the aim to evaluate whether covid- disease map diagrams can be used for pathway modelling approach. to this end, a public rna-seq dataset from human sars-cov- infected lung cells (geo gse ) was used. first, the rna-seq gene expression data was normalized with the trimmed mean of m values (tmm) normalization [ ] , then rescaled to range [ ; ] for the calculation of the signal and normalised using quantile normalisation [ ] . the normalised gene expression values were used to calculate the level of activation of the subpathways, then a case/control contrast with a wilcoxon test was used to assess differences in signaling activity between the two conditions. the activation levels have been calculated using transcriptional data from gse and hipathia mechanistic pathway analysis algorithm. each node represents a gene (ellipse), a metabolite (circle) or a function (square). the pathway is composed of circuits from a receptor gene/metabolite to an effector gene/function, with interactions simplified to inhibitions or activations (see section . , sif format). significantly deregulated circuits are highlighted by color arrows (red: activated in infected cells). the color of the node corresponds to the level of differential expression of each node in sars-cov- infected cells vs normal lung cells. blue: down-regulated elements, red: up-regulated elements, white: elements with not statistically significant differential expression. hipathia calculates the overall circuit activation, and can indicate deregulated interaction even if interacting elements are not individually differentially expressed. results of the apoptosis pathway analysis can be seen in figure and supplementary material . importantly, hipathia calculates the overall activation of circuits (series of causally connected elements), and can indicate deregulated interactions resulting from a cumulative effect, even if interacting elements are not individually differentially expressed. when discussing differential activation, we refer to the circuits, while individual elements are mentioned as differentially expressed. the analysis shows an overactivation of several circuits, specifically the one ending in the effector protein bax. this overactivation seems to be led by the overexpression of the bad protein, inhibiting bcl -mcl -bcl l complex, which in turn inhibits bax. indeed, sars-cov- infection can invoke caspase -induced apoptosis [ ] , where bax together with the ripoptosome/caspase- complex, may act as a pro-inflammatory checkpoint [ ] . this result is supported by studies in sars-cov, showing bax overexpression following infection [ , ] . overall, our findings recapitulate reported outcomes. with evolving contents of the covid- disease map and new omics data becoming available, new mechanism-based hypotheses can be formulated. in the covid disease map community we strive to produce interoperable content and seamless downstream analyses, translating the graphic representations of the molecular mechanisms to executable models. we are also aware of parallel efforts towards modelling of covid- mechanisms, which we plan to include as a part of our ecosystem. these efforts are not yet directly interoperable with the covid disease map content as they use either different notation schemes or require parameters not covered by our biocuration guidelines at the same time, they provide a complementary source of information and the opportunity to create an even broader toolset to tackle the pandemic. the modified edinburgh pathway notation (mepn) scheme [ ] allows for the detailed visual encoding of molecular processes using the yed platform but diagrams are constructed in such a way as to also function as petri nets. these can then be used directly for activity simulations using the biolayout network analysis tool [ ] . the current mepn covid- model details the replication cycle of sars-cov- , integrated with a range of host defence systems, e.g. type interferon signalling, tlr receptors, oas systems, etc. simulations of altered gene expression, interactions with drug targets or changes to interaction kinetics can be represented by introducing relevant transitions or nodes directly in the diagram. currently, models constructed in mepn can be saved as sbgn.ml files, however is a loss of information and the features associated computationally are not compatible with other covid- disease map diagrams (not modelled as petri nets). the covid- disease map can support dynamic kinetic modelling to quantify the behaviour of different pathways and evaluate the dynamic effects of perturbations. however, it is necessary to assign a kinetic equation or a rate law to every reaction in the diagram to be analysed. this process is challenging because any given reaction depends on its cellular and physiological context, which makes it difficult to parameterise. software support of tools like sbmlsqueezer [ ] and reaction kinetics databases like sabio-rk [ ] are indispensable in this effort. nevertheless, the most critical factor is the availability of experimentally validated parameters that can be reliably applied in sars-cov- modelling scenarios. the covid- disease map is both a knowledgebase and a computational repository. on the one hand, it is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. on the other hand, it is a computational resource of curated content for graph-based analyses and disease modelling. it offers a shared mental map for understanding the dynamic nature of the disease at the molecular level and also its dynamic propagation at a systemic level. thus, it provides a platform for a precise formulation of models, accurate data interpretation, monitoring of therapy, and potential for drug repositioning. the covid- disease map spans three platforms and assembles diagrams describing molecular mechanisms of covid- . these diagrams are grounded in the relevant published sars-cov- research, completed where necessary by mechanisms discovered in related beta-coronaviruses. this unprecedented effort of community-driven biocuration resulted in over forty diagrams with molecular resolution constructed since march . it demonstrates that expertise in biocuration, clear guidelines and text mining solutions can accelerate the passage from the published findings to a meaningful mechanistic representation of knowledge. the covid disease map can provide the tipping point to shortcut research data generation and knowledge accumulation, creating a formalized and standardized streamline of well defined tasks. this approach to an emerging pandemic leveraged the capacity and expertise of an entire swath of the bioinformatics community, bringing them together to improve the way we build and share knowledge. by aligning our efforts, we strive to provide covid- specific pathway models, synchronize content with similar resources and encourage discussion and feedback at every stage of the curation process. with new results published every day, and with the active engagement of the research community, we envision the covid- disease map as an evolving and continuously updated knowledge base whose utility spans the entire research and development spectrum from basic science to pharmaceutical development and personalized medicine. moreover, our approach includes a large-scale effort to create interoperable tools and seamless downstream analysis pipelines to boost the applicability of established methodologies to the covid- disease map content. this includes harmonisation of formats, support of standards, and transparency in all steps to ensure wide use and content reusability. preliminary results of such efforts are presented in the case studies. the covid- disease map community is open and expanding as more people with complementary expertise join forces. in the longer run, the map's content will help to find robust signatures related to sars-cov- predisposition or response to various treatments, along with the prioritization of new potential drug targets or drug candidates. we aim to provide the tools to deepen our understanding of the mechanisms driving the infection and help boost drug development supported with testable suggestions. we aim at building armor for new treatments to prevent new waves of covid- or similar pandemics. a pneumonia outbreak associated with a new coronavirus of probable bat origin covid- and the kidney: from epidemiology to clinical practice receptor ace is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues covid- disease map, building a computational repository of sars-cov- virus-host interaction mechanisms systems medicine disease maps: community-driven comprehensive representation of disease mechanisms communitydriven roadmap for integrated disease maps the reactome pathway knowledgebase wikipathways: a multifaceted pathway database bridging metabolomics to other omics research the systems biology graphical notation sbml level : an extensible format for the exchange and reuse of biological models the biopax community standard for pathway data sharing uniform resolution of compact identifiers for biomedical data omnipath: guidelines and gateway for literature-curated signaling pathway resources the imex coronavirus interactome: an evolving map of coronaviridae-host molecular interactions signor . , the signaling network open resource . : update update: integration, analysis and exploration of pathway data fairdomhub: a repository and collaboration environment for sharing systems biology research identifiers.org and miriam registry: community resources to provide persistent identification setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the zbit bioinformatics toolbox: a web-platform for systems biology and expression data analysis sbmlsqueezer : context-sensitive creation of kinetic equations in biochemical networks minerva-a platform for visualization and curation of molecular interaction networks editing, validating and translating of sbgn maps pathvisio : an extendable pathway analysis toolbox modeling and simulation using celldesigner software support for sbgn maps: sbgn-ml and libsbgn systems biology graphical notation markup language (sbgnml) version . cord- : the covid- open research dataset protein interaction data curation: the international molecular exchange (imex) consortium years of pathway figures informing epidemic (research) responses in a timely fashion by knowledge management -a zika virus use case [internet]. pathology from word models to executable models of signaling networks using automated assembly gnormplus: an integrative approach for tagging genes, gene families, and protein domains a sars-cov- protein interaction map reveals targets for drug repurposing biokc: a collaborative platform for systems biology model curation and annotation systems biology markup language (sbml) level package: multistate, multicomponent and multicompartment species, version , release the systems biology markup language (sbml) level package: layout, version core sbml level package: render, version , release controlled vocabularies and semantics in systems biology closing the gap between formats for storing layout information in systems biology cd sbgnml: bidirectional conversion between celldesigner and sbgn formats reactome from a wikipathways perspective sbml qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools automated inference of boolean models from molecular interaction maps using casq cytoscape: a software environment for integrated models of biomolecular interaction networks logical modeling and analysis of cellular regulatory networks with ginsim . ndex: a community resource for sharing and publishing of biological networks human coronavirus: host-pathogen interaction comparative replication and immune activation profiles of sars-cov- and sars-cov in human lungs: an ex vivo study with implications for the pathogenesis of covid- tropism, replication competence, and innate immune responses of the coronavirus sars-cov- in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures pathogenesis of covid- from a cell biology perspective pulmonary postmortem findings in a series of covid- cases from northern italy: a two-centre descriptive study interaction of sars-cov- and other coronavirus with ace (angiotensin-converting enzyme)- as their main receptor: therapeutic implications. hypertens dallas tex type i interferons: diversity of sources, production pathways and effects on immune responses impaired type i interferon activity and inflammatory responses in severe covid- patients interplay between sars-cov- and the type i interferon response the type i interferon response in covid- : implications for treatment type i and type iii interferons -induction, signaling, evasion, and application to combat covid- the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application temporal dynamics in viral shedding and transmissibility of covid- clinical features of patients infected with novel coronavirus in wuhan, china persons evaluated for novel coronavirus -united states epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan the prevalence of olfactory and gustatory dysfunction in covid- patients: a systematic review and meta-analysis identifying airborne transmission as the dominant route for the spread of covid- aerosol and surface stability of sars-cov- as compared with sars-cov- airborne transmission of sars-cov- : theoretical considerations and available evidence cell entry mechanisms of sars-cov- structure of the sars-cov- spike receptorbinding domain bound to the ace receptor sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor functional assessment of cell entry and receptor usage for sars-cov- and other lineage b betacoronaviruses cd l/l-sign and cd /dc-sign act as receptors for sars-cov- and are differentially expressed in lung and kidney epithelial and endothelial cells sars-cov- spike protein interacts with multiple innate immune receptors a multibasic cleavage site in the spike protein of sars-cov- is essential for infection of human lung cells fusion mechanism of -ncov and fusion inhibitors targeting hr domain in spike protein viral and cellular mrna translation in coronavirus-infected cells rna replication of mouse hepatitis virus takes place at double-membrane vesicles identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity liberation of sars-cov main protease from the viral polyprotein: n-terminal autocleavage does not depend on the mature dimerization mode severe acute respiratory syndrome coronavirus envelope protein regulates cell stress response and apoptosis autophagy during viral infection -a double-edged sword autophagy and energy metabolism canonical and noncanonical autophagy as potential targets for covid- digesting the crisis: autophagy and coronaviruses understanding sars-cov- -mediated inflammatory responses: from mechanisms to potential therapeutic tools proteasome activator pa γ-dependent degradation of coronavirus disease (covid- ) nucleocapsid protein coronaviruses hijack the lc -i-positive edemosomes, er-derived vesicles exporting short-lived erad regulators, for replication coronavirus replication complex formation utilizes components of cellular autophagy coronavirus replication does not require the autophagy gene atg coronavirus nsp restricts autophagosome expansion evolutionary analysis of sars-cov- : how mutation of non-structural protein (nsp ) could affect viral autophagy targeting the endocytic pathway and autophagy process as a novel therapeutic strategy in covid- autophagy and sars-cov- infection: apossible smart targeting of the autophagy pathway open questions for harnessing autophagy-modulating drugs in the sars-cov- war: hope or hype? intermittent fasting, a possible priming tool for host defense against sars-cov- infection: crosstalk among calorie restriction, autophagy and immune response murine coronavirus-induced apoptosis in cl- cells involves a mitochondria-mediated pathway and its downstream caspase- activation and bid cleavage the novel severe acute respiratory syndrome coronavirus (sars-cov- ) directly decimates human spleens and lymph nodes middle east respiratory syndrome coronavirus efficiently infects human primary t lymphocytes and activates the extrinsic and intrinsic apoptosis pathways apoptotic pathways: paper wraps stone blunts scissors apoptosis: a review of programmed cell death modulation of host cell death by sars coronavirus proteins spike protein of sars-cov stimulates cyclooxygenase- expression via both calcium-dependent and calcium-independent protein kinase c pathways augmentation of chemokine production by severe acute respiratory syndrome coronavirus a/x and a/x proteins through nf-kappab activation antiapoptotic signalling by the insulin-like growth factor i receptor, phosphatidylinositol -kinase, and akt jnk and pi k/akt signaling pathways are required for establishing persistent sars-cov infection in vero e cells phosphatidylinositol -kinase-dependent pathways oppose fas-induced apoptosis and limit chloride secretion in human intestinal epithelial cells. implications for inflammatory diarrheal states human intestinal epithelial cell survival: differentiation state-specific control mechanisms induction of apoptosis by the severe acute respiratory syndrome coronavirus a protein is dependent on its interaction with the bcl-xl protein the sars-coronavirus membrane protein induces apoptosis via interfering with pdk -pkb/akt signalling frequency and distribution of chest radiographic findings in patients positive for covid- coronavirus disease (covid- ) ct findings: a systematic review and meta-analysis covid- pathophysiology: a review acute respiratory distress syndrome clinical and immunological features of severe and moderate coronavirus disease longitudinal analyses reveal immunological misfiring in severe covid- is a "cytokine storm" relevant to covid- ? urgent avenues in the treatment of covid- : targeting downstream inflammation to prevent catastrophic syndrome incidence of thrombotic complications in critically ill icu patients with covid- abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia clinical course and outcome of patients infected with the novel coronavirus, sars-cov- , discharged from two hospitals in wuhan, china the unique characteristics of covid- coagulopathy treatment of covid- with conestat alfa, a regulator of the complement complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease (covid- ): a meta-analysis hyperinflammation and derangement of renin-angiotensin-aldosterone system in covid- : a novel hypothesis for clinically suspected hypercoagulopathy and microvascular immunothrombosis angiotensin ii up-regulates angiotensin i-converting enzyme (ace), but down-regulates ace via the at -erk/p map kinase pathway sex hormones promote opposite effects on ace and ace activity, hypertrophy and cardiac contractility in spontaneously hypertensive rats sex differences in the aging pattern of renin-angiotensin system serum peptidases sars-cov- receptor and regulator of the renin-angiotensin system: celebrating the th anniversary of the discovery of ace counterregulatory renin-angiotensin system in cardiovascular disease clinical and biochemical indexes from -ncov infected patients linked to viral loads and lung injury the emerging threat of (micro)thrombosis in covid- and its therapeutic implications pathogen recognition and inflammatory signaling in innate immune defenses pattern recognition receptors and inflammation severe acute respiratory syndrome coronavirus m protein inhibits type i interferon production by impeding the formation of traf .tank.tbk /ikkepsilon complex activation of nf-kappab by the full-length nucleocapsid protein of the sars coronavirus sars coronavirus papain-like protease inhibits the tlr signaling pathway through removing lys -linked polyubiquitination of traf and traf antiviral activities of type i interferons to sars-cov- infection interferon priming enables cells to partially overturn the sars coronavirus-induced block in innate immune activation a suspicious role of interferon in the pathogenesis of sars-cov- by enhancing expression of ace sars-cov- is sensitive to type i interferon pretreatment severe acute respiratory syndrome coronavirus orf antagonizes stat function by sequestering nuclear import factors on the rough endoplasmic reticulum/golgi membrane inborn errors of type i ifn immunity in patients with life-threatening covid- autoantibodies against type i ifns in patients with life-threatening covid- human coronaviruses: a review of virus-host interactions regulation of irf- -dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus severe acute respiratory syndrome coronavirus open reading frame (orf) b, orf , and nucleocapsid proteins function as interferon antagonists post-translational modifications of coronavirus proteins: roles and function accessory proteins of sars-cov and other coronaviruses the sars coronavirus a protein causes endoplasmic reticulum stress and induces ligand-independent downregulation of the type interferon receptor accessory proteins b and ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor message in a bottle: lessons learned from antagonism of sting signalling during rna virus infection peroxisomal mavs activates irf -mediated ifn-λ production covid- as a sting disorder with delayed over-secretion of interferon-beta imbalanced host response to sars-cov- drives development of covid- interferon-λ: immune functions at barrier surfaces and beyond decoding type i and iii interferon signalling during viral infection structural basis for translational shutdown and immune evasion by the nsp protein of sars-cov- immunometabolism and pulmonary infections: implications for protective immune responses and host-directed therapies competition for nutrients and its role in controlling immune responses new insights into the nrf- /ho signaling axis and its application in pediatric respiratory diseases heme catabolic pathway in inflammation and immune disorders the hmox pathway as a promising target for the treatment and prevention of sars-cov- of (covid- ) bile pigments in pulmonary and vascular disease heme oxygenase- dampens the macrophage sterile inflammasome response and regulates its components in the hypoxic lung carbon monoxide negatively regulates nlrp inflammasome activation in macrophages heme oxygenase- protects airway epithelium against apoptosis by targeting the proinflammatory nlrp -rxr axis in asthma negative regulators and their mechanisms in nlrp inflammasome activation and signaling targeting the nlrp inflammasome in severe covid- sars-cov- infection and overactivation of nlrp inflammasome as a trigger of cytokine "storm" and risk factor for damage of hematopoietic stem cells severe acute respiratory syndrome coronavirus orf a protein activates the nlrp inflammasome by promoting traf -dependent ubiquitination of asc severe acute respiratory syndrome coronavirus e protein transports calcium ions and activates the nlrp inflammasome role of severe acute respiratory syndrome coronavirus viroporins e, a, and a in replication and pathogenesis. denison mr, editor. mbio coronavirus e protein forms ion channels with functionally and structurally-involved membrane lipids targeting the heme-heme oxygenase system to prevent severe complications following covid- infections genetic polymorphisms complicate covid- therapy: pivotal role of ho- in cytokine storm heme oxygenase- induction contributes to renoprotection by g-csf during rhabdomyolysis-associated acute kidney injury targeting the nrf -heme oxygenase- axis after intracerebral hemorrhage hemin and cobalt protoporphyrin inhibit nlrp inflammasome activation by enhancing autophagy: a novel mechanism of inflammasome regulation remarkable role of indoleamine , -dioxygenase and tryptophan metabolites in infectious diseases: potential role in macrophage-mediated inflammatory diseases inhibition of acute lethal pulmonary inflammation by the ido-ahr pathway -hydroxyanthranilic acid, one of metabolites of tryptophan via indoleamine , -dioxygenase pathway, suppresses inducible nitric oxide synthase expression by enhancing heme oxygenase- expression nitric oxide inhibits indoleamine , -dioxygenase activity in interferon-gamma primed mononuclear phagocytes multiomic immunophenotyping of covid- patients reveals early infection trajectories [internet]. immunology gcn kinase in t cells mediates proliferative arrest and anergy induction in response to indoleamine , -dioxygenase indoleamine , dioxygenase and metabolic control of immune responses an expanding range of targets for kynurenine metabolites of tryptophan ido expands human cd +cd high regulatory t cells by promoting maturation of lps-treated dendritic cells inhibition of allogeneic t cell proliferation by indoleamine , -dioxygenase-expressing dendritic cells: mediation of suppression by tryptophan metabolites cinnabarinic acid generated from -hydroxyanthranilic acid strongly induces apoptosis in thymocytes through the generation of reactive oxygen species and the induction of caspase aryl hydrocarbon receptor negatively regulates dendritic cell immunogenicity via a kynureninedependent mechanism dysregulation of immune response in patients with coronavirus the molecular defect leading to fabry disease: structure of human alpha-galactosidase sirt is a nad-dependent protein lysine demalonylase and desuccinylase shmt desuccinylation by sirt drives cancer cell proliferation substrates and regulation mechanisms for the human mitochondrial sirtuins sirt and sirt imp/gtp balance modulates cytoophidium assembly and impdh activity fba reveals guanylate kinase as a potential target for antiviral therapies against sars-cov- . zenodo teriflunomide in the treatment of multiple sclerosis: current evidence and future prospects cerpegin-derived furo[ , -c]pyridine- , ( h, h)-diones enhance cellular response to interferons by de novo pyrimidine biosynthesis inhibition novel and potent inhibitors targeting dhodh are broad-spectrum antivirals against rna viruses including newly-emerged coronavirus sars-cov- longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of sars-cov- infected patients functional exhaustion of antiviral lymphocytes in covid- patients immunopathological characteristics of coronavirus disease cases in guangzhou detection of sars-cov- -specific humoral and cellular immunity in covid- convalescent individuals sars-cov- spike protein controls natural killer cell activation via the hla-e/nkg a pathway pathological findings of covid- associated with acute respiratory distress syndrome neutrophil-to-lymphocyte ratio and clinical outcome in covid- : a report from the italian front line higher level of neutrophil-to-lymphocyte is associated with severe covid- the comparative immunological characteristics of sars-cov, mers-cov, and sars-cov- coronavirus infections comorbidity and its impact on patients with covid- in china: a nationwide analysis risk factors for developing into critical covid- patients in wuhan, china: a multicenter, retrospective, cohort study covid- and crosstalk with the hallmarks of aging covid- in immunocompromised hosts: what we know so far considering how biological sex impacts immune responses and covid- outcomes public health agency of sweden's brief report: pregnant and postpartum women with severe acute respiratory syndrome coronavirus infection in intensive care in sweden risk of covid- among front-line health-care workers and the general community: a prospective cohort study relationship between the abo blood group and the covid- susceptibility association between abo blood groups and risk of sars-cov- pneumonia relationship between abo blood group distribution and clinical characteristics in patients with covid- genomewide association study of severe covid- with respiratory failure covid- and the abo blood group connection more on "association between abo blood groups and risk of sars-cov- pneumonia abo blood group predisposes to covid- severity and cardiovascular diseases inhibition of the interaction between the sars-cov spike protein and its cellular receptor by anti-histoblood group antibodies covid- and abo blood group: another viewpoint asthma and covid- association of respiratory allergy, asthma, and expression of the sars-cov- receptor ace distinct effects of asthma and copd comorbidity on disease expression and outcome in patients with covid- eleven faces of coronavirus disease covid- and asthma: reflection during the pandemic type inflammation modulates ace and tmprss in airway epithelial cells the possible pathophysiology mechanism of cytokine storm in elderly adults with covid- infection: the contribution of "inflameaging immunosenescence and inflamm-aging as two sides of the same coin: friends or foes? front immunol inflammaging: a new immunemetabolic viewpoint for age-related diseases an update and a model coronavirus disease (sars-cov- ) and colonization of ocular tissues and secretions: a systematic review immunosenescence in aging: between immune cells depletion and cytokines up-regulation clinical characteristics of children and young people admitted to hospital with covid- in united kingdom: prospective multicentre observational cohort study immune responses to sars-cov- infection in hospitalized pediatric and adult patients pathophysiology of covid- : why children fare better than adults? sars-cov- (covid- ): what do we know about children? a systematic review sars-cov- infection in children and newborns: a systematic review an outbreak of severe kawasaki-like disease at the italian epicentre of the sars-cov- epidemic: an observational cohort study multisystem inflammatory syndrome in children during the coronavirus pandemic: a case series hyperinflammatory shock in children during covid- pandemic childhood multisystem inflammatory syndrome -a new challenge in the pandemic genetic variability of human angiotensin-converting enzyme (hace ) among various ethnic populations covid- and individual genetic susceptibility/receptivity: role of ace /ace genes, immunity, inflammation and coagulation. might the double x-chromosome in females be protective against sars-cov- compared to the single x-chromosome in males? ace receptor polymorphism: susceptibility to sars-cov- , hypertension, multi-organ failure, and covid- disease outcome genetic gateways to covid- infection: implications for risk, severity, and outcomes a theory on sars-cov- susceptibility: reduced tlr -activity as a mechanistic link between men, obese and elderly severe covid- is marked by a dysregulated myeloid cell compartment deciphering the role of host genetics in susceptibility to severe covid- amelioration of non-alcoholic fatty liver disease with npc l -targeted igy or n- polyunsaturated fatty acids in mice evidence that vitamin d supplementation could reduce risk of influenza and covid- infections and deaths effect of single-dose injection of vitamin d on immune cytokines in ulcerative colitis patients: a randomized placebo-controlled trial prevalence of vitamin d deficiency among healthy infants and toddlers type and interferon inflammation strongly regulate sars-cov- related gene expression in the airway epithelium a computational framework for complex disease stratification from multiple large-scale datasets integration of multi-omics datasets enables molecular classification of copd similarity network fusion for aggregating data types on a genomic scale integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis diablo: an integrative approach for identifying key molecular drivers from multi-omics assays footprint-based functional analysis of multiomic data the global phosphorylation landscape of sars-cov- infection regulatory network analysis of paneth cell and goblet cell enriched gut organoids using transcriptomics approaches benchmark and integration of resources for the estimation of human transcription factor activities network-based drug repurposing for novel coronavirus -ncov/sars-cov- virus-host interactome and proteomic survey reveal potential virulence factors influencing sars-cov- multi-level proteomics reveals host-perturbation strategies of sars-cov- and sars-cov psicquic and psiscore: accessing and scoring molecular interactions covid- : viral-host interactome analyzed by network based-approach model to study pathogenesis of sars-cov- infection high throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes assessing the impact of mutations found in next generation sequencing data over human signaling pathways actionable pathways: interactive discovery of therapeutic targets using signaling pathway models from expression footprints to causal pathways: contextualizing large signaling networks with carnival the cell collective: toward an open and collaborative approach to systems biology comparing individualbased approaches to modelling the self-organization of multicellular tissues rapid community-driven development of a sars-cov- tissue simulator physiboss: a multiscale agent-based modelling framework integrating physical dimension and cell signalling physicell: an open source physics-based cell simulator for -d multicellular systems maboss . : an environment for stochastic boolean modeling conceptual and computational framework for logical modelling of biological networks deregulated in diseases functional characterization of somatic mutations in cancer using network-based inference of protein activity stat and irf : beyond isgf ifnβdependent increases in stat , stat , and irf mediate resistance to viruses and dna damage edger: a bioconductor package for differential expression analysis of digital gene expression data a comparison of normalization methods for high density oligonucleotide array data based on variance and bias sars-cov- triggers inflammatory responses and cell death through caspase- activation bax/bak-induced apoptosis results in caspase- -dependent il- β maturation in macrophages over-expression of severe acute respiratory syndrome coronavirus b protein induces both apoptosis and necrosis in vero e cells the mepn scheme: an intuitive and flexible graphical system for rendering biological pathways a graphical and computational modeling platform for biological pathways sabio-rk: an updated resource for manually curated biochemical reaction kinetics key: cord- -oc edgd authors: nguyen, trieu; duong bang, dang; wolff, anders title: novel coronavirus disease (covid- ): paving the road for rapid detection and point-of-care diagnostics date: - - journal: micromachines (basel) doi: . /mi sha: doc_id: cord_uid: oc edgd we believe a point-of-care (poc) device for the rapid detection of the novel coronavirus (sars-cov- ) is crucial and urgently needed. with this perspective, we give suggestions regarding a potential candidate for the rapid detection of the coronavirus disease (covid- ), as well as factors for the preparedness and response to the outbreak of the covid- . on january , the world health organization (who) declared a global public health emergency [ ] over the outbreak of the new coronavirus, called the novel coronavirus ( -ncov), which originated in wuhan city, in the hubei province of china. on february, who officially named the disease as the coronavirus disease (covid- ) [ ] . human-to-human transmission (figure ) has been confirmed by who and by the centers for disease control and prevention (cdc) of the united states [ ] , with evidence of person-to-person transmission from three different cases outside china, namely in the us [ ] , germany [ ] , and vietnam [ ] . covid- has continuously spread to countries; the number of confirmed infections reached , on march [ ] , and the death toll in china has overtaken the sars epidemic of - and has risen to [ ] . to slow down the spread of covid- , at least million people in china have been placed under lockdown [ ] . on march , italy also undertook the same measures, with the northern part of the country placed under lockdown, affecting million people [ ] . the definition of coronaviruses is listed in table . the reproduction number r (i.e., the average number of secondary cases generated by a typical infectious individual) is estimated to be . , and the doubling time is estimated to be . days [ ] . [ ] ). current studies have suggested that the intermediate carriers may be snakes [ ] or pangolins [ ] , but according to who the real source is still unknown [ , ] . in this scenario, a point-of-care (poc) device (i.e., a rapid, robust, and cost-efficient device that can be used onsite and in the field, and which does not necessarily require a trained technician to operate [ ] ) is crucial and urgently needed for the detection of covid- . figure shows the dramatic impact of early detection of infectious diseases in controlling an outbreak [ ] [ ] [ ] . such a poc device can be used in (but is not limited to) an emergency situation, such as the diamond princess cruise ship case. recently, it was reported that the diamond princess cruise ship has been quarantined in yokohama, japan, due to a serious spreading of covid- on this cruise, with at least infected cases out of , passengers and crew (reported by who [ ] , february ). the detection of covid- may not have been prompt enough as they did not have enough test kits to diagnose all the passengers on the ship in order to timely respond to the rapid spreading of the disease [ ] . [ ] ). current studies have suggested that the intermediate carriers may be snakes [ ] or pangolins [ ] , but according to who the real source is still unknown [ , ] . a large and diverse family of enveloped, positive-stranded rna viruses, with a~ - kilobase genome [ ] . the coronaviridae cover a broad host range, infecting many mammalian and avian species, and induce upper respiratory, gastrointestinal, hepatic, and central nervous system diseases [ ] . in the last few decades, coronaviruses have been shown to be capable of also infecting humans. the outbreak of severe acute respiratory syndrome (sars) in , and, more recently, middle-east respiratory syndrome (mers) have proved the lethality of covs when they cross the species barrier and infect humans [ ] . novel coronavirus (sars-cov- [ ] ): a new zoonotic human coronavirus, which was reported and announced by the chinese center for disease control and prevention (ccdc) on january [ ] . in spite of the fact that the initial infected cases have been associated with the huanan south china seafood market, the source of covid- is still unknown (figure ). on january , the who declared a global public health emergency regarding the outbreak of covid- . on the march , the who declared the outbreak of covid- a pandemic. the manifestation of the covid- infection is highly nonspecific, including respiratory symptoms, fever, cough, dyspnea, and viral pneumonia [ ] . thus, diagnostic tests specific to this infection are urgently required to confirm suspected cases, screen patients, and conduct virus surveillance. in this scenario, a point-of-care (poc) device (i.e., a rapid, robust, and cost-efficient device that can be used onsite and in the field, and which does not necessarily require a trained technician to operate [ ] ) is crucial and urgently needed for the detection of covid- . figure shows the dramatic impact of early detection of infectious diseases in controlling an outbreak [ ] [ ] [ ] . micromachines , , x of figure . the dramatic impact of the rapid detection of infectious diseases in controlling and preventing an outbreak (adapted to who document [ ] and references [ , ] ). the current standard molecular technique that is now being used to detect covid- is the realtime reverse transcription-polymerase chain reaction (rrt-pcr). this protocol has been documented and available online on the who website since january [ ] . the testing procedure includes: (i) specimen collection; (ii) packing (storage) and shipment of the clinical specimens; (iii) (good) communication with the laboratory and providing needed information; (iv) laboratory testing; (v) reporting the results. this rrt-pcr technique requires sophisticated laboratory equipment that is often located at a central laboratory (biosafety level or above) [ , , ] . sample transportation is inevitable. as a consequence, the time required to obtain the results can be up to or days. in the case of a public health emergency such as the covid- outbreak, this time-consuming process of sample testing is not only extremely disadvantageous, but also dangerous since the virus needs to be contained. in addition, commercial pcr-based methods are expensive and depend upon technical expertise, and the presence of viral rna or dna does not always reflect acute disease [ ] [ ] [ ] . furthermore, using pcr, codetection with other respiratory viruses is frequently encountered in coronaviruses (covs), and the contribution of positive cov pcr results to disease severity is not always explicitly exhibited [ ] [ ] [ ] . furthermore, as of february in the united states, as mentioned in the interim guidelines for collecting, handling, and testing clinical specimens from persons under investigation (puis) for novel coronavirus, the diagnostic testing for covid- can be conducted only at cdc. from february onwards, covid- tests can also be done at laboratories designated by cdc. likewise in china, where the outbreak is ongoing, samples had to be sent to beijing for testing, as reported on january [ ] . on february , china's own cdc deployed a mobile biosafety laboratory to wuhan in the hubei province to assist with the response [ , ] . on february , an emergency test laboratory (biosafety level ) run by bgi genomics, global heartquare: shenzhen, china was set up in wuhan in the hubei province to assist the covid- epidemic [ ] . in order to overcome the current time-consuming and laborious detection technique using rt-qpcr, an alternative molecular amplification technique should be deployed. loop-mediated isothermal amplification (lamp) reaction is a novel nucleic acid amplification technique that amplifies dna with high specificity, efficiency, and rapidity under isothermal conditions. this method uses a set of four specially designed primers, and a dna polymerase with strand displacement activity [ ] to synthesize target dna up to copies in less than an hour at a constant figure . the dramatic impact of the rapid detection of infectious diseases in controlling and preventing an outbreak (adapted to who document [ ] and references [ , ] ). such a poc device can be used in (but is not limited to) an emergency situation, such as the diamond princess cruise ship case. recently, it was reported that the diamond princess cruise ship has been quarantined in yokohama, japan, due to a serious spreading of covid- on this cruise, with at least infected cases out of passengers and crew (reported by who [ ] , february ). the detection of covid- may not have been prompt enough as they did not have enough test kits to diagnose all the passengers on the ship in order to timely respond to the rapid spreading of the disease [ ] . the current standard molecular technique that is now being used to detect covid- is the real-time reverse transcription-polymerase chain reaction (rrt-pcr). this protocol has been documented and available online on the who website since january [ ] . the testing procedure includes: (i) specimen collection; (ii) packing (storage) and shipment of the clinical specimens; (iii) (good) communication with the laboratory and providing needed information; (iv) laboratory testing; (v) reporting the results. this rrt-pcr technique requires sophisticated laboratory equipment that is often located at a central laboratory (biosafety level or above) [ , , ] . sample transportation is inevitable. as a consequence, the time required to obtain the results can be up to or days. in the case of a public health emergency such as the covid- outbreak, this time-consuming process of sample testing is not only extremely disadvantageous, but also dangerous since the virus needs to be contained. in addition, commercial pcr-based methods are expensive and depend upon technical expertise, and the presence of viral rna or dna does not always reflect acute disease [ ] [ ] [ ] . furthermore, using pcr, codetection with other respiratory viruses is frequently encountered in coronaviruses (covs), and the contribution of positive cov pcr results to disease severity is not always explicitly exhibited [ ] [ ] [ ] . furthermore, as of february in the united states, as mentioned in the interim guidelines for collecting, handling, and testing clinical specimens from persons under investigation (puis) for novel coronavirus, the diagnostic testing for covid- can be conducted only at cdc. from february onwards, covid- tests can also be done at laboratories designated by cdc. likewise in china, where the outbreak is ongoing, samples had to be sent to beijing for testing, as reported on january [ ] . on february , china's own cdc deployed a mobile biosafety laboratory to wuhan in the hubei province to assist with the response [ , ] . on february , an emergency test laboratory (biosafety level ) run by bgi genomics, global heartquare: shenzhen, china was set up in wuhan in the hubei province to assist the covid- epidemic [ ] . in order to overcome the current time-consuming and laborious detection technique using rt-qpcr, an alternative molecular amplification technique should be deployed. loop-mediated isothermal amplification (lamp) reaction is a novel nucleic acid amplification technique that amplifies dna with high specificity, efficiency, and rapidity under isothermal conditions. this method uses a set of four specially designed primers, and a dna polymerase with strand displacement activity [ ] to synthesize target dna up to copies in less than an hour at a constant temperature of • c. the final products are stem-loop dnas with multiple inverted repeats of the target, bearing structures with a cauliflower-like appearance. lamp has high specificity and sensitivity and is simple to perform; hence, soon after its initial development it became an enormously popular isothermal amplification method in molecular biology, with application in pathogen detection. lamp uses strand-displacement polymerases instead of heat denaturation to generate a single-stranded template; hence, it has the advantage of running at a constant temperature, simultaneously reducing the cumbersomeness of a thermocycler as well as the energy required. lamp technology is proven to be more stable [ ] and more sensitive [ ] in detection compared to pcr. other advantages of lamp compared to those of pcr are shown in table . we believe that the lamp assay could be a potential candidate for the point-of-care device application in the detection of covid- . an example of using lamp in a point-of-care device for the detection of a zoonotic virus causing respiratory symptoms such as the avian influenza virus (aiv) is the vivaldi (veterinary validation of point-of-care diagnostic instrument) project [ ] . with poc devices such as the vetpod [ ] (veterinary, portable, onsite detection), in the vivaldi project, detection time can be less than h. besides poc devices using disposable polymer chips and lamp assays, as in the vetpod of the vivaldi project, a lateral flow strip (lfs) would also be a suitable candidate for the rapid and on-site detection of covid- . a device such as covid- igm/igg rapid test of biomedomics is a good example [ ] . the sensitivity of the covid- igm/igg rapid test is . %, which is expected to be lower than the sensitivity of tests based on lamp-reaction assays (> %). therefore, a combination of lfs and lamp into one device could be an excellent candidate for poc testing of covid- . table . comparison between pcr and loop-mediated isothermal amplification (lamp) reactions [ , [ ] [ ] [ ] . thermal cycling (multiple heating and cooling cycle; hence, bulky and cumbersome). isothermal and continuous amplification (smaller, simpler, hence portable). always requires sample concentration and preparation (time-consuming). for virus detection, for example, influenza [ ] or human norovirus, lamp assay offers one-step detection [ ] . sample preparation steps are simplified. multiple protocols (complicated and requires a skilled technician). single protocol (faster). inhibitors hinder the reaction. tolerate inhibitors and more stable. diagnostic sensitivity ( %) is currently reported lower than lamp [ , , ] . diagnostic sensitivity > %. established technique. applications using lamp assays are being explored. furthermore, alongside detecting and containing the virus, for the sake of a public health response regarding the dynamics of the outbreak, the socio-economic impact of covid- is equally in urgent need. who announced that to fight the further spread of covid- , the international community has launched a us$ million preparedness and response plan from february through april [ ] . in , the sars-cov virus pulled the world's output down by $ billion. the early estimation for the cost to the global economy as a result of the outbreak of covid- is about $ billion [ ] . this is because china's gdp shares were approximately % globally as of , which was about four times higher than in , and the confirmed infected cases (at the time of doing the economic estimation, i.e., at the beginning of february ) are more than times larger than the total of sars. given that the number of infected cases ( , confirmed cases) is currently approximately times larger than sars cases [ ] , and that the death toll due to covid- has surpassed that of the sars epidemic, the economic impact of covid- might be much larger than $ billion. furthermore, in order to win the battle against this outbreak, information on the epidemiological characteristics, such as the identification of the animal reservoirs [ ] (figure ) and the risk factor of the disease, is also essential. the intermediate host carrying the disease is important to identify not only for the current epidemic, but also to eliminate a future outbreak. together with the all aforementioned factors, the race for a vaccination against covid- is equally essential. although at this stage there is no registered treatment or vaccine for covid- , zhang has recently mentioned some potential interventions [ ] , such as nutritional interventions (vitamin a, b, c, d, e, and other trace minerals such as zinc and iron). due to the high percentage of identicality in the sequence (up to % of the genome structure) between sars-cov- and the sars-cov virus, immuno-enhancers and other specific treatment that have been applied for sars could also be considered [ ] to use for the treatment of sars-cov- . the authors declare no conflict of interest. novel coronavirus ( -ncov ) situation report how -ncov spreads first case of novel coronavirus in the united states transmission of -ncov infection from an asymptomatic contact in germany importation and human-to-human transmission of a novel coronavirus in vietnam situation dashboard strategies shift as coronavirus pandemic looms italy announces lockdown as global coronavirus cases surpass , . available online nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study christening of new coronavirus and its disease name create confusion homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human did pangolins spread the china coronavirus to people? nature . [crossref] . who recommendations to reduce risk of transmission of emerging pathogens from animals to humans in live animal markets updated understanding of the outbreak of novel coronavirus ( -ncov) in wuhan an updated estimation of the risk of transmission of the novel coronavirus ( -ncov) coronavirus spike proteins in viral entry and pathogenesis coronavirus envelope protein: current knowledge return of the coronavirus: -ncov. viruses clinical features of patients infected with novel coronavirus in from lab on a chip to point of care devices: the role of open source microcontrollers world health organization (who) an overview of disease surveillance and notification system in nigeria and the roles of clinicians in disease outbreak prevention and control the french human salmonella surveillance system: evaluation of timeliness of laboratory reporting and factors associated with delays coronavirus infection tally on diamond princess hits as tests for all passengers eyed molecular diagnosis of a novel coronavirus ( -ncov) causing an outbreak of pneumonia rapid detection and monitoring of human coronavirus infections epidemiology and clinical presentations of the four human coronaviruses e, hku , nl , and oc detected over years using a novel multiplex real-time pcr method evaluation of the advansure™ real-time rt-pcr compared with culture and seeplex rv for simultaneous detection of respiratory viruses there's only one way to know if you have the coronavirus, and it involves machines full of spit and mucus the us fast-tracked a coronavirus test to speed up diagnoses accelerated reaction by loop-mediated isothermal amplification using loop primers robustness of a loop-mediated isothermal amplification reaction for diagnostic applications loop-mediated isothermal amplification (lamp) assays for the detection of abaca bunchy top virus and banana bunchy top virus in abaca covid- igm/igg rapid test rapid and simple colorimetric detection of multiple influenza viruses infecting humans using a reverse transcriptional loop-mediated isothermal amplification (rt-lamp) diagnostic platform development of one-step reverse transcription loop-mediated isothermal amplification for norovirus detection in oysters comparison of conventional pcr, multiplex pcr, and loop-mediated isothermal amplification assays for rapid detection of arcobacter species us$ million needed for new coronavirus preparedness and response global plan economic vulnerabilities to the coronavirus: top countries at risk a novel coronavirus outbreak of global health concern a pneumonia outbreak associated with a new coronavirus of probable bat origin potential interventions for novel coronavirus in china: a systematic review key: cord- -kdkyzfjv authors: naghibzadeh, mahmoud; savari, hossein; savadi, abdorreza; saadati, nayyereh; mehrazin, elahe title: developing an ultra-efficient microsatellite discoverer to find structural differences between sars-cov- and covid- date: - - journal: inform med unlocked doi: . /j.imu. . sha: doc_id: cord_uid: kdkyzfjv motivation: recently, the outbreak of coronavirus-covid- has forced the world health organization to declare a pandemic status. a genome sequence is the core of this virus which interferes with the normal activities of its counterparts within humans. analysis of its genome may provide clues toward the proper treatment of patients and the design of new drugs and vaccines. microsatellites are composed of short genome subsequences which are successively repeated many times in the same direction. they are highly variable in terms of their building blocks, number of repeats, and their locations in the genome sequences. this mutability property has been the source of many diseases. usually the host genome is analyzed to diagnose possible diseases in the victim. in this research, the focus is concentrated on the attacker's genome for discovery of its malicious properties. results: the focus of this research is the microsatellites of both sars and covid- . an accurate and highly efficient computer method for identifying all microsatellites in the genome sequences is discovered and implemented, and it is used to find all microsatellites in the coronavirus-covid- and sars . the microsatellite discovery is based on an efficient indexing technique called k-mer hash indexing. the method is called fast microsatellite discovery (fmsd) and it is used for both sars and covid- . a table composed of all microsatellites is reported. there are many differences between sars and covid- , but there is an outstanding difference which requires further investigation. availability: fmsd is freely available at https://gitlab.com/fum_hpclab/fmsd_project, implemented in c on linux-ubuntu system. software related contact: hossein_savari@mail.um.ac.ir. the novel coronavirus outbreak began in wuhan, china, in december (p. zhou et al. a ) and quickly reached a point such that a pandemic state was declared by the world health organization. although it has been controlled in wuhan, overall it is in the throughout the world. knowing the structure of this virus and revealing the hidden properties of its genome could be helpful towards the design of effective treatment procedures of human victims and also the production of a vaccine to provide immunity against this virus. assessment its severity and better understanding this disease is under way (wilson et al. ) . finding all microsatellites in covid- is one direction towards analysis of the virus's structure. lack of a fast, accurate, and memory efficient microsatellite discoverer motivated us to develop such a tool first, and then start analyzing the covid- genome structure. therefore, this research follows two objectives, development of a general microsatellite discoverer which can be used for different genomes, and analysis of the structures of both sars-cov- and that of coronavirus-covid- using this tool and revealing their differences. the final results will assist future investigations towards drug and vaccine design. even very minor assistance in these directions can have a great impact on saving lives and elevating the quality of numerous human lives. tandem repeats, in genomic sequences, are motifs which are continuously repeated many times in dna (deoxyribonucleic acid), gene, genome, or other genomic sequences and, as the name suggests, the orientation of the motif in all repeats are the same. they are classified into three classes, microsatellites, minisatellites and satellites. different researchers and practitioners disagree where to draw the separating line between microsatellites, minisatellites and satellites; however, the number appears very often as the longest length of the core subsequences of microsatellites (pickett et al. ) . the core subsequence of microsatellites will be called motif, from here on. another important feature of microsatellites, minisatellites and satellites is the number of repeats of the corresponding motifs. once again, there is no clear-cut lower bound for the minimum number of repeats. a more general case of micro and mini satellites is called variable number of tandem repeats (vntr) in which other subsequences may appear between motif repeats (pourcel et al. ) . vntrs are very common in the human genome, and it is estimated that % of the human genome is composed of vntrs (farnoud et al. ) . the focus of this research is finding microsatellites with both a fixed number of tandem repeats and those in which the number of repeats vary in different individuals. the variability of the number of repeats in both microsatellites, which is called the number of repeats polymorphism, is a good candidate for an individual's dna signature (lang et al. ; parson ) . could it be the case for different varieties of the coronavirus? this has to be investigated after at least the microsatellites are all detected and reported. the proposed approach to recognition of microsatellites in any genomic sequence as well as that of the novel coronavirus benefits from a hash indexing method called the k-mer hash index (kmhi) (ning et al. ) . in this research, a novel improvement is added to the kmhi to make it both time and space efficient, which is briefly discussed in the following paragraph and the details are clarified in the solution approach section. this novelty not only is usable for finding microsatellites, the topic of this research, but also all other kinds of vntrs in any genomic sequence. generally, each row of the kmhi points to a link list of places where the kmer value corresponding to this row appears in the reference sequence. after the whole input sequence is processed and kmhi and all linked lists are developed, each list is separately processed to find possible microsatellites. the discovery of this research made it possible to remove all linked lists and hence to highly reduce the space requirements and increase the efficiency of the microsatellites' discovery. the processing of each potential microsatellite is done as soon as it is detected during the processing of the input sequence rather than postponing it to after the sequence is completely scanned. the details are described in the solution approach section. the properties and novelties of the presented method, which is named fast microsatellite discoverer (fmsd), for finding all microsatellites of a given gene, dna, rna, or other genome sequences including the novel coronavirus (genbabk ) and sars (rota et al. ) is as follows. • it finds all microsatellites with core sequences, i.e., motifs, of , , …, and characters. • it uses an efficient indexing method which does not require any space for storing k-mer values or their locations in the sequence. • it uses extremely low main memory space and no secondary storage except for the input sequence and the output results. • it is extremely fast. potential microsatellites are processed as they are found, not when the input sequence reaches its end. therefore, although the developed software is not parallel, it can easily become so in the future. using fmsd, both sars and covid- genomes were computationally analyzed and the differences were recognized and highlighted. there seems to be important differences between these two genomes, but their medical significance has to be investigated by geneticists and health specialists. the remainder of the paper is organized in five sections and one references division. section reviews related papers, especially the ones used for comparisons. section is a brief clarification of the problem being solved. section describes the solution approach. section details the evaluation, reports the comparison results, and highlights the structural differences with respect to microsatellites between sars and coronavirus-covid- as a case study. coronavirus infection growth has been very rapid. in less than three months' time it has reached a pandemic state. the need for research is growing, and its priorities are being set (cowling and leung ) . with respect to urgent drug discovery, the immediate effort is focused on repurposing drugs (y. zhou et al. b) . in this respect, the study of virus-host and human-human protein-protein interactome networks is said to be essential (mir et al. ; y. zhou et al. b ). another direction is the discovery of known patterns which have been the source of other diseases, in the genome of the covid- . it is estimated that there are . million microsatellites in the human genome (srivastava et al. ) . amplification of many of these microsatellites have been used for many purposes such as disease diagnosis or human observable characteristics segregation. numerous researches have reported the association between different diseases and certain microsatellites (kelkar et al. ; liu et al. ) . for example, the instability nature of repeats in the microsatellites is associated with many kinds of cancer and a variety of disorders related to the nervous system's degeneration, such as huntington's disease (kovtun and mcmurray ) . even a repeat polymorphism in one of the genes, i.e., il-lra, is shown to be associated with an increased possibility of osteoporotic fractures (raje et al. ; saadati and rajabian ) . having said so, accurately and efficiently locating microsatellites in a given genome or genomic sequence has been and still is an important issue. research on finding tandem repeats has a long history and covers diverse classes of problems with different restrictions and assumptions. generally speaking, the goal is either to find all kinds of tandem repeats (kolpakov et al. ) or a subset of classes of tandem repeats such as microsatellites (kovtun and mcmurray ) with a variable number of repeats in different individuals or without it. from a different point of view, the outcome is either exact or inexact and for the case of inexact, it could be statistical (landau et al. ) , fuzzy (genovese et al. ) , based on distances such as hamming or edit distance (kolpakov et al. ) . to the best of our knowledge, there is no document with a complete classification of methods for finding tandem repeats and the first objective of this research is presenting a new approach to finding these repeats and not reviewing and classifying existing methods. therefore, we will limit ourselves to documents which provide a tide background for the concept and introduce those documents which are used in the comparison sections. the software developed here is capable of finding all microsatellites of genomic sequences whatever their length might be. the main objective of this research is to use the developed system to recognize all microsatellites of the novel coronavirus and that of sars and highlight the differences. a detailed comparison will be provided. kmer-ssr is a package which detects simple sequence repeats of all sizes. the advantage of this method is that it uses a backtracking idea to return to the beginning of the detected sequence and look again for overlapped tandem repeats. this way the precision of the method is increased. the algorithm is an exact one; hence it is not either fuzzy or approximate. this is also the property of the method developed here, which makes it a good candidate to compare our method with (pickett et al. ) . krait (du et al. ) is specifically designed to detect exact microsatellites, similar to what is being done in this paper. however, krait does not find microsatellites of core sizes equal to . to obtain the other six types of microsatellites, the program scans the source sequence six times. it has the capability of using a seed-and-extend concept to detect similar repeats. to check the atomicity of the core sequence, it searches a long list of possible core sequences, which is a time consuming process. although we noticed it does not detect microsatellites with overlapped cores, it is a good candidate for the comparison with the method which is developed here. however, it is a deficiency for sensitive situations such as covid- 's genome study. a software tool called mreps is develop to detect all tandem repeats, including microsatellites, in dna as well as whole genome. their claim is that it is capable to identify fuzzy tandem repeats by defining a resolution parameter. it is general in the sense that it identifies tandem repeats with all core sizes. a feature of mreps is that it can tolerate errors between repeated copies (kolpakov et al. ) . with the generality, of course, comes slowness, usage complexity, and inaccuracy. for the case of coronavirus which is composed of a short genome, fuzziness and inexactness is a weakness of the method. however, the reason for including fuzziness in the search seems to be to decrease the time requirement. for this reason it is decided to include this software in the comparison part to show the superiority of our method even with respect to time. the last work we are going to review is perf (avvaru et al. ) . it is based on the preparation of a repeated set in advance, and comparing all possible subsequences of the input sequence against this set, and then perform further processing, if a match happens. in the default option of this tool, all microsatellites of core lengths to are detected. to build the repeat set, all possible combinations of k-mers, for k= to , are generated, and each one is extended by contiguous repetition of the k-mer to characters. a moving window with length is initialized with the first characters of the input sequence, and it searches in the repeat set. if it is found, further processing will follow to find all repeats; otherwise, the moving window is pushed one place forward and the process continues. the main difficulty with this approach is the search time in the repeat set, especially if microsatellites of longer core sizes are of users' interest. for example, if the core length is seven nucleotides, rows have to be added to the repeat set. one other difficulty is that the tool is not capable of detecting microsatellites with a low number of repeats. for example, it would not be able to detect microsatellites with core size in which the number of repeats are less than . it is possible to change the default values but, a high search time will persist and other problems may arise. a genomic sequence is given as input. it is composed of nucleotides a(adenine), t(thymine), g(guanine), and c(cytosine). for some sequences such as ribonucleic acid (rna) t is replaced by u; however, we have assumed the sequence to be composed of a, t, g, and c. by a simple replacement of u by t in the input sequence, the method presented here will hold valid and applicable. the length of the input sequence could be as long as the whole genome and as small as a few nucleotides. the problem is to find all successive tandem repeats of the same core sequence, i.e., same motif. the core sequences of microsatellites are considered to be of length , , ..., or nucleotides. further, we assume the core sequence is atomic. for example, atat is not atomic because it is composed of two identical ats, and hence it should be reported as a microsatellite of core sequence at, assuming it passes other requirements. using the developed tool, the existence of microsatellites in coronavirus-covid- will be carefully investigated, and all such cases will be reported. the same will apply to sars-cov- , and differences will be specified. possible interpretations of the differences will be discussed, while more complex cases will be left for future investigations. the input sequence is a genome or genomic sequence in which all tandem repeats of type microsatellite will be detected and reported. the approach starts with generating an index table from the input sequence. the index table is called k-mer hash index (kmhi). to generate the kmhi, starting from the beginning of the input sequence, the first six-character subsequence, i.e., characters in positions to , is selected and it is converted to an integer using a two-bit code for each of the letters a, c, g, and t. the corresponding codes of the letters are , , , and , respectively. for example, the subsequence acctga would be converted to the integer in base which is equal to decimal number . decoding this code will take us to row number of the table kmhi. note that the first row is numbered zero. the table has = rows. although all microsatellites of sizes to are to be found, only one kmht is produced, and the unit subsequence for the hashing purpose is always . other options such as units of four were examined, and considering the overall performance and flexibility, was selected. in the following, the details of detecting actual microsatellites will be described using an example. neither the subsequence itself nor the code is stored in the kmhi table. depending on the problem being solved, different information may be stored in rows of the khmi table. this coding system has two major advantages, a no-space requirement for storing search-key values and negligible decoding time requirement. with the big data production and fast analysis requirements, khmi is a good candidate to be used in many fields of bioinformatics. let us say the hash of a search-key value is interpreted as an integer variable x, then its decoding is equivalent to going to kmhi(x), i.e., row x of table kmhi. the simplest approach is to attach a link list to each row of the kmhi, and as the input is scanned, store the position of each k-mer in the link list which corresponds to this k-mer. after the end of the input sequence is reached, then each linked list is separately processed, and microsatellites are detected. in this approach, for each character of the input sequence, a node of a list is formed, and in each node a location and a pointer is stored. therefore, the storage requirement forces the software to rely on the secondary storage which makes the time requirement intolerable. besides, processing the links is another factor which adds to the computation time. in this research, a novel idea was developed which removes all the linked lists and instead, for each kmer includes only three values in the kmhi table. the software system which is developed around this idea to find all microsatellites of a genomic sequence is called fast microsatellite discoverer (fmsd). suppose as the input sequence is being scanned, a -mer gttcgt is seen such that the end character, t, is in position of the input sequence, i.e., this -mer is in locations to of the input sequence. this -mer points to row number of the kmhi table. suppose the same -mer is repeated positions later, i.e., in positions to . this will point to the same row number of the kmhi. with respect to this row, we can guess that perhaps a microsatellite, actually gttc, is forming, because two of them have been already observed. at this point, row will store three values, loc which is equal to , size which is equal to , and count which is equal to . let us assume that the same -mer is repeated in positions to . therefore loc will become , size will not change because it shows the core size of this microsatellite, and count will change to . see figure . a similar case to what was discussed for microsatellites with core subsequences of length is applicable to all microsatellites of sizes one to six. for size seven, a minor extra comparison has to be done. it is clear that size must be but the unit of hashing is six characters. to solve this case, each time an extra comparison for the seventh character has to be performed. there was a compromise between taking the unit of hashing to be seven and reducing the size of the kmhi table by %. for the details of the method see algorithm . figure . the structures of hashing and kmhi table to be able to follow the algorithm , it is important to know what every variable is used for. variable sequence is an array of size n, indexed from zero to n- , which holds the input sequence. table kmhi is the most important variable which is a structure array of size = rows, indexed from to , that is used to hold the location, loc, core size, size, number of repeats, count, of the current potential microsatellite corresponding to this row of the table. this table is considered to be global and all its values are set to zero before entering the algorithm. in each row of the table, after the initial reference, it is always assumed that a potential microsatellite is being detected. if the next reference to this row is not exactly as much as size apart from the previous one then, up to here, is assumed to be a microsatellite, and microsatellite validation routine, msvalidation, is called to do the validation such as checking the number of repeats. otherwise, variables loc and count are updated. fmsd recognizes non-atomic tandem repeats and only reports atomic ones. for example, reporting a microsatellite with core sequence tctc with times repetition is not correct because tctc is not atomic. the correct mi-crosatellite would be tc with times repetition. cyclic repetitions are also eliminated. for example, when a microsatellite with core subsequence tcg with times repetition is reported, geneticists can easily interpret that for example, there is a microsatellite with core sequence cgt which is repeated (or ) times, and there is no need to highly increase the number of reported microsatellites. in addition, if the end of a microsatellite and the start of the next microsatellite have some nucleotides in common, fmsd is able to correctly include the overlapped nucleotides for both microsatellites. it would be the task of the interpreter to decide which one is more important. the developed method was shown to be very effective. it detects all microsatellites, everything is done in one pass of scanning the input sequence, and there is no need for preprocessing or post processing. it is very fast, and even in the worst case it is at least . times faster than the fastest state-of-the- coronavirus is associated with many properties, some of which are listed below. • all ages are susceptible with different probabilities (dong et al. ) . • the fatality rate of covid- is high (wu and mcgoogan ) . • there is no significant gender difference (dong et al. ) . • human-to-human transmission is the norm (dong et al. ). • transmissibility is higher than sars- (wu and mcgoogan ) . • as a consequence, it has forced social distancing throughout the world, and many geographic regions are experiencing a lockdown. • the commonality to all these direct and indirect properties is in its genome. in the following subsection all microsatellites of both sars- and covid- are discovered and reported. the software which is developed here is usable for all genomes of all sizes. it is accurate and exact. it discovers the microsatellites with the smallest number of repeats compared to state-of-the-art packages. it is fast while being a sequential software. since potential microsatellites are detected as the input is scanned, the method which is developed here can easily become parallel to further improve its run time and make use of all cores of computers. it is also memory efficient. since correctness and timing are the most important objectives of such algorithms, table shows the time requirement of different software for different sizes of genomes. the timing of all methods are measured with an intel xeon e - v . gigahertz processor with a gb main memory module. it is clearly notable that the time requirement of fmsd is far less than those of other algorithms. in some cases, it is times faster ,and in the worst case it is at least . times faster than the state-of-the art method. this offers a great advantage, because most genomic sequences are very long and previous methods may not be capable to perform their tasks in a tolerable period of time. the same discussion is true for main memory utilization; however, since other methods did not reported the memory utilization of their algorithms and the source codes (not the executable code) are not available, comparison is not possible. an important objective of this research is to find all microsatellites of both the sars and coronavirous-covid- , and provide the required information for the geneticist to analyze their differences towards drug discovery and vaccine production. this is done in the next subsection. *this package does not find microsatellites of size core substrings. **for some unknown reason, this package was not able to normally complete its task for some sequences. the developed software, fmsd, is applied to both sars-cov- (accession number ay . ) and the novel coronavirus-covid- (accession number nc_ . ) and the results are reported in this section. the results are shown for all microsatellites with atomic core lengths of less than or equal to . the minimum number of repeats is set to except for atomic core lengths of and which is set to and , respectively. table lists all microsatellites in both viruses. a polyadenine (polya) tail is seen in coronavirus-covid- which is absent in sars-cov- . yet the longest sequence of adenine in sars-cov- is of length which is located somewhere within the genome. in addition, the maximum length of atomic simple tandem repeats found in these two genomes were nucleotides (tgtt), which is repeated three times in sars-cov- genome and two times in coronavirus-covid- genome. this fact as well as the absence of longer microsatellites in either of the genomes suggests a selection against longer simple tandem repeats in viral genomes. another microsatellite found in both genomes is caa (poly glutamine, polyq, at protein level). it is shown that polyq is involved in transmissibility of cowpox virus, while lacking of such motif in smallpox leads to less survival of this virus (schein ) . it is worth mentioning that a point mutation in the covid- genome compared to sars-cov- genome might cause the software to find two different microsatellites in the two genomes. for example, segment ttgtgtgtgta can be read as repeats of tg or repeats of gt assuming a recent mutation from g to t at the beginning of the segment. therefore, some differences might not be as significant as they look. since covid- recently jumped from animal to human host, it has not yet adapted to its new environment; hence its genome shows a rapid dynamics perf: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large dna sequences epidemiological research priorities for public health control of the ongoing global novel coronavirus ( -ncov) outbreak title epidemiological characteristics of pediatric patients with coronavirus disease in china krait: an ultrafast tool for genomewide survey of microsatellites and primer design estimation of duplication history under a stochastic model for tandem repeats a census of tandemly repeated polymorphic loci in genic regions through the comparative integration of human genome assemblies a matter of life or death: how microsatellites emerge in and vanish from the human genome mreps: efficient and flexible detection of tandem repeats in dna features of trinucleotide repeat instability in vivo an algorithm for approximate tandem repeats genome-wide distribution of novel ta- a mini-satellite repeats and its use for chromosome identification in wheat and related species', agromomy interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing index: incremental depth extension approach for protein-protein interaction networks alignment ssaha: a fast search method for large dna databases age estimation with dna: from forensic dna fingerprinting to forensic (epi)genomics: a mini-review glutamine repeats and neurodegenerative diseases: molecular aspects' kmer-ssr: a fast and exhaustive ssr search algorithm sa-ssr: a suffix array-based algorithm for exhaustive and efficient ssr discovery in large genetic sequences identification of variable-number tandem-repeat (vntr) sequences in acinetobacter baumannii and interlaboratory validation of an optimized multiple-locus vntr analysis typing scheme genetic epidemiology of osteoporosis across four microsatellite markers near the vdr gene characterization of a novel coronavirus associated with severe acute respiratory syndrome the effect of bisphosphonate on prevention of glucocorticoidinduced osteoporosis polyglutamine repeats in viruses patterns of microsatellite distribution across eukaryotic genomes case-fatality risk estimates for covid- calculated by using a lag time for fatality characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china a pneumonia outbreak associated with a new coronavirus of probable bat origin', nature network-based drug repurposing for novelcoronavirus -ncov/sars-cov- ' the authors would like to thank dr. hassan shafiey for his generous genetics comments during the revision of the paper. dr. shafiey has received his phd in biophysics and his current research interests are computational biology and population genetics. manuscript title: developing an ultra-efficient microsatellite discoverer to find structural the authors whose names are listed immediately below certify that during the revision we have consulted dr. hassan shafiey and this is recorded in the acknowledgement section of the paper. hossein savari abdorreza savadi elahe mehrazin nayyereh saadati towards equilibrium. fmsd, as a simple and fast simple tandem repeat finder, enables biologists to keep track of the distribution and dynamics of repetitive elements in the genome of covid- , which is a great opportunity to watch the biological adaptation dynamics. as an example, repeats of cag, which codes for glutamine, is shown to be unstable (perutz tga tgtt ctt tg gt tta ttc cat ga att agt a tgt t aat ga cga aca gtg ca tgc cga caa tat ctg gtg aag caa a ctg coronavirus-covid- onset occurred at the end of , and soon after a pandemic state was declared. it acts differently than its predecessor sars-cov- which appeared in . being in the same family, it is important to explore the genomic structural differences to look for covid- 's specific behavior. there is a hope that it might help drug repurposing for symptom relief in the short term, and vaccine design in the long term. to this aim, a highly time and space efficient software called fast microsatellite discoverer, fmsd, was developed first. its performance was evaluated and reported to be superior than existing systems. a great novelty that makes fmsd suitable is analysis of genomic sequences of any lengths, whether short, long, or very long. using fmsd, all microsatellites of both sars-cov- and covid- were discovered and reported. there are many differences. although the interpretations of some of the differences are provided, further investigations are needed for possible clues to treatment and drug and vaccine design. note that tandem repeats are reported to be the cause of many diseases. the links to other software used in this project are also provided. in addition, the links to sars and covid genomes are provided at the following links: manuscript title: developing an ultra-efficient microsatellite discoverer and finding the authors whose names are listed immediately below certify that they have no affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers' bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in the research paper with the title mentioned above. hossein savari abdorreza savadi elahe mehrazin nayyereh saadati manuscript title: developing an ultra-efficient microsatellite discoverer and finding the authors whose names are listed immediately below certify that this research is in compliance with standards of research involving humans as subjects. hossein savari abdorreza savadi elahe mehrazin nayyereh saadati key: cord- -rlfsqgm authors: rha, brian title: update: severe respiratory illness associated with a novel coronavirus — worldwide, – date: - - journal: mmwr morb mortal wkly rep doi: nan sha: doc_id: cord_uid: rlfsqgm cdc continues to work closely with the world health organization (who) and other partners to better understand the public health risk posed by a novel coronavirus that was first reported to cause human infection in september . genetic sequence analyses have shown that this new virus is different from any other known human coronaviruses, including the one that caused severe acute respiratory syndrome (sars). as of march , , a total of confirmed cases of novel coronavirus infection have been reported to who, with eight deaths. illness onsets have occurred from april through february . to date, no cases have been reported in the united states. on march , , this report was posted as an mmwr early release on the mmwr website (http://www.cdc.gov/mmwr). cdc continues to work closely with the world health organization (who) and other partners to better understand the public health risk posed by a novel coronavirus that was first reported to cause human infection in september ( ) ( ) ( ) . genetic sequence analyses have shown that this new virus is different from any other known human coronaviruses, including the one that caused severe acute respiratory syndrome (sars) ( ) . as of march , , a total of confirmed cases of novel coronavirus infection have been reported to who, with eight deaths ( ). illness onsets have occurred from april through february ( , ) . to date, no cases have been reported in the united states. three of the confirmed cases of novel coronavirus infection were identified in the united kingdom (uk) as part of a cluster within one family ( ) . the index patient in the cluster, a man aged years with a history of recent travel to pakistan and saudi arabia, developed respiratory illness on january , , before returning to the uk on january ( , , ) . he was hospitalized on january with severe lower respiratory tract disease and has been receiving intensive care ( , , ) . respiratory specimens from this patient taken on february tested positive for influenza a (h n ) virus and for novel coronavirus infection ( ) . the second patient was an adult male household member with an underlying medical condition who became ill on february , after contact with the index patient, and received intensive treatment but died with severe respiratory disease ( , ) . this patient's underlying illness might have made him more susceptible to severe respiratory infection. the third patient is an adult female who developed a respiratory illness on february , following contact with the index patient after he was hospitalized ( , ). she did not require hospitalization and had recovered by february ( , ) . only the index patient had traveled recently outside the uk. based on their ongoing investigation of this cluster of illnesses, the uk health protection agency has concluded that person-to-person transmission likely occurred in the uk within this family ( ) . this recent cluster provides the first clear evidence of human-tohuman transmission of this novel coronavirus, coinfection of this novel coronavirus with another pathogen (influenza a), and a case of mild illness associated with this novel coronavirus infection. in light of these developments, updated guidance has been posted on the cdc coronavirus website (http://www.cdc.gov/coronavirus/ ncv). persons who develop severe acute lower respiratory illness within days after traveling from the arabian peninsula or neighboring countries* should continue to be evaluated according to current guidelines. persons whose respiratory illness remains unexplained and who meet criteria for "patient under investigation" should be reported immediately to cdc through state and local health departments. persons who develop severe acute lower respiratory illness of known etiology within days after traveling from the arabian peninsula or neighboring countries but who do not respond to appropriate therapy may be considered for evaluation for novel coronavirus infection. in addition, persons who develop severe acute lower respiratory illness who are close contacts † of a symptomatic traveler who developed fever and acute respiratory illness within days of traveling from the arabian peninsula or neighboring countries may be considered for evaluation for novel coronavirus infection. testing of specimens for the novel coronavirus will be conducted at cdc. recommendations and guidance on case definitions, infection control (including use of personal protective equipment), case investigation, and specimen collection and shipment for testing, are available at the cdc coronavirus website. additional information and potentially frequent updates will be posted on the cdc coronavirus website. state and local health departments with questions should contact the cdc emergency operations center ( - - ). * countries considered to be on or neighboring the arabian peninsula include bahrain, iraq, iran, israel, jordan, kuwait, lebanon, oman, palestinian territories, qatar, saudi arabia, syria, the united arab emirates, and yemen. † defined as ) any person who provided care for the patient, including a healthcare worker or family member, or who had other similarly close physical contact, or ) any person who stayed at the same place (e.g., lived with or visited) as the patient while the patient was ill. novel coronavirus associated with severe respiratory disease: case definition and public health measures isolation of a novel coronavirus from a man with pneumonia in saudi arabia severe respiratory illness associated with a novel coronavirus-saudi arabia and qatar world health organization. global alert and response (gar): novel coronavirus infection-update rapid risk assessment: severe respiratory disease associated with a novel coronavirus update on family cluster of novel coronavirus infection in the uk. london, united kingdom: health protection agency health protection agency. case of novel coronavirus identified in the uk. london, united kingdom: health protection agency european centre for disease prevention and control. epidemiological update: case of severe lower respiratory tract disease associated with a novel coronavirus further uk case of novel coronavirus. london, united kingdom: health protection agency third case of novel coronavirus infection identified in family cluster key: cord- - s ki g authors: ziebuhr, john title: sars – unprecedented global response to a newly emerging disease date: - - journal: international journal of medical microbiology doi: . / - - sha: doc_id: cord_uid: s ki g abstract no abstract int. j. med. microbiol. , ± ( ) ¹ urban & fischer verlag http://www.urbanfischer.de/journals/ijmm editorial sars ± unprecedented global response to a newly emerging disease severe acute respiratory syndrome (sars) is a life-threatening form of pneumonia that is characterized by fever, chills, myalgia, dry cough, and progressing lung infiltrates (nicholls et al., ; peiris et al., a) . in a substantial number of patients, diarrhea develops in the course of infection. the disease-associated hypoxemia often requires mechanical ventilation. both the high mortality rate associated with the disease and the ease of transmission by aerosols (and likely also the fecal-oral route) requires extreme infectioncontrol measures to prevent further spread of the disease. within only few weeks (february-april ) , sars spread from its likely origin in guang dong province, china, to as much as countries. like in many other infectious diseases, the rapid spread was facilitated by the mobility of contemporary society (including air-travel) and densely populated urban areas. as of june , the world health organization (who) reported cases with deaths. in contrast to the initial phase of the outbreak in which there was a serious danger of a worldwide pandemic, there is now cautious optimism that the outbreak may be contained. without doubt, this is the result of heroic public health efforts to reduce transmission, particularly in the most affected countries, such as china and singapore. however, even though the numbers of new sars cases have dropped substantially over the past three weeks, there is no reason for complacency or negligence. the ongoing epidemic is only the latest in a long list of emerging viral diseases, which all teach us lessons. the current epidemic, however, is unprecedented in several respects. thus, thanks to the advances in molecular diagnostics and the joint efforts of an extraordinary network of laboratories coordinated by the who, the identification of the causative agent of sars, a novel coronavirus designated sars coronavirus (sars-cov), was achieved within only two weeks ksiazek et al., ; peiris et al., b) . again two weeks later, the genomes of two sars-cov isolates, toronto- and urbani, had been completely sequenced (marra et al., ; rota et al., ) and, to date, many other sars-cov sequences have been deposited with public databases. cell culture-grown sars-cov was subsequently shown to cause lower respiratory tract disease in monkeys, fulfilling koch's postulates and providing strong evidence for the novel coronavirus being the cause of sars . because of the large phylogenetic distance to previously known coronaviruses, sars-cov cannot easily be assigned to any of the established coronavirus groups, and recombination between known coronaviruses could be excluded as a possible source of sars-cov. it rather seems likely that the ancestor of sars-cov is an animal coronavirus. consistent with this hypothesis, yuen and colleagues recently isolated a coronavirus from masked palm civets sold in a market in guangdong (enserink, ) . apart from a -nucleotide insertion converting two small orfs in the '-region of the sars-cov genome to one continuous orf, the civet virus was almost identical to sars-cov. more samples are needed to answer the question of whether or not civets are the true origin of the human virus or just got the virus from yet another species, for example by food. interestingly, there is one human isolate, gz , that also carries the extra nucleotides (ruan et al., ) . the patient from which this virus was isolated may have been an early sars case, and it is possible that the deletion found in all other isolates is a result of adaptation of the ancestral virus to humans. despite considerable progress in recent years, the molecular characterization of the coronavirus life cycle is still at a relatively early stage. this is mainly due to the unparalleled size of the coronavirus rna genome which, until recently, has made the devel-opment of reverse genetics systems a major challenge. coronaviruses feature an (among rna viruses) unparalleled complexity in the regulation of their gene expression and they encode a series of (mainly uncharacterized) enzymes not found in other virus families. it can be anticipated that our general understanding of the unique features of coronavirus replication will benefit from the numerous ongoing studies on the biology of sars-cov. only few weeks after the outbreak, the concerted global efforts have resulted in the identification of first coronavirus enzyme inhibitors (anand et al., ; xiong et al., ) that are hoped to be useful for the development of anti-sars drugs. in the future, coronavirus-specific antivirals might also be used to treat common colds in humans and severe animal coronavirus infections, such as feline infectious peritonitis, a fatal disease of cats for which no safe vaccine or therapy is available. obviously, there is also an urgent need to develop sars-cov vaccines, and corresponding efforts are already well underway. in this respect, it should be noted that sequence analysis of multiple sars-cov isolates revealed a remarkable genetic conservation of sars-cov since the outbreak was first documented in february, indicating that the development of vaccines is feasible (ruan et al., ) . however, there is also a number of potential problems that might complicate the development of vaccines, such as the lack of protective immunity in some coronavirus infections, persistent infection and antibodymediated enhancement. it remains to be investigated to which extent these issues also apply to sars-cov or even contribute to the high mortality rate associated with sars. in fact, evidence is now accumulating that, later in infection, lung damage may be caused primarily by the host immune response rather than uncontrolled viral replication (peiris et al., a) . the direction of sars research is now increasingly changing from identification and sequence analysis to other topics, such as the origin of sars-cov, routes of transmission, mechanisms of virulence, viral gene expression (thiel et al., ) , and development of vaccines and antivirals. the period of grace until the next major outbreak will hopefully provide answers to the most urgent questions, which may then allow to combat sars successfully. coronavirus main proteinase ( cl pro ) structure: basis for design of anti-sars drugs identification of a novel coronavirus in patients with severe acute respiratory syndrome infectious diseases. clues to the animal origins of sars aetiology: koch's postulates fulfilled for sars virus sars working group: a novel coronavirus associated with severe acute respiratory syndrome the genome sequence of the sars-associated coronavirus lung pathology of fatal severe acute respiratory syndrome hku/uch sars study group: clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study sars study group: coronavirus as a possible cause of severe acute respiratory syndrome characterization of a novel coronavirus associated with severe acute respiratory syndrome comparative full-length genome sequence analysis of sars coronavirus isolates and common mutations associated with putative origins of infection mechanisms and enzymes involved in sars coronavirus genome expression a d model of sars-cov cl proteinase and its inhibitors design by virtual screening key: cord- - ioiwsd authors: varghese, praveen mathews; tsolaki, anthony g.; yasmin, hadida; shastri, abhishek; ferluga, janez; vatish, manu; madan, taruna; kishore, uday title: host-pathogen interaction in covid- : pathogenesis, potential therapeutics and vaccination strategies date: - - journal: immunobiology doi: . /j.imbio. . sha: doc_id: cord_uid: ioiwsd abstract the current coronavirus pandemic, covid- , is the third outbreak of disease caused by the coronavirus family, after severe acute respiratory syndrome and middle east respiratory syndrome. it is an acute infectious disease caused by severe acute respiratory syndrome coronavirus virus (sars-cov- ). the severe disease is characterised by acute respiratory distress syndrome, septic shock, metabolic acidosis, coagulation dysfunction, and multiple organ dysfunction syndromes. currently, no drugs or vaccine exist against the disease and the only course of treatment is symptom management involving mechanical ventilation, immune suppressants, and repurposed drugs. as such the severe form of the disease has a relatively high mortality rate. last months have seen an explosion of information related to the host receptors, virus transmission, virus structure-function relationships, pathophysiology, co-morbidities, immune response, treatment and most promising vaccines. this review takes a critically comprehensive look at various aspects of host-pathogen interaction in covid- . we examine genomic aspects of sars-cov- , modulation of innate and adaptive immunity, complement-triggered microangiopathy, and host transmission modalities. we also examine its pathophysiological impact during pregnancy, in addition to various gaps in our knowledge. the lessons learnt from various clinical trials involving repurposed drugs have been summarised. we also highlight the rationale and likely success of the most promising vaccine candidates. receptor on enterocytes in the small intestine and is consistent with clinical reports of gastrointestinal symptoms and viral shedding in faeces ( , ) . this has been further resolved with the comprehensive identification of host cells/tissues expressing both ace and tmprss ( figure ). thus, likely targets for sars-cov- primarily include secretory goblets of the nasal mucosa, lung type ii pneumocytes and absorptive erythrocytes of the small intestine ( ) . of note, this study also showed that the ace receptor is an interferonstimulated gene in sars-cov- infection in the cells of the human upper nasal epithelium and lung, predominatly mediated by ifn-α and ifn-γ ( ) . moreover, bystander cells are subject to interferon-mediated effects (upregulation of ace receptor) rather than sars-cov- infected cells, suggesting a mechanism of enhanced viral targeting and entry during pathogenesis and a possible avenue for therapeutic intervention ( ) . analysis of genetic variation in the ace gene has identified single nucleotide polymorphisms (snps) that differ in frequency globally among the human population, particularly between males and females ( ). characterising these snps more fully with epidemiological and clinical data on covid- will in time shed light on the precise molecular mechanisms of transmission and disease. furthermore, in the sars-cov- viral s protein, amino acid substitutions have been described, although these occurred outside the rbd that directly interacts with ace ( ) . of paramount importance is characterising the genetic variation and its consequences in the s protein and its rbd, as this will determine whether the sars-cov- virus is evolving and is likely to be a seasonal infection with new variants for the human population. undoubtedly, variation in the s protein and ace , the central interface of hostpathogen interaction in covid- will have evolved from natural selection contributing to the pathogenesis of this disease. proteins and transported into the endoplasmic reticulum (er). these proteins are processed via the secretory pathway and are transported into the er-golgi intermediate compartment ( , ) , where the full-length viral genomes are packaged with the nucleocapsid n protein, budding from the membrane, and thus forming the enveloped mature virion ( ) . the n protein has two domains that can bind the rna genome, with the aid of nsp protein, and attaching it to the rtc, facilitating the packaging of the virus ( ) ( ) ( ) . the viral m protein has three transmembrane domains and is responsible for the majority of protein-protein interactions needed for virus assembly, including membrane curvature and binding the nucleocapsid ( , ) . pseudo-virus particles can also only be formed when there is a co-expression of m protein and e protein, indicating the requirement of both these two proteins to form the coronavirus envelope ( ) . the viral e protein is also involved in structural shaping of the viral membrane envelope and in inhibiting m protein aggregation, as well as a role in pathogenesis ( ) ( ) ( ) ( ) . after the assembly of the mature virions, they are transported in vesicles, where they are released from the infected cell via exocytosis ( ) . unlike sars, covid- patients had the highest viral load near presentation, which could account for the fast-spreading nature of this epidemic. in a study involving covid- patients in hong kong recorded high viral load on presentation with the onset of symptoms and also when the symptoms are mild ( ) . sars cov- viral rna load was detected in the deep throat (posterior oropharyngeal) saliva samples for days or even longer. the peak of the viral load correlated positively with age. viral load in posterior oropharyngeal saliva samples was higher during the first week of symptom onset, which gradually declined. thus, the location of sample collection and the timing for the onset of symptoms both are important factors to be considered for the detection of sars cov- positive cases. in the same study, most of the patients showed rising antibody titres days after symptom onset, though the serum antibody levels did not show correlation with clinical severity ( ) . the patient's antibody to sars-cov- viral nucleocapsid protein using infected cell lysates was identified on the th day after symptom onset by western blot ( ) . in another study involving patients with covid- , all were tested positive for antiviral igg within days after symptom onset. both igg and igm titres reached a plateau within days after seroconversion ( ) . in wuhan tongji hospital, around convalescent patients tested positive for the igg against the virus, while patients tested negative for igm, where igg titre was higher comparatively. both the antibody titres showed a decrease when tested weeks apart ( ) . thus, titres of sars-cov- antibodies can reflect the progress of viral infection and can be a vital component to understand the development and prognosis of the disease and similarly timing of antibody seroconversion is also crucial for determining the optimum duration for collecting serum specimens for antibody diagnosis. as previously mentioned, several other studies also confirmed the presence of sars-cov- nucleic acids in the faecal, urine samples and rectal swabs of covid- patients and thus it becomes essential to ascertain viral load dynamics in such samples too ( ) ( ) ( ) . transmission sars-cov- is transmitted through "respiratory droplets", which are large droplets of virusladen mucus or through close contact with infected individuals ( ) ( ) ( ) ( ) . at the same time virus has also been reported to spread via asymptomatic but infected individuals in several countries, including china, germany, usa, and india ( , ( ) ( ) ( ) ( ) . a systematic review and meta-analysis of observational studies with no randomised controlled trials and relevant comparative studies in health-care and non-health-care settings revealed transmission of virus decreased as physical distancing increased to metre or more ( ) . eye protection, n or similar respirators in health-care settings and - -layer cotton or surgical masks in the community were found to greatly control the transmission ( ) . studies have also established that the median half-life of the aerosolised virus is ~ . hours under lab conditions, similar to the sars-cov. however currently, no evidence supports real-world airborne transmission of the virus through aerosols ( ) . sars-cov- was found to remain viable for up to hours on copper surfaces, up to hours on cardboard surfaces, and up to hours on plastic and stainless-steel surfaces. thus, there exists a possibility of contact transmission to occur, although no confirmed cases of contact transmission have been reported ( ) . the virus was also found in the faeces of infected patients showing that the virus can survive and replicate in the digestive system ( ) . this suggests that there may be a possibility of an oral-faecal route of transmission, though again no confirmed cases have been reported ( ) . the royal college of obstetricians and gynaecologist uk have reported that transmission from mother to baby antenatally or intrapartum is possible although this requires further study for confirmation; there appears to be no evidence supporting vertical transmission to the foetus ( ) ( ) ( ) . additionally, as reported by who and cdc, the virus has not been found to be transmitted by breastfeeding and has not been found in breastmilk of covid- mothers ( , ) . covid- was found to have low severity and mortality than sars, but it is highly contagious and affecting comparatively more men than women ( , , ) . the difference in fatality rate between males and females may probably be explained by the fact that as ace is located on the x chromosome. there may be alleles that confer resistance to covid- , at the same time, oestrogen and testosterone sex hormones have different immunoregulatory functions that may contribute to protection or severity of the disease ( , ) . the disease has also been found to disproportionately affect older aged persons and people suffering from social deprivation, diabetes, severe asthma, cardiovascular disease, obesity, haematological malignancy, recent cancer, kidney, liver, neurological or autoimmune conditions ( ) . studies have also reported that members of minority communities such as the black and south asian populations, are at a higher risk of the disease ( ) . the incubation period of the disease ranges between to days and the median incubation period is approximately - days before symptom onset ( , , , ) . during the onset of the illness, the common symptoms that most patients exhibited were fever and cough. other symptoms include conjunctivitis, myalgia (muscle pain) or fatigue, headache, dyspnoea (short of breath), chest pain, diarrhoea, nausea, rhinorrhoea (runny nose), vomiting, loss of appetite, abdominal pain, gastrointestinal bleeding, autoimmune haemolytic anaemia, and sometimes haemoptysis (coughing of blood) ( , ( ) ( ) ( ) ( ) ( ) . patients have also reported anosmia (loss of smell), dysgeusia (distortion of the sense of taste) ( ) ( ) ( ) ( ) . for sars-cov- asymptomatic patients, anosmia, hyposmia, or dysgeusia are symptoms that were suggested for screening ( ) . in addition to these, neurological manifestations such as dizziness, headache, impaired consciousness, acute cerebrovascular disease, ataxia, seizure, nerve pain, skeletal muscular injury manifestations, intracerebral haemorrhage, central nervous system vasculitis, encephalopathy, encephalitis, cranial neuropathies and psychosis were reported predominantly in older people ( ) ( ) ( ) . in paediatric patients, an autoimmune and autoinflammatory disease, paediatric inflammatory multisystem syndrome (pims), also known as multisystem inflammatory syndrome in children (mis-c), has been reported to occur after sars-cov- infection ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . cutaneous manifestations of covid- have also been reported ( ) ( ) ( ) . a case report from strasbourg, france reported purpuric lesions in the lower extremity ( ) . an italian study reported patients presenting with an erythematous rash, urticaria and chickenpox-like vesicles mainly in the trunk with little or no itching that did not correspond to disease severity ( ) . the prolonged use of personal protective equipment and repeated washing have also led to an increase in dermal conditions such as pressure injury, contact dermatitis, itch, pressure urticaria, and exacerbation of pre-existing skin diseases ( ) . the first step of infection is the inhalation of viral particles present in respiratory droplets from an infected host. once inhaled, the virion enters the nasal cavity of a healthy host and likely binds to goblet and ciliated cells in the nose that express ace ( ) . at this time, a limited innate immune response may occur, and the virus replicates and moves further down the respiratory tract via the conducting airways. as the virions proliferate and spread towards the upper respiratory tract, usually a robust innate immune response is triggered by the detection of the virions by pattern recognition receptors (prrs) like toll-like receptors, rig- , and mda- . this may present several symptoms starting from dysphonia (hoarseness), ulceration of the epiglottis and subglottis, and profound oedema and granulations in the subglottis and also in the upper trachea ( ) . in a few patients, mild tachypnoea and coarse breath sounds were also observed while the virus is in the upper airway ( ) . furthermore, the detection by prr leads to the expression of type interferons (ifn) in the early stages of infection, which helps establish an anti-viral state in the cells by producing inflammatory cytokines and chemokines. the sars-cov produces an enzyme that adds ' o-methyl group to viral rna, which helps it evade detection by mda- , thereby delaying the induction of ifn. studies have established that unlike an early ifn response, a delayed ifn response causes an inability to control viral replication, leading to cellular damage of airway epithelia and the lung parenchyma and an eventual lethal inflammatory cytokine storm ( ) ( ) ( ) . the sars-cov- papain-like protease, which is essential to generate the rtc, has been shown to preferentially cleave the ubiquitin-like protein isg from interferon responsive factor (irf ), attenuating type i interferon responses ( ) . the c-terminus of the sars-cov- non-structural protein was reported to bind to the s ribosomal subunit and block the mrna entry tunnel ( ) . this obstruction effectively inhibits the rig-i-dependent innate immune response ( ) . accordingly, no significant expression of ifn was detected up to hours post-infection with sars-cov- . only il- , which correlates with respiratory failure, acute respiratory distress syndrome (ards), and adverse clinical outcomes were upregulated. monocyte chemoattractant protein- (mcp ), c-x-c motif chemokine (cxcl) , cxcl , and cxlc , were also upregulated h post-infection with sars-cov- ( ) . the suppression of innate immune activation and annihilation of t cells can help explain the mild or even the lack of symptoms in many infected patients. the increased viral replication efficiency in the respiratory tract early on leads to the highly efficient person-to-person transmission of the virus in the community ( ) . the virions further migrate towards the lower respiratory tract and reaches the alveoli where it binds to the type pneumocytes and begins replication. as the type pneumocytes undergo apoptosis after viral release, they secrete inflammatory mediators like cxlc proteins that attract macrophages and neutrophils ( figure ) ( ) . the stimulated macrophages further secrete cytokines such as il- β, il- and tumor necrotic factor α (tnf-α). the released cytokines trigger a "cytokine storm", which stimulates the release of vascular endothelial growth factor (vegf), monocyte chemoattractant protein- (mcp- ), il- , and additional il- , as well as reduced e-cadherin expression on endothelial cells causing vasodilation and increase capillary permeability ( ) . this causes the plasma to leak into the interstitial spaces and alveoli, increasing interstitial and alveolar oedema. the increased alveolar oedema decreases the level of surfactant in the alveoli. this causes an increase in the surface tension in the alveoli, which leads to alveolar collapse. oedema and alveolar collapse may present as multiple peripheral ground-glass opacities in subpleural regions of both lungs, which is observed in many patients ( ) . chest ct scan of patients also revealed bilateral multifocal infiltrates and mediastinal and hilar lymphadenopathy in some patients ( ) . these decrease the gas exchange efficiency causing hypoxemia and increased work of breathing presenting as dyspnoea (shortness of breath), culminating in ards ( ) . abnormal coagulation parameters, mainly elevated d-dimers seem to be associated with a higher risk of development of ards in covid- patients ( ) . the aberrant wound healing may even lead to fibrosis than other forms of ards ( ) . stimulated neutrophils secrete reactive oxygen species (ros) and proteases which destroy both infected and uninfected type and type pneumocytes, leading to further reduced gas exchange and alveolar collapse, respectively ( ) . furthermore, the dead pneumocytes slough off into alveoli filling them up with fluid, protein deposits, cell debris, macrophages, and neutrophils. this causes pulmonary consolidation, which leads to altered gas exchange and causes hypoxemia ( , ) . the consolidation also leads to productive cough. the hypoxemia can further trigger chemoreceptors that stimulate the sympathetic nervous system (sns) that causes tachycardia (increased heart rate) and tachypnoea (increased respiratory rate) ( , ) . the central nervous system (cns) is also affected by the high concentrations of il- β, il- and tnf-α in the blood, as these cytokines stimulate the hypothalamus to release prostaglandins such as pge , which causes an increased body temperature leading to fever ( ) . studies have also reported elevated levels of myeloperoxidase (mpo)-dna and citrullinated histone h (cit-h ), which are markers used to detect neutrophil extracellular traps (nets), in the serum of covid- patients ( ) . furthermore, control neutrophils treated with covid- patient serum exhibited netosis ( ) . nets, while protecting the host from invasive pathogens, have been attributed to play a role in many autoimmune and vascular diseases. for example, nets are known to contribute to ards, pathogen-induced acute lung injury, thrombosis and can contribute to further cytokine release lading to the inflammation ( ) . an increased frequency of neutrophils, eosinophils and monocytes was reported in severe covid- positive patients; severe patients showed further increase in neutrophils though their activation status had not altered. there was no significant change in the immature granulocyte frequencies. however, there was an inverse correlation between frequency of immature granulocytes in moderate and severe patients with the duration since the appearance of symptoms. severe patients exhibited lower percentages of both conventional and plasmacytoid dendritic cells (dc) ( ) . response syndrome (sirs). the spread of the inflammation from the lungs into the circulatory system causes increased capillary permeability within the systemic circulation. this leads to a decrease in blood volume along with increased vasodilation of systemic arteries, leading to decreased peripheral resistance. the decreased blood volume, along with peripheral resistance, causes hypotension (decreased blood pressure), which decreases perfusion to other organs leading to multisystemic organ failure (mof) ( - ). the cytokine storm has also been shown to trigger autoimmune haemolytic anaemias (aiha) (with warm or cold antibodies) ( , , ) . most of the studies report manifestation of aiha early, during the active phase of covid- (within to days), a timeframe matching that of the cytokine storm ( , , , ) . as a result of ards, sirs and mof, patients suffering from severe sars-cov- infection exhibit significantly elevated levels of, il- , il- , il- , g-csf, gm-csf, mip- α, crp, and ddimer, in addition to il- , il- β and tnf-α ( ). there are reports suggesting that in addition to the lungs, sars-cov- infection may induce the multiorgan injury in patients involving brain, heart, liver, kidney, intestine and eyes ( , ) . covid- associated neurological complications the neurological pathologies observed in covid- are similar to those observed in previous coronavirus epidemics ( ) . myoclonus and demyelination are reported in a few cases ( , , ) . a study conducted in wuhan, china involving covid- patients, reported that patients developed neurological manifestations ( ) . in another study from strasbourg, france where effectively patients were recruited for an observational study, reported agitation in % of the patients, confusion in %, and % of the patients had corticospinal tract signs ( ) . a systemic review and meta-analysis of literature databases for psychiatric and neuropsychiatric presentations in coronavirus infections reported transient encephalopathies with features of delirium and psychosis ( ) . the study also reported cognitive dysexecutive syndrome and delirium with agitation in a few cases ( ) . there is also a reported case of autoimmune encephalitis with the typical clinical features of opsoclonus and myoclonus, and another case of autoimmune encephalitis with a radiological imagery showing typical limbic encephalitis ( ) . the exact mechanism for encephalopathy may be multifactorial (effect of sepsis, hypoxia, and/or cytokine storm) ( ) . a few cases of guillain-barré syndrome (gbs) associated with sars-cov- have been reported from italy ( ) . however, further epidemiological and mechanistic study is required to confirm the incidents of gbs in covid- . the binding of the virus to the ace- receptors on endothelial cells causes extravasation of red blood cells leading to cerebral microbleeds ( , ) . there have also been reports of severe strokes in covid- patients, but further study is required to determine its association with covid- ( ) . magnetic resonance imaging (mri) revealed abnormalities such as meningeal enhancement, ischaemic stroke, perfusion changes, microhaemorrhages, medial temporal lobe signal abnormalities similar to that seen in viral or autoimmune encephalitis ( , ) . very few cases have been reported where sars-cov- was detected in csf and its supportive histopathological features; no reports of the virus in the brain exist yet ( , , ) . thus, it is important to establish whether the above-described syndromes may be caused due to either direct viral injury, hyperinflammation, vasculopathy and/or coagulopathy, autoantibody production to neuronal antigens, sepsis and hypoxia, or a combination of these ( ) . out of the first patients diagnosed with covid- in wuhan, of them had myocardial injury associated with the sars-cov- , which mainly manifested as an increase in highsensitivity cardiac troponin i ( ) . the hemogas analysis showed hypoxia; laboratory tests showed elevation of c-reactive protein, transaminases and lactate dehydrogenase, and lymphopenia ( ) . several patients showed abnormal myocardial zymogram, showing high levels of creatine kinase ( ) . because of an excessive inflammation, hypoxia, immobilisation and diffuse intravascular coagulation (dic), covid- patients may predispose to both venous and arterial thromboembolic disease ( , , ) . it has also been observed that concomitant acute thrombosis of the abdominal aorta and pulmonary embolism induces cardiovascular complications in covid- patients, suggesting an association of hypercoagulable condition with the disease ( ) . covid- patients with abnormal liver function were also documented, where patients had alanine aminotransferase (alt) or aspartate aminotransferase (ast), bilirubin, acute phase recants (apr) like crp, fibrinogen and il- above the normal range ( , ) . sepsis, hypovolaemia, and nephrotoxins were found to be important contributors to kidney damage in covid- patients. cardiorenal syndrome, particularly right ventricular failure, might lead to kidney congestion and acute kidney injury in covid- patients ( ) . symptoms such as olfactory and gustatory dysfunctions were also found to be related to covid- ( ) . sars-cov- , facilitated by tmprss and tmprss , was found to infect and reproduce in ace- + mature enterocytes ( ) . however, the virions released into the intestinal lumen were inactivated by stimulated human colonic fluid and no infectious virions were recovered in stool samples, in spite of the presence of viral rna in stools. this study thus established the intestine as a site of viral replication and its effect on local and systemic illness and overall covid- progression ( ). as in the case respiratory infections by respiratory syncytial virus and sars-cov, the eyes have been shown to act as a portal of entry for the virus. while there have been no reports of sars-cov- transmission in humans via ocular tissues, further studies are required to exclude the eyes as a source of infection and as a portal of entry. moderate conjunctivitis could be the first sign of severe respiratory distress in covid- patients ( ) . studies from china on patients with covid- reported conjunctivitis and other ocular manifestations, such as epiphora, conjunctival congestion, or chemosis in patients with severe covid- ( ) ( ) ( ) ( ) . the studies also reported a few patients with positive conjunctival swab for covid- determined by rt-pcr ( , , ) . similar results were also reported in a study conducted by the national institute for infectious diseases in rome, italy ( ) . in addition to the conjunctivitis, the ocular swabs were positive for sars-cov- even when nasopharyngeal swabs tested negative for the virus. this suggests that the conjunctiva may sustain viral replication for an extended period of time ( ) . there are reports from france, italy, united kingdom and the united states of america, suggesting the presentation of autoimmune and auto inflammatory diseases in children, especially in children of african descent, such as paediatric inflammatory multisystemic syndrome (pims), also known as, multisystemic inflammatory syndrome in children (mis-c) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . this syndrome includes kawasaki-like disease, kawasaki disease shock syndrome, toxic shock syndrome, myocarditis and macrophage activation syndrome ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . the exact cause for kawasaki disease remains unknown; however, it is believed that it is caused by an apparent atypical immune response to pathogens in genetically predisposed individuals ( ) ( ) ( ) . previous studies have implicated the pathogenesis of kawasaki disease with the infection of certain members of the coronavirus family ( , ) . the temporal association between the beginning of covid- , sars-cov- infection and the onset of pims suggest a causal link ( ) . this is further supported by the fact that in most cases, the patients exhibiting pims tested positive for igm or igg sars-cov- antibodies ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . the presence of igg antibodies clearly indicates a delayed onset of pims following sars-cov- infection ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . the onset of pims occurred - weeks after acute covid- ( ) . the patients presented with fever, diffused skin rashes, rash/oedema of hands and feet, conjunctivitis, dry cracked lips, cervical lymphadenopathy and arthritis. the kawasaki-like disease caused by covid- exhibited a few differences in both clinical and biochemical features from patients suffering from kawasaki disease without sars-cov- infection. clinically, the patients suffering from covid- associated kawasaki-like disease were older and the disease occurred in both sexes, unlike the classical kawasaki disease that occurs in younger male children ( ) . the covid- associated kawasaki-like disease also had a higher incidence of abdominal pain and/or more frequent diarrhoea, meningeal and respiratory involvement, and a strikingly different myocarditis severity and frequency when compared to classical kawasaki disease ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . biochemically the patients exhibited leukopenia with thrombocytopenia, increased ferritin, elevated myocarditis markers and high levels of procalcitonin, crp and cytokines were observed when compared to classical kawasaki disease ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . nearly % patients also showed resistance to the initial treatment with intravenous ivig infusion, and required a second infusion for successful treatment ( , ) . while the children exhibited the devastating effects of the cytokine storm associated with covid- , such as heart failure, pneumonia, gastrointestinal, neurological and renal manifestations, the paediatric patients in the french study rarely had respiratory manifestations ( ) . this suggests a different host immune response in children compared to adults. treatment for pims involves the administration of il- receptor antagonist, il- receptor blockers such as tocilizumab or sarilumab, ivig, and steroids or biologics to control inflammation ( , ) . covid- is known to affect older members of the population disproportionately, with adults over the age of years making up to % of hospitalization and having a -fold greater risk of death ( , ) . one possible explanation for this could be the increased baseline inflammation, called inflammaging, commonly observed in individuals over the age of ( ) . studies have shown increased baseline serum concentrations of crp and cytokines such as il- and il- ( ) . inflammaging could be the result of the accumulation of mis-folded proteins, compromised gut barrier, obesity and impaired clearance of dead or dying cells ( , ) . senescent nonlymphoid cells have been known to secrete inflammatory cytokines, chemokines, growth factors, and matrix metalloproteinases ( , ) . this increased baseline inflammation inhibits antigen-specific immunity affecting the efficacy of many vaccines ( ) . studies have shown that treatment with rapamycin, mapk inhibitor or steroids reduces this excessive inflammation and enhances vaccine efficacy ( , , ) . in case of covid- , this baseline inflammation may itself not be detrimental but contributes to the initiation of an inflammatory cascade that ends in the deadly cytokine storm ( ) . furthermore the accumulation of senescent cells in the lungs of older patients could inhibit t cell response, induce nkr ligand expression, which marks the cells for elimination by infiltrating t cells expressing nkrs ( ) . as observed in the case of vaccines against other respiratory viruses, inflammaging may reduce the efficacy of covid- vaccinations in this already disproportionately affected group. as with any infection, both the innate and adaptive arms of the immune system are required to mount a successful defence against a viral incursion. in case of covid- , a decrease in the circulating t helper cells (cd + cells), cytotoxic t cells (cd + cells), b cells, natural killers cells, lymphocytes, monocytes, eosinophils and basophils has been reported ( , , , ) . a retrospective, single-centre study involving patients revealed a significant decrease in the total number of regulatory t cells, memory t cells and suppressor t cells ( ) . the study also reported an increase in the percentage of naïve t cells ( ) . as naïve t cells help respond to novel pathogens that the immune system has not yet encountered by managing release of cytokines, this may help explain the hyperinflammation ( ) . the lower levels of memory t cells reported may also explain the relapses reported in covid- convalescent individuals ( ) . direct infection of thp- cells, human peripheral blood monocyte-derived macrophages and dendritic cells by mers-cov and infection of t cells and macrophages by sars-cov has been reported ( , ) . hence, it can be speculated that sars-cov- may also infect monocytes and macrophages by a mechanism that is yet to be elucidated ( ) . receptors such as cd on the surface of t cells and other immune cells may mediate viral entry ( ) . the clinical trial with anti-cd monoclonal antibody, meplazumab, showed promising efficacy and safety in covid- patients ( ) . however, cd did not show a direct interaction with the s protein of sars-cov- ( ) . similarly, lymphopenia can be attributed to sars-cov- direct infection and lymphocyte death, destruction of the lymphatic organs, and/or high levels of the programmed cell death protein (pd- ) on cd + t cells (which is known to trigger t cell exhaustion) ( , , ) . lymphocytopenia, neutrophilia and neutrophil-to-lymphocyte ratio are being used as a predictor for the severity of the illness during early stages of infection and a poor outcome in covid- ( , , , ) . this further alludes to the hyper-inflammatory nature of covid- . furthermore, covid- patients were reported to have elevated serum levels of highsensitivity c-reactive protein and procalcitonin, whose levels have been associated with high risks of mortality and organ injury ( ) . lower percentage and count of cd + , cd + , and cd + lymphocytes populations serve as a prognostic marker for mortality, organ injury, and severe pneumonia ( ) . sars-cov exposed as well as a subset of non-exposed people exhibit a cross-reactive t cell repertoire ( ) . studies have also reported the presence of sars-cov- spike glycoprotein-reactive cd + t cells in peripheral blood of a subset of donor who were not infected with sars-cov- ( , ) . these s reactive cd + t cells were found to primarily react with the c-terminal of the s epitope ( ) . this binding preference could be attributed to the presence of overlapping human coronavirus mhc-ii epitopes in the c-terminal domain. hence, these cd + t cells are cross reactive clones generated during previous infections with endemic human coronavirus ( ) . a long-term information and knowledge for ageing -camden' (linkage) sub-study is currently underway to study if pre-existing antibodies and specific t cells contribute to the devastating effect observed in old people ( ) . the b cell response occurs alongside the t helper cell response (~ week post infection) in covid- patients and helps mount a humoral response via antibodies that would help neutralise the virus ( ) . characterisation of the transcriptome during the recovery stage of the disease revealed significantly lower levels of naive b cells, while plasma b cell levels had increased in peripheral blood mononuclear cells ( , ) . it was found that a certain subset of patients who contract the disease may not develop long-lasting antibodies against the pathogen; it is possible that these patients may be susceptible to the re-infection ( ) . immune cell profiling of covid- patients in the recovery stage by single-cell sequencing has identified several new b cell-receptor changes such as ighv - and ighv - , and isotypes used earlier for vaccine development including ighv - , ighv - , and igkv - ( ) . the strongest pairing frequencies, ighv - -ighj , has been suggested to indicate a monoclonal state associated with sars-cov- specificity ( ) . antibodies analysed from the serum of covid- patients revealed no cross-reactivity with the s subunit of the sars cov spike antigen, while some reactivity was observed between the nucleocapsid antigens of sars-cov and sars-cov- ( ) . the rbd-specific igm and igg antibodies were significantly elevated in the severe and recovered patients ( ) . investigations conducted on covid- recuperating rhesus macaque models, re-infected with sars-cov- , reported no measurable viral spreading, clinical manifestations, or histopathological changes associated with covid- ( ) . the study found lower viral loads in nasopharyngeal or anal swabs or days after reinfection, compared to the recorded viral loads or days after the initial infection with sars-cov- at similar sites. similarly, increased levels of leukocytes and neutrophils were recorded days after reinfection, compared to the levels measured during the initial infection. significantly higher specific antibody titres were recorded day post reinfection. there were also increased activation of cd + t cells, changes in cd + tcm cells and memory b cells. thus, increased production of neutralising antibodies protected the primates against covid- re-infection ( , ) . a study on covid- convalescent individuals revealed that plasma collected after days of symptom manifestation had a variable half-maximal pseudovirus neutralizing titres of less than : in %, below : , in %, and only % showed titres above : , ( ) . interestingly, in spite of the low titres reported, antibodies specific to three distinct epitopes on the rbd of the sars-cov- s protein neutralized at half-maximal inhibitory concentrations as low as single digit ng/ml ( ) . hence, a vaccine that can elicit the production of such highly potent antibodies, or monoclonal antibodies raised against the rbd of the sars-cov- s protein, may be highly protective. however, studies on sars-cov and mers-cov revealed that neutralizing antibodies to s protein can potentially augment severe lung injury by exacerbating inflammatory responses ( , ( ) ( ) ( ) . hence, therapeutic antibodies should be carefully studied to minimise any unwanted pro-inflammatory activity while retaining maximum virus neutralizing capacity. additional specific insights on the intracellular life cycle have also been gained from nextgeneration sequencing (ngs) studies on the transcriptome and epi-transcriptome profile of sars-cov- virus and infected host cell. this fundamental approach has given an insight into the specific molecular dialogue between the pathogen and the host cell. this dialogue is complex. the sars-cov- transcriptome has been studied in high resolution. it has revealed its highly complex nature, mainly as a result of numerous discontinuous transcription events, revealing canonical and non-canonical rna transcripts with rna modifications ( ) . in addition to the canonical full-length genome and other sgrnas, this study also found numerous non-canonical rna transcripts of unknown orfs that contained rna modifications. putative rna medications were identified at an aagaa motif. these previously unknown orfs represent the epi-transcriptome of sars-cov- and has revealed numerous viral transcripts that may be involved in pathogenesis ( ) . another study looked at transcriptome profiling in the primary human lung epithelium and compared differences between sars-cov- and sars-cov infection and identified several pathways potentially involved in pathogenesis and gender-specific differences in clinical presentation ( ) . among the genes that were upregulated were a cluster involved in the cytokine-mediated signalling pathways, and in particular, the il- signalling pathway ( ) . specifically, cytokine pathways driven by nuclear factor kappa-light-chain-enhancer of activated b cell (nf-κb), toll-like receptors (tlrs), mitogen-activated protein kinase (mapk), bone marrow stromal cell antigen (bst ), il- , tnf alpha induced protein (tnfaip ), tnfaip interacting protein (tn p ), intercellular adhesion molecule (icam- ), intercellular adhesion molecule (icam- ), matrix metallopeptidase (mmp ), baculoviral iap repeat containing (birc ), and rho family gtpase (rnd ), were significantly upregulated during sars-cov- infection, suggesting a significant role in pathogenesis ( ) . moreover, rela (nf-κb p subunit) seems to be significantly upregulated in sars-cov- infection, leading to il- involvement ( ) . of note is the expression of oestrogen receptor (esr ), which was also enhanced under sars-cov- infection, suggesting sex hormones may be involved in differential expression during viral infection and may have implications for the differences in clinical severity seen between genders ( ) . additionally, over and hour post-infection, cxcl- was significantly upregulated in sars-cov- infection compared to sars-cov ( ) . a recent study using single-cell rna-seq in human, non-human primate and mouse tissues/cells was able to resolve further the host cellular targets for sars-cov- and their abundance in specific tissue/cell types ( ) . the study identified ace and tmprss co-expressing cells (lung type ii pneumocytes, ileal absorptive enterocytes and nasal goblet secretory cells) and also determined that that ace is induced by interferon-stimulated gene, suggesting a possible mechanism for enhanced viral infection ( ) . the clinical pathways of covid- disease severity may also depend on host-specific factors that may contribute to the 'cytokine storm', or cytokines release syndrome (crs), which is the massive release of pro-inflammatory cytokines including cytokines (il- β, il- , il- , il- , il- , and tnf-α) and chemokines such as cxcl and ccl in the lungs ( , ) . these genomic approaches also shed light on the specific genetic host factors that predispose individuals to this severe clinical presentation. proteomic and transcriptomic studies on bronchoalveolar lavage (bal) samples from covid- patients have also revealed considerable insights into the expression of sars-cov- receptors, co-receptors, immune responses, as well as risk factors for severe disease e.g. age and co-morbidities. asthma, chronic obstructive pulmonary disease (copd), hypertension, smoking, obesity, and male gender status were all associated with higher expression of ace and cd in bal, as well as bronchial biopsy and blood from covid- patients ( ) . furthermore, there was a positive correlation between the expression of cd -related genes in bal and the age and body mass index (bmi) of covid- patients ( ) . in another study on bal from covid- patients, an association was observed between covid- severity and enhanced levels of certain cytokines, e.g. ccl /mcp- , cxcl /ip- , ccl /mip- a, and ccl /mip b ( ) . this study also found that sars-cov- triggered apoptosis and the p signalling pathway in lymphocytes, probably causing additional lymphopenia in these patients ( ) . a comparison of transcriptome profiles between patients with covid- and influenza a virus infection revealed an absence of significant type i interferon/antiviral responses with sars-cov- infection, with enhanced expression of genes involved in metabolic pathways e.g. haem biosynthesis, oxidative phosphorylation and tryptophan metabolism, suggesting an important role for mitochondria during sars-cov- infection ( ) . furthermore, a meta-analysis on bal data from covid- patients also revealed an excess for neutrophils and chemokines ( ) . in meta-transcriptomic sequencing of bal from covid- patients, the expression of proinflammatory genes, especially chemokines, was significantly elevated in these patients compared to community-acquired pneumonia patients and healthy controls, suggesting hypercytokinemia ( ) . it also revealed enhanced dendritic cell and neutrophil activity ( ) . in contrast to sars-cov, which induces an ineffective interferon response, sars-cov- was found to strongly initiate expression of numerous interferon stimulated genes, which are thought to significantly contribute to immunopathogenesis ( ) . similarly, an analysis of rna-seq data sets of bal from covid- patients identified upregulation of neutrophil, inflammatory genes and chemokines, which may be involved in immunopathology, e.g. tnfr, il- , cxcr , cxcr , adam , gpr , mme, anpep, and lap ( ) . chronic co-morbidities for covid- patients include cardiovascular disease, hypertension, diabetes, stroke and malignant tumour ( ) . it was also found that parameters such as older age, underlying hypertension, high cytokine levels (il- , il- , and tnf-α), and high lactate dehydrogenase level were significantly associated with severe covid- during hospital admission ( ) . in a study involving icu patients with covid- pneumonia, all of them showed an incidence of thrombotic complications such as symptomatic acute pulmonary embolism (pe), deep vein thrombosis, ischemic stroke, myocardial infarction or systemic arterial embolism ( ) . approximately, one-third of patients experienced gastrointestinal symptoms. during hospitalization, a substantial proportion of patients presented cardiac injury, liver, and kidney dysfunction, and hyperglycaemia. icu covid- patients had higher plasma levels of il- , il- , il- , gscf, ip , mcp- , mip- , and tnf-α, compared to non-icu patients. majority of icu patients diagnosed with covid- were found to be at highest thrombotic risk ( ) . patients with severe covid- likely developed ards and died of respiratory failure. biopsy samples at autopsy from a patient who died from severe covid- showed bilateral diffuse alveolar damage with cellular fibromyxoid exudates, and mononuclear inflammatory lymphocytes in both lungs ( , ) . diffuse alveolar damage with fibrin rich hyaline membranes are pathological results of covid- . in a study, covid- -infected cancer patients were found to have underlying diseases, such as hypertension, diabetes and chronic obstructive pulmonary disease ( ) . cancer patients with accompanying covid- infection showed deteriorating conditions and poor outcomes, and thus it was recommended to avoid treatments causing immunosuppression ( ) . the complement system is an integral part of the innate immune response. it consists of a group of plasma proteins produced mainly by the liver or membrane proteins expressed on cell surface. these proteins interact in a cascade that leads to the opsonization of pathogens and the induction of inflammatory responses. the complement system comprises of three distinct activation pathways, i.e. classical, alternative or lectin (mbl). the activation of these pathways is based on different molecules present on the pathogen surfaces. the classical pathway is initiated by the binding of c q to the pathogen surface or antibody complex. the initiation of the alternative pathway is triggered by the binding of a spontaneously activated complement component to pathogen surface. the binding of the mbl to mannose-containing carbohydrates on pathogens triggers the initiation of the lectin pathway. the early events of three pathways eventually converge to generate a protease called, c convertase, which is covalently bound to the pathogen. the c convertase then cleaves c , present in plasma, into c a and c b. the c b binds to the pathogen and targets it for destruction by phagocytes. furthermore, c b binds with the c convertase to form c convertase, which produces c a and c b. c b triggers the late events of the complement cascade, which are a series of polymerization reactions where c , c , c and c interact with each other to form the membrane attack complex (mac). the mac can damage the membrane of certain pathogens by creating a pore in it. the c a and c a produced are important small peptide mediators of inflammation [reviewed in ( ) ]. studies in c -/-(gene-deficient) mice infected with sars-cov revealed the presence of c activation products such as c a, c b, ic b, c c, and c dg day post infection ( ) . the c deficient mice showed significantly less respiratory dysfunction and lower weight loss as compared to control. the mice also showed significantly lower levels of neutrophils and monocytes compared to the control. lower il- , tnf-α and il-  levels were reported in the lungs of the c deficient mice ( ) . the study also reported lower weight loss in mice deficient in factor b or c . in view of the critical role of the complement system in sars-cov infection since the first day of infection, it raised possibility for complement involvement in sars-cov- . levels of the terminal component of the complement system (mac) and c a are increased in patients with ards ( , ) . mac is known to damage endothelial cells, and thus, regulation or inhibition of mac by its known regulators such as cd or clusterin could be a potential treatment for endothelial dysfunction/damage in ards or covid- ( ) ( ) ( ) . considering the lectin pathway of the complement system, mbl was shown to bind sars-cov in vitro and inhibit its infectivity ( ) . the n-protein of sars-cov and sars-cov- has been shown to interact with mbl-associated serine proteases- (masp ), which is known to initiate the lectin pathway ( ) , leading to over-activation of the complement system. this same study also highlighted excess complement proteins found in post-mortem covid- patient lungs ( ) . furthermore, deletion of masp or perturbance of the masp- -n protein interaction was found to reduce lung injury. these studies, along with human proteomic studies, demonstrate the activation of multiple complement pathways during a coronavirus infection. in case of covid- , the alternative and lectin pathways of the complement system seem to be preferentially activated ( ) . increased levels of plasma c a and mac were recorded in patients with moderate and severe covid- ( ) . a post-mortem study of lung and skin vasculature in covid- patients showed significant deposits of mac and c d that colocalized with the sars-cov- s-protein, and masp in the micro-vasculature. this study did not find prominent classical features of ards such as hyaline membranes and inflammation in the histopathological examination ( ) . a recent study reported an increase in levels of c a, which correlated with increased covid- disease severity, as well as high levels of expression of c ar in blood and pulmonary myeloid cells of covid- patients ( ) . furthermore, use of anti-c ar monoclonal antibodies in human c ar knock-in mice was found to successfully prevent c a-mediated myeloid cell recruitment and activation, thereby inhibiting acute lung injury ( ) . a recent genetic study in covid- patients as reported that gene variants associated with complement regulatory protein, cd (decayaccelerating factor, which accelerates the decay of complement proteins, and thus inhibits complement activation) is associated with increased risk in clinical outcome (odds ratio . - . ); gene variants that map to c showed some protective effect (odds ratio . - . ) ( ) . neutrophils along with the complement system are another important component in the defence of the host against invading pathogens. neutrophil infiltration in pulmonary capillaries, acute capillaritis with fibrin deposition, extravasation of neutrophils into the alveolar space, and neutrophilic mucositis have been reported in the case of sars-cov- infection ( ) . the neutrophilic extracellular traps (nets) and the neutrophils activated by sars-cov- infection contain c , factor b and properdin, triggering the alternative pathway of the complement system ( ) . while this is usually beneficial, the sustained activation and nets formation leads to a hyper-inflammatory immune response that damages and destroy surrounding tissue. this aberrant behaviour, in concert with the abnormal complement activation, leads to the well recorded clinical manifestations observed in the case of covid- such as ards and pulmonary inflammation ( ) . additionally, nets have been reported to induce the production of excessive thrombin and subsequently generate c a ( ) . hence, it has been speculated that feedback loop that begins with complement activation leading to netosis causing an increases in thrombin production, that further stimulates the complement activation causing enhanced net formation ( ) . microangiopathy refers to a disease of the small blood vessels. the term is used when small blood vessels pathologically thicken or weaken, which leads to impaired flow of blood as well as leaking of cells and proteins. sustained inflammation in the vascular system due to the sars-cov- infection leads to thrombosis and microangiopathy ( , ) . this is supported by reports of increased lactate dehydrogenase, bilirubin, activation of platelets, elevated d-dimer levels and hyper-fibrinolysis ( ) . a post-mortem case series of patients with covid- found thrombotic microangiopathy, which was restricted to the lungs, along with diffuse alveolar damage could have contributed to causing death ( ) . another such study of cases found similar diffuse alveolar damage with significant capillary congestion and microthrombi despite anti-coagulation therapy ( ) . due to the presence of severe pulmonary vascular dysfunction in ards, it has been argued that ards is a type of vascular microthrombotic disease with lung phenotype involvement. this argument is supported by the association of mortality in ards with thrombocytopenia and mof as a result of disseminated intravascular coagulation ( ) ( ) ( ) . in recent times, a couple of theories on the pathogenesis of ards in sepsis have evolved: the 'two-path unifying theory' in which certain homeostasis mechanisms lead to microthrombogenesis, and the 'twoactivation theory of the endothelium' in which the complement mac leads to inflammation via cytokines and microthrombogenesis via platelet activation ( , ). the complement system plays a key role in the pathogenesis of thrombotic microangiopathy. this is a syndrome characterised by thrombocytopenia (low platelet count), microangiopathic haemolytic anaemia and systemic organ damage. atypical haemolytic uremic syndrome (ahus) is an example of such a disorder that typically leads to kidney damage. it is caused by excessive activation of the alternative pathway due to mutations in complement regulators factor h (common), factor i, membrane-cofactor protein, or c . analysis of renal tissue morphology from autopsies of covid- patients revealed strong c b- staining (via the alternative pathway) on the apical brush border of tubular epithelial cells with minimal deposition on glomeruli and capillaries of the kidney ( ) . treatment with eculizumab (c inhibitor) dramatically improved outcomes of survival in ahus. features similar to complement-mediated thrombotic angiopathy such as kidney and cardiac injury increased lactate dehydrogenase and d-dimer, and decreased platelets were observed in covid- ( , ) . eculizumab was used successfully as part of management of four covid- patients with severe pneumonia or ards in the intensive care unit, and this preliminary data is being used to conduct further full-fledged clinical trials with eculizumab ( ) . considering the overlap with complement-mediated thrombotic angiopathy in covid- , few studies are underway to test the effectiveness of complement regulators. a recent case study demonstrated a favourable outcome for the compstatin-based c inhibitor amy- . the study, which involved a -year-old caucasian male with severe pneumonia and systemic inflammation, found that amy- was safe and had a favourable outcome in improving the clinical presentation of the patient significantly ( ) . furthermore, treatment with a recombinant c a antibody on male covid- patients aged and years showed significant benefit in suppressing complement hyperactivation, which contributes to the excessive immune response causing aggravated inflammatory lung injury, a hallmark of sars-cov- pathogenesis and lethality ( ) . one of the many challenges includes determining patients who have a dysregulated complement activation. c bound to erythrocytes has been detected in patients with covid- ( ) , which may prove to be a useful blood marker as well as in identifying patients who potentially merit intervention with complement regulators ( ) . in covid- , endothelial injury has been found to be a key pathophysiological feature. a case series found direct evidence of viral infection of endothelial cells and endothelial inflammation, leading to endothelial cell death ( ) . in covid- patients, endothelial cell abnormalities were recorded in the kidney, lung, heart, small bowel, and liver. of deceased covid- patients were found to have suffered endothelial cell swelling with variable foamy degeneration in the glomeruli and an additional patients were found to have severe injury to the endothelium due to segmental fibrin thrombi in glomerular capillary loops ( ) ( ) ( ) . mac deposition has been observed in the endothelium of covid- patients ( ) . such studies have led to notion that in covid- , there are strong vascular and inflammatory components as well, which play a significant role in the pathophysiology of the illness ( ) . consistent with endothelial injury, the significantly elevated levels of von willebrand factor found in the patient with severe covid- has led to the idea that the infection of the ace expressing endothelium by sars-cov- induces injury and activates the complement , which sets up a feedback loop that maintains a state of inflammation ( , ( ) ( ) ( ) . it is worth noting that ards may occur in covid- despite well-preserved lung gas volume, which could indicate a key role for inflammatory processes, leading to vascular constriction and subsequent low oxygen levels in the blood ( ) . furthermore, d-dimer (a fibrin degradation product) levels are also found to be elevated in covid- and are associated with poorer prognosis ( , ) . these factors add to the importance of understanding vascular changes in this disease, including microangiopathic processes and coagulopathies in patients with covid- . pregnancy is associated with several maternal adaptations in both immune function (immunosuppression) and cardiovascular physiology (increased cardiac output, physiological anaemia, cardiac hypertrophy) that would likely alter susceptibility to viral respiratory infections including sars-cov- . maternal death occurred in % of patients admitted to the icu for covid- and in % of those who required invasive mechanical ventilation ( ) . to date, the literature consists of case reports, case series and retrospective studies. the most common presenting symptoms of maternal covid- are fever, cough, dyspnoea, and gastrointestinal symptoms ( ) . clinical findings of respiratory manifestations were similar to those seen in the non-pregnant populations, with similar ct findings together with elevations in c-reactive protein with decreased white blood cell counts ( ) . although the portal of entry is inhalational, there are widespread systemic effects. the immobility, hypoxia and acute inflammation lead to a prothrombotic hypercoagulable state, and indeed, elevated ddimers are correlated with disease severity ( ) . covid- is thus associated with venous or arterial thromboembolism ( ) . the mechanism by which this occurs is currently thought to be as a result of inflammatory cytokines ( ) inducing production of tissue factor with subsequent thrombin activation. the elevations of d-dimer (often seen in acute phases of infection) may be related to this increased thrombin generation. while serious maternal morbidity has been seen, the vast majority of pregnant women with sars-cov- infection remained asymptomatic for respiratory symptoms ( ) ( ) ( ) . pregnancy is coupled to physiological changes in cardiorespiratory status ( ) which might be expected to alter susceptibility to a respiratory upset. nevertheless, the evidence suggests that this is less prevalent than thought. however, the changes in immune function and coagulation in pregnancy appear to increase some complications. similarly, the coagulopathies seen in covid- in the non-pregnant population might be expected to have deleterious effects in pregnancy, which is already a prothrombotic state. covid- has been seen to be associated with preeclampsia ( , ) with one non-peerreviewed report suggesting a causal link ( ) . the placenta has also been reported as having vascular malperfusion and thrombosis ( , ) , which may provide an underlying explanation for the preeclampsia, a disease, associated with poor placental perfusion and altered vascular function ( ) . evidence of increased clotting at the placental surface suggests that this mechanism may be responsible (in part) for the increased incidence of preeclampsia. sars-cov- virions have been seen in the syncytiotrophoblast, the part of the placenta responsible for the angiogenic imbalance seen in preeclampsia and effects on the release of known factors associated with the disease (sflt- -soluble fms like tyrosine kinase and plgf -placental growth factor) are unknown. the disease is also linked to preterm premature rupture of membrane (pprom) ( , ) , and preterm labour ( ) , both of which are linked to inflammation. the underlying mechanism by which pprom occurs is not entirely elucidated. however, reports have suggested that activation of the coagulation system and thrombin causes fetal membrane weakening and subsequent rupture of membranes ( , ) . the alterations in clotting and thrombin seen in covid- may well provide a mechanism for this. similarly, thrombin has been related to the induction of preterm labour and weakened fetal membranes by induction of decidual colony-stimulating factor (csf)- ( ). at present, there are no drugs, therapeutics, or vaccines approved for curing, preventing, or treating sars-cov- specifically. as of june , a total of ( in human trails, in preclinical development) therapeutic drugs are under development against covid- . the current treatment for sars-cov- patients involves the management of clinical symptoms and providing supportive care. while research into developing new drugs and treatments against sars-cov- are ongoing, much of the effort currently focuses on the repurposing existing medicines used against viruses, multiple sclerosis, arthritis, blood plasma derivatives and malaria. moreover, although immunosuppressive treatments, e.g. corticosteroids have shown promise for covid- , there is considerable concern about possible side effects. other immunotherapeutic approaches given as adjunct therapy and based on neutralizing inflammatory cytokines and other immunomodulators, passive viral neutralization to reduce lung pathology and viral load, could be a promising approach ( ) . a number of these approaches are discussed below. the antiviral drug remdesivir, developed by gilead sciences, is an adenosine analogue, which incorporates into nascent viral rna chains and results in premature termination, effectively inhibiting viral rna synthesis ( ) . it was developed for the treatment of ebola and marburg virus infections ( ) , and animal studies have shown that it is effective against the other coronavirus ( ) . in vitro studies have established its efficacy against sars-cov- ( ) . an open-label trial across the united states, europe, canada and japan showed clinical improvement of of the covid- patients who were treated with a -day course of remdesivir on a compassionate basis ( ) . however, a follow-up multi-centre, randomized, double-blinded, placebo-controlled trial of patients showed that the drug was not associated with a difference in time to clinical improvement. compared to the placebo, the drug was found to have a non-significant but, numerically faster time to clinical improvement in patients with a symptom duration of days or lower ( ) . currently, japan and the usa have allowed the use of the drug under emergency use authorization for the treatment of covid- . in a randomized, open-label, multi-centre phase clinical trials, a -day course remdesivir brought about a significant clinical improvement compared to standard alone in patients with moderate covid- . this clinical study assessed the effect of -day (n= ) and -day (n= ) investigational remdesivir courses plus standard of care, versus standard of care alone (n= ) on clinical improvement on day ( ) . in case of patients with severe disease, both day and courses of the drug have been found to have similar clinical outcomes, but as the study lacked placebo control, the magnitude of benefit cannot be determined ( ) . umifenovir, marketed as arbidol, is a derivative of indole carboxylic acids used for the treatment of influenza a and b virus infection, and other arboviruses ( ) . it functions by incorporating into cell membranes and interfering with the hydrogen bonding network of phospholipids, blocking both the fusion of the virus to the cell membrane and the virusendosome fusion ( ) . in vitro studies have established anti-viral efficacy against ebola virus, human herpesvirus , hepatitis c virus, tacaribe arena virus, sars-cov and sars-cov- ( ) ( ) ( ) . a retrospective study on sars-cov- patients treated with umifenovir did not reveal any improvement in clinical prognosis or accelerated viral clearance ( ) . currently, two randomized and open-label trials to determine the safety and efficiency of the drug are ongoing in china. favipiravir, another anti-viral drug, developed by fujifilm toyama chemical (as avigan) and zhejiang hisun pharmaceutical, is a pyrazinecarboxamide derivative. it is converted into an active phosphoribosylated form (favipiravir-rtp) in cells and is recognized as a substrate by viral rna polymerase, thereby blocking the activity of rna-dependent rna polymerase. it was developed as a treatment against influenza. the drug is currently approved for the treatment of sars-cov- in china and italy. a study with sars-cov- patients treated using the drug has reported that better efficacy was observed in anti-viral activity and lower adverse reactions compared to the control group that was treated with lopinavir/ritonavir ( ) . another prospective, multi-centre, open-label, randomized superiority study with sars-cov- infected patients was conducted at three hospitals. they showed faster recovery from clinical symptoms when compared to the controls that were treated with umifenovir, even though similar numbers required the use of ventilators and oxygen ( ) . there are currently six trials ongoing in china evaluating the efficiency of this drug against other antivirals for the treatment of covid- and a phase clinal trial to assess its effectiveness and safety is scheduled in japan and usa. anti-malaria drugs, chloroquine and hydroxychloroquine, are lysosomotropic agents that function by increasing late endosomal and lysosomal ph, which results in impaired viral release from the endosome or lysosome ( ) ( ) ( ) . in vitro studies have shown antiviral activity against sars-cov- with hydroxychloroquine, a weak diprotic base, to have higher potency against the virus ( , ) . in sars-cov- , chloroquine, along with its lysosomotropic activity, is believed to reduce glycosylation of ace affecting the binding of the virus to the cells ( ) . furthermore, chloroquine is also shown to block the production of proinflammatory cytokines such as il- preventing ards ( ); hydroxychloroquine was found to possess an anti-inflammatory effect on th -related cytokines (il- , il- and il- ) ( ) . initial clinical studies in china involving sars-cov- infected patients, who were treated with chloroquine, showed amelioration of pneumonia, shortened disease progression, increased resolution of lung lesions on ct, and a better virus-negative conversion ( , ) . hydroxychloroquine and combination therapy with azithromycin was found to reduce viral load in a french open-label non-randomised clinical trial and in an observational pilot study ( , ) . nevertheless, these studies were plagued with several limitations, such as small sample size, very short observation period, no randomisation, lack of reports on clinical progression, poorly described inclusion and exclusion criteria, and low national early warning score ( , , ) . another trial with sars-cov- infected patients treated with hydroxychloroquine for seven days in china and a study with effectively sars-cov- patients, revealed no significant difference in the nasopharyngeal viral carriage when compared to the controls that were provided with the local standard care ( , ) . a third randomized clinical trial conducted in china with patients exhibiting mild sars-cov- when treated with hydroxychloroquine were found to have recovered faster from cough and fever when compared to the placebo. however, the result of this study cannot be extrapolated to patients with severe sars-cov- ( ). a retrospective cohort study of random sample of inpatients with laboratory-confirmed sars-cov- admitted to hospitals in the new york city was conducted. it did not find any significant differences in in-hospital mortality associated with the treatment with hydroxychloroquine, azithromycin, or both, compared to the controls where the patients were given neither of the drugs ( ). the us fda and european medicines agency (ema) and many other countries like india and poland have authorized emergency use of hydroxychloroquine to treat sars-cov- infected patients. however, the fda and ema have issued warnings against the reported side effects of the drugs. these include abnormal electrical activity that affects the heart rhythm (qt interval prolongation, ventricular tachycardia, and ventricular fibrillation), particularly when taken at high doses or in combination with the antibiotic azithromycin. other side effects reported are liver and kidney problems, nerve cell damage that can lead to seizures and hypoglycaemia ( , ) . around clinical trials have been registered to study the effects of hydroxychloroquine and chloroquine independently or in combination with each other on sars-cov- have been registered in the usa and china ( ) . another anti-parasitic drug, ivermectin, has been shown to be effective against sars-cov- in vitro ( ) . a clinical trial to assess the efficiency of ivermectin against sars-cov- has been planned to take place in japan soon. the corticosteroid, dexamethasone, functions as an immunosuppressant. the drug is believed to modulate the lung injury caused by a dysregulated immune system, thereby reducing the progression to respiratory failure and death ( ) . in a randomized, controlled, open-label, adaptive, platform trial, , patients treated with mg of dexamethasone (orally or intravenously) for days were found to have a significantly reduced day mortality rate among those receiving mechanical ventilation by . %, and by % among those receiving oxygen without mechanical ventilation, compared to , patients treated with standard care ( ) . treatment with the drug did not provide any benefit to patients who did not require oxygen or mechanical ventilation, hinting at possible harm. the use of corticosteroid in the case of severe respiratory infections requires the use of "the right dose, at the right time, in the right patient" ( ) . this is because a high or an early dose may help the virus proliferate by suppressing the immune system, instead of reducing inflammation. in case of covid- , the peak of viral shedding is higher early in the disease. the benefit of dexamethasone when patients require respiratory support or after the first week of the disease suggest that this stage is dominated by an irrepressible immune response versus active viral replication ( ) . dexamethasone is the first drug found to reduce mortality in covid- ( ). lopinavir/ritonavir is a drug combination. lopinavir is a protease inhibitor, developed by abbott laboratories against hiv- that functions by blocking essential viral proteases ( ) . due to poor pharmacokinetics, it is administered exclusively in combination with ritonavir which increases lopinavir's plasma half-life through inhibition of cyp a-mediated metabolism of lopinavir, thereby increasing its exposure and improving the anti-viral activity of the drug ( ) . in vitro studies have revealed that lopinavir inhibited the replication of the sars-cov- virus in vero e cell ( ) . in a randomized, controlled, open-label trial with patients with laboratory-confirmed sars-cov- infection, no benefit was observed with lopinavir-ritonavir treatment beyond standard care ( ) . another single-blind randomised controlled trial in china treated patients with mild/moderate covid- for days, or umifenovir or standard care with no antiviral ( ) . in the study, no differences were found in the time taken for viral clearance, as assessed by pcr of nasopharyngeal swabs, fever, cough, or lung ct findings. clinical status deterioration to severe/critical from mild or moderate clinical status and gastrointestinal side effects was seen highest in patients treated with lopinavir/ritonavir when compared to umifenovir treated or those treated with standard care and no antivirals ( ) . both these randomised clinical trials suffer from small sample sizes and lack of blinding. a multi-centre, prospective, open-label, randomised, phase trial in hong kong with sars-cov- infected patients involved treatment for days with only lopinavir-ritonavir (control), or with a combination of lopinavir-ritonavir, ribavirin, an oral hepatitis c virus drug, and ifn-. it found that the combination treatment was effective in reducing symptoms and viral shedding faster, as well as duration of hospital stay ( ) . currently, about a dozen trials are studying the effect of the drug against sars-cov- . one such study is a phase randomized controlled trial in china in which the effectiveness of lopinavir-ritonavir against influenza drugs, umifenovir and oseltamivir, is to be studied. another south korean trial is looking to compare the efficacy of lopinavir-ritonavir against hydroxychloroquine. the who solidarity trial and uk-based recovery trial is looking to study the effectiveness of lopinavir-ritonavir independently; the who solidarity trial also looks to the explore the drug in combination with interferon-. another second-generation protease inhibitor against hiv- , darunavir, has shown significant inhibition of sars-cov- replication (in vitro). according to a press release by johnson & johnson, an unpublished single-centre, open-label, randomized, and controlled trial in china in which sars-cov- patients were treated with darunavir and cobicistat was not effective in treating sars-cov- ( ). however, a further three clinical studies in china are scheduled. other drugs currently being tested against sars-cov- include tocilizumab, a monoclonal antibody against il- developed by roche, which is used for the treatment of moderate to severe rheumatoid arthritis by blocking il- activity. the drug was found to have helped cure of covid- patients in a trial conducted in china ( ) . another open multi-centre randomized controlled trial french study awaits publication, in which patients were split into two groups, i.e. routine treatment with and without tocilizumab: in the group treated with tocilizumab, the combination of ventilation requirement (mechanical or non-invasive) or death was achieved in a significantly lower proportion of patients ( ) . a phase trial to test its efficacy in treating patients with severe covid- has been authorised by the fda. moreover, an italian multi-centre, retrospective study of patients with severe covid- pneumonia, revealed that the use of tocilizumab given either intravenously or subcutaneously was associated with reduced risk of mechanical ventilation and death ( ) . anakinra is a recombinant il- receptor antagonist that has shown promise in treating severe covid- disease. in a retrospective cohort study of patients with covid- and ards that were managed with non-invasive ventilation (outside the icu), their treatment with high-dose anakinra was observed to be safe and associated with clinical improvement in % of patients ( ) . another study has also described the early use of anakinra in covid- patients with cytokine storm syndrome (css) and acute hypoxic respiratory failure (ahrf) which may be beneficial in preventing the need for mechanical ventilation ( ) . these results have encouraged further clinical trials to validate its safety and efficacy ( ) . approaches targeting inhibition of bruton tyrosine kinase (btk) has also shown promise. btk plays a significant role in human innate immune responses. tlrs recognize ssrna of viruses like sars-cov- and induce signalling via btk-dependent activation of nf-κb, initiating a pro-inflammatory response ( ) ( ) ( ) ( ) . btk also plays a key role in the activation of the nlrp inflammasome, resulting in maturation and secretion of il- β, a key pro-inflammatory cytokine ( ) ( ) ( ) . thus, btk seems a favourable target against the cytokine storm in covid- . in one study, acalabrutinib (a selective inhibitor of btk) was given to patients with severe covid- and clinical improvements were observed over a -week treatment period, with reduced biomarkers of inflammation (c-reactive protein and il- ) to normal levels ( ) . other dual inhibitors e.g. ibrutinib which target btk/il- -inducible t-cell kinase (itk) signalling have also shown promise ( ) . in one study of patients given ibutinib for treatment of b-cell malignancies and chronic graft-versus-host disease (cgvhd), there was evidence that ibutinib may also protect against pulmonary injury in covid- , which these patients subsequently had, suggesting ibutinib as a possible prophylactic for vulnerable patient groups ( ) . similar findings demonstrating a possible protective role of btk inhibitors in cancer with covid- have also been subsequently described ( ) ( ) ( ) . these promising findings now merit a controlled randomised trial to demonstrate efficacy and drug safety of these btk inhibitors. intravenous immunoglobulin (ivig) is a pooled preparation of normal igg obtained from several thousand healthy donors. it is generally used in the immunotherapy of several autoimmune and inflammatory diseases, ( ) , and thus has been investigated for treating covid- to mitigate the css. ivig therapy has shown promise through several studies, although careful selection of covid- patients and timing of ivig administration appear to be the key for good clinical outcome. preliminary findings from one multi-centre study showed that early administration of high dose ivig improved the prognosis of critical patients with covid- ( ) . similarly, patients with severe covid- who received high-dose ivig made a satisfactory recovery ( ) . in another study, the use of ivig as an adjuvant treatment for covid- pneumonia within hours of admission to the icu reduced the use of mechanical ventilation, icu and hospital time, and the -day mortality rate of patients with severe covid- pneumonia ( ) . in a case study of a covid- patient with respiratory failure and shock, treatment with plasma exchange before ivig treatment resulted in prompt recovery without the need for mechanical ventilation and may be an additional early treatment step to treat critically ill covid- patients ( ) . ivig treatment of severely-ill covid- patients on mechanical ventilation has also shown promise. in one study of patients, treatment with ivig improved clinical and respiratory outcome, particularly saturation o levels, resulting in earlier extubation of the patients ( ) . furthermore, ct graphs obtained after ivig therapy also revealed improvements in pulmonary lesions of these patients ( ) . convalescent plasma therapy (cpt) is another classical adaptive immunotherapy used for the treatment of infectious disease for over a century. it has currently been approved for covid- by the fda under compassionate use rules. the treatment involves the transfusion of high neutralizing antibody titre containing blood plasma from sars-cov- recovered patients. this provides immediate short-term immunity. this is accomplished by binding of the pathogen to the antibody, which results in the activation of the immune system causing cellular cytotoxicity, phagocytosis, or direct pathogen neutralisation. five clinical studies, conducted involving covid- patients who were treated with cpt, revealed significantly lower viral titres, increased levels of neutralizing antibody, improved clinical symptoms such as apyrexia, resolved ards and unassisted breathing ( ) ( ) ( ) ( ) ( ) . among the cpt-treated patients, no fatalities were recorded, and no severe adverse reactions or treatment complications associated with cpt were reported ( ) ( ) ( ) ( ) ( ) . while providing with valuable initial data, these studies suffer from several limitations such as lack of proper control groups, non-randomized evaluations, concomitant drug treatments, poor participant selection, lack of proper cpt dosage, and duration of therapy ( ) . three clinical trials are currently being evaluated by the fda to test the safety and efficiency of cpt in patients who have been exposed to the virus and are at high risk of developing severe covid- , patients who are admitted in hospital with acute respiratory symptoms, and for covid patients under mechanical ventilation ( ) . further trials are also planned or ongoing in china, columbia, iran, mexico and the netherlands ( ) . early safety indicators of covid- cpt were evaluated in a study of , patients and showed that the mortality rate was not unduly high and concluded that transfusion of convalescent plasma appears safe in hospitalized patients with covid- ( ) . while the repertoire of antivirals and repurposed drugs tested against sars-cov- are expected to help manage the disease, the development of a safe and effective vaccine would help cut down the overall number of deaths and prevent the population from getting the disease in the first place. a recent study suggested that mandatory bcg vaccination can possibly be associated in flattening the curve in the spread of covid- . it analysed the rate of day-wise increase in positive cases in countries and deaths in countries for the first -day period ( ) . while arguments for the potentially beneficial effects of pre-existing vaccines have been sporadically made, including giving mmr (mumps, measles and rubella) vaccines to elderly population, generating a sars-cov- specific vaccine seems a logical and obligatory choice. as of july , the who landscape document reports candidate vaccines developed on various platforms ( figure ) in preclinical stages of development: only are under clinical evaluation. mrna- vaccine is a sequence optimized mrna/lnp expressing a perfusion stabilized form of sars-cov- s- p a transmembrane anchored protein with the native furin cleavage site, developed by moderna in collaboration with the national institute of allergy and infectious diseases vaccine research center ( , ) . the vaccine is undergoing an openlabel phase clinical trial that started in march, with healthy adult ( - -year-old) volunteers for six weeks in three dose cohorts ( µg, µg and µg) as two doses approximately days apart via intramuscular injection in the upper arm. three cohorts of - -year-old volunteers and three cohorts of healthy volunteers aged and above are being enrolled in addition to the initial volunteers. the volunteers will be followed through months after the second vaccination to assess safety data, common vaccination symptoms, review trial data and advise niaid ( ) . a phase ii trial with healthy participants in two cohorts ( - years old adults and adults aged years and above) treated with a placebo, a μg or a μg dose has begun from may, th , . the in vivo studies in murine models suggested the vaccine to be immunogenic and could elicit igg a and igg subclass s-binding antibodies. mrna- immunized mice splenocytes showed higher secretion of ifn- than il- , il- or il- upon re-stimulation with peptide pools (s and s ). a dose of μg of mrna- was found to induce robust cd + t cell response to the s peptide pool with balanced th /th ab isotype response in mice. thus, a μg dose of vaccine has been decided for human trial in phase study, which is equivalent to μg dose induced in mice ( ) . the fda has granted fast track designation for the vaccine. the pfizer licensed biontech's bnt vaccine development programme has developed four coronavirus vaccine candidates ( ) . two of the vaccines contain mrna coding for the spike protein of sars-cov- , while the other two contain only the rbd of the spike protein ( ) . furthermore, the four vaccine candidates are made of three different mrna formats. two of the vaccine are based on nucleoside modified mrna (modrna), which incorporates modified nucleosides in the mrna ( ). this suppresses intrinsic immune activation and the production of anti-drug antibodies against the mrna itself ( ). the suppressed immune activity against the therapeutic mrna helps produce the antigenic protein for longer periods ( ). the next vaccine candidate is based on the optimised unmodified mrna (urna) format ( ). urna uses uridine in the mrna, making it more immunogenic ( ). finally, the last vaccine candidate uses self-amplifying mrna (sarna) ( ). it is based on the principle of viral replication. the sarna, in addition to encoding a protein of interest, also encodes, replicase ( ). this enables the self-amplification of the mrna inside the cell ( ). the dsrna intermediate created during the replication of the rna triggers an immune response making sarna a potent activator of the immune system ( ). a phase / , randomized, placebo-controlled, observer-blind, dose-finding, and vaccine candidate-selection study to evaluate the safety, tolerability, immunogenicity, and potential efficacy of the candidate in healthy adult volunteers is ongoing ( ). another frontrunner among the candidates is cansino bio's ad -ncov ( ) . it is a genetically engineered vaccine candidate with the replication-defective adenovirus type (live virus) as the vector to express sars-cov- spike protein. this would help the body to produce neutralizing antibodies against sars-cov- . it has been shown to induce a strong anti-viral activity against sars-cov- in animal and in vitro studies. a single-centre, non-random, open, and dose-escalation phase i clinical trial for recombinant novel coronavirus vaccine (adenoviral vector) in healthy adults aged between and years were conducted. the vaccine has been administered as a liquid formulation intramuscularly in the deltoid muscle ( ) . three different doses were chosen: (a) low dose of x viral particles/ . ml; (b) intermediate dose of . x viral particles/ml; and (c) high dose combines both low and intermediate dose (one in each arm). the volunteers are assessed for a period for months to study any adverse reactions or other relevant outcomes ( ) . most common systematic adverse reaction observed were fever, fatigue, headache and muscular pain but with no serious adverse effect were noted within days. participants showed four-fold increase in anti-rbd antibodies in all the groups; neutralizing antibodies increased gradually being highest at days post vaccination. ad neutralizing antibody titres were boosted significantly postvaccination. il- and tnf- were detected and polyfunctional memory cd + t cell phenotypes were higher than cd + t cells. this suggested ad vectored covid- vaccine to be immunogenic and capable of stimulating both b and t cell response. for phase clinical trial, intermediate dose was chosen and is expected to be completed by january ( ) . the vaccine may have some negative effects in older age people thus in the nd clinical trial participants above years will be included. t cell response peaked earlier from th day after the st shot of vaccine whereas the antibodies production level peaked at th day post vaccination. the study also highlighted the possibility of negative effect on vaccine elicited immune response due to pre-existing ad immunity ( ) . chadox -ncov is being developed by oxford university, uk ( ) . it is a replication deficient simian adenovirus vector chadox , containing full length s-protein of sars cov- along with a tissue plasminogen activator leader sequence. the vaccine is reported to be effective in inducing an antiviral response in animal models ( ) . chadox -ncov was found to be immunogenic in mice mounting robust anti-viral response. single dose of this vaccine was capable of inducing humoral and cellular immune response in rhesus macaques ( ) . a phase i/ii single-blinded, randomised, multi-centre study to determine efficacy, safety and immunogenicity of the vaccine in about healthy adult volunteers aged - years was initiated on april rd , ( ). the volunteers have been subjected to either one dose of x vp of chadox ncov- , an additional booster dose of . x vp of chadox ncov- , or a control of menacwy vaccine delivered intramuscularly ( ). the volunteers were assessed for a period for months to study any adverse reactions or other relevant outcomes ( ) . the results showed increase in s-specific antibodies with a single dose by th day and increase in neutralizing antibodies with booster dose in all participants. chadox -ncov was also capable of inducing heightened effector t-cell response quite earlier than antibody response. t cell response peaked on day th and sustained up to days. the results showed chadox ncov- vaccine to be safe, tolerant and immunogenic, which further supported phase trial which is now underway ( ) . picovacc is a purified inactivated sars-cov- vaccine candidate which is capable of inducing neutralizing antibodies in mice, rats, and nonhuman primates specific to sars-cov- . cn strain of sars cov- virus was chosen to develop picovacc which was inactivated with β-propiolactone. this inactivated vaccine candidate was able to produce about -fold higher s-specific antibody titres in murine model when compared to covid- recovered patients. efficacy of picovacc was also tested in rhesus macaques with an intramuscular low ( . µg), medium ( µg) and high ( µg) dose administered three times ( , th and th day) and on day nd sars cov- cn strain was inoculated through intratracheal (lungs) route. all vaccinated macaques showed protection towards sars cov- infection and their viral loads declined significantly. no notable haemato-and histopathological changes were observed; human clinical trials are awaited ( ) . a group of us scientists have come up with a series of prototype dna vaccines expressing variants of the sars-cov- spike protein. the efficacy of the dna vaccine candidates was evaluated in rhesus macaques ( - -year-old). intramuscular dose ( mg) of dna vaccine was administered, followed by booster dose on rd week and antigenic challenge ( . x viral particles) on th week (both intranasal and intratracheal route). dna vaccine was found to be protective with dramatic reduction of viral replication and enhanced production of sspecific binding as well as neutralizing antibodies compared to controls. the study has not yet addressed the possibility of mutations that may emerge in escaping neutralizing antibodies, though it seems to be protective in primates against sars-cov- ( ). j o u r n a l p r e -p r o o f ino- , developed by inovio, is a dna vaccine candidate ( ) . the optimized spike protein of sars-cov- virus dna plasmids are introduced into cells by the use of a proprietary platform, cellectra®, via electroporation ( ) . once inserted, the plasmids are expected to strengthen the body's own natural response. a phase i open-label study to evaluate the safety, tolerability and immunogenicity of ino- as a prophylactic vaccine against sars-cov- in healthy volunteers aged - years is ongoing ( ) . the volunteers will be treated with either one or two doses of mg of vaccine administered intradermally followed by electroporation the following day ( ) . the volunteers will be assessed for a period for year to study any adverse reactions or other relevant outcomes ( ) . once the initial safety and immunogenicity of the vaccine are satisfied, phase ii efficacy studies are planned. qualitative and quantitative properties of cd + and cd + t cell responses in covid- and prophylactic vaccine development necessitate identifying viral regions and potential epitopes. thus, a total of peptides ( -to -mer), which span the full proteome of the sars-cov- excluding orf- , were designed and used to assess the memory t cell responses upon challenge on patients following recovery from covid- . peptides were identified containing cd + and/or cd + epitopes. the memory of t cell responses from convalescent individuals with covid- was found to be greater in severe covid- cases compared to mild ones. immunodominant epitope clusters and peptides were most markedly observed to belong to spike, m, and orf proteins. in about % of study groups, strong cd + t cell responses specific to the np protein were observed, suggesting the possibility of inclusion of non-spike proteins in future covid- vaccine design ( ) . in another study, a comprehensive immunogenicity map of the sars-cov- virus was carried out; peptide sequences ( -mers) were generated based on computational algorithms. a single -mer peptide containing multiple epitopes that can possibly present on hla class i and class ii across majority of population and provide long-term immunity in most people acting as b and t cell epitopes had been identified. this in silico analysis needs further evaluation for safety and efficacy as a vaccine ( ) . in an unprecedented short span of time and speed since the beginning of the covid- pandemic, significant progress has been made in our understanding of the pathogenesis of sars-cov- infection. however, there are endless unanswered questions; hopefully and most likely, they will be answered in near future. why there are a huge population that are asymptomatic carriers? what are the genetic contributors to susceptibility and resistance to developing covid- ? how pregnant women are so resilient to developing covidsymptoms; for that matter young children as well! what happens during the period of latency, i.e. between being infected and showing symptoms? how far the lung surfactant system gets affected during severe symptoms? what triggers thrombotic microangiopathy in addition to complement activation. on the adaptive immune aspects, what variations exist within population in terms of the proportion of neutralising antibodies? persistence of neutralising antibodies and recall memory magnitude following second infection (on vaccination trials) will yield serious information about how to finetune the dose, duration and vaccination strategies. in this acute crisis, a number of existing drugs have been repurposed empirically; clinical trials have yielded variable results. it is becoming clear that combination therapies are more likely to be successful. deciphering, at high resolution, the mechanisms and consequences of hostpathogen interactions in covid- will lead to novel therapies and preventative vaccination strategies. primary cellular host and co-receptor for sar-cov- . ) attachment and entry of sar -cov- requires priming by transmembrane serine protease (tmprss ) which cleaves the s protein into s and s portions, facilitating, ), s targeting and binding of the receptor angiotensin-converting enzyme (ace ), followed by receptor-mediated endocytosis of the virion into the host cell. j o u r n a l p r e -p r o o f tmprss is the key protease involved in priming sars-cov- , which forms a receptorprotease complex with ace on the host cell surface, thus facilitating viral targeting and entry to the host cell. co-expression of aec and tmprss has been found in proximal as well in distal airways. the nasal cavity has the highest expression of both the receptors in ciliated and secretory (goblet) cells compared to lung bronchi (ciliated and secretory cells) and lung parenchyma (alveolar type progenitor cells, at ). structural conformation of receptor-binding domain (rbd) present in s region of sars-cov- spike protein is capable of influencing the ace -binding affinity. in case of sars-cov- , the rbd contains a four-residue motif glycine-valine/glutamine-glutamate/threonineglycine which enables the binding loop to take a different conformation. it can undergo two possible conformational changes, a "lying down state" which has low affinity towards aec and a "standing up state" with high binding affinity. sars-cov- rbd is found mostly in lying down state, and thus being less accessible to aec . this hidden conformation of rbd in the spike protein can possibly be a masking strategy for immune evasion by sars-cov- . ( ) the sars-cov- binds to the cell via the ace receptor using the s subunit of the spike protein. once bound, the s subunit facilitates virus-cell membrane fusion by two tandem domains, heptad repeats (hr ) and heptad repeats (hr ) to form a six-helix bundle ( -hb) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. type ii pneumocytes infected with sars-cov trigger the release of cytokines, chemokines and interferons. the secreted inflammatory mediators recruit macrophages, neutrophils and activated t cells. the stimulated macrophages secrete il- , il- and tnf-α. this increases capillary permeability, causing plasma to leak into the interstitial space and the alveolus. the stimulated neutrophils release reactive oxygen species and proteinases, which destroy infected cells. the cell debries and the plasma combine to form a protein-rich fluid. the increasing fluid leads to dyspnoea and pneumonia. it also dilutes the surfactant lining of the alveolus causing alveolar collapse, which leads to hypoxaemia and acute respiratory distress syndrome. the sustained inflammation leads to systemic inflammatory response syndrome, which develops into septic shock causing multi-organ failure and death. coronavirus pathogenesis the structure and functions of coronavirus genomic ' and ' ends novel coronavirus: an emerging global threat identification of a novel coronavirus in patients with severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia a novel coronavirus from patients with pneumonia in china epidemiologic clues to sars origin in china discovery of a rich gene pool of bat sars-related coronaviruses provides new insights into the origin of sars coronavirus summary of probable sars cases with onset of illness from host determinants of mers-cov transmission and pathogenesis middle east respiratory syndrome, mers situation upadate the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- a pneumonia outbreak associated with a new coronavirus of probable bat origin genome composition and divergence of the novel coronavirus ( -ncov) originating in china the architecture of sars-cov- transcriptome isolation and characterization of -ncov-like coronavirus from malayan pangolins a novel coronavirus associated with severe acute respiratory syndrome bat-to-human: spike features determining "host jump" of coronaviruses sars-cov, mers-cov, and beyond angiotensin-converting enzyme : a functional receptor for sars coronavirus efficient activation of the severe acute respiratory syndrome coronavirus spike protein by the transmembrane protease tmprss evidence that tmprss activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response a transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor structure, function, and antigenicity of the sars-cov- spike glycoprotein the cell biology of receptor-mediated virus entry a crucial role of angiotensin converting enzyme (ace ) in sars coronavirusinduced lung injury type ii transmembrane serine proteases activation of influenza viruses by proteases from host cells and bacteria in the human airway epithelium the spike glycoprotein of the new coronavirus -ncov contains a furin-like cleavage site absent in cov of the same clade rare driver mutations in head and neck squamous cell carcinomas converge on notch signaling sars-cov- entry factors are highly expressed in nasal epithelial cells together with innate immune genes single cell rna sequencing of human tissues identify cell types and receptors of human coronaviruses air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding sars-cov- receptor ace is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues structure of the fusion core and inhibition of fusion by a heptad repeat peptide derived from the s protein of middle east respiratory syndrome coronavirus activation of the sars coronavirus spike protein via sequential proteolytic cleavage at two distinct sites host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein inhibitors of cathepsin l prevent severe acute respiratory syndrome coronavirus entry coronavirus membrane fusion mechanism offers a potential target for antiviral development protease-mediated enhancement of severe acute respiratory syndrome coronavirus infection cleavage of the sars coronavirus spike glycoprotein by airway proteases enhances virus entry into human bronchial epithelial cells in vitro cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease modulation of tnf-α-converting enzyme by the spike protein of sars-cov and ace induces tnf-α production and facilitates viral entry tmprss and adam cleave ace differentially and only proteolysis by tmprss augments entry driven by the severe acute respiratory syndrome coronavirus spike protein entry from the cell surface of severe acute respiratory syndrome coronavirus with cleaved s protein as revealed by pseudotype virus bearing cleaved s protein characterization of a highly conserved domain within the severe acute respiratory syndrome coronavirus spike protein s domain with characteristics of a viral fusion peptide ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex a contemporary view of coronavirus transcription coronaviruses post-sars: update on replication and pathogenesis minus-strand copies of replicating coronavirus mrnas contain antileaders recombination between nonsegmented rna genomes of murine coronaviruses rna recombination of coronavirus replication of coronavirus mhv-a in sac-cells: determination of the first site of budding of progeny virions characterization of the budding compartment of mouse hepatitis virus: evidence that transport from the rer to the golgi complex requires only one vesicular transport step molecular interactions in the assembly of coronaviruses modular organization of sars coronavirus nucleocapsid protein identification of in vivo-interacting domains of the murine coronavirus nucleocapsid protein coronaviruses: an overview of their replication and pathogenesis a structural analysis of m protein in coronavirus assembly and morphology differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins s, m and e the production of recombinant infectious di-particles of a murine coronavirus in the absence of helper virus analysis of constructed e gene mutants of mouse hepatitis virus confirms a pivotal role for e protein in coronavirus assembly infectious bronchitis virus e protein is targeted to the golgi complex and directs release of virus-like particles envelope protein palmitoylations are crucial for murine coronavirus assembly characterization of the coronavirus mouse hepatitis virus strain a small membrane protein e the spike protein of sars-cov -a target for vaccine and therapeutic development temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study dynamics of anti-sars-cov- igm and igg antibodies among covid- patients antibody responses to sars-cov- in patients with covid- detection of antibodies against sars-cov- in patients with covid- clinical characteristics of coronavirus disease in china epidemiologic features and clinical course of patients infected with sars-cov- in singapore public health might be endangered by possible prolonged discharge of sars-cov- in stool a rapid advice guideline for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (standard version) first known person-to-person transmission of severe acute respiratory syndrome coronavirus (sars-cov- ) in the usa early transmission dynamics in wuhan, china, of novel coronavirusinfected pneumonia a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster sars-cov- epidemic in india: epidemiological features and in silico analysis of the effect of interventions asymptomatic cases in a family cluster with sars-cov- infection asymptomatic sars-cov- infected patients with persistent negative ct findings transmission of -ncov infection from an asymptomatic contact in germany systematic urgent review group effort (surge) study authors. physical distancing, face masks, and eye protection to prevent person-to-person transmission of sars-cov- and covid- : a systematic review and meta-analysis aerosol and surface stability of sars-cov- as compared with sars-cov- tmprss and tmprss promote sars-cov- infection of human small intestinal enterocytes first case of novel coronavirus in the united states royal college of midwives and royal college of paediatrics and child health, with input from the royal college of anaesthetists phe and hps. covid- virus infection and pregnancy infants born to mothers with a new coronavirus (covid- ) clinical analysis of neonates born to mothers with -ncov pneumonia world health organization. frequently asked questions: breastfeeding and covid- for health care workers if you are pregnant, breastfeeding, or caring for young children gender differences in patients with covid- : focus on severity and mortality clinical features of patients infected with novel coronavirus in wuhan the trinity of covid- : immunity, inflammation and intervention sex hormones determine immune response opensafely: factors associated with covid- death in million patients the clinical dynamics of cases of covid- outside of wuhan, china incubation period of novel coronavirus ( -ncov) infections among travellers from wuhan, china diarrhea during covid- infection: pathogenesis, epidemiology, prevention and management clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study autoimmune haemolytic anaemia associated with covid- infection the ocular manifestations and transmission of covid- : recommendations for prevention taste changes (dysgeusia) in covid- : a systematic review and metaanalysis acute anosmia from covid- infection early recovery following new onset anosmia during the covid- pandemic -an observational cohort study loss of smell and taste as symptoms of covid- : what does the evidence say? -cebm anosmia, hyposmia, and dysgeusia as indicators for positive sars-cov- infection covid- pandemic and the skin: what should dermatologists know? neurologic manifestations of hospitalized patients with coronavirus disease neurological and neuropsychiatric complications of covid- in patients: a uk-wide surveillance study autoimmune and inflammatory diseases following covid- paediatric multisystem inflammatory syndrome temporally associated with sars-cov- mimicking kawasaki disease (kawa-covid- ): a multicentre cohort kawasaki-like multisystem inflammatory syndrome in children during the covid- pandemic an outbreak of severe kawasaki-like disease at the italian epicentre of the sars-cov- epidemic: an observational cohort study clinical characteristics of children with a pediatric inflammatory multisystem syndrome temporally associated with sars-cov- acute heart failure in multisystem inflammatory syndrome in children (mis-c) in the context of global sars-cov- pandemic multisystem inflammatory syndrome in u.s. children and adolescents multisystem inflammatory syndrome in children in new york state classification of the cutaneous manifestations of covid- : a rapid prospective nationwide consensus study in spain with cases covid- and dermatology: a comprehensive guide for dermatologists immune thrombocytopenic purpura in a patient with covid- cutaneous manifestations in covid- : a first perspective appearance and management of covid- laryngo-tracheitis: two case reports ribose '-o-methylation provides a molecular signature for the distinction of self and non-self mrna dependent on the rna sensor mda coronavirus nonstructural protein is a cap- binding enzyme possessing (nucleoside- ′o)-methyltransferase activity sars-cov- and covid- in older adults: what we may expect regarding pathogenesis, immune responses, and outcomes papain-like protease regulates sars-cov- viral spread and innate immunity structural basis for translational shutdown and immune evasion by the nsp protein of sars-cov- comparative replication and immune activation profiles of sars-cov- and sars-cov in human lungs: an ex vivo study with implications for the pathogenesis of covid- comparative pathogenesis of covid- , mers, and sars in a nonhuman primate model cytokine release syndrome in severe covid- ct imaging of the novel coronavirus ( -ncov) pneumonia. radiology covid- associated with acute respiratory distress syndrome abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia pathogenesis of covid- from a cell biology perspective targeting potential drivers of covid- : neutrophil extracellular traps mechanisms of hypoxemia frequency and distribution of chest radiographic findings in covid- positive patients covid- med stille hypoksemi effects of acute hypoxia on heart rate variability, sample entropy and cardiorespiratory phase synchronization cytokines and cytokine inducers stimulate prostaglandin e entry into the brain neutrophil extracellular traps in covid- comprehensive mapping of immune perturbations associated with severe covid- covid- : immunopathology and its implications for therapy coronaviruses and the cardiovascular system: acute and long-term implications covid- and the cardiovascular system cold agglutinin autoimmune haemolytic anaemia associated with novel coronavirus (covid- ) covid- infection associated with autoimmune hemolytic anemia incidence of thrombotic complications in critically ill icu patients with covid- risk factors for severity and mortality in adult covid- inpatients in wuhan the emerging spectrum of covid- neurology: clinical, radiological and laboratory findings sars-cov- can induce brain and spine demyelinating lesions generalized myoclonus in covid- neurologic features in severe sars-cov- infection psychiatric and neuropsychiatric presentations associated with severe coronavirus infections: a systematic review and meta-analysis with comparison to the covid- pandemic covid- : consider cytokine storm syndromes and immunosuppression guillain-barré syndrome associated with sars-cov- brain mri findings in severe covid- : a retrospective observational study early evidence of pronounced brain involvement in fatal covid- outcomes neuropathology of covid- : a spectrum of vascular and acute disseminated encephalomyelitis (adem)-like pathology a rapid fatal evolution of coronavirus disease- (covid- ) in an advanced lung cancer patient with a long time response to nivolumab clinical characteristics of deceased patients with coronavirus disease : retrospective study concomitant acute aortic thrombosis and pulmonary embolism complicating covid- pneumonia covid- and the liver: little cause for concern anosmia and ageusia: common findings in covid- patients unilateral conjunctivitis as first presentation of coronavirus disease (covid- ): a telemedicine diagnosis characteristics of ocular findings of patients with coronavirus disease ophthalmologic evidence against the interpersonal transmission of novel coronavirus through conjunctiva the infection evidence of sars-cov- in ocular surface： a single-center cross-sectional study ocular manifestations of a hospitalised patient with confirmed novel coronavirus disease sars-cov- isolation from ocular secretions of a patient with covid- in italy with prolonged viral rna detection kawasaki disease: insights into pathogenesis and approaches to treatment kawasaki disease: epidemiology and the lessons from it epidemiologic features of kawasaki disease in japan: results of the - nationwide survey association between a novel human coronavirus and kawasaki disease possible involvement of infection with human coronavirus e, but not nl , in kawasaki disease sars-cov- -related paediatric inflammatory multisystem syndrome, an epidemiological study why does covid- disproportionately affect older people? aging immunity may exacerbate covid- inflammaging and 'garbaging blocking elevated p mapk restores efferocytosis and inflammatory resolution in the elderly from discoveries in ageing research to therapeutics for healthy ageing impaired antibody response to influenza vaccine in hiv-infected and uninfected aging women is associated with immune activation and inflammation torc inhibition enhances immune function and reduces infections in the elderly enhancement of cutaneous immunity during aging by blocking p mitogen-activated protein (map) kinaseinduced inflammation a new coronavirus associated with human respiratory disease in china dysregulation of immune response in patients with covid- in wuhan, china immune response in covid- : addressing a pharmacological challenge by targeting pathways triggered by sars-cov- immunopathogenesis of coronavirus infections: implications for sars distribution of ace , cd , cd and other sars-cov- associated molecules in tissues and immune cells in health and in asthma, copd, obesity, hypertension, and covid- risk factors meplazumab treats covid- pneumonia: an open-labelled, concurrent controlled add-on clinical trial no evidence for basigin/cd as a direct sars-cov- spike binding receptor t-cell exhaustion in the tumor microenvironment fighting covid- exhausts t cells cause analysis and treatment strategies of "recurrence" with novel coronavirus pneumonia (covid- ) patients after discharge from hospital neutrophil-to-lymphocyte ratio predicts critical illness patients with coronavirus disease in the early stage immune dysfunction leads to mortality and organ injury in patients with covid- in china: insights from ers-covid- study sars-cov- -specific t cell immunity in cases of covid- and sars, and uninfected controls sars-cov- -reactive t cells in patients and healthy donors sars-cov- -reactive t cells in healthy donors and patients with covid- linkage camden covid- sub-study immune cell profiling of covid- patients in the recovery stage by single-cell sequencing an exploratory randomized, controlled study on the efficacy and safety of lopinavir/ritonavir or arbidol treating adult patients hospitalized with mild/moderate sars-cov- infection protects against rechallenge in rhesus macaques primary exposure to sars-cov- protects against reinfection in rhesus macaques convergent antibody responses to sars-cov- in convalescent individuals transmission of mers-coronavirus in household contacts anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection feasibility of using convalescent plasma immunotherapy for mers-cov infection, saudi arabia transcriptional landscape of sars-cov- infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies systematic comparison of two animal-to-human transmitted human coronaviruses: sars-cov- and sars-cov transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in covid- patients immune and metabolic signatures of covid- revealed by transcriptomics data reuse heightened innate immune responses in the respiratory tract of covid- patients covid- hyperinflammation: what about neutrophils? msphere clinical characteristics and prognosis in cancer patients with covid- : a single center's retrospective study clinical characteristics of covid- -infected cancer patients: a retrospective case study in three hospitals within wuhan, china complement system part i -molecular mechanisms of activation and regulation complement activation contributes to severe acute respiratory syndrome coronavirus pathogenesis accentuated formation of the terminal c b- complement complex in patient plasma precedes development of the adult respiratory distress syndrome association of complement activation and elevated plasma-c a with adult respiratory distress syndrome acute respiratory distress syndrome as an organ phenotype of vascular microthrombotic disease: based on hemostatic theory and endothelial molecular pathogenesis complement-mediated injury and protection of endothelium: lessons from atypical haemolytic uraemic syndrome complement-mediated endothelial cell damage in immune complex vasculitis of the skin: ultrastructurallocalization of the membrane attack complex mannose-binding lectin in severe acute respiratory syndrome coronavirus infection highly pathogenic coronavirus n protein aggravates lung injury by masp- -mediated complement over-activation the complement system in covid- : friend and foe? complement activation in patients with covid- : a novel therapeutic target complement associated microvascular injury and thrombosis in the pathogenesis of severe covid- infection: a report of five cases association of covid- inflammation with activation of the c a-c ar axis immune complement and coagulation dysfunction in adverse outcomes of sars-cov- infection netosis, complement, and coagulation: a triangular relationship the science underlying covid- : implications for the cardiovascular system clinical characteristics of death cases with pulmonary and cardiac pathology in covid- : the first autopsy series from new orleans post-mortem examination of covid patients reveals diffuse alveolar damage with severe capillary congestion and variegated findings of lungs and other organs suggesting vascular dysfunction the significance of disseminated intravascular coagulation on multiple organ dysfunction during the early stage of acute respiratory distress syndrome role of multiple organ dysfunction in ards mortality thrombocytopenia is associated with acute respiratory distress syndrome mortality: an international study hemostasis based on a novel "two-path unifying theory" and classification of hemostatic disorders sepsis and septic shock: endothelial molecular pathogenesis associated with vascular microthrombotic disease human kidney is a target for novel severe acute respiratory syndrome coronavirus (sars-cov- ) infection. medrxiv incidence, clinical characteristics and prognostic factor of patients with covid- : a systematic review and meta-analysis eculizumab treatment in patients with covid- : preliminary results from real life asl napoli nord experience the first case of covid- treated with the complement c inhibitor amy- erythrocytes reveal complement activation in patients with covid- covid- : complement, coagulation, and collateral damage endothelial cell infection and endotheliitis in covid- pathophysiology of sars-cov- : targeting of endothelial cells renders a complex disease with thrombotic microangiopathy and aberrant immune response. the mount sinai covid- autopsy experience renal histopathological analysis of postmortem findings of patients with covid- in china covid- and its implications for thrombosis and anticoagulation severe covid- infection associated with endothelial activation severe covid- infection and thrombotic microangiopathy: success doesn't come easily hypercoagulability of covid- patients in intensive care unit. a report of thromboelastography findings and other parameters of hemostasis covid- does not lead to a "typical" acute respiratory distress syndrome clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study maternal mortality among women with covid- admitted to the intensive care unit sars-cov- in pregnancy: where and what is the evidence? maternal and perinatal outcomes with covid- : a systematic review of pregnancies d-dimer levels on admission to predict in-hospital mortality in patients with covid- confirmation of the high cumulative incidence of thrombotic complications in critically ill icu patients with covid- : an updated analysis coronavirus disease infection among asymptomatic and symptomatic pregnant women: two weeks of confirmed presentations to an affiliated pair of new york city hospitals maternal and neonatal outcomes of pregnant women with covid- pneumonia: a case-control study asymptomatic covid- infection in late pregnancy indicated no vertical transmission cardio-respiratory physiological adaptation of pregnancy clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records sars-cov- infection of the placenta. medrxiv ( ) . . placental pathology in covid- positive mothers: preliminary findings placental pathology in covid- the role of angiogenic factors in the management of preeclampsia coronavirus disease (covid- ) in pregnant women: a report based on cases activation of coagulation system in preterm labor and preterm premature rupture of membranes elevated protease activities in human amnion and chorion correlate with preterm premature rupture of membranes thrombin-induced decidual colony-stimulating factor- promotes abruption-related preterm birth by weakening fetal membranes adjunct immunotherapies for the management of severely ill covid- patients therapeutic efficacy of the small molecule gs- against ebola virus in rhesus monkeys a randomized, controlled trial of ebola virus disease therapeutics broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro compassionate use of remdesivir for patients with severe covid- remdesivir in adults with severe covid- : a randomised, double-blind, placebocontrolled, multicentre trial gilead announces results from phase trial of investigational antiviral remdesivir in patients with severe covid- remdesivir for or days in patients with severe covid- arbidol: a broad-spectrum antiviral compound that blocks viral fusion membranotropic effects of arbidol, a broad anti-viral molecule, on phospholipid model membranes the synthetic antiviral drug arbidol inhibits globally prevalent pathogenic viruses discovering drugs to treat coronavirus disease (covid- ) umifenovir treatment is not associated outcomes in patients with coronavirus disease : a retrospective study favipiravir versus arbidol for covid- : a randomized clinical fluorescence probe measurement of the intralysosomal ph in living cells and the perturbation of ph by various agents targeting endosomal acidification by chloroquine analogs as a promising strategy for the treatment of emerging viral diseases inhibition of endosomal/lysosomal degradation increases the infectivity of human immunodeficiency virus hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro new insights on the antiviral effects of chloroquine against coronavirus: what to expect for covid- ? effects of chloroquine on viral infections: an old drug against today's diseases? hydroxychloroquine decreases th -related cytokines in systemic lupus erythematosus and rheumatoid arthritis patients a systematic review on the efficacy and safety of chloroquine for the treatment of covid- breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in covid- patients with at least a six-day follow up: a pilot observational study hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial no evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe covid- infection a pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease- (covid- ) efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in new york state fda drug safety communication: fda cautions against use of hydroxychloroquine or chloroquine for covid- outside of the hospital setting or a clinical trial due to risk of heart rhythm problems chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (sars-cov- ) infection: preliminary safety results of a randomized, double-blinded, phase iib cl hydroxychloroquine and covid- the fda-approved drug ivermectin inhibits the replication of sars-cov- in vitro effect of dexamethasone in hospitalized patients with first drug to reduce mortality in hospitalised patients with respiratory complications of covid- found epigenetic gene silencing underlies c-fiber dysfunctions in neuropathic pain remdesivir, lopinavir, emetine, and homoharringtonine inhibit sars-cov- replication in vitro a trial of lopinavir-ritonavir in adults hospitalized with severe covid- triple combination of interferon beta- b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with covid- : an open-label, randomised, phase trial lack of evidence to support use of darunavir-based treatments for sars-cov- clinical trial analysis of -ncov therapy registered in china le tocilizumab améliore significativement le pronostic des patients avec pneumonie covid moyenne ou sévère | aphp tocilizumab in patients with severe covid- : a retrospective cohort study interleukin- blockade with high-dose anakinra in patients with covid- , acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study use of anakinra to prevent mechanical ventilation in severe covid- : a case series emerging pharmacotherapies for covid- macrophages eat cancer cells using their own calreticulin as a guide: roles of tlr and btk bruton's tyrosine kinase is required for apoptotic cell uptake via regulating the phosphorylation and localization of calreticulin bruton's tyrosine kinase regulates tlr / -induced tnf transcription via nuclear factor-κb recruitment btk operates a phospho-tyrosine switch to regulate nlrp inflammasome activity bruton's tyrosine kinase is essential for nlrp inflammasome activation and contributes to ischaemic brain injury human nacht, lrr, and pyd domain-containing protein (nlrp ) inflammasome activity is regulated by and potentially targetable through bruton tyrosine kinase inhibition of bruton tyrosine kinase in patients with severe covid- btk/itk dual inhibitors: modulating immunopathology and lymphopenia for covid- therapy the btk inhibitor ibrutinib may protect against pulmonary injury in covid- -infected patients btk inhibitors in cancer patients with covid- : "the winner will be the one who controls that chaos treating leukemia in the time of covid- protective role of bruton tyrosine kinase inhibitors in patients with chronic lymphocytic leukaemia and covid- ivig-mediated effector functions in autoimmune and inflammatory diseases clinical efficacy of intravenous immunoglobulin therapy in critical patients with covid- : a multicenter retrospective cohort study high-dose intravenous immunoglobulin as a therapeutic option for deteriorating patients with coronavirus disease effect of regular intravenous immunoglobulin therapy on prognosis of severe pneumonia in patients with covid- successful treatment with plasma exchange followed by intravenous immunoglobulin in a critically ill patient with covid- recovery of severely ill covid- patients by intravenous immunoglobulin (ivig) treatment: a case series treatment of critically ill patients with covid- with convalescent plasma effectiveness of convalescent plasma therapy in severe covid- patients treatment with convalescent plasma for covid- patients in wuhan use of convalescent plasma therapy in two covid- patients with acute respiratory distress syndrome in korea treatment with convalescent plasma for critically ill patients with severe acute respiratory syndrome coronavirus infection convalescent plasma transfusion for the treatment of covid- : systematic review the resurgence of convalescent plasma therapy early safety indicators of covid- convalescent plasma in , patients mandated bacillus calmette-guérin (bcg) vaccination predicts flattened curves for the spread of covid- world health organization. draft landscape of covid- candidate vaccines - phase i, open-label, dose-ranging study of the safety and immunogenicity of -ncov vaccine (mrna- ) in healthy adults sars-cov- mrna vaccine development enabled by prototype pathogen preparedness a close look at the frontrunning coronavirus vaccines as of may (updated) chinese clinical trial registry. a randomized, double-blinded, placebo-controlled phase ii clinical trial for recombinant novel coronavirus ( -ncov) vaccine (adenovirus vector) safety, tolerability, and immunogenicity of a recombinant adenovirus type- vectored covid- vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial chadox ncov- vaccination prevents sars-cov- pneumonia in rhesus macaques a study of a candidate covid- vaccine (cov ) -full text view -clinicaltrials.gov safety and immunogenicity of the chadox ncov- vaccine against sars-cov- : a preliminary report of a phase / , single-blind, randomised controlled trial development of an inactivated vaccine candidate for sars-cov- dna vaccine protection against sars-cov- in rhesus macaques tolerability and immunogenicity of ino- for covid- in healthy volunteers broad and strong memory cd + and cd + t cells induced by sars-cov- in uk convalescent covid- patients identification of sars-cov- vaccine epitopes predicted to induce long-term population-scale immunity key: cord- -v u h authors: walls, alexandra c.; tortorici, m. alejandra; frenz, brandon; snijder, joost; li, wentao; rey, félix a.; dimaio, frank; bosch, berend-jan; veesler, david title: glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy date: - - journal: nature structural & molecular biology doi: . /nsmb. sha: doc_id: cord_uid: v u h the threat of a major coronavirus pandemic urges the development of suitable strategies to combat these pathogens. hcov-nl is an α-coronavirus that can cause severe lower respiratory tract infections requiring hospitalization. we report here the . Å resolution cryo-electron microscopy reconstruction of the hcov-nl coronavirus spike glycoprotein trimer, which is the conformational machine responsible for entry into host cells and the sole target of neutralizing antibodies during infection. the map resolves the extensive glycan shield obstructing the protein surface and, in combination with mass-spectrometry, provides a structural framework to understand accessibility to antibodies. the structure also reveals a remarkable modular architecture of the receptor-binding subunit and the complete architecture of the fusion machinery including the triggering loop and the c-terminal domains, which contribute to anchoring the trimer to the viral membrane. our data further suggest that hcov-nl and other coronaviruses use molecular trickery, based on masking of epitopes with glycans and activating conformational changes, to evade the immune system of infected hosts. a r t i c l e s coronaviruses are enveloped viruses with large single-stranded positive-sense rna genomes, classified in four genera (α, β, γ and δ). in humans, coronaviruses are responsible for % of respiratorytract infections . in addition, coronaviruses have received substantial attention in the past decade, owing to the emergence of two deadly viruses with tremendous pandemic potential: severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) . to date, there are no approved antiviral treatments or vaccines for any human coronavirus. coronaviruses are zoonotic viruses, and surveillance studies have suggested that both sars-cov and mers-cov originated from bats and that camels are also likely hosts for mers-cov , . moreover, sequencing data have demonstrated that bats serve as a reservoir of coronaviruses that have the potential to cross the species barrier and infect humans. this phenomenon is illustrated by the observation that substitution of three amino acid residues in the spike (s) glycoprotein receptor-binding domain of the bat-infecting hku -cov enhances its affinity for human dpp (the mers-cov receptor) by two orders of magnitude , . in addition, substitution of two other residues enables processing by human proteases and allows the hku -cov s protein to mediate entry into human cells . as a result, cross-species transmission of coronaviruses poses an imminent and long-term threat to human health. recombination with coronaviruses frequently involved in mild respiratory infections may potentially lead to the emergence of highly pathogenic viruses . understanding the pathogenesis, cross-species transmission and recombination of coronaviruses is crucial to prevent or control their spread in humans and to evaluate the potential for long-term emerging diseases. to date, αand β-coronavirus genera have been implicated in human diseases and zoonoses. the human coronavirus nl (hcov-nl ) is an α-coronavirus that is genetically distinct from the β-coronaviruses mouse hepatitis virus (mhv, the prototypical coronavirus), mers-cov and sars-cov, and was first isolated from a -month-old patient with a respiratory-tract infection , . further studies have revealed that hcov-nl infections appear to be common in childhood, and most adult sera contain antibodies that neutralize the virus , . hcov-nl is a major cause of bronchiolitis and pneumonia in newborns worldwide and can cause severe lower-respiratory-tract infections that require hospitalization, especially among young children, the elderly and immunocompromised adults . hcov-nl infections have been reported in countries across europe, asia and north america, thus indicating its circulation among the human population worldwide. other α-coronaviruses related to the human respiratory pathogen hcov- e have recently been identified in camels co-infected with mers-cov , an observation further underscoring the importance of characterizing this coronavirus genus. additionally, the emergence of the highly lethal porcine epidemic diarrhea coronavirus (pedv, α-genus) has recently had devastating consequences for the us swine industry . coronaviruses use s homotrimers to promote cell attachment and fusion of the viral and host membranes. because it is virtually the only antigen present at the virus surface, s is the main target of neutralizing antibodies during infection and a focus of vaccine design . s is a class i viral fusion protein that is synthesized as a single-chain precursor of ~ , amino acids and trimerizes after folding . it is composed of a r t i c l e s an n-terminal s subunit, containing the receptor-binding domain, and a c-terminal s subunit, driving membrane fusion. after virion uptake by target host cells, cleavage at the s ′ site (next to the putative fusion peptide) is required for fusion activation of all coronavirus s proteins, so that they can subsequently transition to the postfusion conformation [ ] [ ] [ ] . our previously reported cryo-em reconstruction of the mhv s glycoprotein at . -Å resolution reveals the prefusion architecture of the machinery mediating entry of β-coronaviruses into cells . it also demonstrates that coronavirus s and paramyxovirus f proteins share a common evolutionary origin. here, we set out to characterize the conservation of the d organization of spike proteins among coronaviruses belonging to different genera. we report the atomic-resolution structure of the pathogenic hcov-nl s-glycoprotein trimer, which belongs to the α-coronavirus genus. the substantial resolution improvement as compared with earlier studies allows visualization of the s glycoprotein at an unprecedented level of detail, which is a prerequisite for guiding drug and vaccine design, and reveals both shared and unique features of the α-genus of human pathogens. our results suggest that hcov-nl and other coronaviruses use molecular trickery, based on epitope masking with glycans and activating conformational changes, to evade the immune system of infected hosts, in a manner similar to that described for hiv- . we used drosophila s cells to produce the hcov-nl s ectodomain n-terminally fused to a gcn trimerization motif downstream from the heptad-repeat (hr ) helix. we imaged frozen-hydrated hcov-nl s ectodomain particles with an fei titan krios electron microscope equipped with a gatan quantum gif energy filter operated in zero-loss mode, with a slit width of ev, and a gatan k summit electron-counting camera (online methods). we determined a d reconstruction of the hcov-nl s at . -Å resolution, using the gold-standard fourier shell correlation (fsc) criterion of . (refs. , ) ( fig. and supplementary fig. ). the final model, which we built and refined with coot and rosetta [ ] [ ] [ ] , includes residues to , with internal breaks between residues - , - and - (supplementary fig. and table ). the hcov-nl s ectodomain is a -Å-long trimer with a triangular cross-section. a notable feature of this structure is the extraordinary number of n-linked oligosaccharides that cover the spike trimer. in the cryo-em npg a r t i c l e s reconstruction, we observed density for n-linked glycans extending tangentially relative to the protein surface ( fig. a, using on-line reversed-phase liquid chromatography with electron transfer/high-energy collision-dissociation tandem ms , we detected n-linked glycosylation sites overlapping with those observed in the cryo-em map and identified three additional sites (fig. c, supplementary fig. and supplementary table ) . we identified these sites from both intact glycopeptides and peptides with the glycan trimmed down to the n-linked core n-acetylglucosamine moiety. the cryo-em and ms data together provide evidence for glycosylation at out of possible nxs/t glycosylation sequons. the intact glycopeptides detected by ms/ms for hcov-nl s expressed in drosophila s cells corresponded to either paucimannosidic glycans containing three mannose residues (with or without core fucosylation) or high-mannose glycans containing four to nine mannose residues. although glycan processing differences exist between insect and mammalian cell expression systems, the same glycosylation sequons are expected to be recognized and glycosylated in both cases. previous reports have suggested that several coronavirus s glycans are of the high-mannose type, as a result of direct budding from the endoplasmic reticulum-golgi intermediate compartment , , thus supporting the biological relevance of the potential glycan structures identified. in the refined model, n-linked glycans cover a substantial amount of the accessible surface of the trimer (fig. a,b) . the higher glycan density per accessible surface area detected for the s subunits ( Å /glycan) compared with the s subunits ( , Å /glycan) may explain why most coronavirus neutralizing antibodies isolated to date target the latter region. because many of the observed glycosylation sites are topologically conserved among coronavirus s proteins, we suggest that the glycan footprint observed here may be representative of those of other s proteins. besides potentially contributing to immune evasion, as discussed below, s glycans have been proposed to play a role in host-cell entry via l-sign lectin, which is an alternative receptor for sars-cov and hcov- e . the hcov-nl and mhv s fusion machineries are structurally similar and can be superimposed with excellent agreement (fig. a and supplementary fig. ; dali z score . , r.m.s. deviation . Å over residues). in contrast to our previous mhv s structure , most of the hcov-nl s ′ trigger loop, which connects the upstream helix to the fusion peptide and participates in fusion activation, is resolved in the reconstruction (fig. b) . the trigger loop runs almost perpendicularly to the long axis of the s subunit and forms three helical segments before looping back to connect to the fusion peptide. multiple arginine residues, forming two putative furin-cleavage sites, are present in the c-terminal region of the s ′ loop ( -rnirssr- ), which is characterized by weaker density, as would be expected from a proteasesensitive polypeptide segment. these observations are consistent with results of previous studies suggesting that fusion activation of the hcov-nl s glycoprotein occurs after s ′ proteolytic processing at the plasma membrane (by trypsin-like proteases such as tmprs ) or in the endosomal pathway (by furin or cysteine proteases) , . the lack of strict amino acid sequence conservation at the s ′ cleavage site among coronavirus s proteins reflects the usage of different proteases found in distinct cellular compartments for fusion activation , . similarly to the additional cleavage site present between the s and s subunits of mers-cov , the multiple glycans present in the vicinity of the s ′ loop probably further influence protease sensitivity (fig. b) . however, we emphasize that s ′ processing occurs at topologically equivalent positions for hcov-nl s, mers-cov s, mhv s and probably most coronavirus s glycoproteins. the hcov-nl s reconstruction (fig. a) resolves a large part of the s c-terminal region that has not been observed in previous studies , . we were able to build an atomic model for the connector domain and the stem helix, which connect to the hr region. the connector folds as a β-rich domain decorated with one short α-helix. at its c-terminal end, the polypeptide chain folds as an α-helix (stem helix, fig. a ,c,d) aligned along the three-fold molecular axis, which turns into the hr domain, corresponding to additional residues not resolved in our map. in the trimer, the connector domains the coronavirus s connector domain and the equivalent paramyxovirus f domain share a related topology, although their tertiary structures are different, and several structural motifs have been added to the latter domain throughout evolution , (fig. e,f) . moreover, the trimer of stem helices assembles as a helical bundle, which initiates the hr domain in a manner reminiscent of the heptad repeat b (hrb) region of paramyxovirus prefusion f structures , . these observations lend further support to the evolutionary connection that we have previously proposed for the fusion machineries of these two viral families . comparison of the prefusion hcov-nl s subunit with the structure of the postfusion core suggests that the c-terminal region of the connector domain and the stem helix must refold and/or change conformation to yield the canonical 'trimer of hairpin' conformation that mediates fusion of the host and viral membrane in all class i fusion proteins , , . the hcov-nl s structure shows the presence of an additional n-terminal domain not present in β-coronaviruses. phylogenetic analyses suggest that this is a canonical feature of most α-coronavirus s glycoproteins (fig. a-c) . this domain, which we named domain , adopts a galectin-like β-sandwich fold supplemented with a three-stranded β-sheet, similarly to domain a ( fig. d-f , dali z score . , r.m.s. deviation . Å over residues), thus suggesting a gene-duplication event. domain interacts with the viral-membraneproximal side of domain a and with domain d. we determined that domain is also structurally similar to the vp * sialic acid-binding domain of the rotavirus vp spike protein ( fig. g ; pdb kqr, dali z score . , r.m.s. deviation . Å over residues). in line with this finding, domain of transmissible gastroenteritis coronavirus (tgev) and of pedv bind to sialic acid, and deletion of this domain in α-coronavirus s appears to correlate with a loss of enteric tropism . we detected no sialic acid binding activity for the hcov-nl s subunit (supplementary fig. ) , thus possibly explaining the strict respiratory tropism of this virus. instead, host-cell heparan sulfate proteoglycans have been shown to participate in hcov-nl anchoring and infection , and we detected binding of heparan sulfate to the hcov-nl s protein by using surface plasmon resonance (spr) (supplementary fig. a) . we hypothesize that these interactions may be mediated either by domain , which exhibits several positively charged patches on its surface ( supplementary fig. b) , or domain a, which has been reported to bind carbohydrates in the case of a bovine coronavirus . a putative immune-evasion strategy domain b, which is the hcov-nl receptor-binding domain, exhibits a structure distinct from those of β-coronavirus b domains, although a topological relatedness has been detected among these β-rich domains . superimposition of the hcov-nl and mhv s subunits highlights that their b domains feature opposite orientations related by an ~ ° rotation (fig. a,b) . as a result, many of the hcov-nl receptor-binding residues are buried through interaction with domain a of the same protomer, are masked by the glycan at residue asn and are not available to engage the host-cell receptor (human angiotensin-converting enzyme , ace ). comparison of the hcov-nl domain-b structure in our cryo-em-derived model with the crystal structure of the same domain in complex with ace (ref. ) revealed that the receptor-binding loop containing residues - undergoes substantial conformational changes after binding (and is defined by weak density ; fig. c ). these findings explain the markedly higher ace binding affinity of hcov-nl domain b, compared with that of the full-length s domain (fig. d) . because the receptor-binding loops elicit potent neutralizing antibodies in the case of tgev , mers-cov and sars-cov - , we speculate that hcov-nl has evolved to limit exposure of this vulnerable site to b-cell receptors via protein-protein interactions and glycan masking. this mechanism is reminiscent of the hiv- immune evasion strategy, which relies on a glycan shield and conformational changes that are triggered by binding of cd and expose the chemokine-receptor-interacting motifs , . viruses have evolved several immune-evasion strategies including rapid antigenic evolution, masking of epitopes and exposure of nonneutralizing immune-dominant 'decoy' epitopes. for example, hiv- (ref. ), lassa virus , hepatitis c virus and epstein-barr virus exhibit extensive n-linked glycosylation, covering exposed protein surfaces, with glycan masses that may exceed that of the protein component. the hcov-nl s trimer is covered by an extensive glycan shield consisting of n-linked oligosaccharides obstructing the protein surface. this observation is reminiscent of descriptions of the hiv- envelope trimer , although the glycan density is % higher in the latter case. furthermore, our data suggest that, similarly to hiv- , coronavirus s glycans mask the protein surface and consequently limit access to neutralizing antibodies and thwart the humoral immune response. this strategy is illustrated by the presence of a glycan linked to asn in the hcov-nl structure reported here. this glycan, along with the proteinaceous moiety of domain a, contributes to masking the receptor-binding loops, which have been shown to elicit potent neutralizing antibodies for other coronaviruses [ ] [ ] [ ] [ ] [ ] [ ] and appear to represent a potential ' achilles' heel' of these viruses. this hypothesis is further supported by the observation of three additional glycans directly protruding from the viral-membranedistal side of domain b. as a result, conformational changes are npg a r t i c l e s required for the hcov-nl s glycoprotein to be able to interact with ace (ref. ). these rearrangements and/or receptor binding are likely to participate in initiating the fusion reaction by disrupting the interactions formed between domain b and the hr c-terminal region. interactions with heparan sulfate proteoglycans present at the host-cell surface might potentially contribute to activating hcov-nl s and promote subsequent interactions with ace . a common theme arising from the analysis of αand β-coronavirus s-glycoprotein structures is that domain-b-mediated host anchoring involves major structural rearrangements that expose the binding motifs , . visualization of the glycan shield obstructing access to the s surface and deciphering the molecular trickery used by some coronaviruses provide a rational basis for understanding the accessibility to neutralizing antibodies and may pave the way for guiding future design of immunogens or therapeutics. we have previously suggested that targeting the fusion machinery bears the promise of finding broadly neutralizing inhibitors of coronavirus infection , and the high density of glycans decorating this region will need to be taken into consideration to increase the likelihood of success. methods and any associated references are available in the online version of the paper. the authors declare no competing financial interests. reprints and permissions information is available online at http://www.nature.com/ reprints/index.html. a gene fragment encoding the hcov-nl s ectodomain (residues - , uniprot q q s ) was pcr-amplified from a plasmid containing the fulllength s gene. the pcr product was ligated to a gene fragment encoding a gcn trimerization motif (likrmkqiedkieeieskqkkieneiarikkik) cryo-em data processing. whole-frame alignment was carried out with dosefgpu driftcorr . the parameters of the microscope contrast-transfer function were initially estimated with ctffind (ref. ) and then with gctf . micrographs were manually masked with appion to exclude the visible carbon edge from images. particles were automatically picked with dogpicker . particle images were extracted and processed with relion . (ref. ) with a box size of pixels and a pixel size of . Å. after reference-free d classification, we retained , out of , particles to run d classification with c symmetry . we used the initial model previously generated for mhv with optimod and low-pass-filtered the data to Å as a starting reference for d classification. , particles were selected and used to run gold-standard d refinement with relion , thus yielding a map at . -Å resolution. after particle-motion and radiation-damage correction with relion particle polishing , another round of d classification with c symmetry was performed to select , particles. after gold-standard d refinement with this subset of particles, we obtained a reconstruction at . -Å resolution. per-particle defocus parameters were estimated with gctf and used to run an identical round of d refinement that yielded the final . -Å-resolution map. post processing was performed with relion to apply an automatically generated b factor of − Å . reported resolutions were based on the gold-standard fsc = . criterion , , and fsc curves were corrected for the effects of soft masking by high-resolution noise substitution . the soft mask used for fsc calculation had a -pixel cosine-edge fall-off. model building and analysis. ucsf chimera and coot , were used to fit atomic models into the cryo-em map. the mhv s subunit was fit into the density and rebuilt manually in coot. the crystal structure of hcov-nl domain b was then fit into the density, and the rest of the s subunit was built with a combination of manual building in coot and de novo building with rosetta - . glycan density coming after an nxs/t motif was initially manually built into the density, and glycan geometry was then refined with rosetta, optimizing the fit-to-density as well as the energetics of protein-glycan contacts. the glycans were not as well defined as the protein region in the reconstruction, owing to flexibility and compositional heterogeneity. the final model was refined by application of strict noncrystallographic symmetry constraints with rosetta, with a training map corresponding to one of the two maps generated by the goldstandard refinement procedure in relion. the second map (testing map) was used only for calculation of the fsc compared with the atomic model and preventing overfitting was used with calibrated charge-dependent etd parameters and a supplemental higher-energy collision dissociation energy of . for the samples with intact glycopeptides and . for the samples treated with endoglycosidases. a resolution setting of , with an agc target of × was used for ms , and a resolution setting of , with an agc target of × was used for ms . the data were searched against a custom database including recombinant coronavirus s-glycoprotein sequences, a list of common contaminant proteins including trypsin, chymotrypsin and the endoglycosidases, as well as decoy reverse yeast sequences, with trypsin or chymotrypsin as the protease, allowing up to two missed cleavages. all searches included carbamidomethylation of cysteine as a fixed modification and oxidation of methionine as a variable modification. an initial comprehensive search for glycosylation revealed that (core-fucosylated) paucimannose and high-mannose structures were the only identified glycan species in the samples. on the basis of these findings, a final search was performed with comet on the same data with the following list of variable modifications of asparagine residues: +hexnac( )hex( ), +hexnac( )hex( )dhex( ), +hexnac( )hex( )dhex( ), +hexnac( )hex( ), +hexnac( )hex( ), +hexnac( )hex( ), +hexnac( )hex( ), +hexnac( )hex( ) and +hexnac( )hex ( ) . the samples treated with endoglycosidases were searched with +hexnac, +hexnac( )dhex( ) and +hexnac( )dhex( ) as variable modifications of asparagine. we used a precursor mass tolerance of p.p.m., . fragment bin size, including b/c/y/z fragments, with monoisotopic masses for both precursor and fragment ions. the search results were filtered for modification of asparagine residues and the presence of an nx(s/t) sequon at the protein level. all appropriate peptide spectrum matches (psms) were manually inspected, and only those with reasonable peptide sequence coverage were kept. in addition, the spectra were inspected for the presence of glycan fragment ions. all glycosylation sites identified by ms listed in supplementary table are based on multiple psms, often with multiple different glycans and additional confirmation from overlap between the trypsin-and chymotrypsin-treated samples. the greatest number of glycopeptide identifications was made in the chymotrypsin-digested samples. hemagglutination assay. the s subunit of hcov-nl c-terminally tagged with the fc portion of human igg (s -fc) was tested alone or premixed with µl of protein a-coupled, -nm-sized nanoparticles (nano-screenmag-protein a beads; chemicell, cat.no. - ) to increase the avidity of s -fc proteins for sialic acids on the erythrocyte surface. the sialic acid-binding s subunit of pedv (strain gdu, genbank afp . ) c-terminally fused to the human fc portion was used as a positive control. 'mock' indicates the conditions in which no s subunit was used (negative control). the initial concentration of s -fc was µg, and two-fold serial dilutions of s -fc-nanoparticle mixtures were made in µl phosphate-buffered saline supplemented with . % bovine serum albumin. µl erythrocyte suspension ( . %) was mixed with µl of s -fc-nanoparticle dilution in v-shaped -well plates and incubated for h on ice, after which the wells were photographed. protein expression of s variants and ace . different s variants of hcov-nl s protein, including s (residues - ), s domain (s - , residues - ) and s domain b (s -b, residues - ), were c-terminally fused to the fc region of mouse igg (mfc), expressed in hek- t cells and affinity purified as previously described . likewise, an s -mfc expression plasmid was made for the sars-cov s domain (isolate cuhk-w , residues - ) and the pedv s domain (strain gdu; residues - ). expression of the human angiotensinconverting enzyme ectodomain (ace ; residues - ) fused to the fc portion of human igg (hfc) was performed as previously described . coronaviruses: drug discovery and therapeutic options middle east respiratory syndrome and severe acute respiratory syndrome isolation and characterization of a bat sars-like coronavirus that uses the ace receptor co-circulation of three camel coronavirus species and recombination of mers-covs in saudi arabia receptor usage and cell entry of bat coronavirus hku provide insight into bat-to-human transmission of mers coronavirus bat origins of mers-cov supported by bat coronavirus hku usage of human receptor cd two mutations were critical for bat-to-human transmission of middle east respiratory syndrome coronavirus identification of a new human coronavirus a previously undescribed coronavirus associated with respiratory disease in humans human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry human coronavirus nl infection and other coronavirus infections in children hospitalized with acute respiratory disease in hong kong deadly pig virus slips through us borders the spike protein of sars-cov: a target for vaccine and therapeutic development the coronavirus spike protein is a class i virus fusion protein: structural and functional characterization of the fusion core complex coronavirus cell entry occurs through the endo-/lysosomal pathway in a proteolysis-dependent manner host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein host cell proteases: critical determinants of coronavirus tropism and pathogenesis cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer electron counting and beam-induced motion correction enable nearatomic-resolution single-particle cryo-em prevention of overfitting in cryo-em structure determination optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions atomic-accuracy models from . -Å cryo-electron microscopy data with density-guided iterative local refinement de novo protein structure determination from near-atomicresolution cryo-em maps high-resolution comparative modeling with rosettacm unambiguous phosphosite localization using electron-transfer/ higher-energy collision dissociation (ethcd) human coronavirus e can use cd l (l-sign) to enter cells identification of n-linked carbohydrates from severe acute respiratory syndrome (sars) spike glycoprotein a single asparagine-linked glycosylation site of the severe acute respiratory syndrome coronavirus spike glycoprotein facilitates inhibition by mannosebinding lectin through multiple mechanisms cd l (l-sign) is a receptor for severe acute respiratory syndrome coronavirus dali server: conservation mapping in d simultaneous treatment of human bronchial epithelial cells with serine and cysteine protease inhibitors prevents severe acute respiratory syndrome coronavirus entry pre-fusion structure of a human coronavirus spike protein structure of rsv fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody structure of the parainfluenza virus f protein in its metastable, prefusion conformation viral membrane fusion core structure of s from the human coronavirus nl spike glycoprotein the rhesus rotavirus vp sialic acid binding domain has a galectin fold with a novel carbohydrate binding site point mutations in the s protein connect the sialic acid binding activity with the enteropathogenicity of transmissible gastroenteritis coronavirus human coronavirus nl utilizes heparan sulfate proteoglycans for attachment to target cells crystal structure of bovine coronavirus spike protein lectin domain evidence for a common evolutionary origin of coronavirus spike protein receptor-binding subunits crystal structure of nl respiratory coronavirus receptor-binding domain complexed with its human receptor structural bases of coronavirus attachment to host aminopeptidase n and its inhibition by neutralizing antibodies junctional and allele-specific residues are critical for mers-cov neutralization by an exceptionally potent germline-like antibody structure of severe acute respiratory syndrome coronavirus receptor-binding domain complexed with neutralizing antibody structural basis of neutralization by a human anti-severe acute respiratory syndrome spike protein antibody, r potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s protein that blocks receptor association potent cross-reactive neutralization of sars coronavirus isolates by human monoclon al antibodies structure of an unliganded simian immunodeficiency virus gp core structure of a v -containing hiv- gp core trimeric hiv- -env structures define glycan shields from clades a, b, and g arenavirus glycan shield promotes neutralizing antibody evasion and protracted infection hepatitis c virus envelope glycoprotein e glycans modulate entry, cd binding, and neutralization structure of the epstein-barr virus major envelope glycoprotein after immobilization quenching, running buffer was flowed for min to ensure a steady baseline before experimental binding. heparan sulfate (sigma aldrich) was reconstituted in running buffer at . mg/ml. two concentrations of heparan sulfate, . mg/ml and . mg/ml, were injected for s with a dissociation time of s. all data were subtracted from the blank flow cell crystal structure of gcn -piqi, a trimeric coiled coil with buried polar residues automated molecular microscopy: the new leginon system ctffind : fast and accurate defocus estimation from electron micrographs real-time ctf determination and correction appion: an integrated, database-driven pipeline to facilitate em image processing dog picker and tiltpicker: software tools to facilitate particle selection in single particle electron microscopy relion: implementation of a bayesian approach to cryo-em structure determination optimod: an automated approach for constructing and optimizing initial models for single-particle electron microscopy beam-induced motion correction for sub-megadalton cryo-em particles high-resolution noise substitution to measure overfitting and validate resolution in d structure determination by single particle electron cryomicroscopy visualizing density maps with ucsf chimera features and development of coot cryo-em model validation using independent map reconstructions molprobity: all-atom structure validation for macromolecular crystallography privateer: software for the conformational validation of carbohydrate structures the interpretation of protein structures: estimation of static accessibility pdb pqr: an automated pipeline for the setup of poisson-boltzmann electrostatics calculations electrostatics of nanosystems: application to microtubules and the ribosome quantifying the local resolution of cryo-em density maps comet: an open-source ms/ms sequence database search tool dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc ace binding elisa. the ability of the hcov-nl s -mfc and s -b-mfc chimeric proteins to bind the ace -hfc receptor was evaluated with an elisa-based assay. µl of hace -hfc ( µg/ml, diluted in pbs) was coated on a -well maxisorb plate overnight at °c. nonspecific binding sites were subsequently blocked with a % (w/v) solution of bovine serum albumin in pbs. plates were washed with washing buffer (pbs with . % tween ) and subsequently incubated with serially diluted s -mfc proteins (starting with equimolar concentrations) for h at room temperature, after which plates were washed three times with washing buffer. mfc-tagged s proteins were detected with hrp-conjugated polyclonal rabbit-anti-mouse immunoglobulins ( : , dilution in pbs with . % bsa; dako, p ; validation on manufacturer's website), and a colorimetric reaction was produced after incubation with tetramethylbenzidine substrate (biofx). the optical density (od) was subsequently measured at nm with an elisa reader (el- , biotek). background (signal from hrp-conjugated anti-mfc antibody alone) was subtracted from the od nm values. the mfc-tagged sars-cov s subunit was used as a positive control, whereas the mfc-tagged hcov-nl s domain (hcov-nl s - -mfc) and pedv s subunit (pedv s -mfc), both of which do not bind ace , were used as negative controls.surface plasmon resonance (spr). spr was performed on a ge healthcare biacore t with a running buffer containing mm hepes, ph . , mm nacl and . % tween- , with a flow rate of µl/min at °c. a carboxymethylated dextran (cm ) chip (ge healthcare) was activated with n-hydroxysulfosuccinimide (nhs) and -ethyl- -( -dimethylaminopropyl) carbodiimide key: cord- -yx golq authors: deng, ziqin; chen, junsheng; wang, ting title: bibliometric and visualization analysis of human coronaviruses: prospects and implications for covid- research date: - - journal: front cell infect microbiol doi: . /fcimb. . sha: doc_id: cord_uid: yx golq human coronaviruses, which can cause a range of infectious diseases, have been studied for nearly years. the field has gained renewed interest from researchers around the world due to the covid- outbreak in late . despite a large amount of research, little is known about the knowledge structure and developing trends of this topic. here, we apply bibliometric analysis along with visualization tools to analyze , publications related to human coronavirus from the scopus database, using indicators on publication and citation, journal, country or territory, affiliation and international cooperation, author, and keyword co-occurrence cluster. the results show that research on human coronavirus is dominated by sars-cov. although there have been many publications, only publications ( . % of total) have more than citations. the top journals with most publications account for . % of total publications and % of total citations. in addition to the united states and some european countries, many asian and african countries are involved in this research, with china holding an important position in this area. leading researchers from various fields of human coronavirus research are listed to facilitate collaboration and promote effective disease prevention and control. the keywords co-occurrence analysis reveals that the research focus on virology, public health, drugs and other hotspot fields, and uncovers changes in the direction of coronavirus research. the research map on human coronavirus obtained by our analysis are expected to help researchers to efficiently and effectively explore covid- . coronaviruses, which were discovered in the s (estola, ) and cause a range of respiratory and intestinal infections in animals and humans (geller et al., ) , are enveloped viruses with positive-sense single-strand rna which belong to the nidovirales order, the coronaviridae family and the coronavirinae subfamily (gonzalez et al., ) . the name "coronavirus" is derived from the latin corona, meaning crown or halo, and refers to the virus's characteristic appearance under an electron microscope, which appears like a crown or solar corona (almeida and tyrrell, ) . there are four genera contained in the coronavirinae subfamily: the alpha-, beta-, gamma-, and deltacoronavairus. these viruses can infect not only birds (gamma-and deltacoronaviruses), but also a range of mammalian species (mainly alpha-and betacoronaviruses), including humans (corman et al., ) . coronaviruses have been known for more than years (saif, ) , while only seven of them have been proven to infect humans so far. plenty of evidence has strongly suggested that human coronaviruses exist with or origin from livestock or some wild animals (corman et al., ) . in this case, diseases caused by coronaviruses can also be defined as a kind of zoonosis. human coronavirus (hcov) had not been considered as a highly pathogenic virus to humans until the severe acute respiratory syndrome (sars) outbreak in (peiris et al., ) and the middle east respiratory syndrome (mers) outbreak in (zumla et al., ) . recently, another coronavirus disease, the covid- , caused by a novel coronavirus, sars-cov- (ciotti et al., ; tan et al., ) , has evoked these painful memories and made people more intensely aware of the pathogenic potential of these microorganisms (cui et al., ) . this is the seventh coronavirus identified so far to infect humans, with the others being hcov- e, hcov-oc , hcov-nl , hcov-hku , sars-cov, and mers-cov (geller et al., ) . hcov- e, hcov-oc , hcov-nl , and hcov-hku are able to cause common cold in humans and majority of these infections only manifest mild symptoms in respiratory system (mackay et al., ; owusu et al., ; annan et al., ) . however, sars-cov and mers-cov are more serious and responsible for high case fatality rates, both of whom belong to genus beta. once the case-fatality rate of sars was ∼ % (cheng et al., ) , while that of mers ranged around % . similar to sars-cov and mers-cov, sars-cov- is also one of the betacoronaviruses, but with quite unique qualities zhu et al., ) . the clinical casefatality rate is not as severe as that of sars-cov and mers-cov, but it is more infectious than either virus (chan et al., ; huang et al., ) . as of : pm cest, july , there have been , , confirmed cases of covid- , including , deaths, reported to who . and the virus had also spread to countries and territories around the world and international conveyances by august , , : gmt. scientists have been studying the human coronavirus since its discovery in the s (hamre and procknow, ; bradburne et al., ; mcintosh et al., ) , and more than , papers related to coronavirus have been published (according to our search) (supplementary figure ) . however, researchers need to devote a significant amount of time to reading and identifying relevant work in related fields due to the long research interval, large amount of data, uneven quality of scientific research papers, the presence of unnecessary duplications, and the differences between human coronaviruses and emerging viruses. therefore, it is particularly urgent to sort out important, effective and meaningful information from large databases in order to guide the scientific research, and promote the proper prevention, control, diagnosis and treatment of human coronavirus. bibliometrics, together with novel visualization methods of scientific information, have been reported to be helpful to identify emerging outbreaks of infectious disease. this is particularly true in the current age, where thousands of reports can be easily exchanged between public health specialists and healthcare providers across the internet (takahashi-omoe and omoe, ; unkel et al., ) . bibliometrics is also recognized as an essential tool and is widely used in a variety of fields to measure and evaluate scientific research quantitatively and qualitatively (aggarwal et al., ; romero and portillo-salido, ; deng et al., ) . therefore, in order to accurately, effectively and systematically reveal connections within the human coronavirus field, our study applied bibliometrics and visualization methods to analyze human coronaviruses-related publications and citations, countries and affiliations, as well as journal performance, author impact and keyword cooccurrence cluster. this study seeks to serve as a valuable reference and guidance for virologists, pharmacists, clinicians and epidemiologists studying the emerging human coronavirus, and to provide novel ideas for finding effective control measures, as well as drugs and vaccines, as soon as possible. our analysis was conducted using the online database scopus (https://www.scopus.com/), which provides a comprehensive collection of different types of scientific peer-reviewed literature (romero and portillo-salido, ; bonilla-aldana et al., ) . the document search was performed on february , . in order to cover as many target documents as possible, we had selected terms that might be used by most scientific publications before the search formula was designed: besides "human coronavirus, " "novel coronavirus" and their abbreviation forms "hcov" and "ncov, " we have the terms "human coronavirus e" ("hcov- e"), "human coronavirus oc " ("hcov-oc "), "human coronavirus nl " ("hcov-nl "), and "human coronavirus hku " ("hcov-hku ") to search for publications related to these four currently known nonseverely pathogenic human coronavirus; for sars related publications, we have "severe acute respiratory syndrome-related coronavirus" ("sarsr-cov" or "sars-cov") and "severe acute respiratory syndrome" ("sars"); for mers related publications, we have "middle east respiratory syndrome-related coronavirus" ("mers-cov") and "middle east respiratory syndrome" ("mers") as well as "mers coronavirus erasmus medical center/ " ("mers coronavirus emc/ , " "hcov-emc/ , " or "emc/ "), "novel coronavirus- " (" -ncov") and "camel flu"; as for the covid- related publications, we have "severe acute respiratory syndrome coronavirus- " ("sars-cov- "), "coronavirus disease- " ("covid- "), " -novel coronavirus" (" -ncov"), " -ncov acute respiratory disease, " "novel coronavirus pneumonia" and "novel coronavirus-infected pneumonia." several writing formats that are not generally accepted, like "corona virus" and "hcov e, " were also taken into consideration after we had found them been used in some publications. notably, when directly using the abbreviation "sars" and "mers" to search, we were provided with a massive number of unrelated results in other fields. we decided to add qualifiers as limitation to these terms to have the accuracy of search optimized ( table ) . and finally, we conducted the search with the following formula, designed according to the search rules of scopus (deng et al., ) : title-abs-key ("human coronavirus" or "human corona virus" or hcov or "novel coronavirus" or "novel corona virus" or ncov or "severe acute respiratory syndrome" or ({sars} and " * cov" or * virus or crisis or outbreak or epidemic or pandemic) or "sarsr-cov" or "middle east respiratory syndrome" or ({mers} and " * cov" or * virus or crisis or outbreak or epidemic or pandemic) or "camel flu" or "emc/ " or "coronavirus disease " or "covid- " or (coronavirus or "corona virus" or " * cov" and e or oc or nl or hku ) or hcov e or hcovoc or hcovnl or hcovhku ) ( table ) . all search results, data and information that were essential for our analysis, including the count of citations and some indicators, were extracted from scopus on february , . complete document lists were exported as csv files, which were then imported into microsoft excel for ranking and counting. bar charts were made by graphpad prism , and vosviewer . . was used to generate the visualization maps. in the analysis of country (or territory), affiliation and author, every co-author was counted equally. in this case, documents with too many authors are not comparable to documents with fewer authors. since only documents with a maximum of authors were counted by scopus, we followed the same strategy when conducting the visualization analysis with vosviewer. our search yielded , results, based on their titles, abstracts and key words. then we limited our results to publications in english and chinese, which yielded , documents in total, including , articles, , reviews and , documents of other types (supplementary figure ) . as expected, the annual publications count was naturally divided into four sections, due to three notable epidemic events in history. before the outbreak of sars, the annual publication amount remained low, reaching a maximum of in . it was not until the sars crisis occurred in that the scientific publications in this field experienced explosive growth. the annual publication number rose suddenly to , in and continued to rise the following year, when it reached , publications. for the next few years, the publication count declined gradually, reaching a low of publications in . it was the first outbreak of mers in the middle east that led to renewed interest in coronavirus and an increase in publications. this lasted for years, during which time the annual number reached another peak, publications in , coinciding with the second outbreak of mers in south korea. notably, the annual publication number has continued to decline since then. for the publications on human coronavirus in , only publications released prior to february were counted. interestingly, the trend for summed citation of annual publications closely aligned with annual publication production prior to (figure ). for our citation analysis, we counted the number of publications with different citation amounts. we found that more than half of the publications, up to , ( . %, , articles, , reviews), had been cited no more than times, including , that had gone uncited ( . %, , articles, reviews). only . % of publications ( publications, articles, reviews) had more than citations, and only publications ( . %) and publications ( . %) had been cited more than and times, respectively (supplementary figure ) . the top most cited articles and non-articles are listed separately in table and supplementary table . among the top articles, six were published in the new england journal of medicine, four in science, three in nature, two in the lancet and the remaining five articles were published in five other journals. in total, these articles were published in nine different journals. most of them were published after , corresponding to the time of the sars outbreak. the research areas of the top articles involve public health, preventive medicine, epidemiology, clinical reports and virological study, including the identification, isolation, and analysis of natural hosts of these coronaviruses. all english and chinese documents came from , different journals. the journals with the most publications on human coronavirus are listed in table . this list includes four journals that published articles that were in the top article list (table ) (new england journal of medicine, science, nature and lancet). these journals produced . % ( , ) of all publications analyzed here and . % of the total citations ( , of , ). among them, the new england journal of medicine had the highest values in two indicators, citations per document and citescore ( ). also, notably, contributions made by chinese journals like hong kong medical journal and chinese medical journal cannot be ignored. figuring out core journals in a specific research field is of considerable importance. this can not only help academic achievements be known and used as much as possible, but also provide those who need the information with more concentrated access. the united states has dominated this field with , citations on its , published documents. china ranked second with a total of , citations for its , documents from researchers in mainland china, , total citations on , documents from researchers in china hong kong and , total citations on documents from researchers in china taiwan. the united kingdom and canada have also contributed significantly to this research area ( in chan, leo l.m. poon and guan yi, which have all garnered high citation counts, cannot be ignored. the studies of those active and emerging researchers with unique ideas rather deserves our attention. it inspired us that more comprehensive and detailed evaluation of researchers will help to identify their specific areas of expertise, and therefore make their work more valued when applicable. a co-occurrence relationship is formed between two keywords when they both occurred in the same paper. keywords with strong co-occurrence relationship can reveal research hotspots more precisely than a single keyword. in our visual representation, strongly connected keywords were colored the same, indicating that they might share something in common. keywords shown in red are roughly connected to public health, preventive medicine and epidemiology. according to these keywords, human coronavirus diseases like "sars, " "mers" and covid- may have something worthwhile for comparison with other "infectious diseases" like "influenza" in their epidemiological characteristics; "healthcare workers, " "transmission, " "surveillance, " "quarantine, " or "isolation" may be the focuses of these studies, which can help to promote current disease control and prevention measures. keywords in blue and yellow are related to virus detection and clinical diagnosis. among them, "serology" and "rt-pcr" are likely to be the methods, the research objects are mainly some kinds of "respiratory viruses, " and the research purposes are mostly on "evolution, " "phylogeny, " and "diagnosis." the words in green are mainly virology-related and also include some immunological and pharmaceutical research: "spike protein, " "nucleocapsid protein, " "receptor-binding domain, " "ace- " and "apoptosis" are mainly on "pathogenesis, " while "epitope, " "antibody, " "vaccine, " "inhibitor, " "interferon, " "ribavirin, " and "antiviral activity" are mainly about antiviral solutions (figure ) . with keyword co-occurrence analysis, we can not only figure out the hotspots, but also discover the limitations, and even come up with new ideas. with the outbreaks of sars in and mers in , along with current covid- pandemic (harapan et al., ) , the world has battled three serious human coronavirus outbreaks during the twenty first century. in particular, the covid- outbreak has surpassed the previous two ones in terms of its transmission scale, largely due to the strong infectivity and long asymptomatic incubation period of the emerging pathogen (epidemiology working group for ncip epidemic response, chinese center for disease control and prevention, ). human coronavirus has been an area of concern for many years, with the first study conducted almost years ago and plenty of scientific documents published in the decades since. however, when the novel virus emerged, controlling the spread of this virus effectively and promptly remained a significant challenge. this is partially due to the unclear knowledge map of human coronavirus research and an inadequate understanding of the present research status, hotspots and development trends. this can result in a large amount of repetitive, insignificant or inefficient research work, which can prevent effective analysis of this virus and further delay the development of targeted prevention and control measures. therefore, we applied an innovative bibliometric and visualization analysis to sort and analyze more than , human coronavirus-related scientific publications spanning years, with the purpose of mapping and managing previous research in this field. the trends in the annual number of publications and summed citation of annual publications on human coronaviruses (figure ) reflect the interest and development of this area over the years (durieux and gevenois, ) . from to , the number of publications was low and remained at a stable amount. strikingly, two explosive growth peaks appear separately in and , matching the onset of the sars and mers outbreaks. this sharp growth seen at these times is reflective of the severe impact of emerging coronaviruses on human health. the number of publications is directly proportional to the extent and spread of the infective disease outbreak (hurtado et al., ) . the peak that emerged during the sars crisis is significantly higher than the one that emerged during the mers outbreak, which is due to the more widespread outbreak and more extensive impact of sars. considering the severity of the covid- outbreak, we can predict that this trend will continue and a large amount of publications will follow. meanwhile, after the short mers outbreak, the summed citation of annual publications dropped quickly and became out of sync with the number of annual publications, which might reflect a gradual declining interest in human coronavirus research. however, it is believed that the covid- outbreak caused by the emerging sars-cov- will bring the research on human coronavirus back to forefront. just as we predicted, the number of literatures on sars-cov- and covid- has doubled in the past months, according to our latest online-searching in august. this has proven that the consequences of covid- are so catastrophic and far-reaching that it has attracted attention worldwide. the citation number of an article represents the extent of its dissemination and influence, and thus partly reflects its quality as well (muniz et al., ) . although there have been over , publications on human coronavirus, only ( . %) have more than citations, while , ( . %) have < citations (supplementary figure ) . this indicates that although there has been much research on human coronavirus, there might be only a small percentage of these studies that are of high quality. it also indicates that the research field is wide but not deep, implying that much remains for researchers to study about this virus, and in-depth exploration in some specialized areas could shift the focus and direction of this field for the future. among the top articles listed in table , six were published in the new england journal of medicine, four in science, three in nature, two in the lancet and the other five articles were published in five different journals. these nine different journals are very responsive to novel emerging viruses and related diseases. moreover, of these top articles are related to the sars outbreak and only one is connected to the mers outbreak. for the top non-article publications listed in supplementary table , there were up to different journals in the list, indicating the attention received by these publications, all of which are related to sars research, from other sources. therefore, sars-cov plays an important and enlightening role in analyzing the research on human coronavirus. despite the fact that all english and chinese publications were obtained from , different sources, the top journals with the most published documents account for . % of all publications and . % of all citations. this is reflective of the authority of these journals, as well as their high degree of interest in research related to human coronaviruses. due to the limitations of scopus, journals can only be sorted by the total number of published documents. however, as shown in table , the new england journal of medicine, proceedings of the national academy of sciences of the united states of america, science, nature and the lancet rank in the top five based on citations per document, which is consistent with the results in table . popular journals and their research trends in a particular field provide researchers with reliable references. in addition, core journals provide researchers with faster search routes and can serve as an important publication guide (zhuang et al., ; wang et al., ) . the united states, the united kingdom, germany and other european countries are usually the most active countries at the forefront of scientific research (sweileh, ) . however, as can be seen from figure a , the situation is quite different in the human coronavirus field. the united states remains dominant in this field, while some asian and african countries, such as china, singapore, saudi arabia, south korea, japan, india and egypt ranked in the top for human coronavirus-related research. this implies that the research on emerging viruses is no longer limited within those developed countries with more developing countries getting involved. one possible factor lies in the wide and fast spread of the diseases, which has enabled more and more people have come to realize the urgency of taking timely actions and having a clear understanding of emerging infectious diseases. additionally, advancements in science and technology, as well as increased funding support from national policies in these regions have been instrumental in discovering and analyzing emerging viral pathogens. in particular, the top affiliations with the highest number of documents published (figure , supplementary table ) reflect chinese scientists' contributions to the human coronavirus field, with nearly a half of the top affiliations coming from china. similarly, a recent article from stanley perlman also praised the contribution of chinese scientists to the study of novel human coronaviruses (perlman, ) . here, we generated a map to show the contributions of different countries to the human coronavirus field and display the cooperative relationship between countries (or territories) intuitively ( figure b ). this map indicates that international cooperation efforts between coronavirus researchers are led by the united states, china, china hong kong, the united kingdom and canada. these results can provide significant guidance for initiating collaborative projects, project applications, and academic exchanges, as well as providing information that can be used in the political sphere in different countries, territories and affiliations concerned with the impact of human coronavirus (fiala, ) . as for the covid- pandemic, the lack of information sharing and collaborative efforts is very detrimental to the prevention of diseases. countries and affiliations are supposed to take on the responsibilities to strengthen mutual trust and international cooperation, so that we can fight against this fatal virus with more joint efforts. analyses of author can help to understand a research field in a more comprehensive manner, and to evaluate the contributions of researchers, as well as their research level and academic status in this field, objectively (podsakoff et al., ) . in our study, the top authors with the most publications were used to screen out those active researchers in this area. as shown in table , yuen kwok-yung has produced the largest number of documents, guan yi has the highest number of citations per document, and joseph sung jao-yiu currently has the highest hindex. these data and indicators provide different perspectives on the research level and academic authority of each researcher. interestingly, consistent with figure , table reveals half of the top researchers are from china, which also reflects the more active state of chinese researchers on human coronaviruses. it should be noted that among all the authors, some are researchers from research institutions at universities, some are doctors from hospitals, and some are experts from the centers for disease control and prevention (cdc), etc. with the current covid- outbreak, it is vital for scientists, clinicians and cdc experts to share and exchange information, and to develop a united approach in emerging viral disease outbreak responses and control (wang et al., a) . in addition, we have learned from the covid- outbreak that at the beginning of a sudden outbreak, the allocation of emergency expert personnel and the expertise, authority and experience of these experts both have a significant impact on the spread of the epidemic. therefore, it is necessary to consult and analyze the literature in order to identify these leaders ahead of another novel human coronavirus emergency. our study is able to supplement and complement these efforts. a large amount of meaningful information can be obtained from keyword co-occurrence analysis, which could enable the identification of hotspots and trends, and guide researchers to related topics in their field (romero and portillo-salido, ) . in figure , four clear research fields within human coronavirus can be seen, which mainly involve aspects of public health, preventive medicine and epidemiology, clinical work and pharmaceutical research. by contrast, the studies on tracing, evolution and animal carriers of human coronavirus account for only a small proportion of the studies performed, suggesting that the research in these areas is still insufficient and there is room for growth. in our study, it is demonstrated that current research on sars-cov- and covid- are mainly focused on prevention and treatment. although there is former experience of sars and mers to learn from, people are still likely to get overwhelmed at first in face of global public health emergencies like this, for its rapid spread on a grand scale (peeri et al., ) . promoting the correct use of protective masks in public places, encouraging a safe social distance and avoiding crowd gathering are all effective alternatives to prevent large-scale public transmission (gasmi et al., ) . and enhancing medical stuff with reasonable allocation of medical resources (emanuel et al., ) , separating different diagnosis and treatment areas, and providing centralized isolation areas for mild patients if necessary (hellewell et al., ) can all help to ease the shortage of medical resources and avoid nosocomial infections. with present absence of specific antiviral drugs or vaccines to covid- , one vital step for now is to prevent the spread of sars-cov- . based on reported data, the effective reproductive number (r o ) of the sars-cov- was estimated to be . approximately , which means that each infected individual can transmit the infection to more than two healthy individuals. it has been indicated that sars-cov- may attach the angiotensin converting enzyme (ace ) receptor with its spike protein, in the way similar to sars-cov, to enter target cells (lu et al., ; walls et al., ) . however, it is still not sufficient enough to explain the high infective efficiency. further research has revealed some possible reasons. on one hand, the case fatality rate of covid- is much lower than that of sars ; on the other hand, x-ray crystal diffraction has implied that the combination between s protein of sars-cov- and ace is a little stronger than that of sars-cov (lan et al., ; shang et al., ) . in fact, different from sars-cov, significant mutation in the s protein of sars-cov- has been identified by genomics analysis, and a specific furin-like protease also plays an essential role in recognition, entry, stability and transmission of the coronavirus (coutard et al., ; drak alsibai, ) . in addition, neutralizing antibody against the virus has also been a hotspot in human coronavirus research nowadays. as for to sars-cov and mers-cov, several types of representative neutralizing antibodies such as monoclonal antibodies, their functional antigen-binding fragment and the single-chain variable region etc., has been found to block the binding between receptor-binding domain(rbd) region of s protein with ace receptor and then to inhibit the infection (jiang et al., ) . this inspires us that the rbd region may be noteworthy when studying the neutralizing antibodies induced by viruses or vaccines. a recent study has reported a human monoclonal antibody d which targets a conserved epitope of the sars-cov- s-s b domain, and might play a role in the prevention and treatment (wang et al., b) . convalescent sera have been applied to treating covid- , but attention needs to be paid to the phenomenon of antibody-dependent enhancement (ade) caused by non-neutralizing antibodies which target in non-rbd regions (du et al., ) . although there are a range of studies on the origin and transmission of human coronaviruses, especially sars-cov, mers-cov, and sars-cov- , current evidences are still not so convincing enough. despite of this, it is widely accepted so far that these three coronaviruses are able to transmit from person to person. they seem to origin from bats and need some intermediate host to facilitate replication, evolution, and variation, and thus can infect human directly. civet cats and dromedary camels are supposed to act as intermediate hosts for sars-cov and mers-cov, respectively azhar et al., ) . according to genome sequencing and evolutionary analysis, bats are also speculated to be the natural host of sars-cov- (guo et al., ) , while turtles, pangolin and snakes are alternatively possible to serve as the intermediate host for its transmission from animal to human (liu et al., ) . study on the origin of the human coronavirus is extremely significant for better understanding, prevention and control of relevant diseases. as it may become the focus of research on emerging human coronaviruses in the near future, more experts, material and financial resources may be urgently needed. in general, previous research on sars-cov and mers-cov can provide important guidance for the study of sars-cov- and speed up the development in therapeutic drugs and vaccines. although the keyword co-occurrence analysis shows the hotspots and trends within human coronavirus research, it also indicates that some fields remain unexplored or underexplored. for example, the relationship between human coronavirus and immune metabolism, the application of rna-seq and single cell sequencing technology in coronavirus research, and the possibility of cocktail therapy in viral treatment have not been studied extensively. due to the short duration of the recent covid- outbreak, studies on sars-cov- were insufficient in various fields. keyword co-occurrence analysis could help researchers studying sars-cov- by providing abundant potential directions in similar fields with other human coronaviruses and revealing the cross-disciplinary exploration potential. today we are experiencing an information data explosion. because researchers have been studying coronavirus for years, there is a massive and complicated array of data. thus, being able to benefit from such an unprecedented amount of data without being overwhelmed poses a significant obstacle for researchers, especially when facing the emergency of a novel infectious disease outbreak, such as covid- . a bibliometric analysis combined with data visualization is critical for exploring and communicating information effectively, and helping researchers to continue to progress (wong, ) . for this reason, we applied bibliometric and visualization methods to analyze , documents of human coronavirus-related studies from the scopus database using various indicators. we hope that our study will indicate potential directions for scientists to explore, promote cooperation with other human coronavirus researchers across disciplines, guide emerging researchers toward specialities that have yet to be fully developed, enable the development and use of new technologies in this field, and provide valuable ideas for the prevention, diagnosis and treatment of covid- . datasets generated for this study will be made available by the authors, to any qualified researcher upon request. the state of lung cancer research: a global analysis the morphology of three previously uncharacterized human respiratory viruses that grow in organ culture similar virus spectra and seasonality in paediatric patients with acute respiratory disease, ghana and germany evidence for camel-to-human transmission of mers coronavirus sars-cov, mers-cov and now the -novel cov: have we investigated enough about coronaviruses? -a bibliometric analysis effects of a "new" human respiratory virus in volunteers a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection covid- outbreak: an overview hosts and sources of endemic human coronaviruses the spike glycoprotein of the new coronavirus -ncov contains a furin-like cleavage site absent in cov of the same clade origin and evolution of pathogenic coronaviruses bibliometric analysis of dendritic epidermal t cell (detc) research from to expression of angiotensin-converting enzyme and proteases in covid- patients: a potential role of cellular furin in the pathogenesis of sars-cov- the spike protein of sars-cov-a target for vaccine and therapeutic development bibliometric indicators: quality measurements of scientific publication fair allocation of scarce medical resources in the time of covid- the epidemiological characteristics of an outbreak of novel coronavirus diseases (covid- ) in china coronaviruses, a new group of animal rna viruses bibliometric analysis of citeseer data for countries individual risk management strategy and potential therapeutic options for the covid- pandemic human coronaviruses: insights into environmental resistance and its influence on the development of new antiseptic strategies a comparative sequence analysis to revise the current taxonomy of the family coronaviridae isolation and characterization of viruses related to the sars coronavirus from animals in southern china the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak -an update on the status a new virus isolated from the human respiratory tract coronavirus disease (covid- ): a literature review feasibility of controlling covid- outbreaks by isolation of cases and contacts clinical features of patients infected with novel coronavirus in wuhan evaluating the frequency of operational research conducted during the - west africa ebola epidemic neutralizing antibodies against sars-cov- and other human coronaviruses structure of the sars-cov- spike receptor-binding domain bound to the ace receptor early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia composition and divergence of coronavirus spike proteins and host ace receptors predict potential intermediate hosts of sars-cov- genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding co-circulation of four human coronaviruses (hcovs) in queensland children with acute respiratory tract illnesses in recovery in tracheal organ cultures of novel viruses from patients with respiratory disease citation analysis and trends in review articles in dentistry human coronaviruses associated with upper respiratory tract infections in three rural areas of ghana the sars, mers and novel coronavirus (covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? coronavirus as a possible cause of severe acute respiratory syndrome another decade, another coronavirus scholarly influence in the field of management: a bibliometric analysis of the determinants of university and author impact in the management literature in the past quarter century trends in sigma- receptor research: a -year bibliometric analysis animal coronaviruses: what can they teach us about the severe acute respiratory syndrome? structural basis of receptor recognition by sars-cov- global research trends of world health organization's top eight emerging pathogens worlwide trends in infectious disease research revealed by a new bibliometric method a novel coronavirus genome identified in a cluster of pneumonia cases -wuhan statistical methods for the prospective detection of infectious disease outbreaks: a review structure, function, and antigenicity of the sars-cov- spike glycoprotein a human monoclonal antibody blocking sars-cov- infection from hendra to wuhan: what has been learned in responding to emerging zoonotic viruses tracking knowledge evolution, hotspots and future directions of emerging technologies in cancers research: a bibliometrics review points of view: visualizing biological data a novel coronavirus from patients with pneumonia in china efficient and robust large medical image retrieval in mobile cloud computing environment middle east respiratory syndrome tw designed the study. zd and jc performed the search. tw, zd, and jc analyzed the data and wrote the manuscript. all authors contributed to the article and approved the submitted version. this work was supported by the national natural science foundation of china ( to tw) and the national undergraduate innovation funding of huazhong university of science and technology ( to tw, a to tw). the supplementary material for this article can be found online at: https://www.frontiersin.org/articles/ . /fcimb. . /full#supplementary-material the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright © deng, chen and wang. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord- -cxc k d authors: saha, jay; chouhan, pradip title: indoor air pollution (iap) and pre-existing morbidities among under- children in india: are risk factors of coronavirus disease (covid- )?() date: - - journal: environ pollut doi: . /j.envpol. . sha: doc_id: cord_uid: cxc k d globally, the coronavirus disease (covid- ) outbreak is linked with air pollution of both indoor and outdoor environments and co-morbidities conditions of human beings. to find out the risk factor zones associated with coronavirus disease among under-five children using pre-existing morbidity conditions and indoor air pollution (iap) environmental factors and also with current fatality and recovery rate of covid- disease in india. data was utilized from the th round of the national family health survey (nfhs), – , and from the ministry of health and family welfare (mohfw) on th may . mean, standard deviation, and z-score statistical methods have been employed to find out the risk factor zones i.e. to execute the objective. findings of this study are, the states and uts which have more likely to very higher to higher risk factors or zones of coronavirus disease (covid- ) are mizoram ( . ), meghalaya ( . ), uttarakhand ( . ), west bengal ( . ), uttar pradesh ( . ), jammu and kashmir ( . ), odisha ( . ), madhya pradesh ( . ), jharkhand ( . ), bihar ( . ), maharashtra ( . risk score), compared to uts like assam (- . ), rajasthan (- . ), goa (- . ), manipur (- . ), chandigarh (- . ), haryana (- . ), delhi (- . ) have moderate risk factors of covid- , and the states and uts like daman and diu (- . ), sikkim (- . ), andaman and nicobar islands (- . ), kerala (- . ), dadra and nagar haveli (- . ), arunachal pradesh ( .- ), karnataka (- . ), and nagaland (- . ) have very low-risk zones of covid- deaths. from a research viewpoint, there is a prerequisite need for epidemiological studies to investigate the connection between indoor air pollution and pre-existing morbidity which are associated with covid- . well-built public health measures, including rapidly searching in high focus areas and testing of covid- , should be performed in vulnerable areas of covid- . coronavirus disease outbreak is a global pandemic frightening the whole world amid unexpected emergence and massive spreading of novel coronavirus ( -ncov) or the severe acute respiratory syndrome coronavirus (sars-cov- ) (who, a (who, , b al-dadah & hing, ; cucinotta & vanelli, ; jin et al., ; lai et al., ; peeri et al., ; saha et al., ; singhal, ; sohrabi et al., ; stahel, ; wang et al., ) . the covid- is a vastly contagious disease rapidly spreading from its origin in wuhan city, hubei province of china to the rest of the world in december . as of may , , the covid- outbreak has hit south-east asia with , confirmed cases; india has the th-largest number of confirmed cases ( , cases), already crossing china (who, a (who, , b . in indoor air pollution (iap), from the indoor biomass combustion, the air pollutants which are emitted include suspended particulate matter (spm), nitrogen oxides (nox), carbon monoxide (co), benzene (c h ), , -butadiene (c h ), methanol (ch o), polycyclic aromatic hydrocarbons (pahs), and several toxic organic compounds (world health organization, ; sukhsohale et al., ; chakraborty et al., ; air quality expert group, ) . the cooking fuels which are generally burned for cooking mostly in a rural home and also in urban areas are coal, lignite, charcoal, wood, straw/shrubs/grass, agricultural crop, animal dung, etc. (iips, ) which are sufficient for the concentration of indoor air pollutants. smoking of cigarettes, bidis, and pipes within the home or indoor environment are also other responsible factors for the increase of smoky indoor environment (bruce et al., ; gilmour et al., ; chaouachi, ), a risk factor of the coronavirus disease among under-five children. the acute respiratory infection (ari), i.e. executes signs like short and rapid breaths (iips, ), cold & cough, and fever among human beings are the primary symptoms of the coronavirus disease and the severe acute respiratory syndrome coronavirus (sars-cov- ) which have widespread effects because it is hazardous or risk factor for children and human beings health having a weak immune system (jin et al., ; lai et al., ; peeri et al., ; singhal, ; wang et al., ; who, a who, , b . these symptoms are quite common among under-five children of developing countries and also in india which have impacts on children's health (ramani et al., ; thota et al., ; krishnan et al., ) . globally, and also in developing countries like india, the under-five children are most vulnerable groups compared to the other age classes, so we considered only underfive age group and in an estimated . million children under the age of years died (unicef, ), mostly from preventable childhood morbidities. for that very reason, areas with these symptoms are vulnerable/risk zone for the covid- deaths in the coming days. several previous studies that have analyzed the indirect effect of the covid- on-air (fattorini & regoli, ; bashir et al., ; collivignarelli et al., ; zambrano-monserrate et al., ) and few studies specifically from that have analyzed the effect of lockdown during the covid- pandemic on air quality in india i.e. pm . had the highest reduction in most of the regions amid the covid- lockdown (sharma et al., ) ; again, pm and pm . concentrations over megacity delhi, have reduced by above % in comparison to the before-lockdown period in india i.e. improvement of air quality during the covid- lockdown (mahato et al., ) . so, compared to the other previous studies in india, this type of study is yet not done, considering this huge research gap and novelty, this study also aims to find out the risk factors associated with the coronavirus disease (covid- ) among under-five children using pre-existing morbidity conditions and indoor air pollution environmental factors which are solid biomass cooking fuel and indoor smoking cigarettes and also with current case fatality ratio (cfr) and recovery rate (rr) of the covid- disease in the high focusing states and union territories of india which are in a risk zone. this very research would be helpful for policymakers, strategy developers, environmentalists, and public health workers to combat the future pandemic situation. for this study, data were utilized from the th round of the national family health survey, e , consisting of nationally representative sample surveys. a total of , living children ( e months) were surveyed by the national family health survey (nfhs)- , among them the under-five children having preexisting morbidities and indoor air pollution characteristics of the states and union territories of india were considered for this study (iips, ) . the data used for this study were retrieved from the public domain after describing the objective of the study. data on the covid- is use from the https://www.mohfw.gov. in/naming 'covd- state-wise status', provides the most updated figures on the daily and a total number of confirmed cases, recovered or cured cases, and deaths (mohfw, ) for each affected states and union territories of india. this data is provided by the ministry of health and family welfare (mohfw), government of india. we have collect information on confirmed cases, the number of deaths, and cured cases as on may , , : ist (gmtþ : ) of affected states and union territories of india. for the analysis of the study, a selection of pre-existing morbidities indicators and indoor air pollution or domestic smoky environmental indicators among under-five children household and recent covid- rates were included. pre-existing morbidities indicators include symptoms of acute respiratory infection (ari) in the two weeks before the survey, the prevalence of cold and cough, and the prevalence of fever among under-five children. indoor domestic smokes indicators include children's family used smoky domestic cooking fuel and children's mother smoke cigarettes and recent covid- rates include case fatality ratio (cfr) and recovery rate (rr) of different affected states and union territories of india ( fig. ). the prevalence of pre-existing childhood morbidities and the percentage of children's family used indoor domestic smokes were computed using the statistical package and data science software stata version . (statacorp lp, college station, tx, usa). after that, the case fatality ratio has been calculated as the ratio of the total figure of deaths due to covd- to the total figure of confirmed cases of the covid- . likewise, the covid- recovery rate is calculated as the ratio of the total figure of recovered cases of the covid- to the total figure of confirmed cases of the covid- . for identification of risk factors zone of the coronavirus disease, the mean composite z-score technique has been employed. all the factors which are taken for this study are positively influenced by the covid- except the factor recovery rate of the covid- . for composing, all the selected variables must be working unidirectional manner. so, the factor recovery rate has been converted into a non-recovery rate i.e. each recovery rate of the covid- of all states and uts is subtracted from . after that, for each variable (x or x and so on) number of observations (states and uts) are sum up and mean was calculated, then standard deviation was calculated as the root mean square deviation from the mean. the zscore i.e. risk score also be calculated for identification of risk or vulnerable zones of the covid- using the following formula- all the z-score values of all variables for each state and uts have been calculated then mean was calculated using total z-score value. high z-score value indicates high-risk factors of the covid- and vice versa. . . indoor air pollution and pre-existing prevalence of morbidities among under-five children and case fatality ratio and recovery rate of the covid- table represents the percentage of under-five children with indoor domestic smokes and pre-existing childhood morbidities and the covid- cfr and rr in states and uts of india. symptoms of ari was higher in the states like meghalaya ( . %), jammu and kashmir ( . %), uttar pradesh ( . %), uttarakhand ( . %), punjab fig. (a) ) compared to the states and uts like assam (À . ), rajasthan (À . ), goa (À . ), manipur (À . ), chandigarh (À . ), haryana (À . ), delhi (À . ) have moderate risk factors of the covid- , showed in color ramp of light yellow to light yellow-greenish ( fig. (a) ) and the states and uts like daman and diu (À . ), sikkim (À . ), andaman and nicobar islands (À . ), kerala (À . ), dadra and nagar haveli (À . ), arunachal pradesh ( .- ), karnataka (À . ), and nagaland (À . ) showed in color ramp of green to light greenish-yellow ( fig. (a) ) have very low-risk factors of covid- . the states and uts with to < . composite score i.e. high ( to À . ), moderate (À . to À . ), and low to very low (À . to À . ) risk score factors of the coronavirus disease ( fig. (b) ). worldwide, till may , as of : p.m. cest, , , confirmed cases of the coronavirus disease, including , deaths have been reported and countries, territories have been affected by the covid- pandemic (who, a (who, , b . in india, as of may , as of : ist (gmtþ : ), ministry of health and family welfare, the government of india reported, a total of , , confirmed cases and deaths have been reported speeded over states and uts (mohfw, ). the present study has examined the risk factors of the coronavirus disease . as the coronavirus has been associated with indoor air pollution and a smoky environment, so, there has a relationship between indoor cooking fuel used with biomass and the coronavirus disease (covid- ) (afshari, ) . the under-five children living in indoor smoky environmental conditions are most vulnerable and risk of the coronavirus disease. this study is consistent with the study done by ahmed et al. ( ) , and a significant relationship between exposure to air pollution and deaths due to the covid- was found in united states . they use of solid biomass for cooking fuels and burning inside their houses with poor vitalization system and no chimneys were found to direct the smoke outside in urban slums of bangalore, india (ghergu et al., ) . so, we found that these indoor air pollution conditions are extremely at risk or vulnerable to the covid- infection. those people staying in an area with intense high amounts of pollutants are, therefore, more likely to develop severe respiratory conditions and also at risk of any infective disease (conticini et al., ) . in this study among children's mothers with smoking cigarettes is a risk factor of the covid- among under-five children in india. this finding is in agreement with another study conducted in china, where hospitalized patients of the covid- with smoking behavior were times high likely to expire or die compared to the patients those were non-smokers (liu et al., ) , and in saudi arab (alraddadi et al., ) . the states and uts with high case fatality ratio and air pollution are risk factors of the covid- in affected states and uts of india. this finding was similar to another study in the people's republic of china i.e. the high prevalence of confirmed/infected cases and deaths of severe acute respiratory syndrome coronavirus (sars-cov- ) were associated with air pollution (cui et al., ) and in northern italy, higher prevalence and mortality of the covid- was also associated with air pollution (conticini et al., ) . indoor air pollution or indoor domestic smoky environment and pre-existing morbidities are the risk factors of health among children with under-five age. indoor air quality directly linked to the respiratory system of living peoples and dependence on hard biomass for cooking and burning or heating exposes respiratory health problem of children of developing countries as well as in india due to use lofty levels of indoor air pollution (padhi and padhy, ; bruce et al., ; mandal et al., ) . pre-existing morbidities like acute respiratory infection (ari), cold & cough, and fever among under-five children in india have also risk factors of the coronavirus disease . in earlier studies, it is found that pre-existing co-morbidities among children are risk factors of the covid- death (sinha et al., ; shekerdemian et al., ) . the measurement of cfr amid the covid- outbreak is not very suitable, because it is sensitive to under-reporting, testing of the covid- cases and moment of reporting and robust estimation of cfr is likely possible only at the end of the covid- pandemic. recovery rate also varies and daily changes during the pandemic situation, so these are few limitations of this study. surveyed women have self-reported about their children's pre-existing childhood morbidities, so there is a possibility of recall bias during the collection of information about children. from a research viewpoint, there is a prerequisite for epidemiological studies to investigate the relationship between indoor air pollution and pre-existing morbidity which are associated with the covid- . more focus needs to place on improving cooking stoves and use clean indoor cooking fuels should become a top concern in the high focus vulnerable region. the children should be kept away from the kitchen during the cooking and burning of fuels. the kitchen room should have extensive space so that air pollutants smokes are not being capable to concentrate within the room for a long period, which reduces indoor air pollution, which is the risk factor of the covid- . smokers of the family should also stay away from indoor house environment when smoking. finally, well-built public health proceedings, including rapidly searching in high focus areas and testing of the covid- , should be performed in vulnerable areas of the covid- . credit authorship contribution statement jay saha: conceptualization, data curation, formal analysis, investigation, methodology, software, supervision, validation, visualization, writing -original draft, writing -review & editing. pradip chouhan: conceptualization, formal analysis, investigation, methodology, software, supervision, validation, visualization, writing -original draft. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. indoor air quality and severity of covid- : where communicable and non-communicable preventive measures meet why inequality could spread covid- the potential air quality impacts from biomass combustion. department for environment, food and rural affairs novel coronavirus (covid- ): a global pandemic risk factors for primary middle east respiratory syndrome coronavirus illness in humans correlation between environmental pollution indicators and covid- pandemic: a brief study in californian context. environmental research indoor air pollution in developing countries: a major environmental and public health challenge who indoor air quality guidelines on household fuel combustion: strategy implications of new evidence on interventions and exposureerisk functions indoor pollution from solid biomass fuel and rural health damage: a micro-environmental study in rural area of burdwan, west bengal a critical review of the relevant literature and the public health consequences lockdown for covid- in milan: what are the effects on air quality? can atmospheric pollution be considered a co-factor in extremely high level of sars-cov- lethality in northern italy? who declares covid- a pandemic air pollution and case fatality of sars in the people's republic of china: an ecologic study role of the chronic air pollution levels in the covid- outbreak risk in italy dealing with indoor air pollution: an ethnographic tale from urban slums in bangalore how exposure to environmental tobacco smoke, outdoor air pollutants, and increased pollen burdens influences the incidence of asthma national family health survey (nfhs- ) virology, epidemiology, pathogenesis, and control of covid- epidemiology of acute respiratory infections in children-preliminary results of a cohort in a rural north indian community severe acute respiratory syndrome coronavirus (sars-cov- ) and corona virus disease- (covid- ): the epidemic and the challenges analysis of factors associated with disease outcomes in hospitalized patients with novel coronavirus disease effect of lockdown amid covid- pandemic on air quality of the megacity delhi impact of domestic smokes on the prevalence of acute respiratory infection (ari) among under-five children: evidence from india covid- statewise status. government of india domestic fuels, indoor air pollution, and children's health: the case of rural india the sars, mers and novel coronavirus (covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? acute respiratory infections among under-five age group children at urban slums of gulbarga city: a longitudinal study lockdown for covid- and its impact on community mobility in india: an analysis of the covid- community mobility reports effect of restricted emissions during covid- on air quality in india characteristics and outcomes of children with coronavirus disease (covid- ) infection admitted to us and canadian pediatric intensive care units a review of coronavirus disease- (covid- ) covid- infection in children. the lancet world health organization declares global emergency: a review of the novel coronavirus (covid- ) how to risk-stratify elective surgery during the covid- pandemic? indoor air pollution from biomass combustion and its adverse health effects in central india: an exposure-response study fever awareness, management practices and their correlates among parents of under five children in urban india children: reducing mortality, key facts a novel coronavirus outbreak of global health concern who coronavirus disease (covid- ) dashboard. world health organization. world health organization air quality guidelines: global update : particulate matter, ozone, nitrogen dioxide, and sulfur dioxide. world health organization situation report exposure to air pollution and covid- mortality in the united states indirect effects of covid- on the environment supplementary data to this article can be found online at https://doi.org/ . /j.envpol. . . key: cord- - au nctt authors: lin, panpan; wang, manni; wei, yuquan; kim, taewan; wei, xiawei title: coronavirus in human diseases: mechanisms and advances in clinical treatment date: - - journal: medcomm (beijing) doi: . /mco . sha: doc_id: cord_uid: au nctt coronaviruses (covs), a subfamily of coronavirinae, are a panel of single‐stranded rna virus. human coronavirus (hcov) strains (hcov‐ e, hcov‐oc , hcov‐hku , hcov‐nl ) usually cause mild upper respiratory diseases and are believed to be harmless. however, other hcovs, associated with severe acute respiratory syndrome, middle east respiratory syndrome, and covid‐ , have been identified as important pathogens due to their potent infectivity and lethality worldwide. moreover, currently, no effective antiviral drugs treatments are available so far. in this review, we summarize the biological characters of hcovs, their association with human diseases, and current therapeutic options for the three severe hcovs. we also highlight the discussion about novel treatment strategies for hcovs infections. f i g u r e genome organization and structure of hcovs human covs generally cause only mild upper respiratory diseases, which is similar to common flu. , a novel cov, named sars-cov- by the world health organization (who), has emerged again at the end of , causing more infections and deaths worldwide than ever before. the absence of effective antiviral treatments and serious consequences of these three covs have highlighted the urgent need for novel drug development to prevent the spread of covs. herein, this review mainly focuses on the biological characters of hcovs, their association with human diseases, and current therapeutic options for the three severe hcovs. we also highlight the discussion about novel treatment strategies for hcovs infections. covs possess a nonsegmented, positive, single-stranded rna genome of - kb. , , all covs have a similar genome arrangement with a ′-methylated cap structure along with ′-polyadenylated tail. the replicase gene, occupying about kb, two-thirds of the genome and comprising two open reading frames (orfs), orf a and orf b, is located at the ′ end. it encodes two large polyproteins (pp) a and ab that can be cleaved by papain-like cysteine protease (plpro) and c-like serine protease ( clpro) into nonstructure proteins, involving some proteases, several rna modification enzymes, as well as rna-dependent rna polymerase (rdrp) and helicase (hel) required for virus replication. additionally, an untranslated region (utr) can also be identified at the ′-end as same as the ′terminal. structure proteins, encompassing the ′-terminal one-third of the genome, are arranged in a certain order of hemagglutinin esterase (he) protein that is present in some beta-covs, spike protein (s), small membrane protein (e), membrane protein (m), and nucleocapsid protein (n). in brief, the arrangement of the cov genome can be shown as ′-utr-replicase gene (orf a and orf b)-he protein (if have)-s protein-e protein-m protein-n protein- ′ utr-poly (a) ( figure ). cov is named for the club-shaped projections eradiating from the envelope, which forms its corona or crow-like morphology. the shape of the viral particles is roughly spherical with approximately - nm in diameters. [ ] [ ] [ ] the nucleocapsid protein and the genome rna intertwine to form a helical structure located inside the envelope. for some covs, the spikes on the surface are not only formed by trimers of s protein, but also he proteins. m protein and e protein, two transmembrane proteins, also participate in the composition of the virus (figure ). s protein, a transmembrane protein, mediates the initiation of cov infection by attaching to the specific receptors on the target cells. [ ] [ ] [ ] for a prototypical cov, s protein is usually cleaved into an extracellular receptor binding subunit (s ) and a membrane-anchored subunit (s ), responsible for virus binding and membrane fusion, respectively. , two heptad repeats (hr and hr ) and enriched alpha-helices are contained in the s domain, a feature typical of fusion protein. [ ] [ ] [ ] the receptor-binding domain (rbd) of s protein specifically binds to target receptors, leading to the conformation change of s /s complex that mediates virus entry. furthermore, the rbd also induces potent neutralizing ab response, which turns s protein into an important antigenic determinant capable of protective immunity induction and provides a vital approach for the development of immunotherapies. [ ] [ ] [ ] [ ] [ ] cov e protein is an integral membrane protein of - amino acids [ ] [ ] [ ] and is present in small amount in virions. [ ] [ ] [ ] it contains a short hydrophilic n-terminal followed by a single predicted hydrophobic domain and a hydrophilic c-terminal. although its membrane topology remains unclear, cov e protein is commonly referred to as a transmembrane protein with one transmembrane domain. [ ] [ ] [ ] accordingly, the e protein mainly targets er and golgi-complex and participates in part of the life cycle of the virus, including virus assembly, budding, particles release, envelope formation, and viral pathogenesis. , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] in addition, cov e protein may have a crucial role in virus production and maturation, because recombinant covs lacking the e protein exhibit significantly reduced viral titers and toxicity. [ ] [ ] [ ] [ ] [ ] the m protein is a small transmembrane protein ( ) ( ) ( ) ( ) ( ) ( ) with three transmembrane segments, an n-terminal ectodomain and a c terminal-endodomain, determining the shape of the virion. , it is considered as the most abundant structural protein and plays a pivotal role in virion assembly via interacting with other structural proteins. [ ] [ ] [ ] binding of s protein and m protein is essential to the virus assembly and the maintenance of s protein in the er-golgi intermediate compartment (ergic)/golgi complex. [ ] [ ] [ ] virus-like particles (vlps) are assembled when the combination of m and e proteins occurs, which suggests that they are required for the formation of the envelope. , [ ] [ ] [ ] additionally, when expressed alone, it can become a homomultimeric complex, the primary driving force of envelope formation. , , furthermore, as to n protein, a stable nucleocapsid and internal core of virions can be achieved when combined with m protein. , the n protein, combined with viral genomic rna to form a helical nucleocapsid inside the viral envelope, is a multifunctional protein. it contains three highly conserved domains: the n-terminal domain (ntd), responsible for rna binding; a c-terminal domain (ctd) that is a hydrophobic and helix-rich terminal, capable of dimerization and oligomerization; and an intrinsically disordered region (rna-binding domain/domain ) that is a serine/arginine-rich domain (sr-domain) with a significant phosphorylation potential. , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] phosphorylation of the n protein can initiate structural modification leading to an increased rna-binding affinity. , , , the n protein binds to the genomic rna through a beads-on-astring form. likewise, except for the interaction between n protein and nucleic, the ability of complex oligomerization is another pivotal activity required for the formation of the ribonucleoprotein complexes for viral assembly. in addition to the role of the n protein in viral core formation and assembly, , [ ] [ ] [ ] it is also involved in other critical processes of viral life cycle such as virus budding and envelope formation, , - genomic mrna replication ,and genomic rna synthesis. , although the pathogenic mechanisms of human covs have not yet been fully understood, the investigation of their unique characteristics of each cov enables to distinguish the various human covs including sars, mers, and sars-cov- . the crucial early step of the infection of human covs into susceptible host cells is the interaction between viral s protein and cellular target receptors. one of the subunits of s protein, s , containing rbd, is responsible for specific recognition and binding of the target receptors. the other subunit, s , is in charge of the membrane fusion. , [ ] [ ] [ ] [ ] [ ] the tissue tropism, as well as the susceptible host species, is mainly determined by the binding of s protein to target receptors. based on lines of known evidence, human covs utilize multiple and different types of cellular receptors rather than use a common receptor. therefore, multiple cellular receptors have been identified as target receptors for the various human covs to date (table ) . angiotensin-converting enzyme (ace ), the first known human homolog of angiotensin-converting enzyme and the receptor for hcov-nl , sars-cov, and sars-cov- , is a vital component of the reninangiotensin system (ras). [ ] [ ] [ ] [ ] [ ] [ ] [ ] it is a secreted enzyme with a transmembrane domain, a single metalloprotease active site and a signal peptide, and predominantly expressed in heart, vascular endothelia, epithelia of the small intestine, kidney, and testis; alveolar macrophage and monocytes of the respiratory tract; and epithelial cells of the trachea, bronchi, and alveoli. , [ ] [ ] [ ] in contrast to its homolog ace that contributes to the promotion of lung failure pathogenesis, induction of lung edemas, and impairment of lung function, ace plays a protective role in severe acute lung injury (ali). imai et al revealed that the deficiency of ace in the murine models of acute respiratory distress syndrome (ards) deteriorated the symptom in lung function, which could be recovered by hcov-nl hcov-hku the recombinant ace . thus, downregulation of ace expression in sars patients could be used as an indicator of severe clinical outcome. besides lung damage caused by sars-cov infection could be attenuated by blocking the renin-angiotensin pathway. overall, ace could serve as a novel therapeutic target for severe respiratory diseases. dipeptidyl peptidase iv (dpp ), a type ii transmembrane protein also known as cd , is identified as a target receptor for mers. it is a prolyl oligopeptidase expressed in various cells including endothelial cells, epithelial cells, and inflammatory cells in the lung and smooth muscle. [ ] [ ] [ ] the multifunctional protein ddp is implicated in the activation of t-cell, the activity regulation of chemokines and growth factors, and the regulation of glucose metabolism. [ ] [ ] [ ] [ ] not only can it be embedded in the plasma membrane in the form of a homodimer, but it also presents in extracellular fluid like plasma as a soluble form. , although ddp is expressed in epithelial cells of the upper respiratory tract in camels, it is principally found in alveoli but rarely in the nasal cavity or conducting airway. , accordingly, in a murine mers model, though monocyte infiltration, alveolar edema and microvascular thrombosis were observed in the mers-cov-infected lungs, any symptoms were seldom found in the airways. aminopeptidase n (apn), a type of ii metalloprotease also called cd , is a ubiquitous enzyme expressed in various organs (lung, intestine, and kidney) and cells (epithelial cells, endothelial cells, leukocyte, and fibroblast). , it serves as a target receptor for hcov- e, but not for hcov-oc . hcov-oc shares the same specific target with hcov-hku , namely -o-acetylated sialic acid. , virus entry is a finely regulated process requiring a series of interactions between the virion and host cell. [ ] [ ] [ ] following the conjunction with the target receptor, cov fuse its envelope with the membrane of the host cell. these processes are forced by the conformational change of s protein, which is triggered by not only the target receptor binding but also ph acidification and proteolytic cleavage led by cell surface or endosomal proteases such as transmembrane protease serine (tmprss ), furin, cathepsin l, elastase, and trypsin. [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] cleavages of s protein are facilitated at two sites: the boundary between the s and s subunit (s /s ) and the conserved site upstream of the fusion peptide (s '). , the former one is aimed at releasing rbd from the membrane fusion subunit, and the latter one is important for the exposure of the fusion peptide, hydrophobic in general, which acts as an anchor to target membrane. , , then the fusion domain adopts two heptad repeats (hr /hr ) to form a compact coiled-coil conformation called -helix bundle or hb. , through direct interactions with lipid bilayers, the fusion domain disrupts two apposed membrane layers and fuses the viral envelope to host cell membrane. ultimately, the viral genome is successfully released into the cytosol of the target cell. in addition to the viral infection through the plasma membrane, the entry of covs into cells can be accomplished by the endocytic pathway, depending on the virus strains and host cells. , sars-cov, whose intermediary host is the palm civet, is a highly pathogenic respiratory virus that emerged in , leading to global pandemic that affected more than people in countries. , patients infected with sars-cov initially present "flu-like" syndrome commonly showing high fever, headache, sore throat, myalgia, and dry cough. [ ] [ ] [ ] during the disease progression, ali or ards is developed in a number of patients. pathological manifestations can be described as three phases. the first step is the disturbance of gas exchange in the first week, owing to the extensive edema, shedding of ciliated epithelial cells, and deposition of hyaline-rich substances on the alveolar membrane. in the next step, pulmonary fibrosis occurs that is characterized as the deposition of fibrin at epithelial cells and the alveolar spaces, as well as the infiltration of inflammatory and fibroblasts. finally, fibrosis of lung tissue, collagen deposition, and proliferation of alveolar and interstitial cells represent the final step of disease, about - weeks. [ ] [ ] [ ] [ ] [ ] diffuse alveolar damage (dad) accompanied by hyaline membrane formation as well as interstitial thickening is common characteristics of sars-cov inducing pulmonary damage. although many investigators have devoted to inquiring into the pathogenesis of such virus, it has not yet been fully understood until now. the immune response is the earliest alert system of the host cells warning virus attacks. ironically, it also aids viral pathogenesis. pattern recognition receptors (prrs) that are retinoic acid-inducible gene i protein (rig-i, member of rlrs family) and melanoma differentiation-associated protein (mda ) recognize viral pathogen-associated molecular patterns (pamps), such as viral components and replication intermediates, to initiate signaling cascades against virus infection. , once the pamps from invaded viruses are detected, rig-i and mda interact with the mitochondrial antiviral signaling protein (mavs) that is a mitochondrial membrane-bound f i g u r e escape mechanisms of innate immune response of sars-cov and mers-cov adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (irf , irf , and nf-κb). activation of nf-κb induces the production of proinflammatory cytokines and chemokines in the nucleus that is a substantial cause of the ards. , phosphorylation of irf and irf by the kinase complexes results in homo-or heterodimerization of irf and irf . the dimerization initiates the transcription of type i interferons (ifns, ifn-α and ifn-β), activating the signal transducer and activator of transcription proteins (stats) to mediate antiviral response ( figure ). [ ] [ ] [ ] several defensive approaches are used by sars-cov to avoid the prrs defense system and, ultimately, host innate immune response. one approach is to replicate themselves within the double membrane vesicles (dmvs) that are protected from the prrs. , the eukaryotic mrnas contain a ′ cap that usually lacks in the viral mrnas. however, some viruses such as sars-cov are capable of building the rna cap through nsp and nsp /nap complex, helping them bypass the recognition by prrs. [ ] [ ] [ ] [ ] in addition, a couple of more proteins encoded by the viruses participate in the suppression of the innate immune response by disrupting the ifn response. among the nonstructural proteins, nsp mainly involves in the degradation of host mrnas, inactivation of host translational machinery as well as the inhibition of stat phosphorylating. [ ] [ ] [ ] sars-cov plpro interferes phosphorylation of irf and disrupts nf-κb signaling probably via interacting with sting. [ ] [ ] [ ] the nsp and nsp are also potential ifn antagonists though the mechanism is not clear. structure proteins such as the n protein and m protein are likely to suppress the type i ifn path-ways. because it was known that n protein inhibits the ifn transcription, the n protein could have a strong potential influence on the viral rna. m protein blocks the formation of signaling kinase complexes, and suppresses the irf and irf activities, suggesting the potential role of the n protein in the viral infection as well. such accessory proteins as orf b protein are able to inhibit the rig-i activity and irf phosphorylation in addition to the transcription of ifn-stimulated genes (isgs) via the isre promoter, while orf blocks the nuclear translocation of stat . , in spite of the number of research findings in vitro, they have not been validated in vivo. therefore, it is urgent to examine the findings in vivo for a clear and solid understanding of the infectious process. besides the immune response of the host, ace also plays an essential role in the pathogenesis of sars-cov. as a negative regulator on the ras, ace has been closely linked to the pathogenesis of pulmonary diseases and considered as a protective factor for ali. consequently, the downregulation of ace mediated by sars-cov binding might give an explanation for the progression of severe lung damage occurred on some sars patients. a decade after sars, another novel cov was identified as the pathogen of mers that caused a higher mortality rate ( %- %) compared with sars (around %). , sars-cov and mers-cov are both emerged from bats, and are disseminated to human through palm civets and dromedary camels, respectively. [ ] [ ] [ ] [ ] mers-cov and sars-cov share some common clinical manifestations ranging from asymptomatic to severe pneumonia in multiple organs, , , and pathological features including inflammatory cells infiltration and dad. similar to sars-cov, mers-cov is also capable of causing immune dysregulation by attenuating the innate immune response ( figure ). , type i interferon is important for the inhibition of mers-cov replication in host cells probably via the suppression of the dmvs formation. , capping viral mrna by nsp and nsp /nap complex protects mers-cov, as well as sars-cov, from the prrs recognition since the structure of nsp /nap complex in both viruses are analogous. besides, several proteins of mers-cov are involved in immune escape mechanism by involving in the signaling cascades. it was reported that irf nuclear translocation and ifn promoter activation are inhibited by m protein, orf a, orf b, and orf , former three of which also restrained the expression from an the isre promoter. inhibition of the phosphorylation of irf might be the mechanism for ifr translocation inhibiting. moreover, mers-cov orf a can interact with ifn-inducible double-stranded dna (dsdna)dependent protein kinase activator a (prkra) and subsequently control the function of rig-i and mda , resulting in the disruption of the ifn response. , orf a and orf b are thought to participate in the nf-κb signaling by downregulating the gene stimulated by nf-κb and affecting the kinase complexes, respectively. functions of plpro and nsp of mers-cov are analogous to the functions of those in sars-cov. , like ace , the entry receptor dpp for mers-cov has also a pivotal role in the disease pathogenesis and is considered as a key factor for the intraspecies variation shown in mers infection. , it is usually expressed in type ii pneumocytes that cover % of the alveolar surface. , approximately % of the surface area is occupied by the type i pneumocytes that are responsible for gas exchange. , but the autopsy reports indicated that both type i and ii pneumocytes in patients died from mers-harbored dpp expression and these pneumocytes were infected by the virus. , mers-cov infection of type i pneumocytes might lead to the damage of the cells in the alveoli subsequently causing the dad. it suggests that type i pneumocytes expressing dpp might be included in the pathogenesis of the disease. this might explain why chronic obstructive pulmonary disease (copd) patients attacked by mers-cov had poor outcomes, since the expression of dpp was predominantly upregulated on type i pneumocytes in such patients. , besides, owing to high expression of dpp shown in the kidney, the renal dysfunction might be caused by either the direct infection or the hypoxic damage. evidence of tubular injury, such as cell debris and tubular dilation, could be observed in the late stage of the infection in mers-cov-infected mice. however, no virus could be detected in such animals in the early stage after infection, meaning such pathologic changes might be related to the hypoxia. the outbreak of covid- , whose pathogen is sars-cov- , now poses a serious threat to the global public health. , since the emergence of the virus, sars-cov- has affected more than million people with more than thousand deaths worldwide as of july . next-generation sequencing of the novel virus has been developed soon after the outbreak, indicating that sars-cov- is closely related to the bat-derived sarslike covs. , it is now believed that bats are likely to be the natural reservoir, , and pangolins are regarded as intermediary host according to the later studies. typical clinical presentations of sars-cov- -infected patients include fever, dyspnea, dry cough fatigue, myalgia, pneumonia, and ards symptoms, similar to those of sars and mers patients. [ ] [ ] [ ] however, intestinal disorders such as diarrhea are less frequent in covid- patients than sars. , , furthermore, in spite of the variation of amino acid at some residues, homology modeling informed that sars-cov- and sars-cov have an analogous rbd structure, and share the same target cell receptor, ace , to mediate the viral entry. , , , [ ] [ ] [ ] it is speculated that ace is involved in the pathogenesis of sars-cov- . owing to the current sparsity of data on the pathological characters of sars-cov- , it is poorly understood. a case report from an infected patient died of this disease showed that dad with hyaline membrane formation, infiltration of inflammatory cells, and pulmonary edema could be found in the samples taken from their lungs, which is notably corresponding with the symptoms of sars and mers patients. additionally, lymphopenia is a common manifestation in covid- patients and might be an effective indicator to estimate the severity of hospitalized covid- patients. lymphopenia is also supposed to be a vital factor related to the pathogenesis that has not been elucidated so far. moreover, the concentration of some cytokines and chemokines detected in the plasma was higher in covid- patients compared with healthy individuals. moreover, higher plasma levels of gscf, il- , il- , il- , mcp , mip a, ip , and tnf-α were linked to the more severe disease. all of the data reveal that immunopathology may occupy a crucial place in the development of the disease, and further researches about the pathogenesis of sars-cov- are urgently needed in the future. owing to the fact that no effective specific antiviral therapies are currently available for sars, mers, and covid- , isolation and symptomatic support cares are the major management strategies for suspected and confirmed cases requiring hospital treatment including oxygen inhalation, fluid management, and rational use of antibiotics, to prevent organ failure and secondary bacterial infection and alleviate the symptoms. , [ ] [ ] [ ] thus, the identification of effective agents against human covs is urgently needed in the response to the current covid- outbreak. all of sars-cov, mers-cov, and sars-cov- encode structure proteins (like s protein), nonstructure proteins (eg, plpro, clpro, rdrp, and helicase), and accessory proteins that are essential for the viral life cycle and that are considered as important targets for the development of antiviral agents ( figure ). , analyses of genomic sequences and protein structure indicated that the catalytic sites of four crucial enzymes and the key drug-binding pockets in viral enzymes were conserved across sars-cov, mers-cov, and sars-cov- . therefore, the therapeutic experience based on sars and mers is capable to guide the treatment of covid- . the idea to disturb the normal life cycle of the virus provides significant insights into the clinical treatment strategy. the s protein is important for the discovery of antiviral agents due to its multifunction in virus infection. rbd located on the s subunit can bind to the host cell receptors (ace for sars-cov and sars-cov- , dpp for mers-cov) initiating the conformational changes in s subunit to get viral and cell membranes closer and trigger membrane fusion. consequently, the interaction between rbd and the host cell receptors serves as a key target for the production of neutralizing antibody followed by the vaccine development. , monoclonal antibodies (mabs) and fusion inhibitors against s and s subunit, respectively, are potential antivirus drugs to conquer the viral infection, and the agents targeting the host receptors also play a similar role. [ ] [ ] [ ] [ ] [ ] likewise, cleavage at the protease site of the s /s complex by host proteases such as tmprss and furin is necessary for the membrane fusion and syncytium formation. , the endosomal cysteine protease cathepsins promote the entry of covs into the host cell via the endosomal pathway. inhibitors of these host proteases can potently block the cell entry, which has been proved in vitro and require further validation on animals studies. once entering the host cells, covs release the nucleocapsid and genomic rna into the cytoplasm and start the translation of the replicase gene. the large replicase pp a and pp ab are cleaved by plpro and clpro to produce nonstructural proteins like rdrp and helicase, forming the replication-transcription complex. numerous agents inhibiting these proteins have shown anti-cov effects in vitro. combination of the hydrophobic domains of the replication-transcription complex to the endoplasmic reticulum membrane can form the typical cov replication structures such as dmvs and convoluted membranes, protecting covs from the detection of prrs. , viral rna synthesis produces genomic and subgenomic rnas. then the subgenomic rnas are translated to generate the structural and accessory proteins, participating in the assembly of the virion that is released into the extracellular compartment via exocytosis. small interfering rnas (sirnas) disturbing these processes could be used in the treatment of covs infections. although covs are capable of disturbing the ifn response, they are still sensitive to the ifn treatment in vitro, indicating that augmented host innate ifn response can be an effective strategy to control the viral infection. , [ ] [ ] [ ] in addition to the enhancement of inf response, several other cell signaling pathways are also regarded as potential anti-cov targets. these include calcineurin-nuclear factor of activated t cells (nfat) pathway and kinase signaling pathways such as erk/mapk and pi k/akt/mtor pathways, the inhibitors of which have exhibited anti-cov activities as well. [ ] [ ] [ ] since the discovery of new interventions may take months or even years, a more efficient approach is to repurpose existing antiviral agents approved for treating related viral infections. the followings are approved drugs or preclinical compounds that have potential antiviral abilities against sars, mers, and covid- . virus-targeted therapeutic strategies all of the major proteases of the virus are attractive druggable targets since they are essential for viral transcription and replication ( table ) . as a key part of replication-transcription complex, rdrp participates in the production of genomic rna and subgenomic rna. nucleoside analogues targeting rdrp is capable of inhibiting viral rna synthesis in a great variety of rna viruses including covs. [ ] [ ] [ ] [ ] [ ] favipiravir (t- ), a guanine analogue approved in japan for influenza treatment, has been proven to effectively interfere the rna synthesis of rna viruses such as influenza virus, ebola virus, and other hemorrhagic fever viruses at rdrp level. [ ] [ ] [ ] [ ] [ ] [ ] several studies concluded that favipiravir could inhibit avian influenza a (h n ) virus and ebola virus infection in mice. , also, favipiravir has been proved with a notable effect increasing the survival rate of ebolainfected patients from . % to . % in sierra leone. a recent study ended with the statement that favipiravir owns the ability against sars-cov- (ec = . um, cc > um, si > . ). covid- patients were enrolled in randomized trials for the evaluation of the efficacy of favipiravir plus inf-α or baloxavir marboxil (chictr and chictr ). another guanosine derivative with broad-spectrum antiviral activity, ribavirin, has been authorized for hcv and respiratory syncytial virus (rsv) treatment. accurate mechanism of ribavirin against virus infection is not clear, but inhibition of mrna capping and viral rna synthesis could be pivotal to its antiviral activity. although high dose of ribavirin has been applied to sars treatment, the anti-mers-cov effects were moderate at such dose in rhesus macaques infected by mers-cov and no obvious survival benefit has been observed in mers patients. , [ ] [ ] [ ] [ ] [ ] [ ] recently, an open-label, randomized phase ii clinical trial (nct ) has revealed that triple combination of ribavirin, interferon, and lopinavirritonavir in covid- treatment was safe and superior to lopinavir-ritonavir therapy alone in remission of symptoms, shortening virus shedding and promoting discharge of mild to moderate covid- patients. remdesivir (gs- ) is a small-molecule monophosphoramidate prodrug of an adenosine analog with the ability to interfere with the rna polymerase and the proofreading exoribonuclease and terminate the nonobligate chain. on day and mg once-daily maintenance for days. however, the first clinical trial (nct ) has been suspended so far and the second trial (nct ) with covid- patients enrolled finally indicated that remdesivir hardly shown any statistically significant clinical benefits. conversely, a research found that of ( %) hospitalized patients suffered from severe covid- and treated with compassionate-use remdesivir could achieve clinical improvement. in addition, a phase iii, randomized, double-blind, placebo-controlled trial (nct ) conducted by beigel et al uncovered the fact that remdesivir prevailed over placebo in shortening the time to recovery in adults patients. though remdesivir has been approved by the food and drug administration (fda) to treat severe covid- patients, further researches are urgently required to determine the efficacy and the indication of remdesivir therapy. a novel synthesized nucleoside analogue, bcx (galidesivir), is designed to inhibit viral rna polymerase activity via terminating nonobligate rna chain. bcx exhibits a promising antiviral capability against a wide array of . it is currently tested in phase i clinical trial (nct ) for marburg virus and can be a potential countermeasure against viral diseases that threaten the public health in the world. a recent study also concluded that penciclovir, another rdrp inhibitor that is approved for hsv, showed effects on reducing sars-cov- infection by high-dose administration (ec = . µm, cc > µm, si > . ). although resistance to nucleoside analogs has rarely been reported, it is worth noting that mutation in rdrp is probably responsible for the acquired resistance and should be monitored for the possible resistance. covs plpro enzymes display proteolytic, deubiquitylating, and deisgylating activities. [ ] [ ] [ ] plpro was first regarded as a druggable target for sars-cov, and then several compounds targeting sars-cov plpro were also found to be effective against mers-cov plpro, recently. , though numerous plpro inhibitors have been identified, many of them only inhibit enzymatic activities and do not affect on the viral replication. , a study from lin et al suggested that an fda-approved alcoholaversive drug, disulfiram could inhibit sars-cov and mers-cov plpro via different mechanisms. and the synergistic inhibition between disulfiram and known plpro inhibitors, like -thioguanine and mycophenolic acid, to mers-cov might offer the potential combination treatments against covs in clinical. another essential protease that cleaves the viral polyproteins during viral replication is clpro. similar to plpro, a great many of inhibitors have been identified with the ability to target covs clpro. among the clpro inhibitors, the human immunodeficiency virus (hiv) protease inhibitors are the most comprehensively studied such as lopinavir, ritonavir, asc f, as well as darunavir and cobicistat. lopinavir and ritonavir, applied in combination to treat hiv infection, have shown improvement in the outcome of sars patients in nonrandomized trials. , though lopinavir alone hardly displayed antiviral activity against mers-cov in vitro, the combination of lopinavir and ritonavir ameliorated the outcome in mers-cov-infected nonhuman primates. , therefore, the efficacy of the lopinavir-ritonavir combination in mers patients should be reappraised (nct ). however, no benefit was observed in lopinavir-ritonavir treatment compared to standard care in a randomized, controlled, open-label clinical trial (chictr ) involving severe covid- patients. further trials are still needed to confirm the therapeutic efficacy. in addition, several other clinical trials have been developed to confirm the efficacy of clpro inhibitors on covid- (nct , nct , nct , chictr , nct , nct , and nct ), as well as darunavir and cobicistat (nct ), asc f combined with oseltamivir (nct ). helicase acts on the duplex oligonucleotides and turns them into single strands in an atp-dependent manner in the cov replication cycle. that helicases in different covs are highly homologous making them potentially strong targets for the covs therapeutic options. based on the mechanism actions, the helicase inhibitors can be approximately classified into two groups. one is able to inhibit both the atpase and helicase activities represented by bananins derivatives, -hydroxychromone derivatives, and triazole derivatives (compound ). , the other group including ssya - and adks has the ability to inhibit the helicase activity with no or little effects on the atpase activity. however, the toxicity of helicase inhibitors needs to be examined before being applied to human patients. the transmembrane glycoprotein, s protein, is also a promising target for antiviral agents' development ( table ). one class of antiviral drugs targeting s protein mostly blocks the spike-mediated membrane fusion. a potent mers-cov inhibitor, nafamostat, has demonstrated to be inhibitive against the sars-cov- infection (ec = . µm, cc > µm, si > . ). griffithsin is a red-alga-derived lectin, which specially binds to oligosaccharides located on the surface of viral glycoproteins, for example, s glycoprotein of sars-cov and hiv glycoprotein . a wide range of human covs infection could be inhibited by griffithsin, comprising hcov- e, hcov-nl , hcov-oc , and sars-cov. , but the value of griffithsin in the treatment or prevention of covid- is needed to be evaluated urgently. s subunit of s protein contains two heptad repeat (hr and hr ). antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as sars-cov, mers-cov, as well as hcov- e. , , hr p, a peptide spanning hr sequences of mers-cov s protein, was capable of interacting with hr region to form a -hb complex, resulting in potent inhibition of viral fusion and replication. its analog hr p-m exhibited an obvious improvement in stability, solubility, and antiviral activity after being modified with hydrophilic residues. additionally, hr p-m intranasal administration effectively prevented experimental mice transduced by adenoviral vectors conveying human dpp from mers-cov infection with a > -fold decrease in viral titers in the lung, and this protection was intensified via the combination of hr p-m and ifn-β. another newly designed fusion inhibitor from mers-cov called mers-five-helix bundle (mers- hb), which is derived from the -hb, also displayed a potent suppression on s protein-mediated syncytial formation. compared with mers- hb, mers- hb lacks one hr , which endows its capability to interact with viral hr to interrupt the membrane fusion. besides, mers- hb could effectively inhibit the entry of pseudotyped mers-cov with % inhibitory concentration (ic ) about µm. altogether, the resistance of these drugs can be overcome by combining antiviral peptides aiming at various domains of s subunit, which may also attain synergistic effects in vitro. as for sirnas, which displayed antiviral activities in vitro as well as in sars-cov-infected rhesus macaques, are still under preclinical development and demand further studies to seek out the reliable drug delivery methods in a human before the clinical application. [ ] [ ] [ ] m, n, and e proteins and some accessory proteins are not only vital to the virion assembly but also involved in viral pathogenesis in which they function in the interruption of host innate immune response to assist viral infection. for instance, m protein as well as accessory proteins a, b, and of mers-cov act as ifn antagonist, and n protein of sars-cov serves as an inhibitor of viral rna. researches carried out by he et al and akerstrom et al emphasized that sirnas silencing m, n, e, orf a, and orf a/ b play an important role in the inhibition of viral replication of the sars-cov. , but the delivery methods still limit their application in human being. nevertheless, various agents related to these proteins are discovered via functional analysis. one example is resveratrol, a natural stilbene derivative demonstrated to reduce inflammation and exert antiviral activity against multiple viruses. [ ] [ ] [ ] [ ] [ ] [ ] in addition, it exhibited significant inhibition of mers-cov infection and prolonged cellular survival after virus challenge in vitro via deregulating the expression of n protein and the apoptosis induced by mers-cov. alternatively, hexamethylene amiloride, a viroporin inhibitor, is capable to suppress the ion channel activity of e protein of covs such as hcov- e and sars-cov. identified as dna metabolism inhibitor, gemcitabine hydrochloride is a deoxycytidine analog inhibiting both sars-cov and mers-cov with micromolar ec and low toxicity, which suggests its potential antiviral capacity for other human covs. lj and jl , two novel lipophilic thiazolidine derivatives, could induce several changes in membrane properties including the decrease in membrane fluidity, contributing to inhibition of membrane fusion, which made them become broad-spectrum enveloped virus entry inhibitors and potential anti-cov agents. host-cell-targeted therapies the host innate immune response is vital to the interruption of viral replication. recombinant interferons have been applicated in treating various viruses as well as many covs (table ) . though the host interferon response can be inhibited by the covs, they are still proved effective against covs infection such as sars-cov and mers-cov in vitro and several animal models. , , , , recombinant interferons are usually combined with other antiviral agents including ribavirin or lopinavir/ritonavir to treat sars-cov and mers-cov infections, , and the anti-covs efficacy of interferons is enhanced when added with ribavirin. a combination of interferon-α b with ribavirin reduced virus replication and improves clinical outcomes in a rhesus macaque model of mers. however, the effectiveness of combination treatments comprising interferons and ribavirin is still controversial in clinical researches. a study of five patients received interferon-α b and ribavirin showed no survival, but the finding might be not reliable owing to the delayed administration. contrarily, in another study (n = ), mortality rates of individuals receiving interferon-α b and ribavirin exhibited a significant reduction in day , compared with the individuals received standard supportive care, but no significant difference was observed in day . moreover, no significant difference in mortality rates between interferon-α b and ribavirin treatment group and interferon-β a and ribavirin ta b l e host-targeted agents for hcovs treating group was observed in a retrospective study. on the other hand, interferon-β b displayed stronger inhibition to the mers-cov replication in vitro compared with other interferons, and combined use of interferon-β b with other antiviral compounds should be evaluated in further research. , nitazoxanide, originally identified as an antiprotozoal agent, was later considered as a broad-spectrum antiviral agent able to inhibit the replication of numerous dna and rna viruses such as rsv, parainfluenza, rotavirus, hbv, hcv, hiv, yellow fever, as well as covs in vitro. several clinical trials have confirmed its potential value in treating influenza, chronic hbv, and hcv. [ ] [ ] [ ] moreover, recent research indicated that nitazoxanide was capable of inhibiting sars-cov- infection at a low micromolar concentration (ec = . µm; cc > . µm; si > . ) , and the in vivo evaluation of this efficacy is demanded. another type i interferon inducer, polyinosinic:polycytidylic acid (poly(i:c)), is an analog of dsdna with a powerful ability to reduce mers-cov load in animal models. and phase ii clinical trials demonstrated that it was well tolerated by malignant gliomas patients when injected intramuscularly. , overall, the use of interferons or interferon inducers may be a valuable strategy against covs infection and should be furtherly accessed in animal models. several host factors are considered essential to covs entry, such as the host receptors that bind to covs s protein, and host proteases that facilitated covs entry through the cell surface or endosomal pathway. thus, these factors become attractive targets for anti-cov agents' development (table ) . antibodies, peptides, and some functional inhibitors targeting the host receptors can effectively interrupt the binding between s protein and the host cells. one example is that the n-( -aminoethyl)- -aziridineethanamine (naae), a small molecular inhibitor, is able to target ace leading to the block of s protein-mediated membrane fusion, so does the synthetic peptides analogous, p and p . , similar agents were also found in mers treatment, one of which, ys , was confirmed to be well tolerated in patients with advance solid tumors. owing to their specificity to appointed receptors, they were regarded as narrow-spectrum drugs. however, the efficacy of these receptor-targeted agents have never been evaluated in any covs-infected patients and the safeties of these agents also remain unclear. host protease such as cathepsins and tmprss play a key role in the cleavage of s protein and the suppression of these proteases with potent inhibitors can obstruct the virus entry through either endosomal pathway or cell surface pathway. k is a cathepsin inhibitor with broad spectrum against enveloped rna virus including sars-cov and mers-cov. , , however, the camostat mesylate, applied in chronic pancreatitis treating, is a tmprss inhibitor that interrupts the tmprss mediated cell surface entry. , the combination of cathepsin inhibitors and tmprss inhibitors is crucial to the complete suppression of mers-cov in vitro. inhibition of another host protease, furin, which is vital to furinmediated s cleavage for covs, also can block membrane fusion and the viral entry like mers-cov. notably, inhibition of host proteases may result in some side effects and need further evaluation. some approved antipsychotic agents (chlorpromazine, triflupromazine, and fluphenazine) and cardiotonic steroids (ouabain and bufalin) can inhibit clathrinmediated endocytosis via affecting the assembly of clathrin-coated pits at the plasma membrane and binding sodium/potassium-transporting atpase subunit α (atp a ), respectively. , , thus, they are considered as clathrin-mediated endocytosis inhibitors. alternatively, endosomal acidification also has a profound impact on endocytosis. increase of endosomal ph shows an inhibitive effect on virus infection, which has been confirmed by chloroquine, a widely used autoimmune disease and antimalarial agents. chloroquine proves to be active against a wide range of rna viruses including hcov- e, hcov-oc , sars-cov, and mers-cov. [ ] [ ] [ ] [ ] [ ] recently, chloroquine is identified to function at both entry and postentry phase of the sars-cov- infection with the ec value of . µm in vero e cells. additionally, as an immunoregulator, its antiviral activity may be synergistically intensified in vivo. therefore, chloroquine is suggested as a potential option against the emerging sars-cov- . significantly, higher dose of chloroquine should not be recommended for severe covid- patients owing to the its drug safety, particularly while simultaneously accepting azithromycin and oseltamivir treatment, which was presented by a randomized clinical trial (nct ). hydroxychloroquine, a chloroquine analog with lower toxicity, was listed as a potential anti-sars-cov- agent and recommended to be applied in covid- treatment by chinese national guideline and fda. however, evidence of the benefits and harms of hydroxychloroquine therapy is still insufficient and conflicting. some small studies show that hydroxychloroquine was capable of decreasing sars-cov- shedding that could be enhanced by the combination of azithromycin and achieving a shorter time to clinical recovery. , but almost no clinical benefit was observed in other studies. , therefore, therapeutic efficacy of hydroxychloroquine is still needed to be reconfirmed. moreover, there are several factors required to be reconsidered before efficacy evaluation, such as the severity of illness, definition of the endpoints, and effects of the comorbidities. except for the innate immune response, host receptors, and other factors affecting the endocytosis, some signaling pathways have also been suggested as useful approaches for discovering anti-cov reagents (table ) . cyclophilins are peptidyl-prolyl isomerases with physiological functions showing as modulating the calcineurin/nfat pathway via reacting with covs nsp , which is important for the immune cell activation. in addition, they are also required for the replication of numerous viruses including hiv, hcv, as well as covs. consequently, inhibition of cyclophilins by cyclosporines, such as cyclosporin a (csa) and its derivatives, has shown to block the replication of a wide range of covs. , , , however, the obvious immune suppressive properties of csa limit its application in antiviral therapy. but alisporivir, a nonimmunosuppressive cyclosporin a-analog, also displayed the inhibition to the covs replication at a lowmicromolar concentration. additionally, the combined use of cyclosporine and interferon or ribavirin in vitro was beneficial to inhibit sars-cov or mers-cov infection, which needed to be furtherly evaluated in animal models. , furthermore, some antiviral agents inhibiting the cellular signaling pathways, in particular, the erk pathway and pi k/akt pathway, also interrupt the replication of covs. , , however, the efficacy and safety against covs infection of these agents still need to be reconsidered. corticosteroids, which were used in sars and mers treatment, have been linked to several complications such as psychosis, diabetes, and avascular necrosis. , they also were pointed out to be associated with viral replication prolongation in mers patients. however, an update on the efficacy of dexamethasone based on a press release publicized recently indicated that severe covid- patients given mg dexamethasone once daily shown a lower mortality (about - %) compared to patients with standard care. , besides, another agent, methylprednisolone, also exhibited potential capacity in reducing the mortality rate and achieving better clinical outcomes in severe covid- patients. , thus, it is wise to apply corticosteroids to the right patients at the right time. but physicians also need to monitor the corticosteroid-related complications. clinical trials of corticosteroid treatments are shown in table . potential immunotherapeutic options s protein of sars-cov proves to be highly immunogenic during infection and responsible for eliciting a humoral immune response in the host. antivirus antibodies could be detected in the plasma of convalescent patients' infected sars-cov and mers-cov. , convalescent plasma therapy has been applicated in treating patients infected by numerous viruses involving ebola virus, junin virus, machupo virus, and lassa fever. [ ] [ ] [ ] [ ] as for sars-cov, higher day- discharge rate and lower mortality rate have been observed among sars patients who received convalescent plasma transfusion before day of the illness. , this is consistent with another small cohorts research concluding infected patients with severe conditions who failed to respond to current therapies but finally survived after transfused with convalescent plasma, with no obvious side effects. similar results were found in mers patients. additionally, plasma adoptive therapy with anti-mers-cov antibodies could block the virus adhesion and accelerate the viral elimination from mers-cov-infected animal models. but the efficacy and safety of convalescent plasma therapy in covid- patients still need to be reevaluated. although convalescent plasma therapy proves to be a potentially effective therapeutic option for emerging covs, several factors still limit its extensive use in clinical, one of which is enough titers of serum neutralizing antibodies. the development of mabs targeting the s protein of covs is regarded as a remedial strategy (table ). potent mabs against s protein of human covs can be attained via transgenic mice immunization, convalescent b cells immortalization, and cloning of small chain variable regions from naïve and convalescent patients. the majority of mabs interact with the rbd of s protein leading to the interruption of rbd-receptor binding and block the viral attachment. a few mabs react with other regions of s protein besides the rbd. although binding to different epitopes, these mabs exhibit capacity to reduce the viral titers. two rbd-specific neutralizing mabs, mers- and mers- , which were derived from single-chain variable regions, revealed suppressive effects against both mers-cov and pseudotyped mers-cov infection at nanomolar concentrations and were recommended as promising candidates for therapeutic interventions to mers. based on similar mechanisms, other human mabs for mers-cov were also capable of competing with dpp for rbd binding and neutralizing the virus. , , [ ] [ ] [ ] [ ] when administrated to individuals at risk, some of the mabs were capable of preventing viral replication and contributing to block the transmission of mers-cov among human. thus, such antibodies could be served as prophylactic strategies in clinical and valuable tools to guild the development of effective anti-covs vaccines. , from sars-cov to sars-cov- , the emergence of severe human covs have taught us many lessons about the importance of rapid diagnostics and effective vaccines to control the outbreak caused by these viruses. due to the persistence of zoonotic sources in endemic areas, lethal covs remain existing in human society and may lead to the epidemic at any time. thus, a priority is to develop vaccines targeting conserved alleles and providing broad-spectrum protection against varied viral strains. since the emergence of sars-cov and mers-cov, several strategies were applicated in vaccine design, including inactivated virus vaccines, live-attenuated virus vaccines, viral vector vaccines, nanoparticles, recombinant protein subunits vaccines, and dna vaccines (table ) . , and clinical trials have also been developed to test the efficacy of the novel vaccines (table ) . effective vaccines are pivotal in blocking the virus spread from animals' reservoirs to human hosts. inactivated virus vaccines, preserving the viral structure and antigenicity but eliminating the infectious ability, could elicit neutralizing antibodies in animal models of sars-cov and show protection against viral replication when administrated with or without adjuvants. which may be related to the disseminated infection observed in immunocompromised patients. in addition, live-attenuated virus vaccines can induce an innate and adaptive immune response and the protective value can last for a long time. besides, other strategies for vaccines development are also evaluated in animal models. based on the experience of sars-cov and mers-cov, the development of novel sars-cov- vaccine is currently underway and requires more research. however, several concerns should be addressed about the vaccination. the first is the disease deterioration caused by vaccination. although this situation only appears in a small subset of sars vaccine studies, it is still a significant problem that needs to be properly solved. second, the variability of s protein can mediate covs escape from neutralization, suggesting that recombinant protein subunits vaccines based on s protein may demand multivalent approaches. last but not least, how to define ta b l e important clinical trials with vaccines for sars-cov, mers-cov, and sars-cov- the emergence and prevalence of highly pathogenic cov severely threaten public health. a task of top priority is to make clear the viral structural and epidemiological characteristics and block the viral dissemination as well as the progression of the disease, at the first case. to date, further understanding of the life cycle and the pathogenesis of emerging human covs makes current therapeutic strategies of antiviral infection more rational. repurposing existing antiviral drugs is an effective short-term strategy to deal with emerging cov such as the ongoing sars-cov- . various agents with different targets have been evaluated in vitro and in vivo. but not all antiviral agents are capable of achieving better efficacy than in vitro, and in vivo studies are needed to select optimal agents. suitable animal models are particularly significant. however, there are only a few effective animal models available for the studies of covs treatment, which may postpone the clinical evaluation of drugs. besides, due to the diversity of viruses and the capacity of rapidly mutating, some antiviral reagents available for existing covs may become invalid. accordingly, sequencing more natural specimens and combination therapy with two or more synergistic agents have become promising solutions. furthermore, the efficacy of current antiviral therapies needs to be estimated in larger scale, well-organized randomized clinical trial the efficacy and safety of the most practicable strategies for the ongoing covid- are urgently needed to be further assessed in clinical trials, involving remdesivir (gs- ), lopinavir/ritonavir, lopinavir/ritonavir combined with ifn-β, convalescent plasma, and mabs, which prove to be potentially effective options against sars-cov- . additionally, to control the future cov pandemics, the development of novel broad-spectrum antiviral agents covering numerous covs will become the ultimate goal. the authors declare no conflict of interest. wei https://orcid.org/ - - - coronavirus diversity, phylogeny and interspecies jumping coronavirus pathogenesis is the discovery of the novel human betacoronavirus c emc/ (hcov-emc) the beginning of another sars-like pandemic? discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus interspecies transmission and emergence of novel viruses: lessons from bats and birds the pdz-binding motif of severe acute respiratory syndrome coronavirus envelope protein is a determinant of viral pathogenesis epidemiology and cause of severe acute respiratory syndrome (sars) in guangdong, people's republic of china middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease cultivation of viruses from a high proportion of patients with colds a new virus isolated from the human respiratory tract epidemiology, genetic recombination, and pathogenesis of coronaviruses molecular evolution of human coronavirus genomes korean society of epidemiology -nco vtft. an interim review of the epidemiological characteristics of novel coronavirus coronavirus envelope protein: a small membrane protein with multiple functions the molecular biology of coronaviruses proteolytic processing of polyproteins a and ab between non-structural proteins and / of coronavirus infectious bronchitis virus is dispensable for viral replication in cultured cells supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy cryo-electron tomography of mouse hepatitis virus: insights into the structure of the coronavirion coronavirus immunogens synthesis and characterization of a native, oligomeric form of recombinant severe acute respiratory syndrome coronavirus spike glycoprotein the m, e, and n structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of viruslike particles pre-fusion structure of a human coronavirus spike protein sars coronavirus: a new challenge for prevention and therapy cellular entry of the sars coronavirus structural characterization of the fusion-active complex of severe acute respiratory syndrome (sars) coronavirus interaction between heptad repeat and regions in spike protein of sars-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors structural characterization of the sarscoronavirus spike s fusion protein core major receptorbinding and neutralization determinants are located within the same domain of the transmissible gastroenteritis virus (coronavirus) spike protein localization of neutralizing epitopes and the receptor-binding site within the aminoterminal amino acids of the murine coronavirus spike protein identification of a receptor-binding domain of the spike glycoprotein of human coronavirus hcov- e receptor-binding domain of sars-cov spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies characterization of the coronavirus mouse hepatitis virus strain a small membrane protein e a highly unusual palindromic transmembrane helical hairpin formed by sars coronavirus e protein exceptional flexibility in the sequence requirements for coronavirus small envelope protein function association of the infectious bronchitis virus c protein with the virion envelope the -kda hydrophobic protein encoded at the ' end of the porcine transmissible gastroenteritis coronavirus genome is membrane-associated mouse hepatitis virus gene b protein is a new virion envelope protein infectious bronchitis virus e protein is targeted to the golgi complex and directs release of virus-like particles a comprehensive comparison of transmembrane domains reveals organelle-specific properties subcellular location and topology of severe acute respiratory syndrome coronavirus envelope protein induction of apoptosis in murine coronavirus-infected cultured cells and demonstration of e protein as an apoptosis inducer assembly of the coronavirus envelope: homotypic interactions between the m proteins sars coronavirus e protein forms cation-selective ion channels differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins s, m and e bcl-xl inhibits t-cell apoptosis induced by expression of sars coronavirus e protein in the absence of growth factors the transmembrane domain of the infectious bronchitis virus e protein is required for efficient virus release biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells role of the coronavirus e viroporin protein transmembrane domain in virus assembly severe acute respiratory syndrome coronavirus envelope protein regulates cell stress response and apoptosis heterologous gene expression from transmissible gastroenteritis virus replicon particles generation of a replication-competent, propagation-deficient virus vector based on the transmissible gastroenteritis coronavirus genome the small envelope protein e is not essential for murine coronavirus replication a severe acute respiratory syndrome coronavirus that lacks the e gene is attenuated in vitro and in vivo absence of e protein arrests transmissible gastroenteritis coronavirus maturation in the secretory pathway characterization of severe acute respiratory syndrome coronavirus membrane protein sequence and topology of a model intracellular membrane protein, e glycoprotein, from a coronavirus genetic evidence for a structural interaction between the carboxy termini of the membrane and nucleocapsid proteins of mouse hepatitis virus the molecular biology of coronaviruses a structural analysis of m protein in coronavirus assembly and morphology envelope glycoprotein interactions in coronavirus assembly efficient assembly and release of sars coronavirus-like particles by a heterologous expression system coronaviruses: an overview of their replication and pathogenesis nucleocapsidindependent assembly of coronavirus-like particles by co-expression of viral envelope protein genes coronavirus pseudoparticles formed with recombinant m and e proteins induce alpha interferon synthesis by leukocytes the cytoplasmic tails of infectious bronchitis virus e and m proteins mediate their interaction the missing link in coronavirus assembly. retention of the avian coronavirus infectious bronchitis virus envelope protein in the pre-golgi compartments and physical interaction between the envelope and membrane proteins characterization of the coronavirus m protein and nucleocapsid interaction in infected cells the membrane m protein carboxy terminus binds to transmissible gastroenteritis coronavirus core and contributes to core stability isolation of coronavirus envelope glycoproteins and interaction with the viral nucleocapsid sequence comparison of the n genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein localization of an rna-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus structure of the n-terminal rna-binding domain of the sars cov nucleocapsid protein the nucleocapsid protein of the sars coronavirus is capable of selfassociation through a c-terminal amino acid interaction domain the dimer interface of the sars coronavirus nucleocapsid protein adapts a porcine respiratory and reproductive syndrome virus-like structure the nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its n-terminal domain and multimerization properties the severe acute respiratory syndrome coronavirus nucleocapsid protein is phosphorylated and localizes in the cytoplasm by - - -mediated translocation recombinant severe acute respiratory syndrome (sars) coronavirus nucleocapsid protein forms a dimer through its c-terminal domain modular organization of sars coronavirus nucleocapsid protein characterisation of the rna binding properties of the coronavirus infectious bronchitis virus nucleocapsid protein amino-terminal region structure of the sars coronavirus nucleocapsid protein rna-binding dimerization domain suggests a mechanism for helical packaging of viral rna phosphorylation of the arginine/serine dipeptide-rich motif of the severe acute respiratory syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization identification of in vivointeracting domains of the murine coronavirus nucleocapsid protein glycogen synthase kinase- regulates the phosphorylation of severe acute respiratory syndrome coronavirus nucleocapsid protein and viral replication oligomerization of the carboxyl terminal domain of the human coronavirus e nucleocapsid protein solution structure of the c-terminal dimerization domain of sars coronavirus nucleocapsid protein solved by the sail-nmr method high affinity interaction between nucleocapsid protein and leader/intergenic sequence of mouse hepatitis virus rna the nucleocapsid protein of sars coronavirus has a high binding affinity to the human cellular heterogeneous nuclear ribonucleoprotein a theoretical aspects of virus capsid assembly analysis of multimerization of the sars coronavirus nucleocapsid protein mass spectroscopic characterization of the coronavirus infectious bronchitis virus nucleoprotein and elucidation of the role of phosphorylation in rna binding by using surface plasmon resonance mapping of the coronavirus membrane protein domains involved in interaction with the spike protein envelope protein palmitoylations are crucial for murine coronavirus assembly the hydrophobic domain of infectious bronchitis virus e protein alters the host secretory pathway and is important for release of infectious virus the coronavirus e protein: assembly and beyond mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes the intracellular sites of early replication and budding of sars-coronavirus cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer glycan shield and epitope masking of a coronavirus spike protein observed by cryoelectron microscopy cryo-electron microscopy structures of the sars-cov spike glycoprotein reveal a prerequisite conformational state for receptor binding immunogenicity and structures of a rationally designed prefusion mers-cov spike antigen cryo-em structures of mers-cov and sars-cov spike glycoproteins reveal the dynamic receptor binding domains a human homolog of angiotensin-converting enzyme. cloning and functional expression as a captopril-insensitive carboxypeptidase angiotensin-converting enzyme is a functional receptor for the sars coronavirus human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry highly conserved regions within the spike proteins of human coronaviruses e and nl determine recognition of their respective cellular receptors genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding receptor recognition by novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars angiotensin-converting enzyme (ace ) in disease pathogenesis a novel angiotensinconverting enzyme-related carboxypeptidase (ace ) converts angiotensin i to angiotensin - quantitative mrna expression profiling of ace , a novel homologue of angiotensin converting enzyme tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis angiotensin-converting enzyme protects from severe acute lung failure a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury dipeptidyl peptidase distribution in the human respiratory tract: implications for the middle east respiratory syndrome dipeptidylpeptidase iv from bench to bedside: an update on structural properties, functions, and clinical aspects of the enzyme dpp iv physiology and pharmacology of dpp- in glucose homeostasis and the treatment of type diabetes dipeptidyl peptidase iv (dpp- ) inhibition alleviates pulmonary arterial remodeling in experimental pulmonary hypertension inhibitors of dipeptidyl peptidase iv (dp iv, cd ) induces secretion of transforming growth factor-beta (tgf-beta ) in stimulated mouse splenocytes and thymocytes dpp- inhibitors and their potential role in the management of type diabetes revisiting an old acquaintance: cd and its molecular mechanisms in t cell function cd /dipeptidylpeptidase iv-chemokine interactions: doubleedged regulation of inflammation and tumor biology cut to the chase: a review of cd /dipeptidyl peptidase- 's (dpp ) entanglement in the immune system differential expression of the middle east respiratory syndrome coronavirus receptor in the upper respiratory tracts of humans and dromedary camels middle east respiratory syndrome coronavirus causes multiple organ damage and lethal disease in mice transgenic for human dipeptidyl peptidase the structure and main functions of aminopeptidase n human aminopeptidase n is a receptor for human coronavirus e molecular determinants of species specificity in the coronavirus receptor aminopeptidase n (cd ): influence of n-linked glycosylation human coronavirus hku spike protein uses o-acetylated sialic acid as an attachment receptor determinant and employs hemagglutininesterase protein as a receptor-destroying enzyme human coronaviruses oc and hku bind to -o-acetylated sialic acids via a conserved receptor-binding site in spike protein domain a virus entry: open sesame the cell biology of receptor-mediated virus entry dynamics of virus-receptor interactions in virus binding, signaling, and endocytosis characterization of severe acute respiratory syndrome-associated coronavirus (sars-cov) spike glycoprotein-mediated viral entry protease-mediated enhancement of severe acute respiratory syndrome coronavirus infection inhibitors of cathepsin l prevent severe acute respiratory syndrome coronavirus entry endosomal proteolysis by cathepsins is necessary for murine coronavirus mouse hepatitis virus type spike-mediated entry activation of the sars coronavirus spike protein via sequential proteolytic cleavage at two distinct sites elastase-mediated activation of the severe acute respiratory syndrome coronavirus spike protein at discrete sites within the s domain cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease evidence that tmprss activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response a transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein mechanisms of coronavirus cell entry mediated by the viral spike protein ready, set, fuse! the coronavirus spike protein and acquisition of fusion competence physiological and molecular triggers for sars-cov membrane fusion and entry into host cells structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme from sars to mers, thrusting coronaviruses into the spotlight isolation and characterization of viruses related to the sars coronavirus from animals in southern china sars: clinical presentation, transmission, pathogenesis and treatment options identification of a novel coronavirus in patients with severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome allelic variation in the toll-like receptor adaptor protein ticam contributes to sars-coronavirus pathogenesis in mice. g (bethesda) a clinicopathological study of three cases of severe acute respiratory syndrome (sars) lung pathology of fatal severe acute respiratory syndrome the spectrum of pathological changes in severe acute respiratory syndrome (sars) pathology and pathogenesis of severe acute respiratory syndrome evolution of pulmonary pathology in severe acute respiratory syndrome sars: prognosis, outcome and sequelae cytosolic surveillance and antiviral immunity sensing of rna viruses: a review of innate immune receptors involved in recognizing rna virus invasion biomarkers in acute respiratory distress syndrome the mercurial nature of neutrophils: still an enigma in ards? sars-cov pathogenesis is regulated by a stat dependent but a type i, ii and iii interferon receptor independent mechanism resolution of primary severe acute respiratory syndrome-associated coronavirus infection requires stat sars coronavirus pathogenesis: host innate immune responses and viral antagonism of interferon ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum functional screen reveals sars coronavirus nonstructural protein nsp as a novel cap n methyltransferase in vitro reconstitution of sars-coronavirus mrna cap methylation biochemical and structural insights into the mechanisms of sars coronavirus rna ribose '-omethylation by nsp /nsp protein complex ribose '-omethylation provides a molecular signature for the distinction of self and non-self mrna dependent on the rna sensor mda severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp and rational design of an attenuated strain a two-pronged strategy to suppress host protein synthesis by sars coronavirus nsp protein sars coronavirus nsp protein induces template-dependent endonucleolytic cleavage of mrnas: viral mrnas are resistant to nsp -induced rna cleavage regulation of irf- -dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of irf and nf-kappab signaling coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of sting-mediated signaling the nucleocapsid protein of coronaviruses acts as a viral suppressor of rna silencing in mammalian cells severe acute respiratory syndrome coronavirus m protein inhibits type i interferon production by impeding the formation of traf .tank.tbk /ikkepsilon complex molecular determinants for subcellular localization of the severe acute respiratory syndrome coronavirus open reading frame b protein severe acute respiratory syndrome coronavirus open reading frame (orf) b, orf , and nucleocapsid proteins function as interferon antagonists pathogenesis of middle east respiratory syndrome coronavirus middle east respiratory syndrome (mers) a review of studies on animal reservoirs of the sars coronavirus middle east respiratory syndrome coronavirus (mers-cov): announcement of the coronavirus study group middle east respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study evidence for camelto-human transmission of mers coronavirus middle east respiratory syndrome tropism of and innate immune responses to the novel human betacoronavirus lineage c virus in human ex vivo respiratory organ cultures active replication of middle east respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis rapid generation of a mouse model for middle east respiratory syndrome antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a positive-strand rna virus coronavirus nonstructural protein : evasion, attenuation, and possible treatments the structural and accessory proteins m, orf a, orf b, and orf of middle east respiratory syndrome coronavirus (mers-cov) are potent interferon antagonists middle east respiratory syndrome coronavirus accessory protein a is a type i interferon antagonist middle east respiratory syndrome coronavirus a protein is a double-stranded rnabinding protein that suppresses pact-induced activation of rig-i and mda in the innate antiviral response middle east respiratory syndrome coronavirus orf b protein inhibits type i interferon production through both cytoplasmic and nuclear targets crystal structure of the middle east respiratory syndrome coronavirus (mers-cov) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression middle east respiratory syndrome coronavirus nsp inhibits host gene expression by selectively targeting mrnas transcribed in the nucleus while sparing mrnas of cytoplasmic origin risk factors for primary middle east respiratory syndrome coronavirus illness in humans, saudi arabia high fatality rates and associated factors in two hospital outbreaks of mers in daejeon, the republic of korea renewal of alveolar epithelium in the rat following exposure to no identification of genes differentially expressed in rat alveolar type i cells clinicopathologic, immunohistochemical, and ultrastructural findings of a fatal case of middle east respiratory syndrome coronavirus infection in the united arab emirates histopathology of middle east respiratory syndrome coronovirus (mers-cov) infection -clinicopathological and ultrastructural study pegylated interferon-alpha protects type pneumocytes against sars coronavirus infection in macaques dpp , the middle east respiratory syndrome coronavirus receptor, is upregulated in lungs of smokers and chronic obstructive pulmonary disease patients first case of novel coronavirus in the united states a novel coronavirus from patients with pneumonia in china genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan genomic characterization and infectivity of a novel sars-like coronavirus in chinese bats a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan a pneumonia outbreak associated with a new coronavirus of probable bat origin epidemiological, demographic, and clinical characteristics of cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by -ncov exploring the mechanism of liver enzyme abnormalities in patients with novel coronavirus-infected pneumonia -ncov: new challenges from coronavirus pathological findings of covid- associated with acute respiratory distress syndrome lymphopenia predicts disease severity of covid- : a descriptive and predictive study the novel coronavirus: a bird's eye view medical treatment of viral pneumonia including sars in immunocompetent adult clinical management and infection control of sars: lessons learned coronaviruses -drug discovery and therapeutic options learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by -ncov structure-based discovery of middle east respiratory syndrome coronavirus fusion inhibitor crossneutralization of human and palm civet severe acute respiratory syndrome coronaviruses by antibodies targeting the receptor-binding domain of spike protein suppression of sars-cov entry by peptides corresponding to heptad regions on spike glycoprotein structure of the fusion core and inhibition of fusion by a heptad repeat peptide derived from the s protein of middle east respiratory syndrome coronavirus potent neutralization of mers-cov by human neutralizing monoclonal antibodies to the viral spike glycoprotein identification of human neutralizing antibodies against mers-cov and their role in virus adaptive evolution exceptionally potent neutralization of middle east respiratory syndrome coronavirus by human monoclonal antibodies middle east respiratory syndrome coronavirus infection mediated by the transmembrane serine protease tmprss role of the spike glycoprotein of human middle east respiratory syndrome coronavirus (mers-cov) in virus entry and syncytia formation protease inhibitors targeting coronavirus and filovirus entry genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans targeting membranebound viral rna synthesis reveals potent inhibition of diverse coronaviruses including the middle east respiratory syndrome virus cell host response to infection with novel human coronavirus emc predicts potential antivirals and important differences with sars coronavirus delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel middle east respiratory syndrome coronavirus: implications for pathogenesis and treatment interferon-β and mycophenolic acid are potent inhibitors of middle east respiratory syndrome coronavirus in cell-based assays antiviral potential of erk/mapk and pi k/akt/mtor signaling modulation for middle east respiratory syndrome coronavirus infection as identified by temporal kinome analysis the sars-coronavirus-host interactome: identification of cyclophilins as target for pancoronavirus inhibitors mers-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin a or interferon-α treatment inhibitors of the hepatitis c virus polymerase; mode of action and resistance approved antiviral drugs over the past years new nucleoside analogues for the treatment of hemorrhagic fever virus infections design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity therapeutic options for the novel coronavirus ( -ncov) t- (favipiravir) induces lethal mutagenesis in influenza a h n viruses in vitro in vitro and in vivo activities of t- against arenavirus and bunyavirus infections activity of t- in a hamster model of yellow fever virus infection in comparison with that of a chemically related compound, t- post-exposure efficacy of oral t- (favipiravir) against inhalational ebola virus infection in a mouse model japanese surveillance systems and treatment for influenza successful treatment of advanced ebola virus infection with t- (favipiravir) in a small animal model efficacy of orally administered t- on lethal avian influenza a (h n ) virus infections in mice clinical and virological characteristics of ebola virus disease patients treated with favipiravir (t- )-sierra leone remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro broad-spectrum antiviral activity of virazole: -beta-d-ribofuranosyl- , , -triazole- -carboxamide depletion of gtp pool is not the predominant mechanism by which ribavirin exerts its antiviral effect on lassa virus development of a standard treatment protocol for severe acute respiratory syndrome the management of coronavirus infections with particular reference to sars treatment with interferon-α b and ribavirin improves outcome in mers-covinfected rhesus macaques ribavirin and interferon alfa- a for severe middle east respiratory syndrome coronavirus infection: a retrospective cohort study ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: an observational study ifn-α a or ifn-β a in combination with ribavirin to treat middle east respiratory syndrome coronavirus pneumonia: a retrospective study triple combination of interferon beta- b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with covid- : an open-label, randomised, phase trial mechanism of inhibition of ebola virus rna-dependent rna polymerase by remdesivir therapeutic efficacy of the small molecule gs- against ebola virus in rhesus monkeys coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease. mbio broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses gs- and its parent nucleoside analog inhibit filo-, pneumo-, and paramyxoviruses remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial compassionate use of remdesivir for patients with severe covid- remdesivir for the treatment of covid- -preliminary report protection against filovirus diseases by a novel broad-spectrum nucleoside analogue bcx mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (t- ), a broad-spectrum antiviral the papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity nidovirus papain-like proteases: multifunctional enzymes with protease, deubiquitinating and deisgylating activities mers-cov papain-like protease has deisgylating and deubiquitinating activities thiopurine analogs and mycophenolic acid synergistically inhibit the papain-like protease of middle east respiratory syndrome coronavirus identification and design of novel small molecule inhibitors against mers-cov papainlike protease via high-throughput screening and molecular modeling the sarscoronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds a noncovalent class of papain-like protease/deubiquitinase inhibitors blocks sars virus replication disulfiram can inhibit mers and sars coronavirus papain-like proteases via different modes treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings broad-spectrum antivirals for the emerging middle east respiratory syndrome coronavirus treatment with lopinavir/ritonavir or interferon-β b improves outcome of mers-cov infection in a nonhuman primate model of common marmoset a trial of lopinavir-ritonavir in adults hospitalized with severe covid- , -bis-arylmethyloxy- -hydroxychromones with antiviral activity against both hepatitis c virus (hcv) and sars-associated coronavirus (scv) design, synthesis and molecular docking of novel triazole derivatives as potential cov helicase inhibitors evaluation of ssya - as a replication inhibitor of severe acute respiratory syndrome, mouse hepatitis, and middle east respiratory syndrome coronaviruses broad-spectrum in vitro activity and in vivo efficacy of the antiviral protein griffithsin against emerging viruses of the family coronaviridae activity of and effect of subcutaneous treatment with the broad-spectrum antiviral lectin griffithsin in two laboratory rodent models inhibition of severe acute respiratory syndrome-associated coronavirus (sars-cov) infectivity by peptides analogous to the viral spike protein peptide-based membrane fusion inhibitors targeting hcov- e spike protein hr and hr domains protective effect of intranasal regimens containing peptidic middle east respiratory syndrome coronavirus fusion inhibitor against mers-cov infection identification of a novel inhibitor against middle east respiratory syndrome coronavirus using sirna in prophylactic and therapeutic regimens against sars coronavirus in rhesus macaque inhibition of sars-cov replication by sirna silencing sars-cov spike protein expression in cultured cells by rna interference inhibition of sars-cov replication cycle by small interference rnas silencing specific sars proteins, a/ b, a/ b and s development of interfering rna agents to inhibit sars-associated coronavirus infection and replication resveratrol suppresses nuclear factor-kappab in herpes simplex virus infected cells resveratrol decreases nitric oxide production by hepatocytes during inflammation polygonum cuspidatum and its active components inhibit replication of the influenza virus through toll-like receptor -induced interferon beta expression studies on trans-resveratrol/carboxymethylated ( , / , )-β-dglucan association for aerosol pharmaceutical applications resveratrol attenuates inflammatory hyperalgesia by inhibiting glial activation in mice spinal cords resveratrol-mediated gamma interferon reduction prevents airway inflammation and airway hyperresponsiveness in respiratory syncytial virus-infected immunocompromised mice effective inhibition of mers-cov infection by resveratrol hexamethylene amiloride blocks e protein ion channels and inhibits coronavirus replication repurposing of clinically developed drugs for treatment of middle east respiratory syndrome coronavirus infection singlet oxygen effects on lipid membranes: implications for the mechanism of action of broad-spectrum viral fusion inhibitors treatment of sars with human interferons inhibition of novel β coronavirus replication by a combination of interferon-α b and ribavirin ribavirin and interferon-beta synergistically inhibit sars-associated coronavirus replication in animal and human cell lines nitazoxanide: a first-in-class broad-spectrum antiviral agent effect of nitazoxanide in adults and adolescents with acute uncomplicated influenza: a double-blind, randomised, placebo-controlled, phase b/ trial clinical trial: randomized, double-blind, placebo-controlled study of nitazoxanide monotherapy for the treatment of patients with chronic hepatitis c genotype induction of cd + tcell responses against novel glioma-associated antigen peptides and clinical activity by vaccinations with {alpha}-type polarized dendritic cells and polyinosinic-polycytidylic acid stabilized by lysine and carboxymethylcellulose in patients with recurrent malignant glioma a multiinstitution phase ii study of poly-iclc and radiotherapy with concurrent and adjuvant temozolomide in adults with newly diagnosed glioblastoma structure-based discovery of a novel angiotensin-converting enzyme inhibitor identification of critical determinants on ace for sars-cov entry and development of a potent entry inhibitor inhibition of middle east respiratory syndrome coronavirus infection by anti-cd monoclonal antibody a cysteine protease inhibitor rescues mice from a lethal cryptosporidium parvum infection cure of hookworm infection with a cysteine protease inhibitor efficacy of camostat mesilate against dyspepsia associated with non-alcoholic mild pancreatic disease pancreatic stellate cells: new target in the treatment of chronic pancreatitis screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture atp a -mediated src signaling inhibits coronavirus entry into host cells anti-malaria drug chloroquine is highly effective in treating avian influenza a h n virus infection in an animal model in vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine inhibition of human coronavirus e infection in human epithelial lung cells (l ) by chloroquine: involvement of p mapk and erk a systematic screen of fda-approved drugs for inhibitors of biological threat agents effects of chloroquine on viral infections: an old drug against today's diseases? chloroquine is a potent inhibitor of sars coronavirus infection and spread effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus (sars-cov- ) infection: a randomized clinical trial hydroxychloroquine in patients with mainly mild to moderate coronavirus disease : open label, randomised controlled trial hydroxychloroquine and azithromycin as a treatment of covid- : results of an openlabel non-randomized clinical trial clinical efficacy of hydroxychloroquine in patients with covid- pneumonia who require oxygen: observational comparative study using routine care data observational study of hydroxychloroquine in hospitalized patients with covid- suppression of coronavirus replication by cyclophilin inhibitors human coronavirus nl replication is cyclophilin a-dependent and inhibited by non-immunosuppressive cyclosporine a-derivatives including alisporivir porcine epidemic diarrhea virus induces caspaseindependent apoptosis through activation of mitochondrial apoptosis-inducing factor alisporivir inhibits mers-and sars-coronavirus replication in cell culture, but not sars-coronavirus infection in a mouse model effect of interferon alpha and cyclosporine treatment separately and in combination on middle east respiratory syndrome coronavirus (mers-cov) replication in a human in-vitro and ex-vivo culture model abelson kinase inhibitors are potent inhibitors of severe acute respiratory syndrome coronavirus and middle east respiratory syndrome coronavirus fusion factors associated with psychosis among patients with severe acute respiratory syndrome: a case-control study corticosteroid therapy for critically ill patients with middle east respiratory syndrome dexamethasone in the management of covid - covid- : demand for dexamethasone surges as recovery trial publishes preprint risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease pneumonia in wuhan a retrospective cohort study of methylprednisolone therapy in severe patients with covid- pneumonia identification of immunodominant sites on the spike protein of severe acute respiratory syndrome (sars) coronavirus: implication for developing sars diagnostics and vaccines virological and serological analysis of a recent middle east respiratory syndrome coronavirus infection case on a triple combination antiviral regimen experience of using convalescent plasma for severe acute respiratory syndrome among healthcare workers in a taiwan hospital the use of lassa fever convalescent plasma in nigeria treatment of ebola hemorrhagic fever with blood transfusions from convalescent patients. international scientific and technical committee treatment of argentine hemorrhagic fever with convalescent's plasma. cases bolivian hemorrhagic fever. a report of four cases retrospective comparison of convalescent plasma with continuing high-dose methylprednisolone treatment in sars patients use of convalescent plasma therapy in sars patients in hong kong middle east respiratory syndrome virus pathogenesis neutralizing human monoclonal antibodies to severe acute respiratory syndrome coronavirus: target, mechanism of action, and therapeutic potential prophylactic and postexposure efficacy of a potent human monoclonal antibody against mers coronavirus a conformation-dependent neutralizing monoclonal antibody specifically targeting receptorbinding domain in middle east respiratory syndrome coronavirus spike protein a humanized neutralizing antibody against mers-cov targeting the receptor-binding domain of the spike protein pre-and postexposure efficacy of fully human antibodies against spike protein in a novel humanized mouse model of mers-cov infection a decade after sars: strategies for controlling emerging coronaviruses sars vaccines: where are we? inactivated sars-cov vaccine elicits high titers of spike protein-specific antibodies that block receptor binding and virus entry a subcutaneously injected uv-inactivated sars coronavirus vaccine elicits systemic humoral immunity in mice vaccines to prevent severe acute respiratory syndrome coronavirus-induced disease escape from human monoclonal antibody neutralization affects in vitro and in vivo fitness of severe acute respiratory syndrome coronavirus presence of middle east respiratory syndrome coronavirus antibodies in saudi arabia: a nationwide, cross-sectional, serological study reversal of the progression of fatal coronavirus infection in cats by a broad-spectrum coronavirus protease inhibitor structure-guided design of potent and permeable inhibitors of mers coronavirus cl protease that utilize a piperidine moiety as a novel design element synthesis and evaluation of phenylisoserine derivatives for the sars-cov cl protease inhibitor identification, synthesis and evaluation of sars-cov and mers-cov c-like protease inhibitors engineering a novel antibodypeptide bispecific fusion protein against mers-cov. antibodies (basel) identification of a peptide derived from the heptad repeat region of the porcine epidemic diarrhea virus (pedv) spike glycoprotein that is capable of suppressing pedv entry and inducing neutralizing antibodies a novel peptide with potent and broad-spectrum antiviral activities against multiple respiratory viruses antiviral activity of k against members of the order nidovirales purified coronavirus spike protein nanoparticles induce coronavirus neutralizing antibodies in mice key: cord- -e m m ut authors: samidurai, arun; das, anindita title: cardiovascular complications associated with covid- and potential therapeutic strategies date: - - journal: int j mol sci doi: . /ijms sha: doc_id: cord_uid: e m m ut the outbreak of coronavirus disease (covid- ), an infectious disease with severe acute respiratory syndrome, has now become a worldwide pandemic. despite the respiratory complication, covid- is also associated with significant multiple organ dysfunction, including severe cardiac impairment. emerging evidence reveals a direct interplay between covid- and dire cardiovascular complications, including myocardial injury, heart failure, heart attack, myocarditis, arrhythmias as well as blood clots, which are accompanied with elevated risk and adverse outcome among infected patients, even sudden death. the proposed pathophysiological mechanisms of myocardial impairment include invasion of sars-cov- virus via angiotensin-converting enzyme to cardiovascular cells/tissue, which leads to endothelial inflammation and dysfunction, de-stabilization of vulnerable atherosclerotic plaques, stent thrombosis, cardiac stress due to diminish oxygen supply and cardiac muscle damage, and myocardial infarction. several promising therapeutics are under investigation to the overall prognosis of covid- patients with high risk of cardiovascular impairment, nevertheless to date, none have shown proven clinical efficacy. in this comprehensive review, we aimed to highlight the current integrated therapeutic approaches for covid- and we summarized the potential therapeutic options, currently under clinical trials, with their mechanisms of action and associated adverse cardiac events in highly infectious covid- patients. coronavirus- is an emerging infectious disease caused by the novel single-stranded rna enveloped severe acute respiratory syndrome-coronavirus- (sars-cov- ). the first case of covid- was reported on december in hubei province of china [ ] and within a short span of time, the disease quickly spread to other parts of the world [ ] and has rapidly evolved as a global pandemic situation. the first confirmed case of covid- in the united states of america (usa) was reported on january in the state of washington when a -year-old man showed symptoms of sars-cov- infection after returning from wuhan, china [ ] . the first person-to-person transmission of a confirmed covid- case in usa was reported in illinois on january after an initial positive diagnosis of covid- on the patient's wife, who returned from wuhan, china in mid-january , and unfortunately, covid- is now widespread in all states across the usa [ , ] . according to johns hopkins coronavirus resource center, as of september , there are , , confirmed covid- cases and , confirmed deaths worldwide [ ] . usa is now the epicenter of the disease; the death toll has reached , with , , confirmed covid- cases [ ] . figure is the graphical representation of most affected regions of confirmed cases with reported deaths across the world. countries with more than , confirmed cases with reported deaths are presented in figure a ,b; and countries with more than , cases (but fewer than , ) and corresponding reported deaths are shown in figure c ,d. understanding the structure and the genetic makeup of sars-cov- is important to appreciate the ongoing efforts to address this disease and for the discovery of drugs and vaccines. sars-cov- is spherical in shape and consists of multiple components which are essential for their replication and transcription: ( ) several club shaped projections on the surface of the envelope, called spike glycoprotein (s), which helps in anchoring to the host cell and acts as an inducer to neutralize antibodies, ( ) a small membrane envelope protein (e), ( ) structural membrane protein (m), which spans the lipid bilayer, ( ) hemagglutinin-esterase glycoprotein (he), which destroys the sialic acid present on the host cell and helps the virus to inject its genetic material, ( ) nucleoprotein (n) and ( ) the key component, the positive-sense single-stranded genomic rna [ ] [ ] [ ] . the typical structure of covid- virus depicting the above-mentioned components is shown in figure a . the genome size of covid- is about . - . kb [ ] and is the largest among all known rna viruses in this category (sars-cov and middle east respiratory syndrome, mers). sars-cov- encompasses several open reading frames (orf) along with its utr and utr regions. orf a/b (frame shift) is the full-length gene ( . kb size) that encodes replicase polyprotein named pp a protein and accessary (non-structural proteins (nsps) and orf b codes for pp b and nsps [ ] [ ] [ ] [ ] . the structural proteins including spike (s), envelope (e), membrane protein (m) and nucleoprotein (n) are coded by orfs and present on the ' utr region. several other essential accessary proteins are coded by orf , orf a, orf b, and orf [ ] . the domain structure of sars-cov- is presented in figure b . the genomic sequencing data obtained from covid- -infected patients in china revealed the distinct features of sars-cov- [ ] . sequence comparison showed the novel sars-cov- was more distantly correlated with sars-cov (about %) and mers-cov (about %). some of the salient features of sars-cov- make it unique and virulent compared to previously known coronaviruses. reports suggest that sars-cov- lacks the orf a protein present in sars-cov and has variation in the c and b proteins [ ] . in addition, a single mutation at n t in the spike protein strengthened the binding efficiency of sars-cov- to angiotensin-converting enzyme (ace ), the primary mode of entry into host cell [ ] . structural details of sars-cov binding to the host cell through spike protein give us the clue about the importance of the mutation in this region [ ] . studies show that this mutation in the spike protein of sars-cov- increases its binding affinity to ace in human by - times higher than sars-cov [ ] . this mutation in the spike protein may be one of the key attributes of sars-cov- that led to its rapid spreading around the world in a very short period. there are six different strains of sars-cov- identified so far, namely, ( ) l strain (originated in wuhan, china and the parent orf -l s strain), ( ) s strain (mutation of orf , l s), ( ) v strain (variant of orf a coding protein ns , g v), ( ) g (mutation in spike protein, d g), ( ) gh strain (mutations in spike protein, d g and orf a, q h) and ( ) gr (mutation in nucleocapsid gene, rg kr) [ , ] . among these variants, g strain is the most widespread, has undergone several mutations since january , and branched into subtypes gr and gh. the g and gr strains are prevalent in europe, including in italy, whereas the gh strain is widespread in germany and france. the most predominant variant found in north america is the gh strain, and this subtype along with the gr clades accounts for % of all global sequences of sars-cov- genome [ ] . as of now, strains g, gh and gr are constantly increasing, globally, and it is yet to be determined whether the unique nature of these strains is associated with the disease intensity. covid- virus is predominantly transmitted from human to human through respiratory droplets or aerosols (> - µm in diameter) and contact routes. inhalation of respiratory droplets and aerosols from covid- -infected persons is the most likely potential mode of transmission of the disease [ ] . once in the host system, sars-cov- follows the traditional steps similar to any other virus for its mode of entry into the host cells [ ] . the spike protein anchors the virus to the surface of the host cell by binding to the ace receptor [ ] . the virus undergoes conformational changes to fuse to the cell membrane of the host cells and engulfs into the cytoplasm of the cell by endosomal pathway. once inside the cell, the virus releases its genomic rna and multiplies using the host's molecular machinery. experimental evidence using hela cells demonstrate that sars-cov- entry into host cell is activated by cell surface proteases and lysosomal proteases such as transmembrane serine protease (tmprss ) and lysosomal cathepsin [ ] . ace is expressed in type ii alveolar cells, the predominant portal of entry in the lungs; it is also expressed in the heart, intestine and kidney as well as on the epithelial cells of oral mucosa and the tongue [ , ] . sars-cov- primarily affects the respiratory tract, and infected patients suffer from pneumonia and flu-like symptoms ( figure ). the patients might need intensive care and artificial ventilation after developing acute respiratory syndrome (ards) or multiple organ dysfunction syndrome (mods). the abundance of sars-cov- compromises the normal function and leads to complications in lungs (inflammation, hypoxia, cytokine storm, pulmonary edema, acute respiratory distress syndrome) and in heart (myocardial infarction, heart failure, myocarditis and arrhythmia). ace , angiotensin i-converting enzyme; ace , angiotensin-converting enzyme ; acei, ace inhibitor; at r, angiotensin type receptor; at r, angiotensin type receptor; arbs, angiotensin ii type-i receptor blockers; ctni, cardiac troponin i; mas, mitochondrial assembly receptor; mras, mineralocorticoid receptor antagonists; tmprss , transmembrane serine protease . the lungs, being a major organ targeted by sars-cov- infection, are severely compromised in delivering their function. one of the common clinical manifestations of covid- at the late stage of the disease is shortness of breath, pneumonia-like symptoms and hypoxia, which ultimately is fatal to the patients. in the pulmonary vasculature, sars-cov- enters through endocytosis and activates adam metallopeptidase domain (adam ), which in turn cleaves ace , which indicates the loss of protection against the renin-angiotensin-aldosterone system (raas), which is mediated by cleaved ace [ , ] . the activation of adam also triggers acute pulmonary inflammation and infiltration of cytokines and leukocytes in the alveolar space and results in pulmonary edema [ , ] . overactive systemic inflammation as a response to covid- infection results in cytokine storm and leads to respiratory difficulties and accounts for majority of the deaths during end stage of the treatment [ ] . pulmonary complications associated with covid- infection include diseases such as acute respiratory distress syndrome (ards), vascular endothelialitis, sepsis, pulmonary edema and pulmonary embolism [ , ] . a multicenter cohort study involving hospitals from countries, which includes patients and cases of confirmed covid- , suggests that up to . % suffer severe pulmonary complications post-surgery and the majority of the deaths are largely due to pulmonary embolism [ ] . lung autopsy reports obtained from covid- patients who died due to ards showed severe alveolar damage and infiltration of perivascular t-cells. histology analysis also demonstrated increased thrombus formation, intussusceptive angiogenesis and microangiopathy in covid- patients compared to influenza [ ] . gene expression analysis using rna isolated from covid- patients showed several inflammatory markers and angiogenesis-related genes were differently regulated compared to healthy lungs. most importantly, there was a significantly increased positive count for ace in covid- tissues compared to control. covid- patients with ards were also characterized by an increased deposition of fibrin and high expression of d-dimers and fibrinogen, suggesting fibrinolysis as a determining factor of mortality [ ] . although pulmonary complication is the dominant clinical manifestation of covid- , underlying cardiovascular complication as well as developed acute cardiac injury enhances the vulnerability of the patient. acute respiratory complication/failure and cytokine storm may cause reduced oxygen supply, which could lead to acute myocardial injury in covid- patients [ ] . patients with cardiovascular disease (cvd) have an increased risk for severity and mortality with covid- infection, mainly because of the abundance of ace receptor in the cardiovascular system, which serves as a gateway for the entry of virus in lungs and heart [ ] . respiratory illness and acute cardiac injury are major clinical manifestations observed in patients infected with sars-cov- during the late stage complications of the disease [ ] . reasonably, patients with coronary artery disease or heart failure are vulnerable to developing major cardiac injury, and once such patients are infected with sars-cov- , they are at greatest risk of serious myocardial impairment or cardiac dysfunction, requiring hospitalization due to unexpected deterioration, and eventual mortality is greater among these patients. a brief view of cardiovascular complications associated with covid- is presented in figure . voluminous available clinical evidence confirms that the severity of covid- is pronounced in patients with a prevalence of underlying cardiovascular diseases, and in many of these patients, the virus causes severe myocardial injury [ ] , including myocardial dysfunction, cardiomyopathy, arrhythmias and heart failure during the course of critical illness [ ] [ ] [ ] [ ] [ ] [ ] [ ] . according to the death data of the cdc (centers for disease control and prevention), different health conditions contribute to the deaths of covid- patients in united states, which are summarized in figure [ ] . deaths that are associated with more than one underlying condition, e.g., deaths involving both diabetes and respiratory arrest or cardiovascular complications and respiratory arrest, etc. hypertension, diabetes, cardiac arrest, ischemic heart disease, and heart failure are the major risk factors and have contributed to the fatalities in covid- cases. the renin-angiotensin-aldosterone system (raas) consists of an enzymatic cascade that controls blood pressure by regulating circulatory homeostasis, body fluid and systemic vascular resistance, all of which are involved in the regulation of a myriad of cardiovascular system [ ] . ace (angiotensin i-converting enzyme) cleaves angiotensin i (ang-i) to angiotensin ii (ang-ii), which binds to and activates angiotensin type receptor (at r), which leads to vasoconstriction, inflammation, fibrosis and proliferation [ ] (figure ). ace converts ang-ii into angiotensin - (ang - ), which has vasodilating and anti-inflammatory effects by binding to mas receptor (mas-r). ace also cleaves ang-i into angiotensin- - , which is further converted into ang - by ace. therefore, ace regulates abnormal activation of the raas, which can prevent the development of hypertension, cardiac hypertrophy, and heart failure [ ] . an increase in ace /ace ratio protects against endothelial dysfunctions and vascular constriction, and exogenous ace activation attenuates thrombus formation and reduces platelet attachment to vessels [ , ] . the etiology of ace -dependent cardiovascular complications with covid- infection is rather complex. sars-cov- enters cardiovascular cells/tissue by binding to the membrane-bound form of ace (ace receptor). elevated levels of ace and its activity are the biomarkers of cardiovascular disease including patients with heart failure [ ] , which indicate that these patients may be more susceptible to covid- infection [ ] , with worsened prognosis of cardiovascular disease treatment [ ] . measuring plasma angiotensin peptides and plasma ace levels can provide a direct evaluation on the progress of treatment and the state of the raas in covid- patients [ ] . nevertheless, earlier clinical studies conveyed that treatment with soluble form of recombinant human ace (rhace ; apn ( . mg/kg, iv, bid for days), gsk : . mg/kg, iv, bid for days) neutralized the excessive sars-cov virus in the system and preserved the protective cellular effects of ace in ards patients [ , ] . consequently, scientists propose the therapeutic potential of soluble recombinant ace , which can overwhelm sars-cov- to prevent its binding to cellular ace [ ] . in addition, ace inhibitors (acei), which upregulate ace expression on the cell surface, have been proven to be successful, and improved the survival rate in patients undergoing covid- treatment [ ] . abundant expression of ace on the cell surface following virus infection may maintain ang-ii degradation, which could reduce at r activation and the risk of deleterious outcomes of covid- . while the ace gene is located on the x-chromosome, gender has an impact among covid- patients, where men are at increased risk of susceptibility to covid- infection and cvd complications due to their hemizygous allele for ace compared to heterozygous allele in female [ ] . interestingly, clinical data from european men and women with heart failure showed elevated level of circulating plasma ace in men than in female [ ] . this data complements with an observation of increased prevalence and susceptibility of covid- in males and demonstrates that abundance of ace receptor in cardiovascular cells can lead to severe clinical complications [ ] [ ] [ ] . considering the importance of ace in the development of hypertension and diabetes mellitus, patients with covid- exhibit severe comorbidities including hypertension and diabetes with poor prognosis. initial evidence from , confirmed cases in china showed . % with cvd and . % with hypertension. however, among the death rate, % had hypertension, . % had diabetes and . % suffered from chronic respiratory disease [ , ] . in another study involving a small population of patients, % had underlying cvd or cerebrovascular disease [ ] . interestingly, data from a small registry of admitted patients showed an alarming % were men, with a median age of [ ] . however, data involving patients (admitted during march to april ) with a median age of from new york city, the epicenter of covid- spread in the usa, showed a slightly different picture [ ] . the most common underlying comorbidities were hypertension ( %), obesity ( %), and diabetes ( %). figure depicts the statistics on distribution of underlying conditions among covid- patients based on the data from center for disease control department (cdc), usa. the data reveals that hypertension is a major comorbid factor for covid- fatalities. an increased risk of covid- death was associated with an age greater than years (mortality of %), cvds (coronary artery disease: . %; heart failure: . %; cardiac arrhythmia: . %), chronic obstructive pulmonary disease ( . %), and current smoking ( . %). another detailed observational meta-analysis ( , confirmed covid- case) of data available from public domains including databases from medline, embase and web of science showed patients with preexisting condition of cvd, diabetes and hypertension are significantly associated with a higher risk of developing severe complication with covid- disease. precisely, the analysis comparing the complications between severe vs non-severe (mild to moderate) covid- cases concluded that cvd was significantly associated with increased illness severity and adverse outcomes among covid- patients [ ] . recently, cdc suggests that children with certain medical conditions, like neurological, genetic, and metabolic conditions, or congenital heart disease might be at increased risk of severe illness from covid- compared to other children. additional study comprising patients from two hospitals in wuhan, china reported % of patients had underlying comorbidity factors: % with hypertension, % with diabetes and % with coronary heart disease [ ] . in another cohort with confirmed covid- patients (during february and march ) with an average median age of from lombardy, italy, % had at least one underlying comorbidity, hypertension ( %), cvd ( %), hypercholesterolemia ( %), or diabetes ( %) [ ] . moreover, a staggering % of the patients were male and the mortality rate was higher in elderly patients aged ≥ years compared to younger patients ( % vs. %). due to the high prevalence of hypertension in the older population, elderly male individuals may be at the highest risk of infection with worse outcomes, and an increased mortality rate with respect to younger patients. patients with hypertension are mostly treated with ace inhibitors (acei) and angiotensin ii type-i receptor blockers (arbs), which substantially increases the expression of ace , due to negative feedback activation caused by low level of ang-i in the system [ ] . considering ace as a preferential receptor of sars-cov- , the patient with antihypertensive therapy with acei/arbs may be at higher risk of developing severe covid- with poor prognosis [ ] . remarkably, clinical studies do not support this hypothesis and found no evidence to demonstrate use of acei or arb as a risk factor in covid- patients [ ] . multiple investigators have demonstrated the beneficial therapeutic effect of acei or arb in prevention of covid- infection [ , ] . independent studies conducted among hypertensive patients found no association between the use of acei or arb and increased risk of mortality in covid- -positive cases [ , ] . a population-based case-control study in the lombardy region of italy with a total of patients with covid- ( february and march ) reported that . % patients were receiving arb and . % patients were receiving acei [ ] . other antihypertensive drugs were also used more in covid- patients than in controls and they had a more frequent history of hospitalization due to cardiovascular complications. however, this study showed no evidence of association of use of anti-hypertrophic drugs including acei or arbs and susceptibility of covid- . another study with , patients in the new york university (nyu) langone health, in which patients were positive for covid- ( . %), reported patients had a history of hypertension ( . %) [ ] . among these hypertensive patients, ( . %) patients were positive for covid- ( . %). this study also identified no substantial adverse effect with the use of antihypertensive drugs including acei or arbs in the covid- positive patients. therefore, prospective research is warranted to clarify the accuracy of existing contradictory hypotheses regarding the use of acei or arbs to control of blood pressure in hypertensive patients during viral infections. fundamentally, after entering into the cells via ace receptors and excessive binding of the sars-cov- result in the downregulation of ace by intracellular degradation and shedding, which could reduce the ang-ii degradation and activation of at r with induction of myocardial hyper-inflammatory reaction in response to covid- [ , ] . due to acei or arb treatment, more ace may be localized in the cell surface after virus binding, which could facilitate ang-ii degradation with reduction of at r activation [ ] . apart from hypertension and age, acute cardiac injury, chronic heart damage and heart failure have all been observed in patients treated for covid- infection [ , ] . due to acute inflammation, procoagulant stimulus and endothelial cell dysfunction, various influenza rna viruses are involved in the development of human atherosclerotic plaques and progression of atherosclerosis. de-stabilization of vulnerable atherosclerotic plaques triggers acute myocardial infarction (mi) or cardiovascular death [ , ] . myocardial infarction, commonly known as heart attack, is a clinical condition, where oxygen supply to the heart is restricted and results in the irreversible loss of cardiomyocytes due to activation of cardiac apoptosis [ ] [ ] [ ] . a large population of patients diagnosed with covid- has died due to mi [ ] . data obtained from a laboratory in lombardy, italy suggest that . % ( out of cases) of patients with confirmed covid- and an existing condition of st-elevation myocardial infarction (stemi) had to undergo a repeated coronary angiogram and coronary lesion was identified as a major cause of the complication [ ] . myocardial injury was also identified as a major contributor of mortality in covid- patients, as derived using data from hospitals in wuhan, china [ ] . strikingly, the cardiac troponin i (ctni) level, a distinct marker of myocardial injury, was noticeably elevated in patients out of hospitalized patients with covid- ( . %) and the mortality was nearly % in these patients with elevated ctni. progressive increased levels of c-reactive protein and n-terminal pro-b-type natriuretic peptide (nt-probnp) coexisted with elevated ctni levels in these covid- patients, which enhance the severity of inflammation and ventricular dysfunction. among patients treated for covid- (admitted to zhongnan hospital of wuhan university during january ), patients had either acute myocardial injury or cardiac arrhythmia, as suggested by their elevated ctni level of . ng/ml versus . ng/ml for those who were treated in non-icu [ ] . several other retrospective multi-center cohort studies from china have also confirmed the significant elevation of biomarkers of myocardial injury over the course of covid- infection that were strongly associated with rapid surge of irreversible clinical deterioration and increased mortality [ , , , ] . although limited data are available on the incidence of heart failure in patients with covid- , the study with hospitalized patients with confirmed covid- (ranging in age from to years) in wuhan, china (until january ) reported that heart failure was identified in patients ( %), among them, ( %) patients died and ( %) patients recovered [ ] . cardiac injury, as a common complication ( . %), was associated with an unexpected high risk of mortality during hospitalization of elderly patients with covid- in wuhan, china [ ] . evidence indicated in another retrospective study that apart from ards and sepsis, acute cardiac injury ( %) and heart failure ( %) were the most common critical complications of death in deceased patients with covid- in wuhan, china [ ] . several other case reports also established that acute or end-stage heart failure was the main pathophysiological manifestation of covid- [ , , ] , which might be associated with hyperinflammation and oxidative stress [ , , ] . interestingly, one recent study indicated a decline in emergency department visits for heart failure during the covid- pandemic, partly due to effective remote clinician-patient interactions [ ] . since patients with cvd are considered to be more vulnerable to sars-cov- infection, with higher risk of negative consequences, these patients avoid frequent hospital visits and prefer alternative remote management. however, analyzing the clinical records during the covid- pandemic (between february and april ) of emergency department of san filippo neri hospital in rome, italy, a study revealed patients with acute heart failure often reported to the emergency department after significant clinical deterioration with high mortality due to failure of routine clinical assessment [ ] . emerging studies indicate that severe covid- -related death is associated with coagulopathy, venous thromboembolism ((vte) and disseminated intravascular coagulation (dic) [ ] . data obtained from the covid- patient population in wuhan, china indicate an abnormal coagulation pattern with prolonged prothrombin time [ ] . there were patients registered in this study and parameters such as (dic), antithrombin activity, prothrombin time (pt) and d-dimer, a fibrin degradation product, were measured and compared between survivors and non-survivors. the results showed elevated levels of dic and d-dimers and prolonged pt in non-survivors and suggest thrombus formation may have contributed to the mortality in these patients. this notion is strongly supported by the observation that treatment of covid- patients with anti-coagulation drug heparin resulted in reduced mortality rate [ ] . the -day mortality study between heparin users and nonusers indicated that only selected covid- patients with markedly higher sepsis-induced coagulopathy (sic) score or elevated d-dimer were benefited from the anticoagulant therapy. notably, anticoagulant treatment may endanger those patients without significant coagulopathy, because the activation of coagulation with local thrombosis/fibrin deposition could limit the survival and dissemination of microbial pathogens and reduce their invasion [ ] . myocarditis is a disease marked by the inflammation of the heart muscle, most often due to viral infection. this inflammation interferes with the electrical system and compromises the pumping capacity of the heart and results in arrhythmia and cardiac arrest [ ] . common diagnosis procedures include electrocardiogram (ecg), mri (magnetic resonance imaging) and a manifestation of increased cardiac troponin i (ctni) level. covid- patients with severe stage of illness manifest systemic hyperinflammation syndrome [ ] . this data suggests an effect of adverse inflammatory reaction or cytokine storm in response to covid- treatment and defines a strong role for ace signaling in covid- disease [ ] . several reports have shown that patients with covid- infection are diagnosed with myocarditis [ , , , ] . in a case report of a -year-old man admitted in lombardy, italy with respiratory difficulties and required mechanical ventilator, with worsening heart condition. transthoracic echocardiography showed mild left ventricle hypertrophy (lvh) with preserved left ventricular ejection fraction and normal wall motion and elevated plasma troponin level (at . ng/ml) [ , ] . cardiovascular mri was suggestive of myocarditis and the patient tested positive for covid- infection demonstrating sars-cov- infection was the most likely cause for the incidence of myocarditis [ ] . similarly, a -year-old healthy woman was diagnosed with acute myopericarditis upon covid- infection. cardiac mri showed a severe left ventricular dysfunction (ejection fraction- %). the patient also had myocyte necrosis with high-sensitivity cardiac troponin t (hstnt) level concentration of . ng/ml [ ] . these reports suggest that patient with covid- infection are prone to myocarditis, and physicians would suspect such conditions along with underlying morbidity factors like hypertension and other cvd. emerging clinical and epidemiological evidence suggests that metabolic disarray, hypoxia and accentuated myocardial inflammation due to sars-cov- infection plays a critical role in the pathophysiology of myocardial injury and prevalence of arrhythmic complications [ ] . in a clinical cohort with patients with covid- in wuhan, china, cardiac arrhythmias were considered a major complication in patients ( . %) who were transferred to the intensive care unit (icu) [ ] . specifically, cardiac arrhythmia was more common in icu patients than in non-icu patients ( . % vs. . %). a recent study from new york-presbyterian/columbia university irving medical center highlighted the spectrum of life-threatening arrhythmias observed in four patients with covid- infection [ ] . fulminant myocarditis with cardiogenic shock could also coexist with atrial and ventricular arrhythmias, which could increase the severity of covid- patients, including death [ , ] . therefore, the expected cardiac arrhythmogenic effect of covid- may be an important underlying risk of disease complication, which needs additional precautions and specialized management. based on the available clinical data, potential myocardial injury is a relevant challenge among hospitalized patients with covid- with increased risk of mortality; therefore, it is essential for multidisciplinary assessment, including blood pressure control in hypertensive patients as well as cardiovascular evaluation and therapy to reduce the morality for covid- infection. strikingly, a recent study in germany involving patients with an average age of years who recently recovered from covid- infection recognized the cardiovascular sequelae, irrespective of preexisting cardiac conditions [ ] . cardiovascular magnetic resonance imaging (cmr) revealed that patients had abnormal cardiac structural changes, had detectable levels of biomarker of cardiac injury, e.g., elevated level of high-sensitivity cardiac troponin t (hstnt), lower left ventricular ejection fraction, higher left ventricle volumes, higher left ventricle mass, and raised native t and t (quantitative assessments of the myocardium composition), commonly found after a heart attack, and had signs of inflammation. the exact molecular mechanism by which sars-cov- virus leads to cardiomyocyte injury is not completely understood. however, the abundant expression of ace- receptors in the heart plays an important role in the accumulation of sars-cov- virus in the cardiac tissue, which eventually results in hyperactivation of inflammation and cardiac tissue injury in patients. recently, autopsy results of patients, who died at early stage of covid- infection in germany, revealed the most likely localization of sars-cov- not to be in the cardiomyocytes, but in interstitial cells or macrophages invading the myocardial tissue [ ] . however, another emerging study using human induced pluripotent stem cell-derived cardiomyocytes (hipsc-cms) shows sars-cov- can directly enter and replicate in hipsc-cms and induce apoptosis, which results in cessation of cardiomyocyte beating after h of infection [ ] . the majority of the covid- patients suffering from cardiovascular complications show a significant elevation of ctni, nt-probnp and interleukin- (il- ) or other cytokines [il b, il ra, il , il , il , il , c-x-c motif chemokine (cxcl ), chemokine (c-c motif) ligand (ccl ), granulocyte-macrophage colony-stimulating factor (gm-csf), and tumor necrosis factor-α (tnf-α)] in their blood stream [ , , ] . severe hyperinflammation or cytokine storm due to immunological dysregulation may be the primary contributor to cardiomyocyte injury [ ] . epidemiological studies with other viral rnas indicated that after entering into the cytoplasm of cardiomyocytes, viral rna is further transcribed and translated into the viral structural proteins to form the complete infectious virion [ ] . ultimately, infected cardiomyocytes would be lysed, which could lead to activation of the innate immune response with induction of pro-inflammatory cytokines, inflammation-induced destabilization of coronary artery plaques and development of left ventricular dysfunction [ ] . collectively, uncontrolled hyperactivated t-lymphocytes with systemic inflammation appears to be the most common mechanisms of the cardiomyocyte injury in covid- patients with profound cardiovascular consequences. in addition to binding to ace of the host cell, the priming of the transmembrane spike (s) glycoprotein of sars-cov- by host proteases (furin, a signature protease of highly pathogenic viruses) through cleavage at the s /s and the s sites could enhance its transmissibility and pathogenicity [ ] . multiple evidences have revealed that the notch signaling plays a major role in maintaining the homeostasis of the cardiovascular system, including atherosclerosis progression and ventricular remodeling after myocardial infarction [ ] [ ] [ ] . furin is transcriptionally induced by notch signaling, but notch is cleaved at the cell membrane by adam /adam to enable final cleavage by γ-secretase to form active notch intracellular domain, which regulates the transcription of target genes in nucleus. therefore, targeting notch activation using inhibitor γ-secretase (gsi) could be a promising therapeutic strategy to block the virus entry into the cardiac cells by reducing furin and increase adam shedding. the notch signaling also modulates the activity of innate and adaptive immune responses by inducing macrophage polarization [ ] . in microphages, it directly binds to il- promoter in response to interferon (ifn)-γ and promotes il- production, which may cause severe myocardial injury due to triggered "cytokine storm" [ ] . our current understanding on the molecular mechanisms of cardiomyocyte injury for sars-cov- infection is limited and future in depth rigorous studies are warranted. early diagnosis of covid- infection in patients is crucial for the recommendation of appropriate treatment strategy and to address associated cvd complications. initial symptoms of sars-cov- infection include high fever or chills, cough, shortness of breath, headache, sore throat, new loss of taste or smell, diarrhea and fatigue that appears during - days after the exposure to the virus. these early indications, though similar to regular viral infection, should be taken seriously during this pandemic time and diagnosed further for the presence of covid- infection. currently, the established diagnostic test for the identification of sars-cov- infection is based on nucleic acid amplification testing (naat) or commonly called real-time reverse transcription-polymerase chain reaction (rt-pcr) assay, nucleic acid-based meta-genomic next-generation sequencing (mngs), reverse transcription loop-mediated isothermal amplification (rt-lamp) and antigen testing performed with nasopharyngeal swab specimen [ , ] . in the absence of any pharmaceutical interventions, traditional public health measures are considered to be the mainstay of management tools to curb this worldwide covid- epidemic. most widely accepted practices are hygienic precautions, isolation and quarantine, social distancing and community containment [ , ] . to minimize cardiovascular complications in highly infectious covid- patients, the patients with covid- infection require routine monitoring of cardiac parameters with echocardiography, telemetry to assess qt interval and electrocardiograph (ecg) to identify the development of cardiomyopathy, arrhythmia, ischemic heart disease and heart failure. potential therapeutic options to impede the propagation of covid- and its associated cardiovascular complication are desperately needed during this ongoing severe pandemic. researchers and clinicians are focusing on developing new drugs against coronavirus as well as repurposing already approved drugs for the treatment of covid- patients. unapproved antiviral drugs for sars-cov- and/or middle east respiratory syndrome coronavirus (mers-cov) diseases are also currently being reevaluated as treatment options for covid- . however, covid- poses unique problems that were not encountered with the previous known viruses. the major issue was to address the cvd complications, systemic and vascular inflammation, and to deal with comorbid risk like hypertension, diabetes and heart failure. initial approaches were to emphasis on obstructing the viral replication and inflammation by using antiviral drugs, such as, remdesivir, liponovir/ritonavir, hydroxy chloroquine (hcq), corticosteroids and broad-spectrum antibiotics like azithromycin, clarithromycin to address inflammation [ , ] . table summarizes the mechanisms of action and beneficial as well as adverse effects of drug treatments used for covid- . the antiviral drug, remdesivir (veklury, gs- ), initially developed for ebola, inhibits rna-dependent rna polymerase and prematurely terminates the viral rna transcription and shows broad-spectrum antiviral activity against rna viruses, including sars-cov- in vitro, and inhibits mers-cov, sars-cov- , and sars-cov- replication in animal models [ ] . remdesivir is a substrate for the drug metabolizing enzymes cyp c , cyp d , and cyp a , as well as a substrate for organic anion transporting polypeptides b (oatp b ) and p-glycoprotein (p-gp) transporters. remdesivir ( - mg/day for days) either treated alone or in combination with anti-inflammatory drugs was effective in curbing the virus and shortening the recovery time of patients undergoing treatment for covid- [ ] . a multicenter randomized, double-blind, clinical trial, involving patients with severe covid- , conducted in ten hospitals in wuhan, china, reported that seriously ill patients, receiving remdesivir ( mg on day followed by mg on days - in single daily infusions) within days of symptom onset, showed a numerically faster time to clinical improvement than those receiving placebo, without any antiviral effect [ ] . the study also reported early termination of the treatment due to multiple adverse events (including gastrointestinal symptoms, aminotransferase or bilirubin increases, and worsened cardiopulmonary status) in the remdesivir-treated patients ( %) ( table ) . in a small pilot study of four critically ill covid- patients with remdesivir, three patients tested negative for sars-cov- rna (swap test) after days of therapy. however, these reports also indicated some adverse side effects including liver injury [ , ] . lopinavir-ritonavir antiviral drugs such as lopinavir-ritonavir (mylan or kaletra; mg and mg, respectively, twice a day for days), hiv protease inhibitors, used in the clinical trial provided only a moderate benefit of reducing the recovery time by day [ ] . although in vivo animal study shows that a combination of remdesivir with lopinavir-ritonavir yields better outcome for coronavirus infection [ ] . however, the treatment with these protease inhibitors (lopinavir-ritonavir) develop cardio-metabolic complications including development of dyslipidemia with an adverse cholesterol profile, which could elicit inflammation with elevated reactive oxygen species (ros) production, altered myocardial ubiquitin proteasome and calcium-handling pathways together with decreased contractile function [ , ] (table ) . lopinavir-ritonavir treatment inhibits the myocardial ups (ubiquitin proteasome system) and leads to elevated calcineurin and connexin expression that may contribute to cardiac contractile dysfunction [ ] . without any benefit, lopinavir-ritonavir may also cause bradycardia, qt and pr interval prolongation due to the interaction with cytochrome p enzymes [ , , ] . baricitinib (olumiant®), an inhibitor of janus kinase (jak and jak ) molecule and a drug for the treatment of rheumatoid arthritis was tested ( mg or mg once daily) in covid- patients [ ] . this drug was repurposed in covid- treatment to curb the occurrence of inflammation process due to the use of ace inhibitors, which moderately reduced the lung inflammation and cytokine [ ] . the management of hyperinflammation or cytokine storm has been challenging and accounts for the majority of the mortality associated with adverse cases of covid- patients. clinical practices to address this complication involves treatment with monoclonal antibody against interleukin- receptor (il- r) such as tocilizumab (actrema®), siltuximab (sylvant®) and sarilumab (kevzara®) to control the infiltration of macrophages and cytokines in the respiratory system and suppression t-cell activation [ , ] . tocilizumab specifically binds membrane-bound (mil- r) and soluble interleukin- receptor (sil- r) and inhibits signal transduction. covid- patients treated with tocilizumab ( to mg/kg with recommended dose of mg with a maximum dose of mg) in addition to routine therapy showed significant improvement of the clinical outcomes, effectively controlled body temperature with improvement of peripheral oxygen saturation and reduction of inflammatory storm [ ] . considering the emergency to identify a drug that is effective in reducing the complications associated with covid- , efforts are also underway to repurpose old drugs that are proven to be clinically safe. data from recovery trial indicates that dexamethasone, a steroid drug generally used as an anti-inflammatory agent, is effective in reducing the mortality rate by one-third in covid- patients subjected to mechanical ventilation or who were on ventilators compared to patients receiving standard therapy [ ] . among registered covid- patients, of them who received mg of dexamethasone for days, had reduced mortality by % compared to patients who were on standard treatment. more importantly, patients on ventilator support during the critical stage of treatment responded better to dexamethasone compared to patients just receiving oxygen therapy. the outcome of this study is considered a breakthrough in the fight against covid- because dexamethasone is a commonly available drug and cost effective. however, further evidence is required to use dexamethasone in covid- patients. another drug that gained much attention for the treatment of covid- is hydroxychloroquine (hcq, plaquenil), an anti-malarial compound, which is also widely used for attenuation of systemic lupus erythematosus (sle), rheumatoid arthritis (ra), juvenile idiopathic arthritis (jia) and sjogren's syndrome [ ] . several clinical studies, including trials from nih (nct ), are testing this drug for covid- treatment, either alone or in combination with azithromycin [ ] . the treatments with hydroxychloroquine alone ( mg by mouth twice daily for day followed by mg by mouth twice daily for days) or in combination with azithromycin ( mg by mouth or intravenous daily for days) lead to a prolongation of the qt interval, possibly increasing the risk of sudden cardiac death [ ] (table ) . another retrospective multicenter cohort study was conducted involving patients admitted across various hospitals in the city of new york who were diagnosed with covid- (between - march ), those receiving either hcq alone (dose ranges: - mg; once or twice a day) or in combination with azithromycin (dose ranges: mg to mg; once or twice a day) or azithromycin alone. the results from the study showed that the probability of death for patients receiving hcq + azithromycin was . % ( out of ), while patients receiving hcq alone was . % ( out of ) and . % ( out of ) in azithromycin alone group. cardiac arrest was significantly high in patients receiving hcq + azithromycin combination than treatment with placebo or hcq alone [ ] . another cohort study performed at an academic tertiary care center in boston, massachusetts, showed similar high risk of qt prolongation with subsequently developed other ventricular arrhythmias in the hcq alone ( mg, twice on day , then mg daily on days through ) or with azithromycin-treated patients with covid- [ ] . an observational study of admitted patients to the hospital with covid- (between march and april ) in new york, revealed that hcq administration alone was not associated with either a greatly lowered or an increased risk of the composite end point of intubation or death [ ] . the treatment regimen of hydroxychloroquine was a loading dose of mg twice on day , followed by mg daily for additional days. however, recently, the u.s. food and drug administration (fda) revoked its approval to use hcq for covid- treatment due to disappointing results [ ] . data from randomized clinical trials suggest that hcq had no beneficial effects compared to placebo and was not successful in decreasing the mortality rate or in hospital stay (based on fda report, updated on july ) [ ] . therefore, rigorous, and large-scale studies with careful risk assessment of hcq should be conducted prior to initiating covid- therapeutics, with close monitoring cardiac manifestations including evaluation of cardiac biomarkers, routine electrocardiograms and electrolyte monitoring. there is an urgency for the development of a safe and effective vaccine for covid- ; however, no specific vaccines against sar-cov- are currently available [ ] . multiple inactivated vaccine candidates for sars-cov- , such as dna-, rna-based formulations, recombinant-subunits containing viral epitopes, adenovirus-based vectors and purified inactivated virus are under development [ , ] . several candidate vaccines are still in the preliminary stage of phase i clinical trial. the mrna-based vaccine prepared by the usa national institute of allergy and infectious diseases against sars-cov- is under phase trial [ ] . ino- , a dna-based vaccine, is also in pipeline and will soon be available for human trial. preliminary results from pilot studies and clinical trials on new vaccine are encouraging and gives hope for a successful availability of an effective vaccine by end of . several pharmaceutical companies, including pfizer, novartis and astrazeneca and moderna, are testing their candidate vaccine. university of oxford in collaboration with astrazeneca are in the development of covid- vaccine and expect to produce million doses in uk by september . jenner institute, oxford, uk is a leader in this effort and launched a phase iii clinical trial of more than people in may. however, due to the suspected adverse event in a person receiving the vaccine in the united kingdom, the clinical trials have been temporarily paused. moderna, a usa-based company in collaboration with switzerland's lonza, released positive outcomes from its phase i clinical trial of their mrna vaccine for sars-cov- [ ] . preliminary results are very promising, showing good immune response, and due to effectiveness and safety profiles, this vaccine is approved by the u.s. food and drug administration (fda) for phase ii and phase iii studies [ , ] . novartis announced its plans to initiate a phase iii clinical trial to study effects of canakinumab, an interleukin (il)- β blocker, in covid- patients with pneumonia [ ] . they aim to rapidly enroll patients at multiple medical centers across france, germany, italy, spain, uk and the usa and randomize them to receive either canakinumab or placebo on top of standard of care (soc) [ ] . pfizer, in partnership with biontech (bnt), has initiated its phase i/ii clinical trial in the usa for its mrna-based vaccine, the bnt prevent covid- [ ] . sinopharm, a wuhan, china-based pharmaceutical company received approval from the national medical products administration (china) and conducting phase ii clinical trials for its inactivated vaccine bbibp-corv. the company already tested doses of this vaccine and expect to release in the marker by the end of the year . sinovac is planning to enter its phase iii clinical trial in collaboration with instituto butantan in brazil after observing positive results in its preclinical trail with the vaccine coronavac [ ] . ad -ncov, an adenovirus type vector-based vaccine developed by cansiobiologics, china is also in phase iii clinical trial and demonstrated promising effects in the early phase of testing on participants [ ] . inovio pharmaceuticals in collaboration with university of pennsylvania and center for pharmaceutical research, kansas city, missouri, is testing its dna-based vaccine ino- [ ] . preclinical experiments conducted in guinea pigs showed antibody titer against ace receptor/sars-cov binding protein. when countries all over the world are racing to develop their own vaccine against covid- , russia has already approved a vaccine candidate for public use named sputnik v, that was developed in collaboration with gamaleya research institute of epidemiology and microbiology in moscow [ ] . the vaccines comprise either recombinant adenovirus type (rad ) or recombinant adenovirus type (rad ) vectors, which contain the gene for sars-cov- spike glycoprotein (rad -s and rad -s). initial results from the ongoing phase i and ii clinical trials are promising, which include total population size of healthy adult volunteers [ ] . among them volunteers were intramuscularly vaccinated with gam-covid-vac lyo (lyophilized vaccine formulation) and other participants were subjected to gam-covid-vac (frozen vaccine formulation) [ ] . both heterologous recombinant adenoviral (rad and rad ) vector-based covid- vaccines induced a strong humoral and cellular immune responses with reported safety profiles in participants. however, further investigations with larger scale population (including different underlying medical complications) are needed to demonstrate the effectiveness of this vaccine for prevention of covid- . nevertheless, scientists globally have serious concerns about unforeseen adverse effects of this vaccine without the outcomes of the phase iii trial. even though, for the development of an efficient vaccine for covid- , extensive preclinical studies and clinical trials are essential to carefully evaluate the adverse effect of vaccine, the aforementioned fast-paced preclinical data are encouraging for advancing the preventive strategies against covid- . several other treatment options such as convalescent plasma therapy (cpt) and monoclonal antibody therapy have been evaluated with some moderate success. cpt is a traditional method where plasma containing the antibody from recovered patients infected with covid- was transfused to the severely ill covid- patients [ , [ ] [ ] [ ] . studies showed that cp therapy was effective, and the level of neutralizing increased as high as : times in patients infected with sars-cov- [ ] . transfusing antibodies from covid- survivors into high-risk patients to neutralize sars-cov- could provide a quick treatment option until an optimistic vaccine will arrive to prevent this viral infection. efforts are also underway to design a monoclonal antibody that can target the specific epitope on the spike protein of sars-cov- and block the virus entry in to the host cell [ , , ] . such efforts are still in their preliminary stage [ ] and are time consuming; however, they could provide a long-lasting solution for dealing with sars viruses in general. recently, stem cell therapies with secreted extracellular vesicles (evs) offer a potential therapeutic benefit in covid- patients by attenuating inflammation with regeneration of the damaged lung. mesenchymal stem cells (mscs)-derived evs-based therapy could be the most promising reparative strategy in people with covid- , because of its high proliferation rate, low invasive nature, and the immunomodulatory, antioxidant and anti-inflammatory properties of mscs [ ] . there are several promising clinical trials with msc-derived evs underway, which could reveal convincing evidence in the encouraging prospect of msc-based therapies for respiratory complications of covid- patients [ , ] . despite the above-mentioned beneficial effects of different therapeutics, the safety profiles of these therapies have not been proficiently identified. specifically, the potential adverse cardiovascular effects of these drugs in covid- patients need urgent attention before rushing the approval of any new drug into clinical application. for most effective treatments for covid- , it is important to pay attention to emerging evidence about potential harmful risk of drug interactions. due to the highly transmissible novel coronavirus, sars-cov- , the covid- outbreak has become an unprecedented worldwide pandemic with a record number of infected individuals and an excess of mortality. the desperate need for effective therapeutics for covid- during this pandemic integrated scientist around the world across multiple research fields while sharing their research findings and knowledge to fast-track the process of drug discovery. considering the high mortality of covid- patients with cardiovascular comorbidities, it is important to understand whether it is attributable to underlying cardiovascular disease (cvd) or if cvd is the consequence of inflammatory response to sar-cov- infection or severe respiratory symptoms. the precise mechanisms linking cvds and worsened prognosis or higher mortality rate in covid- patients remain unknown. recent therapies under investigation for severe multi-organ failure in covid- patients may have adverse cardiovascular effects, while their clinical efficacy for combating covid- is yet to be established. new advanced technological tools, like information technology based on smart phone apps, social media, artificial intelligence (ai), machine learning, etc., accelerate the diagnosis/screening of patients with virus, analysis of available literature, and identification of potential therapeutic targets and other specific clinical features to tackle covid- pandemic. moreover, ai, particularly, plays an important role in predicting the harmful interaction between cardiovascular consequences with the drugs used for covid- , by automated interpretation of collected meta-data from various sources. in the context of disease progression with cardiovascular complications, the researchers are focusing on developing new drugs in parallel to repurposing already clinically approved drugs to avoid a massive surge of covid- patients with a prevalence of cvd. therefore, urgent understanding of molecular mechanism as well as retrospective and prospective studies with robust diagnosis of cardiovascular impairments will be crucial for development of advanced therapies for the treatment of sars-cov- virus, which could mitigate the adverse cardiovascular events among covid- patients and save humankind around the globe from this deadly pandemic. the authors declare no conflict of interest. angiotensin a new coronavirus associated with human respiratory disease in china the continuing -ncov epidemic threat of novel coronaviruses to global health-the latest novel coronavirus outbreak in wuhan first case of novel coronavirus in the united states the covid- pandemic in the usa: what might we expect? first known person-to-person transmission of severe acute respiratory syndrome coronavirus (sars-cov- ) in the usa an interactive web-based dashboard to track covid- in real time genotype and phenotype of covid- : their roles in pathogenesis clinical features of patients infected with novel coronavirus in emerging coronaviruses: genome structure, replication, and pathogenesis rna based mngs approach identifies a novel human coronavirus from two individual pneumonia cases in wuhan outbreak genome composition and divergence of the novel coronavirus ( -ncov) originating in china a novel coronavirus from patients with pneumonia in china pandemic potential of -ncov genomic characterization of a novel sars-cov- genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus structure, function, and evolution of coronavirus spike proteins cryo-em structure of the -ncov spike in the prefusion conformation the proximal origin of sars-cov- a dynamic nomenclature proposal for sars-cov- lineages to assist genomic epidemiology geographic and genomic distribution of sars-cov- mutations. front. microbiol. , , surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient coronaviruses post-sars: update on replication and pathogenesis effectiveness of convalescent plasma therapy in severe covid- patients cell entry mechanisms of sars-cov- high expression of ace receptor of -ncov on the epithelial cells of oral mucosa covid- and individual genetic susceptibility/receptivity: role of ace /ace genes, immunity, inflammation and coagulation. might the double x-chromosome in females be protective against sars-cov- compared to the single x-chromosome in males? sars-cov- receptor ace gene expression and raas inhibitors angiotensin converting enzyme : a double-edged sword lung endothelial adam regulates the acute inflammatory response to lipopolysaccharide pulmonary vascular endothelialitis, thrombosis, and angiogenesis in covid- mortality and pulmonary complications in patients undergoing surgery with perioperative sars-cov- infection: an international cohort study covid- complicated by acute pulmonary embolism and right-sided heart failure fibrinolytic abnormalities in acute respiratory distress syndrome (ards) and versatility of thrombolytic drugs to treat covid- coronavirus disease (covid- ) and cardiovascular disease: a viewpoint on the potential influence of angiotensin-converting enzyme inhibitors/angiotensin receptor blockers on onset and severity of severe acute respiratory syndrome coronavirus infection ace : from vasopeptidase to sars virus receptor presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the cardiovascular implications of fatal outcomes of patients with coronavirus disease clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study association of cardiac injury with mortality in hospitalized patients with covid- in wuhan, china clinical predictors of mortality due to covid- based on an analysis of data of patients from wuhan, china characteristics and outcomes of critically ill patients with covid- in washington state response to covid- in taiwan: big data analytics, new technology, and proactive testing renin-angiotensin-aldosterone system inhibitors in patients with covid- clinical characteristics of coronavirus disease in china weekly updates by select demographic and geographic characteristics the cardiac renin-angiotensin system: conceptual, or a regulator of cardiac function? angiotensin system: are hypertension or its treatments deleterious? front. cardiovasc perspectives for angiotensin profiling with liquid chromatography/mass spectrometry to evaluate ace/ace balance in endothelial dysfunction and vascular pathologies ace activation promotes antithrombotic activity detection of soluble angiotensin-converting enzyme in heart failure: insights into the endogenous counter-regulatory pathway of the renin-angiotensin-aldosterone system covid- and heart failure: from infection to inflammation and angiotensin ii stimulation. searching for evidence from a new disease roles of angiotensin peptides and recombinant human ace in heart failure plasma angiotensin-converting enzyme : novel biomarker in heart failure with implications for covid- angiotensin-converting enzyme (ace ) as a sars-cov- receptor: molecular mechanisms and potential therapeutic target a pilot clinical trial of recombinant human angiotensin-converting enzyme in acute respiratory distress syndrome soluble angiotensin-converting enzyme : a potential approach for coronavirus infection therapy? circulating plasma concentrations of angiotensin-converting enzyme in men and women with heart failure and effects of renin-angiotensin-aldosterone inhibitors risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention epidemiology working group for ncip epidemic response; chinese center for disease control and prevention. the epidemiological characteristics of an outbreak of novel coronavirus diseases (covid- ) in china association of renin-angiotensin system inhibitors with severity or risk of death in patients with hypertension hospitalized for coronavirus disease (covid- ) infection in wuhan, china coronavirus disease (covid- ) and cardiovascular risk: a meta-analysis baseline characteristics and outcomes of patients infected with sars-cov- admitted to icus of the lombardy region are patients with hypertension and diabetes mellitus at increased risk for covid- infection? inhibitors of ras might be a good choice for the therapy of covid- pneumonia urinary angiotensin-converting enzyme in hypertensive patients may be increased by olmesartan, an angiotensin ii receptor blocker renin-angiotensin-aldosterone system blockers and the risk of covid- inhibitors of the renin-angiotensin-aldosterone system and covid- renin-angiotensin-aldosterone system inhibitors and risk of covid- sars-coronavirus modulation of myocardial ace expression and inflammation in patients with sars covid- illness and heart failure: a missing link? jacc heart fail influenza as a trigger for acute myocardial infarction or death from cardiovascular disease: a systematic review seasonal influenza infections and cardiovascular disease mortality cyclic gmp-dependent protein kinase ialpha attenuates necrosis and apoptosis following ischemia/reoxygenation in adult cardiomyocyte apoptosis in human acute myocardial infarction the pathophysiology of acute myocardial infarction and strategies of protection beyond reperfusion: a continual challenge incidence of thrombotic complications in critically ill icu patients with covid- st-elevation myocardial infarction in patients with covid- : clinical and angiographic outcomes clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in elevated troponin in patients with coronavirus disease : possible mechanisms clinical characteristics of deceased patients with coronavirus disease : retrospective study end-stage heart failure with covid- : strong evidence of myocardial injury by -ncov myocardial localization of coronavirus in covid- cardiogenic shock the clinical significance of interleukin- in heart failure: results from the biostat-chf study treating oxidative stress in heart failure: past, present and future short-term outcomes in ambulatory heart failure during the covid- pandemic: insights from pulmonary artery pressure monitoring the impact of the coronavirus disease- pandemic and italian lockdown measures on clinical presentation and management of acute heart failure abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia anticoagulant treatment is associated with decreased mortality in severe coronavirus disease patients with coagulopathy reduced thrombin generation increases host susceptibility to group a streptococcal infection covid- illness in native and immunosuppressed states: a clinical-therapeutic staging proposal myocarditis in a patient with covid- : a cause of raised troponin and ecg changes cardiac and arrhythmic complications in patients with covid- cardiac arrhythmias in covid- infection guidance for cardiac electrophysiology during the covid- pandemic from the heart rhythm society covid- task force; electrophysiology section of the american college of cardiology; and the electrocardiography and arrhythmias committee of the council on clinical cardiology coronavirus fulminant myocarditis saved with glucocorticoid and human immunoglobulin outcomes of cardiovascular magnetic resonance imaging in patients recently recovered from coronavirus disease association of cardiac infection with sars-cov- in confirmed covid- autopsy cases human ipsc-derived cardiomyocytes are susceptible to sars-cov- infection sars-cov- : a potential novel etiology of fulminant myocarditis covid- and the cardiovascular system myocarditis in humans and in experimental animal models. front. cardiovasc. med. , , covid- and the cardiovascular system: implications for risk assessment, diagnosis, and treatment options structure, function, and antigenicity of the sars-cov- spike glycoprotein estrogen-mediated protection against coronary heart disease: the role of the notch pathway the notch pathway: a novel target for myocardial remodelling therapy? eur notch activation enhances lineage commitment and protective signaling in cardiac progenitor cells direct regulation of interleukin- expression by notch signaling in macrophages covid- in the heart and the lungs: could we "notch" the inflammatory storm? -ncov cdc response team. initial public health response and interim clinical guidance for the novel coronavirus outbreak-united states cardiovascular considerations for patients, health care workers, and health systems during the covid- pandemic spatio-temporal characterization of the antiviral activity of the xrn -dcp / aggregation against cytoplasmic rna viruses to prevent cell death remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro remdesivir is a direct-acting antiviral that inhibits rna-dependent rna polymerase from severe acute respiratory syndrome coronavirus with high potency hopes rise for coronavirus drug remdesivir remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial early experience with remdesivir in sars-cov- pneumonia remdesivir in covid- a trial of lopinavir-ritonavir in adults hospitalized with severe covid- comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov altered myocellular and abdominal fat partitioning predict disturbance in insulin action in hiv protease inhibitor-related lipodystrophy cardio-metabolic effectsof hiv protease inhibitors (lopinavir/ritonavir) urgent guidance for navigating and circumventing the qtc-prolonging and torsadogenic potential of possible pharmacotherapies for coronavirus disease (covid- ) role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings baricitinib as potential treatment for -ncov acute respiratory disease covid- : combining antiviral and anti-inflammatory treatments a systematic review on the efficacy and safety of il- modulatory drugs in the treatment of covid- patients interleukin- blockade with sarilumab in severe covid- pneumonia with systemic hyperinflammation: an open-label cohort study effective treatment of severe covid- patients with tocilizumab coronavirus breakthrough: dexamethasone is first drug shown to save lives hydroxychloroquine: from malaria to autoimmunity hydroxychloroquine, and azithromycin on the corrected qt interval in patients with sars-cov- infection association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in risk of qt interval prolongation associated with use of hydroxychloroquine with or without concomitant azithromycin among hospitalized patients testing positive for coronavirus disease observational study of hydroxychloroquine in hospitalized patients with covid- covid- ) update: fda revokes emergency use authorization for chloroquine and hydroxychloroquine fda cautions against use of hydroxychloroquine or chloroquine for covid- outside of the hospital setting or a clinical trial due to risk of heart rhythm problems. does not affect fda-approved uses for malaria, lupus, and rheumatoid arthritis developing covid- vaccines at pandemic speed development of an inactivated vaccine candidate for sars-cov- drugmakers rush to develop vaccines against china virus the covid- vaccine development landscape an mrna vaccine against sars-cov- -preliminary report moderna announces phase cove study of mrna vaccine against covid- (mrna- ) begins. hlh across speciality collaboration u.k. covid- : consider cytokine storm syndromes and immunosuppression novartis announces plan to initiate clinical trial of canakinumab for patients with covid- pneumonia pfizer and biontech dose first participants in the u.s. as part of global covid- mrna vaccine development program. business wire safety, tolerability, and immunogenicity of a recombinant adenovirus type- vectored covid- vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial immunogenicity of a dna vaccine candidate for covid- covid- : russia approves vaccine without large scale testing or published results safety and immunogenicity of an rad and rad vector-based heterologous prime-boost covid- vaccine in two formulations: two open, non-randomised phase / studies from russia treatment with convalescent plasma for critically ill patients with severe acute respiratory syndrome coronavirus infection deployment of convalescent plasma for the prevention and treatment of covid- convalescent plasma as a potential therapy for covid- sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor characterization of the receptor-binding domain (rbd) of novel coronavirus: implication for development of rbd protein as a viral attachment inhibitor and vaccine a human monoclonal antibody blocking sars-cov- infection non-coding rnas in mesenchymal stem cell-derived extracellular vesicles: deciphering regulatory roles in stem cell potency, inflammatory resolve, and tissue regeneration combating covid- with mesenchymal stem cell therapy can stem cells beat covid- : advancing stem cells and extracellular vesicles toward mainstream medicine for lung injuries associated with sars-cov- infections this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license key: cord- - mpymd a authors: khan, muhammad muzamil; noor, amna; madni*, asadullah; shafiq, mudassir title: emergence of novel coronavirus and progress toward treatment and vaccine date: - - journal: rev med virol doi: . /rmv. sha: doc_id: cord_uid: mpymd a in late december , a group of patients was observed with pneumonia‐like symptoms that were linked with a wet market in wuhan, china. the patients were found to have a novel coronavirus genetically related to a bat coronavirus that was termed sars‐cov‐ . the virus gradually spread worldwide and was declared a pandemic by who. scientists have started trials on potential preventive and treatment options. currently, there is no specific approved treatment for sars‐cov‐ , and various clinical trials are underway to explore better treatments. some previously approved antiviral and other drugs have shown some in vitro activity. here we summarize the fight against this novel coronavirus with particular focus on the different treatment options and clinical trials exploring treatment as well as work done toward development of vaccines. coronaviruses are a form of positive-strand non-segmented rna viruses distributed among birds, mammals and humans that cause respiratory and neurological illnesses. there are six different types that can cause disease among humans. four of these (hku , e, nl and oc ) cause only the common cold in patients, due to the broad genetic variation and diversity of coronaviruses and higher chances of animal to human spread they are likely to emerge periodically in future. during december , an outbreak of pneumonia-like symptoms occurred in patients that were linked to the seafood market in wuhan china. investigation identified a new strain of coronavirus called sars-cov- . the detection of this novel coronavirus is key to confirm the cases and proceed to treatment. in an early method for detecting sars-cov- , the samples from bronchoalveolar-lavage fluids were collected, centrifuged to remove debris and inoculated onto human epithelial cells of airway origin. about sequences from each sample were obtained and genome matches showed more than % identity with sars-like betacornavirus. results were also obtained from real-time pcr, and isolated viruses were named sars-cov- . to further characterize sars-cov- , the de-novo sequence was obtained by using nanopore sequencing and illumina methods. the airway epithelial cell cultures were suitable for visualization and identification of the novel coronavirus. check efficacy against this virus. the possible options include nucleoside analogs, interferon that can act as immune modulators and approved antimalarials having antiviral activities such as chloroquine and hydroxychloroquine. the nucleoside analogs such as ribavirin, favipiravir, galidesivir and remdesivir target rna polymerase and block the synthesis of viral rna. favipiravir was effectively used against influenza and has the potential to inhibit viral rna synthesis and a new study also supports its activity against sars-cov- . different clinical trials are underway where patients are being recruited to evaluate the efficacy of a combination of favipiravir and interferon-α and a combination of favipiravir and baloxavir marboxil is being evaluated. ribavirin is a guanine derivative antiviral drug approved for the treatment of hcv and rsv, but it causes anemia at higher doses that limit its use and its efficacy against coronavirus is uncertain. remdesivir is an adenine derivative antiviral drug. it has activity against a variety of viral strains such as sars and mers and a recent study also supports its activity against sars-cov- . a recent patient in us with sars-cov- has shown recovery with intravenous administration of remdesivir. recently, phase-iii clinical trials have been started in usa to evaluate the efficacy of iv remdesivir as mg od or mg od for days. a recent rct apparently reported no significant efficacy, but we await the published findings. small molecular weight drugs such as chloroquine have shown inhibitory effects against sars-cov- (ec = . μm in vero e cells) and is under evaluation in open-label trials.. chloroquine (cq) is a recognized anti-malarial drug but also has antiviral activity. the antiviral activity of chloroquine was first noticed in the late s. chloroquine and its analog hydroxychloroquine both have inhibitory effects against various viruses including sars, enterovirus and zika virus. chloroquine inhibits the virus by increasing endosomal ph and so reducing viral cell fusion and also interferes with cellular receptor glycosylation. the ec value of chloroquine against sars-cov- is . μm that can be achieved with administration of mg dose. remdesivir and chloroquine have shown activity in in vitro studies and can easily be tested in patients with sars-cov- . in another recent study, gao et al found that chloroquine phosphate reduced the symptoms of pneumonia in sars-cov- patients and shortening the duration of disease. the guidelines for the treatment of sars-cov- were revised six times since its issuance on january . the recent guidelines also include ifn-α, remdesivir, ribavirin, ritonavir and chloroquine. the mode of administration of ifn-α is through inhalation at a dose of million units diluted with water for injection. the dose of ritonavir is mg bd for adults. ribavirin may be given in combination with ifn-α or ritonavir at a dose of mg bd or tds. chloroquine phosphate should be administered at a dose of mg bd. arbidol can be given three times a day at mg. hydroxychloroquine (hcq) is an approved disease-modifying antirheumatic drug that also has immunomodulatory effects and prevents organ damage. hcq alters endosomal ph and interrupts the biding between rna/dna and toll-like receptors that leads to suppression of tlr signaling. [ ] [ ] [ ] inside the cytoplasm, hcq also interferes with the interaction between nucleic acid sensor cyclic gmp and cytosolic dna. these two mechanisms lead to increase production of il- , tnf and type- interferon. such mechanism supports the idea that hcq suppress the cytokine release storm (crs) which is due to sars-cov- triggered overreaction of immune system. in a recent study, hcq was found to be more effective than chloroquine; a loading dose of mg twice daily and maintenance dose of mg twice a day is recommended for sars-cov infection. the mechanism involves in antiviral role of hcq and cq is inhibition of receptor binding and fusion of cell membrane. these two are crucial steps that are required for cell entry of sars-cov- . chloroquine interferes with the glycosylation of ace- (angiotensinconverting enzyme receptors) receptors that are considered as cellular receptors for sars-cov- and block the fusion of sars-cov- with host cell. thus, the binding of virus is blocked and infection is prevented. the hcq and cq after entry into the cell tend to concentrate in lysosomes and endosomes. the sars-cov- use endosome as a tool for cellular entry. hcq and cq increase the ph of endosomes and create a negative influence on the binding of sars-c v- with endosomes. lysosomal protease helps in viral fusion with cell membrane. increase lysosomal ph prevents the action of protease and fusion and replication of virus is blocked . the mechanism of action of chloroquine and hydroxychloroquine is represented as (figure ). cinanserin is an antagonist of serotonin receptors. it can inhibit chymotrypsin-like ( c-like) protease and has shown promising results against sars coronavirus. the c-protease was also investigated to be encoded in sars-cov- . flavonoids such as chalcones, flavones and isoflavones produce antioxidant effects but they also have antiviral effects. a study has found that flavonoids can inhibit the entry of hepatitis-c virus. some flavonoids have activity against mers coronavirus, presumably due to inhibition of c-like protease. nitric oxide (no) is a biological gas produced from arginine. no after reaction with superoxide forms peroxynitrite which has cytotoxic bactericidal action. nitric oxide is also known to regulate airway function and reduce inflammation of airways. the beneficial effect of no in sars patients was observed in some studies. no can also inhibit the synthesis of rna and viral protein. a study has found that organic nitric oxide could inhibit the replication cycle of sars-cov- . Αlpha-lipoic acid (ala) is used in hepatic disorders and polyneuropathies. ala is an antioxidant that protects cells against oxidative stress by increasing the glutathione level. some studies support the role of angiotensin-converting enzyme (ace) inhibitors. this is based on the hypothesis that ace- serves as receptor for sars-cov- . , so, ace inhibitor could potentially compete for site binding and reduce the mortality and morbidity associated with sars-cov- . the various ongoing clinical trials are summarized in table . vaccine provides immunity against a particular pathogen before exposure of that infectious agent. several types of vaccines exist that can be nucleic acid based, live attenuated vaccine, subunit proteins or nanoparticle vaccines. different technologies are being utilized to f i g u r e mechanism of action of hcq and cq by blocking binding of virus with ace- receptors and increasing endosomal ph and preventing fusion with the cell develop potential vaccine for sars-cov- including dna and mrnabased nanoparticles. phase-i trials of potential vaccines focus on safety and immunogenicity, for example, against mers. two of the clinical trials on mers vaccine are expected to be complete by the end of , in russia and one in germany by december . the inovo pharmaceutical company has tested its vaccine against mers coronavirus funded by coalition for epidemic preparedness innovation (cepi) using dnabased technology and named as ino- . the university of oxford recombinant chimpanzee adenovirus has also begun phase randomized multicenter trials for intramuscular injection of vaccine chadox against sars-cov- . the participants have been divided into four groups and they will be observed for any serious adverse event for months. the ongoing clinical trials for development of vaccines have been summarized in table and completed vaccine trials for sars and mers viruses have been summarized in table . the fusion of coronavirus with a cell occurs after biding of s protein to a target receptor delivers viral nucleocapsid and initiates replication. the s protein causes syncytial formation at the receptor site. a neutralizing antibody that can target the s protein on the surface of clinical trials for various treatment options for sars-cov- clinical trial registration number trial information date type references the efficacy of newgen beta-gluten probiotic powder in patient with -ncov. march interventional the efficacy of combination of favipiravir + tocilizumab in patient with pneumonia (covid- the immune response was dose-independent and further trials needed to establish efficacy coronavirus pathogenesis epidemiology, genetic recombination, and pathogenesis of coronaviruses origin and evolution of pathogenic coronaviruses epidemiology and cause of severe acute respiratory syndrome (sars) in guangdong, people's republic of china isolation of a novel coronavirus from a man with pneumonia in saudi arabia the role of super-spreaders in infectious disease wuhan municipal health commission. report of clustering pneumonia of unknown etiology in wuhan city china novel coronavirus investigating and research team. a novel coronavirus from patients with pneumonia in china coronaviruses and the human airway: a universal system for virus-host interaction studies new nucleoside analogues for the treatment of hemorrhagic fever virus infections washington state -ncov case investigation team. first case of novel coronavirus in the united states clinical study for safety and efficacy of favipiravir in the treatment of novel coronavirus pneumonia (covid- ) a randomized controlled trial for the efficacy and safety of baloxavir marboxil, favipiravir tablets in -ncov pneumonia (novel coronavirus pneumonia, ncp) patients who are still positive on virus detection under the current antiviral therapy coronavirusesdrug discovery and therapeutic options remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro bin cao yw. mild/moderate -ncov remdesivir rct role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings treatment with lopinavir/ritonavir or interferon-β b improves outcome of mers-cov infection in a nonhuman primate model of common marmoset approved antiviral drugs over the past years clinical management of respiratory syndrome in patients hospitalized for suspected middle east respiratory syndrome coronavirus infection in the paris area from effect of chloroquine on the growth of animal viruses in vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine an evaluation of chloroquine as a broad-acting antiviral against hand, foot and mouth disease fda-approved drug, prevents zika virus infection and its associated congenital microcephaly in mice chloroquine is a potent inhibitor of sars coronavirus infection and spread dose refinements in long-term therapy of rheumatoid arthritis with antimalarials breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies discovering drugs to treat coronavirus disease (covid- ) clinical efficacy and side effects of antimalarials in systemic lupus erythematosus: a systematic review mechanism of endosomal tlr inhibition by antimalarial drugs and imidazoquinolines the ectodomain of toll-like receptor is cleaved to generate a functional receptor immune stimulation mediated by autoantigen binding sites within small nuclear rnas involves toll-like receptors and cutting edge: antimalarial drugs inhibit ifn-β production through blockade of cyclic gmp-amp synthase-dna interaction chloroquine and hydroxychloroquine equally affect tumor necrosis factor-alpha, interleukin , and interferongamma production by peripheral blood mononuclear cells in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) targeting endosomal acidification by chloroquine analogs as a promising strategy for the treatment of emerging viral diseases cinanserin is an inhibitor of the c-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro emerging coronaviruses: genome structure, replication, and pathogenesis flavonoids: an overview flavonoids from pterogyne nitens inhibit hepatitis c virus entry inhibition of sars-cov cl protease by flavonoids a study to evaluate the efficacy and safety of pirfenidone with novel coronavirus infection nitric oxide nitric oxide and airway disease efficacy of inhaled nitric oxide in patients with severe ards an overview on severe acute respiratory syndrome (sars) nitric oxide inhibits the replication cycle of severe acute respiratory syndrome coronavirus efficacy of thioctic acid in the therapy of peripheral diabetic neuropathy biochemical and clinical relevance of alpha lipoic acid: antioxidant and anti-inflammatory activity, molecular pathways and therapeutic potential glucose- -phosphate dehydrogenase deficiency enhances human coronavirus e infection virucidal activity of a scorpion venom peptide variant mucroporin-m against measles, sars-cov and influenza h n viruses convalescent plasma: therapeutic hope or hopeless strategy in the sars-cov- pandemic treatment with convalescent plasma for critically ill patients with sars-cov- infection genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus angiotensin receptor blockers as tentative sars-cov- therapeutics evaluation of the effect of taking newgen beta-gluten probiotic composite powder to nutrition intervention of patients with novel coronavirus pneumonia (covid- ) favipiravir combined with tocilizumab in the treatment of novel coronavirus pneumonia (covid- ) -a multicenter, randomized efficacy and safety of pirfenidone in the treatment of severe post-novel coronavirus pneumonia (covid- ) fibrosis: a prospective exploratory experimental medical study clinical research and preparation development of qingfei detoxification decoction (mixture) for prevention and treatment of novel coronavirus pneumonia clinical study for bronchoscopic alveolar lavage in the treatment of critically trachea intubation patients with new coronavirus pneumonia (covid- ) evaluation of the protective effect of dexmedetomidine on patients with severe novel coronavirus pneumonia (covid- ) coronoavirus clinical trial evaluating the efficacy and safety of bromhexine hydrochloride tablets combined with standard treatment/ standard treatment in patients with suspected and mild novel coronavirus pneumonia (covid- ) fingolimod in covid- eculizumab (soliris) in covid- infected patients (solid-c ) -ncov (wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness potential rapid diagnostics, vaccine and therapeutics for novel coronavirus ( -ncov): a systematic review study of safety and immunogenicity of bvrs-gamvac study of safety and immunogenicity of bvrs-gamvac-combi randomized, double-blind, placebo-controlled, phase ib study to assess the safety and immunogenicity of mva-mers-s_df- inovio selected by cepi to develop vaccine against new coronavirus an obscure biotech stock skyrockets % after saying it's testing a coronavirus antibody (vir) a study of a candidate covid- vaccine (cov ) race to develop coronavirus vaccine j&j scientific officer 'pretty confident' they can create coronavirus vaccine as outbreak widens saskatchewan lab joins global effort to develop coronavirus vaccine china) to collaborate on development of coronavirus vaccine a phase i clinical trial for recombinant novel coronavirus ( -cov) vaccine (adenoviral vector safety and immunogenicity from a phase i trial of inactivated severe acute respiratory syndrome coronavirus vaccine vrc study team. a sars dna vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a phase i clinical trial safety and tolerability of a novel, polyclonal human anti-mers coronavirus antibody produced from transchromosomic cattle: a phase randomised, double-blind, single-dose-escalation study safety and immunogenicity of an anti-middle east respiratory syndrome coronavirus dna vaccine: a phase , open-label, single-arm, dose-escalation trial structural insights into coronavirus entry the ebola epidemic crystallizes the potential of passive antibody therapy for infectious diseases isolation of hcv neutralizing antibodies by yeast display emergence of novel coronavirus and progress toward treatment and vaccine key: cord- - aq authors: cajamarca-baron, jairo; guavita-navarro, diana; buitrago-bohorquez, jhon; gallego-cardona, laura; navas, angela; cubides, hector; arredondo, ana maría; escobar, alejandro; rojas-villarraga, adriana title: sars-cov- (covid- ) in patients with some degree of immunosuppression date: - - journal: nan doi: . /j.reumae. . . sha: doc_id: cord_uid: aq background it is not clear whether patients with some degree of immunosuppression have worse outcomes in sars-cov- infection, compared to healthy people. objective to carry out a narrative review of the information available on infection by sars-cov- in immunosuppressed patients, especially patients with cancer, transplanted, neurological diseases, primary and secondary immunodeficiencies. results patients with cancer and recent cancer treatment (chemotherapy or surgery) and sars-cov- infection have a higher risk of worse outcomes. in transplant patients (renal, cardiac and hepatic), with neurological pathologies (multiple sclerosis (ms), neuromyelitis optica (nmods), myasthenia gravis (mg)), primary immunodeficiencies and infection with human immunodeficiency virus (hiv) in association with immunosuppressants, studies have shown no tendency for worse outcomes. conclusion given the little evidence we have so far, the behaviour of sars-cov- infection in immunosuppressed patients is unclear, but current studies have not shown worse outcomes, except for patients with cancer. in december , a group of five patients with severe pneumonia of unknown origin were reported to have had contact with a seafood market in the city of wuhan, hubei province, china, as an epidemiological link. the chinese centre for disease control and prevention (china cdc), deployed a rapid response for the epidemiological and aetiological investigation of cases and identified a new coronavirus with the ability to cause severe lung disease that can rapidly progress to death in affected patients. , given its rapid progression and the poor knowledge of the infection, how it behaves in patients with multiple comorbidities is not clear, especially patients with some degree of immunosuppression, due either to their underlying disease or to the use of immunosuppressants to manage it. in this review, we will focus on describing the literature on sars-cov- infection in patients with some degree of immunosuppression, other than rheumatological diseases, among these, cancer patients, transplant recipients, primary immunodeficiency, and hiv patients. initially the virus was termed the new coronavirus ( -ncov) and variations of same. sars-cov- is the name currently used for the virus, which shares genetic similarities with the sars-cov virus. covid- (coronavirus disease ) is the name of the disease generated by sars-cov- infection. j o u r n a l p r e -p r o o f epidemiology from december th to th, samples of bronchoalveolar lavage fluid were collected from patients hospitalized for severe pneumonia in the city of wuhan, the epicentre of the pandemic, and the new coronavirus was isolated. results for viruses such as severe acute respiratory syndrome (sars-cov), middle east respiratory syndrome coronavirus (mers-cov), influenza, avian influenza, and other common respiratory pathogens were negative. , on january , a case series of confirmed sars-cov- patients treated at a wuhan hospital was released. most were male ( %), with a median age of years, and less than half had comorbidities ( %) such as diabetes mellitus ( %), hypertension ( %), and cardiovascular disease ( %). of these patients, % had a history of exposure to the seafood market. in another case series of hospitalized patients in wuhan, china, % of the infected patients were presumed to have been infected by nosocomial transmission, % of the patients required icu hospitalization, and mortality was about . %. the infection rapidly escalated and was declared a public health emergency by the world health organization (who) on january , . as of today, june , affected countries have been reported, and the number of confirmed cases worldwide is close to ten million ( , , ) , with a total of , deaths and , , cases that have recovered. the country with the most confirmed cases is currently the united states, followed by brazil and russia. china, the first country affected, has a declining case curve and is now in twentieth place worldwide. in the americas, there are , , confirmed cases with , deaths; the united states and brazil together account for % of all cases and % of all deaths currently reported in the region. infection in children is less frequent and most reported cases are among family members and, to a lesser extent, from close contact with infected patients. j o u r n a l p r e -p r o o f the coronaviruses (cov) are a group of viruses discovered in that have a single strand of rna (~ - kb in length) that codes for structural, envelope, membrane and nucleotide proteins, as well as for non-structural proteins. they belong to the coronaviridae family which in turn is part of a larger family, the nidovirals. the coronaviridae family is divided into two subfamilies: orthocoronavirinae and torovirinae. the former is classified into four genera: alphacoronavirus, betacoronavirus, gammacoronavirus and deltacoronavirus. they are zoonotic viruses, bats have been acknowledged as natural hosts, but six types have been recognized as having the ability to infect humans: two alpha-coronaviruses ( e and nl ) and four betacoronaviruses (oc , hku , sars-cov and mers-cov). , , in , there was an outbreak of sars-cov that caused deaths worldwide. in , mers-cov was discovered in middle eastern countries with a fatality rate of . %. sars-cov- is a betacoronavirus, subgenus sarbecovirus and from the subfamily orthocoronavirinae with an envelope composed of a lipid bilayer derived from the host membrane. the genome encodes for spike glycoprotein (s), small envelope protein (e), membrane protein (m), and nucleocapsid protein (n). it also encodes accessory proteins that interfere with the host's immune response. its name is due to its similarity to a crown, given the spherical morphology of the virus and the projections on its surface that correspond to the s protein, which is glycosylated and mediates the viral entry into the host cells. the m protein gives the shape to the viral particle and together with the e protein directs the assembly of the virus and its maturation. the n protein participates in the packaging of the viral rna during assembly. haemagglutinin is one of the accessory proteins, which binds to sialic acid in host glycoproteins, improving entry into the cell. like sars-cov, sars-cov- uses the receptor for the angiotensin converting enzyme (ace ) as a means of entry into the cell where it binds by means of the s protein, however, unlike the other viruses, sars-cov- binding is much stronger since this protein undergoes a residue substitution in its c-terminal domain that increases affinity for the receptor. , the s protein has two subunits, s which determines the cell tropism and s which mediates the fusion of the virion to the membrane so that it can enter the cell where it rapidly translates two polyproteins that form the replication/transcription complex into a double-membrane vesicle; the virion contained in these vesicles fuses with the plasma membrane to be released later. the viral genome found in cytoplasm acts as pathogen-associated molecular patterns (pamps) and are recognized by the molecular pattern recognition receptors (prrs) that are toll-like receptors (tlr , tlr , tlr and tlr ). the rig-i receptor (retinoic-acid inducible gene-i), the cytosolic receptor mda- (melanoma differentiation-associated gene ) and cgas (nucleotidyltransferase cyclic gmp-amp synthase) recognize viral rna and recruit adaptive molecules that trigger a response cascade leading to the activation of the nuclear transcription factor- and interferon regulatory factor (irf ), producing interferon  and  and pro-inflammatory cytokines. different elevated cytokines have been found in patients with covid- : il- , il , il- , il- , il- , il- , il- , il- , macrophage colony-stimulating factor (mcsf), mcp- , hepatocyte growth factor (hgf), ifn- and tnf-. this supports the fact that lung damage is secondary to a cytokine storm induced by the inflammatory response, resulting in the person entering a critical condition. , the transmission dynamics are not yet fully known. the intermediate host between the natural reservoir and humans is unknown. however, it has been possible to confirm person-to-person transmission, which contributes to the rapid spread of the disease, and this is confirmed by the data found in the case series, which show that as of january , % of cases were linked to the seafood market in wuhan (china); however, of the cases reported after this date, only . % had this link. to date, person-to-person transmission has been considered to occur via respiratory droplets produced by coughing or sneezing. however, the presence of the virus has been detected in other fluids such as blood, faeces, and saliva. , initially, it was believed that spread was by people with clinical manifestations. however, it has been shown that asymptomatic carriers also transmit, and some people have even been recognized as "super spreaders", infecting many people, including health workers. vertical transmission of the virus in pregnancy has not been proven, however it is not known whether there is a risk during delivery through the vaginal canal. clinical manifestations can range from being asymptomatic to acute respiratory distress syndrome and multiorgan dysfunction. the incubation period is estimated at . days; however, this can vary. in the first case series of zhu et al. and ren et al. of patients treated at a hospital in hubei, the predominant symptoms were dry cough, dyspnoea, and fever. lung opacities consistent with a pneumonic process, worsening rapidly (two to four days) and requiring invasive mechanical ventilation, are recorded. , in general, the most common clinical manifestations are fever (although not present in all cases), cough, odynophagia, fatigue, and myalgia. other less frequent symptoms are sputum production, headache, haemoptysis, and diarrhoea. cases of keratoconjunctivitis and fulminant myocarditis have also been described. , , in early stages of the disease, chest x-ray can be normal, but as the disease progresses, bilateral ground glass opacity or consolidation can be found in more than % of patients. chest ct is much more sensitive than radiography. these findings can be found in asymptomatic patients. , it has been reported that up to % of patients will have no radiological changes. as for laboratory findings, lymphopenia was common, found in more than % of patients, with less frequent evidence of thrombocytopenia and leukopenia. a large proportion presented with elevated c-reactive protein, and in fewer cases, elevated alanine aminotransferase, aspartate aminotransferase, creatine kinase, and d-dimer were found. disturbances are pronounced in patients with severe disease. in the different case series and epidemiological reports published since the appearance of sars-cov- , comorbidities have been highlighted as risk factors associated with severity. it has also been established that patients admitted to the intensive care unit have more comorbidities than those in general hospitalization. the most prevalent underlying diseases are high blood pressure, diabetes mellitus, cardiovascular and cerebrovascular disease. , the results of nine metaanalyses in patients with covid- published to date are summarised in tables and . table presents the prevalence of comorbidities in patients with covid- , most of them hospitalized, and analysed through seven meta-analyses. in turn, table shows the risk associated with severity, death, or fatality due to the presence of comorbidities, through seven meta-analyses. the meta-analysis by wang et al. is noteworthy, which identifies arterial hypertension, diabetes mellitus, chronic obstructive pulmonary disease (copd), cardiovascular and cerebrovascular disease as factors that negatively impact mortality. specifically, copd increases by . times the risk of progression and deterioration of patients with covid- . these data are supported by the results of another meta-analysis by zhao et al. where the severity of covid- is four times higher in copd patients; they also assessed the impact of active smoking, which increases the risk of severe covid- two-fold. it has been widely demonstrated that patients suffering from diabetes mellitus are admitted more frequently to the intensive care unit and have a higher mortality, as shown in table . the results of a primary study by roncon et al. are highlighted (or . , % ci . - . ; p < . , i = %). these patients tend to present a more severe pneumonic process, with greater inflammatory response and tissue damage, which makes them more prone to cytokine storm leading to rapid deterioration, which is why patients with this history should be strictly monitored. cardiovascular disease is a risk factor per se increased by covid- infection that generates or aggravates myocardial damage, but when associated with myocardial injury the results are usually fatal for patients. , among other comorbidities, chronic kidney disease is associated with in-hospital mortality, as are cancer and cerebrovascular disease, demonstrated through two meta-analyses that included over fifteen thousand patients ( table ) ; studies suggest that superficial fungal infections and psoriasis confer vulnerability to covid- ; a body mass index (bmi) > kg/m is an independent risk factor for complications from the infection; and there are discouraging results regarding underlying neurological disease and sars-cov- . [ ] [ ] [ ] [ ] in general, the presence of comorbidities should imply strict follow-up of patients to detect early complications; however, more attention should be paid to certain comorbidities where strong associations have been found with covid- infection and its severe outcomes. overall mortality is . % to %, but it changes to % to % among patients requiring hospitalization and increases to % in critically ill patients. studies have shown two peaks, at and days. among the causes of death, respiratory failure prevails, followed by shock due to myocardial dysfunction and finally, the combination of the two. it is important to maintain a high degree of diagnostic suspicion in patients with fever or respiratory symptoms who have travelled to affected areas or have had close contact with j o u r n a l p r e -p r o o f suspected or confirmed cases days before the onset of symptoms. in this scenario, confirmation by molecular testing is required. real-time reverse transcription polymerase chain reaction is performed on specimens collected from the lower or upper respiratory tract if the former cannot be obtained. there are several assays that are performed on serum or plasma for the detection of both viral proteins and antibodies. the most widely used are to detect immunoglobulin g (igg) and immunoglobulin m (igm) antibodies, which are produced in the second week of infection. there are several therapeutic goals and they are directed at different levels: inhibition of virus entry into the cell, inhibition of fusion of the viral envelope to the membrane, transcription inhibition, inhibition of viral proteins and blockade of il- signalling to prevent the cytokine storm. at first, chloroquine (clc) and hydroxychloroquine (hcq) were shown to block sars-cov- in vitro, with better results for the latter and therefore its use was indicated for the management of covid- infection. promising results have been shown in case series; however, the studies have limitations such as the sample size used. however, preliminary results were recently published from the recovery study, a randomized clinical trial to evaluate potential drugs for management of the infection in the united kingdom, in which they concluded no beneficial effect of the use of antimalarials in hospitalized patients, and therefore they stopped including patients for this treatment arm and the recommendation that it should not be used has been extended worldwide. additional results have recently been published in several articles on the efficacy and safety of the antimalarials chloroquine and hydroxychloroquine for the treatment of different phases of sars-cov- infection. however, the data are controversial, some not demonstrating efficacy or reporting a high number of adverse events, primarily associated with cardiac arrhythmias. it is important to note that a number of criticisms and concerns have been raised regarding the accuracy of the data from these studies and they have therefore been withdrawn. to date there are more than clinical trials underway with hcq, and with clq, several of which are in prophylactic use in healthcare workers and others post-exposure. , lopinavir/ritonavir has studies in sars and mers, the data published for covid- are reports and retrospective studies with which the effect cannot be established with certainty. there is a clinical j o u r n a l p r e -p r o o f trial of patients with covid- with no difference in mortality, hospital discharge or recovery. however, despite this, in some centres it is still being used at doses of mg/ mg twice a day for days. ribavirin, like lopinavir/ritonavir, has activity against other coronaviruses and was considered to be a possible treatment for sars-cov- ; however, studies carried out for sars show limited, highdose activity leading to a high rate of haematological and hepatic adverse events, therefore its use is now limited. , other antivirals such as oseltamivir were used in the first cases in hubei, china, because it was suspected to be seasonal influenza; they are now not indicated for use in sars-cov- . remdesivir is a nucleoside analogue that showed in vitro activity against sars-cov- , used later in a -patient cohort in canada, the united states, europe, and japan, achieving a satisfactory response in patients. based on preliminary studies, some drug regulatory agencies (united states and japan), conducted emergency approvals for use in hospitalized patients. results from ongoing studies are expected to evaluate efficacy and safety. currently umifenovir or arbidol is under study, an antiviral that aims to inhibit the interaction between protein s and ace . the use of corticosteroids is limited in sars-cov- infection to scenarios of chronic obstructive pulmonary disease exacerbation and refractory shock, taking into account previous studies in influenza pneumonia where they were associated with increased mortality. recently, preliminary results from the recovery study showed that the use of dexamethasone reduced mortality in one-third of critically ill patients who were on mechanical ventilation, while reduction was onefifth in those receiving non-invasive oxygen. definitive results are expected from this and the more than clinical trials currently underway to define the particular subgroups that would benefit from this treatment. monoclonal antibodies against il- are another therapy studied, in phases of adult respiratory distress syndrome (ards), with promising results in small case series. convalescent plasma is another therapy used as salvage in sars and mers. at the beginning of the pandemic, a case series of five critical patients from china, who were given convalescent plasma, showed improvement in their clinical status. more recently, several case series and preliminary trial results have demonstrated clinical benefits and decreased mortality with its use, particularly in hospitalized patients with moderate to severe involvement; however, results from more than j o u r n a l p r e -p r o o f clinical trials are awaited to clarify the characteristics of the plasma, the donors, and the specific individuals who could benefit. despite the abovementioned therapies, there is still no specific treatment and therefore the recommendations are symptomatic management in mild cases, supportive therapy in cases of critical illness and management of ventilation in cases of ards. immunosuppression and sars-cov- given the suddenness of the pandemic, and its rapid spread, little is known about sars-cov- infection and certain types of condition or disease, this is the case for people with some type of immunosuppression (either primary, associated to underlying or pharmacological diseases), which given the physiopathogenesis of sars-cov- infection known so far, would raise two hypotheses: it could be a possible benefit, since this state of immunosuppression could avoid that uncontrolled immune response or "cytokine storm", but on the other hand, it is equally clear from previous studies that immunosuppressant use or status is associated with increased risk of infection. in epidemics such as the abovementioned sars-cov, immunosuppressed patients, especially transplant recipients, did not have worse outcomes than the general population. , similar findings were presented in the mers epidemic, being male, advanced age and comorbidities such as diabetes mellitus, obesity, pulmonary pathology and renal disease being found as risk factors, and immunosuppression status not being associated as a factor of poor prognosis. to date, the centres for disease control and prevention (cdc) and other international agencies have included as poor prognostic factors patients with some degree of immunosuppression, including people with a history of cancer treatment, smokers, transplant recipients, people with immunodeficiencies, poorly controlled hiv or aids and people with prolonged use of steroids or immunosuppressive drugs, all based on previous studies that associate such diseases with respiratory infections, especially of viral aetiology. current evidence of conditions associated with immunosuppression and sars-cov- infection j o u r n a l p r e -p r o o f c a n c e r on march , liang et al., published a study collecting data from hospitals in china, up until january , , on patients with sars-cov- , comparing those with a history of cancer and those without. they collected , patients, ( %) with a history of cancer. the most frequent neoplasm was lung (five cases [ %]), and of the total cancer patients, four ( %) had undergone chemotherapy or surgery within the previous month, and the rest were cancer survivors, with strict follow-up. in terms of sociodemographic characteristics, the cancer patients were older, had a greater history of exposure to cigarettes, presented more polypnoea and had more severe pulmonary tomographic manifestations. in the analysis of outcomes, they showed that patients with a history of cancer and sar s-cov- infection were at greater risk of serious events (defined as the percentage of patients admitted to the intensive care unit requiring invasive ventilation or death) compared to patients without cancer (seven ( %) of patients vs. ( %) of , patients; p = . ). in addition, patients who underwent chemotherapy or surgery in the last month had a higher risk (three ( %) out of four patients) of clinically severe events than those who had not undergone chemotherapy or surgery (six ( %) out of patients). these data were confirmed by logistic regression (odds ratio (or) . ; % ci . - . ; p = . ) after adjusting for other risk factors such as age and smoking history. in addition, the patients with cancer deteriorated more rapidly than those without cancer (median time to severe events days (ci - vs. days, -unreached; p <. ). furthermore, desai et al., recently published a meta-analysis, in which they included studies, finding a prevalence of cancer in patients with covid- of % (ci . %- . %; i = . %). we should clarify that some authors consider that the current evidence is insufficient in this field, however, the number of research results has been increasing, showing similar results. , taking into account the results mentioned, it can be stated that cancer and its recent treatment are bad prognostic factors for sars-cov- infection. therefore, special recommendations should be considered for these patients, such as postponing adjuvant chemotherapy or elective surgery in people with "stable" cancer, especially in endemic areas, adopting stricter personal protection measures for cancer patients or cancer survivors, and considering stricter surveillance or treatment when cancer patients are infected with sars-cov- . in general, decisions should be made on a "patient-to-patient" basis. , t r a n s p l an t we highlight the study of a case series, two heart and kidney transplants and one liver (paediatric population). the heart transplant patients were confirmed by pcr to be infected, one of them was years old, came with immunosuppression with tacrolimus mg per day and mycophenolate g per day, and attended consultation for fever, fatigue and liquid stools, with characteristic findings of sars-cov- infection on chest tomography. he presented criteria of severe pneumonia, immunosuppression was discontinued, and he was managed with immunoglobulin (ivig) g/day and methylprednisolone mg/day and made adequate medical progress. the second patient, years old, in immunosuppression with tacrolimus . mg a day and mycophenolate g a day, attended with fever and fatigue, had lymphopenia, did not require hospitalization, nor discontinuation of immunosuppression, and was managed with ceftriaxone and ganciclovir, with an adequate outcome. their adequate clinical course suggests that in patients with this type of transplant the disease has a similar presentation to non-transplanted patients. it should be noted that in a series of seven cases (two liver, three kidney, one lung and one heart) an initial attenuated inflammatory response was evident, suggesting that although patients with transplant immunosuppression may have higher susceptibility to sars-cov- infection, their clinical course could be similar to that of immunocompetent patients. with regard to the renal transplantation patients, until the time of the report, a -year-old patient remained in icu managed with lopinavir/ritonavir, requiring suspension of immunosuppression who came under management with tracrolimus, everolimus and prednisolone at intermediate doses. he was admitted for fever and vomiting that progressed to respiratory symptoms, and had thrombocytopenia, lymphopenia, and elevated d-dimer as factors of poor prognosis. the second, a -year-old, under immunosuppression with tacrolimus, mycophenolate, and prednisolone, consulted for fatigue, abdominal pain, dyspnoea, fever, and dry cough, presented lymphopenia and imaging findings typical of sars-cov- infection. he was managed with ivig ( g, then g/day x days), methylprednisolone mg/day and interferon α ( million/u day), in addition to suspension of immunosuppression, and responded adequately to treatment. with regard to this type of transplant, the atypical presentation of the first case is noteworthy, and the adequate response of the second that could be associated with the use of multiple therapies, without it being possible conclude whether renal transplantation is associated or not with a worse prognosis. gandolfini et al., publish two cases of renal transplant and covid- , a -year-old male and a -year-old female patient under management with tacrolimus, corticoids and mycophenolate, who developed severe pneumonia; in addition to suspending immunosuppressants, management with hydroxychloroquine, lopinavir/ritonavir and colchicine was started, due to the unavailability of tocilizumab. the administration of colchicine achieved an impact in decreasing il- serum levels, thanks to its interfering with inflammasome assembly which leads to the production of il- b and other interleukins such as il- . in italy, the paediatric liver transplant group of hospital papa giovanni xxiii bergamo followed up liver transplants (two in the last three months), associated with autoimmune liver diseases ( patients), three additionally in chemotherapy (for hepatoblastoma). of the total number of transplant recipients, three were confirmed to be infected with sars-cov , and all remained asymptomatic without requiring hospitalization or suspension of immunosuppression. additionally, qin et al. , report the case of a patient with hepatocellular carcinoma who underwent liver transplantation and suffered an undetected sars-cov- infection in the perioperative period; immunosuppression was initiated with tacrolimus and glucocorticoids; however, persistence of fever led to confirmation of sars-cov- infection; management with oseltamivir and immunoglobulin was initiated, and despite a prolonged convalescence, they did not present multiorgan failure, thus immunosuppression was maintained. the importance of sars cov- detection is highlighted for organ receptors and donors to reduce the transmission and risk of severe infection or rejection due to adjustments in immunosuppression. given the above, it is not clear whether transplantation and use of immunosuppressants in this context is a risk or severity factor for sars-cov- infection. likewise, in the event of sars-cov- infection, the adjustment or suspension of immunosuppressors should be assessed, and we should always seek to protect graft function with the administration of glucocorticoid doses and support measures, among others. neurology is a continuously growing specialty. many diseases have a component that compromises autoimmune aggression to a greater or lesser extent and therefore go on to require immunosuppressant or immunomodulatory management. within the multiple entities, two diseases have become relevant in recent times, multiple sclerosis and optical neuromyelitis, due on the one hand to their physiopathological mechanism that involves neurodegeneration and inflammation by excessive activity of the immune system derived from antigenic epitopes and proinflammatory molecules, and on the other hand the use of therapies that trigger regulation of immune cells, affecting in some cases innate and adaptive immunity in most cases. if we consider that the response mechanisms to viral infections are based on inhibition of the infection by type i interferons and the death of the infected cells by nk lymphocytes (innate immunity), the generation of antibodies that block the union and entry of the virus into the cells, and the elimination of cells infected by cytotoxic t cells (adaptive immunity), the different drugs currently used could to a greater or lesser extent alter the immune response to sars-cov- infection, and this is why there are now different considerations when initiating or continuing therapies. people with ms are at higher risk of admission to the intensive care unit due to infections, and higher mortality at one year after admission than the general population. the use of diseasemodifying therapies implies a higher risk of infections, however, to date there is no data to indicate that patients with ms are at higher risk of sars-cov- infection, or more severe infection. it is even possible that such disease-modifying therapies and their immunosuppressive effect may play a protective role during -covid infection by preventing or dampening hyperimmune activity that, in some cases, could lead to clinical deterioration; there is even a report of a patient with primary progressive multiple sclerosis receiving treatment with ocrelizumab and becoming infected with sars-cov- , in the context of lymphopenia and hypogammaglobulinema expected for this type of treatment, without generating major clinical complications, this hypothesis is obviously limited for now only to academic deductions and limited information. , in recent results of the multicentre registry covisep, which includes information from patients with ms and covid- , it was demonstrated that age, obesity and highest score in the expanded disability status scale, were independent risk factors for severity of covid- . it is suggested that people with ms and related disorders receiving immunotherapy continue to receive the therapy during mild viral infections. in those with documented mild sars-cov- infection, it may be reasonable to continue treatment. neurologists should have a lower threshold for suspending treatment in people taking therapies with greater immunosuppressant effects. consideration should be given to suspending treatment in those who are hospitalized with severe or complicated sars-cov- infection. treatment may be restarted after four weeks or when symptoms have completely resolved, considering the risk of rebound of ms activity with s p modulators and natalizumab. neurologists should alert intensive care physicians to the importance of fever management in people with ms. in people with ms and disease-modifying treatment, the decision to start, continue, temporarily suspend, or defer doses should be individualized, taking into account factors such as disease activity and the possibility of disease progression, as well as considerations of the mechanism of action of the drugs and their ability to deplete lymphocytes. recommendations from experts suggest not suspending first-line drugs (interferons, glatiramer acetate, teriflunomide, or dimethyl fumarate) and considering deferring therapies such as cladribidine and alemtuzumab based on their ability to deplete lymphocyte counts rapidly and aggressively. , a survey of patients with nmosd or ms from china, from centres, did not find an increased risk of infection by covid- , suggesting as a possibility the role of self-care and protective measures taken by patients and their healthcare team, regardless of their condition and immunosuppression drug. relapses in patients with nmosd can be devastating and patients should be encouraged to continue therapies for the prevention of attacks, including corticosteroids, azathioprine, mycophenolate mofetil, rituximab, tocilizumab and eculizumab. if there is a clinical need to discontinue or delay treatment in patients with nmosd, corticosteroids may be used in moderate doses to prevent relapses in the short-term, it is important to consider individualized therapy and comorbidities when deciding on management of this condition during the covid- pandemic. my a s t h e n i a g r a v i s / l a mb e r t -e a to n my a s t h e n i c s y n d r o me ( mg / l e ms ) because most patients with myasthenia gravis (mg) are on immunosuppressant or immunomodulatory therapies and may also have muscle weakness and ventilatory failure, there is a theoretical concern that they may be at increased risk for infection or experience severe manifestations of sars-cov- infection. in a series of five cases with mg hospitalized for covid- infection, a variable clinical course was demonstrated, with three requiring mechanical ventilation and one presenting mg crises, and although it is difficult to assess the latter due to intubation and sedation in two of the cases, none had a fatal outcome. two additional cases have been reported, one developing crises due to myasthenia and the other with chronic refractory mg, with good outcome, without complications or worsening of their baseline condition. there are numerous recommendations circulating that attempt to provide clarity and guidance. however, the differences between the recommendations have created confusion, because decision-making varies in different countries, and due to the lack of databases with an adequate number of patients. patients with mg/lems should continue their treatment and are advised not to discontinue any existing medications; there is no scientific evidence to suggest that symptomatic therapies such as pyridostigmine increase the risk of infection and they should not be discontinued unless there are other clinical reasons to do so, given the risk of increased disease activity and/or mg exacerbation or crisis. with regard to certain therapies (immunoglobulins, plasmapheresis) there is no information pointing to increased risk of infection, however, the use of immunoglobulin should be based on the individual need of the patient and indiscriminate use should be avoided. in general, these therapies should be reserved for patients with acute exacerbation and if required as maintenance therapy on an exceptional basis, additional precautions should be taken. in patients with severe sars-cov- infection, temporary suspension of immunosuppression may need to be considered. it is important to note that decisions to intensify or change treatment should be individualized based on the relative severity of the sars-cov- infection. there is very little data regarding the impact of sars-cov- infection on primary immunodeficiencies (pi), which is why several international organizations such as the european society for immunodeficiency (esid), the reference centre for hereditary immunodeficiencies (le centre de référence déficits immunitaires héréditaires, ceredih) organization for primary immunodeficiencies (ipop) are collecting data through a survey of physicians in order to gather information and provide them better care. both the idf (immune deficiency foundation) and the ascia (australasian society of clinical immunology and allergy) and other agencies have considered their patients' increased risk of severe respiratory infections or of experiencing a more severe disease course, however, they recognize that it cannot be said whether people with primary immunodeficiencies are at higher or lower risk of severe sars-cov- infection. ascia and ipopi promote measures to prevent the spread of the virus, social isolation, and call for early consultation with medical services when infection is suspected, and recommend maintaining continuity of medication, especially in those receiving immunoglobulin. , virtual resources with patient and medical community education are available in the idf. these experts on the subject have theorized the possible effects of sars-cov- in different populations, for example, in the group of t lymphocyte (tl) immunodeficiency (combined immunodeficiency, digeorge syndrome, among others) measures of isolation and protection must be maximised, since the action of these defence cells is necessary for the control of the virus; in b-lymphocyte deficiency (agammaglobulinaemia, common variable immunodeficiency) the risk of infection is not thought to be higher than in the community, except in patients with structural involvement at the lung level, and in the phagocytosis deficiency immunodeficiency group (neutropenia and chronic granulomatous disease) although neutrophils are not as important in controlling the virus, the possibility of co-infection needs to be considered, while the chronic granulomatous disease group is not thought to be at increased risk of infection or severe manifestation. other recommendations according to the ipopi joint statement on the current coronavirus pandemic, are the use of pcr tests for diagnosis, since for some forms of pi there is no production of antibodies, and therefore tests based on immunoglobulins are not effective. in this same publication, as of april , , sars-cov- cases in different types of pi, exhibiting typical symptoms (fever, cough, and upper respiratory symptoms), of which were under years of age; seven required hospitalization (two developed adult respiratory distress syndrome) and all were under years of age. in the most recent update, based on collected (unpublished) data, there does not appear to be an increased risk of sars-cov- infection, especially in its severe form, however, given the still limited information and risk for these patients, isolation and infection prevention measures should be maintained as much as possible. another important aspect for these patients is the impact during the sars-cov- pandemic on their health-related quality of life (hrqol), requiring strict isolation and a remote care programme. in an italian cohort of patients with pi due to a bl defect, two scales were evaluated, one specific to health-related quality of life, cvidqol (common variable immune deficiency quality of life), and another generic scale to assess anxiety and depression, ghq- ( -item general health questionnaire); finding that the remote care programme does not affect hrqol, however, in the group of patients at risk of anxiety/depression there is impaired quality of life, emphasizing the importance of individualizing each patient and psychosocial support. hu during the stay at this institution infection was documented by nasopharyngeal sample associated with amplification of the betacoronavirus e gene and the specific sars-cov- rdrp gene by pcr, comorbidities such as hypothyroidism and asthma were also identified in these patients. all came under antiretroviral treatment, with cd cell count (> cell/mm in four of the patients). prior classification according to the patient's clinical status as mild, moderate or severe, under the precept that protease inhibitors could have activity against coronavirus protease, cobicistat + darunavir was considered appropriate in two of them, starting ritonavir + lopinavir in the rest combined with hydroxychloroquine, azithromycin, corticosteroids, interferon β- b and even tocilizumab, according to duration and progression. the survival of all is documented up to the time of publication and the conclusion is that patients in advanced stages of the disease should be guaranteed differential diagnosis by opportunistic pulmonary agents, inferring that they may have a poorer outcome, as well as an ominous prognosis. , in a recent study of incidence and severity of covid- involving hiv clinics in spain ( , patients), patients were diagnosed with covid- , were hospitalized, required intensive therapy and died. it was found that patients receiving tenofovir disoproxil fumarate (tdf)-emtricitabine (ftc) reverse transcriptase inhibitors had a lower risk of developing covid- and of hospitalization compared to groups receiving other treatments. there are isolated cases in which patients coinfected with hiv and covid- in management with lopinavir and ritonavir had a favourable clinical response, considering that this reaction can have two effects: inhibition of sars-cov- replication, as well as inhibition of hiv replication, allowing a slight activation of the immune system capable of responding to sars-cov- without the progression of the patient to hyperinflammatory status, even highlighting that lymphopenia would not be considered a marker of poor prognosis but a protective immune effect, being considered an disturbance of the overactive response of the immune system, avoiding serious clinical manifestations. other hypotheses raised as a favourable clinical response dependent on the patient's immune status, coinfection or history of opportunistic infections, mainly at the pulmonary level, the risk or benefit in relation to the use of glucocorticoids and even the benefit of introducing tocilizumab early were not omitted. in patients with hiv and sars-cov- infection it can be concluded that the immune response, prognosis and outcome are highly variable and / or subjective according to the antiretroviral treatment in place, duration in relation to diagnosis and viral suppression, because hiv patients without treatment, newly diagnosed or with no viral suppression may have a compromised immune system (mediated by a low cd count), even being vulnerable not only to the worst outcomes due to sarv-cov- , but alleged coinfection by other agents in pulmonary opportunists. patients with adherence to antiretroviral treatment, who have achieved viral suppression and do not have low cd count, will be affected by sars-cov- with the same chances as immunocompetent patients who develop mild manifestations, regardless of change in antiretroviral treatment or adjustment with ritonavir and lopinavir, however, it is important to emphasize the divergences in approach, management and choice versus antiretroviral treatment documented to date. for this type of patients, as well as those mentioned previously, recommendations have already been published on their management with covid- . the degree of pharmacological immunosuppression is assessed according to the patient's immunological risk, the type of protocol used, the type of target at which the drug or group of drugs is directed, and the type of disease for which it is indicated (e.g., neoplasms, transplants, immunological, etc.). although in all cases it is not easy to directly assess the degree of immunosuppression, some biomarkers have been developed that reflect the individual's response to immunosuppressants, which can range from general tests such as liver function enzymes, to the use of specific genotypes, including cell counts of specific lymphocyte populations, cytokines, leukocyte markers and target enzymes, among others. in other cases, the degree is assessed according to the number of immunosuppressant drugs, dose and time employed, being low when a drug is used in low or moderate doses for a short time, and increasing to a higher degree when two or more immunosuppressants are used in combination, regardless of the dose. there are many drugs used in different medical specialties that are associated with a certain degree of immunosuppression and that render patients vulnerable to one or another infectious process. however, in the field of sars-cov- infection, the data are scarce and unknown. as mentioned throughout the review, comorbidities are the most important risk factors compared to drugs used. the literature search predominantly reveals information about possible drug interactions that can occur with the treatment of covid- , which can clearly also generate damage and worsen the clinical picture. to date there are no data on specific drugs that are associated to a greater or lesser degree with infection by the new coronavirus. there is a warning about possible drug interactions between immunosuppressive drugs and those under investigation for the treatment of covid- , generating alerts and guidelines for the development of this complex task by clinicians. remdesivir, an antiviral with promising results in the treatment of covid- as mentioned, has no data so far on possible drug interactions with immunosuppressive drugs, unlike chloroquine/hydroxychloroquine and lopinavir/ritonavir, which although their use is declining, were initially an active part of treatment, suggesting major interactions with calcineurin inhibitors, mtor (mammalian target of rapamycin inhibitors) and corticosteroids, especially lopinavir/ritonavir. there are recommendations about discontinuing mycophenolate in critically ill transplant recipients, which would also apply to covid- , bearing in mind that during the h n pandemic it was documented that this drug decreased the serological response in transplant recipients. however, given the scarcity of data, this decision must be tailored to each patient in this special subgroup. in reference to calcineurin inhibitors (tacrolimus, cyclosporine), a dose minimization scheme is proposed, with the possibility of increasing the interval for its administration, suggesting safety in these regimens, particularly in individuals with kidney transplantation and covid- . multiple recommendations and guidelines have been generated around the use of immunosuppressors or cytostatics in the oncology field, such as cyclophosphamide, doxorubicin, cytarabine, vinblastine, as well as immunotherapy and the use of biological drugs in the context of cancer, according to the type of neoplasm in the context of risk or presence of covid- infection, suggesting in general a decrease in dose, but always balancing individual cases according to the type of neoplasm, stage and immunosuppressive scheme proposed. the recommendation is to avoid high doses of corticosteroids since they could, as observed in patients with mers-cov, prolong viral replication in patients with covid- . as mentioned above, their use would be reserved for specific subgroups of critically ill patients other drugs, not immunosuppressants, but associated with the physiopathogenesis of the disease, such as angiotensin-converting enzyme inhibitors or renin-angiotensin-aldosterone system j o u r n a l p r e -p r o o f inhibitors, have not been shown to increase the risk of sars-cov- infection, and conversely, their withdrawal could be harmful. considering the evidence available to date on sars-cov- infection outcomes in patients with immunosuppression (either due to their disease or the use of immunosuppressants) its behaviour is not clear in this type of individuals. we can highlight that patients with cancer and recent treatment of cancer (chemotherapy or surgery) have a higher risk of worse outcomes, with faster deterioration than those without cancer, an increased risk of severity and mortality having been shown through two meta-analyses. with regard to transplant patients (kidney, heart and liver), patients with neurological disease associated with the use of immunosuppression (ms, nmods, mg), primary immunodeficiencies and hiv, studies have not shown a tendency to poorer outcomes than patients without these diseases or drugs and have sars-cov- infection, similar to that found in rheumatological diseases. this could perhaps be explained in that the severity of sars-cov- infection has been associated with an aberrant inflammatory response (cytokine storm). for the time being and as more information is obtained, and based on the aforementioned literature and recommendations of societies, it is suggested that immunosuppressant therapy be continued, starting new therapies should be avoided as much as is possible (especially in endemic areas) and in case of infection, depending on its severity, the risk/benefit should be evaluated of suspending it during the period of infection. it should be noted that the presence of comorbidities, such as high blood pressure, diabetes mellitus and copd, increases the risk of severity, intensive care requirements and mortality. no specific grants were received for this research from funding agencies in the public, commercial or non-profit sectors f includes cardiovascular and cerebrovascular, non-meta analysed raw calculation. identification of a novel coronavirus causing severe pneumonia in human a novel coronavirus from patients with pneumonia in china coronavirus disease covid- clinical features of patients infected with novel coronavirus in wuhan clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china coronavirus resource center organizacion panamericana de la salud enfermedad por el coronavirus (covid- ) diagnosis and treatment recommendations for pediatric respiratory infection caused by the novel coronavirus coronavirus diversity, phylogeny and interspecies jumping insights into the recent novel coronavirus (sars-cov- ) in light of past human coronavirus outbreaks the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak -an update on the status a review of coronavirus disease- (covid- ) early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes consistent detection of novel coronavirus in saliva evolving epidemiology and transmission dynamics of coronavirus disease outside hubei province, china: a descriptive and modelling study clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records clinical characteristics of patients infected with sars-cov- in wuhan, china clinical characteristics of coronavirus disease in china care for critically ill patients with covid- comorbidity and its impact on patients with covid- in china: a nationwide analysis prevalence of comorbidities and its effects in patients infected with sars-cov- : a systematic review and meta-analysis does comorbidity increase the risk of patients with covid- : evidence from meta-analysis. aging the impact of copd and smoking history on the severity of covid- : a systemic review and meta-analysis diabetic patients with covid- infection are at higher risk of icu admission and poor short-term outcome diabetes is a risk factor for the progression and prognosis of covid- cardiovascular implications of fatal outcomes of patients with coronavirus disease (covid- ) prevalence and impact of cardiovascular metabolic diseases on covid- in china scoping review of prevalence of neurologic comorbidities in patients hospitalized for covid- covid and the patient with obesity -the editors speak out dermatological diseases presented before covid- : are patients with psoriasis and superficial fungal infections more vulnerable to the covid- ? dermatol ther kidney disease is associated with in-hospital death of patients with covid- world health organization. laboratory testing for novel coronavirus ( -ncov) in suspected human cases in vitro diagnostic assays for covid- : recent advances and emerging trends pharmacologic treatments for coronavirus disease (covid- ): a review chloroquine and hydroxychloroquine as available weapons to fight covid- recovery trial: the uk covid- study resetting expectations for clinical trials retracted: hydroxychloroquine or chloroquine with or without a macrolide for treatment of covid- : a multinational registry analysis. the lancet retraction-hydroxychloroquine or chloroquine with or without a macrolide for treatment of covid- : a multinational registry analysis. the lancet in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome main point : hydroxychloroquine was found to be more potent than chloroquine at inhibiting sars-cov- in vit systematic review of treatment effects compassionate use of remdesivir for patients with severe covid- a promising antiviral candidate drug for the covid- pandemic: a mini-review of remdesivir effect of dexamethasone in hospitalized patients with covid- : preliminary report improved clinical symptoms and mortality on severe/critical covid- patients utilizing convalescent plasma transfusion convalescent plasma in covid- : possible mechanisms of action treatment of critically ill patients with covid- with convalescent plasma severe acute respiratory syndrome in children the facts during the third epidemic. liver transplant off publ am assoc study liver dis int liver transplant soc middle east respiratory syndrome coronavirus: risk factors and determinants of primary, household, and nosocomial transmission comunicar los riesgos para la salud de covid- : una acción clave para ayudar a la población a protegerse y a mitigar su propagación pan american health organization / world health organization centers for disease control and prevention cancer patients in sars-cov- infection: a nationwide analysis in china covid- and cancer: lessons from a pooled meta-analysis risk of covid- for patients with cancer sars-cov- transmission in patients with cancer at a tertiary care hospital in wuhan, china cancer care during the spread of coronavirus disease (covid- ) in italy: young oncologists' perspective. esmo open cancer center recommendations to mitigate covid- impact in patients with cancer: low-resource settings version crucial aspects of the management of solid organ transplant patient with covid- : a narrative review attenuated early inflammatory response in solid organ recipients with covid- case report of covid- in a kidney transplant recipient: does immunosuppression alter the clinical presentation? covid- in kidney transplant recipients perioperative presentation of covid- disease in a liver transplant recipient. hepatol baltim md strategies for prevention and control of the novel coronavirus disease in the department of kidney transplantation inmunología celular y molecular infectionrelated health care utilization among people with and without multiple sclerosis. mult scler houndmills basingstoke engl covida ms patient treated with ocrelizumab: does immunosuppression have a protective role? mult scler relat disord clinical characteristics and outcomes in patients with coronavirus disease and multiple sclerosis treating multiple sclerosis and neuromyelitis optica spectrum disorder during the covid- pandemic disease-modifying therapies and infectious risks in multiple sclerosis decision-making on management of ms and nmosd patients during the covid- pandemic: a latin american survey emcam (multiple sclerosis autonomous community of madrid) document for the management of patients with multiple sclerosis during the sars-cov- pandemic the covid- pandemic and the use of ms disease-modifying therapies risk of covid- infection in ms and neuromyelitis optica spectrum disorders covid- in patients with myasthenia gravis. muscle nerve myasthenic crisis in covid- covid- in refractory myasthenia gravis-a case report of successful outcome guidance for the management of myasthenia gravis (mg) and lambert-eaton myasthenic syndrome (lems) during the covid- pandemic joint statement on the current epidemics of new coronavirus copid <br>worldwide survey of covid- in pid patients latest news on covid and pid immune deficiency foundation covid- and immunodeficiency latest news on covid and pid an idf virtual education event | immune deficiency foundation health-related quality of life in common variable immunodeficiency italian patients switched to remote assistance during the covid- pandemic covid- in patients with hiv: clinical case series co-infection of sars-cov- and hiv in a patient in wuhan city a trial of lopinavir-ritonavir in adults hospitalized with severe covid- centro nacional de información de ciencias médicas incidence and severity of covid- in hiv-positive persons receiving antiretroviral therapy could hiv infection alter the clinical course of sars-cov- infection? when less is better maintaining hiv care during the covid- pandemic biomarkers of immunosuppression immunosuppression for the non-transplant physician: what should you know? breathe pharmacologic treatment of transplant recipients infected with sars-cov- : considerations regarding therapeutic drug monitoring and drug-drug interactions covid- in recent heart transplant recipients: clinicopathologic features and early outcomes should cyclosporine be useful in renal transplant recipients affected by sars-cov- ? when a global pandemic complicates cancer care severe covid- in a renal transplant recipient: a focus on pharmacokinetics clinical course of covid- in a series of patients with chronic arthritis treated with immunosuppressive targeted therapies key: cord- -r bbomvk authors: woo, patrick cy; lau, susanna kp; tsang, chi-ching; lau, candy cy; wong, po-chun; chow, franklin wn; fong, jordan yh; yuen, kwok-yung title: coronavirus hku in respiratory tract of pigs and first discovery of coronavirus quasispecies in ′-untranslated region date: - - journal: emerg microbes infect doi: . /emi. . sha: doc_id: cord_uid: r bbomvk coronavirus hku is a deltacoronavirus that was discovered in fecal samples of pigs in hong kong in . over the past three years, coronavirus hku has been widely detected in pigs in east/southeast asia and north america and has been associated with fatal outbreaks. in all such epidemiological studies, the virus was generally only detected in fecal/intestinal samples. in this molecular epidemiology study, we detected coronavirus hku in . % of the nasopharyngeal samples obtained from pigs in hong kong. samples that tested positive were mostly collected during winter. complete genome sequencing of the coronavirus hku in two nasopharyngeal samples revealed quasispecies in one of the samples. two of the polymorphic sites involved indels, but the other two involved transition substitutions. phylogenetic analysis showed that the two nasopharyngeal strains in the present study were most closely related to the strains pdcov/chjxni / from jiangxi, china, and ch/sichuan/s / from sichuan, china. the outbreak strains in the united states possessed highly similar genome sequences and were clustered monophyletically, whereas the asian strains were more diverse and paraphyletic. the detection of coronavirus hku in respiratory tracts of pigs implies that in addition to enteric infections, coronavirus hku may be able to cause respiratory infections in pigs and that in addition to fecal-oral transmission, the virus could possibly spread through the respiratory route. the presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of coronavirus hku infection. quasispecies were unprecedentedly observed in the ′-untranslated region of coronavirus genomes. coronaviruses (covs) are found in a wide variety of animals, in which they can lead to enteric, hepatic, neurological and respiratory illnesses of differing severity. on the basis of genotypic and serological characterization, covs were traditionally divided into three distinct groups. in , the coronavirus study group of the international committee for taxonomy of viruses replaced the traditional cov groups , and with three genera, alphacoronavirus, betacoronavirus and gammacoronavirus, respectively. in the same year, we discovered three novel covs in avian cloacal swabs. these covs formed a distinct novel cov genus, named deltacoronavirus. subsequently, in a large epidemiological study, we discovered seven additional deltacoronaviruses. interestingly, one of these deltacoronaviruses, which was originally named porcine cov hku , was found in fecal samples of pigs in hong kong, and it is the only mammalian deltacoronavirus. in , the coronavirus study group of the international committee for taxonomy of viruses rectified the species name for this virus to coronavirus hku . over the past three years, coronavirus hku has been widely detected in pigs in east/southeast asia and north america and was found to be associated with fatal outbreaks. [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] in these epidemiological studies, coronavirus hku was generally only detected in fecal/intestinal samples. however, some covs, such as transmissible gastroenteritis cov (tgev)/porcine respiratory cov (prcv) of alphacoronavirus and bovine cov of betacoronavirus , could be detected consistently in both fecal and respiratory samples. , therefore, we hypothesized that coronavirus hku may also be present in respiratory samples of pigs, which has implications for its transmission and potential role in respiratory diseases and for the use of nasopharyngeal sampling as an alternative method of identifying infected pigs. to test this hypothesis, we performed a molecular epidemiology study on nasopharyngeal samples collected from pigs in hong kong. two complete genomes of the 'respiratory' coronavirus hku were sequenced, and comparative genomic and phylogenetic studies were performed. the implications of the presence of coronavirus hku in respiratory samples are also discussed. nasopharyngeal samples from pigs were collected in hong kong over a -month period (january -february ). these samples were obtained from slaughterhouses and pig farms in hong kong with the assistance of the veterinary public health section, food and environmental hygiene department; and the agriculture, fisheries and conservation department of the government of hong kong. immediately after sample collection, each nasopharyngeal swab was submerged in viral transport medium for viral transport and maintenance. rna extraction and reverse transcription viral rnas were extracted from the nasopharyngeal samples of pigs by using μl of inoculated viral transport medium for each sample and by utilizing the ez advanced xl system (qiagen, hilden, germany) and ez virus mini kit v . (qiagen) according to the manufacturer's protocol with rnase-free water as the eluent. reverse transcription (rt) was performed using the superscript iii reverse transcriptase (invitrogen, carlsbad, ca, usa) according to the manufacturer's protocol by random priming. coronavirus hku screening detection of coronavirus hku was performed by polymerase chain reaction (pcr) amplifying a -bp fragment of the rnadependent rna polymerase (rdrp) gene, using the specific primer pair lpw ( ′-aca cac ttg ctg taa cca aa- ′) and lpw ( ′-atc att aga gtc acc acg at- ′). pcr and dna sequencing were carried out following our previous publications with slight modification. , briefly, each pcr mixture contained pcr buffer ( mm of kcl, mm of tris-hcl at ph . and mm of mgcl ; applied biosystems, foster city, ca, usa), μm of each deoxynucleoside triphosphate (roche diagnostics, basel, switzerland), μm of each primer (invitrogen), . u of amplitag gold dna polymerase (applied biosystems) and cdna. the mixtures were subjected to thermocycles of °c for min, °c for min and °c for min, with an initial denaturation at °c for min and a final extension at °c for min for dna amplification using the geneamp pcr system automated thermal cycler (applied biosystems). standard precautions were taken to avoid contamination, and no falsepositive result was observed for the negative controls. pcr products were agarose gel-purified using the qiaquick gel extraction kit (qiagen). both strands of the pcr products were sequenced twice by the abi prism xl genetic analyzer (applied biosystems) using the two pcr primers. the genomes of two coronavirus hku strains detected in the nasopharyngeal samples of two different pigs were sequenced following our previous publications , with modifications. briefly, viral rnas were converted to cdnas using superscript iii reverse transcriptase with a combined random priming and oligo(dt) priming strategy. the cdnas were pcr-amplified by primers (supplementary tables s and s ) that were designed by multiple alignment of the genome sequences of other coronavirus hku strains with complete genomes available or from the results of the first and subsequent rounds of pcr-sequencing. pcrs were performed using the iproof high-fidelity pcr kit (bio-rad laboratories, hercules, ca, usa) according to the manufacturer's protocol, and dna sequencing was performed as mentioned above. when ambiguous peaks were observed consistently in the electropherograms after several attempts of pcr-sequencing for certain genomic regions, cloning followed by plasmid sequencing was performed according to our previous publication, except the zero blunt topo pcr cloning kit (invitrogen) was used to resolve the sequence ambiguities. pcrs using recombinant plasmids as templates were also performed to confirm that indels at mononucleotide polymeric regions were not the result of polymerase slippage. the ′ ends of the viral genomes were amplified and sequenced by the rapid amplification of cdna ends (race) using the smarter race ′/ ′ kit (clontech laboratories, mountain view, ca, usa) according to the manufacturer's protocol with the reverse primers lpw ( ′-tgg gta atg tgt ccg ctg acg ggc ggt g- ′), lpw ( ′-aga agt ggt gga tgg tca gag gaa cgg t- ′) and lpw ( ′-gtg gct ggt ttc cag gta atc ta- ′). the sequences of the pcr products were then assembled manually to obtain the genomes of the two nasopharyngeal strains. pairwise alignment was performed using bioedit . . (optimal global alignment) or emboss stretcher (nucleotide alignment); whereas multiple sequence alignment was performed using muscle . , where the aligned sequences were further manually inspected and edited. tests for substitution models and phylogenetic analysis by the maximum likelihood method were performed using mega . . . divergence times for the coronavirus hku strains were calculated based on the complete genome sequence data, utilizing the bayesian markov chain monte carlo method using beast . . with the substitution model gtr (general time-reversible model)+g (gammadistributed rate variation)+i (estimated proportion of invariable sites), a strict molecular clock, and a constant coalescent. fifty million generations were run with trees sampled every th generation to yield trees. convergence was assessed based on the effective sampling size after a % burn-in using tracer . . . the mean time to the most recent common ancestor (tmrca) and the highest posterior density (hpd) regions at % were calculated. the trees, after a % burn-in, were summarized as a single tree using treeannotator . . by choosing the tree with the maximum sum of posterior probabilities (maximum clade credibility) and viewed using figtree . . . the complete genome sequences of the two nasopharyngeal coronavirus hku strains were deposited into the international nucleotide sequence databases with accession numbers lc and lc . a total of nasopharyngeal samples from pigs were tested. rt-pcr for a -bp fragment of the rdrp gene of coronavirus hku was positive in ( . %) of the nasopharyngeal samples. the samples that tested positive were mostly collected during winter (december-march) ( figure ). dna sequencing showed that seven sequence variants were detected among the positive samples, and pairwise alignment showed that these seven sequence variants possessed . %- % sequence identity to the corresponding region in the rdrp gene of coronavirus hku strain hku - that we previously found in fecal samples of pigs in hong kong (supplementary figure s ). complete genome sequencing and genome analysis complete genome sequencing was performed for the coronavirus hku found in two of the positive nasopharyngeal samples (s n and s n) . excluding the ′ poly(a) tail, the genomes of s n and s n were - and nucleotides long, respectively. the genome organization of the two strains was the same as that of other coronavirus hku strains. the lengths of the seven open reading frames (orfs) of the two strains s n/ s n were / , , , , , and bp, respectively. the genomes of the two strains possessed . %- . % sequence identity to that of the representative isolate hku - . quasispecies were detected in one of the samples (s n) at the ′ genomic region via two independent nested pcrs targeting the nd- th bases of the genome using two different primer pairs for the first round and the same primer pair for the second round of reaction. for s n, direct sequencing of the pcr products yielded ambiguous peaks in the sequencing electropherograms, which could only be resolved after cloning (figure ). post-cloning dna sequencing revealed that there were six sequence variants, with four polymorphic sites, for this genomic region ( figure ) . two of the polymorphic sites, located at the th and th nucleotide positions, involved indels (Δt and Δa/c, respectively), whereas the other two polymorphic sites, located at the nd and th nucleotide positions, involved transition substitutions (t → c and g → a, respectively). additionally, pcr-dna sequencing using the recombinant plasmids as amplification templates did not generate the same sequence ambiguities observed in the pre-cloning experiment. phylogenetic analysis of the complete genomes of the two nasopharyngeal strains and other coronavirus hku strains showed that the outbreak strains in the united states possessed highly similar genome sequences and that they were all clustered together monophyletically, whereas the asian strains were more diverse and paraphyletic, with the lao and thai strains occupying the basal lineage; however, the south korean strain knu - was more similar to the us strains than to the other asian strains (figure and supplementary figure s the estimated mean evolutionary rate of the complete genome sequence data set was . × − ( % hpd: . - . × − ) substitutions per site per year, which is approximately . -fold higher than that estimated in a previous study. the root of the tree was september ( % hpd: june -march ). the tmrca of the diversity of coronavirus hku was dated to june ( % hpd: november -june ); and the tmrca of the thai/laos strains was traced back to september ( % hpd: may -january ). the tmrcas for the clade containing us/korean strains was estimated to be october ( % hpd: june -january ), which is slightly delayed compared with that estimated in a previous study. for the two nasopharyngeal strains characterized in this study (s n and s n) , they were estimated to have diverged from their respective mrcas in december ( % hpd: . six intra-strain quasispecies were found. post-cloning plasmid-dependent pcr-sequencing confirmed that the presence of indels at positions and was not due to polymerase slippage. quasispecies and were detected in both nested pcr using first round primers lpw /lpw and second round primers lpw /lpw as well as nested pcr using first round primers lpw /lpw and second round primers lpw /lpw . however, quasispecies and were only detected in nested pcr using first round primers lpw / lpw and second round primers lpw /lpw , whereas quasispecies and were only detected in nested pcr using first round primers lpw /lpw and second round primers lpw /lpw . coronavirus hku was detected in nasopharyngeal samples of pigs. although coronavirus hku has been widely detected in various locations around the pacific ocean, including canada, china, , , , hong kong, laos, , mexico, south korea, , thailand, , vietnam and the united states, [ ] [ ] [ ] [ ] [ ] [ ] , , , the virus has principally been found in fecal or intestinal specimens. there have been a few exceptional circumstances; in one study, the presence of coronavirus hku was reported in the blood, liver, lung and kidney of one pig, and in a few other studies, coronavirus hku was found to exist in the blood (n = ), mesenteric lymph node (n = ) and saliva (n = )/oral fluid (n = ) of pigs, , , implying that coronavirus hku can cause systemic infections in occasional cases. in this study, coronavirus hku was found in . % of the nasopharyngeal samples of pigs, which is similar to the . % positive rate of coronavirus hku in fecal samples of pigs that we reported previously. seasonal variation in the detection rate of coronavirus hku from pigs was noted, where most of the positive samples were collected in winter. this is similar to the pattern of seasonal variation in a surveillance study carried out in the united states, where the detection rate for coronavirus hku was much lower during summer. it has recently been confirmed that coronavirus hku is able to cause swine enteric infections by infecting gnotobiotic and conventional pigs with coronavirus hku . the detection of coronavirus hku in respiratory tracts of pigs has the following implications. first, in addition to enteric infections, coronavirus hku may be able to cause respiratory infections in pigs. second, in addition to fecal-oral transmission, the virus may be able to spread through the respiratory route. third, the presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of coronavirus hku infection. further studies will determine the full spectrum of clinical diseases and pathologies associated with coronavirus hku . from the data of the present study, both the 'enteric' and 'respiratory' coronavirus hku may possess similar properties. a number of animal covs possess dual or multiple tissue tropisms. for example, tgev, which is another enteropathogenic cov that infects pigs, could also be found in the nasopharynx of pigs as prcv, which is a deletion mutant of tgev. moreover, bovine cov is both an enteric and a respiratory pathogen in cattle. similar to tgev/ prcv, coronavirus hku is recovered from both respiratory and gastrointestinal samples. however, unlike tgev/prcv, in which there is a - nucleotide deletion at the ′ end of the spike (s) gene leading to a loss of - antigenic sites in prcv, comparative genome analysis of coronavirus hku from respiratory and fecal samples did not show any obvious difference in their s proteins or other parts of their genomes. phylogenetic analysis also did not reveal a separate clustering of fecal/intestinal and nasopharyngeal isolates ( figure ). further cell culture experiments are required to confirm whether all strains of this species possess intrinsic tropism to both enteric and respiratory tissues. this is also the first report of cov quasispecies in the ′untranslated region (utr). in one (s n) of the two coronavirus hku genomes that we sequenced in this study, variant sites were observed at four positions; two of them were due to nucleotide substitutions, and the other two were results of indels at mononucleotide polymeric regions ( th and th bases). these two indels were genuine variant sites instead of being due to polymerase slippage during the amplification process because recombinant plasmiddependent pcr-sequencing no longer resulted in sequence ambiguities in the electropherograms. although the existence of quasispecies has been reported in covs, the variant sites were found in coding regions or ′-utr. [ ] [ ] [ ] [ ] in the case of severe acute respiratory syndromerelated coronavirus, all of the variant sites observed in the quasispecies were located at the s gene. for bovine cov, one of the two strains with naturally occurring intra-isolate quasispecies had all seven variant sites located at orf a, whereas for the other strain with naturally occurring intra-isolate quasispecies, there were polymorphic sites scattered across orf a (n = ), orf b (n = ), kda-non-structural protein (nsp) gene (n = ), hemagglutinin esterase (he) gene (n = ), s gene (n = ), . kda-nsp gene (n = ), . kda-nsp gene (n = ), membrane (m) gene (n = ), nucleocapsid (n) gene (n = ) and ′-utr (n = ). similar to bovine cov, middle east respiratory syndrome-related coronavirus also possessed all the intra-host single nucleotide variations throughout its genome except the ′-utr. , in this study, all four variant sites ( Δt, t → c, g → a and Δa/c) were present in the ′-utr and were not located in the leader sequence or the transcription regulatory sequence. we speculate that the existence of quasispecies in covs may play a role in cov evolution, in addition to the more well-known high-recombination and mutation rates in cov genomes. virus taxonomy: ninth report of the international committee on taxonomy of viruses, international union of microbiological societies, virology division comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group c coronavirus discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus create new species in the family coronaviridae complete genome characterization of korean porcine deltacoronavirus strain kor/knu - / full-length genome sequence of porcine deltacoronavirus strain usa/ia/ / rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus complete genome sequence of strain sdcv/ usa/illinois / , a porcine deltacoronavirus from the united states detection and genetic characterization of deltacoronavirus in pigs porcine coronavirus hku detected in us states complete genome sequence of porcine coronavirus hku strain in from the united states full-length genome characterization of chinese porcine deltacoronavirus strain ch/sxd / porcine deltacoronavirus in mainland china isolation and characterization of porcine deltacoronavirus from pigs with diarrhea in the united states origin, evolution, and virulence of porcine deltacoronaviruses in the united states newly emerged porcine deltacoronavirus associated with diarrhoea in swine in china: identification, prevalence and full-length genome sequence analysis complete genome sequence of porcine deltacoronavirus strain ch/sichuan/s / from mainland china porcine deltacoronavirus: histological lesions and genetic characterization characterization and evolution of porcine deltacoronavirus in the united states detection and phylogenetic analysis of porcine deltacoronavirus in korean swine farms the first detection and full-length genome sequence of porcine deltacoronavirus isolated in lao pdr different lineage of porcine deltacoronavirus in thailand, vietnam and lao pdr in studies on the relationship between coronaviruses from the intestinal and respiratory tracts of calves porcine respiratory coronavirus: molecular features and virus-host interactions discovery of a novel coronavirus, china rattus coronavirus hku , from norway rats supports the murine origin of betacoronavirus and has implications for the ancestor of betacoronavirus lineage a discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in gammacoronavirus intra-genomic internal transcribed spacer region sequence heterogeneity and molecular diagnosis in clinical microbiology bioedit: a user-friendly biological sequence alignment editor and analysis program for windows / /nt the embl-ebi bioinformatics web and programmatic tools framework muscle: multiple sequence alignment with high accuracy and high throughput mega : molecular evolutionary genetics analysis version . bayesian phylogenetics with beauti and the beast . respiratory and fecal shedding of porcine respiratory coronavirus (prcv) in sentinel weaned pigs and sequence of the partial s-gene of the prcv isolates sars-associated coronavirus quasispecies in individual patients quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation middle east respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in saudi arabia middle east respiratory syndrome coronavirus intrahost populations are characterized by numerous high frequency variants comparative analysis of coronavirus hku genomes reveals a novel genotype and evidence of natural recombination in coronavirus hku kong. the funding sources had no role in study design, data collection, analysis, interpretation, or writing of the report. the authors alone are responsible for the content and the writing of the manuscript. the authors thank the staff from the veterinary public health section, food and environmental hygiene department as well as the agriculture, fisheries and conservation department of the hong kong government for their help in collecting the porcine nasopharyngeal samples. key: cord- -v kk i authors: dhama, kuldeep; khan, sharun; tiwari, ruchi; sircar, shubhankar; bhat, sudipta; malik, yashpal singh; singh, karam pal; chaicumpa, wanpen; bonilla-aldana, d. katterine; rodriguez-morales, alfonso j. title: coronavirus disease –covid- date: - - journal: clin microbiol rev doi: . /cmr. - sha: doc_id: cord_uid: v kk i in recent decades, several new diseases have emerged in different geographical areas, with pathogens including ebola virus, zika virus, nipah virus, and coronaviruses (covs). recently, a new type of viral infection emerged in wuhan city, china, and initial genomic sequencing data of this virus do not match with previously sequenced covs, suggesting a novel cov strain ( -ncov), which has now been termed severe acute respiratory syndrome cov- (sars-cov- ). although coronavirus disease (covid- ) is suspected to originate from an animal host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. compared to diseases caused by previously known human covs, covid- shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. compared to other emerging viruses, such as ebola virus, avian h n , sars-cov, and middle east respiratory syndrome coronavirus (mers-cov), sars-cov- has shown relatively low pathogenicity and moderate transmissibility. codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. early diagnosis by real-time pcr and next-generation sequencing has facilitated the identification of the pathogen at an early stage. since no antiviral drug or vaccine exists to treat or prevent sars-cov- , potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating sars-cov, mers-cov, and other emerging viral diseases. in this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus. o ver the past decades, coronaviruses (covs) have been associated with significant disease outbreaks in east asia and the middle east. the severe acute respiratory syndrome (sars) and the middle east respiratory syndrome (mers) began to emerge in and , respectively. recently, a novel coronavirus, severe acute respiratory syndrome coronavirus (sars-cov- ), causing coronavirus disease (covid- ) , emerged in late , and it has posed a global health threat, causing an ongoing pandemic in many countries and territories ( ) . health workers worldwide are currently making efforts to control further disease outbreaks caused by the novel cov (originally named -ncov), which was first identified in wuhan city, hubei province, china, on december . on february , the world health organization (who) announced the official designation for the current cov-associated disease to be covid- , caused by sars-cov- . the primary cluster of patients was found to be connected with the huanan south china seafood market in wuhan ( ) . covs belong to the family coronaviridae (subfamily coronavirinae), the members of which infect a broad range of hosts, producing symptoms and diseases ranging from the common cold to severe and ultimately fatal illnesses, such as sars, mers, and, presently, covid- . sars-cov- is considered one of the seven members of the cov family that infect humans ( ) , and it belongs to the same lineage of covs that causes sars; however, this novel virus is genetically distinct. until , six covs were known to infect humans, including human cov e (hcov- e), hcov-nl , hcov-oc , hcov-hku , sars-cov, and mers-cov. although sars-cov and mers-cov have resulted in outbreaks with high mortality, others remain associated with mild upper-respiratory-tract illnesses ( ) . newly evolved covs pose a high threat to global public health. the current emergence of covid- is the third cov outbreak in humans over the past decades ( ) . it is no coincidence that fan et al. predicted potential sars-or mers-like cov outbreaks in china following pathogen transmission from bats ( ) . covid- emerged in china and spread rapidly throughout the country and, subsequently, to other countries. due to the severity of this outbreak and the potential of spreading on an international scale, the who declared a global health emergency on january ; subsequently, on march , they declared it a pandemic situation. at present, we are not in a position to effectively treat covid- , since neither approved vaccines nor specific antiviral drugs for treating human cov infections are available ( ) ( ) ( ) . most nations are currently making efforts to prevent the further spreading of this potentially deadly virus by implementing preventive and control strategies. in domestic animals, infections with covs are associated with a broad spectrum of furthermore, it acts as a critical factor for tissue tropism and the determination of host range ( ) . notably, s protein is one of the vital immunodominant proteins of covs capable of inducing host immune responses ( ) . the ectodomains in all covs s proteins have similar domain organizations, divided into two subunits, s and s ( ) . the first one, s , helps in host receptor binding, while the second one, s , accounts for fusion. the former (s ) is further divided into two subdomains, namely, the n-terminal domain (ntd) and c-terminal domain (ctd). both of these subdomains act as receptorbinding domains, interacting efficiently with various host receptors ( ) . the s ctd contains the receptor-binding motif (rbm). in each coronavirus spike protein, the trimeric s locates itself on top of the trimeric s stalk ( ) . recently, structural analyses of the s proteins of covid- have revealed amino acid substitutions within a , -amino-acid stretch ( ) . six substitutions are located in the rbd (amino acids to ), while four substitutions are in the rbm at the ctd of the s domain ( ) . of note, no amino acid change is seen in the rbm, which binds directly to the angiotensinconverting enzyme- (ace ) receptor in sars-cov ( , ) . at present, the main emphasis is knowing how many differences would be required to change the host tropism. sequence comparison revealed nonsynonymous changes between the early sequence of sars-cov- and the later isolates of sars-cov. the changes were found scattered over the genome of the virus, with nine substitutions in orf ab, orf ( substitutions), the spike gene ( substitutions) , and orf a (single substitution) ( ) . notably, the same nonsynonymous changes were found in a familial cluster, indicating that the viral evolution happened during person-to-person transmission ( , ) . such adaptive evolution events are frequent and constitute a constantly ongoing process once the virus spreads among new hosts ( ) . even though no functional changes occur in the virus associated with this adaptive evolution, close monitoring of the viral mutations that occur during subsequent human-to-human transmission is warranted. the m protein is the most abundant viral protein present in the virion particle, giving a definite shape to the viral envelope ( ) . it binds to the nucleocapsid and acts as a central organizer of coronavirus assembly ( ) . coronavirus m proteins are highly diverse in amino acid contents but maintain overall structural similarity within different genera ( ) . the m protein has three transmembrane domains, flanked by a short amino terminus outside the virion and a long carboxy terminus inside the virion ( ) . overall, the viral scaffold is maintained by m-m interaction. of note, the m protein of sars-cov- does not have an amino acid substitution compared to that of sars-cov ( ) . the coronavirus e protein is the most enigmatic and smallest of the major structural proteins ( ) . it plays a multifunctional role in the pathogenesis, assembly, and release of the virus ( ) . it is a small integral membrane polypeptide that acts as a viroporin (ion channel) ( ) . the inactivation or absence of this protein is related to the altered virulence of coronaviruses due to changes in morphology and tropism ( ) . the e protein consists of three domains, namely, a short hydrophilic amino terminal, a large hydrophobic transmembrane domain, and an efficient c-terminal domain ( ) . the sars-cov- e protein reveals a similar amino acid constitution without any substitution ( ) . the n protein of coronavirus is multipurpose. among several functions, it plays a role in complex formation with the viral genome, facilitates m protein interaction needed during virion assembly, and enhances the transcription efficiency of the virus ( , ) . it contains three highly conserved and distinct domains, namely, an ntd, an rna-binding domain or a linker region (lkr), and a ctd ( ) . the ntd binds with the = end of the viral genome, perhaps via electrostatic interactions, and is highly diverged both in length and sequence ( ) . the charged lkr is serine and arginine rich and is also known as the sr (serine and arginine) domain ( ) . the lkr is capable of direct interaction with in vitro rna interaction and is responsible for cell signaling ( , ) . it also modulates the antiviral response of the host by working as an antagonist for interferon (ifn) and rna interference ( ) . compared to that of sars-cov, the n protein of sars-cov- possess five amino acid mutations, where two are in the intrinsically dispersed region (idr; positions and ) , one each in the ntd (position ), lkr (position ), and ctd (position ) ( ) . besides the important structural proteins, the sars-cov- genome contains nsps, nsp to nsp and nsp to nsp , and accessory proteins ( a, b, p , a, b, b, b, and orf ) ( ) . all these proteins play a specific role in viral replication ( ) . unlike the accessory proteins of sars-cov, sars-cov- does not contain a protein and has a longer b and shorter b protein ( ) . the nsp , nsp , envelope, matrix, and p and b accessory proteins have not been detected with any amino acid substitutions compared to the sequences of other coronaviruses ( ) . the virus structure of sars-cov- is depicted in fig. . sequence percent similarity analysis. we assessed the nucleotide percent similarity using the megalign software program, where the similarity between the novel sars-cov- isolates was in the range of . % to %. among the other serbecovirus cov sequences, the novel sars-cov- sequences revealed the highest similarity to bat-sl-cov, with nucleotide percent identity ranges between . and . %. meanwhile, earlier reported sars-covs showed . to . % similarity to sars-cov- at the nucleotide level. further, the nucleotide percent similarity was . %, . % to . %, . % to . %, and . % to . % to the other four subgenera, namely, hibecovirus, nobecovirus, merbecovirus, and embecovirus, respectively. the percent similarity index of current outbreak isolates indicates a close relationship between sars-cov- isolates and bat-sl-cov, indicating a common origin. however, particular pieces of evidence based on further complete genomic analysis of current isolates are necessary to draw any conclusions, although it was ascertained that the current novel sars-cov- isolates belong to the subgenus sarbecovirus in the diverse range of betacoronaviruses. their possible ancestor was hypothesized to be from bat cov strains, wherein bats might have played a crucial role in harboring this class of viruses. splitstree phylogeny analysis. in the unrooted phylogenetic tree of different betacoronaviruses based on the s protein, virus sequences from different subgenera grouped into separate clusters. sars-cov- sequences from wuhan and other countries exhibited a close relationship and appeared in a single cluster (fig. ). the covs from the subgenus sarbecovirus appeared jointly in splitstree and divided into three subclusters, namely, sars-cov- , bat-sars-like-cov (bat-sl-cov), and sars-cov (fig. ) . in the case of other subgenera, like merbecovirus, all of the sequences grouped clinical microbiology reviews than italy. a john hopkins university web platform has provided daily updates on the basic epidemiology of the covid- outbreak (https://gisanddata.maps.arcgis.com/ apps/opsdashboard/index.html#/bda fd b e ecf ) ( ) . covid- has also been confirmed on a cruise ship, named diamond princess, quarantined in japanese waters (port of yokohama), as well as on other cruise ships around the world ( ) (fig. ) . the significant events of the sars-cov- /covid- virus outbreak occurring since december are presented as a timeline in fig. . at the beginning, china experienced the majority of the burden associated with covid- in the form of disease morbidity and mortality ( ), but over time the covid- menace moved to europe, particularly italy and spain, and now the united states has the highest number of confirmed cases and deaths. the covid- outbreak has also been associated with severe economic impacts globally due to the sudden interruption of global trade and supply chains that forced multinational companies to make decisions that led to significant economic losses ( ) . the recent increase in the number of confirmed critically ill patients with covid- has already surpassed the intensive care supplies, limiting intensive care services to only a small portion of critically ill patients ( ) . this might also have contributed to the increased case fatality rate observed in the covid- outbreak. the novel coronavirus was identified within month ( days) of the outbreak. this is impressively fast compared to the time taken to identify sars-cov reported in foshan, guangdong province, china ( days) ( ) . immediately after the confirmation of viral etiology, the chinese virologists rapidly released the genomic sequence of sars-cov- , which played a crucial role in controlling the spread of this newly emerged novel coronavirus to other parts of the world ( ) . the possible origin of sars-cov- and the first mode of disease transmission are not yet identified ( ) . analysis of the initial cluster of infections suggests that the infected individuals had a common exposure point, a seafood market in wuhan, hubei province, china (fig. ). the restaurants of this market are well-known for providing different types of wild animals for human consumption ( ) . the huanan south china seafood market also sells live animals, such as poultry, bats, snakes, and marmots ( ) . this might be the point where zoonotic (animal-to-human) transmission occurred ( ) . although sars-cov- is alleged to have originated from an animal host (zoonotic origin) with further humanto-human transmission (fig. ), the likelihood of foodborne transmission should be ruled out with further investigations, since it is a latent possibility ( ). additionally, other clinical microbiology reviews potential and expected routes would be associated with transmission, as in other respiratory viruses, by direct contact, such as shaking contaminated hands, or by direct contact with contaminated surfaces (fig. ) . still, whether blood transfusion and organ transplantation ( ) , as well as transplacental and perinatal routes, are possible routes for sars-cov- transmission needs to be determined (fig. ). from experience with several outbreaks associated with known emerging viruses, higher pathogenicity of a virus is often associated with lower transmissibility. compared to emerging viruses like ebola virus, avian h n , sars-cov, and mers-cov, sars-cov- has relatively lower pathogenicity and moderate transmissibility ( ) . the risk of death among individuals infected with covid- was calculated using the infection fatality risk (ifr). the ifr was found to be in the range of . % to . %, which is comparable to that of a previous asian influenza pandemic ( to ) ( , ) . notably, the reanalysis of the covid- pandemic curve from the initial cluster of cases pointed to considerable human-to-human transmission. it is opined that the exposure history of sars-cov- at the wuhan seafood market originated from humanto-human transmission rather than animal-to-human transmission ( ) ; however, in light of the zoonotic spillover in covid- , is too early to fully endorse this idea ( ). following the initial infection, human-to-human transmission has been observed with a preliminary reproduction number (r ) estimate of . to . ( , ) , and recently it is estimated to be . to . ( ) . in another study, the average reproductive number of covid- was found to be . , which is significantly higher than the initial who estimate of . to . ( ) . it is too early to obtain the exact r value, since there is a possibility of bias due to insufficient data. the higher r value is indicative of the more significant potential of sars-cov- transmission in a susceptible population. this is not the first time where the culinary practices of china have been blamed for the origin of novel coronavirus infection in humans. previously, the animals present in the liveanimal market were identified to be the intermediate hosts of the sars outbreak in china ( ) . several wildlife species were found to harbor potentially evolving coronavirus strains that can overcome the species barrier ( ) . one of the main principles of chinese food culture is that live-slaughtered animals are considered more nutritious ( ) . after months of struggle that lasted from december to march , the covid- situation now seems under control in china. the wet animal markets have reopened, and people have started buying bats, dogs, cats, birds, scorpions, badgers, rabbits, pangolins (scaly anteaters), minks, soup from palm civet, ostriches, hamsters, snapping turtles, ducks, fish, siamese crocodiles, and other animal meats without any fear of covid- . the chinese government is encouraging people to feel they can return to normalcy. however, this could be a risk, as it has been mentioned in advisories that people should avoid contact with live-dead animals as much as possible, as sars-cov- has shown zoonotic spillover. additionally, we cannot rule out the possibility of new mutations in the same virus being closely related to contact with both animals and humans at the market ( ) . in january , china imposed a temporary ban on the sale of live-dead animals in wet markets. however, now hundreds of such wet markets have been reopened without optimizing standard food safety and sanitation practices ( ) . with china being the most populated country in the world and due to its domestic and international food exportation policies, the whole world is now facing the menace of covid- , including china itself. wet markets of live-dead animals do not maintain strict food hygienic practices. fresh blood splashes are present everywhere, on the floor and tabletops, and such food customs could encourage many pathogens to adapt, mutate, and jump the species barrier. as a result, the whole world is suffering from novel sars-cov- , with more than , , cases and , deaths across the globe. there is an urgent need for a rational international campaign against the unhealthy food practices of china to encourage the sellers to increase hygienic food practices or close the crude live-dead animal wet markets. there is a need to modify food policies at national and international levels to avoid further life threats and clinical microbiology reviews economic consequences from any emerging or reemerging pandemic due to close animal-human interaction ( ) . even though individuals of all ages and sexes are susceptible to covid- , older people with an underlying chronic disease are more likely to become severely infected ( ) . recently, individuals with asymptomatic infection were also found to act as a source of infection to susceptible individuals ( ) . both the asymptomatic and symptomatic patients secrete similar viral loads, which indicates that the transmission capacity of asymptomatic or minimally symptomatic patients is very high. thus, sars-cov- transmission can happen early in the course of infection ( ) . atypical clinical manifestations have also been reported in covid- in which the only reporting symptom was fatigue. such patients may lack respiratory signs, such as fever, cough, and sputum ( ) . hence, the clinicians must be on the look-out for the possible occurrence of atypical clinical manifestations to avoid the possibility of missed diagnosis. the early transmission ability of sars-cov- was found to be similar to or slightly higher than that of sars-cov, reflecting that it could be controlled despite moderate to high transmissibility ( ) . increasing reports of sars-cov- in sewage and wastewater warrants the need for further investigation due to the possibility of fecal-oral transmission. sars-cov- present in environmental compartments such as soil and water will finally end up in the wastewater and sewage sludge of treatment plants ( ) . therefore, we have to reevaluate the current wastewater and sewage sludge treatment procedures and introduce advanced techniques that are specific and effective against sars-cov- . since there is active shedding of sars-cov- in the stool, the prevalence of infections in a large population can be studied using wastewater-based epidemiology. recently, reverse transcription-quantitative pcr (rt-qpcr) was used to enumerate the copies of sars-cov- rna concentrated from wastewater collected from a wastewater treatment plant ( ) . the calculated viral rna copy numbers determine the number of infected individuals. the increasing reports of virus shedding via the fecal route warrants the introduction of negative fecal viral nucleic acid test results as one of the additional discharge criteria in laboratory-confirmed cases of covid- ( ) . the covid- pandemic does not have any novel factors, other than the genetically unique pathogen and a further possible reservoir. the cause and the likely future outcome are just repetitions of our previous interactions with fatal coronaviruses. the only difference is the time of occurrence and the genetic distinctness of the pathogen involved. mutations on the rbd of covs facilitated their capability of infecting newer hosts, thereby expanding their reach to all corners of the world ( ) . this is a potential threat to the health of both animals and humans. advanced studies using bayesian phylogeographic reconstruction identified the most probable origin of sars-cov- as the bat sars-like coronavirus, circulating in the rhinolophus bat family ( ) . phylogenetic analysis of whole-genome sequences of sars-cov- showed that they are related to two covs of bat origin, namely, bat-sl-covzc and bat-sl-covzxc , which were reported during in china ( ) . it was reported that sars-cov- had been confirmed to use ace as an entry receptor while exhibiting an rbd similar to that of sars-cov ( , , , ) . several countries have provided recommendations to their people traveling to china ( , ) . compared to the previous coronavirus outbreaks caused by sars-cov and mers-cov, the efficiency of sars-cov- human-to-human transmission was thought to be less. this assumption was based on the finding that health workers were affected less than they were in previous outbreaks of fatal coronaviruses ( ) . superspreading events are considered the main culprit for the extensive transmission of sars and mers ( , ) . almost half of the mers-cov cases reported in saudi arabia are of secondary origin that occurred through contact with infected asymptomatic or symptomatic individuals through human-tohuman transmission ( ) . the occurrence of superspreading events in the covid- outbreak cannot be ruled out until its possibility is evaluated. like sars and mers, covid- can also infect the lower respiratory tract, with milder symptoms ( ) . the basic reproduction number of covid- has been found to be in the range of . to . based on real-time reports and . to . based on predicted infected cases ( ) . coronavirus infection in humans is commonly associated with mild to severe respiratory diseases, with high fever, severe inflammation, cough, and internal organ dysfunction that can even lead to death ( ) . most of the identified coronaviruses cause the common cold in humans. however, this changed when sars-cov was identified, paving the way for severe forms of the disease in humans ( ) . our previous experience with the outbreaks of other coronaviruses, like sars and mers, suggests that the mode of transmission in covid- as mainly human-to-human transmission via direct contact, droplets, and fomites ( ) . recent studies have demonstrated that the virus could remain viable for hours in aerosols and up to days on surfaces; thus, aerosol and fomite contamination could play potent roles in the transmission of sars-cov- ( ) . the immune response against coronavirus is vital to control and get rid of the infection. however, maladjusted immune responses may contribute to the immunopathology of the disease, resulting in impairment of pulmonary gas exchange. understanding the interaction between covs and host innate immune systems could enlighten our understanding of the lung inflammation associated with this infection ( ) . sars is a viral respiratory disease caused by a formerly unrecognized animal cov that originated from the wet markets in southern china after adapting to the human host, thereby enabling transmission between humans ( ) . the sars outbreak reported in to had , confirmed cases with total deaths ( . %) ( ) . the outbreak severely affected the asia pacific region, especially mainland china ( ) . even though the case fatality rate (cfr) of sars-cov- (covid- ) is lower than that of sars-cov, there exists a severe concern linked to this outbreak due to its epidemiological similarity to influenza viruses ( , ) . this can fail the public health system, resulting in a pandemic ( ) . mers is another respiratory disease that was first reported in saudi arabia during the year . the disease was found to have a cfr of around % ( ) . the analysis of available data sets suggests that the incubation period of sars-cov- , sars-cov, and mers-cov is in almost the same range. the longest predicted incubation time of sars-cov- is days. hence, suspected individuals are isolated for days to avoid the risk of further spread ( ) . even though a high similarity has been reported between the genome sequence of the new coronavirus (sars-cov- ) and sars-like covs, the comparative analysis recognized a furin-like cleavage site in the sars-cov- s protein that is missing from other sars-like covs ( ) . the furin-like cleavage site is expected to play a role in the life cycle of the virus and disease pathogenicity and might even act as a therapeutic target for furin inhibitors. the highly contagious nature of sars-cov- compared to that of its predecessors might be the result of a stabilizing mutation that occurred in the endosome-associated-protein-like domain of nsp protein. similarly, the destabilizing mutation near the phosphatase domain of nsp proteins in sars-cov- could indicate a potential mechanism that differentiates it from other covs ( ) . even though the cfr reported for covid- is meager compared to those of the previous sars and mers outbreaks, it has caused more deaths than sars and mers combined ( ) . possibly related to the viral pathogenesis is the recent finding of an -nucleotide (nt) deletion in orf , which appears to reduce the replicative fitness of the virus and leads to attenuated phenotypes of sars-cov- ( ) . coronavirus is the most prominent example of a virus that has crossed the species barrier twice from wild animals to humans during sars and mers outbreaks ( , ) . the possibility of crossing the species barrier for the third time has also been suspected in the case of sars-cov- (covid- ) . bats are recognized as a possible natural reservoir host of both sars-cov and mers-cov infection. in contrast, the possible intermediary host is the palm civet for sars-cov and the dromedary camel for mers-cov infection ( ) . bats are considered the ancestral hosts for both sars and mers ( ) . bats are also considered the reservoir host of human coronaviruses like clinical microbiology reviews hcov- e and hcov-nl ( ) . in the case of covid- , there are two possibilities for primary transmission: it can be transmitted either through intermediate hosts, similar to that of sars and mers, or directly from bats ( ) . the emergence paradigm put forward in the sars outbreak suggests that sars-cov originated from bats (reservoir host) and later jumped to civets (intermediate host) and incorporated changes within the receptor-binding domain (rbd) to improve binding to civet ace . this civetadapted virus, during their subsequent exposure to humans at live markets, promoted further adaptations that resulted in the epidemic strain ( ) . transmission can also occur directly from the reservoir host to humans without rbd adaptations. the bat coronavirus that is currently in circulation maintains specific "poised" spike proteins that facilitate human infection without the requirement of any mutations or adaptations ( ) . altogether, different species of bats carry a massive number of coronaviruses around the world ( ) . the high plasticity in receptor usage, along with the feasibility of adaptive mutation and recombination, may result in frequent interspecies transmission of coronavirus from bats to animals and humans ( ) . the pathogenesis of most bat coronaviruses is unknown, as most of these viruses are not isolated and studied ( ) . hedgehog coronavirus hku , a betacoronavirus, has been identified from amur hedgehogs in china. studies show that hedgehogs are the reservoir of betacoronavirus, and there is evidence of recombination ( ) . the current scientific evidence available on mers infection suggests that the significant reservoir host, as well as the animal source of mers infection in humans, is the dromedary camels ( ) . the infected dromedary camels may not show any visible signs of infection, making it challenging to identify animals actively excreting mers-cov that has the potential to infect humans. however, they may shed mers-cov through milk, urine, feces, and nasal and eye discharge and can also be found in the raw organs ( ) . in a study conducted to evaluate the susceptibility of animal species to mers-cov infection, llamas and pigs were found to be susceptible, indicating the possibility of mers-cov circulation in animal species other than dromedary camels ( ) . following the outbreak of sars in china, sars-cov-like viruses were isolated from himalayan palm civets (paguma larvata) and raccoon dogs (nyctereutes procyonoides) found in a live-animal market in guangdong, china. the animal isolates obtained from the live-animal market retained a -nucleotide sequence that was not present in most of the human isolates ( ) . these findings were critical in identifying the possibility of interspecies transmission in sars-cov. the higher diversity and prevalence of bat coronaviruses in this region compared to those in previous reports indicate a host/ pathogen coevolution. sars-like coronaviruses also have been found circulating in the chinese horseshoe bat (rhinolophus sinicus) populations. the in vitro and in vivo studies carried out on the isolated virus confirmed that there is a potential risk for the reemergence of sars-cov infection from the viruses that are currently circulating in the bat population ( ) . the disease caused by sars-cov- is also named severe specific contagious pneumonia (sscp), wuhan pneumonia, and, recently, covid- ( ) . compared to sars-cov, sars-cov- has less severe pathogenesis but has superior transmission capability, as evidenced by the rapidly increasing number of covid- cases ( ) . the incubation period of sars-cov- in familial clusters was found to be to days ( ) . the mean incubation period of covid- was found to be . days, ranging from . to . days ( ) . among an early affected group of patients, years was the median age, of which more males were affected ( ) . similar to sars and mers, the severity of this ncov is high in age groups above years ( , ) . symptoms of covid- include fever, cough, myalgia or fatigue, and, less commonly, headache, hemoptysis, and diarrhea ( , ) . compared to the sars-cov- -infected patients in wuhan during the initial stages of the outbreak, only mild symptoms were noticed in those patients that are infected by human-to-human transmission ( ) . the initial trends suggested that the mortality associated with covid- was less than that of previous outbreaks of sars ( ) . the updates obtained from countries like china, japan, thailand, and south korea indicated that the covid- patients had relatively mild manifestations compared to those with sars and mers ( ). regardless of the coronavirus type, immune cells, like mast cells, that are present in the submucosa of the respiratory tract and nasal cavity are considered the primary barrier against this virus ( ) . advanced in-depth analysis of the genome has identified amino acid substitutions between the amino acid sequences of sars-cov- and the sars/sarslike coronaviruses. these differences in the amino acid sequences might have contributed to the difference in the pathogenic divergence of sars-cov- ( ) . further research is required to evaluate the possible differences in tropism, pathogenesis, and transmission of this novel agent associated with this change in the amino acid sequence. with the current outbreak of covid- , there is an expectancy of a significant increase in the number of published studies about this emerging coronavirus, as occurred with sars and mers ( ) . sars-cov- invades the lung parenchyma, resulting in severe interstitial inflammation of the lungs. this is evident on computed tomography (ct) images as ground-glass opacity in the lungs. this lesion initially involves a single lobe but later expands to multiple lung lobes ( ) . the histological assessment of lung biopsy samples obtained from covid- -infected patients revealed diffuse alveolar damage, cellular fibromyxoid exudates, hyaline membrane formation, and desquamation of pneumocytes, indicative of acute respiratory distress syndrome ( ) . it was also found that the sars-cov- infected patients often have lymphocytopenia with or without leukocyte abnormalities. the degree of lymphocytopenia gives an idea about disease prognosis, as it is found to be positively correlated with disease severity ( ) . pregnant women are considered to have a higher risk of getting infected by covid- . the coronaviruses can cause adverse outcomes for the fetus, such as intrauterine growth restriction, spontaneous abortion, preterm delivery, and perinatal death. nevertheless, the possibility of intrauterine maternal-fetal transmission (vertical transmission) of covs is low and was not seen during either the sars-or mers-cov outbreak ( ) . however, there has been concern regarding the impact of sars-cov- /covid- on pregnancy. researchers have mentioned the probability of in utero transmission of novel sars-cov- from covid- -infected mothers to their neonates in china based upon the rise in igm and igg antibody levels and cytokine values in the blood obtained from newborn infants immediately postbirth; however, rt-pcr failed to confirm the presence of sars-cov- genetic material in the infants ( ) . recent studies show that at least in some cases, preterm delivery and its consequences are associated with the virus. nonetheless, some cases have raised doubts for the likelihood of vertical transmission ( ) ( ) ( ) ( ) . covid- infection was associated with pneumonia, and some developed acute respiratory distress syndrome (ards). the blood biochemistry indexes, such as albumin, lactate dehydrogenase, c-reactive protein, lymphocytes (percent), and neutrophils (percent) give an idea about the disease severity in covid- infection ( ) . during covid- , patients may present leukocytosis, leukopenia with lymphopenia ( ), hypoalbuminemia, and an increase of lactate dehydrogenase, aspartate transaminase, alanine aminotransferase, bilirubin, and, especially, d-dimer ( ) . middle-aged and elderly patients with primary chronic diseases, especially high blood pressure and diabetes, were found to be more susceptible to respiratory failure and, therefore, had poorer prognoses. providing respiratory support at early stages improved the disease prognosis and facilitated recovery ( ) . the ards in covid- is due to the occurrence of cytokine storms that results in exaggerated immune response, immune regulatory network imbalance, and, finally, multiple-organ failure ( ) . in addition to the exaggerated inflammatory response seen in patients with covid- pneumonia, the bile duct epithelial cell-derived hepatocytes upregulate ace expression in liver tissue by compensatory proliferation that might result in hepatic tissue injury ( ) . coronavirus can cause disease in several species of domestic and wild animals, as well as humans ( ) . the different animal species that are infected with cov include horses, camels, cattle, swine, dogs, cats, rodents, birds, ferrets, minks, bats, rabbits, snakes, and various other wild animals ( , , , , , , ) . coronavirus infection is linked to different kinds of clinical manifestations, varying from enteritis in cows and pigs, upper respiratory disease in chickens, and fatal respiratory infections in humans ( ) . among the cov genera, alphacoronavirus and betacoronavirus infect mammals, while gammacoronavirus and deltacoronavirus mainly infect birds, fishes, and, sometimes, mammals ( , , ) . several novel coronaviruses that come under the genus deltacoronavirus have been discovered in the past from birds, like wigeon coronavirus hku , bulbul coronavirus hku , munia coronavirus hku , white-eye coronavirus hku , night-heron coronavirus hku , and common moorhen coronavirus hku , as well as from pigs (porcine coronavirus hku ) ( , ) . transmissible gastroenteritis virus (tgev), porcine epidemic diarrhea virus (pedv), and porcine hemagglutinating encephalomyelitis virus (phev) are some of the coronaviruses of swine. among them, tgev and pedv are responsible for causing severe gastroenteritis in young piglets with noteworthy morbidity and mortality. infection with phev also causes enteric infection but can cause encephalitis due to its ability to infect the nervous system ( ) . bovine coronaviruses (bocovs) are known to infect several domestic and wild ruminants ( ) . bocov inflicts neonatal calf diarrhea in adult cattle, leading to bloody diarrhea (winter dysentery) and respiratory disease complex (shipping fever) in cattle of all age groups ( ) . bocov-like viruses have been noted in humans, suggesting its zoonotic potential as well ( ) . feline enteric and feline infectious peritonitis (fip) viruses are the two major feline covs ( ) , where feline covs can affect the gastrointestinal tract, abdominal cavity (peritonitis), respiratory tract, and central nervous system ( ) . canines are also affected by covs that fall under different genera, namely, canine enteric coronavirus in alphacoronavirus and canine respiratory coronavirus in betacoronavirus, affecting the enteric and respiratory tract, respectively ( , ) . ibv, under gammacoronavirus, causes diseases of respiratory, urinary, and reproductive systems, with substantial economic losses in chickens ( , ) . in small laboratory animals, mouse hepatitis virus, rat sialodacryoadenitis coronavirus, and guinea pig and rabbit coronaviruses are the major covs associated with disease manifestations like enteritis, hepatitis, and respiratory infections ( , ) . swine acute diarrhea syndrome coronavirus (sads-cov) was first identified in suckling piglets having severe enteritis and belongs to the genus alphacoronavirus ( ) . the outbreak was associated with considerable scale mortality of piglets ( , deaths) across four farms in china ( ) . the virus isolated from the piglets was almost identical to and had % genomic similarity with horseshoe bat (rhinolophus species) coronavirus hku , suggesting a bat origin of the pig virus ( , , ) . it is also imperative to note that the sads-cov outbreak started in guangdong province, near the location of the sars pandemic origin ( ) . before this outbreak, pigs were not known to be infected with bat-origin coronaviruses. this indicates that the bat-origin coronavirus jumped to pig by breaking the species barrier. the next step of this jump might not end well, since pigs are considered the mixing vessel for influenza a viruses due to their ability to be infected by both human and avian influenza a viruses ( ) . similarly, they may act as the mixing vessel for coronaviruses, since they are in frequent contact with both humans and multiple wildlife species. additionally, pigs are also found to be susceptible to infection with human sars-cov and mers-cov, making this scenario a nightmare ( , ) . it is only a matter of time before another zoonotic coronavirus results in an epidemic by jumping the so-called species barrier ( ) . the host spectrum of coronavirus increased when a novel coronavirus, namely, sw , was recognized in the liver tissue of a captive beluga whale (delphinapterus leucas) ( ) . in recent decades, several novel coronaviruses were identified from different animal species. bats can harbor these viruses without manifesting any clinical disease but are persistently infected ( ) . they are the only mammals with the capacity for self-powered flight, which enables them to migrate long distances, unlike land mammals. bats are distributed worldwide and also account for about a fifth of all mammalian species ( ) . this makes them the ideal reservoir host for many viral agents and also the source of novel coronaviruses that have yet to be identified. it has become a necessity to study the diversity of coronavirus in the bat population to prevent future outbreaks that could jeopardize livestock and public health. the repeated outbreaks caused by bat-origin coronaviruses calls for the development of efficient molecular surveillance strategies for studying betacoronavirus among animals ( ) , especially in the rhinolophus bat family ( ) . chinese bats have high commercial value, since they are used in traditional chinese medicine (tcm). therefore, the handling of bats for trading purposes poses a considerable risk of transmitting zoonotic cov epidemics ( ) . due to the possible role played by farm and wild animals in sars-cov- infection, the who, in their novel coronavirus (covid- ) situation report, recommended the avoidance of unprotected contact with both farm and wild animals ( ) . the live-animal markets, like the one in guangdong, china, provides a setting for animal coronaviruses to amplify and to be transmitted to new hosts, like humans ( ) . such markets can be considered a critical place for the origin of novel zoonotic diseases and have enormous public health significance in the event of an outbreak. bats are the reservoirs for several viruses; hence, the role of bats in the present outbreak cannot be ruled out ( ) . in a qualitative study conducted for evaluating the zoonotic risk factors among rural communities of southern china, the frequent human-animal interactions along with the low levels of environmental biosecurity were identified as significant risks for the emergence of zoonotic disease in local communities ( , ) . the comprehensive sequence analysis of the sars-cov- rna genome identified that the cov from wuhan is a recombinant virus of the bat coronavirus and another coronavirus of unknown origin. the recombination was found to have happened within the viral spike glycoprotein, which recognizes the cell surface receptor. further analysis of the genome based on codon usage identified the snake as the most probable animal reservoir of sars-cov- ( ) . contrary to these findings, another genome analysis proposed that the genome of sars-cov- is % identical to bat coronavirus, reflecting its origin from bats ( ) . the involvement of bat-derived materials in causing the current outbreak cannot be ruled out. high risk is involved in the production of bat-derived materials for tcm practices involving the handling of wild bats. the use of bats for tcm practices will remain a severe risk for the occurrence of zoonotic coronavirus epidemics in the future ( ) . furthermore, the pangolins are an endangered species of animals that harbor a wide variety of viruses, including coronaviruses ( ) . the coronavirus isolated from malayan pangolins (manis javanica) showed a very high amino acid identity with covid- at e ( %), m ( . %), n ( . %), and s genes ( . %). the rbd of s protein in cov isolated from pangolin was almost identical (one amino acid difference) to that of sars-cov- . a comparison of the genomes suggests recombination between pangolin-cov-like viruses with the bat-cov-ratg -like virus. all this suggests the potential of pangolins to act as the intermediate host of sars-cov- ( ) . human-wildlife interactions, which are increasing in the context of climate change ( ) , are further considered high risk and responsible for the emergence of sars-cov. covid- is also suspected of having a similar mode of origin. hence, to prevent the occurrence of another zoonotic spillover ( ), exhaustive coordinated efforts are needed to identify the high-risk pathogens harbored by wild animal populations, conducting surveillance among the people who are susceptible to zoonotic spillover events ( ) , and to improve the biosecurity measures associated with the wildlife trade ( ) . the serological surveillance studies conducted in people living in proximity to bat caves had earlier identified the serological confirmation of sars-related covs in humans. people clinical microbiology reviews living at the wildlife-human interface, mainly in rural china, are regularly exposed to sars-related covs ( ) . these findings will not have any significance until a significant outbreak occurs due to a virus-like sars-cov- . there is a steady increase in the reports of covid- in companion and wild animals around the world. further studies are required to evaluate the potential of animals (especially companion animals) to serve as an efficient reservoir host that can further alter the dynamics of human-to-human transmission ( ) . to date, two pet dogs (hong kong) and four pet cats (one each from belgium and hong kong, two from the united states) have tested positive for sars-cov- ( ) . the world organization for animal health (oie) has confirmed the diagnosis of covid- in both dogs and cats due to human-to-animal transmission ( ) . the similarity observed in the gene sequence of sars-cov- from an infected pet owner and his dog further confirms the occurrence of human-to-animal transmission ( ) . even though asymptomatic, feline species should be considered a potential transmission route from animals to humans ( ) . however, currently, there are no reports of sars-cov- transmission from felines to human beings. based on the current evidence, we can conclude that cats are susceptible to sars-cov- and can get infected by human beings. however, evidence of cat-to-human transmission is lacking and requires further studies ( ) . rather than waiting for firmer evidence on animal-to-human transmission, necessary preventive measures are advised, as well as following social distancing practices among companion animals of different households ( ) . one of the leading veterinary diagnostic companies, idexx, has conducted large-scale testing for covid- in specimens collected from dogs and cats. however, none of the tests turned out to be positive ( ) . in a study conducted to investigate the potential of different animal species to act as the intermediate host of sars-cov- , it was found that both ferrets and cats can be infected via experimental inoculation of the virus. in addition, infected cats efficiently transmitted the disease to naive cats ( ) . sars-cov- infection and subsequent transmission in ferrets were found to recapitulate the clinical aspects of covid- in humans. the infected ferrets also shed virus via multiple routes, such as saliva, nasal washes, feces, and urine, postinfection, making them an ideal animal model for studying disease transmission ( ) . experimental inoculation was also done in other animal species and found that the dogs have low susceptibility, while the chickens, ducks, and pigs are not at all susceptible to sars-cov- ( ) . similarly, the national veterinary services laboratories of the usda have reported covid- in tigers and lions that exhibited respiratory signs like dry cough and wheezing. the zoo animals are suspected to have been infected by an asymptomatic zookeeper ( ) . the total number of covid- -positive cases in human beings is increasing at a high rate, thereby creating ideal conditions for viral spillover to other species, such as pigs. the evidence obtained from sars-cov suggests that pigs can get infected with sars-cov- ( ). however, experimental inoculation with sars-cov- failed to infect pigs ( ) . further studies are required to identify the possible animal reservoirs of sars-cov- and the seasonal variation in the circulation of these viruses in the animal population. research collaboration between human and animal health sectors is becoming a necessity to evaluate and identify the possible risk factors of transmission between animals and humans. such cooperation will help to devise efficient strategies for the management of emerging zoonotic diseases ( ) . rna tests can confirm the diagnosis of sars-cov- (covid- ) cases with real-time rt-pcr or next-generation sequencing ( , , , ) . at present, nucleic acid detection techniques, like rt-pcr, are considered an effective method for confirming the diagnosis in clinical cases of covid- ( ) . several companies across the world are currently focusing on developing and marketing sars-cov- -specific nucleic acid detection kits. multiple laboratories are also developing their own in-house rt-pcr. one of them is the sars-cov- nucleic acid detection kit produced by shuoshi biotechnology (double fluorescence pcr method) ( ) . up to march , the u.s. food and drug administration (fda) had granted in vitro diagnostics emergency use authorizations (euas), including for the rt-pcr diagnostic panel for the universal detection of sars-like betacoronaviruses and specific detection of sars-cov- , developed by the u.s. cdc (table ) ( , ) . recently, full-length genomic sequences of saras-cov- strains available in the national center for biotechnology information and gisaid databases were subjected to multiple-sequence alignment and phylogenetic analyses for studying variations in the viral genome ( ) . all the viral strains revealed high homology of . % ( . % to %) at the nucleotide level and . % ( . % to %) at the amino acid level. overall variation was found to be low in orf regions, with variation sites recognized in a, b, s, a, m, , and n regions. mutation rates of . % ( / ) and . % ( / ) were observed at nt (orf ) and nt (orf a) positions, respectively. owing to such selective mutations, a few specific regions of sars-cov- should not be considered for designing primers and probes. the sars-cov- reference sequence could pave the way to study molecular biology and pathobiology, along with developing diagnostics and appropriate prevention and control strategies for countering sars-cov- ( ) . nucleic acids of sars-cov- can be detected from samples ( ) such as bronchoalveolar lavage fluid, sputum, nasal swabs, fiber bronchoscope brush biopsy specimen, pharyngeal swabs, feces, blood, and urine, with different levels of diagnostic performance (table ) ( , , ) . the viral loads of sars-cov- were measured using n-gene-specific quantitative rt-pcr in throat swab and sputum samples collected from covid- -infected individuals. the results indicated that the viral load peaked at around to days following the onset of symptoms, and it ranged from to copies/ml during this time ( ) . in another study, the viral load was found to be higher in the nasal swabs than the throat swabs obtained from covid- symptomatic patients ( ) . although initially it was thought that viral load would be associated with poor outcomes, some case reports have shown asymptomatic individuals with high viral loads ( ) . recently, the viral load in nasal and throat swabs of symptomatic patients was determined, and higher viral loads were recorded soon after the onset of symptoms, particularly in the nose compared to the throat. the pattern of viral nucleic the results of the studies related to sars-cov- viral loads reflect active replication of this virus in the upper respiratory tract and prolonged viral shedding after symptoms disappear, including via stool. thus, the current case definition needs to be updated along with a reassessment of the strategies to be adopted for restraining the sars-cov- outbreak spread ( ) . in some cases, the viral load studies of sars-cov- have also been useful to recommend precautionary measures when handling specific samples, e.g., feces. in a recent survey from confirmed cases of sars-cov- infection with available data (representing days to after onset), stool samples from nine cases ( %; days to after onset) were positive on rt-pcr analysis. although the viral loads were lower than those of respiratory samples (range, copies per ml to . ϫ copies per ml), this has essential biosafety implications ( ) . the samples from sars-cov- -positive patients in singapore who had traveled from wuhan to singapore showed the presence of viral rna in stool and whole blood but not in urine by real-time rt-pcr ( ) . further, novel sars-cov- infections have been detected in a variety of clinical specimens, like bronchoalveolar lavage fluid, sputum, nasal swabs, fibrobronchoscope brush biopsy specimens, pharyngeal swabs, feces, and blood ( ) . the presence of sars-cov- in fecal samples has posed grave public health concerns. in addition to the direct transmission mainly occurring via droplets of sneezing and coughing, other routes, such as fecal excretion and environmental and fomite contamination, are contributing to sars-cov- transmission and spread ( ) ( ) ( ) ( ) . fecal excretion has also been documented for sars-cov and mers-cov, along with the potential to stay viable in situations aiding fecal-oral transmission. thus, sars-cov- has every possibility to be transmitted through this mode. fecal-oral transmission of sars-cov- , particularly in regions having low standards of hygiene and poor sanitation, may have grave consequences with regard to the high spread of this virus. ethanol and disinfectants containing chlorine or bleach are effective against coronaviruses ( ) ( ) ( ) ( ) . appropriate precautions need to be followed strictly while handling the stools of patients infected with sars-cov- . biowaste materials and sewage from hospitals must be adequately disinfected, treated, and disposed of properly. the significance of frequent and good hand hygiene and sanitation practices needs to be given due emphasis ( ) ( ) ( ) ( ) . future explorative research needs to be conducted with regard to the fecal-oral transmission of sars-cov- , along with focusing on environmental investigations to find out if this virus could stay viable in situations and atmospheres facilitating such potent routes of transmission. the correlation of fecal concentrations of viral rna with disease severity needs to be determined, along with assessing the gastrointestinal symptoms and the possibility of fecal sars-cov- rna detection during the covid- incubation period or convalescence phases of the disease ( ) ( ) ( ) ( ) . the lower respiratory tract sampling techniques, like bronchoalveolar lavage fluid aspirate, are considered the ideal clinical materials, rather than the throat swab, due to their higher positive rate on the nucleic acid test ( ) . the diagnosis of covid- can be made by using upper-respiratory-tract specimens collected using nasopharyngeal and oropharyngeal swabs. however, these techniques are associated with unnecessary risks to health care workers due to close contact with patients ( ) . similarly, a single patient with a high viral load was reported to contaminate an entire endoscopy room by shedding the virus, which may remain viable for at least days and is considered a great risk for uninfected patients and health care workers ( ) . recently, it was found that the anal swabs gave more positive results than oral swabs in the later stages of infection ( ) . hence, clinicians have to be cautious while discharging any covid- infected patient based on negative oral swab test results due to the possibility of fecal-oral transmission. even though the viral loads in stool samples were found to be less than those of respiratory samples, strict precautionary measures have to be followed while handling stool samples of covid- suspected or infected patients ( ) . children infected with sars-cov- experience only a mild form of illness and recover immediately after treatment. it was recently found that stool samples of sars-cov- -infected children that gave negative throat swab results were positive within ten days of negative results. this could result in the fecal-oral transmission of sars-cov- infections, especially in children ( ) . hence, to prevent the fecal-oral transmission of sars-cov- , infected covid- patients should only be considered negative when they test negative for sars-cov- in the stool sample. a suspected case of covid- infection is said to be confirmed if the respiratory tract aspirate or blood samples test positive for sars-cov- nucleic acid using rt-pcr or by the identification of sars-cov- genetic sequence in respiratory tract aspirate or blood samples ( ) . the patient will be confirmed as cured when two subsequent oral swab results are negative ( ) . recently, the live virus was detected in the selfcollected saliva of patients infected with covid- . these findings were confirmative of using saliva as a noninvasive specimen for the diagnosis of covid- infection in suspected individuals ( ) . it has also been observed that the initial screening of covid- patients infected with rt-pcr may give negative results even if they have chest ct findings that are suggestive of infection. hence, for the accurate diagnosis of covid- , a combination of repeated swab tests using rt-pcr and ct scanning is required to prevent the possibility of false-negative results during disease screening ( ) . rt-pcr is the most widely used test for diagnosing covid- . however, it has some significant limitations from the clinical perspective, since it will not give any clarity regarding disease progression. droplet digital pcr (ddpcr) can be used for the quantification of viral load in the samples obtained from lower respiratory tracts. hence, based on the viral load, we can quickly evaluate the progression of infection ( ) . in addition to all of the above findings, sequencing and phylogenetics are critical in the correct identification and confirmation of the causative viral agent and useful to establish relationships with previous isolates and sequences, as well as to know, especially during an epidemic, the nucleotide and amino acid mutations and the molecular divergence. the rapid development and implementation of diagnostic tests against emerging novel diseases like covid- pose significant challenges due to the lack of resources and logistical limitations associated with an outbreak ( ) . sars-cov- infection can also be confirmed by isolation and culturing. the human airway epithelial cell culture was found to be useful in isolating sars-cov- ( ). the efficient control of an outbreak depends on the rapid diagnosis of the disease. recently, in response to the covid- outbreak, -step quantitative realtime reverse transcription-pcr assays were developed that detect the orf b and n regions of the sars-cov- genome ( ) . that assay was found to achieve the rapid detection of sars-cov- . nucleic acid-based assays offer high accuracy in the diagnosis of sars-cov- , but the current rate of spread limits its use due to the lack of diagnostic assay kits. this will further result in the extensive transmission of covid- , since only a portion of suspected cases can be diagnosed. in such situations, conventional serological assays, like enzyme-linked immunosorbent assay (elisa), that are specific to covid- igm and igg antibodies can be used as a high-throughput alternative ( ) . at present, there is no diagnostic kit available for detecting the sars-cov- antibody ( ) . the specific antibody profiles of covid- patients were analyzed, and it was found that the igm level lasted more than month, indicating a prolonged stage of virus replication in sars-cov- -infected patients. the igg levels were found to increase only in the later stages of the disease. these findings indicate that the specific antibody profiles of sars-cov- and sars-cov were similar ( ) . these findings can be utilized for the development of specific diagnostic tests against covid- and can be used for rapid screening. even though diagnostic test kits are already available that can detect the genetic sequences of sars-cov- ( ), their availability is a concern, as the number of covid- cases is skyrocketing ( , ) . a major problem associated with this diagnostic kit is that it works only when the test subject has an active infection, limiting its use to the earlier stages of infection. several laboratories around the world are currently developing antibody-based diagnostic tests against sars-cov- ( ). chest ct is an ideal diagnostic tool for identifying viral pneumonia. the sensitivity of chest ct is far superior to that of x-ray screening. the chest ct findings associated with covid- -infected patients include characteristic patchy infiltration that later progresses to ground-glass opacities ( ) . early manifestations of covid- pneumonia might not be evident in x-ray chest radiography. in such situations, a chest ct examination can be performed, as it is considered highly specific for covid- pneumonia ( ) . those patients having covid- pneumonia will exhibit the typical ground-glass opacity in their chest ct images ( ) . the patients infected with covid- had elevated plasma angiotensin levels. the level of angiotensin was found to be linearly associated with viral load and lung injury, indicating its potential as a diagnostic biomarker ( ) . the chest ct imaging abnormalities associated with covid- pneumonia have also been observed even in asymptomatic patients. these abnormalities progress from the initial focal unilateral to diffuse bilateral ground-glass opacities and will further progress to or coexist with lung consolidation changes within to weeks ( ). the role played by radiologists in the current scenario is very important. radiologists can help in the early diagnosis of lung abnormalities associated with covid- pneumonia. they can also help in the evaluation of disease severity, identifying its progression to acute respiratory distress syndrome and the presence of secondary bacterial infections ( ) . even though chest ct is considered an essential diagnostic tool for covid- , the extensive use of ct for screening purposes in the suspected individuals might be associated with a disproportionate risk-benefit ratio due to increased radiation exposure as well as increased risk of cross-infection. hence, the use of ct for early diagnosis of sars-cov- infection in high-risk groups should be done with great caution ( ) . more recently, other advanced diagnostics have been designed and developed for the detection of sars-cov- ( , , ( ) ( ) ( ) . a reverse transcriptional loopmediated isothermal amplification (rt-lamp), namely, ilaco, has been developed for rapid and colorimetric detection of this virus ( ) . rt-lamp serves as a simple, rapid, and sensitive diagnostic method that does not require sophisticated equipment or skilled personnel ( ) . an interactive web-based dashboard for tracking sars-cov- in a real-time mode has been designed ( ) . a smartphone-integrated home-based point-of-care testing (poct) tool, a paper-based poct combined with lamp, is a useful point-of-care diagnostic ( ) . an abbott id now covid- molecular poct-based test, using isothermal nucleic acid amplification technology, has been designed as a pointof-care test for very rapid detection of sars-cov- in just min ( ) . a crispr-based sherlock (specific high-sensitivity enzymatic reporter unlocking) diagnostic for rapid detection of sars-cov- without the requirement of specialized instrumentation has been reported to be very useful in the clinical diagnosis of covid- ( ) . a crispr-cas -based lateral flow assay also has been developed for rapid detection of sars-cov- ( ) . artificial intelligence, by means of a three-dimensional deep-learning model, has been developed for sensitive and specific diagnosis of covid- via ct images ( ) . tracking and mapping of the rising incidence rates, disease outbreaks, community spread, clustered transmission events, hot spots, and superspreader potential of sars-cov- /covid warrant full exploitation of real-time disease mapping by employing geographical information systems (gis), such as the gis software kosmo . , web-based real-time tools and dashboards, apps, and advances in information technology ( - ). researchers have also developed a few prediction tools/models, such as the prediction model risk of bias assessment tool (probast) and critical appraisal and data extraction for systematic reviews of prediction modeling studies (charms), which could aid in assessing the possibility of getting infection and estimating the prognosis in patients; however, such models may suffer from bias issues and, hence, cannot be considered completely trustworthy, which necessitates the development of new and reliable predictors ( ) . recently emerged viruses, such as zika, ebola, and nipah viruses, and their grave threats to humans have begun a race in exploring the designing and developing of advanced vaccines, prophylactics, therapeutics, and drug regimens to counter emerging viruses ( ) ( ) ( ) ) . several attempts are being made to design and develop vaccines for cov infection, mostly by targeting the spike glycoprotein. nevertheless, owing to extensive diversity in antigenic variants, cross-protection rendered by the vaccines is significantly limited, even within the strains of a phylogenetic subcluster ( ) . due to the lack of effective antiviral therapy and vaccines in the present scenario, we need to depend solely on implementing effective infection control measures to lessen the risk of possible nosocomial transmission ( ) . recently, the receptor for sars-cov- was established as the human angiotensin-converting enzyme (hace ), and the virus was found to enter the host cell mainly through endocytosis. it was also found that the major components that have a critical role in viral entry include pikfyve, tpc , and cathepsin l. these findings are critical, since the components described above might act as candidates for vaccines or therapeutic drugs against sars-cov- ( ) . the majority of the treatment options and strategies that are being evaluated for sars-cov- (covid- ) have been taken from our previous experiences in treating sars-cov, mers-cov, and other emerging viral diseases. several therapeutic and preventive strategies, including vaccines, immunotherapeutics, and antiviral drugs, have been exploited against the previous cov outbreaks (sars-cov and mers-cov) ( , , ( ) ( ) ( ) ( ) . these valuable options have already been evaluated for their potency, efficacy, and safety, along with several other types of current research that will fuel our search for ideal therapeutic agents against covid- ( , , , , ) . the primary cause of the unavailability of approved and commercial vaccines, drugs, and therapeutics to counter the earlier sars-cov and mers-cov seems to owe to the lesser attention of the biomedicine and pharmaceutical companies, as these two covs did not cause much havoc, global threat, and panic like those posed by the sars-cov- pandemic ( ) . moreover, for such outbreak situations, the requirement for vaccines and therapeutics/drugs exists only for a limited period, until the outbreak is controlled. the proportion of the human population infected with sars-cov and mers-cov was also much lower across the globe, failing to attract drug and vaccine manufacturers and clinical microbiology reviews producers. therefore, by the time an effective drug or vaccine is designed against such disease outbreaks, the virus would have been controlled by adopting appropriate and strict prevention and control measures, and patients for clinical trials will not be available. the newly developed drugs cannot be marketed due to the lack of end users. the s protein plays a significant role in the induction of protective immunity against sars-cov by mediating t-cell responses and neutralizing antibody production ( ) . in the past few decades, we have seen several attempts to develop a vaccine against human coronaviruses by using s protein as the target ( , ) . however, the developed vaccines have minimal application, even among closely related strains of the virus, due to a lack of cross-protection. that is mainly because of the extensive diversity existing among the different antigenic variants of the virus ( ) . the contributions of the structural proteins, like spike (s), matrix (m), small envelope (e), and nucleocapsid (n) proteins, of sars-cov to induce protective immunity has been evaluated by expressing them in a recombinant parainfluenza virus type vector (bhpiv ). of note, the result was conclusive that the expression of m, e, or n proteins without the presence of s protein would not confer any noticeable protection, with the absence of detectable serum sars-cov-neutralizing antibodies ( ) . antigenic determinant sites present over s and n structural proteins of sars-cov- can be explored as suitable vaccine candidates ( ) . in the asian population, s, e, m, and n proteins of sars-cov- are being targeted for developing subunit vaccines against covid- ( ) . the identification of the immunodominant region among the subunits and domains of s protein is critical for developing an effective vaccine against the coronavirus. the c-terminal domain of the s subunit is considered the immunodominant region of the porcine deltacoronavirus s protein ( ) . similarly, further investigations are needed to determine the immunodominant regions of sars-cov- for facilitating vaccine development. however, our previous attempts to develop a universal vaccine that is effective for both sars-cov and mers-cov based on t-cell epitope similarity pointed out the possibility of cross-reactivity among coronaviruses ( ) . that can be made possible by selected potential vaccine targets that are common to both viruses. sars-cov- has been reported to be closely related to sars-cov ( , ) . hence, knowledge and understanding of s protein-based vaccine development in sars-cov will help to identify potential s protein vaccine candidates in sars-cov- . therefore, vaccine strategies based on the whole s protein, s protein subunits, or specific potential epitopes of s protein appear to be the most promising vaccine candidates against coronaviruses. the rbd of the s subunit of s protein has a superior capacity to induce neutralizing antibodies. this property of the rbd can be utilized for designing potential sars-cov vaccines either by using rbd-containing recombinant proteins or recombinant vectors that encode rbd ( ) . hence, the superior genetic similarity existing between sars-cov- and sars-cov can be utilized to repurpose vaccines that have proven in vitro efficacy against sars-cov to be utilized for sars-cov- . the possibility of cross-protection in covid- was evaluated by comparing the s protein sequences of sars-cov- with that of sars-cov. the comparative analysis confirmed that the variable residues were found concentrated on the s subunit of s protein, an important vaccine target of the virus ( ) . hence, the possibility of sars-cov-specific neutralizing antibodies providing cross-protection to covid- might be lower. further genetic analysis is required between sars-cov- and different strains of sars-cov and sarslike (sl) covs to evaluate the possibility of repurposed vaccines against covid- . this strategy will be helpful in the scenario of an outbreak, since much time can be saved, because preliminary evaluation, including in vitro studies, already would be completed for such vaccine candidates. multiepitope subunit vaccines can be considered a promising preventive strategy against the ongoing covid- pandemic. in silico and advanced immunoinformatic tools can be used to develop multiepitope subunit vaccines. the vaccines that are engineered by this technique can be further evaluated using docking studies and, if found effective, then can be further evaluated in animal models ( ) . identifying epitopes that have the potential to become a vaccine candidate is critical to developing an effective vaccine against covid- . the immunoinformatics approach has been used for recognizing essential epitopes of cytotoxic t lymphocytes and b cells from the surface glycoprotein of sars-cov- . recently, a few epitopes have been recognized from the sars-cov- surface glycoprotein. the selected epitopes explored targeting molecular dynamic simulations, evaluating their interaction with corresponding major histocompatibility complex class i molecules. they potentially induce immune responses ( ) . the recombinant vaccine can be designed by using rabies virus (rv) as a viral vector. rv can be made to express mers-cov s protein on its surface so that an immune response is induced against mers-cov. the rv vector-based vaccines against mers-cov can induce faster antibody response as well as higher degrees of cellular immunity than the gram-positive enhancer matrix (gem) particle vector-based vaccine. however, the latter can induce a very high antibody response at lower doses ( ) . hence, the degree of humoral and cellular immune responses produced by such vaccines depends upon the vector used. dual vaccines have been getting more popular recently. among them, the rabies virus-based vectored vaccine platform is used to develop vaccines against emerging infectious diseases. the dual vaccine developed from inactivated rabies virus particles that express the mers-cov s domain of s protein was found to induce immune responses for both mers-cov and rabies virus. the vaccinated mice were found to be completely protected from challenge with mers-cov ( ) . the intranasal administration of the recombinant adenovirus-based vaccine in balb/c mice was found to induce long-lasting neutralizing immunity against mers spike pseudotyped virus, characterized by the induction of systemic igg, secretory iga, and lung-resident memory t-cell responses ( ) . immunoinformatics methods have been employed for the genomewide screening of potential vaccine targets among the different immunogens of mers-cov ( ) . the n protein and the potential b-cell epitopes of mers-cov e protein have been suggested as immunoprotective targets inducing both t-cell and neutralizing antibody responses ( , ) . the collaborative effort of the researchers of rocky mountain laboratories and oxford university is designing a chimpanzee adenovirus-vectored vaccine to counter covid- ( ) . the coalition for epidemic preparedness innovations (cepi) has initiated three programs to design sars-cov- vaccines ( ) . cepi has a collaborative project with inovio for designing a mers-cov dna vaccine that could potentiate effective immunity. cepi and the university of queensland are designing a molecular clamp vaccine platform for mers-cov and other pathogens, which could assist in the easier identification of antigens by the immune system ( ) . cepi has also funded moderna to develop a vaccine for covid- in partnership with the vaccine research center (vrc) of the national institute of allergy and infectious diseases (niaid), part of the national institutes of health (nih) ( ) . by employing mrna vaccine platform technology, a vaccine candidate expressing sars-cov- spike protein is likely to go through clinical testing in the coming months ( ( ) . the process of vaccine development usually takes approximately ten years, in the case of inactivated or live attenuated vaccines, since it involves the generation of long-term efficacy data. however, this was brought down to years during the ebola emergency for viral vector vaccines. in the urgency associated with the covid- outbreaks, we expect a vaccine by the end of this year ( ) . the development of an effective vaccine against covid- with high speed and precision is the combined result of advancements in computational biology, gene synthesis, protein engineering, and the invention of advanced manufacturing platforms ( ) . the recurring nature of the coronavirus outbreaks calls for the development of a pan-coronavirus vaccine that can produce cross-reactive antibodies. however, the success of such a vaccine relies greatly on its ability to provide protection not only against present versions of the virus but also the ones that are likely to emerge in the future. this can be achieved by identifying antibodies that can recognize relatively conserved epitopes that are maintained as such even after the occurrence of considerable variations ( ) . even though several vaccine clinical trials are being conducted around the world, pregnant women have been completely excluded from these studies. pregnant women are highly vulnerable to emerging diseases such as covid- due to alterations in the immune system and other physiological systems that are associated with pregnancy. therefore, in the event of successful vaccine development, pregnant women will not get access to the vaccines ( ) . hence, it is recommended that pregnant women be included in the ongoing vaccine trials, since successful vaccination in pregnancy will protect the mother, fetus, and newborn. the heterologous immune effects induced by bacillus calmette guérin (bcg) vaccination is a promising strategy for controlling the covid- pandemic and requires further investigations. bcg is a widely used vaccine against tuberculosis in high-risk regions. it is derived from a live attenuated strain of mycobacterium bovis. at present, three new clinical trials have been registered to evaluate the protective role of bcg vaccination against sars-cov- ( ) . recently, a cohort study was conducted to evaluate the impact of childhood bcg vaccination in covid- pcr positivity rates. however, childhood bcg vaccination was found to be associated with a rate of covid- -positive test results similar to that of the nonvaccinated group ( ) . further studies are required to analyze whether bcg vaccination in childhood can induce protective effects against covid- in adulthood. population genetic studies conducted on genomes identified that the sars-cov- virus has evolved into two major types, l and s. among the two types, l type is expected to be the most prevalent (ϳ %), followed by the s type (ϳ %) ( ) . this finding has a significant impact on our race to develop an ideal vaccine, since the vaccine candidate has to target both strains to be considered effective. at present, the genetic differences between the l and s types are very small and may not affect the immune response. however, we can expect further genetic variations in the coming days that could lead to the emergence of new strains ( ) . there is no currently licensed specific antiviral treatment for mers-and sars-cov infections, and the main focus in clinical settings remains on lessening clinical signs and providing supportive care ( ) ( ) ( ) ( ) . effective drugs to manage covid- patients include remdesivir, lopinavir/ritonavir alone or in a blend with interferon beta, convalescent plasma, and monoclonal antibodies (mabs); however, efficacy and safety issues of these drugs require additional clinical trials ( , ) . a controlled trial of ritonavirboosted lopinavir and interferon alpha b treatment was performed on covid- hospitalized patients (chictr ) ( ) . in addition, the use of hydroxychloroquine and tocilizumab for their potential role in modulating inflammatory responses in the lungs and antiviral effect has been proposed and discussed in many research articles. still, no fool-proof clinical trials have been published ( , , , ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . recently, a clinical trial conducted on adult patients suffering from severe covid- revealed no benefit of lopinavir-ritonavir treatment over standard care ( ) . the efforts to control sars-cov- infection utilize defined strategies as followed against mers and sars, along with adopting and strengthening a few precautionary measures owing to the unknown nature of this novel virus ( , ) . presently, the main course of treatment for severely affected sars-cov- patients admitted to hospitals includes mechanical ventilation, intensive care unit (icu) admittance, and symptomatic and supportive therapies. additionally, rna synthesis inhibitors (lamivudine and tenofovir disoproxil fumarate), remdesivir, neuraminidase inhibitors, peptide (ek ), antiinflammatory drugs, abidol, and chinese traditional medicine (lianhuaqingwen and shufengjiedu capsules) could aid in covid- treatment. however, further clinical trials are being carried out concerning their safety and efficacy ( ) . it might require months to a year(s) to design and develop effective drugs, therapeutics, and vaccines against covid- , with adequate evaluation and approval from regulatory bodies and moving to the bulk production of many millions of doses at commercial levels to meet the timely demand of mass populations across the globe ( ) . continuous efforts are also warranted to identify and assess viable drugs and immunotherapeutic regimens that revealed proven potency in combating other viral agents similar to sars-cov- . covid- patients showing severe signs are treated symptomatically along with oxygen therapy. in such cases where the patients progress toward respiratory failure and become refractory to oxygen therapy, mechanical ventilation is necessitated. the covid- -induced septic shock can be managed by providing adequate hemodynamic support ( ) . several classes of drugs are currently being evaluated for their potential therapeutic action against sars-cov- . therapeutic agents that have anti-sars-cov- activity can be broadly classified into three categories: drugs that block virus entry into the host cell, drugs that block viral replication as well as its survival within the host cell, and drugs that attenuate the exaggerated host immune response ( ) . an inflammatory cytokine storm is commonly seen in critically ill covid- patients. hence, they may benefit from the use of timely anti-inflammation treatment. anti-inflammatory therapy using drugs like glucocorticoids, cytokine inhibitors, jak inhibitors, and chloroquine/hydroxychloroquine should be done only after analyzing the risk/benefit ratio in covid- patients ( ). there have not been any studies concerning the application of nonsteroidal anti-inflammatory drugs (nsaid) to covid- -infected patients. however, reasonable pieces of evidence are available that link nsaid uses with the occurrence of respiratory and cardiovascular adverse effects. hence, as a cautionary approach, it is better to recommend the use of nsaids as the first-line option for managing covid- symptoms ( ) . the use of corticosteroids in covid- patients is still a matter of controversy and requires further systematic clinical studies. the guidelines that were put forward to manage critically ill adults suggest the use of systemic corticosteroids in mechanically ventilated adults with ards ( ) . the generalized use of corticosteroids is not indicated in covid- , since there are some concerns associated with the use of corticosteroids in viral pneumonia. stem cell therapy using mesenchymal stem cells (mscs) is another hopeful strategy that can be used in clinical cases of covid- owing to its potential immunomodulatory capacity. it may have a beneficial role in attenuating the cytokine storm that is observed in severe cases of sars-cov- infection, thereby reducing mortality. among the different types of mscs, expanded umbilical cord mscs can be considered a potential therapeutic agent that requires further validation for managing critically ill covid- patients ( ) . repurposed broad-spectrum antiviral drugs having proven uses against other viral pathogens can be employed for sars-cov- -infected patients. these possess benefits of easy accessibility and recognized pharmacokinetic and pharmacodynamic activities, stability, doses, and side effects ( ) . repurposed drugs have been studied for treating cov infections, like lopinavir/ritonavir, and interferon- ␤ revealed in vitro anti-mers-cov action. the in vivo experiment carried out in the nonhuman primate model of clinical microbiology reviews common marmosets treated with lopinavir/ritonavir and interferon beta showed superior protective results in treated animals than in the untreated ones ( ) . a combination of these drugs is being evaluated to treat mers in humans (miracle trial) ( ) . these two protease inhibitors (lopinavir and ritonavir), in combination with ribavirin, gave encouraging clinical outcomes in sars patients, suggesting their therapeutic values ( ) . however, in the current scenario, due to the lack of specific therapeutic agents against sars-cov- , hospitalized patients confirmed for the disease are given supportive care, like oxygen and fluid therapy, along with antibiotic therapy for managing secondary bacterial infections ( ) . patients with novel coronavirus or covid- pneumonia who are mechanically ventilated often require sedatives, analgesics, and even muscle relaxation drugs to prevent ventilator-related lung injury associated with human-machine incoordination ( ) . the result obtained from a clinical study of four patients infected with covid- claimed that combination therapy using lopinavir/ritonavir, arbidol, and shufeng jiedu capsules (traditional chinese medicine) was found to be effective in managing covid- pneumonia ( ) . it is difficult to evaluate the therapeutic potential of a drug or a combination of drugs for managing a disease based on such a limited sample size. before choosing the ideal therapeutic agent for the management of covid- , randomized clinical control studies should be performed with a sufficient study population. several classes of routinely used antiviral drugs, like oseltamivir (neuraminidase inhibitor), acyclovir, ganciclovir, and ribavirin, do not have any effect on covid- and, hence, are not recommended ( ) . oseltamivir, a neuraminidase inhibitor, has been explored in chinese hospitals for treating suspected covid- cases, although proven efficacy against sars-cov- is still lacking for this drug ( ) . the in vitro antiviral potential of fad-approved drugs, viz., ribavirin, penciclovir, nitazoxanide, nafamostat, and chloroquine, tested in comparison to remdesivir and favipiravir (broad-spectrum antiviral drugs) revealed remdesivir and chloroquine to be highly effective against sars-cov- infection in vitro ( ) . ribavirin, penciclovir, and favipiravir might not possess noteworthy in vivo antiviral actions for sars-cov- , since higher concentrations of these nucleoside analogs are needed in vitro to lessen the viral infection. both remdesivir and chloroquine are being used in humans to treat other diseases, and such safer drugs can be explored for assessing their effectiveness in covid- patients. several therapeutic agents, such as lopinavir/ritonavir, chloroquine, and hydroxychloroquine, have been proposed for the clinical management of covid- ( ) . a molecular docking study, conducted in the rna-dependent rna polymerase (rdrp) of sars-cov- using different commercially available antipolymerase drugs, identified that drugs such as ribavirin, remdesivir, galidesivir, tenofovir, and sofosbuvir bind rdrp tightly, indicating their vast potential to be used against covid- ( ). a broadspectrum antiviral drug that was developed in the united states, tilorone dihydrochloride (tilorone), was previously found to possess potent antiviral activity against mers, marburg, ebola, and chikungunya viruses ( ) . even though it had broad-spectrum activity, it was neglected for an extended period. tilorone is another antiviral drug that might have activity against sars-cov- . remdesivir, a novel nucleotide analog prodrug, was developed for treating ebola virus disease (evd), and it was also found to inhibit the replication of sars-cov and mers-cov in primary human airway epithelial cell culture systems ( ) . recently, in vitro study has proven that remdesivir has better antiviral activity than lopinavir and ritonavir. further, in vivo studies conducted in mice also identified that treatment with remdesivir improved pulmonary function and reduced viral loads and lung pathology both in prophylactic and therapeutic regimens compared to lopinavir/ritonavir-ifn-␥ treatment in mers-cov infection ( ) . remdesivir also inhibits a diverse range of coronaviruses, including circulating human cov, zoonotic bat cov, and prepandemic zoonotic cov ( ) . remdesivir is also considered the only therapeutic drug that significantly reduces pulmonary pathology ( ) . all these findings indicate that remde-sivir has to be further evaluated for its efficacy in the treatment of covid- infection in humans. the broad-spectrum activity exhibited by remdesivir will help control the spread of disease in the event of a new coronavirus outbreak. chloroquine is an antimalarial drug known to possess antiviral activity due to its ability to block virus-cell fusion by raising the endosomal ph necessary for fusion. it also interferes with virus-receptor binding by interfering with the terminal glycosylation of sars-cov cellular receptors, such as ace ( ) . in a recent multicenter clinical trial that was conducted in china, chloroquine phosphate was found to exhibit both efficacy and safety in the therapeutic management of sars-cov- -associated pneumonia ( ) . this drug is already included in the treatment guidelines issued by the national health commission of the people's republic of china. the preliminary clinical trials using hydroxychloroquine, another aminoquinoline drug, gave promising results. the covid- patients received mg of hydroxychloroquine daily along with azithromycin as a single-arm protocol. this protocol was found to be associated with a noteworthy reduction in viral load. finally, it resulted in a complete cure ( ) ; however, the study comprised a small population and, hence, the possibility of misinterpretation could arise. however, in another case study, the authors raised concerns over the efficacy of hydroxychloroquine-azithromycin in the treatment of covid- patients, since no observable effect was seen when they were used. in some cases, the treatment was discontinued due to the prolongation of the qt interval ( ) . hence, further randomized clinical trials are required before concluding this matter. recently, another fda-approved drug, ivermectin, was reported to inhibit the in vitro replication of sars-cov- . the findings from this study indicate that a single treatment of this drug was able to induce an ϳ , -fold reduction in the viral rna at h in cell culture. ( ) . one of the main disadvantages that limit the clinical utility of ivermectin is its potential to cause cytotoxicity. however, altering the vehicles used in the formulations, the pharmacokinetic properties can be modified, thereby having significant control over the systemic concentration of ivermectin ( ) . based on the pharmacokinetic simulation, it was also found that ivermectin may have limited therapeutic utility in managing covid- , since the inhibitory concentration that has to be achieved for effective anti-sars-cov- activity is far higher than the maximum plasma concentration achieved by administering the approved dose ( ) . however, ivermectin, being a host-directed agent, exhibits antiviral activity by targeting a critical cellular process of the mammalian cell. therefore, the administration of ivermectin, even at lower doses, will reduce the viral load at a minor level. this slight decrease will provide a great advantage to the immune system for mounting a large-scale antiviral response against sars-cov- ( ). further, a combination of ivermectin and hydroxychloroquine might have a synergistic effect, since ivermectin reduces viral replication, while hydroxychloroquine inhibits the entry of the virus in the host cell ( ) . further, in vivo studies and randomized clinical control trials are required to understand the mechanism as well as the clinical utility of this promising drug. nafamostat is a potent inhibitor of mers-cov that acts by preventing membrane fusion. nevertheless, it does not have any sort of inhibitory action against sars-cov- infection ( ) . recently, several newly synthesized halogenated triazole compounds were evaluated, using fluorescence resonance energy transfer (fret)-based helicase assays, for their ability to inhibit helicase activity. among the evaluated compounds, -(cyclopent- -en- -ylamino)- -[ -( -iodophenyl) hydrazinyl]- h- , , -triazole- -thiol and -(cyclopent- -en- -ylamino)- -[ -( -chlorophenyl) hydrazinyl]- h- , , -triazole- -thiol were found to be the most potent. these compounds were used for in silico studies, and molecular docking was accomplished into the active binding site of mers-cov helicase nsp ( ) . further studies are required for evaluating the therapeutic potential of these newly identified compounds in the management of covid- infection. monoclonal antibodies (mabs) may be helpful in the intervention of disease in clinical microbiology reviews cov-exposed individuals. patients recovering from sars showed robust neutralizing antibodies against this cov infection ( ) . a set of mabs aimed at the mers-cov s protein-specific domains, comprising six specific epitope groups interacting with receptor-binding, membrane fusion, and sialic acid-binding sites, make up crucial entry tasks of s protein ( , ) . passive immunization employing weaker and strongly neutralizing antibodies provided considerable protection in mice against a mers-cov lethal challenge. such antibodies may play a crucial role in enhancing protective humoral responses against the emerging covs by aiming appropriate epitopes and functions of the s protein. the cross-neutralization ability of sars-cov rbd-specific neutralizing mabs considerably relies on the resemblance between their rbds; therefore, sars-cov rbd-specific antibodies could cross-neutralized sl covs, i.e., bat-sl-cov strain wiv (rbd with eight amino acid differences from sars-cov) but not bat-sl-cov strain shc ( amino acid differences) ( ) . appropriate rbd-specific mabs can be recognized by a relative analysis of rbd of sars-cov- to that of sars-cov, and cross-neutralizing sars-cov rbd-specific mabs could be explored for their effectiveness against covid- and further need to be assessed clinically. the u.s. biotechnology company regeneron is attempting to recognize potent and specific mabs to combat covid- . an ideal therapeutic option suggested for sars-cov- (covid- ) is the combination therapy comprised of mabs and the drug remdesivir (covid- ) ( ) . the sars-cov-specific human mab cr is found to bind with sars-cov- rbd, indicating its potential as a therapeutic agent in the management of covid- . it can be used alone or in combination with other effective neutralizing antibodies for the treatment and prevention of covid- ( ) . furthermore, sars-cov-specific neutralizing antibodies, like m and cr , failed to bind the s protein of sars-cov- , indicating that a particular level of similarity is mandatory between the rbds of sars-cov and sars-cov- for the cross-reactivity to occur. further assessment is necessary before confirming the effectiveness of such combination therapy. in addition, to prevent further community and nosocomial spread of covid- , the postprocedure risk management program should not be neglected ( ) . development of broad-spectrum inhibitors against the human coronaviral pathogens will help to facilitate clinical trials on the effectiveness of such inhibitors against endemic and emerging coronaviruses ( ) . a promising animal study revealed the protective effect of passive immunotherapy with immune serum from mers-immune camels on mice infected with mers-cov ( ) . passive immunotherapy using convalescent plasma is another strategy that can be used for treating covid- -infected, critically ill patients ( ) . the exploration of fully human antibodies (human single-chain antibodies; huscfvs) or humanized nanobodies (single-domain antibodies; sdab, vh/vhh) could aid in blocking virus replication, as these agents can traverse the virus-infected cell membranes (transbodies) and can interfere with the biological characteristics of the replicating virus proteins. such examples include transbodies to the influenza virus, hepatitis c virus, ebola virus, and dengue virus ( ) . producing similar transbodies against intracellular proteins of coronaviruses, such as papain-like proteases (plpro), cysteinelike protease ( clpro), or other nsps, which are essential for replication and transcription of the virus, might formulate a practical move forward for a safer and potent passive immunization approach for virus-exposed persons and rendering therapy to infected patients. in a case study on five grimly sick patients having symptoms of severe pneumonia due to covid- , convalescent plasma administration was found to be helpful in patients recovering successfully. the convalescent plasma containing a sars-cov- specific elisa (serum) antibody titer higher than : , and neutralizing antibody titer more significant than was collected from the recovered patients and used for plasma transfusion twice in a volume of to ml on the day of collection ( ) . at present, treatment for sepsis and ards mainly involves antimicrobial therapy, source control, and supportive care. hence, the use of therapeutic plasma exchange can be considered an option in managing such severe conditions. further randomized trials can be designed to investigate its efficacy ( ) . potent therapeutics to combat sars-cov- infection include virus binding molecules, molecules or inhibitors targeting particular enzymes implicated in replication and transcription process of the virus, helicase inhibitors, vital viral proteases and proteins, protease inhibitors of host cells, endocytosis inhibitors, short interfering rna (sirna), neutralizing antibodies, mabs against the host receptor, mabs interfering with the s rbd, antiviral peptide aimed at s , and natural drugs/medicines ( , , ) . the s protein acts as the critical target for developing cov antivirals, like inhibitors of s protein and s cleavage, neutralizing antibodies, rbd-ace blockers, sirnas, blockers of the fusion core, and proteases ( ) . all of these therapeutic approaches have revealed both in vitro and in vivo anti-cov potential. although in vitro research carried out with these therapeutics showed efficacy, most need appropriate support from randomized animal or human trials. therefore, they might be of limited applicability and require trials against sars-cov- to gain practical usefulness. the binding of sars-cov- with ace leads to the exacerbation of pneumonia as a consequence of the imbalance in the reninangiotensin system (ras). the virus-induced pulmonary inflammatory responses may be reduced by the administration of ace inhibitors (acei) and angiotensin type- receptor (at r) ( ) . several investigations have suggested the use of small-molecule inhibitors for the potential control of sars-cov infections. drugs of the fda-approved compound library were screened to identify four small-molecule inhibitors of mers-cov (chlorpromazine, chloroquine, loperamide, and lopinavir) that inhibited viral replication. these compounds also hinder sars-cov and human covs ( ) . therapeutic strategies involving the use of specific antibodies or compounds that neutralize cytokines and their receptors will help to restrain the host inflammatory responses. such drugs acting specifically in the respiratory tract will help to reduce virus-triggered immune pathologies in covid- ( ) . the later stages of coronavirus-induced inflammatory cascades are characterized by the release of proinflammatory interleukin- (il- ) family members, such as il- and il- . hence, there exists a possibility that the inflammation associated with coronavirus can be inhibited by utilizing anti-inflammatory cytokines that belong to the il- family ( ) . it has also been suggested that the actin protein is the host factor that is involved in cell entry and pathogenesis of sars-cov- . hence, those drugs that modulate the biological activity of this protein, like ibuprofen, might have some therapeutic application in managing the disease ( ). the plasma angiotensin level was found to be markedly elevated in covid- infection and was correlated with viral load and lung injury. hence, drugs that block angiotensin receptors may have potential for treating covid- infection ( ) . a scientist from germany, named rolf hilgenfeld, has been working on the identification of drugs for the treatment of coronaviral infection since the time of the first sars outbreak ( ) . the sars-cov s subunit has a significant function in mediating virus fusion that provides entry into the host cell. heptad repeat (hr ) and heptad repeat (hr ) can interact and form a six-helix bundle that brings the viral and cellular membranes in close proximity, facilitating its fusion. the sequence alignment study conducted between covid- and sars-cov identified that the s subunits are highly conserved in these covs. the hr and hr domains showed . % and % overall identity, respectively ( ) . from these findings, we can confirm the significance of covid- hr and hr and their vital role in host cell entry. hence, fusion inhibitors target the hr domain of s protein, thereby preventing viral fusion and entry into the host cell. this is another potential therapeutic strategy that can be used in the management of covid- . other than the specific therapy directed against covid- , general treatments play a vital role in the enhancement of host immune responses against the viral agent. inadequate nutrition is linked to the weakening of the host immune response, clinical microbiology reviews making the individual more susceptible. the role played by nutrition in disease susceptibility should be measured by evaluating the nutritional status of patients with covid- ( ) . for evaluating the potential of vaccines and therapeutics against covs, including sars-cov, mers-covs, and the presently emerging sars-cov- , suitable animal models that can mimic the clinical disease are needed ( , ) . various animal models were assessed for sars-and mers-covs, such as mice, guinea pigs, golden syrian hamsters, ferrets, rabbits, nonhuman primates like rhesus macaques and marmosets, and cats ( , ( ) ( ) ( ) ( ) ( ) ( ) . the specificity of the virus to hace (receptor of sars-cov) was found to be a significant barrier in developing animal models. consequently, a sars-cov transgenic mouse model has been developed by inserting the hace gene into the mouse genome ( ) . the inability of mers-cov to replicate in the respiratory tracts of animals (mice, hamsters, and ferrets) is another limiting factor. however, with genetic engineering, a - ϩ/ϩ mers-cov genetically modified mouse model was developed and now is in use for the assessment of novel drugs and vaccines against mers-cov ( ). in the past, small animals (mice or hamsters) have been targeted for being closer to a humanized structure, such as mouse dpp altered with human dpp (hdpp ), hdpp -transduced mice, and hdpp -tg mice (transgenic for expressing hdpp ) for mers-cov infection ( ) . the crispr-cas gene-editing tool has been used for inserting genomic alterations in mice, making them susceptible to mers-cov infection ( ) . efforts are under way to recognize suitable animal models for sars-cov /covid- , identify the receptor affinity of this virus, study pathology in experimental animal models, and explore virus-specific immune responses and protection studies, which together would increase the pace of efforts being made for developing potent vaccines and drugs to counter this emerging virus. cell lines, such as monkey epithelial cell lines (llc-mk and vero-b ), goat lung cells, alpaca kidney cells, dromedary umbilical cord cells, and advanced ex vivo three-dimensional tracheobronchial tissue, have been explored to study human covs (mers-cov) ( , ) . vero and huh- cells (human liver cancer cells) have been used for isolating sars-cov- ( ) . recently, an experimental study with rhesus monkeys as animal models revealed the absence of any viral loads in nasopharyngeal and anal swabs, and no viral replication was recorded in the primary tissues at a time interval of days post-reinfection in reexposed monkeys ( ) . the subsequent virological, radiological, and pathological observations indicated that the monkeys with reexposure had no recurrence of covid- , like the sars-cov- -infected monkeys without rechallenge. these findings suggest that primary infection with sars-cov- could protect from later exposures to the virus, which could help in defining disease prognosis and crucial inferences for designing and developing potent vaccines against covid- ( ). in contrast to their response to the sars outbreak, china has shown immense political openness in reporting the covid- outbreak promptly. they have also performed rapid sequencing of covid- at multiple levels and shared the findings globally within days of identifying the novel virus ( ) . the move made by china opened a new chapter in global health security and diplomacy. even though complete lockdown was declared following the covid- outbreak in wuhan, the large-scale movement of people has resulted in a radiating spread of infections in the surrounding provinces as well as to several other countries. large-scale screening programs might help us to control the spread of this virus. however, this is both challenging as well as time-consuming due to the present extent of infection ( ) . the current scenario demands effective implementation of vigorous prevention and control strategies owing to the prospect of covid- for nosocomial infections ( ) . follow-ups of infected patients by telephone on day and day are advised to avoid any further unintentional spread or nosocomial transmission ( ) . the availability of public data sets provided by independent analytical teams will act as robust evidence that would guide us in designing interventions against the covid- outbreak. newspaper reports and social media can be used to analyze and reconstruct the progression of an outbreak. they can help us to obtain detailed patient-level data in the early stages of an outbreak ( ) . immediate travel restrictions imposed by several countries might have contributed significantly to preventing the spread of sars-cov- globally ( , ) . following the outbreak, a temporary ban was imposed on the wildlife trade, keeping in mind the possible role played by wild animal species in the origin of sars-cov- /covid- ( ) . making a permanent and bold decision on the trade of wild animal species is necessary to prevent the possibility of virus spread and initiation of an outbreak due to zoonotic spillover ( ) . personal protective equipment (ppe), like face masks, will help to prevent the spread of respiratory infections like covid- . face masks not only protect from infectious aerosols but also prevent the transmission of disease to other susceptible individuals while traveling through public transport systems ( ) . another critical practice that can reduce the transmission of respiratory diseases is the maintenance of hand hygiene. however, the efficacy of this practice in reducing the transmission of respiratory viruses like sars-cov- is much dependent upon the size of droplets produced. hand hygiene will reduce disease transmission only if the virus is transmitted through the formation of large droplets ( ) . hence, it is better not to overemphasize that hand hygiene will prevent the transmission of sars-cov- , since it may produce a false sense of safety among the general public that further contributes to the spread of covid- . even though airborne spread has not been reported in sars-cov- infection, transmission can occur through droplets and fomites, especially when there is close, unprotected contact between infected and susceptible individuals. hence, hand hygiene is equally as important as the use of appropriate ppe, like face masks, to break the transmission cycle of the virus; both hand hygiene and face masks help to lessen the risk of covid- transmission ( ) . medical staff are in the group of individuals most at risk of getting covid- infection. this is because they are exposed directly to infected patients. hence, proper training must be given to all hospital staff on methods of prevention and protection so that they become competent enough to protect themselves and others from this deadly disease ( ) . as a preventive measure, health care workers caring for infected patients should take extreme precautions against both contact and airborne transmission. they should use ppe such as face masks (n or ffp ), eye protection (goggles), gowns, and gloves to nullify the risk of infection ( ) . the human-to-human transmission reported in sars-cov- infection occurs mainly through droplet or direct contact. due to this finding, frontline health care workers should follow stringent infection control and preventive measures, such as the use of ppe, to prevent infection ( ) . the mental health of the medical/health workers who are involved in the covid- outbreak is of great importance, because the strain on their mental well-being will affect their attention, concentration, and decision-making capacity. hence, for control of the covid- outbreak, rapid steps should be taken to protect the mental health of medical workers ( ) . since the living mammals sold in the wet market are suspected to be the intermediate host of sars-cov- , there is a need for strengthening the regulatory mechanism for wild animal trade ( ) . the total number of covid- confirmed cases is on a continuous rise and the cure rate is relatively low, making disease control very difficult to achieve. the chinese government is making continuous efforts to contain the disease by taking emergency control and prevention measures. they have already built a hospital for patients affected by this virus and are currently building several more for accommodating the continuously increasing infected population ( ) . the effective control of sars-cov- /covid- requires high-level interventions like intensive contact tracing, as well as the quarantine of people with suspected infection and the isolation of infected individuals. the implementation of rigorous control and preventive measures together might control the r number and reduce the transmission risk ( ) . clinical microbiology reviews considering the zoonotic links associated with sars-cov- , the one health approach may play a vital role in the prevention and control measures being followed to restrain this pandemic virus ( ) ( ) ( ) . the substantial importation of covid- presymptomatic cases from wuhan has resulted in independent, self-sustaining outbreaks across major cities both within the country and across the globe. the majority of chinese cities are now facing localized outbreaks of covid- ( ) . hence, deploying efficient public health interventions might help to cut the spread of this virus globally. the occurrence of covid- infection on several cruise ships gave us a preliminary idea regarding the transmission pattern of the disease. cruise ships act as a closed environment and provide an ideal setting for the occurrence of respiratory disease outbreaks. such a situation poses a significant threat to travelers, since people from different countries are on board, which favors the introduction of the pathogen ( ). although nearly cruise ships from different countries have been found harboring covid- infection, the major cruise ships that were involved in the covid- outbreaks are the diamond princess, grand princess, celebrity apex, and ruby princess. the number of confirmed covid- cases around the world is on the rise. the success of preventive measures put forward by every country is mainly dependent upon their ability to anticipate the approaching waves of patients. this will help to properly prepare the health care workers and increase the intensive care unit (icu) capacity ( ) . instead of entirely relying on lockdown protocols, countries should focus mainly on alternative intervention strategies, such as large-scale testing, contract tracing, and localized quarantine of suspected cases for limiting the spread of this pandemic virus. such intervention strategies will be useful either at the beginning of the pandemic or after lockdown relaxation ( ) . lockdown should be imposed only to slow down disease progression among the population so that the health care system is not overloaded. the reproduction number (r ) of covid- infection was earlier estimated to be in the range of . to . ( ); recently, it was estimated to be . to . ( ) . compared to its coronavirus predecessors, covid- has an r value that is greater than that of mers (r Ͻ ) ( ) but less than that of sars (r value of to ) ( ) . still, to prevent further spread of disease at mass gatherings, functions remain canceled in the affected cities, and persons are asked to work from home ( ) . hence, it is a relief that the current outbreak of covid- infection can be brought under control with the adoption of strategic preventive and control measures along with the early isolation of subsequent cases in the coming days. studies also report that since air traffic between china and african countries increased many times over in the decade after the sars outbreak, african countries need to be vigilant to prevent the spread of novel coronavirus in africa ( ) . due to fear of virus spread, wuhan city was completely shut down ( ) . the immediate control of the ongoing covid- outbreaks appears a mammoth task, especially for developing countries, due to their inability to allocate quarantine stations that could screen infected individuals' movements ( ) . such underdeveloped countries should divert their resources and energy to enforcing the primary level of preventive measures, like controlling the entry of individuals from china or countries where the disease has flared up, isolating the infected individuals, and quarantining individuals with suspected infection. most of the sub-saharan african countries have a fragile health system that can be crippled in the event of an outbreak. effective management of covid- would be difficult for low-income countries due to their inability to respond rapidly due to the lack of an efficient health care system ( ) . controlling the imported cases is critical in preventing the spread of covid- to other countries that have not reported the disease until now. the possibility of an imported case of covid- leading to sustained human-to-human transmission was estimated to be . . this can be reduced to a value of . by decreasing the mean time from the onset of symptoms to hospitalization and can only be made possible by using intense disease surveillance systems ( ) . the silent importations of infected individuals (before the manifestation of clinical signs) also contributed significantly to the spread of disease across the major cities of the world. even though the travel ban was implemented in wuhan ( ) , infected persons who traveled out of the city just before the imposition of the ban might have remained undetected and resulted in local outbreaks ( ) . emerging novel diseases like covid- are difficult to contain within the country of origin, since globalization has led to a world without borders. hence, international collaboration plays a vital role in preventing the further spread of this virus across the globe ( ) . we also predict the possibility of another outbreak, as predicted by fan et al. ( ) . indeed, the present outbreak caused by sars-cov- (covid- ) was expected. similar to previous outbreaks, the current outbreak also will be contained shortly. however, the real issue is how we are planning to counter the next zoonotic cov epidemic that is likely to occur within the next to years or even sooner (fig. ) . several years after the global sars epidemic, the current sars-cov- /covid- pandemic has served as a reminder of how novel pathogens can rapidly emerge and spread through the human population and eventually cause severe public health crises. further research should be conducted to establish animal models for sars-cov- to investigate replication, transmission dynamics, and pathogenesis in humans. this may help develop and evaluate potential therapeutic strategies against zoonotic cov epidemics. present trends suggest the occurrence of future outbreaks of covs due to changes in the climate, and ecological conditions may be associated with humananimal contact. live-animal markets, such as the huanan south china seafood market, represent ideal conditions for interspecies contact of wildlife with domestic birds, pigs, and mammals, which substantially increases the probability of interspecies transmission of cov infections and could result in high risks to humans due to adaptive genetic recombination in these viruses ( ) ( ) ( ) . the covid- -associated symptoms are fever, cough, expectoration, headache, and myalgia or fatigue. individuals with asymptomatic and atypical clinical manifestations were also identified recently, further adding to the complexity of disease transmission dynamics. atypical clinical manifestations may only express symptoms such as fatigue instead of respiratory signs such as fever, cough, and sputum. in such cases, the clinician must be vigilant for the possible occurrence of asymptomatic and atypical clinical manifestations to avoid the possibility of missed diagnoses. the present outbreak caused by sars-cov- was, indeed, expected. similar to clinical microbiology reviews previous outbreaks, the current pandemic also will be contained shortly. however, the real question is, how are we planning to counter the next zoonotic cov epidemic that is likely to occur within the next to years or perhaps sooner? our knowledge of most of the bat covs is scarce, as these viruses have not been isolated and studied, and extensive studies on such viruses are typically only conducted when they are associated with specific disease outbreaks. the next step following the control of the covid- outbreak in china should be focused on screening, identification, isolation, and characterization of covs present in wildlife species of china, particularly in bats. both in vitro and in vivo studies (using suitable animal models) should be conducted to evaluate the risk of future epidemics. presently, licensed antiviral drugs or vaccines against sars-cov, mers-cov, and sars-cov- are lacking. however, advances in designing antiviral drugs and vaccines against several other emerging diseases will help develop suitable therapeutic agents against covid- in a short time. until then, we must rely exclusively on various control and prevention measures to prevent this new disease from becoming a pandemic. history is repeating itself: probable zoonotic spillover as the cause of the novel coronavirus epidemic return of the coronavirus: -ncov china novel coronavirus investigating and research team. . a novel coronavirus from patients with pneumonia in china evolutionary perspectives on novel coronaviruses identified in pneumonia cases in china a novel coronavirus emerging in china-key questions for impact assessment bat coronaviruses in china drug treatment options for the -new coronavirus ( -ncov) comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov recent discovery and development of inhibitors targeting coronaviruses epidemiology, genetic recombination, and pathogenesis of coronaviruses understanding bat sars-like coronaviruses for the preparation of future corona virus outbreaks-implications for coronavirus vaccine development coronavirus infections reported by promed origin and evolution of the novel coronavirus clinical findings in a group of patients infected with the novel coronavirus (sars-cov- ) outside of wuhan, china: retrospective case series pathogenicity and transmissibility of -ncov-a quick overview and comparison with other emerging viruses genome composition and divergence of the novel coronavirus ( -ncov) originating in china genomic characterization and epidemiology of novel coronavirus: implications for virus origins and receptor binding clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province this scientist hopes to test coronavirus drugs on animals in locked-down wuhan coronavirus infection in equines: a review . design, synthesis and molecular docking of novel triazole derivatives as potential cov helicase inhibitors una nueva zoonosis viral de preocupación global: covid- , enfermedad por coronavirus coronavirus pathogenesis coronavirus infections and immune responses who. . coronavirus disease (covid- ) situation report- severe acute respiratory syndrome-related coronavirus: the species and its viruses-a statement of the coronavirus study group emerging coronaviruses: genome structure, replication, and pathogenesis coronaviridae: the viruses and their replication discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus coronaviruses: an overview of their replication and pathogenesis genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan coronavirus genome structure and replication viral and cellular mrna translation in coronavirus-infected cells ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex identification of novel subgenomic rnas and noncanonical transcription initiation signals of severe acute respiratory syndrome coronavirus emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments identification of a novel coronavirus causing severe pneumonia in human: a descriptive study bat origin of human coronaviruses discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing bats, civets and the emergence of sars middle east respiratory syndrome coronavirus and the one health concept the molecular biology of coronaviruses mechanisms of coronavirus cell entry mediated by the viral spike protein architecture of the sars coronavirus prefusion spike structure, function, and evolution of coronavirus spike proteins isolation and characterization of a bat sars-like coronavirus that uses the ace receptor bat origin of a new human coronavirus: there and back again a structural analysis of m protein in coronavirus assembly and morphology differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins s, m and e a conserved domain in the coronavirus membrane protein tail is important for virus assembly coronavirus envelope protein: current knowledge severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis structure and inhibition of the sars coronavirus envelope protein ion channel a severe acute respiratory syndrome corona virus that lacks the e gene is attenuated in vitro and in vivo modular organization of sars coronavirus nucleocapsid protein analysis of preferred codon usage in the coronavirus n genes and their implications for genome evolution and vaccine design the coronavirus nucleocapsid is a multifunctional protein the covid- clinical microbiology reviews nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its n-terminal domain and multimerization properties identification of in vivointeracting domains of the murine coronavirus nucleocapsid protein specific interaction between coronavirus leader rna and nucleocapsid protein subcellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein the nucleocapsid protein of coronaviruses acts as a viral suppressor of rna silencing in mammalian cells discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin the first novel coronavirus case in nepal the covid- epidemic economic impacts of wuhan -ncov on china and the world china critical care clinical trials group (cccctg). . intensive care during the coronavirus epidemic preparedness and proactive infection control measures against the emerging wuhan coronavirus pneumonia in china emerging viruses without borders: the wuhan coronavirus china coronavirus: what do we know so far? the continuing -ncov epidemic threat of novel coronaviruses to global health-the latest novel coronavirus outbreak in wuhan, china outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle the rate of underascertainment of novel corona virus ( -ncov) infection: estimation using japanese passengers data on evacuation flights initial cluster of novel coronavirus ( -ncov) infections in wuhan, china, is consistent with substantial human-to-human transmission china coronavirus: cases surge as official admits human to human transmission preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a data-driven analysis in the early phase of the outbreak the reproductive number of covid- is higher compared to sars coronavirus isolation and characterization of viruses related to the sars coronavirus from animals in southern china identification of alpha and beta coronavirus in wildlife species in france: bats, rodents, rabbits, and hedgehogs. viruses diagnosis, treatment, and prevention of novel coronavirus infection in children: experts' consensus statement interpretation of guidelines for the diagnosis and treatment of novel coronavirus ( -ncov) infection by the national health commission (trial version ) sars-cov- viral load in upper respiratory specimens of infected patients preliminary prediction of the basic reproduction number of the wuhan novel coronavirus -ncov bat-origin coronaviruses expand their host range to pigs the global spread of -ncov: a molecular evolutionary analysis receptor recognition by novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars the next big threat to global health? novel coronavirus ( -ncov): what advice can we give to travellers? interim recommendations january , from the latin-american society for travel medicine (slamvi) going global-travel and the novel coronavirus severe acute respiratory syndrome middle east respiratory syndrome coronavirus: risk factors and determinants of primary, household, and nosocomial transmission mast cells contribute to coronavirus-induced inflammation: new anti-inflammatory strategy consensus document on the epidemiology of severe acute respiratory syndrome (sars) epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in hong kong a new emerging zoonotic virus of concern: the novel coronavirus (covid- ) isolation, quarantine, social distancing and community containment: pivotal role for old-style public health measures in the novel coronavirus ( -ncov) outbreak middle east respiratory syndrome coronavirus (mers-cov) does sars-cov- has a longer incubation period than sars and mers? the spike glycoprotein of the new coronavirus -ncov contains a furin-like cleavage site absent in cov of the same clade covid- : the role of the nsp and nsp in its pathogenesis coronavirus covid- has killed more people than sars and mers combined, despite lower case fatality rate from sars to mers, thrusting coronaviruses into the spotlight another decade, another coronavirus a decade after sars: strategies for controlling emerging coronaviruses a sars-like cluster of circulating bat coronaviruses shows potential for human emergence origin and evolution of pathogenic coronaviruses identification of a novel betacoronavirus (merbecovirus) in amur hedgehogs from china who mers global summary and assessment of risk livestock susceptibility to infection with middle east respiratory syndrome coronavirus overview of the novel coronavirus ( -ncov): the pathogen of severe specific contagious pneumonia (sscp) -ncov: new challenges from coronavirus a familial cluster of pneumonia associated with the novel coronavirus indicating personto-person transmission: a study of a family cluster incubation period of novel coronavirus ( -ncov) infections among travellers from wuhan, china feng z. . early transmission dynamics in epidemiological, demographic, and clinical characteristics of cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study clinical features of patients infected with novel coronavirus in wuhan sars-cov, mers-cov and now the -novel cov: have we investigated enough about coronaviruses? a bibliometric analysis early detection and disease assessment of patients with novel coronavirus pneumonia pathological findings of covid- associated with acute respiratory distress syndrome potential maternal and infant outcomes from (wuhan) coronavirus -ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections clinical and biochemical indexes from -ncov infected patients linked to viral loads and lung injury the keypoints in treatment of the critical novel coronavirus pneumonia patient exploring the mechanism of liver enzyme abnormalities in patients with novel coronavirus-infected pneumonia fenner's veterinary virology sars-cov related betacoronavirus and diverse alphacoronavirus members found in western old-world genomic characterization and phylogenetic classification of bovine coronaviruses through whole genome sequence analysis biological and genetic characterization of a hemagglutinating coronavirus isolated from a diarrhoeic child feline coronaviruses: pathogenesis of feline infectious peritonitis canine enteric coronaviruses: emerging viral pathogens with distinct recombinant spike proteins canine respiratory coronavirus: an emerging pathogen in the canine infectious respiratory disease complex emergence of avian infectious bronchitis virus and its variants need better diagnosis, prevention and control strategies: a covid- clinical microbiology reviews global perspective pathogenesis and diagnostic approaches of avian infectious bronchitis the biology and pathogenesis of coronaviruses fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin complete genome sequence of bat coronavirus hku from chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome the pig as an intermediate host for influenza a viruses between birds and humans sars-associated coronavirus transmitted from human to pig identification of a novel coronavirus from a beluga whale by using a panviral microarray rapid classification of betacoronaviruses and identification of traditional chinese medicine as potential origin of zoonotic coronaviruses novel coronavirus: from discovery to clinical diagnostics a qualitative study of zoonotic risk factors among rural communities in southern china brazil burning! what is the potential impact of the amazon wildfires on vector-borne and zoonotic emerging diseases? a statement from an international experts meeting homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (manisjavanica). viruses : isolation and characterization of -ncov-like coronavirus from malayan pangolins a strategy to prevent future epidemics similar to the -ncov outbreak serological evidence of bat sars-related coronavirus infection in humans efficient management of novel coronavirus pneumonia by efficient prevention and control in scientific manner evolving status of the novel coronavirus infection: proposal of conventional serologic assays for disease diagnosis and infection monitoring measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in wuhan viral load of sars-cov- in clinical samples consistent detection of novel coronavirus in saliva molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes chest ct for typical -ncov pneumonia: relationship to negative rt-pcr testing emergence of a novel coronavirus disease (covid- ) and the importance of diagnostic testing: why partnership between clinical laboratories, public health agencies, and industry is essential to control the outbreak molecular diagnosis of a novel coronavirus ( -ncov) causing an outbreak of pneumonia labs scramble to produce new coronavirus diagnostics therapeutic and triage strategies for novel coronavirus disease in fever clinics radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study outbreak of novel coronavirus (covid- ): what is the role of radiologists? advances in developing therapies to combat zika virus: current knowledge and future perspectives advances in designing and developing vaccines, drugs, and therapies to counter ebola virus nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies-a comprehensive review a dna vaccine induces sars coronavirus neutralization and protective immunity in mice role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings anti-sars coronavirus agents: a patent review ( -present) characterization of the immune response of mers-cov vaccine candidates derived from two different vectors in mice the spike protein of sars-cov-a target for vaccine and therapeutic development one-health: a safe, efficient, dual-use vaccine for humans and animals against middle east respiratory syndrome coronavirus and rabies virus contributions of the structural proteins of severe acute respiratory syndrome coronavirus to protective immunity identification of the immunodominant neutralizing regions in the spike glycoprotein of porcine deltacoronavirus t-cell immunity of sars-cov: implications for vaccine development against mers-cov an emerging coronavirus causing pneumonia outbreak in wuhan, china: calling for developing therapeutic and prophylactic strategies use of the informational spectrum methodology for rapid biological analysis of the novel coronavirus -ncov: prediction of potential receptor, natural reservoir, tropism and therapeutic/vaccine target sars vaccine development immunoinformatics-aided identification of t cell and b cell epitopes in the surface glycoprotein of -ncov superior immune responses induced by intranasal immunization with recombinant adenovirus-based vaccine expressing full-length spike protein of middle east respiratory syndrome coronavirus epitope-based vaccine target screening against highly pathogenic mers-cov: an in silico approach applied to emerging infectious diseases analysis of the genome sequence and prediction of b-cell epitopes of the envelope protein of middle east respiratory syndromecoronavirus niaid. . developing therapeutics and vaccines for coronaviruses cepi. . cepi to fund three programmes to develop vaccines against the novel coronavirus, ncov- moderna announces funding award from cepi to accelerate development of messenger rna (mrna) vaccine against novel coronavirus novel inhibitors of severe acute respiratory syndrome coronavirus entry that act by three distinct mechanisms treatment with interferon-␣ b and ribavirin improves outcome in mers-cov-infected rhesus macaques middle east respiratory syndrome coronavirus (mers-cov): challenges in identifying its source and controlling its spread covid- , an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics potential antiviral therapeutics for novel coronavirus a novel coronavirus outbreak of global health concern coronavirusesdrug discovery and therapeutic options treatment with lopinavir/ritonavir or interferon-␤ b improves outcome of mers-cov infection in a nonhuman primate model of common marmoset treatment of middle east respiratory syndrome with a combination of lopinavir-ritonavir and interferon-␤ b (miracle trial): study protocol for a randomized controlled trial clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected clinical characteristics and therapeutic procedure for four cases with novel coronavirus pneumonia receiving combined chinese and western medicine treatment remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses chloroquine is a potent inhibitor of sars coronavirus infection and spread breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies towards a solution to mers: protective human monoclonal antibodies targeting different domains and functions of the mers-coronavirus spike glycoprotein characterization of novel monoclonal antibodies against merscoronavirus spike protein crossneutralization of sars coronavirus-specific antibodies against bat sars-like coronaviruses new coronavirus threat galvanizes scientists potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody cell-based antiviral screening against coronaviruses: developing virus-specific and broad-spectrum inhibitors passive immunotherapy with dromedary immune serum in an experimental animal model for middle east respiratory syndrome coronavirus infection potential interventions for novel coronavirus in china: a systemic review human transbodies that interfere with the functions of ebola virus vp protein in genome replication and transcription and innate immune antagonism inhibitors of ras might be a good choice for the therapy of covid- pneumonia screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses sars-cov, mers-cov, and -ncov fusion mechanism of -ncov and fusion inhibitors targeting hr domain in spike protein animal models for sars and mers coronaviruses recent advances in the vaccine development against middle east respiratory syndromecoronavirus virology: sars virus infection of cats and ferrets a live attenuated severe acute respiratory syndrome coronavirus is immunogenic and efficacious in golden syrian hamsters animal models and vaccines for sars-cov infection infection with mers-cov causes lethal pneumonia in the common marmoset vaccines for the prevention against the threat of mers-cov molecular basis of coronavirus virulence and vaccine development mice transgenic for human angiotensin-converting enzyme provide a model for sars coronavirus infection genetically engineering a susceptible mouse model for mers-cov-induced acute respiratory distress syndrome prospects for a mers-cov spike vaccine a mouse model for mers coronavirus-induced acute respiratory distress syndrome replicative capacity of mers coronavirus in livestock cell lines entry of human coronavirus nl into the cell china's response to a novel coronavirus stands in stark contrast to the sars outbreak response novel coronavirus is putting the whole world on alert early epidemiological analysis of the coronavirus disease outbreak based on crowdsourced data: a population-level observational study estimation of the transmission risk of the -ncov and its implication for public health interventions the mental health of medical workers in wuhan, china dealing with the novel coronavirus the progress of novel coronavirus ( -ncov) event in china nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study response to the emerging novel coronavirus outbreak potential for global spread of a novel coronavirus from china novel coronavirus, poor quarantine, and the risk of pandemic novel coronavirus outbreak in wuhan, china, : intense surveillance is vital for preventing sustained transmission in new locations risk for transportation of novel coronavirus disease from wuhan to other cities in china infections without borders: a new coronavirus in wuhan, china an interactive web-based dashboard to track covid- in real time limiting spread of covid- from cruise ships-lessons to be learnt from japan clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records a case of novel coronavirus in a pregnant woman with preterm delivery clinical features and obstetric and neonatal outcomes of pregnant patients with covid- in wuhan, china: a retrospective, single-centre, descriptive study a pregnant woman with covid- in central america latin american network of coronavirus disease -covid- research (lancovid- ). . clinical, laboratory and imaging features of covid- : a systematic review and meta-analysis comparison of different samples for novel coronavirus detection by nucleic acid amplification tests detection of sars-cov- in different types of clinical specimens a well infant with coronavirus disease with high viral load clinical presentation and virological assessment of hospitalized cases of coronavirus disease in a travel-associated transmission cluster public health might be endangered by possible prolonged discharge of sars-cov- in stool screening of faecal microbiota transplant donors during the covid- outbreak: suggestions for urgent updates from an international expert panel evidence for gastrointestinal infection of sars-cov- enteric involvement of coronaviruses: is faecal-oral transmission of sars-cov- possible? viral load kinetics of sars-cov- infection in first two patients in korea sars-cov- cell entry depends on ace and tm-prss and is blocked by a clinically proven protease inhibitor structure, function, and antigenicity of the sars-cov- spike glycoprotein discovery of a -nt deletion during the early evolution of sars-cov- aerosol and surface stability of sars-cov- as compared with sars-cov- laboratory diagnosis of emerging human coronavirus infections-the state of the art covid- ) emergency use authorization (eua) information-in vitro diagnostic euas the establishment of reference sequence for sars-cov- and variation analysis chloroquine and hydroxychloroquine as available weapons to fight covid- a systematic review on the efficacy and safety of chloroquine for the treatment of covid- new insights on the antiviral effects of chloroquine against coronavirus: what to expect for covid- ? aminoquinolines against coronavirus disease (covid- ): chloroquine or hydroxychloroquine of chloroquine and covid- in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) covid- : a recommendation to examine the effect of hydroxychloroquine in preventing infection and progression increased incidence of gastrointestinal side effects in patients taking hydroxychloroquine: a brand-related issue? clinical trials registry-chloroquine. covid- province and health commission of guangdong province for chloroquine in the treatment of novel coronavirus. . expert consensus on chloroquine phosphate for the treatment of novel coronavirus pneumonia covid- clinical microbiology reviews results of an open-label non-randomized clinical trial in vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine a trial of lopinavir-ritonavir in adults hospitalized with severe covid- reinfection could not occur in sars-cov- infected rhesus macaques severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection community-acquired respiratory viruses in transplant patients: diversity, impact, unmet clinical needs respiratory infections in the u.s. military: recent experience and control middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease two years after pandemic influenza a/ /h n : what have we learned? emerging respiratory viruses: challenges and vaccine strategies virus receptors: implications for pathogenesis and the design of antiviral agents an update on sars-cov- /covid- with particular reference on its clinical pathology, pathogenesis, immunopathology and mitigation strategies-a review can sars-cov- infection be acquired in utero? more definitive evidence is needed wuhan virus: chinese animal markets reopened with almost no precautions china must close down "wet markets will they ever learn? chinese markets are still selling bats and slaughtering rabbits on blood-soaked floors as beijing celebrates "victory sars-cov- : jumping the species barrier, lessons from sars and mers, its zoonotic spillover, transmission to humans, preventive and control measures and recent developments to counter this pandemic virus novel coronavirus outbreak research team. . epidemiologic features and clinical course of patients infected with sars-cov- in singapore air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus (sars-cov- ) from a symptomatic patient detectable sars-cov- viral rna in feces of three children during recovery period of covid- pneumonia quantitative detection and viral load analysis of sars-cov- in infected patients ct screening for early diagnosis of sars-cov- infection characterization of spike glycoprotein of sars-cov- on virus entry and its immune cross-reactivity with sars-cov preliminary identification of potential vaccine targets for the covid- coronavirus (sars-cov- ) based on sars-cov immunological studies insights into cross-species evolution of novel human coronavirus -ncov and defining immune determinants for vaccine development vaccine designers take first shots at covid- precision vaccinations. . coronavirus vaccines draft landscape of covid- candidate vaccines- features, evaluation and treatment coronavirus (covid- ) therapeutic opportunities to manage covid- /sars-cov- infection: present and future the use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease (covid- ): the experience of clinical immunologists from china non-steroidal anti-inflammatory drugs and covid- surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease (covid- ) expanded umbilical cord mesenchymal stem cells (uc-mscs) as a therapeutic strategy in managing critically ill covid- patients: the case for compassionate use ribavirin, remdesivir, sofosbuvir, galidesivir, and tenofovir against sars-cov- rna dependent rna polymerase (rdrp): a molecular docking study tilorone: a broad-spectrum antiviral invented in the usa and commercialized in russia and beyond no evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe covid- infection the fdaapproved drug ivermectin inhibits the replication of sars-cov- in vitro prevention of nosocomial sars-cov- transmission in endoscopy: international recommendations and the need for a gold standard treatment of critically ill patients with covid- with convalescent plasma a novel treatment approach to the novel coronavirus: an argument for the use of therapeutic plasma exchange for fulminant covid- coronavirus (covid- ) outbreak: what the department of endoscopy should know covid- : face masks and human-tohuman transmission. influenza other respir viruses does hand hygiene reduce sars-cov- transmission? reply to "does hand hygiene reduce sars-cov- transmission? clinical characteristics of medical staff with covid- : a retrospective study in a single center in wuhan revisiting the one health approach in the context of covid- : a look into the ecology of this emerging disease emerging coronavirus disease (covid- ), a pandemic public health emergency with animal linkages: current status update covid- , an emerging coronavirus infection: current scenario and recent developments-an overview cdc cruise ship response team, california department of public health covid- team, solano county covid- team. . public health responses to covid- outbreaks on cruise ships-worldwide preparing for the covid- pandemic: our experience in new york covid- : extending or relaxing distancing control measures sars-cov- : an emerging coronavirus that causes a global threat the novel coronavirus disease (covid- ) pandemic: a review of the current evidence profile of specific antibodies to sars-cov- : the first report sars-cov- and the hidden carriers-sewage, feline, and blood transfusion first confirmed detection of sars-cov- in untreated wastewater in australia: a proof of concept for the wastewater surveillance of covid- in the community what do we know about the sars-cov- coronavirus in the environment? susceptibility of ferrets, cats, dogs, and other domesticated animals to sars-coronavirus a critical needs assessment for research in companion animals and livestock following the pandemic of covid- in humans we should err on side of caution with covid- advice can cats become infected with covid- ? can companion animals become infected with covid- ? leading veterinary diagnostic company sees no covid- cases in pets avma. . sars-cov- in animals coronavirus disease (covid- ) outbreak: could pigs be vectors for human infections? xenotransplantation :e infection and rapid transmission of sars-cov- in ferrets current therapeutic applications and pharmacokinetic modulations of ivermectin hydroxychloroquine and ivermectin: a synergistic combination for covid- chemoprophylaxis and/or treatment? the approved dose of ivermectin alone is not the ideal dose for the treatment of covid- ivermectin and covid- : a report in antiviral research, widespread interest, an fda warning, two letters to the editor and the authors' responses rapid covid- vaccine development global efforts on vaccines for covid- : since, sooner or later, we all will catch the coronavirus abbott-launches-molecular-point-of-care-test-to -detect-novel-coronavirus-in-as-little-as-five-minutes era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned crispr-cas -based detection of sars-cov- diagnostic testing for severe acute respiratory syndrome-related coronavirus- : a narrative review artificial intelligence distinguishes covid- from community acquired pneumonia on chest ct development of a novel reverse transcription loop-mediated isothermal amplification method for rapid detection of sars-cov- global threat of sars-cov- /covid- and the need for more and better diagnostic tools diagnosing covid- : the disease and tools for detection in vitro diagnostic assays for covid- : recent advances and emerging trends point-of-care rna-based diagnostic device for covid- rapid colorimetric detection of covid- coronavirus using a reverse transcriptional loop-mediated isothermal amplification (rt-lamp) diagnostic plat-form: ilaco mapping the incidence of the covid- hotspot in iran-implications for travellers covid- : preparing for superspreader potential among umrah pilgrims to saudi arabia geographical tracking and mapping of coronavirus disease covid- /severe acute respiratory syndrome coronavirus (sars-cov- ) epidemic and associated events around the world: how st century gis technologies are supporting the global fight against outbreaks and epidemics policy decisions and use of information technology to fight novel coronavirus disease prediction models for diagnosis and prognosis of covid- infection: systematic review and critical appraisal consider pregnancy in covid- therapeutic drug and vaccine trials rational vaccine design in the time of covid- bacillus calmette guérin (bcg) vaccination use in the fight against covid- -what's old is new again? sars-cov- rates in bcg-vaccinated and unvaccinated young adults high throughput and comprehensive approach to develop multiepitope vaccine against minacious covid- on the origin and continuing evolution of sars-cov- covid- : the race for a vaccine all authors substantially contributed to the conception, design, analysis, and interpretation of data and checking and approving the final version of the manuscript, and we agree to be accountable for its contents.this compilation is a review article written, analyzed, and designed by its authors and required no substantial funding to be developed.all authors declare that there are no existing commercial or financial relationships that could, in any way, lead to a potential conflict of interest. with years of research and teaching experience in the areas of microbiology, immunology, virology, public health, medicine, and biomedicine as an eminent researcher, he has developed several diagnostics, vaccines, immunomodulatory modules, and hypotheses to counter infectious diseases of animals, poultry, and public health concerns. he has to his credit publications, books, and book chapters. dr. dhama has been recognized as an extremely productive researcher in the journal nature. he has been honored with best paper awards and other recognitions. he is an naas (national academy of agricultural science, india) associate and has worked as nodal officer, wto, and member, wildlife health specialist group (iucn). he is actively serving as editor-in-chief, co-eic, editor, and member, editorial board, of nearly scientific journals. his google scholar h-index is and scopus h-index is . sharun khan, m.v.sc., is currently working as a researcher in the stem cell laboratory, division of surgery, icar-indian veterinary research institute, izatnagar, india. his area of interest is regenerative medicine with a focus on understanding cell biology and molecular pathways involved in the maintenance and differentiation of stem cells originating from different tissues. he has particular interest and knowledge in the fields of veterinary medicine, pharmacology, infectious diseases of animals, wildlife diseases, diagnosis and therapy of animal diseases, nutrition, and biomedicine. with excellent academic records, he has received awards and recognitions (fellowships and scholarships) and participated in national and international workshops, training programs, and courses. he has a keen interest in learning excellent scientific writing skills and has published papers, including in international journals of repute. he is highly enthusiastic about gaining knowledge of advancements in educational and scientific research areas.ruchi tiwari is currently working as assistant professor in the department of veterinary microbiology, college of veterinary sciences, duvasu, mathura, india. she is currently pursuing her ph.d. (hons) degree from duvasu. with an excellent academic record and years of research and teaching experience, she has expertise in the field of diagnosis, prevention, and control of important livestock/poultry diseases/pathogens having public health significance, along with particular reference to veterinary microbiology, immunology, ethnoveterinary medicine, alternative and complementary therapies, and bacteriophage therapy. dr. tiwari has published research/review articles and book chapters. she has been honored with the young scientist award, best paper awards ( ) key: cord- -t azymo authors: yi, ye; lagniton, philip n.p.; ye, sen; li, enqin; xu, ren-he title: covid- : what has been learned and to be learned about the novel coronavirus disease date: - - journal: int j biol sci doi: . /ijbs. sha: doc_id: cord_uid: t azymo the outbreak of coronavirus disease (covid- ), caused by severe acute respiratory syndrome (sars) coronavirus (sars-cov- ), has thus far killed over , people and infected over , in china and elsewhere in the world, resulting in catastrophe for humans. similar to its homologous virus, sars-cov, which caused sars in thousands of people in , sars-cov- might also be transmitted from the bats and causes similar symptoms through a similar mechanism. however, covid- has lower severity and mortality than sars but is much more transmissive and affects more elderly individuals than youth and more men than women. in response to the rapidly increasing number of publications on the emerging disease, this article attempts to provide a timely and comprehensive review of the swiftly developing research subject. we will cover the basics about the epidemiology, etiology, virology, diagnosis, treatment, prognosis, and prevention of the disease. although many questions still require answers, we hope that this review helps in the understanding and eradication of the threatening disease. the spring festival on january , has become an unprecedented and unforgettable memory to all chinese who were urged to stay indoors for all the holiday and for many weeks after due to the outbreak of a novel viral disease. the virus is highly homologous to the coronavirus (cov) that caused an outbreak of severe acute respiratory syndrome (sars) in ; thus, it was named sars-cov- by the world health organization (who) on february , , and the associated disease was named cov disease- (covid- ) [ ] . the epidemic started in wuhan, china, and quickly spread throughout the entire country and to near others all over the world. as of march , , the virus has resulted in over , confirmed cases of covid- , with more than , patients discharged and over , patients who died. who warns that covid- is "public enemy number " and potentially more powerful than terrorism [ ] . according to pubmed (https://www.ncbi.nlm. nih.gov/pubmed/), in less than two months, over papers have been published on covid- including its virology, epidemiology, etiology, diagnosis, and treatment since the first report on january , that determined the sequence of the virus isolated from multiple patients [ ] . this review attempts to summarize the research progress in the new and swiftly developing subject area. whenever possible, we will try to compare covid- with sars and another cov-caused disease, middle east respiratory syndrome (mers, an outbreak in ). we will also discuss what we have learned so far regarding the prevention and prognosis of the disease as well as some remaining yet urgent questions. covs have been traditionally considered nonlethal pathogens to humans, mainly causing approximately % of common colds [ ] . however, in this century, we have encountered highly pathogenic human covs twice, i.e., sars-cov and mers-cov, which caused an outbreak originally in china in ivyspring international publisher and saudi arabia in , respectively, and soon spread to many other countries with horrible morbidity and mortality [ ] . therefore, the current covid- is the third cov outbreak in the recorded history of humans. as shown in fig. , clusters of pneumonia that had unknown origins were first reported from wuhan on december , to the china national health commission [ ] . seven days later the sequence of the cov was released [ ] . on january , the first fatal case from wuhan was reported [ ] . meanwhile, the epidemic rapidly spread to the neighboring cities, provinces, and countries. on january , the infection of health-care providers was reported, suggesting that human-to-human transmission was possible [ ] . on january , the city of wuhan was locked down with all its public transportation stopped. on january the first clinical study on the disease reported that, out of patients with confirmed cases, only had direct contact with the wuhan seafood market that was considered the starting site of the infection from an unknown animal source [ ] . on january , who declared the outbreak a global health emergency. by the time of this report, the disease has already spread throughout china and near other countries all over the world (fig. ) . as the situation is rapidly evolving, the final scope and severity of the outbreak remain to be determined. on february , , a multi-center study on , patients including , confirmed covid- patients presented a more updated illustration of the epidemic as follows (https://mp.weixin.qq.com/s/ ulbi-hx_rhpxa qha bhda). • sars-cov- infected people of all ages, but mainly at the age of - . almost half ( . %) of the infected individuals were over years old, very few were under , and only infected individuals were under the age of . • sars-cov- infected more men ( . / , ) than women ( . / , ). • covid- expanded in clusters mainly in and around hubei. • covid- took an average of ( - ) days from onset to diagnosis. the average incubation period was . ( . - . ) days. the average time from onset to death was . ( . - ) days. • the basic reproductive number (r ) was . ( % ci: . - . ), and the adjusted r was . - . . • the number of infected people increased exponentially before jan. , matching the time of massive transportation before the spring festival in china. • the mortality of patients with confirmed cases was . % ( % ci: . - . %), and the adjusted mortality of all the patients was . % ( % ci: . - . %). • three major risk factors for covid- were sex (male), age (≥ ), and severe pneumonia. covs are a subfamily of large and enveloped viruses containing a single strand of sense rna. they can be divided into four genera, i.e., alpha, beta, gamma, and delta, of which alpha-and beta-covs are known to infect humans [ ] . the envelope spike (s) glycoprotein binds to its cellular receptors angiotensin-converting enzyme (ace ) and dipeptidyl peptidase (dpp ) for sars-cov and mers-cov, respectively, and then membrane fusion occurs [ ] . the viral rna genome is released into the cytoplasm; after replication of the viral genome, genomic rna accompanied by envelope glycoproteins and nucleocapsid proteins forms virion-containing vesicles, which then fuse with the plasma membrane to release the virus [ ] . the first genomic sequence of sars-cov- was reported on january , [ ]. sars-cov- was found to be a new type of beta-cov with more than . % genetic identity among sequenced samples collected from the original site of the outbreak, the huanan seafood market in wuhan. sars-cov- is genetically more similar to sars-cov than to mers-cov [ ] [ ] [ ] . through transmission electron microscopy, sars-cov- particles were found in ultrathin sections of human airway epithelium [ ] . human ace was found to be a receptor for sars-cov- as well as sars-cov [ , , ] . however, the s protein of sars-cov- binds to human ace more weakly than that of sars-cov, which is coincident with the fact that sars-cov- causes less severe infection in patients than sars-cov [ ] . sars-cov- can also form a novel short protein encoded by orf b and a secreted protein encoded by orf . the orf b of sars-cov- may play a role in the viral pathogenicity and inhibit the expression of ifnβ; however, orf does not contain any known functional domain or motif [ ] . on february , , zhou, et al., reported the cryo-em structure of the full-length human ace at . Å resolution in complex with the amino acid transporter b at [ ] . they found that the complex, which had open and closed conformations, was assembled as a dimer and the ace -b at complex can bind two s proteins, which provides evidence for cov recognition and infection. b at may become a therapeutic target for drug screening to suppress sars-cov- infection. it has been known that both sars-cov and mers-cov originated from bats and were transmitted to humans via civet cats and camels, respectively. through a phylogenetic comparison of sars-cov- with other covs, bats were considered the native host of sars-cov- as the new virus is % identical to two sars-like covs from bats called bat-sl-covzx and bat-sl-covzx [ ] [ ] [ ] ] . however, what intermediate host helped the virus cross the species barrier to infect humans remains unknown, and the transmission route is yet to be elucidated. ji, et al., proposed snakes as a carrier of the virus from bats to humans which involved homologous recombination within the s protein [ ] . according to a study, researchers in guangzhou, china, suggested that pangolins -long-snouted, anteating mammals often used in traditional chinese medicine -are the potential intermediate host of sars-cov- based on % genetic homology in a cov discovered in pangolins and sars-cov- [ ] . however, % difference spread all over two genomes is still a big difference; thus, conclusive results for concrete evidence are awaited (fig. ) . the physicochemical properties of sars-cov- are largely not yet known. sars-cov and mers-cov can survive in vitro for hours in a dry environment and up to days under °c and %- % humidity [ ] [ ] [ ] . sars-cov- may possess similar properties. it has been reported that sars-cov- is sensitive to ultraviolet rays and heat at °c for minutes; ether, % ethanol, chlorine-containing disinfectant, peracetic acid, chloroform, and other fatty solvents, but not chlorhexidine, can effectively inactivate the virus [ ] . the entire human population generally lacks immunity to sars-cov- and hence is susceptible to the novel virus. currently, no detailed study has been reported regarding the immunological response to sars-cov- . thus, we can only refer to previous studies on other covs, especially sars-cov and mers-cov (fig. ) . in general, after a virus invades the host, it is first recognized by the host innate immune system through pattern recognition receptors (prrs) including c-type lectin-like receptors, toll-like receptor (tlr), nod-like receptor (nlr), and rig-ilike receptor (rlr) [ ] . through different pathways, the virus induces the expression of inflammatory factors, maturation of dendritic cells, and synthesis of type i interferons (ifns) which limit the spreading of the virus and accelerate macrophage phagocytosis of viral antigens [ ] . however, the n protein of sars-cov can help the virus escape from the immune responses [ ] . soon, the adaptive immune response joins the fight against the virus. t lymphocytes including cd + and cd + t cells play an important role in the defense. cd + t cells stimulate b cells to produce virus-specific antibodies, and cd + t cells directly kill virus-infected cells. t helper cells produce proinflammatory cytokines to help the defending cells. however, cov can inhibit t cell functions by inducing apoptosis of t cells. the humoral immunity including complements such as c a and c a and antibodies is also essential in combating the viral infection [ , ] . for example, antibodies isolated from a recovered patient neutralized mers-cov [ ] . on the other hand, an overreaction of the immune system generates a large number of free radicals locally that can cause severe damages to the lungs and other organs, and, in the worst scenario, multi-organ failure and even death [ ] . the sars-cov- infection, featured by clustering onset, is more likely to affect elderly people with comorbidities and pregnant women [ ] . it is common that for people who are exposed to a large number of viruses or whose immune functions are compromised, they have higher chance to be infected than others. the estimated mean incubation period of sars-cov- is - days, mostly - days based on a study of the first cases in wuhan [ ] . however, a study on , cases demonstrates that the incubation period was days on average and ranged from to days [ ] . a more recent study, as described above, demonstrates that the incubation period was . ( . - . ) days based on the demography of , cases [ ] . it is very important for health authorities to adjust the effective quarantine time based on the most accurate incubation period, thus preventing infected but symptomless people from transmitting the virus to others [ ] . as a common practice, individuals exposed to, or infected by, the virus are usually required to be quarantined for days. should the quarantine time be extended to days? fever is often the major and initial symptom of covid- , which can be accompanied by no symptom or other symptoms such as dry cough, shortness of breath, muscle ache, dizziness, headache, sore throat, rhinorrhea, chest pain, diarrhea, nausea, and vomiting. some patients experienced dyspnea and/or hypoxemia one week after the onset of the disease [ ] . in severe cases, patients quickly progressed to develop acute respiratory syndrome, septic shock, metabolic acidosis, and coagulopathy. patients with fever and/or respiratory symptoms and acute fever, even without pulmonary imaging abnormalities, should be screened for the virus for early diagnosis [ ] [ ] [ ] . a demographic study in late december of showed that the percentages of the symptoms were % for fever, % for dry cough, % for dyspnea, and % for diarrhea; % of the patients required ventilation support [ ] . similar findings were reported in two recent studies of a family cluster and a cluster caused by transmission from an asymptomatic individual [ , ] . comparably, a demographic study in showed that mers-cov patients also had fever ( %), dry cough ( %), and dyspnea ( %) as their main symptoms. however, % of them required ventilation support, much more than covid- patients and consistent with the higher lethality of mers than of covid- . diarrhea ( %) and sore throat ( %) were also observed with mers patients. in sars patients, it has been demonstrated that fever ( %- %), dry cough ( %- %), dyspnea ( %- %), diarrhea ( - %), and sore throat ( - %) were the major symptoms and ventilation support was required for approximately %- % of the patients [ ] . by february , the mortality of covid- was % when the confirmed cases reached , globally. comparably, the mortality of sars by november was % of , confirmed cases [ ] . for mers, based on a demographic study in june , the mortality was % of , confirmed cases [ ] . an earlier study reported that the r of sars-cov- was as high as . with a % confidence interval (ci) of . - . [ ] , whereas the r of sars-cov only ranged from to [ ] . a comparison of sars-cov- with mers-cov and sara-cov regarding their symptoms, mortality, and r is presented in table . the above figures suggest that sars-cov- has a higher ability to spread than mers-cov and sars-cov, but it is less lethal than the latter two [ ] . thus, it is much more challenging to control the epidemic of sars-cov- than those of mers-cov and sars-cov. clustered onset often happens in the same family or from the same gathering or vehicle such as a cruise ship. patients often have a history of travel or residence in wuhan or other affected areas or contact with infected individuals or patients in the recent two weeks before the onset [ ] . however, it has been reported that people can carry the virus without symptoms longer than two weeks and cured patients discharged from hospitals can carry the virus again [ ] , which sends out an alarm to increase the time for quarantine. patients have normal or reduced number of peripheral white blood cells (especially lymphocytes) at the early stage. for example, lymphopenia with white blood cell count < × /l including lymphocyte count < × /l, and elevated aspartate aminotransferase levels and viremia were found in , covid- patients [ ] . the levels of liver and muscle enzymes and myoglobin were increased in the blood of some patients, and c-reactive protein and erythrocyte sedimentation were increased in the blood of most patients [ ] . in patients with severe cases, the level of d-dimer, a fibrin degradation product present in the blood, was elevated, and lymphocyte count was progressively reduced [ ] . abnormalities in chest radiography are found in most covid- patients and featured by bilateral patchy shadows or ground glass opacity in the lungs. patients often develop an atypical pneumonia, acute lung injury, and acute respiratory distress syndrome (ards) [ ] . when ards happens, uncontrolled inflammation, fluid accumulation, and progressive fibrosis severely compromise the gas exchange. dysfunction of type-i and type-ii pneumocytes decreases the surfactant level and increases surface tension, thus reducing the ability of the lungs to expand and heightening the risk of lung collapse [ , ] . therefore, the worst chest radiographic findings often parallel the most severe extent of the disease [ ] . on february , , the first pathological analysis of covid- demonstrated the desquamation of pneumocytes, hyaline membrane formation, and interstitial lymphocyte infiltration, and multinucleated syncytial cells in the lungs of a patient who died of the disease, consistent with the pathology of viral infection and ards [ ] and similar to that of sars and mers patients [ , ] . the detection of sars-cov- rna via reversetranscriptase polymerase chain reaction (rt-pcr) was used as the major criteria for the diagnosis of covid- . however, due to the high false-negative rate, which may accelerate the epidemic, clinical manifestations started to be used for diagnosis (which no longer solely relied on rt-pcr) in china on february , . a similar situation also occurred with the diagnosis of sars [ ] . therefore, a combination of disease history, clinical manifestations, laboratory tests, and radiological findings is essential and imperative for making an effective diagnosis. on february , , the feng zhang group described a protocol of using the crispr-based sherlock technique to detect sars-cov- , which detects synthetic sars-cov- rna fragments at × - mol/l to × - mol/l ( - copies per microliter of input) using a dipstick in less than an hour without requiring elaborate instrumentation [ ] . hopefully, the new technique can dramatically enhance the sensitivity and convenience if verified in clinical samples. due to the lack of experience with the novel cov, physicians can mainly provide supportive care to covid- patients, while attempting a variety of therapies that have been used or proposed before for the treatment of other covs such as sars-cov and mers-cov and other viral diseases ( table ) . these therapies include current and potential treatments with antiviral drugs, immunosuppressants, steroids, plasma from recovered patients, chinese medicine, and psychological support. even plasma from recovered patients was proposed to be used for treatment [ ] . pharmaceutical companies are racing to develop antibodies and vaccines against the virus [ ] . sars-cov- mainly attacks the lungs in the beginning and probably also attacks, to a lesser degree, other organs that express ace , such as the gastrointestinal system and the kidneys. nevertheless, respiratory dysfunction and failure are the major threat to the patients and the major cause of death. thus, respiratory support is critical to relieve the symptoms and save lives and includes general oxygen therapy, high-flow oxygen, noninvasive ventilation, and invasive mechanical ventilation depending on the severity of the disease. patients with severe respiratory symptoms have to be supported by extracorporeal membrane oxygenation (ecmo), a modified cardiopulmonary bypass technique used for the treatment of life-threatening cardiac or respiratory failure. in addition, the maintenance of electrolyte balance, the prevention and treatment of secondary infection and septic shock, and the protection of the functions of the vital organs are also essential for sars-cov- patients [ ] . it has been known that a cytokine storm results from an overreaction of the immune system in sars and mers patients [ ] . cytokine storm is a form of systemic inflammatory response featured by the release of a series of cytokines including tnfα, il- β, il- , il- , ifnα, ifnβ, ifnγ, and mcp- . these cytokines induce immune cells to release a vast number of free radicals which are the major cause of ards and multiple organ failure [ ] . immunosuppression is essential in the treatment of cytokine storms, especially in severe patients. corticosteroids and tocilizumab, an anti-il monoclonal antibody, have been used to treat cytokine storm [ ] . other immunosuppression treatments for cytokine storm include the modulation of t cell-directed immune response; the blockade of ifn-γ, il- , and tnf; jak inhibition [ ] ; blinatumomab [ ] ; suppressor of cytokine signaling [ ] ; and hdac inhibitors [ ] . steroids, as immunosuppressants, were widely used in the treatment of sars to reduce the severity of inflammatory damage [ ] . however, steroids at high dosages were not beneficial to severe lung injury in sars and covid- patients [ , ] . instead, they may cause severe side effects, especially avascular osteonecrosis, dramatically affecting the prognosis [ ] . nevertheless, short courses of corticosteroids at low-to-moderate doses have been recommended to be used prudently for critically ill covid- patients [ ] . at the time of writing, no effective antiviral therapy has been confirmed. however, intravenous administration with remdesivir, a nucleotide analog, has been found to be efficacious in an american patient with covid- [ ] . remdesivir is a novel antiviral drug developed by gilead initially for the treatment of diseases caused by ebola and marlburg viruses [ ] . later, remdesivir also demonstrated possible inhibition of other single stranded rna viruses including mers and sars viruses [ , ] . based on these, gilead has provided the compound to china to conduct a pair of trials on sars-cov- infected individuals [ ] , and the results are highly anticipated. in addition, baricitinb, interferon-α, lopinavir/ ritonavir, and ribavirin have been suggested as potential therapies for patients with acute respiratory symptoms [ , ] . diarrhea, nausea, vomiting, liver damage, and other adverse reactions can occur following combined therapy with lopinavir/ritonavir [ ] . the interaction of these treatments with other drugs used in the patients should be monitored carefully. the collection of the blood from patients who recovered from a contagious disease to treat other patients suffering from the same disease or to protect healthy individuals from catching the disease has a long history [ ] . indeed, recovered patients often have a relatively high level of antibodies against the pathogen in their blood. antibodies are an immunoglobulin (ig) produced by b lymphocytes to fight pathogens and other foreign objects and they recognize unique molecules in the pathogens and neutralize them directly [ ] . based on this, plasma was collected from the blood of a group of patients who recovered from covid- and was injected into seriously ill patients. their symptoms improved within hours, accompanied by reduced inflammation and viral loads and improved oxygen saturation in the blood. however, verification and clarification are necessary to propose the method for large-scale use before specific therapies are not yet developed. in addition, given the therapeutic effects, some disadvantages associated with the plasma should be considered carefully. for example, antibodies can overstimulate the immune response and cause cytokine release syndrome, which is potentially a life-threatening toxicity [ ] . the concentration of antibodies in the blood is usually low, and the demand for the plasma is large to treat critically ill patients. it is difficult to develop and produce specific antibodies rapidly enough to fight against a global epidemic [ ] . thus, it is more critical and practical to isolate b cells from recovered patients and identify the genetic codes encoding effective antibodies or screen for effective antibodies against essential proteins of the virus. this way, we can readily scale up the production of the antibodies. tcm has been used to treat a variety of diseases in china for thousands of years. however, its effects largely rely on a combination of multiple components in a formula that varies depending on the diagnosis of a disease based on the theories of tcm. most of the effective components remain unknown or are vague as it is difficult to extract and verify such components or their optimal combinations. currently, due to the lack of effective and specific therapy for covid- , tcm has become one of the major alternative treatments for patients with light to moderate symptoms or for those who have recovered from severe stages [ ] . for example, shu feng jie du capsules and lian hua qing wen capsules were found to be effective for covid- treatment [ ] . top cure rates in the treatment of covid- patients were observed in several provinces in china that used tcm in % of their patients, including gansu ( . %), ningxia ( %), and hunan ( %), whereas hubei province, which used tcm in only approximately % of its covid- patients, had the lowest cure rate ( %) [ ] . however, this is quite a rough comparison as many other impact factors such as the number and severity of the patients should be included in the evaluation. on february , , boli zhang and coworkers published a study to compare western medicine (wm) treatment alone with combined treatment of wm and tcm [ ] . they found that the times needed for body temperature recovery, symptom disappearance, and hospitalization were remarkably shorter in the wm+tcm group than in the wm only group. most impressively, the rate for symptomatic worsening (from light to severe) was remarkably lower for the wm+tcm group than for the wm only group ( . % versus . %) and the mortality was lower in the wm+tcm group than wm only group ( . % versus %). nevertheless, the efficacy and safety of tcm still await more well-controlled trials at larger scales and in more centers. it would also be intriguing to characterize the mechanism of actions and clarify the effective components of tcm treatments or their combinations if possible. patients with suspected or confirmed covid- mostly experience great fear of the highly contagious and even fatal disease, and quarantined people also experience boredom, loneliness, and anger. furthermore, symptoms of the infection such as fever, hypoxia, and cough as well as adverse effects of the treatments such as insomnia caused by corticosteroids can lead to more anxiety and mental distress. in the early phase of the sars outbreak, a range of psychiatric morbidities including persistent depression, anxiety, panic attacks, psychomotor excitement, psychotic symptoms, delirium, and even suicidality were reported [ , ] . mandatory contact tracing and quarantine, as a part of the public health responses to the covid- outbreak, can make people more anxious and guilty about the effects of the contagion, quarantine, and stigma on their families and friends [ ] . thus, mental health care should be provided to covid- patients, suspected individuals, and people in contact with them as well as the general public who are in need. the psychological support should include the establishment of multidisciplinary mental health teams, clear communications with regular and accurate updates about the sars-cov- outbreak and treatment plans and the use of professional electronic devices and applications to avoid close contact with each other [ ] . effective vaccines are essential for interrupting the chain of transmission from animal reservoirs and infected humans to susceptible hosts and are often complementary to antiviral treatment in the control of epidemics caused by emerging viruses. efforts have been made to develop s protein-based vaccines to generate long-term and potent neutralizing antibodies and/or protective immunity against sars-cov [ , ] . live-attenuated vaccines have been evaluated in animal models for sars [ ] . however, the in vivo efficacy of these vaccine candidates in elderly individuals and lethal-challenge models and their protection against zoonotic virus infection have yet to be determined before a clinical study is initiated. this is probably because sars died down years ago and no new case has been reported since. in contrast, sporadic cases and clusters of mers continue to occur in the middle east and spread to other regions owing to the persistence of zoonotic sources in endemic areas. vaccination strategies have been developed for mers by using inactivated virus, dna plasmids, viral vectors, nanoparticles, virus-like particles and recombinant protein subunits and some have been evaluated in animal models [ ] . the development of a safe and effective vaccine against sars-cov- for non-immune individuals is an urgent and critical task for controlling the ongoing epidemic. however, it is challenging to overcome the difficulty because of the long period of time (averaged months) needed for vaccine development and the dynamic variations of covs. as a novel disease, covid- has just started to manifest its full clinical course throughout thousands of patients. in most cases, patients can recover gradually without sequelae. however, similar to sars and mers, covid- is also associated with high morbidity and mortality in patients with severe cases. therefore, building a prognosis model for the disease is essential for health-care agencies to prioritize their services, especially in resourceconstrained areas. based on clinical studies reported thus far, the following factors may affect or be associated with the prognosis of covid- patients (table ) : • age: age was the most important factor for the prognosis of sars [ ] , which is also true for covid- . covid- mainly happened at the age of - with . % of those patients being over in a study of , cases as described above [ ] . patients who required intensive care were more likely to have underlying comorbidities and complications and were significantly older than those who did not (at the median age of versus ) [ ] , suggesting age as a prognostic factor for the outcome of covid- patients. • sex: sars-cov- has infected more men than women ( . / , versus . / , ), as described above [ ] . • comorbidities and complications: patients with covid- who require intensive care are more likely to suffer from acute cardiac injury and arrhythmia [ ] . cardiac events were also the main reason for death in sars patients [ , , ] . it has been reported that sars-cov- can also bind to ace -positive cholangiocytes, which might lead to liver dysfunctions in covid- patients [ ] . it is worth noting that age and underlying disease are strongly correlated and might interfere with each other [ ] . • abnormal laboratory findings: the c-reactive protein (crp) level in blood reflects the severity of inflammation or tissue injury and has been proposed to be a potential prognostic factor for disease, response to therapy, and ultimate recovery [ ] . the correlation of crp level to the severity and prognosis of covid- has also been proposed [ ] . in addition, elevated lactate dehydrogenase (ldh), aspartate aminotransferase (ast), alanine aminotransferase (alt), and creatine kinase (ck) may also help predict the outcome. these enzymes are expressed extensively in multiple organs, especially in the heart and liver, and are released during tissue damage [ , ] . thus, they are traditional markers for heart or liver dysfunctions. • major clinical symptoms: chest radiography and temporal progression of clinical symptoms should be considered together with the other issues for the prediction of outcomes and complications of covid- . • use of steroids: as described above, steroids are immunosuppressant commonly used as an adjunctive therapy for infectious diseases to reduce the severity of inflammatory damage [ ] . since a high dosage of corticosteroids was widely used in severe sars patients, many survivors suffered from avascular osteonecrosis with life-long disability and poor life quality [ ] . thus, if needed, steroids should be used at low dosage and for a short time in covid- patients. • mental stress: as described above, during the covid- outbreak many patients have suffered from extraordinary stress as they often endured long periods of quarantine and extreme uncertainty and witnessed the death of close family members and fellow patients. it is imperative to provide psychological counseling and long-term support to help these patients recover from the stress and return to normal life [ ] . according to demographic studies so far, covid- seems to have different epidemiological features from sars. in addition to replicating in the lower respiratory tract, sars-cov- can efficiently replicate in the upper respiratory tract and causes mild or no symptoms in the early phase of infection, similar to other covs that cause common colds [ ] . therefore, infected patients at the early phase or incubation period can produce a large amount of virus during daily activities, causing great difficulty for the control of the epidemic. however, the transmission of sars-cov was considered to occur when the patients are severely ill, while most transmission did not happen at the early phase [ ] . thus, the current outbreak of covid- is much more severe and difficult to control than the outbreak of sars. great efforts are currently underway in china including the lockdown of wuhan and surrounding cities and continuous quarantine of almost the entire population in hopes of interrupting the transmission of sars-cov- . although these actions have been dramatically damaging the economy and other sectors of the country, the number of new patients is declining, indicating the slowdown of the epidemic. the most optimistic estimate is that the outbreak will end by march and the downswing phase will last for - months [ ] . however, some other experts are not that optimistic. paul hunter, et al., estimated that covid- , which seems substantially more infectious than sars, will not end in [ ] . ira longini, et al., established a model to predict the outcome of the epidemic and suggested that sars-cov- could infect two-thirds of the global population [ ] . a canadian group reported that sars-cov- was detected in both mid-turbinate and throat swabs of patients who recovered and left the hospital weeks earlier [ ] , which indicates that the newly identified virus could become a cyclical episode similar to influenza. however, promising signs have occurred in china based on the declining number of new cases, indicating the current strategies might have been working. ebola was originally predicted to cause up to a million cases with half a million deaths. however, via strict quarantine and isolation, the disease has eventually been put under control [ , ] . it is possible, similar to sars-cov, that sars-cov- might become weaker in infectivity and eventually die down or become a less pathogenic virus co-existent with humans. a comparison of the epidemic of covid- with that of sars and mers is provided below (fig. ). sars-cov- is highly transmittable through coughing or sneezing, and possibly also through direct contact with materials contaminated by the virus [ ] . the virus was also found in feces, which raises a new possibility of feces-to-mouth transmission [ ] . a recent study on cases reported that % of the cases were possibly caused by nosocomial infections, including patients with other prior diseases and health-care providers [ ] . thus, great precaution should be used to protect humans, especially health-care providers, social workers, family members, colleagues, and even bystanders in contact with patients or infected people. the first line of defense that could be used to lower the risk of infection is through wearing face masks; both the use of surgical masks and n respirator masks (series # s) helps control the spread of viruses [ ] . surgical face masks prevent liquid droplets from a potentially infected individual from traveling through the air or sticking onto surfaces of materials, where they could be passed on to others [ ] . however, only n (series # s) masks can protect against the inhalation of virions as small as to nm, with only % of the virions being able to penetrate completely; sars-cov- is similar to sars-cov in size and both are approximately nm [ ] . since particles can penetrate even five surgical masks stacked together, health-care providers in direct contact with patients must wear n (series # s) masks but not surgical masks [ ] . in addition to masks, health-care providers should wear fitted isolation gowns in order to further reduce contact with viruses. viruses can also infect an individual through the eyes. on january , , a doctor was infected with sars-cov- although he wore an n mask; the virus might have entered his body through his inflammatory eyes [ ] . thus, health-care providers should also wear transparent face shields or goggles while working with patients. for the general public in affected or potentially affected areas, it is highly suggested that everybody wash their hands with disinfectant soaps more often than usual, try to stay indoors for self-quarantine and limit contact with potentially infected individuals. three feet is considered an appropriate distance for people to stay away from a patient [ ] . these actions are effective methods to lower the risk of infection as well as prevent the spread of the virus. although sars-cov- came as a new virus to the human world, its high homology to sars-cov as reported on january [ ] should have caused high alert to china based on her deep memory of the sars outbreak in . however, not until january did the director of the center of disease control of wuhan comfort the citizens by saying that the novel virus has low contagiousness and limited reproductivity from human to human and that it is not a problem to prevent and contain the disease. this message remarkably relaxed the alarm of the public, especially when the entire country was preparing for the spring festival, and the critical time was missed to contain the disease at its minimal scale in wuhan. the disease control agencies in china may take this hard lesson and make critical improvements in the future. for example, these agencies should be ( ) more careful when making public announcements as every word counts to citizens and can change their attitude and decisions; ( ) more sensitive and reactive to unusual information from clinics rather than waiting for formal reports from doctors or officials; ( ) more restrictive to contain a potential epidemic at its early stage rather than attempting to comfort the public; and ( ) more often to issue targeted and effective drills to increase the public's awareness about epidemic diseases and to test and improve the response system of the society periodically. the outbreak of covid- caused by the novel virus sars-cov- started in the end of december . in less than two months, it has spread all over china and near other countries globally at the time of this writing. since the virus is very similar to sars-cov and the symptoms are also similar between covid- and sars, the outbreak of covid- has created a sense of sars recurring. however, there are some remarkable differences between covid- and sars, which are essential for containing the epidemic and treating the patients. • covid- affects more elderly individuals than youth and more men than women, and the severity and death rate are also higher in elderly individual than in youth. • sars has higher mortality than covid- ( . % versus . %). • covid- patients transmit the virus even when they are symptomless whereas sars patients do so usually when they are severely ill, which causes much greater difficulty to contain the spread of covid- than sars. this partially explains why sars-cov- spread much faster and broader than sars-cov. • the regular rna assay for sars-cov- can be negative in some covid- patients. on the other hand, cured patients can be positive for the virus again. these findings dramatically increase the risk of virus spreading. given such rapid progress in research on covid- , several critical issues remain to be solved, as follows: • where did sars-cov- come from? although % genetic homolog was found between sars-cov- and two bat sars-like covs, we still cannot conclude that sars-cov- is from bats. • what animal was the intermediate species to transmit the virus from the original host, say bats, to humans? without knowing answers to # and , we cannot efficiently cut the transmission, and the outbreak can relapse at any time. • although molecular modeling and biochemical assays have demonstrated that sars-cov- binds to ace , how exactly does the virus enter the airway cells and cause subsequent pathological changes? does the virus also bind ace -expressing cells in other organs [ ] ? without clear answers to these questions, we cannot achieve fast and accurate diagnosis and effective treatment. • how long will the epidemic last? how is the virus genetically evolving during transmission among humans? will it become a pandemic worldwide, die down like sars or relapse periodically like the flu? it is essential but may take some time to search for answers to the above and many other questions. however, with whatever expense it may demand, we have no other choice but to stop the epidemic as soon as possible and bring our life back to normal. the covid- epidemic a: who warns coronavirus, now dubbed covid- , is 'public enemy number ' and potentially more powerful than terrorism sars and mers: recent insights into emerging coronaviruses coronavirus infections-more than just the common cold a novel coronavirus outbreak of global health concern cdc: novel coronavirus clinical characteristics of coronavirus disease in china reliefweb: johns hopki university. coronavirus covid- global cases by johns hopkins csse an interactive web-based dashboard to track covid- in real time host factors in coronavirus replication dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc insights into rna synthesis, capping, and proofreading mechanisms of sars-coronavirus genomic and protein structure modelling analysis depicts the origin and infectivity of -ncov evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding. the lancet a novel coronavirus from patients with pneumonia in china functional assessment of cell entry and receptor usage for lineage b β-coronaviruses, including -ncov discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan structure of dimeric full-length human ace in complex with b at homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross-species transmission from snake to human isolation and characterization of -ncov-like coronavirus from malayan pangolins stability of sars coronavirus in human specimens and environment and its sensitivity to heating and uv irradiation human coronaviruses: insights into environmental resistance and its influence on the development of new antiseptic strategies stability and inactivation of sars coronavirus nhc: diagnosis and treatment of pneumonia caused by new coronavirus (trial version modulation of murine dendritic cell function by adenine nucleotides and adenosine: involvement of the a( b) receptor sars-cov nucleocapsid protein antagonizes ifn-beta response by targeting initial step of ifn-beta induction pathway, and its c-terminal region is critical for the antagonism molecules great and small: the complement system an efficient method to make human monoclonal antibodies from memory b cells: potent neutralization of sars coronavirus ultrapotent human neutralizing antibody repertoires against middle east respiratory syndrome coronavirus from a recovered patient pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan coronavirus infections and immune responses early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia epidemiological and clinical features of the novel coronavirus outbreak in china epidemiologic and clinical characteristics of novel coronavirus infections involving patients outside wuhan epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study severe acute respiratory syndrome-related coronavirus: the species and its virusesa statement of the coronavirus study group identification of a novel coronavirus causing severe pneumonia in human: a descriptive study clinical features of patients infected with novel coronavirus in wuhan transmission of -ncov infection from an asymptomatic contact in germany importation and human-to-human transmission of a novel coronavirus in vietnam imaging changes in patients with -ncov summary of probable sars cases with onset of illness from nvember mers situation update estimation of the transmission risk of the -ncov and its implication for public health interventions consensus document on the epidemiology of sars organizaition wh. global surveillance for human infection with novel coronavirus epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study surfactant alteration and replacement in acute respiratory distress syndrome molecular pathology of emerging coronavirus infections clinical manifestations, laboratory findings, and treatment outcomes of sars patients pathological findings of covid- associated with acute respiratory distress syndrome the clinical pathology of severe acute respiratory syndrome (sars): a report from china immunohistochemical, and ultrastructural findings of a fatal case of middle east respiratory syndrome coronavirus infection in the united arab emirates clinical findings, treatment and prognosis in patients with severe acute respiratory syndrome (sars) a protocol for detection of covid- using crispr diagnostics bloomberg: china seeks plasma from recovered patients as virus treatment wired: niiler e. darpa cranks up antibody research to stall coronavirus differential role for t cells in the development of fibrotic lesions associated with reovirus /l-induced bronchiolitis obliterans organizing pneumonia versus acute respiratory distress syndrome first case of novel coronavirus in the united states clinical features and short-term outcomes of patients with sars in the greater toronto area timely mental health care for the novel coronavirus outbreak is urgently needed into the eye of the cytokine storm current concepts in the diagnosis and management of cytokine release syndrome review: cytokine storm syndrome: looking toward the precision medicine era cytokine release syndrome suppressor of cytokine signaling (socs ) protects against severe cytokine storm and enhances viral clearance during influenza infection hdac inhibitor reduces cytokine storm and facilitates induction of chimerism that reverses lupus in anti-cd conditioning regimen clinical evidence does not support corticosteroid treatment for -ncov lung injury osteonecrosis of hip and knee in patients with severe acute respiratory syndrome treated with steroids on the use of corticosteroids for -ncov pneumonia. the lancet therapeutic efficacy of the small molecule gs- against ebola virus in rhesus monkeys gs- and its parent nucleoside analog inhibit filo-, pneumo-, and paramyxoviruses broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses the new york times: denise grady. china begins teating an antiviral drug in coronavirus patients ecil- ): guidelines for diagnosis and treatment of human respiratory syncytial virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus coronaviruses -drug discovery and therapeutic options primary immunodeficiency disorders: a historic and scientific perspective immunoglobulins and virus antibody titers: of past needs, current requirements, and future options current concepts in the diagnosis and management of cytokine release syndrome drug treatment options for the -new coronavirus ( -ncov) covind- epidemic situation in real time clinical study on cases of covid- treated with combined traditional chinese and western medicine (in chinese) a revisit on older adults suicides and severe acute respiratory syndrome (sars) epidemic in hong kong prevalence of psychiatric morbidity and psychological adaptation of the nurses in a structured sars caring unit during outbreak: a prospective and periodic assessment study in taiwan the spike protein of sars-cov--a target for vaccine and therapeutic development sars vaccines: where are we? antibodies and vaccines against middle east respiratory syndrome coronavirus clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study patient characteristics infected with middle east respiratory syndrome coronavirus infection in a tertiary hospital a comparative study of clinical presentation and risk factors for adverse outcome in patients hospitalised with acute respiratory disease due to mers coronavirus or other causes therapeutic options for middle east respiratory syndrome coronavirus (mers-cov)--possible lessons from a systematic review of sars-cov therapy clinical and laboratory findings of middle east respiratory syndrome coronavirus infection clinical prognostic rules for severe acute respiratory syndrome in low-and high-resource settings specific ace expression in cholangiocytes may cause liver damage after -ncov infection applications of acute phase reactants in infectious diseases aspartate aminotransferase: bridging carbohydrate and energy metabolism in plasmodium falciparum lactate dehydrogenase in sickle cell disease induction of proinflammatory cytokines in human macrophages by influenza a (h n ) viruses: a mechanism for the unusual severity of human disease? avascular necrosis of bone in severe acute respiratory syndrome a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster the severe acute respiratory syndrome reality and future about covid- how long will covid- outbreak last bloomberg: lauerman j. coronavirus could infect two-thirds of globe, research shows first imported case of novel coronavirus in canada, presenting as mild pneumonia ebola, the day after the world after ebola: an overview of ebola complications, vaccine development, lessons learned, financial losses, and disease preparedness sciencealert: latest study suggests the new coronavirus is also spreading via feces clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan a quantitative assessment of the efficacy of surgical and n masks to filter influenza virus in patients with acute influenza infection do n respirators provide % protection level against airborne viruses, and how adequate are surgical masks? protecting healthcare staff from severe acute respiratory syndrome: filtration capacity of multiple surgical masks -ncov transmission through the ocular surface must not be ignored cdc: guideline for isolation precautions: preventing transmission of infectious agents in healthcare settings ace expression in kidney and testis may cause kidney and testis damage after -ncov infection y.y. and r.x. conceived and designed the manuscript. y.y., p.l., s.y., e.l. and r.x. wrote the manuscript. r.x gave the final approval of the manuscript. r.x. is a founder of imstem biotechnology, inc., a stem cell company. the other authors declare no competing financial interests. key: cord- - czqs q authors: pennisi, manuela; lanza, giuseppe; falzone, luca; fisicaro, francesco; ferri, raffaele; bella, rita title: sars-cov- and the nervous system: from clinical features to molecular mechanisms date: - - journal: int j mol sci doi: . /ijms sha: doc_id: cord_uid: czqs q increasing evidence suggests that severe acute respiratory syndrome-coronavirus- (sars-cov- ) can also invade the central nervous system (cns). however, findings available on its neurological manifestations and their pathogenic mechanisms have not yet been systematically addressed. a literature search on neurological complications reported in patients with covid- until june produced a total of studies. overall, these papers report that patients may exhibit a wide range of neurological manifestations, including encephalopathy, encephalitis, seizures, cerebrovascular events, acute polyneuropathy, headache, hypogeusia, and hyposmia, as well as some non-specific symptoms. whether these features can be an indirect and unspecific consequence of the pulmonary disease or a generalized inflammatory state on the cns remains to be determined; also, they may rather reflect direct sars-cov- -related neuronal damage. hematogenous versus transsynaptic propagation, the role of the angiotensin ii converting enzyme receptor- , the spread across the blood-brain barrier, the impact of the hyperimmune response (the so-called “cytokine storm”), and the possibility of virus persistence within some cns resident cells are still debated. the different levels and severity of neurotropism and neurovirulence in patients with covid- might be explained by a combination of viral and host factors and by their interaction. coronaviruses (covs) are a group of large enveloped non-segmented positive-sense rna viruses, causing respiratory and enteric diseases in animals and humans [ ] . a highly pathogenic cov, named severe acute respiratory syndrome (sars)-cov- (formerly known as -ncov), emerged in december in the hubei region of china, and in the city of wuhan in particular. the initial cases, presenting with a dry cough, sore throat, fever, dyspnea, and bilateral lung infiltrates on chest imaging, were all linked to the wuhan's huanan seafood wholesale market, which trades fish and a variety of live animals, including bats, poultry, marmots, and snakes [ ] . this novel cov has caused an outbreak viral antigen and more rapid antibody detection systems (such as the enzyme-linked immunosorbent assay) are currently being developed, although their accuracy is still limited by the relatively high rate of false-negative cases and, therefore, needs to be improved [ ] . more recently, other studies are trying to propose droplet digital pcr-based methods as more effective diagnostic strategies for the identification of sars-cov- positive patients with low viral load [ ] . to date, there is no effective treatment for patients with covid- . adenosine analogs (e.g., remdesivir, favipiravir, ribavirin, and galidesivir) acting on the rna-dependent polymerase and blocking the viral rna synthesis are promising. chloroquine (cq) and hydroxychloroquine (hcq) can effectively inhibit sars-cov- in vitro, but their efficacy in vivo is under evaluation, as well as the effect of serum rich in anti-sars-cov- antibodies obtained from convalescent subjects [ ] . very recently, a systematic review assessed the efficacy and safety of cq/hcq for treatment or prophylaxis of adult patients with covid- [ ] . thirty-two studies were included, of which randomized clinical trials (rcts) and non-randomized, with a total of , participants. overall, studies suggest that the treatment of hospitalized patients with cq/hcq may not reduce the risk of death compared to standard care. high dose regimens or combination with macrolides may be associated with harm, particularly qtc prolongation and cardiac arrhythmias [ ] . post-exposure prophylaxis may not reduce the rate of infection, although the quality of the evidence is low. the authors concluded that patients should be treated with cq/hcq only if monitored and in the context of high-quality rcts [ ] . therefore, rationalization of the use of these drugs is also advised [ ] . other non-specific immune modulators include human immunoglobulin and corticosteroids, such as dexamethasone, a glucocorticoid that has proved to be the first life-saving drug in these patients. in particular, dexamethasone mg once daily (either per os or by intravenous injection) for days may result in a reduction in mortality by / in patients on ventilators and by / in those receiving oxygen [ ] . other treatment options include specific monoclonal antibodies that bind the receptor-receptor domain of sars-cov- and antibodies that block inflammatory interleukins (il), such as tocilizumab. finally, several vaccines are under analysis and include live attenuated viruses, inactivated viruses, use of recombinant dna, and vaccines based on sars-cov- specific proteins and subunits [ ] . until these therapeutic options are confirmed, the main measures are prevention, isolation, social distancing, frequent hand washing, and the use of personal protective equipment. some experimental and clinical studies previously performed on other covs and preclinical models seem to converge on the evidence that these viruses may have a tropism into the central nervous system (cns). seven types of covs are currently known that can infect humans and cause neurological damage [ ] . in some animal and human covs (including those causing sars and mers), a neuroinvasive potential has been demonstrated [ ] . although there are limitations in the epidemiological studies carried on covid- , as well as limited case records for determining the actual incidence of these complications, some patients reported neurological symptoms, but clinical findings and pathogenic features have not yet systematically addressed. the penetration of several respiratory viruses into the cns has already been shown, a mechanism called "neuroinvasion," affecting both glia and neurons [ ] . in some cases and under certain conditions, the neurotropism can cause neurovirulence, which refers to the development of neurological manifestations [ ] . in the case of sars-cov- , the existence of these phenomena is supported by previous evidence showing human cns infection from other respiratory viruses, the cns of other species infected by covs, animal and in vitro models of cns infection by human covs, and the occurrence of neurological complications in the course of other human covs infections. the aims of this review are i) to summarize the available information on the relationship between covs and the nervous system, ii) to identify the potential targets and routes of entry of sars-cov- into the nervous system, and iii) to describe the range of the neurological features reported to date in patients with covid- and the proposed pathogenic mechanisms. all the common respiratory viruses affecting humans, such as influenza, covs, and respiratory syncytial virus (rsv), can be associated with various neurological manifestations, particularly in subjects experiencing severe pulmonary symptoms [ ] . for instance, the effects that rsv may cause include seizures, encephalitis, ataxia, and cerebellitis, and the virus has been detected in the cerebrospinal fluid (csf). influenza is known to cause neurological complications, such as encephalitis, myelitis, meningitis, and guillain-barré syndrome (gbs) [ ] . respiratory viruses, including the cov family, affect the cns of other species, such as birds, felines, and livestock [ ] . meningitis and spinal cord inflammation have been reported in cats affected by a pathogenic feline cov [ ] . a % homology resemblance has been assessed between the human oc cov and the swine hemagglutinating encephalomyelitis virus (hev), which can invade the porcine brain by retrograde neuronal propagation through the peripheral nerves [ ] . a subspecies of murine covs, called mouse hepatitis virus, induces a demyelinating disease resembling multiple sclerosis (ms) [ ] . human covs can induce acute or persistent infections in neuronal cell lineages, neuroglia, and oligodendrocytes [ ] [ ] [ ] . moreover, flaccid paralysis and demyelination in animal models can be caused by the human oc cov [ ] . in particular, it has been shown that the spread of the oc in susceptible mice runs from the olfactory bulb to the brainstem and spinal cord, and uses the axonal transport system as the avenue for the neuron-to-neuron spread [ ] . further, neuron-to-neuron propagation strategies observed in cell cultures include both passive viral particle diffusion and axonal transport [ ] . sars-cov, which may enter the cns through the olfactory bulb and transneuronally spread to other brain regions, can cause neuronal death in the human ace receptor transgenic mouse [ ] . at least four types of human covs have shown neuroinvasive capacity based on the detection of viral rna or other nucleic acids in the human brain [ ] . in a -month-old infant with severe immunodeficiency, a case of fatal oc cov-related encephalitis was confirmed through rna sequencing techniques and rt-pcr in samples of brain biopsy [ ] . immunohistochemical study of the brain showed a microglial reaction, t lymphocyte infiltrates, and presence of the oc cov nucleocapsid in neurons. in a -year-old adolescent with disseminated acute encephalomyelitis associated with oc cov infection, magnetic resonance imaging (mri) disclosed demyelination in the subcortical white matter, cerebellum, and spinal cord [ ] . the oc cov was detected in the csf and nasopharynx secretions by using the pcr. there has also been a report of gbs associated with e and oc cov co-infection in a pediatric patient [ ] . encephalitis, ischemic stroke, and polyneuropathy can result from sars-cov exposure, with viral rna detectable in the csf [ , ] . in a necropsy study carried out on victims of sars-cov, infected neurons were found in the cortex and hypothalamus, and genomic sequences of sars-cov were detected in all cases by using the rt-pcr [ ] . encephalomyelitis and vasculitis may result also from mers-cov infection. a series of three patients showed that they all suffered from an altered level of consciousness, ranging from confusion to coma, along with ataxia and motor deficit [ ] . at brain mri, bilateral lesions were evident in the white matter of the frontal, parietal, and temporal lobes, as well as in the basal ganglia and corpus callosum. two of these patients showed an increased protein level in the csf, while all had lymphocytopenia and severe multiple organ involvement, including kidney, liver, and the cardiovascular system [ ] . during the mers-cov infection, other neurological complications were reported: brainstem encephalitis, gbs [ ] , and cerebral hemorrhage in the context of thrombocytopenia and disseminated intravascular coagulation [ ] . a retrospective study involving mers patients reported that . % had seizures, while four had gbs in a series of cases. the latency of the neurological symptoms ranged from and days after the onset of the pulmonary disease [ ] . a pubmed-based literature search was performed to find all relevant reports published until june . the search queries were "covid- and nervous system", "brain", "neurology", "neurological", "encephalopathy", "encephalitis", "stroke", "seizures", "neuropathy". the search was also repeated by using the above-mentioned keywords and the term "sars-cov- " instead of "covid- ". the authors selected all the articles based on the abstract and full-text examination and without a priori appraisal of inclusion/exclusion criteria. indeed, the number of studies reporting neurological complications of covid- is still limited and the majority include case reports/case series or retrospective samples, without a systematic specific assessment of the neurological complications. the references of the articles retrieved were also examined in search of more data. after this process, a total of studies were included. figure summarizes the main neurological manifestations of covid- and proposed mechanisms. reported: brainstem encephalitis, gbs [ ] , and cerebral hemorrhage in the context of thrombocytopenia and disseminated intravascular coagulation [ ] . a retrospective study involving mers patients reported that . % had seizures, while four had gbs in a series of cases. the latency of the neurological symptoms ranged from and days after the onset of the pulmonary disease [ ] . a pubmed-based literature search was performed to find all relevant reports published until june . the search queries were "covid- and nervous system", "brain", "neurology", "neurological", "encephalopathy", "encephalitis", "stroke", "seizures", "neuropathy". the search was also repeated by using the above-mentioned keywords and the term "sars-cov- " instead of "covid- ". the authors selected all the articles based on the abstract and full-text examination and without a priori appraisal of inclusion/exclusion criteria. indeed, the number of studies reporting neurological complications of covid- is still limited and the majority include case reports/case series or retrospective samples, without a systematic specific assessment of the neurological complications. the references of the articles retrieved were also examined in search of more data. after this process, a total of studies were included. figure summarizes the main neurological manifestations of covid- and proposed mechanisms. the available research on the neurological involvement in sars-cov- makes it hard to causally link a specific neurological manifestation to the viral infection. as a general rule, severe forms of covid- are more likely to produce neurological complications when compared to the mild forms ( . % versus %). an autopsy study on deceased patients with covid- due to respiratory failure indicated the presence of cerebral edema and neuronal degeneration in these subjects [ ] . a study in wuhan (china), reported neurological findings in hospitalized patients with covid- [ ] . another systematic study in france [ ] noted neurological symptoms in of patients, including confusion, encephalopathy, and cortico-spinal tract signs at clinical examination, along with leptomeningeal enhancement and perfusion abnormalities on brain mri. overall, the most common neurological symptoms reported in some patients with covid- were headache, anosmia, ageusia, asthenia, and myalgia, followed by encephalopathy, seizures, stroke, and encephalitis [ ] . elderly patients and those with previous cognitive decline, multiple comorbidities, other infections, severe medical illness, poor premorbid functional status, malnutrition, and vascular risk factors (especially hypertension) have a higher risk to show an altered level of consciousness related to covid- [ , , ] . moreover, metabolic or endocrine derangements, including hypoor hypernatremia, hypo-or hypercalcemia, hypo-or hyperglycemia, renal and/or liver dysfunction, among others, put patients at further risk for encephalopathy. sepsis and the subsequent inflammatory and the so-called "cytokine storm" may also contribute to encephalopathy with il- , il- , il- , and tumor necrosis factor α (tnfα) being implicated in confusional states [ ] . finally, patients with previous neurological disorders and acute respiratory symptoms seem to be at increased risk for encephalopathy as the initial symptom of covid- . coherently, in the study by mao et al. [ ] , % of patients with a severe form of the disease presented an altered level of consciousness. toxic and metabolic causes, as well as the effects of drugs or hypoxia, may result in covid- -associated encephalopathy [ ] . interestingly, an electroencephalography (eeg) report on a patient with altered mental status who was unable to follow verbal orders as the presenting symptom of covid- showed diffuse slow waves, particularly in the left temporal region, whereas pathological findings demonstrated cerebral edema without inflammatory signs [ ] . in these cases, treatment is symptomatic and includes fever control, treatment of hypoxia, and antiepileptic medications [ ] . a case of covid- -associated (confirmed by rt-pcr in a nasopharyngeal sample) acute hemorrhagic necrotizing encephalopathy has also been described [ ] . brain computed tomography (ct) detected a symmetrical bilateral hypodense area in the medial thalamic nucleus, whereas mri showed contrast-enhanced hemorrhagic lesions, with multifocal and symmetrical disposition, in both thalami, insula, and the mesial region of temporal lobes [ ] . although relatively rare, acute necrotizing encephalopathy can be a severe complication of some viral infections, including the influenza virus. the authors postulated that the pathogenesis might be related to the "cytokine storm" induced by covid- [ ] . a posterior reversible encephalopathy-like syndrome, associated with transient cortical blindness, was also reported [ ] . based on the available evidence, sars-cov- should be included in the differential diagnosis algorithm of viral encephalitis. typical symptoms are fever, headache, seizures, behavioral disorders, and altered level of consciousness. in these patients, an early diagnosis is of crucial importance to increase the survival rate, especially in those with severe pneumonia and hypoxia [ ] . in a report of a -year-old woman from wuhan with covid- , the brain ct remained normal but the diagnosis of encephalitis was confirmed through the isolation of sars-cov- in the csf using genomic sequencing techniques [ ] . the case of a -year-old japanese man presenting with multiple generalized epileptic seizures and decreased level of consciousness led to a diagnosis of meningoencephalitis [ ] . brain mri showed hyperintense areas in the right mesial region of the temporal lobe and hippocampus. while the sars-cov- rna was not detected in the nasopharynx, it was identified in the csf by using rt-pcr, although it was unclear if some of the patient features were present in the context of seizures due to other causes [ ] . anyhow, high levels of proinflammatory cytokines in the csf can cause breakdown and increased permeability of the blood-brain barrier (bbb) which may, in turn, lead to viral invasion and clinical manifestation [ ] . seizures have already been reported in cov infections, and there has been a high proportion of breakthrough seizures in patients with epilepsy who developed covid- [ ] . nevertheless, a recent analysis of patients with covid- [ ] reported two seizure-like events only, with no confirmed cases of new-onset seizures. however, the study was limited by a lack of instrumental investigation (e.g., eeg, neuroimaging) and by its retrospective approach. a case report of a patient with no history of epilepsy who had multiple apparent tonic-clonic seizures in the context of covid- might be interpreted as an unmasked seizure disorder or a direct effect of covid- on the brain, although further confirmations are needed [ ] . when compared to younger subjects without comorbidities, elderly patients with covid- and vascular risk factors appear to be at greater risk for developing cerebrovascular complications [ ] . in a retrospective study of patients [ ] , ( %) presented with ischemic stroke, one ( . %) with cerebral venous thrombosis, and one ( . %) with a cerebral hemorrhage. the risk factors for stroke in this population were: advanced age (mean age: . years), severe pulmonary disease, hypertension, diabetes, marked inflammatory or procoagulant response (e.g., increased c-reactive protein and d-dimer), and previous cerebrovascular events [ ] . other researchers described five patients with stroke ( % ischemic), who had severe forms of covid- , increased d-dimer, thrombocytopenia, and multiple organ failure [ ] . notably, a study in the usa demonstrated that young patients (aged < years) more likely developed large-vessel strokes in the context of covid- , suggesting that all ages are vulnerable [ ] . regarding pathomechanisms, the increased risk of cerebrovascular disease during the covid- infection is likely multifactorial. it has been shown that sars-cov- can bind to the ace receptor on endothelial cells, which might result in increased blood pressure. both ischemic and hemorrhagic strokes can be secondary to the increase in blood pressure, together with the presence of thrombocytopenia and coagulation disorders. the "cytokine storm" may act as another pathogenic mechanism [ ] . the levels of c-reactive protein, ferritin, d-dimer, lactate dehydrogenase, and the leukocyte count have often been found to be elevated in these patients [ ] . moreover, increased inflammatory markers and hypercoagulability state seem to characterize severe cases, along with a substantially enhanced risk of stroke [ ] . the likelihood of ischemic or hemorrhagic stroke may be also increased by some viral-related mechanisms, including vascular endothelial cell infection and consequent vessel damage. on the other hand, it is well known that infection-associated systemic inflammation, thrombosis, or vasculitis increase the risk of stroke [ ] . finally, systemic vasculitis and cns vasculitis have been demonstrated at autopsy in patients with sars-cov [ ] . most patients with covid- complain of headaches. guan et al. [ ] found that . % of a series of more than patients reported headache, and in % of those with severe forms. the intensity of headache was generally referred to be mild, although the study did not mention whether a prior history of headache or any meningeal sign was present. in a recent case series [ ] , headaches were a predominant complaint, along with fever, cough, sore throat, and breathlessness. the prevalence varies in different reports, but headache may affect up to / of patients [ , ] . headache is a well-known clinical feature of meningitis, encephalitis, intracranial hypertension, cerebrovascular diseases, and vasculitis, whereas scarce pathophysiological data link it to covid- . in some cases, cytokines and chemokines released by macrophages may activate nociceptive sensory neurons [ ] , with a neuroinflammatory mechanism similar to that involved in pain [ ] . in this scenario, screening patients for secondary causes of headache, including covid- , is mandatory, especially for patients in whom frequency or severity of headache change, or present with systemic symptoms, or do not respond to first-line or habitual treatments. anosmia and secondarily taste disorders are commonly reported in patients with covid- and may appear suddenly [ ] . in italy, . % of patients had some form of chemosensory dysfunction [ ] , whereas in a case register of twelve european hospitals, the prevalence of olfactory and gustatory dysfunction in patients with covid- with mild-to-moderate symptoms [ ] was . % and %, respectively. notably, % of them declared the olfactory dysfunction as the initial symptom and % had no runny nose or nasal obstruction [ ] . indeed, although anosmia is noted in many other respiratory infections, such as cold and influenza, in covid- it is typically not accompanied by nasal swelling or rhinitis [ , , ] . given the reports of anosmia presenting as an early symptom of covid- , dedicated testing may offer the potential for early detection of sars-cov- infection. nevertheless, the chemosensory deficit in covid- has not yet been systematically investigated, although it is a current research "hot topic", both at the clinical-epidemiological and cellular level. initial observations and early studies suggested as possible mechanisms for anosmia in covid- the cleft syndrome, nasal obstruction and rhinorrhea, "cytokine storm", direct damage to olfactory receptor neurons (orns), and impairment of the brain olfactory centers. the most obvious cause would be a direct damage to orns, since other human covs (e.g., oc ) have shown to directly bind to orns. however, although anosmia is linked with human viruses causing the common cold, such as influenza and other covs (respiratory or not), the exact mechanism has not yet been clearly established. a new model of olfactory dysfunction in covid- has been recently drawn from the observation that sustentacular cells (suss) are the primary target of the virus and that suss infection triggers a cascade of events leading to anosmia [ ] . suss express ace and would be infected first. impairment of sus would negatively affect orns, leading to the inhibition of the odor perception. simultaneously, rapid immune response would be induced in a subset of orns and microvillar cells, which would lead to activation of lymphocytes and macrophages and their infiltration into the olfactory epithelium, as well as secretion of proinflammatory cytokines. stem cell infection may potentially explain why a small fraction of patients with covid- experience long-term dysosmia [ ] . of note, such a model does not imply that sars-cov- travels from the olfactory epithelium to the brain along the olfactory axons. indeed, no axonal transport of sars-cov- to the brain has been demonstrated in the hamster model during the first two weeks after infection [ ] , and no viral accumulation or persistence has been reported in cerebral olfactory regions of autopsy material from patients with covid- [ ] . on the other hand, rapid sars-cov- accumulation in the brain after intranasal injection was recently shown using the new humanized ace knock-in mouse [ ] . yet, this is not synonymous with transport along olfactory axons, as other routes are also possible. if sars-cov- travels within the olfactory axons, this would require an ace -independent passage of the virus from suss to orns within the olfactory epithelium. in addition, it would be relevant to examine progenitor or stem cell infection, as these olfactory epithelium cells also express significant levels of ace . probably, also host genetic factors play a role in individual susceptibility to anosmia in covid- and the characterization of these factors is of particular interest [ ] . regarding gustatory dysfunction in covid- , it is known that the ability to separate flavors depends on the retronasal stimulation pathway. therefore, in patients with ageusia, retronasal olfactory dysfunction is commonly suggested, although some studies reported high ace expression on the oral cavity mucosa and epithelial cells of the tongue [ ] . another possibility is that sars-cov- may have a direct effect on the taste buds or receptors [ ] . gbs (i.e., acute inflammatory demyelinating polyneuropathy) can follow a gastrointestinal or respiratory infection. a molecular mimicry mechanism, in which infecting viruses likely share epitopes similar to some peripheral nerve components, is believed to occur and to stimulate autoreactive t or b lymphocytes. antibodies against the virus cross-react and bind to peripheral nerve components, thus causing neuronal dysfunction and clinical manifestations. after sars-and mers-cov infections, both gbs and acute motor axonal neuropathy have been described [ , ] . reports of gbs in patients with covid- are emerging. a case series [ ] reported five cases of gbs in italy, and four of them presented with lower-extremity weakness and paresthesia. patients developed symptoms five to days after the onset of the viral infection. at electromyography, two patients had gbs and three acute motor axonal neuropathy [ ] . another patient in iran [ ] and an italian patient with the miller-fisher gbs variant [ ] were also reported. in a -year-old patient presenting with motor weakness of the lower extremities and covid- symptoms, gbs associated with sars-cov- infection was observed a week later [ ] . an increase in proteins ( mg/dl) but not in cells was found in the csf, while at neurophysiological examination increased distal latencies and f-waves absence was detected, suggesting a severe and diffuse peripheral nerve demyelination. although the authors reported that the patient was infected by sars-cov- at the onset of gbs symptoms (because the patient had lymphopenia and thrombocytopenia), it cannot be excluded that covid- and gbs presented coincidentally [ ] , and therefore further evidence is needed. some of the most frequently described non-specific symptoms are myalgia, unsteadiness, and fatigue. of note, . % of patients with covid- admitted in a wuhan hospital exhibited neurological manifestations [ ] , which were categorized as "cns involvement" ( . %), "peripheral involvement" ( . %), and "muscular-skeletal involvement" ( . %). among the latter, % of the non-severe patients reported myalgia, while . % had elevated levels of creatine kinase. two cases of rhabdomyolysis ( . %) were also described [ ] . apart from a general unspecific reaction to the awareness of infection, some psychiatric illnesses might directly result from exposure to human covs. in patients with psychotic symptoms compared to non-psychiatric controls, a higher prevalence of immune reactivity for hku and nl covs was found [ ] , suggesting that viral exposure may represent a comorbid risk factor in neuropsychiatric disease. however, the role that sars-cov- may play in the etiopathogenesis of psychiatric diseases needs to be explored. sars-cov entry into the human host cell seems to be mediated primarily by cellular receptors ace , which are expressed in the lung, kidney, vascular endothelia, small intestine, and human airway epithelia [ ] [ ] [ ] . conversely, mers-cov may enter human host cells primarily through the dipeptidyl peptidase- (dpp ) protein located in the membrane of cells of the immune system, liver, small intestine, and lower respiratory tract [ , ] . however, ace or dpp alone are not enough to make the host cell susceptible to infections. this is particularly true when considering that sars or mers infections were also reported in the cns, where ace or ddp expression level is low under normal conditions [ ] . the exact route through which sars and mers covs enter the cns is still not clear, although the glymphatic or a pure hematogenous path seems to be unlikely, particularly in the initial infection stage, during which no virus particle is detected in the brain [ , , ] . however, some evidence indicates that covs might initially invade peripheral nerve terminals, and later the cns through a synapse-connected route [ ] [ ] [ ] [ ] . coherently, the sars infection seems to be able to cause significant neuronal damage without substantial inflammatory infiltration [ ] . earlier studies have shown the presence of viral particles in the brain of patients with sars, located exclusively in the neurons [ , ] . in vivo experiments using transgenic mice showed that, when sars or mers covs are given intranasally, they can enter the brain via the olfactory nerve, and quickly spread to specific brain regions, such as the brainstem and the thalamus [ , ] . in these cases, the brain expresses ace receptors, that have been detected in neurons and glial cells, making them a potential target for covid- . another important observation is that in mice infected with mers-cov with low inoculum doses, virus particles are not detected in the lung but only in the brain, which indicates that the cns infection is relevant for the high mortality of the disease [ ] . however, although murine models develop cns infection, mers-cov has never been detected in the human cns, thus suggesting a different disease model [ ] . viruses are present in the brain of patients with sars-covs [ ] . baig et al. [ ] have recently suggested a putative transcribral sars-cov- route to the brain and the presence of its rna in the csf would be the conclusive evidence to support the covid- neurovirulence. however, the pathomechanisms underlying the cns invasion seem to be more complex. a cns invasion can occur in both the initial and late phases of sars-cov- infection [ ] . however, research is yet to determine the exact route for the entrance of the virus into the brain. a direct entry along the olfactory nerve can be considered among the potential mechanisms. in particular, the nasal olfactory epithelium is the probable site of enhanced binding of sars-cov- . multiple non-neuronal cell types within the olfactory epithelium express two host receptors, ace and transmembrane protease serine (tmprss ), that facilitate sars-cov- binding, replication, and accumulation. moreover, a subsequent brain infection beginning from the olfactory neurons might be considered, as well as the possibility that orns may initiate a rapid immune response at the early stages of the disease [ ] . using a mouse model, bilinska et al. [ ] determined whether cells in the olfactory epithelium expressed the receptors allowing the entry of the sars-cov- virus. they showed that ace and tmprss were expressed in the suss of the olfactory epithelium but not, or much less, in most olfactory receptor neurons, suggesting that suss are involved in sars-cov- virus entry and smell impairment. moreover, the expression of the entry proteins increased in older animals, thus possibly explaining, if verified also in humans, why older individuals are more susceptible to sars-cov- infection [ ] . translationally, these preliminary findings suggest that damage to the olfactory epithelium may not only underlie clinical anosmia but also represent a preferential gate to the brain. namely, sars-cov- might spread via the transcribral route from the olfactory epithelium along the olfactory nerve to the olfactory bulb within the cns or spread retrogradely via transsynaptic transfer using an endocytosis or exocytosis mechanism and a fast axonal transport mechanism of vesicle transport moving the virus along microtubules back to neuronal cell bodies [ ] . additionally, another possible transsynaptic route from the nasal respiratory epithelium to the brain via the trigeminal nerve branch has recently been hypothesized, although replication of the findings is needed [ ] . the biological plausibility of the retrograde transsynaptic pathway from the peripheral nerve endings is based on the evidence that some covs appear to be capable of penetrating the cns through the cribriform plate of the ethmoid bone, even if the olfactory bulb is efficient enough to control viral invasion [ ] . according to li et al. [ ] , mechanoreceptors and chemoreceptors in the lung and respiratory tract can act as a possible retrograde pathway for sars-cov- , as the nucleus of the solitary tract receives sensory information from these anatomical structures. indeed, a dysfunction of the cardiac-respiratory control centers in the medulla oblongata would aggravate the symptoms till death [ ] . however, the neurogenic hypothesis of respiratory failure is not supported by other researchers [ ] , as they argue that patients with covid- pneumonia do develop hypoxia and low co levels accompanied by increased respiratory rate. while these patients can breathe spontaneously, they do it with great effort; thus, a respiratory failure resulting from a neurological origin would be characterized by a reduced respiratory rate, low oxygen levels, and high co levels [ ] . further virologic, histopathological, and immunohistochemical studies are necessary to demonstrate a specific neurotropism of sars-cov- for the brain respiratory control centers. the hypotheses behind sars-cov- transsynaptic propagation are further corroborated by other studies demonstrating that the virus may use a transsynaptic route for infecting the cns. one of the first pieces of evidence was provided in by gosztonyi [ ] , who described the axonal transport of viral nucleic acid of some neurotropic viruses. in particular, he described that the rabies virus (rv) could be transmitted to other neurons by transsynaptic passage, without involving the complete virus replication, thus reaching various brain areas. li et al. [ ] demonstrated that hev was able to propagate into cns via transsynaptic routes. namely, the peripheral inoculation of hev in both piglets and rodents results in encephalomyelitis via the primary motor cortex, where membranous-coating-mediated endo-/exocytosis events favor the hev transsynaptic transfer. in a recent review, taylor and enquist [ ] deeply described the axonal route of propagation of several neuroinvasive viruses, including herpes simplex, varicella-zoster, pseudorabies, rhabdoviridae (including rv), flaviviridae, vesicular stomatitis (vsv), and theiler's murine encephalitis virus (belonging to the picornaviridae). they also described the mechanisms by which viruses were able to move in and out axons, both anterogradely or retrogradely, thanks to coupled or separate transports (mediated by vesicles or not, respectively) [ ] . the anterograde and retrograde transsynaptic propagation lead researchers to adopt this viral feature for mapping the axon transports of neuronal impulses, viruses, and other factors. in this context, the transsynaptic transport of vsv has been used for tracing and mapping neuronal circuits by using specific virus-labeling techniques [ , ] . of note, transsynaptic propagation is not a prerogative of cns viruses. for instance, the measles virus (mv) can reach the cns and cause subacute sclerosing panencephalitis, which is often fatal. the cns complications of mv infection are known to be the results of transsynaptic viral propagation thanks to the binding between mv envelope f protein and several host proteins, including hemagglutinin and neurokinin- [ ] . taken together, these observations support the concept that some viruses, including respiratory viruses like the sars-cov- , may propagate through the cns via a transsynaptic transport. the cell invasion of sars-cov- and its rapid replication seem to be supported by the ace receptor [ ] . the damaging effects of angiotensin ii may be enhanced because of the depletion of the ace receptor on the cell membrane, which leads to an acute deterioration in lung function. therefore, the down-regulation of the ace receptor could put the hypertensive and diabetic population at higher risk for covid- due to the increase in angiotensin ii. a hypothesis related to this issue is that ace inhibitors, when used in patients with covid- , can lead to an increased expression of ace , thus probably making the cells more vulnerable to sars-cov- infection [ ] . a study examining the risk factors for mortality in patients with covid- found that % of the deceased people presented single or multiple comorbidities, with high blood pressure being the most common ( %) [ ] . the neurovirulence of sars-cov- could be related to the degree of expression of the ace receptor in the cns, although this receptor is expressed in endothelial cells, so it is necessary to further investigate its role in the etiopathogenesis of some neurological complications, such as stroke [ ] . the viral s protein might allow the virus interaction in brain microcirculation with ace receptors expressed in the capillary endothelium, possibly leading to endothelial cells infection and subsequent spreading to the neurons after that the endothelial damage has occurred [ ] . damage of the epithelial barrier by covs may occur, thus allowing the virus to reach the bloodstream or the lymphatic system and to spread to other tissues, including the brain. in this scenario, however, it is important to distinguish between the nasal olfactory epithelium and the nasal respiratory epithelium. while the former has been indicated as the main route for the trans-synaptic propagation of covs, the latter seems to be involved in the hematogenous propagation [ ] . nevertheless, it is not well clearly understood how this could take place, although the bbb seems to be involved. two hypotheses have been proposed for the crossing of the bbb by sars-cov- . the first mechanisms would involve the infection and transport across vascular endothelial cells, which express ace and, as such, are at risk for sars-cov- infection [ ] . sars-cov- particles have been found in capillary endothelia and neurons of a frontal lobe specimen from an autopsy case study [ ] . in particular, viral particles were packaged in intraneuronal dilated vesicles, and endocytosis or exocytosis of viral particles across endothelial cells were detected by electron microscopic imaging [ ] . as soon as the virus enters vascular and neuronal cells, it might interact with ace on neurons, glia, and vessels, and then begin a cycle of viral budding, thus further damaging both vascular and neuronal tissue [ ] . the second hypothesis is based on the so-called "trojan horse mechanism," through the infection of leukocytes that pass the bbb [ ] . as lymphocytes, granulocytes, and monocytes all express ace , the sars-cov might able to infect them [ , [ ] [ ] [ ] , and it is likely that sars-cov- too may act in the same manner. moreover, the covid- -related systemic inflammation would increase the bbb permeability, thus facilitating the invasion of the cns by the infected immune cells [ ] . covid- -related hypoxia may be responsible for indirect neuronal damage as it induces anaerobic metabolism in the cns cells, ischemia, interstitial edema, and vasodilatation in the cerebral circulation, which eventually causes stroke, syncope, and anoxic crisis [ ] . the fact that covs can infect macrophages, astroglia, and microglia makes it possible for the host's immune-mediated response to playing a role. in some patients who died because of covid- , a multiple organ failure and a hyperinflammatory syndrome (the "cytokine storm") were hypothesized as possible underlying causes [ ] . in this context, a previous study in mice showed t-lymphocyte infiltration into the cns and significantly increased levels of the proinflammatory cytokine il- and the chemokine monocyte chemoattractant protein- after cov exposure [ ] . finally, in genetically predisposed individuals, the persistence of covs in some cns resident cells cannot be excluded, where they would act as a cofactor of clinical exacerbations. serological techniques have identified covs in various neurological diseases, such as parkinson's disease, ms, and optic neuritis [ ] [ ] [ ] [ ] . therefore, it was proposed that a persistent cov infection might be a pathogenic factor in the development and course of some neurological diseases. for instance, infectious agents may play a triggering role in ms, with viruses being the most likely culprit in genetically predisposed individuals [ ] . taken together, all the mechanisms discussed here might, at least in part, explain why and how sars-cov- could be moved in or within the cns despite the low expression of ace receptor in the brain. further studies are needed to better understand these pivotal aspects of neuroinfection. the research on the neurological manifestations of covid- has recently made significant progress, although the exact neuropathogenic mechanisms of sars-cov- are not yet completely clear. essential questions are emerging with the identification of people with covid- and cns involvement. although these patients may exhibit a wide range of neurological complications, it remains to be determined whether these can be an indirect and unspecific consequence of the pulmonary disease, hypoxia, or generalized inflammatory state on the cns, or if they may rather reflect a direct viral-related neuronal damage. some symptoms, such as headache and unsteadiness, are non-specific manifestations of several viral infections but, in some cases, they might accompany more severe diseases, such as meningitis, encephalitis, and stroke. a hematogenous versus a transsynaptic propagation is still debated, as well as the role of the ace receptor, the impact of hyperimmune response, and the viral persistence within some cns cells. the different levels and severity of human neurotropism and neurovirulence in patients with covid- might be explained by a combination of viral and host factors and their interaction. although researchers are yet to elucidate the real degree of neurovirulence of sars-cov- , there is a demonstration of its presence in the csf or tissue samples at autopsy. however, in the current epidemic, some difficulties may occur in performing mri or a lumbar puncture, especially in severely affected patients and in those admitted in intensive care units. nevertheless, it remains of pivotal importance for all patients with altered consciousness or any unexplained neurological manifestation to receive an accurate neurological exam and appropriate instrumental investigations (i.e., neuroimaging, eeg, evoked potentials, csf), when necessary [ ] . another warning related to this topic is that lymphopenia in immunosuppressed patients with covid- can be a serious risk factor; these are not only patients with cancer or with systemic autoimmune diseases but also patients with neurological disorders. indeed, taking high-dose corticosteroids or immunosuppressive/biological treatments is relevant for diseases like cerebral vasculitis, neuromyelitis optica, neurosarcoidosis, polymyositis, myasthenia gravis, or ms, and the scientific community should rapidly develop ad hoc guidelines for the management (especially in terms of reevaluation of dosages and treatment cycles) of these diseases during the covid- era. another relevant consideration concerns the possibility of developing anti-covid- drugs to cross the bbb and to selectively target the sars-cov- inside the brain. the role of the bbb needs to be further explored in patients with covid- . hence, the possible neuroinvasion may be a significant mechanism to take into account for treating and preventing covid- . in this context, the design of safe and effective brain penetrating drugs would be very helpful in preventing and possibly treating the neurological complications of covid- , although the studies on this "cutting-edge topic" are still at their beginning [ ] . the differences in the sequence of spike proteins between sars-cov and sars-cov- will enable scientists to identify epitopes in covid- patients for the development of monoclonal antibodies against this virus. basic research studies on sars-cov- and host interactions are the key to several unanswered questions in the prevention and control of the disease, including the challenging question of why not all patients with covid- show neuroinvasion and why, among those experiencing neuroinvasion, not all show neurotropism or neurovirulence [ ] . moreover, the difference in terms of neurological involvement and pathomechanisms between the current pandemic and the sars and mers infections needs to be further studied. lastly, longitudinal neurological assessments of patients after their recovery will be crucial in the understanding of the natural history of covid- in the cns and for monitoring potential neurological sequelae. reaching a more global vision of covid- neuroinfection is also crucial, for instance how sars-cov- may affect the clinical expression of other infections or co-infectious diseases within the cns (i.e., the human immunodeficiency virus). further studies on clinical features of patients and pathogenetic mechanisms will provide guidance to deal with this pandemic infection, which seems to go well beyond pneumonia and whose multifaceted aspects warrant an urgent need for multidisciplinary and multidimensional research. the authors declare no conflict of interest. angiotensin-converting enzyme- bbb blood-brain barrier cns mechanisms of host defense following severe acute respiratory syndrome-coronavirus (sars-cov) pulmonary infection of mice outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle world health organization declares global emergency: a review of the novel coronavirus (covid- ) coronavirus disease (covid- ) pandemic. who: geneva, switzerland the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak aerosol and surface stability of sars-cov- as compared with sars-cov- early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia updated understanding of the outbreak of novel coronavirus ( -ncov) in wuhan epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in single-cell rna-seq data analysis on the receptor ace expression reveals the potential risk of different human organs vulnerable to -ncov infection origin and evolution of pathogenic coronaviruses evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding a pneumonia outbreak associated with a new coronavirus of probable bat origin the origin of covid- and why it matters measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in wuhan from sars to mers, thrusting coronaviruses into the spotlight an overview of their replication and pathogenesis cryo-em structures of mers-cov and sars-cov spike glycoproteins reveal the dynamic receptor binding domains coronavirus spike protein and tropism changes clinical management of severe acute respiratory infection when covid- is suspected neurological complications of coronavirus and covid- evidence of the covid- virus targeting the cns: tissue distribution, host-virus interaction, and proposed neurotropic mechanisms coronavirus and the race to distribute reliable diagnostics sensitivity assessment of droplet digital pcr for sars-cov- detection a systematic review on the efficacy and safety of chloroquine for the treatment of covid- review: hydroxychloroquine and chloroquine for treatment of sars-cov- (covid- ). open forum infect therapeutic use of chloroquine and hydroxychloroquine in covid- and other viral infections: a narrative review pharmaco-immunomodulatory therapy in covid- emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus : biology and therapeutic options neurological manifestations in severe acute respiratory syndrome human coronaviruses and other respiratory viruses: underestimated opportunistic pathogens of the central nervous system? viruses neurologic alterations due to respiratory virus infections neuroinvasive and neurotropic human respiratory coronaviruses: potential neurovirulent agents in humans diagnostic features of clinical neurologic feline infectious peritonitis virus isolated and immunofluorescence in different organs of pigs infected with hemagglutinating encephalomyelitis virus acute and persistent infection of human neural cell lines by human coronavirus oc persistent infection of human oligodendrocytic and neuroglial cell lines by human coronavirus e neuroinvasion by human respiratory coronaviruses glutamate excitotoxicity is involved in the induction of paralysis in mice after infection by a human coronavirus with a single point mutation in its spike protein axonal transport enables neuron-to-neuron propagation of human coronavirus oc severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ace human coronavirus oc associated with fatal encephalitis detection of coronavirus in the central nervous system of a child with acute disseminated encephalomyelitis a rare cause of acute flaccid paralysis: human coronaviruses detection of sars coronavirus rna in the cerebrospinal fluid of a patient with severe acute respiratory syndrome possible central nervous system infection by sars coronavirus multiple organ infection and the pathogenesis of sars severe neurologic syndrome associated with middle east respiratory syndrome corona virus (mers-cov) neurological complications during treatment of middle east respiratory syndrome neurological complications of middle east respiratory syndrome coronavirus: a report of two cases and review of the literature clinical aspects and outcomes of patients with middle east respiratory syndrome coronavirus infection: a single-center experience in saudi arabia novel coronavirus infection (covid- ) in humans: a scoping review and meta-analysis neurological complications of coronavirus disease (covid- ): encephalopathy. cureus , , e self-reported olfactory and taste disorders in sars-cov- patients: a cross-sectional study clinical characteristics of coronavirus disease in china clinical and epidemiologic profile of the initial covid- patients at a tertiary care centre in india. monaldi arch miller fisher syndrome and polyneuritis cranialis in covid- neurologic features in severe sars-cov- infection rhabdomyolysis as potential late complication associated with covid- epidemiological, clinical and virological characteristics of cases of coronavirus-infected disease (covid- ) with gastrointestinal symptoms frequent convulsive seizures in an adult patient with covid- : a case report. iran. red crescent med transient cortical blindness in covid- pneumonia; a pres-like syndrome: case report olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (covid- ): a multicenter european study acute cerebrovascular disease following covid- : a single center, retrospective, observational study new onset acute symptomatic seizure and risk factors in coronavirus disease : a retrospective multicenter study neurologic manifestations of hospitalized patients with coronavirus disease a first case of meningitis/encephalitis associated with sars-coronavirus- large-vessel stroke as a presenting feature of covid- in the young covid- -associated acute hemorrhagic necrotizing encephalopathy: ct and mri features guillain barre syndrome associated with covid- infection: a case report guillain-barré syndrome associated with sars-cov- anosmia and ageusia: common findings in covid- patients first case of novel coronavirus disease with encephalitis guillain-barré syndrome associated with sars-cov- infection: causality or coincidence? pathological findings of covid- associated with acute respiratory distress syndrome neuropathogenesis and neurologic manifestations of the coronaviruses in the age of coronavirus disease : a review risk factors for incident delirium among older people in acute hospital medical units: a systematic review and meta-analysis a neurologist's approach to delirium: diagnosis and management of toxic metabolic encephalopathies hlh across speciality collaboration, uk. covid- : consider cytokine storm syndromes and immunosuppression analysis of clinical characteristics and laboratory findings of cases of novel coronavirus pneumonia in wuhan, china: a retrospective analysis the interface between stroke and infectious disease: infectious diseases leading to stroke and infections complicating stroke the clinical pathology of severe acute respiratory syndrome (sars): a report from progression in migraine: role of mast cells and pro-inflammatory and anti-inflammatory cytokines the pathogenesis and treatment of the 'cytokine storm' in covid- analysis of the clinical effect of olfactory training on olfactory dysfunction after upper respiratory tract infection anosmia in covid- : a bumpy road to establishing a cellular mechanism massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by sars-cov- in golden syrian hamsters olfactory transmucosal sars-cov- invasion as port of central nervous system entry in covid- patients a mouse model of sars-cov- infection and pathogenesis prevalence of chemosensory dysfunction in covid- patients: a systematic review and meta-analysis reveals significant ethnic differences smell and taste dysfunction in patients with sars-cov- infection: a review of epidemiology, pathogenesis, prognosis, and treatment options. asian pac high expression of ace receptor of -ncov on the epithelial cells of oral mucosa coronavirus immunoreactivity in individuals with a recent onset of psychotic symptoms a novel angiotensin-converting enzyme-related carboxypeptidase (ace ) converts angiotensin i to angiotensin - tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis quantitative mrna expression profiling of ace , a novel homologue of angiotensin converting enzyme the multifunctional or moonlighting protein cd /dppiv expression of cd (dipeptidyl peptidase iv) on resting and activated human t-lymphocytes dipeptidyl peptidase iv, which probably plays important roles in alzheimer disease (ad) pathology, is upregulated in ad brain neurons and associates with amyloid plaques organ distribution of severe acute respiratory syndrome (sars) associated coronavirus (sars-cov) in sars patients: implications for pathogenesis and virus transmission pathways detection of severe acute respiratory syndrome coronavirus in the brain: potential role of the chemokine mig in pathogenesis immunofluorescence studies on the pathogenesis of hemagglutinating encephalomyelitis virus infection in pigs after oronasal inoculation neurotropic virus tracing suggests a membranous-coating-mediated mechanism for transsynaptic communication coronavirus infection of rat dorsal root ganglia: ultrastructural characterization of viral replication, transfer, and the early response of satellite cells the vagus nerve is one route of transneural invasion for intranasally inoculated influenza a virus in mice the evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets middle east respiratory syndrome coronavirus causes multiple organ damage and lethal disease in mice transgenic for human dipeptidyl peptidase cov- : olfaction, brain infection, and the urgent need for clinical samples allowing earlier virus detection expression of the sars-cov- entry proteins, ace and tmprss , in cells of the olfactory epithelium: identification of cell types and trends with age covid- and herpes zoster co-infection presenting with trigeminal neuropathy the neuroinvasive potential of sars-cov may play a role in the respiratory failure of covid- patients respiratory failure alone does not suggest central nervous system invasion by sars-cov- axonal spread of neuroinvasive viral infections anterograde or retrograde transsynaptic circuit tracing in vertebrates with vesicular stomatitis virus vectors anterograde or retrograde transsynaptic labeling of cns neurons with vesicular stomatitis virus vectors neurokinin- enables measles virus trans-synaptic spread in neurons structural basis for the recognition of sars-cov- by full-length human ace clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study central nervous system involvement by severe acute respiratory syndrome coronavirus- (sars-cov- ) time course and cellular localization of sars-cov nucleoprotein and rna in lungs from fatal cases of sars interaction of severe acute respiratory syndrome-associated coronavirus with dendritic cells monocytic angiotensin-converting enzyme relates to atherosclerosis in patients with chronic kidney disease systemic inflammation and the brain: novel roles of genetic, molecular, and environmental cues as drivers of neurodegeneration nervous system involvement after infection with covid- and other coronaviruses mutations in the spike glycoprotein of human coronavirus oc modulate disease in balb/c mice from encephalitis to flaccid paralysis and demyelination cerebrospinal fluid antibodies to coronavirus in patients with parkinson's disease two coronaviruses isolated from central nervous system tissue of two multiple sclerosis patients antibodies to coronaviruses oc and e in multiple sclerosis patients coronaviruses in spinal fluid of patients with acute monosymptomatic optic neuritis epidemiologic evidence for multiple sclerosis as an infection height, and sex on motor evoked potentials: translational data from a large italian cohort in a clinical environment cns penetration of potential anti-covid- drugs the emergence of a novel coronavirus (sars-cov- ) disease and their neuroinvasive propensity may affect in covid- patients key: cord- -gowtohr authors: cox, rebecca c.; jessup, sarah c.; luber, maxwell j.; olatunji, bunmi o. title: pre-pandemic disgust proneness predicts increased coronavirus anxiety and safety behaviors: evidence for a diathesis-stress model date: - - journal: j anxiety disord doi: . /j.janxdis. . sha: doc_id: cord_uid: gowtohr although health anxiety and corresponding safety behaviors can facilitate disease transmission avoidance, they can be maladaptive in excess, including during the coronavirus pandemic. disgust proneness (i.e., tendency to experience and be sensitive to disgust) is one factor that may predict elevated coronavirus anxiety and safety behaviors during the pandemic, given the role of disgust in avoiding disease transmission. the present study examined the relations between pre-pandemic disgust proneness and coronavirus anxiety and safety behaviors in community adults who completed a study and were re-contacted on / / (n = ). interactions between pre-pandemic disgust proneness and current perceived stress were tested to examine a diathesis-stress model of the role of disgust proneness in anxiety response to the pandemic. increased pre-pandemic disgust proneness predicted increased coronavirus anxiety and safety behaviors, controlling for number of covid- cases by state. consistent with a diathesis-stress model, current perceived stress moderated this effect, such that highest coronavirus anxiety and safety behaviors were reported by those with high disgust proneness and high stress. trait disgust proneness may be a vulnerability factor for anxiety responses to the coronavirus pandemic, particularly among individuals experiencing high stress. assessing disgust proneness and current stress may facilitate targeted anxiety intervention during the pandemic. the coronavirus pandemic and its resulting condition, covid- have devastated society in a multitude of ways, such as the loss of human life, negative economic consequences, enforced social distancing, and the unemployment of countless workers. among these outcomes, there is concern about the impact of the pandemic on mental health, and who may be most vulnerable to psychological distress. it may be the case that individuals with certain personality traits (e.g., a heightened propensity to experience disgust) are at a greater risk of experiencing heightened coronavirus anxiety, or what a recently proposed model of fear during the coronavirus pandemic describes as fear for the body (schimmenti, billieux, & starcevic, ) . disgust proneness, health anxiety, and contamination fears (blakey et al., ; brand et al., ; wheaton et al., ) . these studies indicate the existence of identifiable predictors of anxiety during viral outbreaks and suggest the need for similar research during the coronavirus pandemic. compared to previous viral outbreaks, covid- appears to have a higher rate of transmissibility and a longer incubation period, the latter of which is associated with higher risk of asymptomatic individuals unknowingly infecting others prior to symptom onset (xie and chen, ). high rates of asymptomatic transmission are thought to contribute to rapid spread of the coronavirus (li et al., ) and may result in increased coronavirus anxiety due to decreased certainty about the health status of others and decreased predictability of one's own health status and role as potential disease vector. coronavirus anxiety may be conceptualized as a specific form of health anxiety, or obsessive and irrational worry about contracting a serious medical condition. indeed, recent studies indicate coronavirus anxiety responses are largely characterized by fear of contracting the virus (e.g., ahorsu et al., ; lee, ). an appropriate level of health anxiety facilitates adaptive reactions to physical symptoms to prevent and alleviate illness. however, health anxiety that is chronic and/or greater than the severity of the health-related threat may become maladaptive (taylor, mckay, & abramowitz, ) . health anxiety may also be accompanied by excessive safety behaviors (e.g., salkovskis, ) . although safety behaviors are intended to minimize the risk of illness (e.g., avoidance of contaminants, excessive washing, or overuse of medical supplies), they can also exacerbate distress and functional impairment by preventing the correction of mistaken anxious beliefs (see helbig-lang & petermann, for a review). indeed, one recent study found that health anxiety and excessive internet research on the coronavirus is associated with increased coronavirus anxiety (jungmann and witthöft, ) . thus, identifying additional theoretically informed risk factors that predict coronavirus anxiety and safety behaviors may inform treatment and preventive strategies amidst the pandemic. it has been theorized that a complex "behavioral immune system" functions to help humans avoid the harmful effects of pathogens (curtis, de barra, & aunger, ; schaller & duncan, ) . this system includes facilitated detection of potential infectious pathogens in the environment and pathogens-avoidance behaviors. evolutionary approaches contend that disgust is mobilized by this system to protect humans from disease (tybur, lieberman, & griskevicius, ). there may be individual differences in the extent to which the experience of disgust is deployed as a psychological first line of defense against pathogen threats in the environment. this individual difference process has been operationalized as disgust proneness, a personality trait that consists of two core components, disgust propensity or an individual's tendency to experience disgust, and disgust sensitivity, an individual's negative appraisal of a disgust experience (van overveld, de jong, peters, cavanagh, & davey, ) . disgust proneness may serve an adaptive function by facilitating avoidance of stimuli that present risk for uncleanliness, contamination, and disease. however, this trait has also been implicated as a risk factor for anxiety-related disorders characterized by contamination symptoms (olatunji, williams, lohr, & sawchuk, ) and has been shown to predict excessive health anxiety symptoms (e.g., thorpe, patel, & simonds, ; davey & bond, ; fan & olatunji, ) , further supporting a functional link between disgust and disease avoidance. disgust proneness may also confer risk for excessive coronavirus anxiety. consistent with this view, disgust proneness was correlated with swine flu anxiety during the swine flu pandemic (wheaton et al., ) . although those high in disgust proneness may be more likely to experience elevated anxiety related to the coronavirus pandemic, it is unknown whether this effect may be impacted j o u r n a l p r e -p r o o f disgust, stress, and coronavirus by features of an individual's current context. one such contextual feature is perceived stress. data from china suggest that nearly % of the general population reported experiencing moderate to severe levels of distress in the early stages of the pandemic (qiu et al., ; wang et al., ) . the coronavirus pandemic has also been a significant source of stress for reasons extending beyond fears of infection. indeed, economic instability due to loss of work, difficulties balancing childcare and work responsibilities while working from home, and diminished social support due to social distancing may contribute to psychosocial stress. importantly, there may also be differences in the amount of stress experienced given variability in the extent to which the individual perceives the stress as uncontrollable, unpredictable, and severe, and deems coping resources as insufficient. consistent with a diathesis-stress model (monroe and simons, ) , perceived stress may amplify the effects of an underlying diathesis, such as disgust proneness. though research on predictors of mental health during the coronavirus is nascent, one study found that increased stress during the pandemic was associated with maladaptive coping strategies, including behavioral disengagement and substance use, among adults with disabilities and chronic conditions (umucu et al., ) , and another study found higher resilience, or the ability to effectively cope with stress, is associated with lower anxiety during the pandemic (liu et al., ) . together these findings suggest that perceived stress may be an important process that modulates the effect of disgust proneness on coronavirus anxiety and safety behaviors. the identification of predictors of coronavirus-related anxiety responses is crucial to effectively address mental health issues during the pandemic. disgust proneness may be conceptualized as a diathesis, or predisposition, that interacts with the individual's subsequent stress response to produce maladaptive responses during the pandemic. thus the diathesis-stress model can be a useful framework for exploring how pre-existing traits j o u r n a l p r e -p r o o f disgust, stress, and coronavirus (diatheses) interact with environmental influences (stressors) to produce excessive coronavirusrelated anxiety responses. accordingly, the present study examines the relations between disgust proneness, perceived stress, and coronavirus-related anxiety and safety behaviors in a sample of adults who were assessed in and were re-contacted in the early stages of the coronavirus pandemic in the united states. it was hypothesized that pre-pandemic disgust proneness would predict increases in coronavirus anxiety and safety behaviors during the pandemic, and those with high current perceived stress and high disgust proneness years prior to the pandemic would report the highest coronavirus anxiety and safety behaviors. the sample consisted of adults who completed a survey study on anxiety-related symptoms who were re-contacted to participate in the present study (n = ). the sample included adults aged - who were recruited for a survey study related to sleep and anxiety symptoms (n = ). of the sample, . % participated when re-contacted. the sample was . % female with a mean age of . (sd = . ) at follow-up, ranging from to . the ethnicity composition was as follows: white (n = ; . %), african american (n = ; . %), asian (n = ; . %), hispanic/latino (n = ; . %), other (n = ; . %). information on state of residence and corresponding number of covid- cases can be found in table . . the cai is a -item self-report measure of fear related to the coronavirus pandemic (items are listed in table ). the cai was adapted for this study from a similar measure of ebola-related fear, the ebola fear inventory (efi; blakey et al., ) . in previous research, the efi demonstrated small to medium, significant correlations j o u r n a l p r e -p r o o f disgust, stress, and coronavirus with measures of disgust and contamination concerns (blakey et al., ) . items on the cai are rated on a likert scale from (not at all) to (very much), and higher scores indicate higher coronavirus fear. the cai demonstrated adequate internal consistency (α = . ) at time . (csbc) . the csbc is a -item self-report measure of engagement in behaviors to prevent contracting coronavirus (items are listed in table ). the csbc was adapted for this study from a similar measure of ebola-related safety behaviors, the ebola safety behaviors checklist (blakey et al., ) . in previous research, the efi demonstrated small to medium, significant correlations with measures of disgust and contamination concerns (blakey et al., ) . items on the csbc are rated on a likert scale from (none) to (extreme amount), and higher scores indicate higher engagement in coronavirus-related safety behaviors. the csbc demonstrated adequate internal consistency (α = . ) at time . (dpss-r; van overveld, de jong, peters, cavanagh, & davey, ) . the dpss-r is a -item self-report measure of the tendency to experience disgust in various contexts (i.e., disgust proneness). items on the dpss-r are rated on a likert scale from (never) to (always), and higher scores indicate increased disgust propensity. the dpss-r demonstrated good internal consistency (α = . ) at time . cohen, sheldon, kamarck, tom, & memelstein, ). the pss is a -item self-report measure of the degree to which an individual perceives their life to be unpredictable, uncontrollable, and overburdened in the past month. items on the pss are rated on a likert scale from (never) to (very often), and higher scores indicate increased stress. the pss demonstrated adequate internal consistency (α = . ) at time . data analysis was conducted in spss . prior to data analysis, for scale totals with one item missing, mean imputation was used to replace the missing item. measures with more than one missing item were considered missing and not included in analysis. two hierarchical linear regression models were tested to examine the predictive effect of pre-pandemic disgust j o u r n a l p r e -p r o o f disgust, stress, and coronavirus proneness on coronavirus fear and safety behaviors, respectively. number of covid- cases by state (i.e., the number of covid- cases in a given participant's state on / / ) was included as a covariate to control for relative risk of exposure to coronavirus. two moderation models were tested using the process macro (hayes, ) to examine whether current stress level moderated the relation between pre-pandemic disgust proneness and coronavirus fear and safety behaviors, respectively, controlling for number of covid- cases by state. predictor variables were mean-centered prior to analysis. significant interactions were probed with both a simple slopes analysis (aiken & west, ) and regions of significance analysis using the johnson-neyman technique (johnson & neyman, ) . descriptive statistics and associations between study variables are shown in table . prepandemic disgust proneness demonstrated small, significant, and positive associations with current stress and coronavirus fear and safety behaviors. table for the results of the regression model. two exploratory follow-up models testing disgust propensity and sensitivity as predictors j o u r n a l p r e -p r o o f disgust, stress, and coronavirus revealed that pre-pandemic disgust propensity but not sensitivity individually predicted coronavirus anxiety (p < . ). significantly contribute to the model, f( , ) = . , p = . . introducing pre-pandemic disgust proneness to the model explained an additional . % of the variance in coronavirus safety behaviors, and the r change was significant (p < . ). when number of covid- cases by state and pre-pandemic disgust proneness were included in the model, pre-pandemic disgust proneness predicted a small increase in coronavirus safety behaviors, b = . ,  = . , p < . . see table for the results of the regression model. two exploratory follow-up models testing disgust propensity and sensitivity as predictors revealed that pre-pandemic disgust propensity and sensitivity predicted coronavirus safety behaviors (p's < . ). . . coronavirus anxiety. there was a trend-level interaction between pre-pandemic disgust proneness and current stress level to predict coronavirus anxiety, r = . , f = . , p = . (see table ). conditional effects analysis revealed that there was no significant relation between pre-pandemic disgust proneness and coronavirus fear at low and medium levels of current stress (p's > . ). however, at high levels of current stress, there was a significant, positive relation between pre-pandemic disgust proneness and coronavirus anxiety, b = . , t = . , p < . (see figure ) . a regions of significance analysis identified . as the score on the pss at which the relation between pre-pandemic disgust proneness and coronavirus anxiety becomes significant. that is, those with current pss scores below . exhibited no link between pre-pandemic disgust proneness and coronavirus anxiety; in contrast, for those with j o u r n a l p r e -p r o o f disgust, stress, and coronavirus current pss scores of . or higher, coronavirus anxiety increase with increasing prepandemic disgust proneness. there was a significant interaction between prepandemic disgust proneness and current stress level to predict coronavirus safety behaviors, r = . , f = . , p < . (see table ). conditional effects analysis revealed that there was no significant relation between pre-pandemic disgust proneness and coronavirus safety behaviors at low levels of current stress (p > . ). however, there were significant, positive relations between pre-pandemic disgust proneness and coronavirus safety behaviors at medium, b = . , t = . , p < . , and high levels of current stress b = . , t = . , p < . (see figure ) . a regions of significance analysis identified . as the score on the pss at which the relation between prepandemic disgust proneness and coronavirus safety behaviors becomes significant. that is, those with current pss scores below . exhibited no link between pre-pandemic disgust proneness and coronavirus safety behaviors; in contrast, for those with current pss scores of . or higher, coronavirus safety behaviors increase with increasing pre-pandemic disgust proneness. the present study examined the predictive effect of pre-pandemic disgust proneness on coronavirus anxiety and safety behaviors during the pandemic, as well as the moderating effect of current levels of perceived stress. results of the regression models found that pre-pandemic disgust proneness significantly predicted increases in both coronavirus anxiety and safety behaviors, controlling for number of covid- cases by state. these findings replicate previous studies implicating disgust proneness as one factor associated with responses to previous viral outbreaks, including the swine flu pandemic (wheaton et al., ) and the ebola (blakey et al., ) and zika outbreaks (blakey and abramowitz, ) . evidence for an effect of prior disgust responses to viral outbreaks were due to acutely elevated disgust in response to said outbreaks (i.e., state disgust). the present study suggests that disgust proneness in the absence of a disgustrelevant threat (i.e., pre-pandemic trait disgust) contributes to an elevated anxiety response during the coronavirus pandemic. in other words, disgust proneness may be one individual difference factor that confers vulnerability for experiencing increased anxiety and engaging in excessive safety behaviors during the coronavirus pandemic. the present findings show that heightened disgust proneness before the pandemic results in an increased use of protective behaviors in the midst of the pandemic. this likely reflects the adaptive functions of the complex "behavioral immune system" that functions to help humans avoid contacts with pathogens (curtis et al., ) . indeed, it has been posited that experiencing disgust is a primary mechanism that is employed by the "behavioral immune system" to facilitate disease avoidance (olatunji et al., ) . it is important to note that disgust levels will also increase, as part of the "behavioral immune system", during pandemics given the threat of infection. this heightened disgust may then facilitate adaptive avoidance of situations and stimuli where contamination is likely to occur. one mechanism may be that those high in preexisting disgust proneness (trait) may experience even higher levels of (state) disgust during the pandemic which then motivates the use of more safety behaviors. although this process is largely adaptive, disgust proneness has been found to contribute to excessive safety behavior j o u r n a l p r e -p r o o f disgust, stress, and coronavirus usage in conditions like contamination-based ocd (e.g., phillips, senior, fahy, & david, ; woody & teachman, ) , as well as illness anxiety disorder (davey & bond, ) . heightened pre-pandemic disgust proneness may contribute to a response to the pandemic that exceeds that which is evolutionarily adaptive. this may occur when those with elevated pre-pandemic disgust proneness negatively appraise disgust-relevant stimuli and/or situations (e.g., "i will get sick and die if a stranger sneezes in close proximity to me," "i would not be able to tolerate the disgust associated with touching something a stranger has touched") in a way that exacerbates a fear response to the coronavirus pandemic. indeed, research has previously shown that disgust is significantly associated with both danger and germ spread appraisals (dorfan & woody, ) . safety behaviors are actions performed to prevent, escape, or minimize feared catastrophes and/or associated distress. safety behaviors become maladaptive when individuals misattribute their safety to the behavior itself, rather than the low probability of the feared outcome (e.g., "i am only safe because i washed my hands," rather than "it is unlikely i will get sick;" salkovskis, ). heightened pre-pandemic disgust proneness may also contribute to usage of safety behaviors that exceeds that which is adaptive. of note, safety behaviors are functionally related to anxious beliefs and are logical, if unnecessary (blakey & abramowitz, ) . for those high in disgust proneness, there may be a tendency to engage in safety behaviors (e.g., excessive handwashing) when such protective acts are not required. this may subsequently facilitate safety misattributions that maintain anxiety during the pandemic. this view is consistent with previous research indicating disgust proneness significantly mediates the relationship between contamination-related obsessive-compulsive symptoms and beliefs (e.g., overestimations of threat) and swine flu behaviors and fear (brand et al., ) . in moderation analyses also revealed that current perceived stress significantly interacted with pre-pandemic disgust proneness to predict coronavirus safety behaviors, while the interactive effect for coronavirus anxiety was at trend level. specifically, increased pre-pandemic disgust proneness predicted increased coronavirus safety behaviors for those reporting high and medium current perceived stress. in contrast, those reporting low current perceived stress did not demonstrate a significant relation between pre-pandemic disgust proneness and coronavirus safety behaviors. similarly, though at trend level, increased pre-pandemic disgust proneness predicted increased coronavirus anxiety for those reporting high, but not medium or low, current perceived stress. these findings are consistent with a diathesis-stress framework, such that the vulnerability for an anxiety response to the coronavirus pandemic conferred by elevated prepandemic disgust proneness is "activated" by stress. likewise, when perceived stress is low, prepandemic disgust proneness has no impact on response to the pandemic. indeed, a recent study found heightened covid- distress is associated with difficulties coping during the pandemic (taylor, landry, paluszek, fergus, & mckay, a) . one of the unanswered questions in the literature is why people vary in the degree to which they experience disgust (tybur, cinar, karinen, & perone, ) . these findings suggest that perceived stress may contribute to variability in disgust proneness and this variability may effect subsequent coronavirus fear and safety behaviors. this diathesis-stress approach offers preliminary insight into who may be most vulnerable to a disproportionate response to the coronavirus pandemic. the present findings may also have implications for clinical intervention during the pandemic. clinicians may consider assessing for disgust proneness and stress to facilitate identifying those who may be experiencing particularly high distress. further, stress reduction interventions may be beneficial for off-setting the detrimental effects of pre-pandemic vulnerability factors, such as disgust proneness. however, the findings of the present study must be considered in light of the study limitations. first, the sample was largely white and female, which limits generalizability to various demographic groups. second, this study used self-report instruments that may be incomplete measures of disgust proneness, stress, and coronavirus fear and safety behaviors, such that these subjective responses may diverge from responses to clinical interviews or behavioral tasks. third, although the longitudinal design establishes the temporal precedence of disgust proneness, the lack of manipulation of disgust limits causal interpretations. finally, given the unprecedented nature of the pandemic, the level of coronavirus fear and safety behaviors that can be considered maladaptive or disproportionate is presently unknown. thus, future research is needed to identify thresholds at which the distress response to the coronavirus is clinically significant and whether disgust proneness contributes to exceeding such a threshold. compliance with ethical standards. all procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/ or national research committee and with the helsinki declaration and its later amendments or j o u r n a l p r e -p r o o f comparable ethical standards. this article does not contain any studies with animals performed by any of the authors. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. ms. cox collected the data, performed the statistical analysis, and contributed to drafts of the manuscript. ms. jessup contributed to drafts of the manuscript. mr. luber contributed to drafts of the manuscript and data entry. dr. olatunji contributed to study design, oversaw data collection, and assisted with statistical analysis and manuscript preparation. all authors contributed to and have approved of the final manuscript. behaviors at values of current stress, controlling for number of covid- cases by state. prepandemic disgust and current stress were mean-centered prior to analysis, such that low, medium, and high represent the sample mean +/-one standard deviation. importantly, this effect is at trend-level. j o u r n a l p r e -p r o o f step the fear of covid- scale: development and initial validation multiple regression: testing and interpreting interactions the effects of safety behaviors during exposure therapy for anxiety: critical analysis from an inhibitory learning perspective psychological predictors of health anxiety in response to the zika virus tracing "fearbola": psychological predictors of anxious responding to the threat of ebola the relationship between obsessive compulsive beliefs and symptoms, anxiety and disgust sensitivity, and swine flu fears a global measure of perceived stress research electronic data capture (redcap): a metadata-driven methodology and workflow process for providing translational research informatics support introduction to mediation, moderation, and conditional process analysis: a regression-based approach stress-induced cortisol level elevations are associated with reduced negative affect after stress: indications for a mood-buffering cortisol effect health anxiety, cyberchondria, and coping in the current covid- pandemic: which factors are related to coronavirus anxiety? acute hpa axis responses, heart rate, and mood changes to psychosocial stress (tsst) in humans at different times of day coronavirus anxiety scale: a brief mental health screener for covid- related anxiety substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov- ) factors associated with depression, anxiety, and ptsd symptomatology during the covid- pandemic: clinical implications for u.s. young adult mental health anxiety regarding contracting covid- related to interoceptive anxiety sensations: the moderating role of disgust propensity and sensitivity diathesis-stress theories in the context of life stress research: implications for the depressive disorders risk factors for hypochondriacal concerns in a sample of military veterans key: cord- -fuaq ujb authors: gong, yue; ma, ting-can; xu, yang-yang; yang, rui; gao, lan-jun; wu, si-hua; li, jing; yue, ming-liang; liang, hui-gang; he, xiao; yun, tao title: early research on covid- : a bibliometric analysis date: - - journal: innovation doi: . /j.xinn. . sha: doc_id: cord_uid: fuaq ujb abstract in december , an outbreak of pneumonia, which was named covid- , emerged as a global health crisis. scientists worldwide are engaged in attempts to elucidate the transmission and pathogenic mechanisms of the causative coronavirus. covid- was declared a pandemic by the world health organization in march , making it critical to track and review the state of research on covid- to provide guidance for further investigations. here, bibliometric and knowledge mapping analyses of studies on covid- were performed, including more than papers on covid- available in the pubmed and cnki databases from january , to march , . in this review, we found that because of the rapid response of researchers worldwide, the number of covid- -related publications showed a high growth trend in the first ten days of february; among these, the largest number of studies originated in china, the country most affected by pandemic in its early stages. our findings revealed that the epidemic situation and data accessibility of different research teams have caused obvious difference in emphases of the publications. besides, there was an unprecedented level of close cooperation and information sharing within the global scientific community relative to previous coronavirus research. we combed and drew the knowledge map of the sars-cov- literature, explored early status of research on etiology, pathology, epidemiology, treatment, prevention, and control, and discussed knowledge gaps that remain to be urgently addressed. future perspectives on treatment, prevention, and control were also presented to provide fundamental references for current and future coronavirus research. in december , a cluster of cases of pneumonia with unknown cause was detected in wuhan city, hubei province of china. a novel coronavirus was identified as the causative virus by chinese authorities on january . the coronavirus study group (csg) of the international committee on taxonomy of viruses designated the causative virus as severe acute respiratory syndrome coronavirus (sars-cov- ), and the disease, which subsequently spread globally, was named coronavirus disease of covid- , covering topics such as etiology, diagnosis, epidemiology, treatment, prognosis, nursing, prevention and control, were available in the pubmed and china national knowledge infrastructure (cnki) databases. in this review, the global literature related to covid- were analyzed via bibliometric methods, citation analysis, and knowledge mapping methods. studies reporting temporal patterns, main countries affected and core subjects were identified, and the status and trends in covid- research were explored from january to march to reveal the conceptual knowledge map in sars-cov- . the results provide a reference for current and future coronavirus research and policymaking worldwide. the sources of literature used in this review were pubmed (for publications in beijing has covered all aspects of sars-cov- , with a focus on treatment, prevention, etiology, and prognosis, ranking first in china in terms of number of publications. in however, their inter-provincial collaborative rates were quite different: liaoning, over %; tianjin, over %; and sichuan, only about % (table ) . sequence analysis showed that the orf regions, such as orf ab, orf b, and orf , are important functional domains that may be related to protein stability and nucleophilic effects, as well as to mutations subject to selection pressure (e.g., nsp and nsp , aa -aa , . the spike glycoprotein on the virion surface mediates receptor recognition and membrane fusion. the conserved rbd core domain in subunit s may be involved in the novel coronavirus's ability to cross species barriers imposed by receptor specificity. the c-terminus/ n-terminus of the s subunit may also be responsible for direct interaction with the host receptor. traceability early epidemiological investigations have found that most covid- patients in china had a history of travel to wuhan, as well as a history of exposure to wildlife. the phylogenetic tree of coronaviruses suggested that the natural host of the novel coronavirus is the bat (rhinolophus affinis) , , and that sars-cov- represents a recombination, on the s protein, between the bat coronavirus and an origin-unknown coronavirus. turtles and pangolins were suggested to be potential intermediate hosts for sars-cov- based on analyses using the mega program . spread the transmission of sars-cov- between bats and intermediate hosts might be attributed to the contamination of food environments by animal droppings, restricted air flow in the environment, or the aggregation behavior of animals . transmission between humans did not exclude the fecal-oral route, and the transmission intensity depended on the length of the incubation period and the importance of asymptomatic carriers with regard to disease transmission , . the high replication rate and strong immunologic pressure in humans might be conducive to the adaptive evolution of the virus the incubation period was generally considered to be no more than days, with the median ranging from to days. other research on cluster cases showed that covid- was still contagious during the incubation period . the median interval between primary and secondary cases was . days, which is much shorter for those with direct infection ( days) . pregnant women and children were the priority groups for covid- prevention as pregnant women were considered an at-risk group while the low infection rates among children might be due to having more mild cases that aren't reported. related studies have reported clinical recommendations for diagnosis, prevention, and control among these groups . in order to prevent clustered infections, the government has strengthened the management and control of people's movements. medical staff have designed remote diagnosis and treatment guidelines for cancer patients been optimized in a timely manner. however, prevention and control measures taken by the international community have exposed shortcomings related to various aspects such as emergency reserve supplies as well as fundamental disease prevention and control systems in response to public health emergencies. it is suggested that the construction of advanced institutional mechanisms to reform the public health response in addition to an increased focus on coordination and cooperation among scientists, public health professionals, entrepreneurs, and government officials would be conducive to global joint defense against pandemics in the future. in addition to the above general suggestions, there are some other specific efforts that china must undertake. regional differences in previous studies reflect the importance of developing an equitable health system and accelerating the construction of modern information systems to improve governmental coordination for effective pandemic preparedness and response , , , . analysis of the global coronavirus related research status and its enlightenment for the present and future. chin research advances of novel coronavirus disease (covid- ) current status of research on coronavirus cross-species transmission of the newly identified coronavirus -ncov bioinformatics analysis of the novel coronavirus genome analysis of myocardial injury in patients with covid- and association between concomitant cardiovascular diseases and severity of covid- quantifying the association between domestic travel and the exportation of novel coronavirus ( -ncov) cases from wuhan, china in : a correlational analysis escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease (covid- ) due to sars-cov- in hong kong severe acute respiratory syndrome coronavirus (sars-cov- ) and coronavirus disease- (covid- ): the epidemic and the challenges insights into the recent novel coronavirus (sars-cov- ) in light of past human coronavirus outbreaks genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan genome composition and divergence of the novel coronavirus ( -ncov) originating in china emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments cross-species transmission of the newly identified coronavirus -ncov first respiratory transmitted food borne outbreak? enteric involvement of coronaviruses: is faecal-oral transmission of sars-cov- possible? advances on presymptomatic or asymptomatic carrier transmission of covid- . chin viral escape mechanisms--escapology taught by viruses evolution of virulence in emerging epidemics a glimpse into the origins of genetic diversity in sars-cov- genomic diversity of sars-cov- in coronavirus disease patients novel coronavirus is undergoing active recombination angiotensin-converting enzyme (ace ) as a sars-cov- receptor: molecular mechanisms and potential therapeutic target pathogenicity and transmissibility of -ncov-a quick overview and preliminary study of the relationship between novel coronavirus pneumonia and liver function damage: a multicenter study exploring the mechanism of liver enzyme abnormalities in patients with novel coronavirus-infected pneumonia pulmonary pathology of early-phase novel coronavirus (covid- ) pneumonia in two patients with lung cancer clinical diagnosis and treatment of critical patients with novel coronavirus pneumonia (report of cases). chin analysis of factors associated with disease outcomes in hospitalized patients with novel coronavirus disease clinical and biochemical indexes from -ncov infected patients linked to viral loads and lung injury the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak novel coronavirus pneumonia related liver injury: etiological analysis and treatment strategy cause analysis of liver injury in patients infected by novel coronavirus and suggestion of drug monitoring understanding sars-cov- -mediated inflammatory responses: from mechanisms to potential therapeutic tools puzzle of highly pathogenic human coronaviruses pregnant women with new coronavirus infection: a clinical characteristics and placental pathological analysis of three cases. chin covid- and the cardiovascular system therapeutic glucocorticoids: mechanisms of actions in rheumatic diseases detection of novel coronavirus ( -ncov) by real-time rt-pcr nanoplasmonic on-chip pcr for rapid genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding a rapid advice guideline for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (standard version) an anti-influenza drug against life-threatening rna virus infections drug interaction monitoring of lopinavir / ritonavir in covid- patients with cancer learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by -ncov breakthrough: chloroquine phosphate has shown potential antiviral therapeutics for novel coronavirus we should pay close attention to some issues in the process of respiratory therapy of covid- current status of application of convalescent plasma in acute viral infectious diseases and its prospect in therapy of covid- . chin epidemiological characteristics of novel coronavirus pneumonia in henan epidemiologic characteristics of early cases with novel coronavirus ( -ncov) disease in korea early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia clinical analysis of cases of novel coronavirus infection in children from six provinces (autonomous region) of northern china epidemiologic features and clinical course of patients infected with sars-cov- in singapore pattern of early human-to-human transmission of wuhan passengers' destinations from china: low risk of novel coronavirus ( -ncov) transmission into africa and south america risk for transportation of novel coronavirus disease from wuhan to other cities in china early phylogenetic estimate of the effective reproduction number of sars-cov- the time scale of asymptomatic transmission affects estimates of epidemic potential in the covid- outbreak epidemiological analysis on a family cluster of covid- . chin novel coronavirus (sars-cov ): a global emergency that needs new approaches? novel corona virus disease (covid- ) in pregnancy: what clinical recommendations to follow? acta clinical management of lung cancer patients during the outbreak of novel coronavirus disease (covid- ) initial public health response and interim clinical guidance for the novel coronavirus outbreak -united states covid- : school closures and bans on mass gatherings will need to be considered, says england's cmo covid- in singapore-current experience: critical global issues that require attention and action first cases of coronavirus disease (covid- ) in france: surveillance, investigations and control measures a bibliometric analysis on coronavirus coronavirus: three things all governments and their science advisers must do now how to help the free market fight coronavirus challenges to the system of reserve medical supplies for public health emergencies: reflections on the outbreak of the severe acute respiratory syndrome coronavirus (sars-cov- ) epidemic in china the importance of strengthening the ability of fundamental disease prevention and control system from the perspective of the epidemic situation of covid- thoughts and suggestions on modern construction of disease prevention and control system covid- : what is next for public health? key: cord- - kevsl z authors: agarwal, krishna mohan; mohapatra, swati; sharma, prairit; sharma, shreya; bhatia, dinesh; mishra, animesh title: study and overview of the novel corona virus disease (covid- ) date: - - journal: nan doi: . /j.sintl. . sha: doc_id: cord_uid: kevsl z in december , a new disease with pneumonia-like symptoms was spreading throughout wuhan in china which was entitled as novel coronavirus disease or covid - caused by the virus sars cov- . within a span of a few days, this disease became a global threat and was termed as a pandemic by the world health organization (who) on th march , since then the disease has affected more than . crore people worldwide and around . lakh people in india as of th july . the origin of the covid- disease has been traced back to the bats, but the intermediary contact is unknown. the disease spreads by respiratory droplets and contaminated surfaces. in most cases, the virus shows mild symptoms like fever, fatigue, dyspnea, cough, etc. which may become severe if appropriate precautions are not adhered to. for people with comorbidities (usually elderly) the disease may turn deadly and cause pneumonia, acute respiratory disease syndrome (ards), and multi-organ failure, thereby affecting a person's ability to breathe leading to being put on the ventilator support. the reproduction number (rℴ) of covid- is much higher than its predecessors and genetically similar diseases like sars-cov and mers-cov. this paper discusses the epidemiological characteristics of the sars-cov- virus, its phylogenetic relationship with the previous pandemic causing viruses such as sars-cov- and mers-cov and analyzes the various responses to this global pandemic worldwide, focusing on the actions taken by india and their outcomes. the current global pandemic is caused by the "novel coronavirus disease ( -ncov) or severe acute respiratory syndrome coronavirus- (sars-cov- ) popularly known as covid- hunan seafood market was sealed, on th january roughly a week after china's notification of a possible outbreak the disease was confirmed to be the novel coronavirus disease or covid- which has more than % homology with bat coronavirus and almost % similarity to the sars cov- virus. (singhal, ) environmental samples collected from the hunan seafood market were tested positive with traces of covid- , indicating it as the origin of the virus (singhal, ) . in the ensuing days, more cases from the above data, we can infer that the ∘ of covid- is much higher than that of sars or mers, hence the total number of cases is also exponentially higher than those of other similar viruses. on the other hand, sars and mers are much deadlier than covid- with their fatality rates at . % and %, respectively. a greater number of people succumbed to the virus with the ratio of those infected. other than the varying ∘ and fatality rate the three viruses are quite similar in their mode of transmission and general effect on the health of an individual suffering from these diseases. all three diseases had bats as their primary reservoir and were crossed with humans via an intermediary host (which is not yet confirmed in the case of covid- ). the disease is transmitted by human to human contact, generally through respiratory droplets. the viruses cause ards (acute respiratory disease syndrome) in their worst cases forcing the patient to be put on ventilators to aid in their breathing. according to a research which tested the viruses viability in different mediums and surfaces such as aerosol, stainless steel, copper, and cardboard providing essential information that these surfaces can be easily disinfected within a minute using certain chemicals like sodium hypochlorite, to % an infected covid- patient can have two major states of infection, the asymptomatic state, and the symptomatic state. the symptomatic stage can develop into acute respiratory disease syndrome (ards) then raising infection can lead to multi-organ failure which can be fatal to the patient. an asymptomatic patient does not exhibit any symptoms of the disease due to high immunity but is still capable of infecting others, this state is extremely dangerous for the community and ( %) exhibit critical severity of illness, from this study it was also found that the case fatality rate stood at - % and most deaths( %) occurred in patients with critical illness severity. amongst the most affected by sars-cov- are the people with underlying medical conditions like cardiovascular diseases, diabetes, respiratory diseases, hypertension, and cancer. age is another strong risk factor for severe illness, complications, and death. the graph below depicts that the older an individual is, the higher is the case fatality rate (cfr), the ( j o u r n a l p r e -p r o o f at the time of writing this paper, neither vaccine nor approved drug treatment for covid- is discovered, prevention of the disease is therefore crucial to avoid the transmission. although certain aspects of the virus pose serious hindrances in prevention aspects, such as no onset of symptoms until an average of days during the days incubation period or in some cases no symptoms, while at the same time the patient is shedding viral load similar to the symptomatic patient and prolonged duration of the illness and transmission even after clinical recovery. keeping these aspects in mind there some guidelines suggested by major institutes in a bid to prevent the spread of the virus. at the community, level to slow the spread initially avoid large gatherings, defer non-essential travel for work or recreation, it is recommended to wear masks whenever heading out of the house for essential work the mask need not be surgical like n a simple mask made of cloth would suffice. j o u r n a l p r e -p r o o f . to flatten the curve so as not to overwhelm the healthcare infrastructure: flatten the curve is a statement used during healthcare emergencies, its basic concept is to limit the spread of the virus such that at any given time during a pandemic the total number of patients required to be hospitalized is less than the maximum capacity of the state's health infrastructure. when compared to other countries india's doubling rate is a lot less due to early implementation of the lockdown which has helped in bringing down the doubling rate from an initial of five days to nearly thirteen days. currently, the rate of growth of confirmed cases is at . % (sinha, ) use this lockdown to boost the healthcare system's capacity. the lockdown period acts as a pause button on cases requiring urgent medical attention this period can be used to ramp up the infrastructure of hospitals so that when the lockdown is lifted and cases rise medical attention could be given to every serious case thus aiding in preventing potential deaths. the uk published its first advisory for their citizens asking people with cough and fever to selfisolate for days. schools were asked to cancel trips abroad and people above the age of were advised to avoid cruises (coronavirus: people with fever or 'continuous' cough told to self-isolate, ). with no respite in-site, the uk again updated its advisory on th march which recommended citizens to avoid non-essential travel and contact with others. citizens were also recommended to avoid pubs, clubs, and theatres and try to work from home as much as possible. (coronavirus: pm says everyone should avoid office, pubs and travel, ) on rd march restrictions were placed on citizens with weeks of lockdown. all non-essential activities were suspended, only essential workrelated travel was allowed everyone was advised to stay at home unless there was an emergency. approximately after a month, sweden had , cases and three deaths due to the virus. from recorded data, it is revealed that the confirmed cases took - days to double initially. as the days progressed the doubling rate increased to days and then a month, this indicated that sweden was j o u r n a l p r e -p r o o f sweden's massive investment in its health architecture over the past years has made the system one of the finest, and it has returned the reward in the ongoing covid- pandemic. however, a high number of old-age deaths have become a big concern. on th june, the most recorded deaths in sweden lied in the - years age group at , which was followed by deaths in the years and above age group and deaths in the - years age group (jha, ) . this illustrates the fact that the elderly had to bear the brunt of the disease. although sweden was able to slow the spread of the virus, it still had a very high case fatality ratio, particularly among the elderly. a high number of people who got infected died due to the disease as compared to other countries. on th january, the very first case of covid- was recorded in the usa (corley, ) . in the case of covid- , there is currently no vaccine and the best way for us to come out of this pandemic with minimal human casualties is aggressive social distancing and lockdowns. at the same time relaxation in lockdowns enhances the rate of cases and deaths as we saw after june st in india when relaxations were implemented, daily confirmed cases rose significantly. the current review highlights that even though india's lockdown strategy has been able to flatten the curve to a certain extent, it has essentially been unable to create a reversion in this trend or in isolating the disease. therefore, substantial reforms in policies need to be implemented to seize the spread of covid- . this pandemic has resulted in the loss of a lot of lives, clearly indicating the lack of planning and understanding of various biological species that remain a threat to our civilization. extensive research is still of paramount importance to develop the vaccine and ensure the process of interaction. every state should be prepared beforehand to avoid such a significant rise in preventable deaths by assessing and studying about the covid- pandemic carefully. j o u r n a l p r e -p r o o f coronaviruses; origin and evolution hunt for contacts of coronavirus-stricken pair in york the first british national to contract coronavirus had been in singapore. from the guardian coronavirus disease (covid- ): a primer for emergency physicians emerging coronaviruses genome structure, replication, and pathogenesis novel coronavirus: where we are and what we know but how does it compare to other countries? from forbes covid- ) advice for the public coronavirus: people with fever or 'continuous' cough told to self-isolate coronavirus: pm says everyone should avoid office, pubs, and traveling covid- coronavirus real-time pcr kit covid- : guidance for staff in the transport sector from the economic times covid- testing: what are the tests and testing procedures being carried out in india? from indian express explained: how the antibody test for covid- is different from the pcr test aerosol and surface stability of sars-cov- as compared with sars-cov- a review of cardiovascular implications of novel covid- coronaviruses: an overview of their replication and pathogenesis govt bans airlines from boarding passengers from china to india three emerging coronaviruses in two decades: the story of sars, mers, and now covid- clinical features of patients infected with novel coronavirus in wuhan, china. the lancet india may run out of icu beds for covid- patients by july end: study interim clinical guidance for management of patients with confirmed coronavirus disease (covid- ) sweden's 'soft' covid- strategy: an appraisal how did new zealand become covid- free? from bbc news days of lockdown: measuring india's success in arresting covid- the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application the first case of neonate infected with novel coronavirus pneumonia in china explained: how rapid antigen test detects covid- , where it will be used emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments middle east respiratory syndrome coronavirus (mers-cov) covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? government responses to covid- . blavatnik school of government covid- , sars, and mers: are they closely related? police can issue 'unlimited fines' to those flouting coronavirus social distancing rules, says health secretary clinical virology ourworldindata.org. from coronavirus pandemic (covid- coronavirus pandemic (covid- ). from ourworldindata transmission of -ncov infection from an asymptomatic contact in germany annexure to ministry of home affairs order no: - / -d covid- infection: origin, transmission, and characteristics of human a review of coronavirus disease- (covid- ) india coronavirus numbers explained: cases in four states growing faster than the national average nearly lakh coronavirus cases in india recent advancements in the diagnosis, prevention, and prospective drug therapy of covid- . frontiers in public health cell the authors report no conflict of interest for submitting paper titled "study and overview of the novel corona virus disease (covid- krishna mohan agarwal has done his b. tech. in mechanical engineering from knit energy from iit he is working as the capacity of assistant professor grade iii in amity university uttar pradesh, noida, india since his broad research area lies in the field of materials & design (microstructure and mechanical behavior of materials alternative fuels for ic engines, solar energy) and business & management (management concepts and human resource management) usa where he was leading a multidisciplinary team of researchers. he is also the recipient of "inae fellowship award" in by indian national academy of engineering. he was selected as one of the twelve young biomedical scientists by the indian council of medical research (icmr), govt. of india to pursue research fellowship ( - ) in the field of sensory prosthetics at university of glasgow, scotland, uk. he has attended biomechanics and human gait training at munich, germany in march and training of use of rtms, eeg and emg equipment(s) in disabled children in ivanovo she completed her major project on the topic heavy metals status of water and soil of okhla bird sanctuary and najafgarh jheel under the guidance of assistant professor dr.pamposh bhat at the department of environment management a nature enthusiast with a green thumb her research interests lie in the field of microbial molecular biotechnology and its application in the field of environmental biotechnology, medical biotechnology, she is also very enthusiastic about the growing importance of bioinformatics and its application in biological data analysis his recent internship on the topic "design of physical structure of icu ventilators for covid- " with inxee systems pvt. ltd. led him to research more about covid- when he felt the lack of a compiled holistic guide to the novel coronavirus disease. prairit during his engineering has researched on topics like "aerodynamics of formula one cars" ( ) and completed projects like "prototype construction of an arduino controlled cnc machine swati mohapatra obtained her master's degree in applied microbiology from kalinga institute industrial technology, bhubaneswar and ph.d. on the topic "bio-prospecting and characterization of polyhydroxyalkanoates from bacillus sp. isolated from rhizospheric soil" from odisha university of agriculture & technology bhubaneswar, odisha, india in and respectively. she is currently working as assistant professor in the department of microbial her research work pertains to biopolymer & composite materials with its biomedical & agricultural applications she supervised p.g and ongoing ph.d. students. she has published scientific publications including research, review & popular science articles in different journals of national & international repute and book chapters in different books with teaching and research experience of more than years. he was the recipient of the indian society of cardiology fellowship ( ), and many other fellowships key: cord- -tojgojjf authors: segars, james; katler, quinton; mcqueen, dana b.; kotlyar, alexander; glenn, tanya; knight, zac; feinberg, eve c.; taylor, hugh s.; toner, james p.; kawwass, jennifer f. title: prior and novel coronaviruses, covid- , and human reproduction: what is known? date: - - journal: fertil steril doi: . /j.fertnstert. . . sha: doc_id: cord_uid: tojgojjf structured abstract objective to summarize current understanding of the effects of novel and prior coronaviruses on human reproduction, specifically male and female gametes, and in pregnancy. design review of english publications in pubmed and embase to april , . methods manuscripts were screened for reports including coronavirus, reproduction, including pathophysiology and pregnancy. intervention(s) none. main outcome measure(s) reproductive outcomes; effects on gametes; pregnancy outcomes; neonatal complications. results seventy-nine reports formed the basis of the review. coronavirus binding to cells involves the s domain of the spike protein to receptors present in reproductive tissues, including angiotensin converting enzyme- (ace ), cd , ezrin, and cyclophilins. sars-cov- may cause severe orchitis leading to germ cell destruction in males. reports indicate decreased sperm concentration and motility for - days following covid- infection. gonadotropin-dependent expression of ace was found in human ovaries, but it is unclear whether sars-cov- adversely affects female gametogenesis. evidence suggests that covid- infection has a lower maternal case fatality rate than sars or mers, but anecdotal reports suggest that infected, asymptomatic women may develop respiratory symptoms postpartum. covid- infections in pregnancy are associated with preterm delivery. postpartum neonatal transmission from mother to child has been reported. conclusion covid- infection may adversely affect some pregnant women and their offspring. additional studies are needed to assess effects of sars-cov- infection on male and female fertility. the rapid spread of the severe acute respiratory syndrome coronavirus (sars-cov- ) has led to a pandemic of coronavirus disease (covid- ) across the globe. as of april , , there are over . million cases and , deaths attributed to the virus worldwide. as a result, nations have implemented suppression and mitigation strategies to control community spread, including mandated social distancing, restrictions to non-urgent medical care, and closure of non-essential businesses. despite these efforts, the spread of sars-cov- is ongoing, creating a public health crisis and impacting the population world-wide. coronaviruses are a group of viruses that can cross species barriers and become human pathogens. all seven identified human coronaviruses originated from animal reservoirs including domestic animals, bats, or mice. while most human coronaviruses cause mild illness, severe acute respiratory syndrome coronavirus (sars-cov), middle east respiratory syndrome coronavirus (mers-cov) and the novel sars-cov- have been associated with severe lower respiratory tract infections, acute respiratory distress syndrome, and death ( ). the novel sars-cov- virus spreads rapidly, with - people infected from every index case, a reproduction number (r ) or transmission rate of . - . ( ) . in contrast, the h n seasonal influenza had an r of . - . . the incubation period for sars-cov- ranges from - days, and asymptomatic spread occurs prior to onset of symptoms ( , ) . transmission is thought to be mainly through respiratory droplets and fomites ( ) . in one experiment, viable virus was detected in aerosols for up to three hours, with an estimated half-life of . hours. in addition, virus was detected on surfaces for days after application, with viable sars-cov- identified on plastic and stainless steel up to hours ( ). sars-cov- rna has also been detected in blood and stool and it is not yet known whether the infection can be acquired through exposure to non-respiratory bodily fluids ( ) . symptoms of sars-cov- infection include fever, cough, fatigue, shortness of breath, sputum production, headache and myalgias. in addition, patients may report gastrointestinal symptoms ( ) or anosmia. the severity of infection ranges from asymptomatic carriers, to mild flu-like disease, to critical illness and death. critically-ill patients may experience respiratory failure, shock or multiorgan dysfunction. approximately % of infections are mild with flu-like symptoms, - % are severe, requiring hospitalization and supplemental oxygen, and % are critical and require mechanical ventilation ( ). risk factors for severe illness include age and underlying medical comorbidities such as cardiovascular disease, diabetes, chronic respiratory disease, hypertension and cancer ( ) . death may occur in up to % of infections. death from sars-cov- is more common in individuals over age or with underlying medical issues but can occur in younger persons, perhaps related to the inoculum. associated cardiac arrhythmias may be fatal. while persons of advanced age are most likely to experience severe symptoms, women of reproductive age are also at risk for development of severe disease and death. furthermore, reproductive age women can act as asymptomatic carriers and increase viral transmission. the aim of this review is to summarize what is currently known about the impact of prior coronaviruses and the novel sars-cov- infection on reproduction and pregnancy. a systematic search in the literature published in the pubmed and embase databases was conducted in accordance with the guidelines of the preferred reporting items for systematic reviews and meta-analyses (prisma). literature review of available literature in english, both published and peer-reviewed on-line publications from -april , . additional sources were identified from citations of retrieved literature. search strategy for the pubmed and embase searches is shown below. there was no limitation on sample size. published reports of experiences with the sars-cov- virus have increased greatly in the past months, but no randomized trials to date regarding possible treatments were identified. most reports pertaining to reproduction or pregnancy involved small cohorts, case reports, guidelines, and editorials. similarly, prior publications of other coronaviruses were limited in number. we reviewed all titles for eligibility. all reports including pregnancy or reproductive tissues were included. we excluded editorials and publications of guidelines. we excluded papers that were duplicates or did not contain information related to pregnancy or reproduction, the presence of virus in reproductive tissues, effects on gametes, pregnancy outcomes, or neonatal complications. case reports were included. because of the limited nature of the reports and the absence of randomized trials we did not use the cochrane rob . tool. similarly, because of the limited scope of the cohort studies, we did not use the newcastle-ottawa scale to rate the studies. full text articles were then reviewed and evaluated for inclusion by authorship teams. two independent reviewers (j.s. and z.k.) any disagreements were resolved through discussion with third reviewer (j.k.). the authors acknowledge the number of publications about the novel sars-cov- virus is increasing at an exponential rate and there may be bias toward reporting of positive findings. we used a broad inclusive search strategy so as not to miss a seminal contribution. the the search revealed manuscripts after removal of duplicates. ninety-seven manuscripts related to pregnancy and coronavirus and only were related to embryos or early reproduction. small cohorts, case reports, comments on guidelines, guidelines, editorials were retrieved. after exclusion, manuscripts were included in the review based on relevance and new data. a review of the coronavirus structure and function help to inform us on the pathophysiology of coronavirus infectivity. coronaviruses are large, single-stranded, enveloped rna viruses approximately kb ( ) . the viral rna genome is housed inside a nucleocapsid, which itself is contained within a viral envelope ( ) . this envelope comprises three distinct proteins: a "membrane protein" and "envelope protein," which are both directly responsible for viral assembly, as well as a "spike protein," which mediates viral entry into host cells ( ) . when viewed with electron microscopy, these spike proteins are surface-exposed markers that produce a recognizable "crown-like" appearance to the virus. the spike proteins serve a critical step in initiating human infection, as well as determining host tissue specificity and inducing host immune response ( ) ( ) ( ) . the coronavirus spike protein is composed of two unique subunits that facilitate viral-host binding ( ) ( ) ( ) ( ) . the s domain of the spike protein functions in viral binding and attachment to the host cell membrane. numerous receptors on the human cell membrane that are involved in s subunit binding have been identified to date, including angiotensin converting enzyme- (ace ), cd , ezrin, and cyclophilins ( , ) . the s domain of the spike protein is responsible for fusion of the viral and host cell membranes, allowing the sars-cov- viral genome to enter the host cell. this process involves a complex interaction between viral and host machinery, which culminates in rapid viral replication within target cells. international research efforts are currently underway aimed at using the s domain of the spike protein as a target for therapeutic anti-viral therapy, as well as vaccine development. the involvement of sars-cov- infection within human male and female reproductive systems has yet to be fully elucidated. however, results from other coronavirus subtypes, specifically sars-cov, help inform knowledge of tissue-specific viral pathophysiology. current data suggest that the female reproductive system may be spared from viral infection. immunohistochemical and in situ hybridization studies on tissues from a small cohort of deceased patients that were infected with sars-cov failed to identify sars-cov viral rna within the female reproductive tract, including both ovarian and uterine tissue ( ) , though ace receptors can be found there. importantly, there is evidence to suggest that coronavirus infection may impact the male reproductive tract. the ace protein, a main receptor for coronavirus viral entry, is selectively expressed by leydig cells of the adult testes ( ) . there are numerous reports of male reproductive injury after sars-cov infection. leading theories postulate that this is an immune-mediated response to infection since direct inoculation of the coronavirus rna within testicular tissue has not been described. in a study of eight postmortem sars-cov patients, testicular tissue contained focal atrophy despite lacking identifiable sars viral rna ( ) . accordingly, there have been reported cases of sars-cov causing severe orchitis, as evidenced by extensive igg precipitation in testicular interstitial tissue causing germ cell destruction and widespread testicular leukocyte infiltration ( ) . further studies on the reproductive involvement of coronavirus infections are warranted, particularly within recovered patients. there are limited data regarding the impact of sars-cov- on human reproduction as the virus is novel and has only recently infected humans. to date, there have been no reports of the virus in the female reproductive tract, in vaginal secretions, in amniotic fluid or in peritoneal fluid. although there is nothing to suggest that female or male gametes would be impacted directly by infection with sars-cov- or other coronaviruses, there is evidence that fever can impact spermatogenesis. therefore, male fertility may be diminished for - days following covid- due to decreased sperm concentration and motility ( , ) . the sars-cov- virus utilizes ace receptors to gain entry into the human cells. the male reproductive system expresses ace within adult leydig cells in the testis and there are data to suggest that ace plays a role in spermatogenesis. the presence of ace receptors is much more prominent in the male reproductive system than the female reproductive system, but gonadotropin-dependent expression of ace has been reported in human ovaries ( , ) . at this time, it is unknown if the sars-cov- virus utilizes ace receptors in the reproductive system and what, if any, impact this would have on oocyte quality, embryo development, or ensuing pregnancy. gametes obtained from patients with other viral illnesses, such as hiv and hepatitis, must be treated with special precautions aimed at reducing exposure of the non-infected partner and cross contamination of reproductive tissue within the laboratory ( ) . these precautions are not currently recommended for sars-cov- , given the lack of evidence for transmission through blood or sexual contact ( ) . similarly, there is no current recommendation for screening oocyte or sperm donors for sars-cov- . these are areas in which further investigation is necessary in order to assure the safety of stored gametes and the safety of patients undergoing assisted reproduction. the case fatality rate for all reported cases of sars in pregnancy (n= ) was % ( - ), and was higher among pregnant women. mechanical ventilation was required three times more often in pregnant versus non-pregnant women. a case control study comparing ten pregnant to forty non-pregnant women affected by sars reported a % icu admission rate and a % case fatality rate (cfr) in the pregnant group compared to only an % and % rate in the nonpregnant group ( ). four of seven pregnant patients with sars miscarried in the first trimester ( ) . four of five women infected after weeks gestation were delivered prematurely, largely due to their deteriorating maternal condition from sars, at , and weeks gestation ( ) . the infants born at and weeks developed rds requiring surfactant, but were normal weight for gestational age. however, among infants born weeks ( to ) after initial infection, fetal growth restriction and fibrin deposition on placental interface was seen in two of three pregnancies, suggesting compromise. there was no evidence of vertical transmission. overall, sars was a very serious disease for pregnant women and their fetuses. among pregnant patients with mers (n= ), % were admitted to the icu ( / ) and three died (cfr of %) ( ) ( ) ( ) ( ) ( ) . the only woman known to contract mers in the first trimester went on to deliver a healthy infant at term ( ) . of those contracting the disease after the first trimester (n= ), one had a spontaneous loss at week gestation ( ) , one presented at weeks gestation with pre-eclampsia and had an intrauterine fetal demise ( ) , and a third with preexisting respiratory issues developed mers at weeks gestation and then ards. despite ventilation and cesarean delivery, both the neonate and mother subsequently died ( ) . three of nine other patients were delivered preterm due to maternal hypoxia. mers also had a high fatality rate and premature delivery rate. through april , , there have been case reports or series and case-control reports of intrauterine growth restriction (iugr), were delivered prematurely, were small for gestational age (sga) and was large for gestational age (lga). one stillbirth and one neonatal death were reported. table summarizes the pregnancy-related experience of the three coronavirus epidemics. peerreviewed case reports to date suggest the following: • covid- has a lower maternal case fatality rate than either sars or mers. • pregnant patients display similar signs and symptoms of covid- as non-pregnant patients. • pregnant patients are not more susceptible to coronavirus infection, nor at higher risk for severe illness. • severe illness may precipitate premature labor or lead to early delivery. • adverse infant outcomes have been reported, but it is unclear whether these outcomes are directly related to covid- infection. given the teratogenicity concerns associated with viruses such as zika, there remains the however, a recent case report in jama ( ) suggests that vertical transmission may be possible. in this case report, an otherwise healthy infant was born by cesarean section to a -year-old with rt-pcr confirmed sars-cov- infection. this infant was immediately placed into isolation and a blood sample at two hours of age was noted to show an elevated sars-cov- igg. while the igg can be secondary to transplacental transfer, the infant was also positive for sars-cov- igm which cannot be explained by maternal-fetal transfer ( ) . furthermore, igm antibodies only appear three-to-seven days after infection. all five rt-pcr tests on the infant were negative for sars-cov- ( ). the antibody profile of this infant is suggestive of exposure to sars-cov- in-utero. a follow-up study done on six infants born to covid- positive mothers showed positive igm antibodies in two of them. yet, all throat swabs and blood samples from the neonates tested negative for the virus. overall, evidence of vertical transmission in the setting of covid- infection is currently inconclusive. continued observation is necessary as more data is gathered during the course of this pandemic. as of march , , there were no identified vaccines or targeted therapies for the treatment of covid- . currently, treatment is aimed at supportive methods such as oxygenation/mechanical ventilation and treating complications. as no effective treatment has been identified, a barrage of potential therapies are being trialed both within and outside of research protocols. although this list is ever-changing, the majority of these medications target the ability of the virus to replicate or are designed to suppress or modulate the immune system, thereby limiting inflammatory damage ( , ) . during pregnancy these potential remedies fall into three different departments: those established to be safe in pregnancy, those with unknown status, and those which have clear or relative contraindications during pregnancy. it is imperative to consider that although some of these interventions are safe in pregnancy, none so far have been identified as definitive treatment and all have potential risks. these concerns need to be considered as an additional risk assumed by pregnant women; some potential therapies may carry risk to the fetus or be unavailable to pregnant women. several investigated medical treatments for covid- are known either to be safe or nonteratogenic in pregnancy. these include various immune modulators such as hydroxychloroquine/chloroquine, methylprednisolone/glucocorticoids, and the anti-viral medications lopinavir-ritonavir ( ) ( ) ( ) ( ) ( ) . it is important to note that although non-teratogenic, the use of glucocorticoids in pregnancy has been associated with diabetes, weight gain, preterm premature rupture of membranes, hypertension, and intrauterine growth restriction. interferon therapy, often used in hepatitis c treatment, has been well established to be safe in pregnancy ( ) . the use of convalescent plasma, or plasma derived from individuals who previously contracted covid- , has been shown to reduce disease sequela in those with severe disease ( ) . given that its risk profile should be similar to a blood transfusion, there are no overt contraindications in pregnancy. east respiratory syndrome coronavirus in monkeys ( ) . although current clinical studies exclude pregnant women, remdesivir may be administered in critically-ill pregnant patients (nct ) ( ) . to date, no information is available concerning the effects of remdesivir in pregnancy. due to the increased release of cytokines and subsequent inflammatory damage during covid- , tocilizumab, a monoclonal antibody that binds the receptor il- , has been used in china, with at least one clinical trial that is ongoing (nct ) ( , ) . a major concern for pregnant patients is that igg isotype antibodies cross the placenta at an increasing rate in accordance with gestational age ( ) . however, the effect of each medication on fetal development is unknown. furthermore, in the rheumatology literature it is recommended that tocilizumab be avoided during pregnancy given the lack of data on adverse fetal effects ( ) . other anti-viral medications which have been utilized that have clear evidence of teratogenicity, either in humans or animal models, include favipiravir and ribavirin ( , , ) . notably, the aforementioned medications are experimental, thus it is imperative to have a risk-benefit discussion with patients given the medication side-effect profiles, potential effects in pregnancy, and unknown benefits. until randomized trials with adequate controls are completed, it is difficult to draw definitive conclusions concerning the efficacy of any of these treatments ( ) . thus far, there has been no indication that infants born to covid- positive mothers experience any significant morbidity or mortality. in the aforementioned case series of nine covid- -positive patients who underwent cesarean section, all of their infants had negative covid- testing and had -min apgar scores of - and -min apgar scores of - . in addition, none of the infants in this series experienced asphyxia or neonatal death ( ) . three newborns have been confirmed with covid- and their infection was likely secondary to exposure to infected caregivers. all three neonates experienced either fever, cough, or vomiting, then subsequently recovered with no severe sequelae ( ) . given the disease course seen in older children, the disease severity can be expected to be worse for neonates with pre-existing cardiac or pulmonary conditions such as congenital heart disease ( ). there are a significant number of unknowns concerning covid- and pregnancy, especially regarding the infectivity of a pregnant woman. therefore, the majority of data are extrapolated from previous experience with other coronaviruses, sars-cov and mers-cov, as well as influenza pandemics such as the flu and the asian flu in the late s ( , ) . however, pregnant women are not more likely than non-pregnant woman to become infected with sars-cov- , based on data from regions with the first covid- exposures and from previous pandemics ( ) . nor do pregnant women appear to suffer a more severe disease course or higher mortality rate compared to non-pregnant women of a similar age. it has been established that sars-cov- is spread by respiratory droplets, yet the potential for other routes of transmission, particularly during labor, is unknown ( ) . limited data are available for covid- , but it is possible to extrapolate from limited information available on sars-cov- and other coronaviruses. in the sars-cov outbreak, small case reports showed no viral rna in placental, umbilical cord blood, amniotic fluid, or breastmilk ( , , ) . it is important to note that fecal matter that was aerosolized via the flushing of toilets was noted to spread disease ( ) . one could hypothesize that amniotic fluid could become aerosolized and infect others if viral rna was present through mixing with fecal matter. mers-cov had an extremely high death toll, however only twelve cases were documented in pregnancy, and no information is available on viral rna in pregnancy-specific tissue ( ) . to date, there is limited information concerning which fluids in labor could potentially transmit sars-cov- directly or by aerosolization. while a single maternal vaginal swab in the only suspected case of vertical transmission was negative, it is too early to conclude whether transmission can occur via vaginal secretions ( ) . rectal swabs have not been obtained in pregnant patients; however, a series of ten pediatric patients did confirm sars-cov- rna in rectal specimens ( ) . thus, information regarding vaginal deliveries, while limited, remains concerning. as previously noted, case reports have shown no viral rna in amniotic fluid, cord blood, or breast milk ( ) . until more information is gathered, it is prudent for personnel present during delivery to treat all fluids as potentially contagious and wear appropriate personal protective equipment. on january , thanks to the initial efforts of the late dr. jixian zhang, the sars-cov- virus was identified as a cause of severe cases of pneumonia that began on december in wuhan, china. in the first three months of , the novel virus has infected over . million people and caused more than , deaths. declared a pandemic by the who on march , , the sickness has overwhelmed healthcare resources as it spread. containment of sars-cov- has proven exceptionally difficult due to asymptomatic and pre-symptomatic spread of disease, as well as the relatively high person-to-person transmission. as the virus moved from host to host, as is typical of the single-stranded rna viruses, sars-cov- has mutated. notably, there is an enormous phenotypic difference in disease severity from asymptomatic infection to death, but the reasons for this striking variability remains obscure. despite the overwhelming magnitude of the disease and its worldwide prevalence, information regarding the effects of the novel coronavirus on human reproduction are currently limited. this lack of evidence should not be considered reassuring, since only three months have elapsed since the novel coronavirus jumped species and infected humans. there is reason to be concerned based on data from other coronaviruses. as is typical of this family of viruses, the sars-cov- spike protein binds the ace receptor, a protein found in many reproductive tissues, including the testis. of concern, evidence exists that related coronaviruses have caused severe orchitis. while sperm counts can be reduced by high fever alone, the question of other possible long-term effects on male and female gametes is pressing. specifically, whether there might be shedding of virus in some individuals that might affect the safety and storage of gametes. as noted, evidence continues to emerge regarding effects of the novel coronavirus in pregnancy and some initial reports suggest that complications, particularly after delivery, may be increased. additional studies are urgently needed. because of the risk of viral transmission between patients, staff, physicians and providers, and to comply with local restrictions for non-emergency surgeries, many programs of assisted reproduction have suspended procedures throughout the globe during the height of the pandemic. as the assisted reproductive technology (art) programs resume operations it will be important to gather information regarding the status of individuals infected with the novel coronavirus, and to assess gametes and reproductive outcomes for those who had covid- . these studies will be enabled by the availability of serologic testing and more widespread rna testing for the novel coronavirus. likewise, researchers should collect data regarding outcomes of pregnancies in women who became infected during pregnancy. while a vaccine may prevent disease, until one is available, information is needed on the safety of medical treatments and outcomes in pregnancy. one limitation of this review is that because of the rapidly increasing number of publications, it is possible that new information may be published contradicting the findings. because of concern about possible adverse effects, there may be a risk of bias toward reporting positive outcomes. additionally, since reports have focused on the acuity of treatment, the reproductive effects may be present, but not yet reported. the strength of the report is that our search was comprehensive and conducted, as much as possible, in accordance with prisma guidelines. the immense impact of the covid- pandemic in lives lost, healthcare expenses, and economic consequences of countries and individuals is inestimable because the epidemic is still rampant throughout the globe. while data are limited, and incomplete at this time, there is justifiable concern that reproductive consequences of the novel coronavirus may have lasting effects for male reproduction and for some pregnant women and children. zoonotic origins of human coronaviruses preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a data-driven analysis in the early phase of the outbreak early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention aerosol and surface stability of sars-cov- as compared with sars-cov- professionals: frequently asked questions and answers clinical characteristics of covid- patients with digestive symptoms in hubei, china: a descriptive, cross-sectional, multicenter study interim clinical guidance for management of patients with confirmed coronavirus disease (covid- ) role of changes in sars-cov- spike protein in the interaction with the human ace receptor: an in silico analysis structure, function, and evolution of coronavirus spike proteins human coronaviruses oc and hku bind to -o-acetylated sialic acids via a conserved receptorbinding site in spike protein domain a structural insights into coronavirus entry human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza c viruses cryo-electron microscopy structures of the sars-cov spike glycoprotein reveal a prerequisite conformational state for receptor binding tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion cryo-em structures of mers-cov and sars-cov spike glycoproteins reveal the dynamic receptor binding domains ezrin interacts with the sars coronavirus spike protein and restrains infection at the entry stage cryo-em structure of the sars coronavirus spike glycoprotein in complex with its host cell receptor ace organ distribution of severe acute respiratory syndrome (sars) associated coronavirus (sars-cov) in sars patients: implications for pathogenesis and virus transmission pathways the novel angiotensin-converting enzyme (ace) homolog, ace , is selectively expressed by adult leydig cells of the testis multiple organ infection and the pathogenesis of sars orchitis: a complication of severe acute respiratory syndrome (sars) history of febrile illness and variation in semen quality influence of genital heat stress on semen quality in humans angiotensin-converting enzymes play a dominant role in fertility recommendations for reducing the risk of viral transmission during fertility treatment with the use of autologous gametes: a committee opinion patient management and clinical recommendations during the coronavirus (covid- ) pandemic a case-controlled study comparing clinical course and outcomes of pregnant and non-pregnant women with severe acute respiratory syndrome severe acute respiratory syndrome (sars) in neonates and children sars and pregnancy: a case report potential maternal and infant outcomes from (wuhan) coronavirus -ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections infants born to mothers with severe acute respiratory syndrome pregnancy and perinatal outcomes of women with severe acute respiratory syndrome impact of middle east respiratory syndrome coronavirus (mers-cov) on pregnancy and perinatal outcome middle east respiratory syndrome coronavirus infection during pregnancy: a report of cases from saudi arabia mers-cov infection in a pregnant woman in korea middle east respiratory syndrome coronavirus during pregnancy emergency cesarean section in an epidemic of the middle east respiratory syndrome: a case report middle east respiratory syndrome coronavirus (mers-cov) infection during pregnancy: report of two cases & review of the literature stillbirth during infection with middle east respiratory syndrome coronavirus covid- in pregnancy: early lessons clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records clinical analysis of pregnant women with novel coronavirus pneumonia infants born to mothers with a new coronavirus (covid- ). in: front pediatr possible vertical transmission of sars-cov- from an infected mother to her newborn should we worry? clin infect dis pregnancy and perinatal outcomes of women with coronavirus disease (covid- ) pneumonia: a preliminary analysis maternal and neonatal outcomes of pregnant women with covid- pneumonia: a case-control study premature baby in serious condition after coronavirus infection coronavirus disease (covid- ) during pregnancy: a case serie a case report of neonatal covid- infection in china a case of novel coronavirus in a pregnant woman with preterm delivery clinical features and obstetric and neonatal outcomes of pregnant patients with covid- in wuhan, china: a retrospective, single-centre, descriptive study a pregnant woman with covid- in central america antibodies in infants born to mothers with covid- pneumonia neonatal early-onset infection with sars-cov- in neonates born to mothers with covid- in wuhan, china clinical analysis of neonates born to mothers with -ncov pneumonia effects of coronavirus infections in children middle east respiratory syndrome an analysis of pregnant women with covid- , their newborn infants, and maternal-fetal transmission of sars-cov- : maternal coronavirus infections and pregnancy outcomes coronavirus disease (covid- ) and neonate: what neonatologist need to know development of a standard treatment protocol for severe acute respiratory syndrome immune modulating therapies in pregnancy and lactation a trial of lopinavir-ritonavir in adults hospitalized with severe covid- treating covid- -off-label drug use, compassionate use, and randomized clinical trials during pandemics recommendations for the use of antiretroviral drugs in pregnant women with hiv infection and interventions to reduce perinatal hiv transmission in the united states effects of chloroquine on viral infections: an old drug against today's diseases? a systematic review of the fetal safety of interferon alpha treatment of critically ill patients with covid- with convalescent plasma prophylactic and therapeutic remdesivir (gs- ) treatment in the rhesus macaque model of mers-cov infection adaptive covid- treatment trial (actt) favipiravir combined with tocilizumab in the treatment of corona virus disease the eular points to consider for use of antirheumatic drugs before pregnancy, and during pregnancy and lactation favipiravir as a potential countermeasure against neglected and emerging rna viruses the ribavirin pregnancy registry: an interim analysis of potential teratogenicity at the mid-point of enrollment pneumonia in pregnancy interim considerations for infection prevention and control of coronavirus disease (covid- ) in inpatient obstetric healthcare settings covid- : faecal-oral transmission? the authors thank drs. catherine racowsky and dr. ricardo azziz. key: cord- -i um iu authors: hoskins, johnny d. title: coronavirus infection in cats date: - - journal: veterinary clinics of north america: small animal practice doi: . /s - ( ) - sha: doc_id: cord_uid: i um iu cats are susceptible to natural infection with several strains of feline coronavirus that result in either effusive and noneffusive feline infectious peritonitis or enteritis. excretion of coronavirus by infected cats into the environment occurs by way of feces, oronasal secretions, and possibly urine. clinical diagnosis of coronavirus infection is made by evaluating the case history, physical findings, laboratory results, and coronavirus antibody titers as well as ruling out analogous diseases. an intranasal temperature-sensitive feline infectious peritonitis coronavirus vaccine is available for use in healthy cats weeks of age or older. in many species of animals, coronaviruses have a relatively restricted organ tropism. they infect the respiratory or gastrointestinal system, or both. fip coronavirus, feline enteric coronavirus, canine coronavirus (ccv), transmissible gastroenteritis virus (tgev) of swine, and human respiratory tract coronavirus comprise an antigenic cluster of closely related viruses within the family coronaviridae. the major structural proteins of these coronaviruses are antigenically similar to the extent that most investigators consider these coronaviruses as host-range variants rather than individual corona virus species. strains of feline coronavirus that infect cats have been divided into those that cause fip and those that induce subclinical to severe enteritis (table ) . strains of fip coronavirus differ from those of feline enteric coronavirus in that fip coronavirus is able to escape from the gastrointestinal tract and spread to replication sites in other organs. strains of fip coronavirus and feline enteric coronavirus probably represent pathogenic variants of a single coronavirus type.' alternatively, strains of fip coronavirus may arise as mutants of feline enteric coronavirus strains. current knowledge of the cell culture-adapted strains of feline coronavirus is based on their morphologic, structural, and antigenic relationship to tgev and ccv; the nature of the disease caused in the host; growth characteristics in cell culture systems; and the degree of relatedness to ccv in virus neutralization tests. the most virulent strains of fip coronavirus, such as fipv- - and fipv-df , cause fatal fip disease in most cats inoculated oronasally, whereas strains of intermediate virulence, such as fipv-ucdl, cause fip disease in cats undergoing extended exposure. strains of low virulence, such as fipv-ucd and fipv-ucd , can become established as asymptomatic infections; fatal fip disease occurs only if the immunologic responsiveness of the host later becomes compromised. most cases of fip disease result from infection with strains similar to fipv-tn and not with those strains of fip coronavirus that are closely related to ccv. most asymptomatic cats with positive coronavirus-antibody titers have been previously infected by strains of feline enteric coronavirus or fip coronavirus, which usually do not cause fatal disease by natural routes of infection. asymptomatic cats, however, may later succumb if exposed to a more virulent strain of fip coronavirus. coronavirus antibody-positive cats that resist later challenge probably seroconvert as a result of a systemic infection with a virulent strain of fip corona virus. various strains of fip coronavirus evidently survive in the environment much longer than originally was believed. in recent studies/ fip coronavirus was recovered from contaminated dry surfaces for to weeks. the amount of infectious virus recovered decreases with time. because relatively large quantities of fip coronavirus are required to establish natural infection in a susceptible cat, strains of coronavirus probably are not contagious to cats for longer than or weeks after an environment, bedding, food bowl, or water bowl is contaminated. infectivity of feline coronavirus strains is destroyed by most household disinfectants and detergents. feline enteric coronaviruses, such as strains of fecv- - and fecv-ucd, are highly infectious by the oral route to all cats of any age and have an affinity for the apical columnar epithelia of the duodenum, jejunum, and ileum. adult cats often endure subclinical infections; low-grade fever, vomiting, and diarrhea may be observed in newly weaned kittens. natural infection with strains of feline enteric coronavirus results in production of antibodies that presently are serologically indistinguishable from the antibodies produced by infection with fip coronavirus, ccv, or tgev. most cats infected with a strain of feline enteric coronavirus remain persistently infected and periodically shed coronavirus in their feces. coronavirus antibodies do not, however, protect most cats from later exposure with virulent strains of fip coronavirus. these antibodies may actually sensitize cats to later exposures, thereby hastening the disease process caused by a virulent strain of fip coronavirusy investigators remain unsure of the routes of natural transmission by which feline coronaviruses are passed between cats. excretion of coronavirus by infected cats into the environment occurs by way of feces, oronasal secretions, and, possibly, urine. initial infection of susceptible cats most likely results from ingestion and/or inhalation of the corona virus. close contact between cats is probably required for the most effective transmission of coronavirus, although the possibility of virus transmission by fomites (contaminated clothing, bedding, and dishware) also exists. transmission of fip coronavirus in utero, as suggested by several reports/ • has not been convincingly shown to occur. domestic cat and other felidae, including lions, mountain lions, leopards, jaguars, cheetahs, lynxes, sand cats, and pallas cats, are susceptible to infection with fip corona virus. • in domestic cats, fip disease occurs predominantly in young animals, although all ages are susceptible. a higher incidence occurs between and months of age, whereas a lower incidence is noted from to years of age, followed by an increased incidence in cats older. male and female cats are. affected equally. fip occurs more frequently in purebred cats than in other breeds. after natural infection, localization and replication of fip coronavirus occur in large mononuclear cells of regional lymphoid tissue at or near the site of initial virus penetration (fig. ). • a primary viremia results with free virus and virus-infected mononuclear cells being transported to other body organs, especially to the liver, spleen, and lymph nodes. these organs are subsequently involved because they contain large populations of macrophages, which are the principal target cells for fip corona virus infection. a secondary macrophage-associated viremia then occurs, resulting in further spread of fip coronavirus throughout the body! the susceptibility of cats to fip disease may involve several predisposing factors, including age at time of exposure, genetic susceptibility, physical condition, stress, presence of concurrent disease (especially feline leukemia virus and feline immunodeficiency virus infections), challenge dose and strain of feline coronavirus, route of infection, previous sensitization with nonprotective corona virus antibodies, and cell-mediated immunocompetence. • if an effective cell-mediated immune response is exhibited during the primary phase of coronavirus infection, viremia will probably be terminated, thereby protecting the cat against fip disease. most cats subsequently do not show clinical evidence of fip coronavirus infection. some cats, however, may develop a transient fever that lasts for to days and mild mesenteric iymphadenopathy. if the infected cat is unable to mount an effective cellmediated immune response and produces coronavirus antibodies that do not neutralize the virus, infection progresses rapidly into a fulminating form of fip disease. a similar situation may occur if the cat has already acquired coronavirus antibodies through previous infection with a strain of feline enteric coronavirus or fip coronavirus of low virulence. in the absence of an effective cell-mediated immune response, a strong nonprotective humoral response may result in effusive form of fip disease. cats that exhibit a partial cell-mediated immune response may develop noneffusive fip disease. u an effective cell-mediated immune response does not always eliminate fip coronavirus from the body. in some recovered cats, the infection may persist in various places in the body, such as the gastrointestinal tract or associated lymph nodes. factors that depress cell-mediated immune responsiveness, such as feline leukemia virus and feline immunodeficiency virus infections, concurrent disease, and advanced age, may allow recrudescence of macrophageassociated infection with periodic shedding of fip corona virus, thereby resulting in effusive or noneffusive disease. • an exaggerated and nonprotective humoral response results in excessive levels of coronavirus antibodies and the formation of large immune complexes that are rapidly phagocytized by reticuloendothelial cells. immune complexes deposited in small blood vessels fix and activate complement, thereby resulting in the release of the third component of complement. phagocytosis of aggregates containing coronavirus, immunoglobulin, and complement is aided by the presence of receptors for immunoglobulin and complement on the macrophage surface. macrophages that are in perivascular locations ingest aggregates of intact fip coronavirus, immunoglobulin, and complement and thus encourage replication of the virus and the release of new virus and complement components. uptake and processing of fip coronavirus in these macrophages may be enhanced by an impaired cell-mediated immune response. recurrent complement-mediated damage results in the release of chemotactic complement components and the attraction of neutrophils. release of proteolytic enzymes from degenerated neutrophils exacerbates tissue damage. in cases of fip disease, degenerative and proliferative changes occur in blood vessels, particularly in the endothelial and medial layers of small veins and arteries in the peritoneal serosa and in the interstitial connective tissue of parenchymatous organs. the vascular lesion results in a pyogranulomatous lesion. in effusive disease, complement-mediated damage to the vascular endothelium results in increased vascular permeability and leakage of a nonseptic exudate rich in fibrin and immunoglobulin. severe damage to the vascular endothelium also contributes to disseminated intravascular coagulation. the development of multiple clotting abnormalities, including thrombocytopenia, increased quantity of fibrin-fibrinogen degradation products, and decreased activity of clotting factors vii, viii, ix, xi, and xii, is evident in fatal cases of fip disease. although most cats undergoing the primary phase of fip coronavirus infection recover, many cats remain persistently infected, that is, they are persistent carriers of fip corona virus. a small number of these cats subsequently develop the fatal fip disease weeks to months after the primary phase of infection. in the early phase of fip disease, cats with the effusive form may be presented with nonspecific signs, such as nonresponsive fever, anorexia, lethargy, weight loss, and pale mucous membranes. icterus may be seen in patients with severe liver involvement. • recurring episodes of diarrhea and constipation may be observed. progressive abdominal distention occurs from an accumulation of ascitic fluid in the peritoneal cavity. the volume of fluid present in cases of effusive disease varies and is generally a reflection of disease chronicity. • in chronic cases, a liter or more of fluid may accumulate within the peritoneal cavity. abdominal palpation usually elicits no response of pain. in some cats, the omentum may be palpated as a firm, contracted mass in the anteroventral abdomen. • pleural effusion with clinical signs of respiratory distress infrequently occurs in cats with effusive fip disease. these cats are presented with decreased exercise tolerance, dyspnea, and muffled heart and lung sounds. pericardia! effusion may be present. ocular and central nervous system signs are seldom seen in cats with effusive disease. • cats that recover from effusive disease usually undergo a period of time with noneffusive disease before they show clinical evidence of complete recovery. clinical diagnosis of the noneffusive fip disease usually is impeded by a lack of specific signs. onset of noneffusive disease is more insidious than is onset of the effusive form and is frequently associated with organ-specific signs resulting from disseminated pyogranulomatous lesions in various organs. nonspecific signs of weight loss, nonresponsive fever, and malaise may occur for several weeks before any organ-specific manifestations are present. • signs of renal or hepatic insufficiency and pancreatic, central nervous system, or ocular disease may be seen in cats with severe organ impairment! abdominal palpation may reveal mesenteric lymphadenopathy and nodular irregularities that are caused by surface-oriented pyogranulomata on various viscera, especially the kidneys. • pneumonia with clinical signs of respiratory distress infrequently occurs. when present, pulmonary lesions consist of mixed inflammatory cell infiltrates in peribronchiolar areas that may radiographically appear as ill-defined, patchy, interstitial, and peribronchiolar densities. ocular involvement usually is associated with other clinical signs of noneffusive disease, but may be present as a single manifestation. ocular lesions result from a necrotizing and pyogranulomatous uveitis that localizes around vascular structures. • changes in the anterior chamber include corneal edema, aqueous flare, hypotonia, iritis, hyphema, hypopyon, and keratic precipitates. on ophthalmoscopic examination, flame-shaped or boat-shaped hemorrhages may be present. engorgement of retinal vessels and perivascular cuffing is often noted. choroidal inflammation may cause subretinal fluid accumulation and secondary bullous or linear retinal detachments. neurologic signs in cats with noneffusive fip disease are variable and may include incoordination, posterior paresis, nystagmus, convulsions, intention tremors, cranial and peripheral nerve deficits, hyperesthesia, generalized ataxia, head tilt, behavioral changes, and urinary incontinence.n signs reflecting central nervous system and ocular involvement frequently occur together in noneffusive disease. lesions of central nervous system are usually multifocal or diffuse pyogranulomas and are located around the smaller blood vessels. the lesions are surface-oriented and primarily affect the choroid plexus, meninges, and ependyma. • in cases of noneffusive disease, many patients that do not show neurologic involvement have histopathologic evidence of central nervous system involvement.> hemograms of cats with fip disease often show a mild to moderate normocytic, normochromic anemia and leukocytosis that may be associated with absolute neutrophilia. absolute leukopenia may develop in some cats, especially in more fulminating or fatal cases. lymphopenia is commonly observed and is profound in cats with concurrent feline leukemia virus infection . on serum chemistry profiles, elevations in blood urea nitrogen and serum creatinine may be present in cats with either effusive or noneffusive fip and may reflect dehydration and inflammatory lesions in the kidneys. elevations in serum alanine transaminase and serum alkaline phosphatase as well as hyperbilirubinemia may occur if the inflammatory process involves the liver. • total serum proteins exceed . g/dl in % of cats with effusive disease and in % of cats with noneffusive disease because of varied increases in alpha- , beta- , and gamma globulins. this polyclonal gammopathy is not pathognomonic for fip disease but reflects its inflammatory nature. hyperglobulinemia also may occur in other inflammatory conditions that are associated with persistent antigenic stimulation of antibody-producing cells. aspirated peritoneal fluid typically is clear to slightly opaque or pale yellow to golden as well as being viscous in consistency. a stable foam often develops after shaking, presumably reflecting a protein content in excess of g/dl. • fluid specimens may contain fibrin strands and flakes that settle with time and may clot when exposed to room air. cellular count of fluid usually is between to , cells/ill. stained smears from a concentrated fluid sample commonly show a mixture of intact neutrophils, macrophages, plasma cells, lymphocytes, mesothelial cells, and a few erythrocytes. cultures of aspirated fluid for fungi, bacteria, and mycoplasmas usually reveal no growth. clinical diagnosis of pip disease is made by evaluating the presenting history, physical findings, laboratory results, coronavirus antibody titers, and exclusion of analogous diseases. • • these diagnostic maneuvers, however, do not provide conclusive evidence that a cat has pip disease, especially in cases of noneffusive disease in which accumulative abdominal fluid is not available for examination. tissue biopsy is the only diagnostic procedure that definitively confirms the presence of pip disease in apparently healthy cats or sick cats with either effusive or noneffusive disease. • any diagnosis of pip disease made without tissue biopsy or eventual necropsy examination must be considered, at best, to be a presumptive diagnosis. several serologic test procedures are available for detecting coronavirus antibodies in cats, including biologic assays, such as virus neutralization, and nonbiologic assays, such as indirect immunofluorescent antibody test, enzymelinked immunosorbent assay, kinetics-based enzyme-linked immunosorbent assay, agar gel immunodiffusion, and passive hemagglutination techniques. the target antigen used in these assays may be either a pip coronavirus (in liver sections of experimentally infected cats or in cell culture) or another coronavirus in the pip coronavirus antigenic cluster, usually tgev or ccvy coronavirus antibodies may be found in serum of apparently healthy cats, in cats with disorders other than effusive or noneffusive disease, and in cats with pip disease. excluding cats in catteries and in multiple-cat households, % to % of cats in the general feline population have coronavirus antibodies in their serum. if cats are housed together, the rate of seropositivity is completely absent or present in % to % of the cats, depending on whether feline corona virus is enzootic in that cat population. there are several situations in which assay results for the detection of coronavirus antibody are potentially helpful to the clinician and the cat owner. serotesting for feline coronavirus may be used as a screening procedure to determine if coronavirus is enzootic in a cat population and as an adjunct in the diagnosis of pip disease. most cats with histopathologically confirmed pip disease have high coronavirus-antibody titers. titers greater than : usually are associated with noneffusive disease, whereas titers of : to : may be found in cats with effusive and noneffusive disease and in cats with feline enteric coronavirus infection. in some cats with pip disease, negative titers or a decrease in titers may be seen terminally; this is a grave prognostic sign. in addition to correlating the positive coronavirus-antibody titer with other diagnostic information on the patient, the clinician should be aware that differences in assay results can be found between diagnostic laboratories and in the clinician's own interpretation of assay results. a few cats with histopathologically confirmed pip disease may have negative coronavirus-antibody titers. reasons for negative titers include disappearance of coronavirus antibodies in the terminal stages of pip disease, formation of immune complexes that leave little if any free coronavirus antibodies to react in the assay procedure, use of assay systems that are not sensitive enough to detect low levels of coronavirus antibodies, and presence of small amounts of coronavirus antibodies in fulminating cases of effusive diseasey in addition, bovine serum components found in some commercial feline vaccines may induce antibody production in cats vaccinated with those prod-ucts. these antibodies may react with antigenically similar bovine serum components in cell cultures that are used to propagate target viruses of the fip coronavirus antigenic cluster for immunochemical assays. resultant reactivity may be mistaken for coronavirus antibodies in serum of a recently vaccinated cat. because of this potential interference, it is recommended that elective serotesting of healthy cats for evidence of exposure to feline coronavirus should be delayed until at least to months after the last parenteral vaccine was given. at the time of this writing, available serologic assays for detecting coronavirus antibodies do not identify the strain of coronavirus that is responsible for the eat's seroconversion; also, the presence of coronavirus-antibody titers merely indicates that the cat has been infected with a coronavirus in the coronavirus antigenic cluster. • most healthy cats with positive coronavirusantibody titers have probably been infected with strains of feline enteric coronavirus, with non-fip disease-producing strains of fip coronavirus, or with fip disease-producing strains. most healthy coronavirus antibody-positive cats are probably not immune carriers of highly virulent fip coronavirus. it is impossible to predict accurately the long-term prognosis of healthy coronavirus antibody-positive cat. positive antibody titers do not indicate that a cat is protected against future development of fip disease, will later develop fip disease, or is definitely a hazard to other cats. because effective treatment is unavailable for complet~ elimination of coronavirus infection, long-term prognosis for cats definitively diagnosed with fip disease is extremely poor. antiviral drugs are not available for effective treatment of affected cats, although research is ongoing to evaluate various antiviral compounds. most treatment regimens provide, at best, only shortterm remission. palliative therapy is effective for cats with fip disease that are in good physical condition, have a good appetite, and are free of severe anemia or neurologic deficits; however, few cats with fip disease conform to these standards or are presented early enough in the course of disease to be given meaningful palliative therapy. effective drug therapy for fip disease relies on the use of systemic corticosteroids (such as oral prednisolone, to mg/kg daily) to decrease the disseminated corona virus antibody-mediated vasculitis. although corticosteroids may provide short-term remission, long-term use is not curative in cats with disease resulting from defective cell-mediated immune response. the general well-being of cats that receive systemic corticosteroids should be monitored weekly to monthly. if the cat shows a favorable response to therapy during the first few weeks, treatment should be continued for at least months. if the cat is in complete remission at the end of months, the corticosteroids may be slowly withdrawn. treatment should be reinstated, however, if signs of the disease recur. progressive physical deterioration of the cat during treatment is a poor prognostic sign. cats that develop pyogranulomatous lesions that only affect the eyes, especially unilateral or bilateral uveitis, respond relatively well to topical and/ or systemic corticosteroid therapy along with subconjunctival injection of methylprednisolone or triamcinolone acetonide (figure ). if ocular inflammation is severe and sight has been lost, enucleation may be indicated. initial incidence of new cases of fip disease in catteries and multicat households may be reduced by promptly isolating all cats with signs associated with fip disease, removing all cats infected with feline leukemia virus or feline immunodeficiency virus infection, and reducing overcrowding as well as by improving hygiene and nutrition, selecting queens that have good mothering instincts and are able to raise healthy litters, and only admitting cats that have negative corona virus-antibody titers. using coronavirus-antibody serotesting as part of a test-and-removal program to control fip disease (similar to successful programs used to reduce incidence of feline leukemia virus and feline immunodeficiency virus infections) cannot be recommended. serologic assays used in detecting coronavirus antibodies in cats have poor specificity compared with the high accuracy of enzymelinked immunosorbent assay and indirect fluorescent antibody testing procedures used to detect feline leukemia virus p antigen or levels of feline immunodeficiency virus antibodies. removal of healthy coronavirus antibodypositive cats from catteries or multicat household is justified only if strong evidence that the cat is a source of fip coronavirus infection for other cats exists. a first-generation temperature-sensitive fip coronavirus (ts-fipv) vaccine that protects cat against fip coronavirus challenge is available (primucell-fip, smithkline beecham animal health, exton, p a) . the ts-fipv vaccine contains attenuated live virus and is derived by the following laboratory procedure. the original wild-type strain of fip coronavirus, known as fipv-df isolate, is attenuated by passages in norden laboratories feline kidney (nlfk) cell line, of which passages to are propagated at °c. the th passage of fipv-df is made temperature-sensitive by exposure to ultraviolet irradiation. the ts-fipv is again propagated on nlfk cells for eight more passages and then lyophilized for subsequent vaccine·use. the attenuated ts-fipv strain replicates primarily in the upper respiratory tract and associated regional lymph nodes (mandibular, medial retropharyngeal, and cervical) of cats (figs. and ) . the ts-fipv proteins stimulate local immunoglobulin a and a cell-mediated immune response, as well as a systemic cell-mediated immune response that may deter systemic dissemination of the fip corona virus. • • the manufacturer (smithkiine beecham animal health) recommends administering the primucell-fip vaccine intranasally to healthy cats weeks of age or older. initial vaccination is given with two doses to weeks apart. annual revaccination with a single dose is recommended. vaccinated pregnant cats, dexamethasone-suppressed cats, feline leukemia virus-infected cats, and feline enteric coronavirus-infected cats have not shown a febrile response or blood dyscrasias. various feline enteric coronavirus strains produce clinical signs that resemble those produced by tgev in swine and by ccv in puppies. feline enteric coronavirus infection is most severe in recently weaned kittens; most infected adult cats, however, remain apparently healthy.>' clinical signs in kittens include low-grade fever, intermittent vomiting, depression, and mild to moderately severe diarrhea that lasts for to days. kittens with severe disease may be anorectic for to days. in kittens with more severe infection, a transient neutropenia may accompany the onset of diarrhea. the most severe lesions, such as villous atrophy, fusion of adjacent villi, and sloughing of the mature columnar epithelium from the upper portion of the villi, occur in the mature columnar epithelia of the duodenum, jejunum, and ileum. • mortality is negligible, and nearly all affected kittens recover. diagnosis a definitive diagnosis of feline enteric coronavirus infection is difficult to obtain. clinical resemblance of feline enteric coronavirus infection to other enteritides can confound diagnosis." electron microscopy of stool specimens to search for coronavirus particles is expensive, time-consuming, and fraught with false-negative and false-positive results. furthermore, true-positive results provide only presumptive evidence of the cause of diarrhea. coronavirus antibody assays do not provide the information for a definitive diagnosis of feline enteric coronavirus infection. • histopathologic lesions also are not sufficiently specific for the diagnosis, and viral isolation is impractical for routine use. supportive care is the only treatment option for feline enteric coronavirus infection in kittens. - food and water should be withheld during the more severe phases of infection, and a balanced electrolyte solution be given parenterally if there is moderate to severe dehydration. antimicrobial therapy usually is not required . in a study at louisiana state university, primucell-fip vaccine was administered to -week-old, specific-pathogen-free kittens according to the manufacturer's instructions. a similar group of nonvaccinated animals served as controls. all of the kittens were oronasally challenged with virulent feline enteric coronavirus weeks after final vaccination. the extent of clinical signs caused by feline enteric coronavirus infection in the vaccinated and nonvaccinated kittens is shown in figure . the vaccinated kittens experienced milder enteric disease after challenge exposure than did age-matched nonvaccinated kittens. the febrile response on days and postchallenge were significantly lower in the vaccinated kittens (p < . ). there was also a significant reduction (p < . ) in the amount of feline enteric coronavirus isolated from the jejunum, duodenum, and mesenteric lymph nodes of vaccinated kittens. morphometric analysis of the duodenum and the jejunum indicated that villus height was less affected in the vaccinated kittens than in nonvaccinated kittens ( figure ). there was a significant difference (p < . ) in villus height in the jejunum but not in the . morphometric results of the small intestines from ten nonvaccinated kittens and ten kittens vaccinated twice intranasally with ts·fipv vaccine following feline enteric coronavirus challenge. five kittens served as age-matched (nonvaccinated-nonchallenged) controls. duodenum of the vaccinated group. in addition, the nonvaccinated kittens lost significantly more weight than the vaccinated kittens. the results of this study indicated that the ts-fipv vaccine partially protected the kittens against disease caused by feline enteric coronavirus infection. various feline enteric coronavirus strains are very common in the general cat population. the virus is found in virtually every cattery and multicat household and in approximately % of all outdoor cats. thus, it is nearly impossible to prevent kittens and adult cats from being exposed to feline enteric coronavirus. nature limits the severity of feline enteric coronavirus infection by providing young kittens with maternal antibody protection until to weeks of age. cats are susceptible to natural infection with several strains of feline coronavirus that may result in either effusive and noneffusive fip disease or in subclinical to severe enteritis. investigators are still unsure of the routes by which strains of coronavirus are transmitted between cats. excretion of coronavirus by infected cats into the environment occurs by way of feces, oronasal secretions, and, possibly, urine. fip coronavirus remains stable outside the host for as long as to weeks and is rapidly inactivated by most household disinfectants. clinical diagnosis of coronavirus infection is made by evaluating the presenting history, physical findings, laboratory results, coronavirus antibody titers, and by excluding analogous diseases. the presence of coronavirus antibodies can be used to screen cats for the presence of coronavirus infection and as an adjunct in diagnosing clinical coronavirus infection. a intranasal ts-fipv vaccine that protects against natural coronavirus challenge is available for healthy cats weeks of age or older. a study of naturally occurring feline coronavirus infections in kittens feline viral diseases preventive health care and infectious disease control feline infectious peritonitis: an immune-mediated coronaviral vasculitis barlough je: cats, coronaviruses and coronavirus antibody tests do feline coronavirus antibody tests provide a conclusive diagnosis serodiagnosis aids and management practices for feline retrovirus and coronavirus infections infectious diseases of the dog and cat feline infectious peritonitis experimental inoculation of cats with canine coronavirus and subsequent challenge with feline infectious peritonitis virus feline infectious peritonitis characterization of a temperature sensitive feline infectious peritonitis coronavirus cdna cloning and sequence analysis of the gene encoding the peplomer protein of feline infectious peritonitis virus diagnostic features of an epizootic of feline infectious peritonitis in captive cheetahs new approaches to feline infectious peritonitis prevention in feline infectious peritonitis: current status. lawrenceville, nj, veterinary learning systems protection against feline infectious peritonitis by intranasal inoculation of a temperature sensitive-fipv vaccine characterization of an attenuated temperature sensitive feline infectious peritonitis vaccine virus systemic vascular lesions in feline infectious peritonitis the virology and pathogenesis of feline infectious peritonitis. brief review antibody immune complexes and complement activity fluctuations in kittens with experimentally induced feline infectious peritonitis intraocular inflammation in cats as a manifestation of systemic diseases feline infectious peritonitis. the central nervous system form epigenetic transmission of feline infectious peritonitis feline infectious peritonitis coronavirus diseases (coronavirus enteritis, feline infectious peritonitis) virologic and immunologic aspects of feline infectious peritonitis virus infection feline infectious peritonitis and feline enteric coronavirus infections. part i. feline enteric coronaviruses feline infectious peritonitis and feline enteric coronavirus infections. part ii. feline infectious peritonitis attempted immunization of cats against feline infectious peritonitis pathogenic differences between various coronavirus isolates immunologic phenomena in the effusive form of feline infectious peritonitis an enteric coronavirus of cats and its relationship to feline infectious peritonitis experimental studies with three new strains of feline infectious peritonitis virus: fipv-ucd , fipv-ucd , and fipv-ucd . compend contin educ pract vet antigenic relationship of the feline infectious peritonitis virus to coronaviruses of other species coronaviruses: structure and genome expression update on fip the real and unreal feline coronaviruses feline infectious peritonitis the veterinary annual, issue early death after feline infectious peritonitis virus challenge due to recombinant vaccinia virus immunization the biology and pathogenesis of coronaviruses disseminated intravascular coagulation in experimentally induced feline infectious peritonitis pathogenesis of feline infectious peritonitis . nature and development of viremia pathogenesis of feline infectious peritonitis: pathologic changes and immunofluorescence cross protection studies between feline infectious peritonitis and porcine transmissible gastroenteritis virus key: cord- -otsrexqu authors: goel, saurav; hawi, sara; goel, gaurav; thakur, vijay kumar; pearce, oliver; hoskins, clare; hussain, tanvir; agrawal, anupam; upadhyaya, hari m.; cross, graham; barber, asa h. title: resilient and agile engineering solutions to address societal challenges such as coronavirus pandemic date: - - journal: mater today chem doi: . /j.mtchem. . sha: doc_id: cord_uid: otsrexqu the world is witnessing tumultuous times as major economic powers including the us, uk, russia, india, and most of europe continue to be in a state of lockdown. the worst-hit sectors due to this lockdown are sales, production (manufacturing), transport (aerospace and automotive) and tourism. lockdowns became necessary as a preventive measure to avoid the spread of the contagious and infectious “coronavirus disease ” (covid- ). this newly identified disease is caused by a new strain of the virus being referred to as severe acute respiratory syndrome coronavirus (sars cov- ; formerly called -ncov). we review the current medical and manufacturing response to covid- , including advances in instrumentation, sensing, use of lasers, fumigation chambers and development of novel tools such as lab-on-the-chip using combinatorial additive and subtractive manufacturing techniques and use of molecular modelling and molecular docking in drug and vaccine discovery. we also offer perspectives on future considerations on climate change, outsourced versus indigenous manufacturing, automation, and antimicrobial resistance. overall, this paper attempts to identify key areas where manufacturing can be employed to address societal challenges such as covid- . coronaviruses (covs) belong to the family coronaviridae which includes four genera: α, β, γ and δ as well as several subgenera and species [ ] . sars cov- is a β-coronavirus with a single-stranded rna genome of ~ kb [ ] . recent topical research has revealed several new covs (three α-coronaviruses, three new βcoronaviruses, and one previously described α-coronavirus) from bats captured from myanmar and future emergence of new diseases caused by these covs due to change of land use has been speculated [ ] . furthermore, newer mutations of the virus that originally spread from wuhan were confirmed as deadlier in some countries compared to others, which has led to added confusion and concern [ ] . sars cov- was first identified from the outbreak of respiratory illness cases in wuhan city in the hubei province of china. initial reports of the virus were made to the world health organisation (who) on december , . this was followed by the who declaring covid- as a global health emergency on january , due to rapid spreading, and a later pandemic declaration on march , . the disease has quickly engulfed most of the world and has caused severe infection to populations across numerous countries as shown in figure . covid- is shorthand for "coronavirus disease " which is caused by the sars cov- virus, also called coronavirus in typical usage. viruses cause disease by binding to receptors on cells in the human body and then replicating at a rapid rate which triggers a variety of pathogenic processes. in the case of covid- , the structures on the surface of the virus bind to receptors in the airway or the lungs of human beings. the lungs may become inflamed, making breathing more difficult. for some people, the infection becomes severe and leads to critical care requirements. the anatomy of sars cov- , including its internal biological structure of spike protein legs, envelope protein, and membrane protein, surrounding the genomic rna is shown in figure (a). the virus shown in figure (a) highlights a large diameter of about . µm with variations in sizes reported by different researchers. the spike-shaped protein legs that make up a portion of the outer capsule of the virus create the crown-like or corona-like appearance. thus, the name coronavirus. the mechanism of infection due to the surface interactions between the spike protein and the lung cells is depicted in figure (b). this understanding was gathered from the genetic analysis which revealed that the mutations located in the spike surface glycoprotein might induce conformal changes and play an essential role in binding to receptors on the host cell (lungs) and determine host tropisms by leading to possible changing antigenicity [ ] . viruses are fundamentally different to bacteria so the classically developed work on nano-structuring and biomimicking surfaces, such as the cicada wing, primarily targeting bacterial killing, should not be confused as a readily available knowledge to kill sars cov- . physically, a bacterium is larger than a virus (the biggest size of a virus is smaller than the smallest known bacteria). bacteria are living cells which are ± nm capable of prolific reproduction independently, whereas viruses are non-living particles, requiring a host cell for replication. also, bacteria possess a cell-wall engulfing a chromosome, whereas viruses consist of genetic material, either dna or rna, covered by a protein coating. bacterial infections can therefore be treated with high success using antibiotic drugs. although some antiviral medicines are now available, the susceptibility of viruses to react to the treatment rate of medicines is significantly reduced as they are non-living. hence, the only long-term option to eradicate viruses is the development of vaccines that stimulate the natural production of antibodies. studies suggest that the source of sars cov- could either be ratg from horseshoe bats (rhinolophus affinis), pangolins (manis javanica), or a mix of both. their transmission has occurred by zoonotic mechanisms [ , ] . however, the coronavirus isolated from pangolins is % similar in a specific region of the spike protein, which corresponds to the amino acids involved in the angiotensin-converting enzyme (ace ) receptor binding domain, which allows the virus to enter human cells to infect them as shown in figure (b). the virus ratg isolated from rhinolophus affinis bats is highly divergent in this specific region (only % similarity). this observation indicates that the coronavirus isolated from pangolins can enter human cells, whereas coronavirus isolated from rhinolophus affinis bats is unable to enter human cells. the sars cov- has a high transmissible efficiency and covid- has high morbidity and mortality. a popular but possibly flawed measure for assessing fatality of disease is the use of deaths/case counts. this measure would yield a fatality rate of . % for covid- as of th may [ ] . the problem with this measure is that case counts reflect the number of tests that were done rather than infections, and the deaths lag the cases because fatality (if observed) may happen several days after the case is identified. a lag in reporting case numbers and incorrect tests may also occur. an alternative measure is the case fatality rate (cfr), which is the ratio of deaths / (deaths + recovered cases). this measure would yield a fatality rate of . % [ ] . the consensus is that the covid- disease has high fatality and can exceed the fatality ratio of the century-old "spanish flu", which had a % cfr [ ] . however, the data analysis of callaway et al. [ ] shown in figure suggests that covid- 's cfr is lower than that of mers and ebola and that its infection rate (r -the expected number of cases directly generated by one case in a population where all individuals are susceptible to infection) suggests that the infection can spread more easily than other diseases, including seasonal influenza. a further comparison of three different episodes of epidemics and pandemics caused by the family of coronavirus, namely, sars cov- , mers and sars cov- , is depicted in table . the exact mechanism of these drugs towards the virus is yet to be completely understood. however, the mechanism where a drug affects the replication of viruses in-vivo is a broadly accepted concept. in general, viruses replicate via protein processing using endosomes within golgi bodies. a drug such as hcq increases the ph of the golgi bodies making them more basic, thus disrupting the integrity of the internal nucleocapsid protein (see figure a ). this denatures the protein of the coronavirus rendering it dysfunctional. therefore, the rationale for using hcq is built on the premise that the change in ph brought about by the drug inhibits the endosomal transport necessary to spread the infection, hence the patient recovers. another short-term treatment being implemented by some hospitals across the world is to infuse patients with the antibody-rich blood plasma of people who have recovered from covid- [ ] . this approach has been used during disease outbreaks for over a century. however, the approach carries significant risk in terms of the already immunocompromised patients' immune response after administration, and results may vary between patients. as an early effort of investigation of the problem from scratch, researchers at toho university in japan used high-sensitivity cameras and laser beam guidance experiments to deduce that saliva spray during a sneeze (potentially containing thousands of viruses) can be classified into large vs small droplets or droplets vs aerosols. the droplets, due to their heavier weight, fall off, whereas aerosols remain airborne for a few hours due to their relatively small size. prima facie evidence suggests that the coronavirus has escalated to a pandemic due to the high contagion occurring via this 'airborne' spread model. recently, the possibility of asymptomatic or oligosymptomatic infection has also been highlighted [ ] . the aerosols may circulate near an infected patient in an airborne condition depending on the local conditions (airflow rate, humidity, dryness) for up to a few hours, even after the infected person has left the location. hence, the chances of contracting coronavirus are relatively high by merely occupying the same vicinity where an infected person has been or passed through. researchers have experimentally evaluated the stability of sars cov- recently, and these comparisons are shown in figure [ , ] . it is noteworthy that sars cov- was stable in the aerosol (airborne) form for up to hours. as opposed to this, the virus appears to be stable on surgical masks or stainless-steel surfaces for up to days and for up to days on smooth surfaces such as glass or currency notes. the same research also shows that the application of hand soap does not immediately deactivate the virus but rather takes up to minutes. therefore, a -minute waiting period after a handwash is required before bringing hands in contact with face, mouth or nose. covid- is not only present in the airway secretions of infected patients when they sneeze, but also when they simply breathe out or speak. studies have shown that covid- is also present in other body fluids of infected people, such as faeces, blood [ ], oral fluids, anal secretions [ ] , tears [ ] , and urine [ ] . the virus primarily attacks the respiratory system, however, new evidence shows the virus is not filtered by the kidneys, as traces of virus can be seen in sewage systems [ ] . therefore, as a mitigation strategy, testing of these fluids, which can be available and abundant in the wider population can be done for identifying the most effective areas. overall, when people are in close contact with one another, then transmission is more likely. most sources for infection worldwide have happened in an enclosed space, including homes, offices, public transport and restaurants. a second spreading pathway for the virus is through touching a surface or object that has the virus on it and then touching one's own mouth, nose, or eyes. if one is in a wellventilated space with fewer people, even for a longer period, the risk of infection is low. sustained contact with an infected person, even for a short period, even without a cough or sneeze, can spread the infection. by the virtue of disturbing the cell programming, covid- possesses the capability to cause a surprise attack on almost any part of the body ranging from lungs, heart, blood vessels, brain, eyes, nose, liver, kidneys and intestine. a schematic representation of this adverse impact is shown in figure (a) [ ] . recent literature suggests that apart from the airway, the human brain may also be targeted by the virus -see figure (b) and figure [ ] . patients have reported having mild (anosmia and ageusia) to severe (encephalopathy) neurological manifestations, and if true, it makes sars cov- more lethal. [ ] (b) tissue distribution of ace receptors in humans [ ] (c) possible neuro disorders due to sars cov- [ ] and (d) life cycle of sars cov- in host cells [ ] . (figures reprinted with permission) our nasal lining tissue contains a rich number of cell receptors called angiotensinconverting enzyme (ace ), which are favourable sites for the sars cov- to attach its spiked protein to, thus paving way for the entrance of the virus inside the body. once attached to the cell, sars cov- can change cell programming, replicate itself, and attack new cells at a very rapid pace. within a week of entrance into the body, the virus exhibits effects. during this time, the person may show early symptoms such as fever, dry cough, sore throat, loss of smell and taste, or head and body aches. at this point, the failure of the immunity in defeating the virus means giving the virus a way forward to enter into the respiratory system, where the lungs are attacked. the lungs also have a cell lining rich in ace [ ] . as the immune system continues to fight the sars cov- , the supply of healthy oxygen is disrupted. as the disease progresses inside the body, the white blood cells release inflammatory molecules or chemokines, which attack and kill the virusinfected immune cells, leaving the dead cells and pus behind. this affects healthy oxygen transfer in the lungs and is the stage where the patient starts to complain of pneumonia, coughing, fever, and rapid, shallow respiration. acute respiratory distress syndrome may develop. at this stage, the lungs start to be filled with opaque black spots signifying closure of the air pores, and such patients require ventilator support. the survivors of this severity of infection can end up having long-term complications. a few hospitals have successfully applied artificial intelligence to monitor the recovery rate by monitoring the coronascorea general term used to quantify the extent of the blocked pores (in cm ) [ ] long-term research measures, advanced manufacturing and metrology have pivotal roles to play in containing a pandemic. specifically, the development of engineering innovations is timely for the control of the covid- pandemic. for diagnostic testing to be useful for informing doctors and governments about the true incidence at any one time of coronavirus in the population, it needs to be inexpensive, high in sensitivity and specificity (sensitivity refers to the ability of a test to correctly identify those with the disease or true positive rate, whereas specificity refers to the ability of a test to correctly identify those without the disease or true negative rate) and easy to use for non-experts. as doctors are treating infected patients in this emergent time in an unprepared state, emergent manufacturing measures can help design better testing equipment and thus help in both short and long term to tackle this problem. the most significant challenge now lies in probing early-stage symptoms of covid- . for a relatively late stage detection in severe cases, chest computer tomography (ct) using x-ray probes (providing > % sensitivity) has proved to be a more reliable test assay in comparison to the reverse-transcription polymerasechain-reaction (rt-pcr) test and other sensor-based detection methods currently being pursued [ ] . since the nervous system and respiratory dysregulation are both likely to co-exist, covid- testing should be done by combining brain mri and rt-pcr tests as shown in figure (a) [ ] . however, caution is required in the analysis of results, such that covid- should not be confused with drug-resistant tuberculosis (tb) as both would show symptoms of damages in the lungs. in an attempt to boost the testing in a populous country such as india, the indian council of medical research (icmr) has approved the use of diagnostic machines used for testing drug-resistant tuberculosis under the guidance that the throat/nasal swabs are collected in the viral transport medium [ ] . interestingly, the pcr test cannot identify asymptomatic infections or those people who were exposed to or infected with covid- in the past and did not suffer from the disease or have recovered from covid- and may still be spreading the virus (carriers). therefore, different tests may be required to collate vital information required by government bodies to carry out a risk-benefit analysis to relax lockdown measures to protect their economies. immunodiagnostic kits such as a lab-on-a-chip are being developed for asymptomatic detection of covid- [ ] . a lab-on-chip (figure (b) works on the principle of detecting the presence of patient-generated antibodies against the virus that causes a specific disease, in this case, covid- . the test uses a lateral flow immunoassay to assess the presence of an analyte from a patient sample or specimen and detects two types of antibody isotypes: igm and igg. igm antibodies are the first antibodies to appear in response to a novel antigen and imply a more recently initiated infection while igg antibodies are generated later in the course of infection and possess a higher affinity for the target antigen, meaning they are more specifically able to bind the substance which caused the immune response. a test is declared positive if either one or both antibodies are detected during the test, similar to widely used pregnancy tests. the test consists of an anti-human igg coating in the g test line region and an igm coating the m test line region (see figure (b). during testing, the sample (blood, urine etc) reacts with sars-cov- antigen-coated gold nanoparticles (aunp) in the conjugation pad of the test cassette. any antibody in the patient sample that recognises the sars-cov- antigen binds to the antigen-aunp complex. the mixture then migrates laterally across the membrane by capillary action/lateral flow. as these human antibody/antigen/aunp complexes move across the test lines, they are captured at the anti-human igm 'm' line, the anti-human igg 'g' line, or both, depending on the antibody contents of the specimen. the sample first reaches the anti-human igm antibodies which coat the m line. if the specimen contains igm antibodies to sars-cov- , a coloured line will appear in the m test line region. next, the sample reaches the anti-human igg antibodies which coat the g line. if a specimen contains igg antibodies to sars-cov- , the conjugate-specimen complex reacts with anti-human igg. a coloured line appears in the g test line region as a result. the rabbit igg-aunp complexes are captured by the control line (which contains anti-rabbit-igg). this visible line indicates that there has been successful lateral flow across the detection strip. the last check ensures that the sample had enough volume to move across the entirety of the test cassette. only human antibody/sars-cov- antigen/aunp complexes will produce a visible red or pink line at the m or g line. other antibodies produce no colour. the accuracy of these lab-on-chip tests is still being debated as it depends on two key parameters, sensitivity and specificity. to date, igg related sensitivity and specificity has been found to be higher than that of igm. a schematic diagram in figure (c) and figure (d) shows that unlike currently available diagnostic methods, field-effect transistor (fet)-based biosensing devices may have several advantages, including the ability to make highly sensitive and instantaneous measurements using small amounts of analytes [ ] . the fet sensor shown in figure (d) makes use of a graphene sheet since graphene-based fet biosensors can detect surrounding changes on their surface and provide an optimal sensing environment for ultrasensitive and low-noise detection. from this standpoint, graphene-based fet technology is attractive for applications related to the sensitive immunological diagnosis. graphene as a sensing material is selected, and sars-cov- spike antibody is conjugated onto the graphene sheet via -pyrenebutyric acid n-hydroxysuccinimide ester [ ] (figures reprinted with permission) a group of researchers at mit and harvard are developing coronavirus-identifying sensor embedded face masks. this ongoing work is an extension to their previous work where they developed a low-cost method to detect a zika virus [ ] . in this technique, the sensor is made by using genetic material such as the rna or the dna which binds to the viruses. the researchers used a lyophilizer to freeze-dry the genetic material onto the fabric of the mask. the material deposited onto the fabric remains stable for many months (at room temperature) and the detection process starts merely by the presence of moisture (such as saliva). the detection signal is small (in terms of voltage) and can be detected by an additional fluorimeter device that can quantify this signal and emit in form of a fluorescent light. thus, one can expect to see light glowing masks to detect coronavirus in the future. fumigation chambers allow quick disinfection of a person while visiting areas such as hospitals, universities or airports. the aim is to use tubes releasing hydrogen peroxide in a chamber designed to be five-feet wide and seven-feet tall. the fumigation chamber usually seals automatically after the person's entry to avoid any leakage outside of the chamber and has designated sensors facilitating the chamber entry. the disinfection lasts for five seconds. it is to be noted here that hydrogen peroxide has also been recommended by the food and drug administration (fda) to be used as a sterilisation material to decontaminate n or n -equivalent respirators for reuse by health care workers in hospital settings [ ] . a populist view is that sunlight and high temperature during peak summers kills the coronavirus, which would help containment of its spread. it is reported that sars cov- does not survive beyond min after being exposed to ºc [ ] . however, it has yet to be ascertained as to how long does sunlight take to deactivate sars cov- and at what intensity. a more specific question is whether ultra-violet (uv) light can kill coronavirus? sunlight usually contains three types of uv: uva ( - nm), uvb ( - nm), and uvc ( - nm). uva and uvb can both cause sunburn, however, uvc is shorter and a more energetic wavelength of light. while uvc is effective at destroying genetic material, whether in humans or viral particles, it is filtered by the ozone layer and does not reach the earth's surface. preliminary findings from the national biodefense analysis and countermeasures centre of the usa (which houses a bsl- level lab) indicate that "sunlight seems to be very detrimental to the virus… within minutes, the majority of the virus is inactivated on surfaces and in the air in direct sunlight." [ ] . research on the use of uv as a treatment is still evolving and the behaviour of sars cov- under uv light is unknown. results were relatively favourable for sars cov- treatment with uvc [ , ] . sars cov- was efficiently inactivated after minutes of uvc exposure (at about a wavelength of nm), whereas addition of psoralen (a light-sensitive drug) to uva enhances inactivation of the sars cov- . popular press reports suggest that uv light booths are capable of deactivating coronavirus without any human contact and are proposed to be deployed ( figure ). one must be cautious, since uvc can be dangerous to the skin, causing burns within seconds and harmful to the eyes if observed directly. therefore, risk assessment and associated precautions would need to be deployed that may render this strategy difficult in the short-term. . . . antimicrobial coatings chouirfa et al. [ ] summarised nanomaterials based coatings for antibacterial applications and xing et al. [ ] have summarised the potential of natural polymer chitosan as an antimicrobial agent ( figure ). their research on antimicrobial properties of a nanocomposite coating formed by polysaccharide -deoxylactit- -yl chitosan (chitlac) and silver nanoparticles (nag) on methacrylate thermosets showed satisfactory results. figure : antimicrobial mechanism of chitosan-based coating with antimicrobial agents. reprinted with permission from [ ] . antimicrobial surfaces are based on three main mechanisms (see figure ): the anti-biofouling mechanism which repels microbes and prevents them from adhering to the surface, the release-killing mechanism where microbes are killed in the nearsurface environment with a release of antimicrobial agents and the contact-killing mechanism where microbes adhere and are killed on the surface [ , ] . researchers have also experimented with developing long-lasting antimicrobial surfaces to stop spreading pathogenic microbes through commonly touched surfaces or at-risk surfaces and have focused on the use of antimicrobial/antiviral materials such as copper. experimental trials for copper oxide impregnated respiratory protective facemasks have yielded % efficiency in eradicating the infectivity of human and avian influenza a virus in simulated breathing conditions [ ] . warnes et al. [ ] have shown that the surfaces of dry copper alloys are lethal to viruses such as mnv- at room temperature, with higher copper content being more time-efficient. generally, the antimicrobial activity of copper is attributed to oxidative behaviour of copper and the solubility properties of copper oxides [ ] . more recently, surface texturing of copper via cold spray methods has shown enhanced promise as an antiviral agent [ ] . combining the aforementioned antimicrobial contact-killing properties of copper, the anti-adhesion properties of polymeric micelles and the release-kill abilities of chlorine dioxide (clo ), li et al. [ ] developed a multifunctional coating viricidal for influenza virus h n . this multifunctional coating is composed of clo encapsulated in polymeric micelles (with slow on-demand release) on which copper nanoparticles were covalently tethered. other studies have investigated hydrophobic polycationic coatings as antimicrobial coatings [ ] [ ] [ ] . hsu et al. [ ] investigated the mechanism by which the n,n-dodecyl,methyl-polyethelenimine (pei) coated surfaces killed the influenza a virus. it was concluded that upon contact with the coated surface, the virus adheres irreversibly and through hydrophobic and electrostatic interactions, the virus' disintegration is then initiated resulting in rna leakage into the solution. the incorporation of pei into protective mask textiles has also been investigated with nearly a -fold improvement in the capture of the t d bacteriophage virus of escherichia coli b [ ] . finally, the direct mechanical action of sharp nanostructures such as darts, blades and spikes as a kind "mechano-cide" has been shown to have some success for bacteria, but remains largely unexplored for viruses [ ] . from a contact mechanics perspective, the combined effect of sharp ( somewhat surprisingly, while researchers have investigated bactericidal properties of nanoparticles of silver, yet the current understanding of the interaction of these nanoparticles with viruses is limited. however, some positive results are reported and, based on these reports, this direction of manufacturing research holds a good promise to tackle sars cov- . previous studies showed that the size of nanoparticle is critical to manifest a viricidal effect. for example, a nanoparticle size of less than nm was found to be effective against tacaribe virus [ ] , while a particle size of between to nm worked well against herpes simplex virus (hsv) type / and human parainfluenza virus type- [ ] . nakamura et al. [ ] reported that materials with immobilised silver nanoparticles possess enhanced microbicidal activities against the virus. these researchers developed a material using silver nanoparticle absorbed on a chitin sheet having a nanoscale fibre-like surface structure shown in figure and obtained favourable results against h n influenza a virus. figure : the mechanism of viricidal activity of silver (ag) nanoparticles (np) chitin nanofiber sheets showing strong antimicrobial activity via reactive oxygen species (ros) and silver ions on the substrate. reprinted with permission from [ ] . moreover, the unique characteristics of metallic nanoparticles such as high surface to volume ratio, surface-enhanced raman scattering and localized surface plasmon resonance can be utilised for virus detection and therapy via destruction through laser-induced localised hypothermia as well. some of the candidate nanoparticles are metallic and high entropy alloy nanoparticles (agauptpdcu high entropy nanoparticles, feo nps, ag nps, tio nps, au nps, ag-au core-shell nps) [ ] . for this purpose, uv-visible spectroscopy can be deployed to study the surface plasmon resonance, refractive index, and fluorescence change when nanoparticles interact with virus particles. nanoparticle-based investigation can help detect and inactivate viruses (figure ). specific to coronavirus, graphene oxide sheets with silver nanoparticles (go-ag nps) were reported to inhibit the growth of feline coronavirus (fcov) by up to %, in comparison to pure go that inhibited it only up to % [ ] . additionally, chiral biosensor with self-assembled chiral gold nanohybrids (cau nps) on account of multiple plasmonic scattering showed better detection performance on coronavirus [ ] . figure : nanoparticle based therapy for sars cov- . reprinted with permission from [ ] as with all fundamental and translation nanomaterial research, progress is not immediate. caution is required with nanomaterial technologies, as the long-term impact on human health and the environment of free nanoparticles has not been ascertained, and this may ultimately pose greater risk, particularly in the liver and respiratory tract of human beings and in ecosystems. lack of governmental regulation strategies for nanomaterials can also hinder the speed of approval and ultimately the availability in the marketplace. nevertheless, a call has gone out to nanomedicine researchers to utilise their existing knowledge base and translate their technologies towards covid- , should the outbreak last more than months [ ] . filtration efficiency is a strong measure of penetration prevention of aerosols through mask filters and is usually required to be above % for surgical face masks [ ] . ultrasonic welding is usually deployed to produce filters with sufficient filtration efficiency. both polymer and textile-based masks are popular and can benefit from the adoption of sequential micromachining techniques [ ] . a surgical mask (procedure mask) is worn by health professionals during surgery to avoid exposure to aerosols. such masks are not designed to protect the wearer from inhaling airborne bacteria or virus particles and are less effective than respirators, such as n or niosh masks which provide better protection due to their material, shape and tight seal. the who laboratory biosafety manual necessitates biosafety level (bsl- ) requirements for non-propagative diagnostic laboratories and bsl- for laboratories handling high concentrations of live sars-cov- . according to the manual and the who biosafety guidance for sars-cov- , the exhaust air from such laboratories should be discharged through high-efficiency particulate air (hepa) filters. it is worth mentioning that particle collection efficiency of such mechanical filtering methods decreases to about % at particle sizes of . µm due to diffusion and diffusioninterception regimes of particles with sizes in the range from . up to µm [ ] . therefore, hepa filters are not ideal in screening the viruses like sars cov- which has a typical diameter from nm to nm [ ] . mass production of appropriate filters to screen the virus entry is a micromanufacturing challenge. this could potentially involve technologies such as direct laser micromachining or punch-based microstamping methods. for this purpose, a plasma spraying, or laser micromachining method may be used to obtain a well-suited punch which can be used to stamp (pierce) polymer sheets (e.g., pet), to achieve appropriate filter sizes. another candidate process of subtractive manufacturing is metal anisotropic reactive ion etching with oxidation (mario) [ ] . an illustration of how the proposed micromachining strategies can be deployed for scalable fabrication of filters to screen virus scale particles is shown in figure . while self-assembly techniques such as block copolymers have shown promise filtering small viral particles such as human rhinovirus [ ] , direct printing methods allow greater engineering control over pore size and spacing, critical to tuning membrane efficiency, fluid resistance and mechanical strength. protection of surrounding or nearby people is important and an infected patient can help to control the spread by wearing a mask, leading to the concept of social distancing suggested by various governments. the safe distance guideline is an important concept especially in populous countries where an assembly of people on the streets can cause the spread to grow exponentially. keeping this in mind, the who urged people to maintain a safe social physical distance of about ft (~ m), while the centre of disease control and prevention recommends this to be ft (~ m). these limits are now challenged by recent research that suggests this safe distance should be to ft ( to m) [ ] . the same study also suggested that the currently available commercial masks need to be redesigned. it was suggested that the masks available at present are not suitable for containment of sprayed aerosols (during a sneeze) travelling at the velocity of kmph [ ] , as this increases the possibility of escape of viruses through contaminated droplets from edges of the mask making nearby people more vulnerable to contracting the coronavirus. also, chin et al. [ ] tested the strength of the virus and suggested that the virus is highly stable at ºc as well as in the ph range of to . the virus was found to be detectable on a mask surface even after days. these findings suggest a product design strategy to develop more appropriate masks for handling exhalations travelling at high speeds by considering human ergonomics, material aspects, antimicrobial nature and structural aspect. while the design and strategies for developing these new types of masks are underway, a possible technique for deploying the extant fabrication methods would be to merge the two approaches, namely, additive and subtractive manufacturing methods described above. this development would mean that even in the current landscape, a new mask-making strategy would provide more protection than the currently available masks. astm f - is the relevant international standard that details specifications of materials to be used in medical face masks. however, the current standards do not capture the techniques required to make the mask reusable especially as the current materials are yet to be tested against sars cov- . as of now, curad antiviral isolation masks making use of a cocktail coating (citric acid, zinc and copper) are available as an option to disinfecting the outer surface of the mask. these are useful for medical professionals as they can come in contact with the virus infected aerosols more frequently. another concept is that of a 'germ trap' surface [ ] , which is akin to fooling a virus. the team at the university of manchester, uk identified specific glycoproteins that have carbohydrates attached to their surface, similar to those seen on the surface of the cell of the nasal passages. this study suggests that a glycoprotein biocoating on a snood surface [ ] denatures a virus by causing the same interfacial chemical reaction between the spike proteins and carbohydrate cell surface as the one when the coronavirus attaches to the ace receptors, but due to unavailability of any physical cells to invade on the snood surface, the virus decomposes and becomes deactivated immediately after landing on the textile surface (see figure ). the efficiency of germ trap coating in achieving its goal is indicated to be %. based upon the existing literature, an immediate measure to functionalise the personal protective equipment's (ppes) could be to introduce the use of antimicrobial coatings comprising of proven materials (e.g., zinc and sodium [ , ] based compounds) on the surface of ppes, especially the shields and visors. such coatings can be deposited by additive methods such as spraying (in d) or via roll to roll (r r) manufacturing. in terms of processing techniques, one limitation of thermal spraying is that it requires heat resistant feedstock materials, limiting the use of most of the chemical species traditionally used to functionalise surfaces, such as polyethylene glycol (peg) [ ] . in view of this limitation, a possible research avenue is to develop functional coatings with viricidal properties such that the coating ingredients do not degrade at high temperatures, thus providing a controlled release over time. with this goal in mind, a suitable processing and material matrix availability is crucial to obtain a coating to possess desirable advantages in the medical field. on the other hand, the use of thermal sprayed hydroxyapatite (ha) coatings on orthopaedic implants has been widely adopted in the medical field since the late s [ ] . as reported in the early s [ ] , the use of thermal sprayed ha coatings on metal implants presents several advantages and a positive potential for its use in the medical field [ ] . taking into consideration the status of ha as the standard in thermal sprayed coatings and the decades of research on its behaviour and response to living tissue [ ] , the choice of ha as a base material for the development of anti-microbial functional coatings has been most popular to date. at a personal level, deploying smart ppe incorporating viral detection capability into masks, gloves or wearing "viral dosimeter" badges might help monitor the strength of direct transmission vectors as well as environmental exposure rates and accumulation. conversely, masks could collect exhaled viral particles for early detection of infection [ ] . detection could be implemented as microfluidic channels functionalized with bioelectronic miniaturized detection schemes [ , ] with specific virus sensitivity [ , ] . local area smart sensing filter textiles incorporated into mobile or in-place ventilation systems designed to both filter and detect could also help provide early alert alarms and protection in buildings and other areas of restricted air replacement. the importance of wearing a mask by the infected person and by a healthy person coming in the vicinity of the infected person is ranked on the priority order shown by the cartoon model in figure . safe disposal of materials used in the treatment of infected patients such as gloves, masks, test samples, clothes or the human waste, especially in icu patients who may be closer to death is a challenging task. in addition to the possibility of an infection, this waste could lead to other secondary issues including emergence of a new category of virus/bacteria. hence, safe disposal of biomedical waste is very important. additionally, gaining support from members of the public to adequately dispose of their used personal masks etc. is essential. recently, an absorbent gel with embedded disinfecting material has been developed at sree chitra tirunal institute for medical sciences and technology, india for liquid respiratory and other body fluid solidification and disinfection for the safe management of infected respiratory secretions. this material helps to solidify the liquid respiratory secretions from icu patients or those with copious secretions treated in the wards. the material so collected becomes fit for disposal through the usual incineration system for biomedical wastes. newer guidelines are required to refine the existing risk assessments procedures [ ] . big data analytics and extant research utilizes accelerated development of techniques for data mining, machine learning and use of artificial intelligence (ai) that shows promise in the treatment of sars cov- . as a direct benefit to this approach, a digitalised shadow of the data to study plausible scenarios of certainty of an event becomes easier. as for sars cov- , genome data now exist offering scope for soft-computing application researchers as well as those involved in ai based research to offer new insights into the area. as an example, the global initiative on sharing all influenza data (gisaid) database (https://www.gisaid.org), made available in march , contains a compilation of over , sars-cov- complete and partial genomes from all over the globe since december [ ] . recently, researchers from cambridge used phylogenetic network on complete genomes of sars cov- [ ] to predict probable mutation and migration paths of the coronavirus. atomistic modelling and molecular docking [ ] can hold the key to a scientific breakthrough to address questions surrounding sars cov- . the development of vaccines, antibodies and diagnostics is dependent in a large measure on our understanding of the interfacial science between the spike (s) glycoprotein of sars cov- and ace receptor in human lung cell (as shown earlier in figure ). wrapp et al. [ ] obtained a cryo-electron microscopy structure of the sars cov- s trimer in the metastable prefusion conformation, showing it undergoes a transient (hide and active states) structural rearrangement. their results relying on surface plasmonic resonance elucidated a stronger affinity of sars cov- with ace compared to sars cov- , and shed light on two states, namely, a "down state" or receptorinaccessible and an "up state" or receptor-accessible state shown in figure in yet another interesting study [ ] , computer-aided drug screening was used to run a test assay over , compounds as inhibitors to a key cov enzyme, m pro . ebselen was found to exhibit antiviral activity and illustrate a way forward use of this potentially promising modelling strategy to discover targeted drug and vaccine down: transient hidden state of rbd up: active binding state of rbd development. a molecular docking example shown in figure (b) is yet another effective example of accelerating the drug discovery [ ] . recently, liu et al. [ ] carried out an aerodynamic analysis by measurement of the rna of sars cov- . they used pre-sterilized gelatin filters (pore size of μm) to collect the aerosols from different areas of two wuhan hospitals. this study classified the sampling location in three areas: ( surprisingly, the researchers detected maximum stains of sars cov- in patients' toilet areas, while the levels were low in the isolation wards and ventilated patient rooms. also, the medical staff areas showed peaks of high concentrations with aerosol size ranging from . micrometres to . micrometres and they were neutralised after rigorous sanitisation procedures. the study suggests that there is a likelihood of resuspension of virus-laden aerosols from the surface of medical staff's protective equipment including surgical masks during their removal while having lunch, visiting toilets or breaks etc. the source of these virus suspensions was speculated to be from the direct deposition of patient's respiratory droplets or airborne sars-cov- onto the protective apparel. the researchers also found that the sars-cov- in aerosol forms had relatively longer residence time, implying the infection remains for a relatively longer time causing further transmissions. this study serves as a practice guide on the requirements and specification after the lockdown procedures are eased to avoid recurrent infection. the exit-strategy after the lockdown must consider carefully the ventilation of offices/classrooms, maximum use of open space (preferable sunlight), regular sanitisation of clothes, hairs and hands, and proper use and disinfection of toilet areas. the data obtained by toho university (figure ) suggests that laser technology can be employed efficiently to monitor the streamlines and microdroplets movements from a sneeze. this monitoring could be a highly effective lab-scale activity to not just guide the futuristic cfd models but also to efficiently design new masks effective for preventing diseases caused by high velocity spray caused by a sneeze. while engineering and manufacturing will undoubtedly play their part over the coming years, the interventions proposed herein can help avoid the recurrent spread and emergence of new infections. the patients who have survived while battling against covid- showed that they have developed antibodies to the virus. antibodies are virus-specific proteins, which have a memory of the exposure to the virus and will recognize the virus on a second exposure. antibodies help prevent future infections by detecting the virus and binding to their surfaces signalling the body's immune system to destroy such viruses or virus-infected cells. while reasons are not clear, common wisdom is that the human body does not have an adequate immune response to hiv. for covid- , an adequate immune response does exist. therefore, a vaccine is more likely to be created successfully for sars cov- . additionally, the observation that a large majority of people recover, either without any symptoms or with minimal symptoms such as fever and body ache, also bodes well for the development of a vaccine. three major scenarios are currently being pursued or envisaged in tackling the disease. (i) research and trials on vaccines: clinical trials are being conducted across the globe into novel vaccines and fast-tracking approval processes are being deployed. however, scientists fear that the virus itself, like the flu, can mutate and form different strains. therefore, immunity after immunisation or contracting and surviving covid- may only last as short as two years. (ii) therapeutic trials using available drugs: attention is being focused to drug repurposing and advanced formulations, including antimalarial, hiv, and other antiviral and immune-modulating drugs and biomolecules. (iii) nanotechnology: study of molecules that show promise but exhibit poor physiochemical properties or toxicity is currently being formulated across the globe into advanced nanomedicine platforms, translating the knowledge gained in drug targeting and efficacy enhancement from conditions such as cancer and cardiovascular disease. such technologies aim to provide better treatment prognosis for those patients who fall ill with coronavirus related diseases. attention to immunemodulating molecules is growing, as patients who contracted severe forms of covid- were reported to experience notorious cytokine storms which ultimately m m lead to their death. ability to suppress such immunological responses could be one key to controlling the progression of the virus from mild to severe infection. lessons learned during this pandemic will also impact the outlook for other viruses. these include governmental pandemic funding allocation, stockpiling of medical protective equipment and emergency aid strategies within and between countries across the globe. as the coronavirus problem increased across the globe in , many questions have been raised regarding what more governments could have done, why they did not act more quickly, and what were the fundamental failures within their policy. over time, addressing these issues will pave the way for a more streamlined and effective future response. in addition to this, contact tracing technology is being heavily invested in across the globe, with the intention that citizens would be able to download mobile applications, which could inform them (and the authorities) if they had been exposed to another person who tested positive to covid- . whilst early trials seem positive, the longer-term question remains over privacy and ownership of personal data collected by such applications. access to death records inside countries and across continents will allow identification of high-risk population categories which will aid risk prevention. the positive news is that this pandemic has cemented the importance of scientific integrity, the inclusion of scientific advisors into government, and the role of science in society. while this may offer little solace at such an upsetting time, yet, with the power of science, this disease will be managed unlike many other viral threats over the years. currently, vaccine trials are ongoing at various phases of progress in different countries (see table ) and good news may be expected soon. [ ] . the world has seen a surge in the use of digital tools being growingly used for teaching, research, consultation, banking and day to day activities. digital health innovation has been a prime example. these approaches culminated in the development of telemedicine consultation. the current situation has also driven many changes in work-life routines such as less travel and digital technology-based remote work. the coronavirus pandemic has brought significant disruption and caused severe emotional, sentimental and financial losses. there is even a chance that life on the planet will never be the same again and many stringent safety measures will continue to be followed in the time to come while using public transport, air travel, or while visiting touristic places. the continued extension of lockdowns (e.g., lockdown . to lockdown . in india) has resulted in making people restless when staying indoors. countries who were not very resilient in adapting to the situation even saw disrupted supply chains, disturbed migrant workers, lack of food and other supplies and unavailability of essential items -a situation comparable to a natural disaster. however, every disaster brings forth a new cycle of life and the episode of covid- did bring some good things. countries facing severe pollution in air, water, and land saw a life not seen in the last many decades. social websites and digital tools were used heavily to share the beauty of nature. rivers got cleaner, the air became more breathable, and the sky got clearer [ ] . as a result of this transition, even climate change and transition in weather were observed in many places and it will be befitting to say that we witnessed how "nature self-heals and mends itself". a prime example of climate change as a result of lockdown can be seen in china, europe and in india (see figure ). india has faced two major challenges for many years in the wake of rapid urbanisation: alarming levels of air pollution and a rapid decrease in the availability of clean water, especially from rivers like the ganga. the government of india had earlier set up a mega project called "namami gange" [ ] for freeing the rivers from industrial wastes. the project is of such importance that when addressing the indian community at madison square garden in new york in , the prime minister of india mr narendra modi had said, "if we can clean the ganga, it will be a huge help for % population of the country." covid- has rejuvenated the ganga and many other rivers around the world, making them cleaner to a point that their water was reported to be potable [ ] . the learning from the episode of covid- has been that resources offered by mother nature are meant to be used and not to be "exploited". if this simple rule is forgotten, then the world may continue to witness a regular self-healing cycle. on this occasion it was covid- but the next time, it could be readjustments in the ecosystem caused by a surge in the carbon emissions. researchers are reporting a decrease in solar activity leading to an increased flux of energetic particles in our galaxy [ ] . before it is too late to realize, and the entire human race wipes-off the face of the earth due to the climate change, we must take this pandemic as a wake-up call towards being considerate to the environment. what has apparently come clearer though is that problems like biohazards primarily emerge due to our lifestyle (e.g., consumption patterns including eating habits) or mishandling of biowastes (see figure ). there is an absolute necessity to pay utmost attention to biosafety and implementation of effective iso standards worldwide. health of people is also closely connected to the health of animals and our shared environment. this is because people, animals, plants, and our environment are interdependent [ ] and this direction of research considers the concept of "one health". in the wake of the covid- pandemic, the world witnessed an all-time-high demand of ventilators, ppe's, masks, bed liners, other essential health supplies and medicines. the pandemic struck everywhere, including the largest manufacturing economiesand pretty much all at once. as a result, most nations experienced manufacturing shocks. the two shocks that have impacted manufacturing worldwide are: • supply shock: the containment measures (such as lockdowns and social distancing) kept the workers away and resulted in reduced productivity and output. • demand shock: customer consumption patterns started changing (e.g., movement away from "non-essentials") and this affected the demand for a large variety of manufactured goods and associated services. as the pandemic spread, a few countries were resilient enough to cope with the pace of transformed supply chain requirements while many others who had earlier (in pre-covid- era) aligned themselves to outsourced or cloud-based manufacturing, primarily driven by low-cost, became hugely dependent for their essential supplies on other countries (primarily china the manufacturing related lesson learned from the covid- episode is that pandemics can affect manufacturing in several geographical locations simultaneously and therefore can affect an individual nation's surge capacity to deliver essential supplies such as diagnostics, drugs and vaccines to its population. going forward, this lesson will critically affect thoughts on manufacturing strategy and low-cost based outsourcing, and we may see a sustained push towards development of resilient indigenous manufacturing capabilities and a decreasing reliance on low-cost based outsourced manufacturing. a second trend that we perceive is an increasing focus on digitised automation and use of automated production systems including the use of robotics in day to day life as well as deployment of embedded robotics in manufacturing operations. an example of a futuristic automation capability was displayed at the indian institute of technology guwahati who developed remote controlled food delivery robot for covid- isolation wards (see figure ) . the robot was designed for hours run when fully charged. antimicrobial resistance (amr) refers to the resistance of microbes to antimicrobial drugs or "microbial immunity". the who as well as several national health organizations have identified antibiotic resistance as one of the greatest threats to global public health, economic growth, agriculture, economic security and national security. around the globe, people are being admitted to hospitals with infections that do not respond to antibiotic treatment. the problem of amr is rooted in the fact that when microbes are repeatedly exposed to antibiotics, they mutate to produce strains that are resistant to the antibiotic and are therefore able to resist the effects of medication that could successfully treat the microbe. in , lord jim o'neill and his team published a review commissioned by the united kingdom government entitled, "antimicrobial resistance: tackling a crisis for the health and wealth of nations" (the amr review) which is in line to the question that de kraker et al. [ ] asked "will million people die a year due to amr by ?" the problem of amr is connected to that of covid- with respect to the emergence of zoonotic diseases. the trend of overuse and/or misuse of antimicrobials, excess use of certain antibiotics in animals, and pharmaceutical industry pollution can lead to continuous emergence of zoonotic diseases. excessive use of antimicrobials stresses the naturally occurring microbiome and allows for resistant bacteria to become dominant. indeed, research has suggested that amr might spread to humans through food products of animal origin, the environment, and by direct contact in the case of agricultural workers. addressing the issue of amr as well as others shown in figure is thus a global priority as its impact on claiming lives is no less than that of covid- [ ]. the rapid emergence of the covid- pandemic provided minimal time for welldirected resource mobilization, and almost every country was tested for its resilience in its medical and manufacturing abilities during the first half of . the number of tragic health cases pushed organizations such as the fda to allow emergency use authorisation of various drugs without a systematic testing protocol, and among the drugs tried, favipiravir and tocilizumab were rated most effective. amidst the chaotic situation, the growing use of digital tools for professional communications and artificial intelligence to monitor the recovery of covid- patients showed some positive outcomes. a major question remains open to date, "how can the symptoms of covid- be detected in their early stages?" while more research is needed on the instrumentation and manufacturing sides, there are clear opportunities identified from the available scientific knowledgebase. in relatively advanced stages of the symptoms, rapid measurements by combining chest computer tomography (ct) and reverse-transcription polymerase-chain-reaction (rt-pcr) tests seem to provide a high confidence level in the screening. more work is needed on the sensing side for detection of the virus in the primitive stages. definitive promise has been exhibited using laser technology to monitor the aerosol spread and to detect the rna of the virus and gain a deeper understanding of the aerodynamic properties of emergent viruses. further development of fumigation chambers and ultra-violet chambers seem to hold promise as precautionary measures that can be implemented in public places like malls, airports, theatres and train stations etc. in this paper, we have also highlighted the possibilities of developing novel tools such as lab-on-the-chip, in addition to developing advanced personal protective equipment (ppe) using combinatorial additive and subtractive manufacturing techniques such as roll-to-roll manufacturing and thermal spray. these technologies allow the capability to filter the coronavirus, which has a diameter in the range of ± nm. it is envisioned that in future, wearing masks and social distancing would be mandated to avoid the recurrent spread of the virus. in the long term, micro-manufacturers, medical professionals, metrology engineers, material scientists and virologists will need to work in a more interdisciplinary way to develop modelling informed fabrication strategies. accelerated use of molecular modelling approaches -like molecular dynamics and molecular dockingalso seems to hold promise in drug and vaccine discovery to end this pandemic from its root. as society progresses to meet challenges such as covid- , many overarching issues will become important. strong measures will need to be implemented to ensure careful handling of biowastes, indigenous capability-based manufacturing focus will become stronger and issues such as antimicrobial resistance will demand increased attention. our hope is that the post-pandemic society will better heed the warning signs from nature and work on making manufacturing systems resilient to address emerging threats. . figure : airborne spread tracked by the laser experiments at toho university, japan laboratory diagnosis of emerging human coronavirus infections-the state of the art the architecture of sars-cov- transcriptome detection of novel coronaviruses in bats in myanmar patient-derived mutations impact pathogenicity of sars-cov- . medrxiv the proximal origin of sars-cov- methods for estimating the case fatality ratio for a novel, emerging infectious disease how blood from coronavirus survivors might save lives virological assessment of hospitalized patients with covid- aerosol and surface stability of sars-cov- as compared with sars-cov- stability of sars-cov- in different environmental conditions. medrxiv molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes. emerging microbes & infections evaluation of coronavirus in tears and conjunctival secretions of patients with sars-cov- infection novel coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples. medrxiv a rampage through the body. neurological insights of covid- pandemic evidence of the covid- virus targeting the cns: tissue distribution, host-virus interaction, and proposed neurotropic mechanisms remdesivir: a review of its discovery and development leading to emergency use authorization for treatment of covid- correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases updates on what acs reported: emerging evidences of covid- with nervous system involvement rapid detection of covid- causative virus (sars-cov- ) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor diagnosing covid- : the disease and tools for detection rapid, low-cost detection of zika virus using programmable biomolecular components issues-second-emergency-use-authorization-decontaminate-n inactivation of the coronavirus that induces severe acute respiratory syndrome, sars-cov evaluation of inactivation methods for severe acute respiratory syndrome coronavirus in noncellular blood products review of titanium surface modification techniques and coatings for antibacterial applications chitosan-based coating with antimicrobial agents: preparation, property, mechanism, and application effectiveness on fruits and vegetables antibacterial polymeric membranes: a short review surface modification of polyurethane with a hydrophilic, antibacterial polymer for improved antifouling and antibacterial function a novel anti-influenza copper oxide containing respiratory face mask inactivation of norovirus on dry copper alloy surfaces contact killing and antimicrobial properties of copper effectiveness of nanomaterial copper cold spray surfaces on inactivation of influenza a virus a smart multi-functional coating based on anti-pathogen micelles tethered with copper nanoparticles via a biosynthesis method using l-vitamin c polymeric coatings that inactivate both influenza virus and pathogenic bacteria hydrophobic polycationic coatings inactivate wild-type and zanamivir-and/or oseltamivir-resistant human and avian influenza viruses preparation, application and testing of permanent antibacterial and antiviral coatings mechanism of inactivation of influenza viruses by immobilized hydrophobic polycations a new material for airborne virus filtration mechano-bactericidal nanostructures and where to find them interaction of silver nanoparticles with tacaribe virus antiviral activity of mycosynthesized silver nanoparticles against herpes simplex virus and human parainfluenza virus type . international journal of nanomedicine synthesis and application of silver nanoparticles (ag nps) for the prevention of infection in healthcare workers nano-based approach to combat emerging viral (nipah virus) infection antiviral activity of graphene-silver nanocomposites against non-enveloped and enveloped viruses self-assembled star-shaped chiroplasmonic gold nanoparticles for an ultrasensitive chiro-immunosensor for viruses nano research for covid- surgical face masks: manufacturing methods and classification current trends and future of sequential micromachining processes on a single machine tool high-aspect-ratio bulk micromachining of titanium virus filtration membranes prepared from nanoporous block copolymers with good dimensional stability under high pressures and excellent solvent resistance the production of nanostructures by mechanical forming a direct-write, resistless hard mask for rapid nanoscale patterning of diamond. diamond and related materials turbulent gas clouds and respiratory pathogen emissions: potential implications for reducing transmission of covid- respiratory virus shedding in exhaled breath and efficacy of face masks structural basis for human coronavirus attachment to sialic acid receptors zn + inhibits coronavirus and arterivirus rna polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture universal and reusable virus deactivation system for respiratory protection. scientific reports thermal/oxidative degradation and stabilization of polyethylene glycol addressing processing problems associated with plasma spraying of hydroxyapatite coatings material fundamentals and clinical performance of plasma-sprayed hydroxyapatite coatings: a review the thermal spray roadmap chemical implant fixation using hydroxyl-apatite coatings: the development of a human total hip prosthesis for chemical fixation to bone using hydroxyl-apatite coatings on titanium substrates organic field-effect transistor sensors: a tutorial review interfacial electronic effects in functional biolayers integrated into organic field-effect transistors human influenza virus detection using sialyllactose-functionalized organic electrochemical transistors functional sensing interfaces of pedot: pss organic electrochemical transistors for chemical and biological sensors: a mini review covid- : a risk assessment perspective phylogenetic network analysis of sars-cov- genomes anti-hiv drug repurposing against sars-cov- cryo-em structure of the -ncov spike in the prefusion conformation fast identification of possible drug treatment of coronavirus disease- (covid- ) through computational drug repurposing study structure of mpro from covid- virus and discovery of its inhibitors aerodynamic analysis of sars-cov- in two wuhan hospitals covid- : a new digital dawn? covid- , climate change, and renewable energy research: we are all in this together, and the time to act is now pandemic spotlight on urban water quality. ecological processes update on galactic cosmic ray integral flux measurements in lunar orbit with crater. space weather biosafety materials: an emerging new research direction of materials science from covid- outbreak will million people die a year due to antimicrobial resistance by ? plos medicine authors are very much thankful to the research support provided by the ukri via grants no.: (ep/k / , ep/l / , ep/s / , ep/t / , ep/s / and ep/t / ) as well as the gcrf/ epsrc supported sunrise program (ep/p / ). additionally, we acknowledge the support received from h (cost actions (ca , ca , ca and ca ) and euramet empir a ( )), royal academy of engineering grant no. iapp - \ (indo-uk partnership), royal academy of engineering grant no. tsp (south africa-uk partnership) and newton fellowship award from the royal society (nif\r \ ). also, numerical calculations performed on the isambard bristol, uk and archer hpc were made available by the epsrc resource allocation panel (rap). all data in the manuscript will be available through cranfield university open repository. key: cord- -uu p rgi authors: mansueto, gelsomina title: covid- : brief check point through the pathologist's eye (autopsy archive) date: - - journal: pathol res pract doi: . /j.prp. . sha: doc_id: cord_uid: uu p rgi during the covid- pandemic many deaths have been caused, especially of patients with cardiovascular comorbidities and old age. many questions have been asked and few simple answers have been given. the autopsy data are few and the aspects often observed are pulmonary diffuse alveolar damage (dad), myocarditis, acute myocardial infarction (ami), and disseminated intravascular coagulation (dic); these aspects are not only in covid- but also in other viral infections and associated sepsis. we must not lose sight of the fact that coronavirus with its pathological organ changes have already been described in the years preceding the pandemic. a few but long months have passed since the "unknown" and "doubtful" beginning of the pandemic induced by novel sars-cov- coronavirus (severe acute respiratory syndrome coronavirus), named cov- . many things have been said about this rna virus which is responsible of acute respiratory distress syndrome (ards), cardiovascular and multiple organ failure till death. the same has been said about the structure of the virus and its ability to interfere with ace receptor, with the heme synthesis, and with the immune system ( , , , , , ) during the pandemic many deaths have been caused, especially of patients with cardiovascular comorbidities and old age ( , , ) . the research has developed quantitative and qualitative serological tests, but the only reliable test was the nasopharyngeal swab that detects the virus when it is in replication phase; various therapies have been tried without a unique protocol or vaccine ( , , , ) . few autopsies were carried out for fear that the virulent agent could spread even more and for purely organizational reasons of the italian autopsy rooms often not up to standard for infectious diseases. many questions have been asked and few simple answers have been given. in this brief summary, i would like to induce the reader's reflection to the fact that coronavirus appears already before the pandemic in many texts of medical doctrine and that the pathological findings related to lung and multi-organ damage are described similar to those induced by other viral pathogens both from the same or different family. the autopsy pathologists can confirm that many deaths are due to complications from viral infections especially in subjects with comorbidities and they can also confirm that the aspects often observed are diffuse alveolar damage (dad), cardiac damage from myocarditis or acute myocardial infarction (ami), or even disseminated intra-vascular coagulation (dic); these findings are also present in sepsis associated with various viral infections. ( , , , , , , ) . my observation wants to induce the reader to focus on the common histopathological findings that are present in various viral infections, through the clarification of some salient points. the sars-cov- is an rna virus of the coronaviridiae family, that infect epithelial cells of the upper respiratory tract, pulmonary pneumocytes and different epithelial cells types, endothelial cells of arteries and veins, smooth muscle cells, and immune cells the main mechanisms of interaction between sars-cov- and host are represented by the binding with angiotensin-converting enzyme receptors (ace ), the inhibition of heme synthesis through competition for the binding of porphyrin to iron, the interference in the native immune response which trigger the expression and activation of anti-viral mediators, recruitment of inflammatory cells, and the dysregulation of host dna replication with transcription anomalies with triggering of the apoptotic pathways. the dysregulation of major homeostatic cell systems is responsible for primary lung injury with interstitial pneumonia and dad, and is responsible for secondary heart and multi-organ damage and hyperagulability occurring mainly in the comorbid population ( , , , , , , , , ) . lung histopathology in cov- disease is characterized by interstitial pneumonia, dad, oedema, haemorrhage, multinucleated cells, exfoliation associated with or without viral inclusions and associated with reactive aspect of rehash as alveolar epithelial hyperplasia, fibrosis and emphysema. these aspects are described in books as well as in scientific articles and are frequent autoptic findings from direct alveolar demage by viruses, atypical agents and associated with functional vascular and cardiac imbalance ( , , , ) . the microscopic observation provides a large spectrum of pathological findings that are not different or peculiar in many viral disease. in acute myocarditis which can be associated with sars cov- , histology is characterized by lymphomonocytic infiltrate, interstitial oedema, myocytolisys, as observed in myocarditis which is associated with other etiological agents according to dallas criteria ( ) . it is cause of sudden cardiac death ( , ) , (fig. ) . in ami contraction band necrosis, areas of coagulative necrosis, edema and inflammatory infiltrate are the most characteristic aspect of hypoxia and of response within the timeframe from the beginning of the damage to the attempted resolution. also, in this case the damage is common to many conditions including myocarditis by different viral agents and therefore not peculiar to the cov- infection ( , ) (fig. ) . finally, platelet and fibrin aggregation with micro-thrombotic j o u r n a l p r e -p r o o f events and diffuse vascular occlusion are responsible of poor prognosis to death in dic entity. as resumed in table , many different viral and non-viral agents can be induce dic ( , , , ) , (tab. ) (fig. , ) . since other etiological agents may also be implicated in etiopathogenesis such as bacteria, it cannot be excluded that these pathologies may be determined by the superposition of the latter. also in this case the differential diagnosis with identification of the agent is not easy since there is often no evidence of the virus in the myocardium and the morphological changes are the indirect result of the damage caused which manifests itself as inflammatory infiltrate in myocarditis, with necrosis in ima and with increased state of coagulability and thrombosis in dic. in the diagnosis of sars-cov- infection in cases with suspected clinical history and symptoms, the detection of the viral genome with pcr from the upper respiratory tract are currently the most valid. the test is primarily used to detect sars-cov- and to distinguish it from other viral agents responsible for similar types of pneumonia. in a correct differential diagnosis, first instance laboratory investigations must be accompanied above all to establish the patient's status as well as more specific laboratory investigations aimed at assessing the patient's pre-existing and recent status with the aim of excluding autoimmune, neoplastic or cardiovascular diseases. regarding therapy, the respiratory support is considered for patients with hypoxemia, and there is no evidence to support a specific drug treatment and antiviral therapies against sars-cov- have a range of variability. however, the number of antivirals was reduced especially considering the side effects and drug interactions. there have been no changes in the use of corticosteroids, and the treatment plan only considers severe and critical cases. the immunotherapy is described as a therapeutic option ( , ) . it is clear that both in cases of exclusive pulmonary involvement and in cases with multi-organ dysfunction, treatment must aim at improving the symptoms especially in the population with comorbidities, while active prevention must aim at safeguarding populations especially with comorbidities with the aim of controlling the possible complications that are the real responsible for the deaths. only what is unknown is not understandable. infections induced by viruses belonging to the sars family have already been described although today we have called the new virus as sars cov- and a disease as covid- . in truth, for the first time we found ourselves in a pandemic and this scared us. the lack of autopsy findings did not allow us to evaluate with greater serenity what was happening and to understand that the specific pulmonary histological pictures and the secondary multiorgan damage in the patients with comorbidities were very similar to those already observed for other viral infections. early knowledge of the changes in the organs would have speeded up the therapeutic approach by targeting complications rather than the viral agent as such. infact pulmonary pathology with systemic complication can currently be considered not very different from those caused by other viruses which can lead to systemic failure with worsening up to death. deaths are currently reduced due to early diagnosis in subjects at risk and for the use of generic antiviral and symptomatic therapies, however non-specific directed towards sars-cov- , and diagnoses have increased thanks to the use of nasopharyngeal swabs that highlighted the presence of the virus even in younger asymptomatic subjects. this shows that although sars-cov- has high virulence, it behaves like other viruses, that in the population the symptoms occur in subjects often with comorbidities and that deaths are due to complications in the same way as it happens for other viral agents. finally, the therapy for complications in the different cases has proved effective. not applicable. the images from the forensic autopsy archive of mansueto gelsomina md, phd. not applicable. the images from the forensic autopsy archive of doctor mansueto. structure, function, and evolution of coronavirus spike proteins tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis renin-angiotensin-aldosterone system inhibitors in patients with covid- angiotensin-converting enzyme is a functional receptor for the sars coronavirus transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in covid- patients covid- :attacks the -beta chain of hemoglobin and captures the porphyrin to inhibit human heme metabolism casscells sw rd. influenza epidemics and acute respiratory disease activity are associated with a surge in autopsy-confirmed coronary heart disease death:results from years of autopsies in , subjects prevalence and impact of cardiovascular metabolic diseases on covid- in china prevalence of comorbidities in the novel wuhan coronavirus (covid- ) infection: a systematic review and meta-analysis virology, epidemiology, pathogenesis, and control of covid- . viruses zhong ns; china medical treatment expert group for covid- . clinical characteristics of coronavirus disease in china controversial treatments: an updated understanding of the coronavirus disease case of the index patient who caused tertiary transmission of covid- infection in korea: the application of lopinavir/ritonavir for the treatment of covid- infected pneumonia monitored by quantitative rt-pcr pulmonary eosinophilic inflammatory infiltration post-intensive care in a nearly drowned young man with papillary fibroelastoma: a rare complication discovered by forensic autopsy the dating of thrombus organization in cases of pulmonary embolism: an autopsy study fatal exertional rhabdomyolysis. literature review and our experience in forensic thanatology late histological findings in symptomatic covid- patients a case report can covid disease induce a specific cardiovascular damage or it exacerbates pre-existing cardiovascular diseases? lung pathology of severe acute respiratory syndrome (sars): a study of autopsy cases from singapore immunosenescence exacerbates the covid- cardiovascular involvement during covid- and clinical implications in elderly patients. a review post-mortem diagnosis of invasive pulmonary aspergillosis after alemtuzumab treatment for multiple sclerosis a histopathologic definition and classification sudden cardiac death caused by myocarditis in persons aged - years: a nationwide study of deaths in denmark acute myocardial infarctions, strokes and influenza: seasonal and pandemic effects acute myocardial infarction after laboratory-confirmed influenza infection abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia disseminated intravascular coagulation: an update on pathogenesis, diagnosis, and therapeutic strategies diagnosis and treatment protocol for novel coronavirus pneumonia (trial version ) the - novel coronavirus (severe acute respiratory syndrome coronavirus ) pandemic: a joint american college of academic international medicine-world academic council of emergency medicine multidisciplinary covid- working group consensus paper ima. areas of coagulative necrosis of the myocardium as initial hypoxic damage. a. hiv (e&e stain x ). b. coronavirus (e&e stain x ) key: cord- -e f sfl authors: tripathi, shweta; tripathi, mayukh mani title: the covid- : current understanding date: - - journal: vet world doi: . /vetworld. . - sha: doc_id: cord_uid: e f sfl in december , china reported several cases of a new coronavirus disease (covid- ). the covid- outbreak, which was initially limited to wuhan, china, has rapidly spread worldwide. infection of the disease occurs through exposure to the virus through inhalation of respiratory droplets or if a person touches a mucosal surface after touching an object with the virus on it. the common symptoms of covid- are fever, dry cough, dyspnea (difficult or labored breathing), fatigue, chest pain, and myalgia (muscle pain), etc. real-time polymerase chain reaction is used to detect the virus in sputum, throat, nasal swabs, and secretion of lower respiratory samples. early diagnosis, isolation, and supportive care are necessary for the treatment of the patients. the present review aims to provide recent information on covid- related to its epidemiology, clinical symptoms, and management. this article also summarizes the current understanding of severe acute respiratory syndrome coronavirus- and its history of origin. on december , , the municipal health authority of wuhan in the hubei province of china reported several cases of pneumonia of an unknown etiology. all the patients had a common exposure to the hunan seafood market [ ] [ ] [ ] . on january , , the chinese center for disease control and prevention discovered a novel coronavirus from a throat swab sample of one of those patients. initially, the world health organization named it ncov [ , ] , but later on february , , it was renamed as severe acute respiratory syndrome coronavirus- (sars-cov- ) by icvt, and who designated the disease as coronavirus disease [ , ] . before the covid- , the two outbreaks of coronavirus are middle east respiratory syndrome coronavirus (mers-cov) and sars-cov. both occurred over the past years, mers was first detected in saudi arabia in and affected people with mortalities [ ] , and sars was originated from guangdong (china) in and resulted in more than infections and deaths in countries [ ] . the covid- outbreak, which was initially limited to wuhan, has rapidly spread worldwide. as of now, august , , , , cases, and , deaths have been reported globally [ ] . covid- made its entry into india through various international travels. the first laboratory-confirmed case of covid- was reported from kerala on january , [ ] . now, it has spread in almost every part of india. according to the ministry of health and family welfare, currently, there are , active cases of covid- in india [ ] . researchers from all over the world are working very closely and efficiently on this pandemic [ , ] . as several studies are currently in progress, new revelations are emerging every day. therefore, this article aims to provide recent information about the covid- and the relation to its epidemiology, clinical symptoms, and treatments. this article also summarizes the current understanding of sars-cov- and its history of origin. covid- causing virus (sars-cov- ) belongs to the coronaviridae family under nidovirales order [ ] . further, this family consists of two subfamilies; coronavirinae and torovirinae, and within the coronavirinae, there are four genera: (a) alphacoronavirus; this includes the human coronavirus human coronavirus (hcov)- e and hcov-nl , (b) beta-coronavirus; this contains sars-hcov, hcov-hkv , and mers-cov, (c) gamma-coronavirus; this covers the viruses of whales and birds, and (d) delta-coronavirus; this includes viruses from pigs and birds [ ] . sars-cov- comes within the beta-coronavirus genus, which also contains two deadly viruses: sars-cov and mers-cov. betacoronavirus genus consists of many subgroups. the sars-cov- , sars-cov, and bat sars-like cov belong to sarbecovirus, whereas the mers-cov belongs to merbecovirus [ , ] . sars-cov- is an enveloped, single-stranded, and positive-sense rna copyright: tripathi and tripathi. open access. this article is distributed under the terms of the creative commons attribution . international license (http://creativecommons.org/licenses/ by/ . /), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the creative commons license, and indicate if changes were made. the creative commons public domain dedication waiver (http:// creativecommons.org/publicdomain/zero/ . /) applies to the data made available in this article, unless otherwise stated. virus [ ] . the size of this virus ranges from to nm in diameter, and the size of single-stranded rna varies from to kbs [ ] . the crown-like spikes on the outer surface of the virus give it the name of corona [ ] . spikes are glycoprotein in nature and responsible for host attachment [ ] . other proteins of coronaviruses include nucleoprotein, membrane proteins, and accessory proteins [ , ] . beta-coronavirus found in pangolins and bat coronavirus (ratg ) isolated from rhinolophus affinis might be the parental viruses responsible for the origin of sars-cov- [ , ] . bat coronavirus (ratg ) shares . % genome sequence identity with sars-cov- [ ] . despite the genomic similarity, ratg might not be the immediate ancestor of sars-cov- because of disparity in receptor binding protein domain (unlike the sars-cov- , it does not use the ace receptor of the host cell for entrance). whereas, virus from pangolins uses the same receptor (ace ) but differs in the overall genome sequence, thus, ruling out its possibility of being an immediate ancestor of sars-cov- too. however, the virus isolated from pangolins is closely related to both; sars-cov- and ratg . therefore, bats might be the original host of sars-cov- [ ] . in late december , several residents of wuhan, the capital of the hubei province of china, visited the hospital with complaints of fever, dry cough, fatigue, and infrequent gastrointestinal symptoms [ ] . all the cases had a common exposure to a seafood wholesale wet market, the hunan wholesale seafood markets [ ] . however, the first laboratory-confirmed case of covid- was on december , [ ] . on december , , china issued an epidemiologic alert and notified who about this mysterious disease. on january , , authorities shut down the hunan seafood market, assuming it the source of this virus, as several environmental samples of this market had tested positive for sars-cov- [ ] . however, based on a genomic study, research suggested that the virus came into the market from an unknown location [ ] . in china, patients were increasing rapidly, and soon after, a large number of patients started coming into the hospital with no history of exposure to the live market. reported cases of clusters of families suggested human to human transmission of this virus [ ] . due to heavy transportation load and the massive migration of the chinese population, during the chinese new year festival, several new cases were being reported in many cities and provinces of china. as several tourists had also visited china during this period, they returned to their home country with this deadly virus. thailand recorded the first exported case of covid- on january , [ ] . soon after, several other countries reported its first confirmed cases. on january , , india started thermal screening of passengers arriving from china at seven airports (delhi, mumbai, kolkata, chennai, bangalore, hyderabad, and cochin) to fight covid- . later, the government extended thermal screening to up to airports [ ] . these efforts did not work as effectively as hoped, and india recorded its first case of covid- of a student from kerala on january , ; she had just returned from wuhan [ ] . soon after, other states reported its first confirmed cases of covid- . as numbers of cases were increasing daily, the govt. of india imposed a nationwide lockdown on march , , to control the spread of this disease [ ] . till the date of writing this article (august , ), a total number of + laboratory-confirmed cases of covid- from states and union territories, out of which , , ( . %) recovered, while , ( . %) deaths are reported in india [ , ] . maharashtra is the worst affected state with a total number of confirmed cases of , (https://arogya. maharashtra.gov.in/ /novel--corona-virus seen on august , ). the frequency of confirmed cases has been increasing rapidly, and india is on the rd position in a tally of worst-affected countries globally [ ] . genome analysis of sars-cov- revealed that the ' end of the sars-cov- genome contains orf ab, and this orf ab occupies the majority of the genome. orf ab encodes for polyprotein pp ab and which comprises nonstructural proteins. the '-end of the genome contains four structural proteins and eight accessory proteins such as a, , , , and [ ] . viruses can undergo mutation, and the genome of rna viruses can mutate million times higher than the host genome. these mutations can be either harmful or beneficial to the virus [ ] . phylogenetic analysis of indian sars-cov- isolates suggests that these are strongly related to isolates reported from other parts of the world. most orfs are highly conserved, whereas mutations were also identified in some orfs. the study further revealed that most isolates from india have key mutations at th position of the s protein and th position of the orf , which has been reported to be associated with high virulence and high transmission rate [ ] . soon, it was clear that the infection of covid- occurs through exposure to the virus through inhalation of respiratory droplets or if a person touches a mucosal surface after touching an object with the virus on it [ ] . a study reported the presence of sars-cov- in stools suggesting the possibility of fecal-oral route transmission [ ] . infection through conjunctiva is also possible [ ] . initially, scientists believed that newborns could get an infection from covid- positive mothers. however, a researcher ruled out the intrauterine transmission in its study, where nine newborns did not contract the disease from their mothers [ ] . although all age groups and genders are susceptible to the attack of this virus, mostly male patients of the - age group have been reported [ , ] . elderly and people with weak immune function and hepatic dysfunction are more at risk [ ] . available at www.veterinaryworld.org/vol. /september- / .pdf sars-cov- is highly infectious, with an effective reproductive number of . (higher than sars-cov- . ) [ , ] . the mortality rate of covid- is . % globally and . % in india [ ] . the lower mortality rate in india might be due to its demographic constitution. however, due to lack of testing and surveillance, there is a possibility that the number of deaths related to covid- could not be differentiated hence not reported. india reported a . % recovery rate for covid- [ ] . according to the world health organization, covid- affects different people in different ways. on average, it takes - days from when someone is infected with the virus for symptoms to show; however, it could also possibly take up to days [ ] . most infected people will develop mild-to-moderate illness symptoms and recover without hospitalization. the most common symptoms include fever, dry cough, and tiredness, and less common symptoms are aches and pains, sore throat, diarrhea, conjunctivitis, headache, loss of taste or smell, and a rash on the skin, or discoloration of fingers or toes [ ] . severe symptoms such as difficulty in breathing or shortness of breath, chest pain or pressure, and loss of speech or movement, require immediate medical attention [ ] . according to the ministry of family and health welfare of india; a suspected case is defined as a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease, e.g., cough, and shortness of breath) and a history of travel to or residence in a location reporting community transmission of covid- , days prior of the beginning of symptoms. it is also defined as a patient with an acute respiratory illness and has been in contact with a confirmed or probable covid- case in the past days before symptom onset; ora patient with severe acute respiratory illness (fever and at least one sign/ symptom of respiratory disease, e.g., cough, shortness of breath; and requiring hospitalization). in the absence of an alternative diagnosis that thoroughly explains the clinical presentation, a probable case is a suspect case for whom testing for the covid- virus is inconclusive or a suspect case for whom testing could not be performed for any reason, and, a confirmed case is a person with laboratory confirmation of covid- infection, irrespective of clinical signs and symptoms [ ] . the definition of a confirmed or suspected case differs from country to country. the testing strategy in india used for covid- is discussed below [ ] ; real-time polymerase chain reaction (rt-pcr) is the gold standard test for detecting cases of covid- . the average time taken is around - h from receipt of a sample to getting the result. the advantage of this platform lies in its accuracy of detection as well as the ability to run up to samples in a single run. whenever possible, it is advised to use rt-pcr as the frontline test for the diagnosis of sars-cov- . the truenat and cbnaat systems have also been deployed for the diagnosis of covid- given the availability of customized cartridges. these platforms have a quick turnaround time ( - min), but only - samples can be tested in one run, limiting the maximum numbers that can be tested to - samples/day only. rapid point-of-care antigen detection test (for diagnosis along with rt-pcr): this test is a promising tool for quick diagnosis of sars-cov- in field settings. the assay is known as standard q covid- ag kit and has been developed by sd biosensor with a manufacturing unit at manesar, gurugram. on validation, the test has been found to have a very high specificity with moderate sensitivity. igg antibody test for covid- (only for surveillance and not diagnosis): igg antibodies generally start appearing after weeks of the onset of infection, once the individual has recovered after infection, and last for several months. to ramp up testing capacity, icmr has approved a total of covid- testing labs in both public ( ) and private sector ( ). this includes rt-pcr labs ( ); truenat labs ( ); and cbnaat labs ( ) [ ] . at present, there is no specific treatment available for covid- [ ] . isolation is the first step in managing the virus. symptomatic supportive care such as oxygen therapy, fluid management, maintenance of vital signs and blood pressure, and treatment of secondary bacterial infection with the antibiotic is recommended [ ] . some victims of covid- developed ards and septic shock very rapidly, eventually leading to multiple organ failure [ , ] . therefore, early recognition of the suspected case and immediate isolation for the containment of disease is necessary [ ] . national institute of health (nih), usa, recommended the following guidelines to treat covid- and severe conditions caused by covid- [ ] . it is an old anti-malarial drug, which has shown an in vitro inhibitory effect on the growth of sars-cov- [ ] . recent studies from china and france observed that the administration of this drug in covid- patients produced significant results in both clinical outcomes as well as in viral clearance [ , ] . chloroquine/hydroxychloroquine, when given with azithromycin, yielded better results [ ] . the govt. of india has also recommended the same combination of these drugs for the management of covid- [ ] . however, the usa food and drug administration (fda) only allows this drug for the treatment of particular adolescent and adult patients hospitalized for covid- . recently, the world health organization suspended all its clinical trials as few studies suggested a high mortality risk of this drug. therefore, more researches are needed to establish the safety and efficacy of this drug. this therapy utilizes plasma of covid- recovered patients to treat other patients. several studies reported a shorter hospital stay and lower mortality rate in sars patients treated with convalescent plasma than those who were not treated with it [ ] [ ] [ ] . recently a medical practitioner from shanghai used plasma therapy to treat covid- patients and yielded positive results with rapid recovery, suggesting it could be a potential treatment for covid- patients. however, more clinical trials are needed to prove the safety and effectiveness of convalescent plasma transfusion in sars-cov- infected patients [ ] . researchers developed this antiviral drug to treat ebola, mers, and sars-cov. it is a monophosphide prodrug that acts as a nucleotide inhibitor and causes premature termination of viral rna replication [ ] . it has also shown interference with the nsp polymerase of sars-cov- in the in vitro study [ ] . some studies also reported that remdesivir alone and in combination with chloroquine and beta interferon blocked the sars-cov- [ , , ] . patients with severe covid- can develop a systemic inflammatory response that can lead to lung injury and multisystem organ dysfunction. it has been suggested that the anti-inflammatory effects of corticosteroids might prevent or mitigate these deleterious effects [ ] . therefore, the covid- treatment guidelines panel of the nih recommends using dexamethasone mg/day for up to days for the treatment of covid- in mechanically ventilated (ai) patients and in those patients who require supplemental oxygen but not the mechanical ventilation (bi) [ ] . apart from these therapies, researches on antiviral drugs and vaccines are in progress which includes: lopinavir and ritonavir are the two most critical potential candidates against sars-cov- . the combination of these two drugs (usually a component of haart regiment to treat aids) has shown an in vitro antiviral activity against sars-cov- . however, more randomized trials are mandatory to prove its effectiveness against this novel coronavirus [ ] . mscs are multipotent adult stem cells that are present in most human tissues, including in the umbilical cord. mscs can self-renew by dividing and can differentiate into multiple types of tissues, including osteoblasts, chondroblasts, adipocytes, hepatocytes, and others, which has led to a robust clinical research agenda in regenerative medicine [ ] it is hypothesized that mscs could reduce the acute lung injury and inhibit the cell-mediated inflammatory response induced by sars-cov- [ ] . mscs are investigational products that have been studied extensively for broad clinical applications in regenerative medicine [ ] and their immunomodulatory properties [ ] . no mscs are approved by the fda for the treatment of covid- . there are insufficient data to assess the use of mscs for the treatment of covid- . the fda has recently issued several warnings about patients becoming potentially vulnerable to stem cell treatments that are illegal and potentially harmful [ ] . tocilizumab, a recombinant monoclonal antibody against the interleukin- receptor, has been used to mitigate the cytokine release syndrome associated with chimeric antigen receptor t-cell therapy and has been proposed as a potential therapy for the cytokine storm syndrome associated with severe covid- pneumonia based on small phase two studies [ ] [ ] [ ] [ ] [ ] [ ] [ ] . an observational study reported reduced mortality in icu requiring covid- patients who had received tocilizumab [ ] . the indian council of medical research has recommended the use of tocilizumab in mechanically ventilated patients not improving despite the use of steroids [ ] . however, more trials are needed before its efficacy can be established. at present, no vaccine is available for the treatment of covid- . however, much research is in progress to develop an effective vaccine against this virus. according to the world health organization, candidate vaccines are in clinical evaluation, and are in preclinical evaluation. india is developing three vaccines that are under clinical trial and listed in table- , along with other clinical candidate vaccines [ ] . the sars-cov- has existed in the world for over months. during this short duration, it has spread across countries/territories/areas of the world. even developed countries could not prevent themselves from the damages caused by this virus. several measures, such as lockdown, random testing, and various researches related to therapies, have been taken to contain the spread of this disease. some drugs have shown promising results to fight against the sars-cov- , which results in a higher recovery rate. as there are no specific drugs or vaccines are available, it is impossible to predict the end of this pandemic. however, several vaccines are under clinical trials, but it will take a minimum of - months before it reaches the general population. moreover, viruses tend to mutate, so we can never be confident that vaccines will work. therefore, we will have to rely on preventive measures such as frequent hand washing, use of masks, restricted traveling, personal hygiene, and healthy eating to keep ourselves covid- free until the proper and specific treatment is available. st drafted and revised the manuscript. mmt read, edited and approved the final manuscript. both authors read and approved the final manuscript. clinical features of patients infected with novel coronavirus in wuhan epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china notice of the national health commission of the people's republic of china on revising the english name of novel coronavirus pneumonia isolation of a novel coronavirus from a man with pneumonia in saudi arabia ministry of health and family welfare. ( ) update on novel coronavirus: one positive case reported in kerala one of the lowest globally, india's case fatality rate below % and sliding covid- infection: origin, transmission, and characteristics of human coronaviruses coronaviruses: an overview of their replication and pathogenesis a novel coronavirus from patients with pneumonia in china another decade, another coronavirus evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission a new coronavirus associated with human respiratory disease in china identification of -ncov related corona viruses in malayan pangolins in southern china the outbreak of covid- : an overview china's cdc detects a large number of new coronavirus in the south china seafood market in wuhan decoding the evolution and transmissions of the novel pneumonia coronavirus (sars-cov- /hcov- ) using whole genomic data ministry of health and family welfare. ( ) the outbreak of novel corona virus in china: actions taken by the health ministry pm calls for complete lockdown of the entire nation for days: pm addresses the nation on covid- genome composition and divergence of the novel coronavirus ( -ncov) originating in china genome analysis of sars-cov- isolates occurring in india: present scenario central for diseases control and prevention. ( ) how covid- spreads situation reports ) -ncov transmission through the ocular surface must not be ignored clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records early transmission dynamics in wuhan quick guide to the diagnosis and treatment of pneumonia for novel coronavirus infections. herald of medicine. rd ed.medical expert group of tongji hospital time-varying transmission dynamics of novel corona virus pneumonia in china epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (covid- ) during the early outbreak period: a scoping review government of india ministry of health and family welfare directorate general of health services (emr division). ( ) clinical management of covid- protocol newer additional strategies for covid- testing emergence of a novel coronavirus causing respiratory illness from wuhan the novel coronavirus: a bird's eye view global surveillance for covid- caused by human infection with covid- global-surveillance-for-covid- -caused-by-humaninfection-with-covid- -virus-interim-guidance coronavirus disease (covid- ) treatment guidelines remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies hydroxychloroquine and azithromycin as a treatment of covid- : preliminary results of an open-label non-randomized clinical trial treatment of severe acute respiratory syndrome retrospective comparison of convalescent plasma with continuing high-dose clinical microbiology and infection use of convalescent plasma therapy in sars patients in hong kong anca-associated vasculitis-refining therapy with plasma exchange and glucocorticoids a comprehensive literature review on the clinical presentation and management of the pandemic coronavirus disease (covid- ) perinatally administered losartan augments renal ace expression but not cardiac or renal mas receptor in spontaneously hypertensive rats comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon-beta against mers-cov first case of novel coronavirus in the united states the national heart, lung, and blood institute acute respiratory distress syndrome (ards) clinical trials network remdesivir, lopinavir, emetine, and homoharringtonine inhibit sars-cov- replication in vitro concise review: multifaceted characterization of human mesenchymal stem cells for use in regenerative medicine hypothesis for the management and treatment of the covid- -induced acute respiratory distress syndrome and lung injury using mesenchymal stem cell-derived exosomes interactions between mesenchymal stem cells and the immune system fda warns about stem cell therapies fda approval summary: tocilizumab for treatment of chimeric antigen receptor t cell-induced severe or life-threatening cytokine release syndrome ) pathological findings of covid- associated with acute respiratory distress syndrome effective treatment of severe covid- patients with tocilizumab tocilizumab treatment in covid- : a single center experience efficacy and safety of tocilizumab in severe covid- patients: a single-centre retrospective cohort study off-label use of tocilizumab for the treatment of sars-cov- pneumonia in tocilizumab for the treatment of severe covid- pneumonia with hyperinflammatory syndrome tocilizumab among patients with covid- in the intensive care unit: a multicentre observational study draft landscape of covid- candidate vaccines the authors did not receive any funds for this study. the authors declare that they have no competing interests.veterinary world remains neutral with regard to jurisdictional claims in published institutional affiliation. key: cord- -wio b i authors: carmona-gutierrez, didac; bauer, maria a.; zimmermann, andreas; kainz, katharina; hofer, sebastian j.; kroemer, guido; madeo, frank title: digesting the crisis: autophagy and coronaviruses date: - - journal: microbial cell doi: . /mic . . sha: doc_id: cord_uid: wio b i autophagy is a catabolic pathway with multifaceted roles in cellular homeostasis. this process is also involved in the antiviral response at multiple levels, including the direct elimination of intruding viruses (virophagy), the presentation of viral antigens, the fitness of immune cells, and the inhibition of excessive inflammatory reactions. in line with its central role in immunity, viruses have evolved mechanisms to interfere with or to evade the autophagic process, and in some cases, even to harness autophagy or constituents of the autophagic machinery for their replication. given the devastating consequences of the current covid- pandemic, the question arises whether manipulating autophagy might be an expedient approach to fight the novel coronavirus sars-cov- . in this piece, we provide a short overview of the evidence linking autophagy to coronaviruses and discuss whether such links may provide actionable targets for therapeutic interventions. the ongoing outbreak of the respiratory disease covid- (coronavirus disease ) is endangering individuals, governments and societies around the world. indeed, this pandemic has unprecedented global consequences at the economic and social levels as it challenges the medical and research communities. the first case of covid- was reported in december in wuhan (china) [ ] and, despite increasingly drastic efforts to contain the disease, the infection rapidly spread across the planet, leading the who to declare it, first, a global health emergency (in january ) and eventually a pandemic (on march , ) [ , ] . as of april th , more than countries and territories have reported covid- cases with a total of over three million confirmed cases and more than . confirmed deaths [ ] . in the current absence of effective treatments and vaccines, these numbers will continue to grow inexorably. the main clinical features of given the devastating scenario that covid- has already generated, a multitude of potential approaches against sars-cov- are currently being conceived. in that sense, we think that the manipulation of autophagy might be worth exploring. macroautophagy (hereafter referring to autophagy) is an intracellular catabolic mechanism that regulates the elimination of unwanted, superfluous or defective cell components [ ] . in this process, the targeted molecules/organelles are enclosed in double-membrane vesicles called autophagosomes, which eventually fuse with lysosomes for degradation of the delivered contents. this process is induced upon energy deprivation and/or physical activity in order to secure sufficient nutrient supply and is thus often referred to as a cellular self-digestion system. the compounds resulting from lysosomal degradation (e.g., fatty acids, amino acids) may be released into the cytoplasm for the generation of new macromolecules and/or bioenergetics reactions. autophagy, therefore, represents a recycling mechanism under circumstances of low resource availability [ ] . the digestion of damaged and thus potentially detrimental cargo also increases the fitness at the cellular and consequently at the organismal level. accordingly, the induction of autophagy by dietary interventions (e.g., caloric restriction, fasting regimens), behavioral cues (e.g., exercise) or pharmacological agents (e.g., caloric restriction mimetics like spermidine, rapamycin, resveratrol or specific chalcones [ ] [ ] [ ] [ ] [ ] ) has been consistently linked to beneficial effects on health [ ] . in turn, reduced autophagic capacity is connected to aging progression and a number of pathologies including cardiovascular disease, cancer and neurogeneration [ ] . the autophagic machinery can retrieve its cargo in bulk, but it can also selectively target distinct intracellular components and organelles via specific adapter proteins that interact with both the individual substrates and the autophagosomes [ ] . specifically, these autophagy adaptors (e.g., p /sqstm , optineurin) contain both a ubiquitin-binding domain (ubd) and an lc -interacting region (lir). the ubd recognizes ubiquitin tags decorating the specific target, while the lir allows binding of lc proteins attached to nascent phagophores, the structures that eventually close to form autophagosomes [ ] . accordingly, autophagic subforms have been defined that describe, for example, the specific removal of damaged mitochondria (mitophagy), the disposal of protein aggregates (aggrephagy), the digestion of lipid droplets (lipophagy), etc [ ] . yet another selective autophagy subroutine is xenophagy, the specialized elimination of intracellular pathogens, including fungi, bacteria and viruses [ ] . the xenophagic disposal of viruses (sometimes also termed virophagy) has been described for different viral pathogens, including human immunodeficiency virus- (hiv- ) [ , ] and herpes simplex virus- (hsv- ) [ , ] . however, many viruses (including hiv- and hsv- ) and other pathogens have also evolved strategies to escape or inhibit autophagy and sometimes even to manipulate the autophagic machinery for their replicative benefit [ ] . thus, autophagy emerges as a crucial element in the evolutionary-driven arms race of host against pathogen. this further underlines the significance of xenophagy as a central antimicrobial mechanism, but also limits the potential of autophagy induction to fight infections. the question whether autophagy induction might be beneficial to specifically counteract sars-cov- infection cannot be answered at this point. however, the existing data on other covs suggest that -despite some conflicting results -autophagy induction might be a valid approach that should be subjected to further evaluation. the autophagylysosomal system does indeed seem to play a central role during the infection with different covs, including sars-covs [ ] [ ] [ ] [ ] . nevertheless, the diverse putative roles of autophagy during viral infection [ ] require that two opposite aspects be covered by this overview: (i) is there evidence for autophagy being used for the survival or replication of covs (proviral effects)? (ii) can autophagy induction reduce cellular infection, and does the virus actively inhibit autophagy (suggesting antiviral effects for autophagy)? of note, cellular manipulation of autophagic levels during infection may also reflect desperate attempts of the cell to reestablish homeostasis, either through restriction of viral entry by actively shunting endocytosis/endosomal trafficking (possibly resulting in autophagy reduction as a sideeffect) [ ] or to counteract virally induced cell death by increasing cytoprotective autophagy. as a third major as-open access | www.microbialcell.com pect, (iii) the autophagic effects on antiviral immunity must be taken into consideration. over the last years, a number of studies have addressed these issues in the context of the "old" covs, those that historically precede sars-cov- . covs rely on the formation of replication complexes at double membrane vesicles (dmvs), where viral genome replication and transcription occurs [ , ] . as it may be at least partly the case for autophagosomes, dmvs probably depend on er-derived membranes for their generation [ , ] . therefore, it was initially suspected that covs might usurp the autophagosomal machinery for dmv formation. in fact, an early study using atg knockout cells implied that autophagy may promote mouse hepatitis virus (mhv) replication via formation of dmvs [ ] . in a follow-up work, the same authors reported the co-localization of specific replication proteins (nsp , nsp , nsp ) with endogenous lc , suggesting a connection between replication and autophagosome formation [ ] . other studies reported that the porcine covs transmissible gastroenteritis virus (tgev) [ ] and porcine epidemic diarrhea virus (pedv) [ ] may induce autophagy to promote replication. however, the link between autophagy and replication of covs has been challenged by a number of different reports, showing that deletion of the essential autophagy genes atg or atg does not affect the replication of mhv [ , ] or sars-cov [ ] . furthermore, the co-localization of lc (or gfp-lc ) with the sars-cov rna replication complex could not be confirmed [ ] . a study using pharmacological induction (rapamycin) or genetic inhibition (knockdown of lc , atg , or atg ) of autophagy even demonstrated that tgev replication is negatively regulated by autophagy [ ] . in addition, rapamycin reduced infectivity of pedv [ ] . altogether, although some conflicting results exist, autophagy may not be primarily engaged in promoting cov replication. however, single components of the autophagic machinery may be hijacked independently of their activity in autophagic processing. non-lipidated lc , for instance, is used for membrane derivation for dmvs in covs, and downregulation of lc but not inactivation of autophagy, counteracts cov infection [ ] . notably, some components of the canonical autophagy machinery can target invading pathogens by promoting phagosome-to-lysosome fusion [ ] . during lc -associated phagocytosis (lap), for instance, which does not involve sequestration in autophagosomes, lc is recruited to phagosome membranes to facilitate lysosomal fusion and degradation [ ] . in addition, it has been proposed that non-canonical autophagy and intruding viruses, both of which can be inhibited by the fungal compound brefeldin a, may converge in the retrieval of membranes [ ] . non-canonical autophagy includes atg -and atg -independent as well as beclin- independent autophagy [ , ] . altogether, these observations add further layers of possible modulation of autophagic processes in trying to attenuate viral infection (figure ). intriguingly, a body of evidence indicates that covs may actually inhibit autophagy, which in turn teleologically suggests an antiviral role for autophagy. accordingly, a number of studies have shown that increasing autophagic capacity may be beneficial against infection (figure ) . a temporal kinome analysis of mers-cov-infected hepatocytes demonstrated selective activation of the erk/mapk and pi k/akt/mtor signaling responses, both of which have inhibitory effects on autophagy [ ] . accordingly, pharmacological inhibition of these pathways was able to inhibit mers-cov infection [ ] . moreover, although one of the central replicase proteins (nsp ) of avian infectious bronchitis virus (ibv) seems to promote autophagosome formation at the omegasome level [ ] , nsp also limits further autophagosomal expansion [ ] , thus compromising autophagic delivery of viral components to lysosomes. interestingly, nsp is also present in other covs, including sars-cov- [ ] . overexpression of the protease plp of sars-cov and mers-cov in different cell lines inhibited autophagosomelysosome fusion and autophagic flux [ ] . a recent report corroborated the autophagy-inhibitory activity of mers-cov and showed that induction of autophagy can reduce mers-cov replication [ ] . specifically, the authors found that pharmacological inhibition of the ubiquitin ligase skp increases the levels of beclin- , a central regulator of phagophore formation [ ] . skp executes lysine- -linked poly-ubiquitination of beclin- , targeting it for proteasomal degradation, the inhibition of which promoted autophagy and efficiently reduced mers-cov replication. this work also shows that ectopic expression of at least three viral proteins (nsp , p b, p ) restricts autophagy [ ] . while nsp may limit autophagosome expansion (see above), p b inhibits rnase l activation (a pro-autophagic event [ ] ), and p has been connected to the blockage of ifn-β induction [ , ] , which itself may be linked to autophagy [ ] . accordingly, deletion of p b or p resulted in reduced mers-cov growth, although disputing some previous observations, which the authors explain by methodological differences [ ] . thus, the group-specific accessory proteins, which by definition are not essential for viral replication but are involved in the modulation of host cells and immune evasion [ , ] , may represent targets for reducing the autophagy-inhibitory effects of covs. the fda-approved anti-malarial drugs chloroquine and hydroxychloroquine have been suggested to be repurposed for the treatment of covid- [ ] [ ] [ ] , but this remains widely controversial [ ] [ ] [ ] . although chloroquine is a lysosomotropic agent that blocks autophagic degradation, possibly by impairing autophagosome fusion with lysosomes [ ] , the putative effects on autophagy may not be necessarily causal for the antiviral activity. in fact, endosomal acidification after endocytosis is critical for sars-cov- entry [ ] , and chloroquine inhibits this acidification [ ] . in addition, chloroquine limits terminal glycosylation of the metallopeptidase ace , the functional receptor for sars-cov and sars-cov- cell entry [ , , ] . nonglycosylated ace seems to interact less efficiently with open access | www.microbialcell.com the sars-cov spike protein, thus reducing viral entry [ ] . these modes of action would target the virus upstream of autophagy, making it unlikely that autophagy modulation contributes to the outcome of chloroquine treatment at that point. additionally, chloroquine has been shown to induce autophagy-independent effects, for instance, golgi disorganization [ ] and pulmonary vasodilation [ ] that may contribute to its controversial clinical activity. interestingly, the net effects on autophagy may differ depending on parameters like cell type and dose: for instance, chloroquine-mediated lysosomal stress may promote the nuclear translocation of the pro-autophagic transcription factors tfeb and tfe [ , ] . altogether, further clinical work must clarify if chloroquine and hydroxychloroquine have major effects on covid- and at which (early?) phase of the disease these drugs should be administered. if chloroquine or its derivative turned out to be clinically useful against covid- , it will be important to understand to which extent such effects are connected to the modulation of autophagy. indeed, repurposing of known (especially currently fda-approved) drugs might offer a welcome shortcut to rapidly developing treatments against covid- . obviously, even in the present period of desperate search for pharmacological treatments, the efficacy (and lack of sideeffects) of anti-covid- treatments needs to be proven by clinical studies subjected to rigorous scientific scrutiny. while data regarding such attempts remain preliminary at this stage, several currently available preprints allow the speculation of autophagy as a possible druggable target. for instance, a recent preprint mapping the sars-cov- interactome in human host cells identifies several host factors connected to autophagy [ ] . amongst others, the authors find viral-human interactions with proteins directly modulated by mammalian target of rapamycin complex (mtorc ) [ ] , a master regulator of cell proliferation and autophagy known to be affected by other viruses [ , ] . intriguingly, another recent preprint presents in vitro data showing that sars-cov- infection restricts autophagy and that, in turn, pro-autophagic compounds -including spermidine -may inhibit viral propagation [ ] . admittedly, open access | www.microbialcell.com spermidine has a plethora of physiological functions, including regulation of rna-to-protein translation, as well as amelioration of rna and dna stability [ ] , and these effects need further investigation, specifically in relation with a possible autophagy induction. in fact, the role of spermidine during infection may be pleiotropic. on the one hand, spermidine is an autophagy inducer [ , [ ] [ ] [ ] [ ] and may promote viral xenophagy; also, it may contribute to endosomal ph buffering [ ] and thus block viral entry. on the other hand, polyamines are essential for viral replication [ ] , and the overexpression of spermidine/spermine-n( )acetyltransferase by the host, which drives spermidine (and spermine) depletion, is a common cellular response to viral infections, including that of rna viruses [ ] . this underlines once more that any pharmacological candidate for the fight against sars-cov- should be examined for its (possible) pleiotropy during infection. autophagy directly impacts immune signaling, and autophagy induction hence may counteract covs by promoting immunological defense mechanisms (figure ) . for instance, autophagy regulates, and can be regulated by, socalled pattern recognition receptors (prrs), which sense molecules specifically derived from microorganisms (pathogen-associated molecular patterns, pamps) [ , ] . prrs are present in various cells of the innate immune system and many epithelial cells [ ] . there, they are distributed at diverse locations (either at the cell surface or in the cytoplasm), providing a recognition system for different life cycle phases of a given pathogen [ ] . pamp-induced signaling triggers a multitude of pathways, including proinflammatory responses, that result in the synthesis of immunostimulatory molecules including cytokines, chemokines and immunoreceptors [ ] . autophagy further assists immune responses by processing and supporting the presentation of antigens on major histocompatibility complex (mhc) class ii, responsible for loading extracellular antigens [ , ] . in addition, autophagy can deliver exogenous viral antigens into mhc-i molecules for cross-presentation (the mhc-i pathway is usually employed for loading endogenous antigens) [ , ] . moreover, autophagy directly impacts the activation, proliferation and differentiation of immune cells [ ] . amongst others, autophagy has been connected to the differentiation of cd + t-cells into cytotoxic t lymphocytes, to dendritic cell and b cell development, to plasma cell differentiation, and to macrophage differentiation, therefore covering multiple instances of the innate and adaptive immune systems [ ] . of note, autophagy activation by caloric restriction mimetics (including hydroxycitric acid and spermidine) also improves anticancer immunosurveillance [ ] . in addition, the general cellular pro-survival effects of autophagy extend to several immune cell types. pharmacological autophagy induction by spermidine [ ] , for instance, has been demonstrated to promote the maintenance and survival of memory cd + t cells [ ] as well as to counteract b lymphocyte senescence [ ] . the interplay of autophagy and inflammation is complex, since it does not only encompass positive but also negative regulatory mechanisms. for example, autophagy can digest the interleukin precursors produced by inflammasomes (e.g. pro-il- ), but also directly target inflammasome components (e.g. nlrp , aim and asc) [ ] . in sum, autophagy ensures acute inflammatory responses while preventing excessive and prolonged hyperinflammation. finally, it should be noted that autophagy may have paracrine functions in the form of unconventional secretion [ ] , thus adding yet another layer of non-cell autonomous effects. in the context of viral infections, this mechanism may be used to induce protective responses in cells neighboring an infection site [ , ] . in primary human placental trophoblasts, for instance, autophagy induction promotes packaging and exosome-dependent delivery of specific mirnas, which induce autophagy in non-placental recipient cells, conferring resistance to a variety of viruses [ ] . this may be (one of) the mechanism(s) through which placental and maternal cells optimize their defense against viral infections during pregnancy. the existing evidence allows the speculation that autophagy induction might counteract cov infection at different levels, although more specific data are certainly required. as mentioned above, the restriction of calorie intake is the most robust method to induce autophagy. however, the fight against acute infections also requires sufficient energy supply, suggesting that autophagy induction via caloric restriction or fasting regimens may be counterproductive, at least in the short-term during (as well as shortly before) infection. therefore, caloric restriction mimetics [ , ] , natural or synthetic compounds with the ability to induce autophagy, may circumvent this problem. irrespectively of whether autophagy modulation will eventually be part of the strategies against covid- , the current pandemic outbreak is a shocking reminder that emerging (and re-emerging) infectious pathogens are (and will be) a major challenge. in view of the exposed vulnerability of our medical structures and socioeconomic wellbeing, this pandemic underlines how essential it is to further establish and secure global healthcare as well as to promote and extend robust research against infectious diseases. open access | www.microbialcell.com project "epiage". gk is supported by the ligue contre le cancer (équipe labellisée); agence national de la recherche (anr) -projets blancs; anr under the frame of e-rare- , the era-net for research on rare diseases; ammica us /cnrs ums ; association pour la recherche sur le cancer (arc); association "le cancer du sein, parlons-en!"; cancéropôle ile-de-france; chancelerie des universités de paris d.c-g., g.k. and f.m. are the scientific co-founders of samsara therapeutics, a company that develops novel pharmacological autophagy inducers. a.z. has equity interests in samsara therapeutics. f.m. and d.c-g. have equity interests in tll (the longevity labs), a company that develops natural food extracts. covid- : what has been learned and to be learned about the novel coronavirus disease potential treatments for covid- ; a narrative literature review a pneumonia outbreak associated with a new coronavirus of probable bat origin clinical characteristics of coronavirus disease in china the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study identification of a novel coronavirus causing severe pneumonia in human: a descriptive study the covid- epidemic coronavirus envelope protein: current knowledge molecular evolution of human coronavirus genomes epidemiology, genetic recombination, and pathogenesis of coronaviruses coronavirus infections: epidemiological, clinical and immunological features and hypotheses sars and mers: recent insights into emerging coronaviruses zoonotic origins of human coronaviruses autophagy: machinery and regulation induction of autophagy by spermidine promotes longevity autophagy in the pathogenesis of disease a diversity of selective autophagy receptors determines the specificity of the autophagy pathway cargo recognition and trafficking in selective autophagy cargo recognition and degradation by selective autophagy autophagy restricts hiv- infection by selectively degrading tat in cd + t lymphocytes autophagy plays an important role in the containment of hiv- in nonprogressor-infected patients trim mediates virus-induced autophagy via activation of tbk a neuron-specific role for autophagy in antiviral defense against herpes simplex virus autophagy during viral infection -a double-edged sword the interaction between nidovirales and autophagy components sars-coronavirus open reading frame- b triggers intracellular stress pathways and activates nlrp inflammasomes sars-coronavirus open reading frame- a drives multimodal necrotic cell death skp attenuates autophagy through beclin -ubiquitination and its inhibition reduces mers-coronavirus infection viruses and the autophagy pathway autophagy and the endo/exosomal pathways in health and disease rna replication of mouse hepatitis virus takes place at doublemembrane vesicles targeting membrane-bound viral rna synthesis reveals potent inhibition of diverse coronaviruses including the middle east respiratory syndrome virus sarscoronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum coronavirus replication complex formation utilizes components of cellular autophagy identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins mitophagy in tgev infection counteracts oxidative stress and apoptosis porcine epidemic diarrhea virus induces autophagy to benefit its replication coronaviruses hijack the lc -i-positive edemosomes, er-derived vesicles exporting short-lived erad regulators, for replication coronavirus replication does not require the autophagy gene atg severe acute respiratory syndrome coronavirus replication is severely impaired by mg due to proteasomeindependent inhibition of m-calpain ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex rapamycin-induced autophagy restricts porcine epidemic diarrhea virus infectivity in porcine intestinal epithelial cells autophagy and viruses: adversaries or allies? lc -associated phagocytosis at a glance alternative autophagy, brefeldin a and viral trafficking pathways discovery of atg /atg -independent alternative macroautophagy unsaturated fatty acids induce non-canonical autophagy antiviral potential of erk/mapk and pi k/akt/mtor signaling modulation for middle east respiratory syndrome coronavirus infection as identified by temporal kinome analysis coronavirus nsp proteins generate autophagosomes from the endoplasmic reticulum via an omegasome intermediate coronavirus nsp restricts autophagosome expansion genomic characterization of the novel humanpathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan coronavirus membrane-associated papain-like proteases induce autophagy through interacting with beclin to negatively regulate antiviral innate immunity new advances in our understanding of the "unique" rnase l in host pathogen interaction and immune signaling the structural and accessory proteins m, orf a, orf b, and orf of middle east respiratory syndrome coronavirus (mers-cov) are potent interferon antagonists ifnb /interferon-β-induced autophagy in mcf- breast cancer cells counteracts its proapoptotic function attenuation of replication by a nucleotide deletion in sarscoronavirus acquired during the early stages of human-to-human transmission accessory proteins of sars-cov and other coronaviruses chloroquine is a potent inhibitor of sars coronavirus infection and spread hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro regulators split on antimalarials for covid- chloroquine and hydroxychloroquine in covid- should chloroquine and hydroxychloroquine be used to treat covid- ? a rapid review chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor targeting endosomal acidification by chloroquine analogs as a promising strategy for the treatment of emerging viral diseases structure, function, and antigenicity of the sars-cov- spike glycoprotein inhibition of endoplasmic reticulum-resident glucosidases impairs severe acute respiratory syndrome coronavirus and human coronavirus nl spike pro-microbial cell tein-mediated entry by altering the glycan processing of angiotensin iconverting enzyme chloroquine is a potent pulmonary vasodilator that attenuates hypoxia-induced pulmonary hypertension the nutrient-responsive transcription factor tfe , promotes autophagy, lysosomal biogenesis, and clearance of cellular debris the transcription factor tfeb links mtorc signaling to transcriptional control of lysosome homeostasis a sars-cov- -human protein-protein interaction map reveals drug targets and potential drug-repurposing. biorxiv adapting the stress response: viral subversion of the mtor signaling pathway comprehending a killer: the akt/mtor signaling pathways are temporally high-jacked by the highly pathogenic influenza virus analysis of sars-cov- -controlled autophagy reveals spermidine, mk- , and niclosamide as putative antiviral therapeutics version functions of polyamines in mammals spermidine in health and disease cardioprotection and lifespan extension by the natural polyamine spermidine spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome restoring polyamines protects from age-induced memory impairment in an autophagy-dependent manner chloride accumulation and swelling in endosomes enhances dna transfer by polyamine-dna polyplexes polyamines and their role in virus infection interferon-induced spermidine-spermine acetyltransferase and polyamine depletion restrict zika and chikungunya viruses the interplay between pattern recognition receptors and autophagy in inflammation pathogen recognition and innate immunity autophagy promotes mhc class ii presentation of peptides from intracellular source proteins autophagy beyond intracellular mhc class ii antigen presentation autophagy enhances the presentation of endogenous viral antigens on mhc class i molecules during hsv- infection the relationship between autophagy and the immune system and its applications for tumor immunotherapy caloric restriction mimetics enhance anticancer immunosurveillance autophagy is a critical regulator of memory cd + t cell formation polyamines control eif a autophagy and inflammasomes secretory autophagy human placental trophoblasts confer viral resistance to recipient cells human tank-binding kinase is required for early autophagy induction upon herpes simplex virus infection a discovery platform for the identification of caloric restriction mimetics with broad health-improving effects caloric restriction mimetics against age-associated disease: targets, mechanisms, and therapeutic potential the authors are grateful to the austrian science fund fwf (sfblipotox f &f , w , p , p , p ) and the austrian federal ministry of education, science and research and the university of graz for grants "unkonventionelle forschung" and "flysleep" (bmwfw- . / -wf/v/ b/ ).the authors also acknowledge the funding of dk metabolic and cardiovascular disease (fwf) and the doctoral college "metabolic and cardiovascular disease" (fwfw ) as well as support from nawi graz and the biotechmed-graz flagship open access | www.microbialcell.com key: cord- -d b gd authors: vabret, a.; dina, j.; brison, e.; brouard, j.; freymuth, f. title: coronavirus humains (hcov) date: - - journal: pathol biol (paris) doi: . /j.patbio. . . sha: doc_id: cord_uid: d b gd coronaviruses are a large group of viruses and infect a lot of species of mammals and birds. five coronaviruses currently infect humans: hcovs e and oc , identified in the s, sars-cov identified in march during the sars epidemic, and the hcovs nl and hku , identified in and respectively. the genome of the coronaviruses is a linear, non-segmented, positive-sense single-stranded rna molecule of approximately kb. the evolution of these viruses occurs through some features: the generation of multiple mutants during the replication resulting on a quasispecies structure of the viral population, the demonstrated ability of coronaviruses to establish persistent infections, the flexibility of the genome due to a high frequency of homologue or heterologue recombinations, the ability to jump barrier species and to adapt to the new environment. two epidemiologic pictures of hcov infections have to be distinguished: as suggested by recent studies, hcovs except sars-cov, are distributed worldwide and cocirculate during seasonal outbreaks. the distribution of the different hcov species varies according to the geographic area and season. in contrast, the sars-cov is responsible of the first emerging infectious disease of this millennium, infecting more than people between november and july . its circulation has been stopped by drastic public health policy. human coronaviruses may be also involved in enteric and neurologic diseases. the detection of these viruses is difficult and mainly based on molecular assays (rt-pcr). there is no established specific therapy to date. la survenue récente, en à , de l'épidémie de sras (ou syndrome respiratoire aigu sévère), et l'identification de l'agent pathogène responsable, un coronavirus émergent dans la population humaine, ont conduit à un vif regain d'intérêt et une intensification importante des recherches sur ces virus. les premiers coronavirus humains ont été identifiés dans les années dans le cadre d'infections respiratoires hautes d'allure bénigne. ils ont été longtemps considérés comme un des agents principaux, avec les rhinovirus, du rhume banal. même si rapidement, certains travaux ont suggéré leur implication dans des infections respiratoires plus graves, des pathologies entériques et neurologiques, ces virus sont longtemps restés un sujet marginal en médecine humaine. la plupart des données virologiques sur les coronavirus avant le sras intéresse le domaine vétérinaire, où ces virus peuvent être à l'origine d'infections graves avec de lourdes conséquences économiques sur les élevages de volailles et de porcs en particulier. depuis , nouveaux coronavirus ont été identifiés, trois chez l'homme, dix chez les autres mammifères, et chez les oiseaux. le nombre de séquences de coronavirus référencées dans genbank en juillet est de l'ordre de , incluant génomes complets de espèces de coronavirus différents, soit une croissance exponentielle des données génétiques disponibles concernant ces virus [ ] . les recherches menées pour identifier les réservoirs animaux du sars-cov ont mis en évidence le fort potentiel évolutif de ces virus, leur très large spectre d'hôtes, et leur importante diversité génétique. l'objectif de cette revue est de présenter, de façon non exhaustive, les principales données virologiques, épidémiologiques et cliniques accumulées depuis plus de ans sur ce groupe de virus. le genre « coronavirus » a été créé en et a regroupé à partir de critères essentiellement morphologiques des virus animaux connus depuis les années (virus de la bronchite infectieuse ou ibv, virus de l'hépatite murine ou mhv, virus de la gastroentérite porcine ou tgev) et des virus alors récemment identifiés chez l'homme (souches b , e, oc , oc , ) [ ] [ ] [ ] . le terme « coronavirus » évoque l'aspect en couronne des virions en microscopie électronique (fig. ) . la taxinomie virale a ensuite été régulièrement revue : l'ordre des nidovirales, créé en , regroupe actuellement trois familles, les coronaviridae, les arteriviridae, et les roniviridae. tous ces virus ont en commun l'organisation du génome arn et la stratégie de réplication, mais ils diffèrent dans leur morphologie, la structure de leur capside, et la taille de leur génome, qui va de nucléotides pour les arterivirus à nucléotides pour les coronavirus. la famille des coronaviridae est constituée de deux genres, les coronavirus et les torovirus. parmi les nidovirales, seul le genre coronavirus comprend des virus identifiés chez l'homme [ ] . les (carcinome rectal humain) ; hcov-nl (souche amsterdam ) a été isolé en sur la lignée llc-mk , le sars-cov sur cellules vero e ; seul hcov-hku à ce jour n'a jamais été isolé en culture cellulaire et a été uniquement caractérisé par biologie moléculaire. il est important de noter qu'en dehors des souches prototypes, les coronavirus restent très difficiles à cultiver et il existe peu d'isolats. rappelons enfin que ces virus sont des agents de classe , sauf le sars-cov qui nécessite un laboratoire de confinement de niveau pour sa manipulation. les coronavirus sont des particules virales enveloppées pléomorphes de à nm de diamètre. l'aspect en couronne visible en microscopie électronique est dû à la présence sur l'enveloppe virale de spicules en forme de massue de nm de hauteur et constitués de la protéine de surface s (fig. ). les autres glycoprotéines d'enveloppe sont la protéine m, la protéine e et, pour les coronavirus du groupe , l'hémaglutinine-estérase he. la capside virale est de symétrie hélicoïdale, elle est constituée de la protéine n, qui est étroitement liée à l'arn génomique (fig. ) . la protéine s est une glycoprotéine membranaire de type i, elle est organisée en trimères, et est composée de deux sous-unités nommées s (partie globulaire) et s (partie en forme de tige). la protéine s joue un rôle primordial dans les premières étapes du cycle viral : elle est responsable de l'attachement du virion à la cellule cible par sa sous-unité s , et détermine en grande partie le tropisme tissulaire du virus et son spectre d'hôte ; elle est également responsable de la fusion membranaire par sa sousunité s . par ailleurs, elle est la cible principale de la réponse immunitaire cellulaire et humorale et induit la formation d'anticorps neutralisants [ ] . de ce fait, comme la plupart des protéines de surface, elle présente des régions hypervariables, lui permettant d'échapper à la pression immunitaire, et, le cas échéant, de pouvoir élargir son tropisme cellulaire. la protéine s des coronavirus possède une faible activité hémagglutinante et se lie aux acides sialiques. cependant, l'entrée dans les cellules cibles semble requérir l'interaction avec un récepteur protéique spécifique. ainsi, des récepteurs cellulaires sont identifiés pour certains coronavirus : molécule ceacam pour le virus de l'hépatite murine mhv, l'aminopeptidase n (apn) ou cd pour plusieurs coronavirus du groupe (hcov- e, coronavirus porcins tgev et prcv, coronavirus canins et félins), la molécule ace pour hcov-nl et le sars-cov [ ] [ ] [ ] [ ] . les interactions entre protéine s et récepteur semblent complexes, et de nombreuses données restent incomprises : le site de liaison de s à son récepteur (receptor binding domain [rbd]) est localisé dans différentes régions de la protéine selon l'espèce de coronavirus, le clivage de s en ses deux sous-unités s et s est variable selon le coronavirus et le type cellulaire, le rôle de la liaison aux acides sialiques n'est pas déterminé (corécepteur ?) [ , [ ] [ ] [ ] . certaines données expérimentales sont inattendues : malgré des séquences en aminoacides conservées au niveau de la protéine s des hcov e et nl , ces deux coronavirus humains utilisent des récepteurs différents (apn et ace , respectivement) ; par ailleurs, le sars-cov utilise le même récepteur cellulaire que nl alors que les séquences s sont éloignées, cependant le rbd des deux virus semble proche et il est absent chez les sl-cov. l'hypothèse est posée d'une acquisition de ce domaine par recombinaison entre le sars-cov et un autre coronavirus proche de nl lors de son évolution chez l'homme [ ] . l'apparente plasticité de la protéine s et du rbd permettrait aux coronavirus de s'adapter à différents récepteurs protéiques ou à des récepteurs hétérologues dans différentes espèces et serait un atout pour émerger chez de nouveaux hôtes. les coronavirus du groupe a sont caractérisés par l'existence d'une protéine he qui forme une double rangée de petits spicules de nm de hauteur à la surface du virion. il s'agit d'une protéine dimérique possédant une activité hémagglutinante et acétyl-estérase. le gène codant cette protéine est caractéristique des cov du groupe a, cependant son expression est très variable. ainsi, dans la plupart des isolats mhv, des mutations, délétions ou insertions ont conduit à la perte de la phase ouverte de lecture de ce gène [ ] [ ] [ ] [ ] [ ] . parmi les coronavirus humains, seules les souches oc et hku possèdent le gène codant he. il existe une homologie d'environ % entre la protéine de surface hef du virus influenza c et la protéine he du hcov-oc et des coronavirus bovins (bcov). les virus influenza c et hcov-oc infectant les mêmes tissus chez l'homme, cette homologie suggère l'acquisition de ce gène par recombinaison. il est à noter que la protéine hef du virus influenza c possède une activité de fusion membranaire, absente chez la protéine he des cov [ , , , ] . les propriétés biologiques de cette protéine restent obscures. elle reconnaît les récepteurs le génome des coronavirus est une molécule d'arn linéaire, non segmentée, directement infectieuse. sa caractéristique principale est sa taille qui est de à nucléotides. il s'agit du plus grand arn viral connu. l'organisation génomique est conservée parmi toutes les espèces de coronavirus. les deux premiers tiers du génome, soit environ nucléotides, sont constitués de deux cadres de lecture orf a et b chevauchant codant deux précurseurs protéiques d'une taille et d'une complexité sans précédent. ces précurseurs sont clivés en à fragments qui forment le complexe de réplication. en aval, on trouve les quatre à cinq gènes codant les protéines structurales, dans un ordre précis et conservé (he-s-e-m-n). le génome des coronavirus comprend aussi des gènes codant des protéines non structurales dont la fonction n'est pas encore connue. la réplication des coronavirus dans les cellules eucaryotes est entièrement intracytoplasmique, elle fait appel à une stratégie particulière aboutissant à la synthèse discontinue d'arn subgénomiques de taille décroissante, ayant tous la même extrémité '. la taille du génome et la complexité du mode de réplication ont longtemps été un obstacle à l'étude des coronavirus. les récents progrès réalisés dans les études de génétique inverse et de biochimie structurale permettront probablement de répondre aux nombreuses questions sur la biologie de ces virus [ ] [ ] [ ] . l'importante plasticité du génome des coronavirus fait de ces virus des agents à fort potentiel évolutif. les deux modes d'évolution majeurs des coronavirus sont les mutations et les recombinaisons (fig. [ ] [ ] [ ] [ ] [ ] . la très grande taille du génome permet l'émergence de variants présentant de larges délétions, et permet l'utilisation de ces virus comme vecteurs viraux. l'exemple le plus connu est l'émergence du coronavirus porcin respiratoire ou prcv, dans les années . le prcv est un variant spontané du coronavirus porcin entérique ou tgev. il présente une délétion en phase de nucléotides ( acides aminés) dans le gène codant la protéine s . une des conséquences biologiques de cette grande délétion est le changement de tropisme du virus qui, d'entérique pour le tgev, est devenu respiratoire pour le prcv [ ] de nombreuses études ont été menées à la recherche du réservoir animal du sars-cov. dès l'identification, en mars , du coronavirus responsable de l'épidémie de sars, l'hypothèse d'un réservoir animal a été retenue. les premières données sérologiques provenant de la province de canton, ont montré une séroprévalence significativement plus élevée chez les personnes travaillant au contact des animaux, notamment sur les marchés vivants [ ] . rappelons que ces marchés hébergent pour une période limitée de nombreuses espèces animales ne partageant pas la même écologie dans les conditions naturelles ou les conditions d'élevage, ils constituent donc pour les virus une interface favorable au franchissement interspécifique. la première étude animale a été menée dès mai , et a inclus animaux appartenant à huit espèces différentes. parmi eux, six civettes masquées (paguma larvata) et un chien viverrin (nyctereutes procyonoides) ont été trouvés porteurs de sl-cov essentiellement par rt-pcr à partir de prélèvements nasaux et fécaux [ ] . dès cette époque, l'alarme a été donnée concernant la consommation de civettes, qui ont été éliminées des menus des restaurants suite à un abattage massif. la consommation de viande de civette est devenue populaire en chine depuis les années ; on estime qu'en , environ civettes masquées étaient élevées dans fermes sur l'ensemble du territoire chinois [ ] . ces animaux supportent la réplication du sl-cov sans symptôme apparent et constituent le ou une partie du réservoir animal. une étude ultérieure a montré que les civettes semblaient être contaminées lors de leur passage dans les marchés, le pourcentage de civettes prélevées dans les fermes d'élevage et sl-cov positives étant nul [ ] . ces résultats sont cependant controversés [ ] . actuellement, dix génomes complets de sl-cov provenant de civettes ont été séquencés. leur comparaison avec les séquences de sars-cov humains montrent, sur environ nucléotides, un total de positions de variation, dont dans une région codante protéique ( de ces sont silencieuses) [ ] . l'épidémie de sars a été divisée en trois périodes, précoce, intermédiaire, et tardive, sur la base des données moléculaires des souches prélevées chez les patients : la période précoce s'étend de novembre à janvier , l'intermédiaire de janvier à février , et la tardive de février à juillet . À cette date, la transmission interhumaine de sars-cov a été déclarée interrompue. les séquences de sars-cov de la période précoce sont proches des séquences de sl-cov des civettes, en particulier l'existence d'une séquence de nucléotides située au niveau de l'orf , qui a ensuite disparue lors de l'adaptation du virus à l'homme (délétion de nt) [ ] . au cours de l'évolution du sars-cov, la mutation du résidu aminoacide (de serine chez la civette en thréonine chez l'homme) de la protéine s semble avoir contribué de façon importante à l'adaptation du sars-cov au récepteur humain ace [ ] . certaines chauves-souris du genre rhinolophus ont récemment été identifiées comme le réservoir naturel de sl-cov par deux équipes indépendantes [ , ] . en particulier, le bat sl-cov a été détecté par rt-pcr chez l'espèce rhinolophus [ ] . en dehors des civettes masquées et des chauves-souris, d'autres animaux ont été testés ( espèces différentes, familles, huit ordres, deux classes), et certains (sept espèces) ont été trouvés porteurs du virus dans certaines circonstances. les essais d'infection expérimentales, en vue d'obtenir des modèles, notamment pour le développement de vaccins, ont montré que de nombreux mammifères supportaient la réplication du sars-cov (singes, chats, furets, souris, porcs, cobayes, hamsters), cependant, la transmission de virus à partir des animaux inoculés semble difficile [ ] . en conclusion, l'hypothèse actuellement retenue est l'existence d'un réservoir naturel de sl-cov chez les chauves-souris. ces animaux, seuls mammifères volants, constituent à eux seuls % de l'ensemble des mammifères, ils sont répartis sur tout le globe, et sont identifiés comme le réservoir de nombreux virus émergents ou réémergents dans la population humaine : virus hendra, virus nipah, lyssavirus, virus ebola. il est à noter que les chauves-souris hébergent d'autres coronavirus, notamment un bat-cov du groupe . ce réservoir naturel serait à l'origine de la contamination de plusieurs espèces animales trouvées sur les marchés, parmi elles, les civettes paguma larvata auraient un rôle amplificateur important et serait à l'origine de la contamination des humains (fig. ). la connaissance des modes de transmission constitue l'un des éléments les plus importants pour la prévention des infections respiratoires virales, et cela d'autant plus qu'il n'existe pas encore de traitement spécifique pour beaucoup d'entre elles. les durées d'incubation des infections à coronavirus humains sont courtes : de l'ordre de trois jours pour les cov classiques, et de deux à dix jours pour le sars-cov. les durées d'excrétion virale dans les voies respiratoires sont moins bien connues, l'arn des hcov classiques est détectable pendant environ jours dans les voies respiratoires [ ] . l'arn du sars-cov peut être détecté par rt-pcr dans les sécrétions respiratoires, les selles, et les urines des patients jusqu'à environ jours après le début des signes cliniques. cependant, l'isolement en culture de formes infectieuses n'a pas été possible à partir de ces prélèvements après trois semaines de maladie [ ] . l'apparente dissociation des résultats moléculaires et cellulaires peuvent être le fait d'un manque de sensibilité des systèmes de culture, ou la neutralisation des formes infectieuses par l'immunité locale. la transmission des cov se fait principalement de façon directe par les gouttelettes de sécrétions oropharyngées dispersées par la toux d'une personne infectée et symptomatique. au cours du sras, les personnes infectées étaient essentiellement celles qui avaient eu un contact rapproché avec un cas (vie commune ou prise en charge). le port de masque et le lavage des mains sont les mesures de prévention les plus efficaces [ ] . la dissémination virale aérienne semble peu fréquente ainsi que la transmission indirecte « manu-portée » ; cependant, ces voies de transmission doivent être prises en compte pour le contrôle des épidémies, notamment en milieu de soins. les études de « survie » ou de maintien de l'infectiosité dans l'air sont rares et difficiles. l'absence de standardisation et de maîtrise de nombreux paramètres rendent difficilement comparables les données de la littérature. quoi qu'il en soit, les coronavirus perdent leur infectiosité au contact des désinfectants et fixateurs les communément utilisés [ ] . le nombre de cas secondaires à partir d'un cas index n'a été étudié que dans le cadre du sras en . ce virus est modérément contagieux, avec un nombre moyen de cas secondaires estimé de , à , . cependant, des évènements de superpropagation avec plusieurs dizaines de cas secondaires ont été décrits, et ont joué un rôle important dans la diffusion de la maladie [ ] . le sras constitue une histoire particulière au sein des infections à coronavirus ; cette épidémie a été particulièrement bien documentée. elle a été divisée rétrospectivement en trois périodes décrites plus haut. la phase précoce consiste en l'émergence de plusieurs cas de pneumopathies atypiques chez des individus sans lien épidémiologique dans la province de canton. la phase intermédiaire débute par une épidémie nosocomiale hospitalière ( cas secondaires à partir d'un patient index). la phase tardive correspond à la diffusion mondiale de l'épidémie à partir de l'hôtel métropole à hong kong. dans cet hôtel, un patient index contaminera personnes logeant au même étage, et en transfert vers des destinations variées [ , ] . l'alerte mondiale est donnée par l'oms le mars . environ cas probables et décès ont été déclarés, la grande majorité en chine. le taux de mortalité estimé est égal à % pour les sujets de moins de ans, de % pour les sujets de à ans, et de % chez les sujets de plus de ans. la fin de la transmission interhumaine est déclarée par l'oms en juillet , elle a été obtenue grâce aux mesures sanitaires drastiques appliquées dans les différents pays. en france, l'institut de veille sanitaire a été chargé de la surveillance et de l'investigation épidémiologique nationale des cas de sras. en mai , cas possibles ont été notifiés, sept ont été considérées comme probables et seulement quatre ont été confirmés par la biologie [ ] . depuis juillet , plusieurs cas de contamination de laboratoire ont été rapportés en asie. enfin, les rapports épidémiologiques émanant du guangdong center for disease control and prevention ont rapporté qu'en janvier , soit six mois après la fin de l'épidémie, quatre patients ont été hospitalisés pour une infection bénigne par le sars-cov. l'étude moléculaire de ces souches a conclu qu'elles dérivaient de la même source que les souches épidémiques de à [ ] . ces résultats sont importants car ils montrent que la réémergence du sars-cov reste possible, et doit faire l'objet d'une surveillance, notamment dans cette région du monde, où d'autres virus respiratoires potentiellement émergent circulent largement. le diagnostic virologique des infections respiratoires même bénignes est un élément central de cette surveillance. concernant les autres coronavirus humains, des données épidémiologiques anciennes étaient disponibles avant le sras pour les coronavirus classiques e et oc . parmi toutes les souches isolées dans les années , seules celles-ci ont été maintenues en culture et étudiées. ces données proviennent des grandes études d'épidémiologie descriptive menées notamment aux États-unis dans les années [ ] [ ] [ ] [ ] . ces études ont montré que les hcov représentaient un groupe de pathogènes respiratoires importants pour tous les groupes d'âge. ils sont, avec les rhinovirus, les principaux agents des infections respiratoires hautes, et sont aussi impliqués dans les infections respiratoires basses (bronchite, bronchiolite, pneumopathies, exacerbations d'asthme). les primo-infections surviennent dans les premières années, et les réinfections sont fréquentes toute au long de la vie. ces réinfections sont symptomatiques dans environ % des cas. le taux d'infection est relativement uniforme dans tous les groupes d'âge ; cette situation est particulière, et diffère de celle observée pour des virus respiratoires comme le virus respiratoire syncytial (vrs), pour lequel les taux d'infection diminuent avec l'âge. les coronavirus classiques circulent sur un mode épidémique, le plus souvent entre janvier et mai dans les zones à climat tempéré. le caractère cyclique et alternatif des souches e et oc avait été souligné, ainsi que l'existence probable d'autres sérotypes, suggérée par l'utilisation combinée de plusieurs techniques sérologiques telles que la fixation du complément, l'inhibition de l'hémagglutination, et la séroneutralisation [ ] . concernant les nouveaux coronavirus nl et hku , leur identification récente rend compte d'un nombre réduit de données épidémiologiques. plusieurs points sont à souligner concernant leur découverte. le hcov-nl est un coronavirus de groupe découvert trois fois par trois équipes différentes [ , , ] . la « paternité » de ce virus revient cependant à lia van der hoek et al. qui ont identifié ce virus par une technique moléculaire originale à partir d'un prélèvement respiratoire d'un nourrisson de sept mois hospitalisé pour bronchiolite en janvier . la souche prototype a été appelée amsterdam [ ] . une autre équipe hollandaise a identifié le même virus à partir d'un prélèvement respiratoire réalisé en chez un garçon souffrant d'une pneumopathie [ ] . cette observation, et d'autres études rétrospectives ont montré que nl n'était pas un virus émergent, mais un virus circulant déjà dans la population humaine, et nouvellement identifié. certains auteurs pensent qu'il s'agit peut-être de la souche b , isolé dans les années , et perdue ensuite en laboratoire [ , [ ] [ ] [ ] [ ] [ ] [ ] [ ] . le hcov-hku , lui, est un coronavirus du groupe a, découvert à hong kong en , chez un patient de ans hospitalisé pour une pneumonie. ce virus a été caractérisé sur le plan moléculaire, et n'a pas encore été adapté à la culture cellulaire. la même équipe a ensuite déterminé trois génotypes différents a, b, et c de hcov-hku , le génotype c étant un recombinant des génotypes a et b [ , ] . là encore, ce virus n'est pas responsable d'une maladie nouvelle, seule sa connaissance est émergente [ ] [ ] [ ] . en et , un certain nombre d'études a été publié sur la circulation des quatre hcov hors sars-cov. ces études sont peu comparables dans la mesure où un grand nombre de paramètres diffèrent d'une étude à l'autre : région, saison, population cible (enfants, adultes, hospitalisés ou non, terrain immunitaire), et méthodes de détection moléculaire utilisées. elles ont néanmoins confirmé le caractère épidémique des infections à coronavirus, à la jonction hiver-printemps (pic en février). les quatre hcovs co-circulent, avec cependant des variations dans la distribution des différentes espèces selon la géographie et les années. le caractère annuel régulier des épidémies reste à étudier. les coronavirus sont en général placés en quatrième ou cinquième position dans la détection des virus respiratoires, derrière les rhinovirus, le vrs, l'hmpv et les virus influenza ; avec une fréquence équivalente à celle des virus parainfluenza (fig. ). le taux de détection moléculaire dans les prélèvements va de à % [ ] [ ] [ ] [ ] [ ] [ ] [ ] . les hcovs sont essentiellement étudiés dans le cadre d'infections respiratoires. leur implication précise dans des pathologies digestives et neurologiques chez l'homme est encore controversée. les hcov sont détectables dans les selles. ils ont été mis en cause dans les entérocolites nécrosantes du nourrisson dans les années , et dans les diarrhées aiguës et chroniques, suite à l'observation en microscopie électronique de particules virales dans les selles : ces particules à la morphologie caractéristique ont été alors désignées sous le nom de human enteric coronavirus (hevc) ou coronavirus-like particles (cvlps) [ , ] . l'arn des hcov est détectable dans les selles de patients présentant des infections respiratoires à hcov accompagnées de signes digestifs [ ] . s'agit-il seulement d'une excrétion digestive ou de la détection d'un agent responsable des symptômes entériques ? il faut noter qu'un certain nombre de coronavirus animaux sont responsables d'authentiques pathologies entériques graves, avec une mortalité importante, notamment chez les nouveau-nés. concernant le système nerveux central, les hcov font partie de la longue liste d'agents potentiellement responsables de pathologies démyélinisantes, notamment de la sclérose en plaque. certaines études ont montré le caractère neuroinvasif des hcov classiques et suggèrent l'existence d'infections persistantes dans le tissu cérébral [ , ] . rappelons que le paradigme de la sep est l'encéphalomyélite induite par l'infection expérimentale de souris par certaines souches neurotropes de coronavirus murins (mhv). les hcov sont essentiellement responsables d'infections respiratoires. comme de nombreux virus, leur responsabilité n'est pas toujours prouvée par le contrôle des critères du postulat de koch adapté aux virus par rivers en (ensemble de six critères établissant un virus comme cause de la maladie). cependant, certaines preuves directes ou indirectes ont pu être apportées pour les coronavirus classiques et les infections respiratoires hautes (inoculation à des volontaires sains), pour hcov-hku et les infections respiratoires basses (séroconversion), et pour le sars-cov (inoculation expérimentale à l'animal) [ , , ] . les études récentes montrent que les patients infectés par un hcov hors sars-cov peuvent présenter une infection respiratoire haute (rhinite, laryngite, otite) ou basse (bronchite, bronchiolite, ou pneumopathies) [ ] [ ] [ ] [ ] , [ ] [ ] [ ] [ ] [ ] [ ] . quelques particularités ont été soulignées dans certaines études, comme l'association plus fréquente de l'infection par hcov-nl et la survenue de laryngite [ ] syndrome de détresse respiratoire grave nécessitant une ventilation assistée. cette aggravation de la symptomatologie se fait alors qu'une réponse immunitaire s'est mise en place, suggérant un mécanisme immunopathologique. de nombreux patients atteints de sras ont reçu divers protocoles incluant ribavirine et corticoïdes. l'issue se fait soit vers la mort par défaillance multiviscérale, soit vers la guérison. chez certains patients, des signes de fibrose pulmonaire séquellaires visible au scanner ont été décrites après plusieurs mois d'évolution. il est à noter que des cas d'infections peu symptomatiques par le sars-cov ont été décrites [ , ] . la détection des hcov est réalisée dans un nombre restreint de laboratoires de virologie, et uniquement sur des prélèvements respiratoires. les techniques moléculaires sont les méthodes de choix pour la détection des hcov, virus difficilement cultivables, et pour lesquels il n'existe pas d'anticorps spécifiques validés pour une utilisation à visée diagnostique. la détection de l'arn des hcov est réalisée par rt-pcr, suivie soit d'une pcr nichée, soit d'une hybridation moléculaire confirmant la spécificité du produit amplifié. actuellement, comme pour tous les virus, ces techniques ont tendance à être remplacées par des pcr en temps réel, qui présentent l'avantage de réaliser une amplification spécifique en une seule réaction et en tube fermé. il existe de nombreuses techniques originales publiées pour chaque espèce de hcov depuis de nombreuses années. cependant, l'identification de nouveaux coronavirus (hcov nl et hku ) et la mise en évidence pour certains de différents génotypes rendent de plus en plus complexe la détection de ces virus. la disponibilité de séquences de plus en plus nombreuses et d'origine géographique diverse permet d'apprécier la diversité génétique de ce groupe de virus, et d'affiner le choix des amorces d'amplification. l'objectif principal d'un outil de détection des hcov est de disposer d'une technique fiable, sensible, et dont le coût et la faisabilité reste raisonnable. deux principales stratégies sont développées. la première consiste à développer des techniques « consensus », contenant des amorces choisies dans la région du génome la plus conservée au sein des groupes et des coronavirus, soit le premier cadre de lecture (orf a/b). ces amorces contiennent un nombre variable de positions dégénérées, de façon à amplifier en théorie les , voire les hcov. l'autre stratégie est le développement de techniques dites multiplex, utilisant simultanément, dans le même mélange réactionnel plusieurs couples d'amorces spécifiques des différents hcov. les régions du génome choisies sont en général les gènes de structure n ou m. cette stratégie reste encore difficile à appliquer aux techniques temps réel. elle semble néanmoins plus sensible que les techniques consensus [ , ] . concernant le sars-cov, il existe deux techniques commerciales de pcr temps réel (realart hpa coronavirus lc kit, artus, et light cycler sars-cov quantification kit roche), ces techniques ont été développées à partir des souches circulant en , elles devront être réévaluées en cas de résurgence de ce virus. la détection des hcov hors sars-cov sur d'autres prélèvements tels que les selles est possible, mais uniquement dans le cadre d'études visant à clarifier leur rôle dans la survenue de pathologies digestives. rappelons que les selles ont constitué le meilleur prélèvement pour le diagnostic virologique du sras [ ] . la détection des hcov hors sars-cov est utile notamment pour un diagnostic virologique précis des infections respiratoires dans le cadre hospitalier, regroupant la majorité des formes sévères, elle reste cependant lourde à mettre en place, et ne constitue pas toujours une priorité, étant donné le nombre grandissant de virus identifiés dont l'étude est importante à développer. les coronavirus ont bénéficié d'une large couverture médiatique secondaire à l'épidémie de sras de à . de nombreux laboratoires ont alors consacré leur recherche à ce groupe de virus. les progrès réalisés sur la connaissance de ces virus depuis cinq ans sont très significatifs, et permettent de mieux appréhender leur complexité et leur potentiel évolutif, notamment via le franchissement de barrière d'espèces. ces connaissances sont importantes pour l'ensemble du monde viral qui comprend la quasi-totalité des malades infectieuses émergentes ; elles permettent aussi d'élargir les collaborations entre différents professionnels, eux-mêmes enfermés dans les différentes « niches écologiques » : chercheurs, virologues médicaux et vétérinaires, cliniciens, zoologistes. . . covdb: a comprehensive database for comparative analysis of coronavirus genes and genomes the morphology of three previously uncharacterized human respiratory viruses that grow in organ culture a new virus isolated from the human respiratory tract recovery in tracheal organ cultures of novel viruses from patients with respiratory disease nidovirales: a new order comprising coronaviridae and arteriviridae a comparative sequence analysis to revise the current taxonomy of the family coronaviridae identification of a novel coronavirus in patients with severe acute respiratory syndrome characterization of a novel coronavirus associated with severe acute respiratory syndrome identification of a new human coronavirus characterization and complete genome sequence of a novel coronavirus, coronavirus hku , from patients with pneumonia coronavirus binding and entry human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry angiotensin-converting enzyme is a functional receptor for the sars coronavirus human aminopeptidase n is a receptor for human coronavirus e coronavirus spike proteins in viral entry and pathogenesis localization of neutralizing epitopes and the receptor-binding site within the amino-terminal amino acids of the murine coronavirus spike protein a -amino acid fragment of the sars coronavirus s protein efficiently binds angiotensinconverting enzyme the s proteins of human coronavirus nl and severe acute respiratory syndrome coronavirus bind overlapping regions of ace the coronavirus hemagglutinin-esterase glycoprotein expression of hemagglutinin esterase protein from recombinant mouse hepatitis virus enhances neurovirulence structure and expression of the bovine coronavirus hemagglutinin protein luxury at a cost? recombinant mouse hepatitis viruses expressing the accessory hemagglutinin esterase protein display reduced fitness in vitro heterogeneity of gene expression of the hemagglutinin-esterase (he) protein of murine coronaviruses human and bovine coronaviruses recognize sialic acid-containing receptors similar to those of influenza c viruses the hemagglutinin/esterase gene of human coronavirus strain oc : phylogenetic relationships to bovine and murine coronaviruses and influenza c virus analysis of cellular receptors for human coronavirus oc sialic acids as receptor determinants for coronaviruses coronavirus rna synthesis: transcription the molecular biology of coronaviruses the coronavirus replicase gene: special enzymes for special viruses evolution of mouse hepatitis virus (mhv) during chronic infection: quasispecies nature of the persisting mhv rna detection of infectious bronchitis virus by real-time reverse transcriptase-polymerase chain reaction and identification of a quasispecies in the beaudette strain preliminary studies on feline coronavirus distribution in naturally and experimentally infected cats quasispecies development by high frequency rna recombination during mhv persistence inter-and intra-variant genetic heterogeneity of human coronavirus oc strains in france le coronavirus porcin prcv: un virus émergent pas comme les autres feline coronavirus type ii strains - and - originate from a double recombination between feline coronavirus type i and canine coronavirus evolutionary history of the closely related group coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus oc circulation of genetically distinct contemporary human coronavirus oc strains complete genomic sequence of human coronavirus oc : molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event biological and genetic analysis of a bovine-like coronavirus isolated from water buffalo (bubalus bubalis) calves detection of a group coronavirus in dogs with canine infectious respiratory disease characterization of a coronavirus isolated from a diarrheic foal biologic, antigenic, and full-length genomic characterization of a bovinelike coronavirus isolated from a giraffe analysis of the genome sequence of an alpaca coronavirus isolation and characterization of viruses related to the sars coronavirus from animals in southern china a review of studies on animal reservoirs of the sars coronavirus molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms development and evaluation of a multitarget real-time taqman reverse transcription-pcr assay for detection of the severe acute respiratory syndrome-associated coronavirus and surveillance for an apparently related coronavirus found in masked palm civets cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human molecular evolution of the sars coronavirus during the course of the sars epidemic in china structure of sars coronavirus spike receptor-binding domain complexed with receptor severe acute respiratory syndrome coronavirus-like virus in chinese horseshoe bats bats are natural reservoirs of sars-like coronaviruses frequent detection of human coronaviruses in clinical specimens from patients with respiratory tract infection by use of a novel real-time reverse-transcriptase polymerase chain reaction detection of sars coronavirus in patients with suspected sars effectiveness of precautions against droplets and contact in prevention of nosocomial transmission of severe acute respiratory syndrome (sars) efficacy of various disinfectants against sars coronavirus superspreading sars events sars: retrospective cohort study among german guests of the hotel 'm introduction of sars in france virologic studies of acute respiratory disease in young adults. v. coronavirus e infections during six years of surveillance seroepidemiologic survey of coronavirus (strain e) infections in a population of children seroepidemiologic survey of coronavirus (strain oc ) related infections in a children's population the tecumseh study of respiratory illness. vi. frequency of and relationship between outbreaks of coronavirus infection coronavirus humains evidence of a novel human coronavirus that is associated with respiratory tract disease in infants and young children a previously undescribed coronavirus associated with respiratory disease in humans new human coronavirus, hcov-nl , associated with severe lower respiratory tract disease in australia human coronavirus nl- infections in children: a -year study human coronavirus nl infection and other coronavirus infections in children hospitalized with acute respiratory disease in hong kong detection of human coronavirus-nl in children in japan human coronavirus nl , france croup is associated with the novel coronavirus nl comparative analysis of twelve genomes of three novel group c and group d coronaviruses reveals unique group and subgroup features evidence of human coronavirus hku and human bocavirus in australian children detection of the new human coronavirus hku : a report of cases clinical and molecular epidemiological features of coronavirus hku -associated community-acquired pneumonia impact of human coronavirus infections in otherwise healthy children who attended an emergency department a prospective hospital-based study of the clinical impact of non-severe acute respiratory syndrome (non-sars)-related human coronavirus infection genetic variability of human coronavirus oc -, e-, and nl -like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients human respiratory coronavirus hku versus other coronavirus infections in italian hospitalised patients clinical disease in children associated with newly described coronavirus subtypes coronavirus hku and other coronavirus infections in hong kong human (non-severe acute respiratory syndrome) coronavirus infections in hospitalised children in france association of coronavirus infection with neonatal necrotizing enterocolitis intestinal lesions containing coronavirus-like particles in neonatal necrotizing enterocolitis: an ultrastructural analysis neuroinvasion by human respiratory coronaviruses persistent infection of neural cell lines by human coronaviruses effects of a ''new'' human respiratory virus in volunteers koch's postulates fulfilled for sars virus a major outbreak of severe acute respiratory syndrome in hong kong clinical progression and viral load in a community outbreak of coronavirusassociated sars pneumonia: a prospective study a novel pancoronavirus rt-pcr assay: frequent detection of human coronavirus nl in children hospitalized with respiratory tract infections in belgium key: cord- -n ee authors: kakhki, reza kamali; kakhki, mohammad kamali; neshani, alireza title: covid- target: a specific target for novel coronavirus detection date: - - journal: gene rep doi: . /j.genrep. . sha: doc_id: cord_uid: n ee an ongoing outbreak of pneumonia associated with a novel coronavirus has been reported worldwide and become a global health problem; hence, the diagnosis and differentiation of this virus from other types of coronavirus is essential to control of the disease. to this end, the analysis of genomics data plays a vital role in introducing a stronger target and consequently provides better results in laboratory examinations. the modified comparative genomics approach helps us to find novel specific targets by comparing two or more sequences on the nucleotide collection database. we, for the first time, detected orf gene as a potential target for the detection of the novel coronavirus. unlike previous reported genes (rdrp, e and n genes), orf is entirely specific to the novel coronavirus (covid- ) and has no cross-reactivity with other kinds of coronavirus. accordingly, orf gene can be used as an additional confirmatory assay. coronaviruses are enveloped positive-sense rna viruses belonging to the family coronaviridae and the order nidovirales spread among humans and animals (richman, whitley, & hayden, ) . although most of the coronavirus species (e.g., e, oc , nl , and hku ) cause common cold in humans, some other species such as the middle east respiratory syndrome coronavirus (mers-cov) and the severe acute respiratory syndrome coronavirus (sars-cov) cause severe respiratory diseases with mortality rates of % and %, respectively (mers-cov; organization, ) . the world health organization (who) announced the outbreak of another coronavirus in china at the end of and named this novel coronavirus (covid- ), which is currently a worldwide pandemic (organization, ) . the increasing cumulative incidence of different coronavirus genotypes throughout many countries poses a challenge to the public health laboratories in terms of diagnostic. although molecular methods such as rt-pcr and real-time pcr are among the most common procedures in detecting coronavirus, the use of specific targets still is the first critical step in the accurate diagnosis of the agent. bioinformatics analysis can assist in the identification of specific targets based on genetic diversity. the present study aimed to introduce a novel specific target and evaluate the known target genes in order to analyze covid- bioinformatically. in this study, covid- novel target was detected using the modified comparative genomic analysis (kakhki, najafzadeh, kachuei, & ghazvini, ; kakhki et al., ; neshani et al., ) . the genome of wuhan seafood market pneumonia virus isolate wuhan-hu- (nc_ ) was considered as reference strain and compared with the other types of coronavirus isolates. the gene exhibiting less cross-reaction with the other coronaviruses was considered as the conserved sequences of covid- . then the primers and a probe were designed by primer premier software version . (premier biosoft intl., ca usa), and then the secondary structures and the predicted melting temperature were checked. afterwards, the specificity of the primers was determined bioinformatically using blast software for all databases to check any cross-reactivity with other bacterial or human genomes. furthermore, we analyzed the targets, primers, and probes, which were introduced previously (v. m. corman et al., ) for the detection of the novel coronavirus using the basic local alignment search tool (blast) search. coronavirus, as published in and using primer-blast (https://www.ncbi.nlm.nih.gov/tools/primer-blast/). we also designed a specific probe (k_cov-p ) for the novel coronavirus to differentiate covid- from all other human coronaviruses. the location and characteristics of the designed primers and probe are illustrated in figure and development of a cost-effective line probe assay for rapid detection and differentiation of mycobacterium species: a pilot study diagnostic detection of wuhan coronavirus by real-time rt-pcr. world health organization detection of novel coronavirus ( -ncov) by real-time rt-pcr targeting novel genes for simultaneous detection of five fungal and bacterial agents from bal samples using multiplex pcr assay the short-chain dehydrogenases/reductases (sdr) gene: a new specific target for rapid detection of mycobacterium tuberculosis complex by modified comparative genomic analysis. infection hcv genotypes and their determinative role in hepatitis c treatment who| middle east respiratory syndrome coronavirus (mers-cov). who emergency page on mers-cov modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using mycobacterium tuberculosis complex as an example summary of probable sars cases with onset of illness from j o u r n a l p r e -p r o o f key: cord- -f d bykp authors: longardt, ann carolin; winkler, vincent patrick; pecks, ulrich title: perinatale aspekte der sars-cov- infektion date: - - journal: z geburtshilfe neonatol doi: . /a- - sha: doc_id: cord_uid: f d bykp the novel coronavirus sars-cov- has developed into a pandemic, yet still has many unknowns. the modalities of transmission, different symptoms and manifestations as well as concomitant circumstances of the disease are insufficiently characterized. especially patient groups in special situations like pregnant women and newborns have to be considered separately. the current knowledge about pregnancy, labor and the first days of life is characterized by particular uncertainty due to the scarce data available. however, there is currently no evidence of significant unfavorable maternal and perinatal outcome. many pregnant women with sars-cov- infection remain asymptomatic. the possibility of vertical transmission to the child cannot be excluded with certainty. however, indications of vertical transmission were detected only in individual cases. newborn infections are also rather rare, unspecific and usually mild, with respiratory symptoms dominating. in this article, the data available to date are examined in order to provide better information, advice and treatment for pregnant women and newborns with sars-cov- and to provide suggestions for future research. zu schwangerschaft, geburt und den ersten lebenstagen ist aufgrund der spärlichen datenlage von besonderer unsicherheit geprägt. es bestehen aber derzeit keine hinweise für eine signifikante verschlechterung im maternalen und perinatalen outcome. viele schwangere mit sars-cov- -infektion bleiben asymptomatisch. die möglichkeit einer vertikalen transmission auf das kind kann nicht sicher ausgeschlossen werden. hinweise hierauf ergaben sich jedoch bislang nur aus einzelfällen. auch neugeboreneninfektionen sind eher selten, unspezifisch und verlaufen meist mild, wobei respiratorische symptome dominieren. in diesem artikel wird die bisherige datenlage beleuchtet, um eine bessere aufklärung, beratung und behandlung der schwangeren und neugeborenen mit sars-cov- zu ermöglichen und um anregungen für die zukünftige forschung zu geben. the novel coronavirus sars-cov- has developed into a pandemic, yet still has many unknowns. the modalities of transmission, different symptoms and manifestations as well as concomitant circumstances of the disease are insufficiently characterized. especially patient groups in special situations like pregnant women and newborns have to be considered separately. the current knowledge about pregnancy, labor and the first days of life is characterized by particular uncertainty due to the scarce data available. however, there is currently no evidence of significant unfavorable maternal and perinatal outcome. many pregnant women with sarscov infection remain asymptomatic. the possibility of vertical transmission to the child cannot be excluded with certainty. however, indications of vertical transmission were detected only in individual cases. newborn infections are also rather rare, unspecific and usually mild, with respiratory symptoms dominating. in this article, the data available to date are examined in order to provide better information, advice and treatment for pregnant women and newborns with sars-cov- and to provide suggestions for future research. men verlaufen [ ] . typische symptome sind trockener husten, halsschmerzen, myalgien und fieber, sowie eine olfaktorische dysfunktion [ , ] . hauptübertragungsweg scheint die tröpfcheninfektion zu sein, kontaktinfektionen sind nicht auszuschließen. eine vertikale transmission von mutter zum kind wird diskutiert [ ] [ ] [ ] [ ] [ ] . berichte zu infektionen von schwangeren [ ] [ ] [ ] ] , sowie peri-und postnatale infektionen [ ] [ ] [ ] [ ] werden zunehmend publiziert. es besteht weiterhin große unsicherheit betreffend der maternofetalen transmission, dem infektionsverlauf bei schwangeren, dem risiko für frühgeburten sowie dem postnatalen verlauf. diese spiegelt sich auch in kontroversen zum management unter geburt wider [ ] . die vorliegende Übersicht befasst sich mit der aktuellen publikationslage zu sars-cov- in der schwangerschaft mit dem schwerpunkt der materno-fetalen transmission beziehungsweise der postnatalen infektion des neonaten. bei sars-cov- handelt es sich um ein einzelstrang rna-virus, das zu den sarbecoviren der gattung betacoronavirus gehört [ ] . sars-cov- wird rasch inaktiviert zum beispiel durch minütige exposition bei °c, % ethanol, oder peressigsäure beziehungsweise chlorhaltige desinfektionsmittel [ ] . das virus vermehrt sich bereits in einem frühen stadium der infektion stark im rachenraum. der eintritt in die zelle findet über den sarscov rezeptor angiotensinkonvertierendes enzym (ace ) statt [ ] . die expression von ace ist signifikant höher in der asiatischen im vergleich zur europäischen und amerikanischen bevölkerung, sowie höher bei männern als bei frauen. dies ist eine mögliche erklärung für höhere infektionszahlen im asiatischen raum sowie in der männlichen bevölkerung [ , ] . in bezug auf die transmission wird die tröpfcheninfektion als hauptübertragungsweg gesehen, neben der kontakttransmission und transmission durch aerosole [ ] . eine fäkal-orale Übertragung ist möglich [ ] da studien zu influenza, sars und mers eine erhöhte morbidität und mortalität bei schwangeren im vergleich zu nicht-schwangeren frauen nahelegten [ , [ ] [ ] [ ] [ ] [ ] , war die sorge bei sarscov groß. in einzelnen fallserien wurde nun aber über einen vergleichbaren klinischen verlauf bei schwangeren wie bei nicht-schwangeren erwachsenen berichtet [ , ] . typische symptome sind fieber, trockener husten, sowie myalgien, halsschmerzen und laborchemisch eine lymphopenie [ , ] . die symptomatik kann von milden grippeähnlichen symptomen bis hin zu schweren pneumonien reichen [ ] . eine systematische untersuchung, bei der alle zur geburt aufgenommenen frauen zwischen dem . märz bis . april an zwei krankenhäusern in new york auf sars-cov- gescreent wurden, deckte eine prävalenz von % auf. wichtig ist die beobachtung, dass nur der betroffenen frauen zum zeitpunkt des abstrichs symptomatisch waren. nur der asymptomatischen frauen entwickelten im weiteren verlauf symptome [ ] . in einer studie aus den kliniken in wuhan wurden frauen mit covid- zwischen dezember und märz erfasst; zeigten einen milden verlauf und ( %) einen schweren verlauf mit hypoxämie, eine hiervon wurde beatmet. zum zeitpunkt der publikation wurden frauen ohne weitere komplikationen entlassen, so auch alle frauen mit schwerem verlauf. vier frauen wünschten wegen covid die abruptio, frauen hatten einen spontanen abort und frauen eine extrauteringravidität; frauen ( %) wurden in dieser zeit entbunden. bemerkenswert ist dabei die hohe sectio-rate von %, die sich insbesondere aus der unsicherheit im umgang mit der erkrankung ergab [ ] . in einem systematischen review aus publikationen mit schwangeren frauen wurde über einen milden verlauf in , %, einen schweren verlauf in , % und über kritisch kranke patientinnen in , % berichtet [ ] . einschränkend ist hier jedoch zu erwähnen, dass die qualität der aktuell sehr rasch und im schnellverfahren publizierten studien dem sonst üblichen wissenschaftlichen anspruch nicht standhalten und diese daten daher mit vorsicht zu bewerten sind. mitte mai sind auf pubmed alleine publikationen zu den schlagworten "covid and pregnancy" zu finden. ob ein erhöhtes risiko für fehlgeburten, intrauterinen fruchttod, frühgeburt, oder "fetal distress" sowie für andere maternale oder perinatale komplikationen besteht bleibt aktuell noch unklar. pathologische veränderungen der fetalen herzfrequenz können bei schwangeren mit covid- ein frühes zeichen einer maternalen respiratorischen verschlechterung sein [ ] . eine vertikale transmission bezeichnet die intrauterine transplazentare, peripartale oder durch muttermilch übertragene infek tion des neugeborenen. in bezug auf die intrauterine vertikale transmission von sars-cov- gibt es keinen sicheren nachweis. da das virus selten (ca. %) im blut betroffener zu finden ist [ ] , macht dies eine Übertragung über die plazenta unwahrscheinlich. mehrere fallserien gingen dieser frage letztlich genauer nach: untersuchungen bei neugeborenen von sars-cov- -positiven müttern ergaben keinen virusnachweis in fruchtwasser, nabelschnurblut oder im kindlichen nasen-rachenabstrich [ ] [ ] . vier publikationen beschreiben eine analyse von plazenten von frauen, die zum zeitpunkt der geburt covid- aufwiesen. in keiner der insgesamt untersuchten plazenten konnte das sars-cov- -virus nachgewiesen werden [ , [ ] [ ] [ ] . abgesehen davon, dass das virus selten im blut detektiert wurde, stellt sich auch die frage nach der expres sion des sars-cov- -rezeptors ace im bereich der maternofetalen grenzfläche beziehungsweise in der plazenta. herse et al. beschrieben, dass ace in der plazenta deutlich geringer exprimiert wird als in der dezidua [ ] . dem gegenüber zeigte eine kürzlich veröffentlichte auswertung bestehender onlinedatenbanken zu single cell sequencing eine hohe expression des ace in stromalen und perivaskulären zellen der dezidua, im zytotrophoblast und synzytiotrophoblast der plazenta, aber auch in spezifischen zellen des fetalen herzens, der leber und der lunge. zudem unterliegt die dichte des rezeptors im gewebe zumindest in der maus einer dynamik im laufe der embryonalen entwicklung [ ] . somit stellt sich auch die frage nach einer vulnerablen phase in der schwangerschaft. daten aus dem . oder . trimenon sind so spärlich, dass eine bewertung nicht möglich ist. ein fallbericht aus der schweiz wies das virus in der plazenta bei einem spätabort einer symptomatischen patientin im . trimenon nach [ ] . ob das virus in diesem speziellen fall von pathogenetischer bedeutung war, ist unklar, aber möglich. ein weiterer fall eines neugeborenen einer jährigen peruanischen covid positiven mutter wirft fragen zum transmissionsweg auf. die patientin wurde wegen ihrer respiratorischen symptomatik in der schwangerschaftswoche entbunden. das kind zeigte sich mit lebensstunden positiv für sarscov im nasenrachenabstrich. da das frühgeborene unmittelbar nach der entbindung durch sectio von der mutter isoliert und nicht durch die mutter gestillt wurde, erscheint eine postpartale infektion nach angaben der autoren unwahrscheinlich und damit eine vertikale transmission naheliegend [ ] . seit februar sind igg und igmantikörpertests für sars cov auf dem markt verfügbar [ ] . [ , ] , die dann den Übertritt großmolekularer mütterliche partikel zum fötus erleichtert. ebenfalls unklar ist, ob eine Übertragung über die muttermilch erfolgen kann. chen et al. untersuchten in einer fallserie muttermilch von müttern; alle proben waren negativ für sars-cov- [ ] . in einer kohorte aus wuhan ( frauen mit covid ) wurde in einer von muttermilchproben virus-rna nachgewiesen [ ] . gesichert ist der infektionsweg durch eine sars-cov- -Übertragung über die muttermilch damit jedoch nicht. möglicherweise liegt das hauptrisiko eher in der tröpfcheninfektion aus den mütterlichen atemwegen während des stillens (horizontale transmission) [ ] . obwohl das stillen für das neugeborene und für die bindung zwischen mutter und kind wichtig ist, vermieden kollegen in china noch im februar eine klare positionierung für oder gegen das stillen bei isolierten neugeborenen [ ] . anzunehmen ist aber auch die weitergabe von sarscov antikörpern über die muttermilch an das kind, was den klinischen verlauf einer kindlichen infektion positiv beeinflussen könnte, ähnlich wie es bei der sars-epidemie / berichtet wurde [ ] . weitere untersuchungen sind dringend erforderlich, um einerseits das risiko einer "muttermilchkontamination" mit virusrna andererseits den möglichen nutzen durch die weitergabe von antikörpern abzuschätzen. die symptome bei infizierten neu und insbesondere frühgeborenen sind weniger spezifisch und eindeutig als bei erwachsenen. symptome wie atemnotsyndrom, temperaturinstabilität, gastrointestinale sowie kardiovaskuläre manifestationen könnten auch die folgen der geburtsumstände oder einer frühgeburt sein. in der oben bereits erwähnten retrospektiven auswertung durch zhu et al. wurden zwischen dem . januar und . februar neugeborene in wuhan untersucht, die von müttern mit covid- geboren wurden; der neugeborenen von müttern (ein zwilling) wurden symptomatisch, neugeborene hatten eine atemstörung, eine zyanose, erbrechen und nahrungsintoleranz, fieber, ein kind war tachykard. laborchemisch wurden zwei kinder durch eine thrombopenie und pathologische leberwerte auffällig. ein kind verstarb am . lebenstag im multiorganversagen. diese viel beachtete publikation warf aufgrund der signifikanten komplikationsrate der kinder fragen auf, insbesondere deshalb, da die nasen-rachenabstriche auf sars-cov- bei allen kindern negativ waren. das ungünstige outcome der kinder erklärt sich somit einerseits möglicherweise durch die folgen der frühgeburt, der kinder wurden vor der vollendeten . schwangerschaftswoche geboren, wobei die umstände, die zu der frühgeburt führten, nicht ausführlich beschrieben wurden [ ] . auf der anderen seite ist unklar, wie intensiv die kinder tatsächlich auf eine sarscov infektion getestet wurden oder wie hoch die falsch negativ-rate der abstriche war. die publikation zeigt deutlich die allgemeinen mängel der v. a. zu beginn der pandemie möglicherweise unkritisch im eilverfahren veröffentlichten berichte. chen et al. berichteten über weitere kinder von covid- positiven schwangeren. alle frauen wurden durch sectio entbunden. keine der sectiones war allein aufgrund von covid symptomen indiziert. jedoch spielte die unsicherheit im umgang mit der infektion eine rolle. obwohl der kinder als frühgeborene ( + bis + schwangerschaftswochen) zur welt kamen, benötigte keines der kinder eine spezielle neonatologische versorgung oder wurde respiratorisch auffällig. ein kind zeigte leicht erhöhte myokardiale enzymwerte im blut [ ] . die wohl größte fallserie mit neugeborenen von frauen mit covid beschreibt nachweislich sars cov infizierte kinder. alle drei neugeborenen hatten anzeichen der pneumonie, zwei kinder hatten fieber und nur eines der drei neugeborenen schwere respiratorische symptome, die aber auch auf die frühgeburt ( + schwangerschaftswochen) bezogen werden können. zudem berichtet die studie nicht, wie systematisch die kinder postpartal getestet wurden, oder ob abstriche nur durchgeführt wurden, wenn die kinder symptomatisch wurden [ ] . somit stellt sich der neonatale verlauf bei kindern von covid- positiven müttern in den meisten fällen milde bis asymptomatisch dar. die sorge vor rascher respiratorischer verschlechterung in einzelfällen sowie die eingeschränkten behandlungsmöglichkeiten lassen neugeborene von covid- -positiven müttern jedoch als risikogruppe einstufen [ ] . Ähnliche effekte im kindesalter wurden in bezug auf sars und mers gesehen -insgesamt scheint auch hier in dieser altersgruppe der verlauf deutlich milder als bei erwachsenen zu sein [ , ] . die langzeitauswirkungen der sars-cov- -infektion auf das neugeborene sollten gegenstand künftiger forschung sein. [ ] . Ähnliche veröffentlichungen gehen auch von who, unicef und viele andere fachgesellschaften (z. b. royal college of obstetricians and gynecologists) aus [ , ] . dennoch bestanden und bestehen international kontroversen in bezug auf das stillen. einzelne autoren rieten explizit hiervon ab, ohne sich dazu näher zu erklären oder auf sinnvolle haltbare evidenz zu stützen [ , ] . dies war und ist sicher der herrschenden unsicherheit und angst vor einer transmission auf das neugeborene geschuldet und unterstreicht die notwendigkeit von studien hierzu. eine aktuelle umfrage der cochrane collaboration lässt interessante schlüsse auf die bestehende unsicherheit beim peripartalen management von schwangeren mit covid- zu. besonders interessant sind dabei die aspekte, bei denen kein konsens unter experten erreicht werden konnte [ ] : [ ] . who declares covid- a pandemic sarscov : is it the newest spark in the torch? olfactory dysfunction: a highly prevalent symptom of covid with public health significance clinical features of patients infected with novel coronavirus in wuhan, china unlikely sarscov vertical transmission from mother to child: a case report vertical transmission of coronavirus disease (covid- ) from infected pregnant mothers to neonates: a review possible vertical transmission of sars-cov- from an infected mother to her newborn clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records perinatal transmission of covid associated sarscov : should we worry? online ahead of print an analysis of pregnant women with covid , their newborn infants, and maternalfetal transmission of sars cov : maternal coronavirus infections and pregnancy outcomes clinical characteristics of novel coronavirus disease (covid- ) in newborns, infants and children coronavirus disease (covid- ) and neonate: what neonatologist need to know novel coronavirus in a dayold neonate with clinical signs of sepsis, a case report novel coronavirus disease (covid- ) in newborns and infants: what we know so far genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding association of angiotensin-converting enzyme gene polymorphism and enzymatic activity with essential hypertension in different gender: a casecontrol study molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes detection of sarscov in different types of clinical specimens effects of influenza on pregnant women and infants viral infections during pregnancy potential maternal and infant outcomes from (wuhan) coronavirus -ncov infecting pregnant women: lessons from sars, mers, and other human coronavirus infections middle east respiratory syndrome coronavirus infection during pregnancy: a report of cases from saudi arabia a casecontrolled study comparing clinical course and outcomes of pregnant and non-pregnant women with severe acute respiratory syndrome clinical analysis of neonates born to mothers with -ncov pneumonia universal screening for sarscov in women admitted for delivery clinical characteristics of pregnant women with covid- in wuhan, china a systematic scoping review of covid during pregnancy and childbirth coronavirus disease (covid ) and pregnancy: what obstetricians need to know infants born to mothers with a new coronavirus (covid ) pregnant women with new coronavirus infection: a clinical characteristics and placental pathological analysis of three cases covid- ) during pregnancy: a case series a case of novel coronavirus in a pregnant woman with preterm delivery dysregulation of the circulating and tissuebased reninangiotensin system in preeclampsia the sars-cov- receptor ace expression of maternalfetal interface and fetal organs by singlecell transcriptome study secondtrimester miscarriage in a pregnant woman with sars-cov- infection severe covid- during pregnancy and possible vertical transmission antibodies in infants born to mothers with covid- pneumonia virus disease , a growing threat to children? coronavirus disease among pregnant chinese women: case series data on the safety of vaginal birth and breastfeeding proposal for prevention and control of the novel coronavirus disease in newborn infants sars and pregnancy: a case report neonatal earlyonset infection with sars-cov- in neonates born to mothers with covid- in wuhan, china middle east respiratory syndrome coronavirus and children severe acute respiratory syndrome among children empfohlene präventionsmaßnahmen für die geburtshilfliche versorgung in deutschen krankenhäusern und kliniken im zusammenhang mit dem coronavirus umgang mit neugeborenen sars-cov- positiver mütter mit oder ohne klinische erkrankung (covid ) coronavirus/ covid- und stillen: aktuelle internationale empfehlungen faq für schwangere frauen und ihre familien us nicus and donor milk banks brace for covid breastfeeding and coronavirus disease : ad interim indications of the italian society of neonatology endorsed by the union of european neonatal & perinatal societies chinese expert consensus on the perinatal and neonatal management for the prevention and control of the novel coronavirus infection guidelines for pregnant women with suspected sars-cov- infection key: cord- -xi zy ow authors: allam, zaheer title: the third days: a detailed chronological timeline and extensive review of literature documenting the covid- pandemic from day to day date: - - journal: surveying the covid- pandemic and its implications doi: . /b - - - - . - sha: doc_id: cord_uid: xi zy ow this chapter surveys the global unfolding of events during the third days of the covid- pandemic that originated from china. the third days of the unfolding of the events showcased how city-wide lockdowns were started to be considered globally, the moving of the epicenter from china to europe, and major industries being impacted worldwide. to document this, an extensive review of the literature provides a daily overview of the situation covering health, economic, political, and social perspectives and outlines key events during the unfolding of the pandemic. this chapter surveys, and establishes a chronological timeline of the outbreak from day to day , covering issues appertaining to health policy and dwells into socioeconomic measures and impacts during the unfolding of the pandemic. the past days of the covid- pandemic had been eventful, as the reality of the disease was clear globally, where no single continent had been spared. the next days (day to day ) were marked with major milestones, challenging and most trying in different spheres of life as is demonstrated in succeeding sections. to start with, during this period, the number of confirmed cases increased from slightly above , to a high of million and counting (spotlight, ) , with the number of casualties increasing from deaths to over , deaths across the globe by the end of the days. in addition, the number of affected countries increased from countries to countries and territories (worldometer, ) . another change that was witnessed within the third days is the shifting of the covid- pandemic epicenter from europe to the united states, where the numbers of confirmed cases in the country, beingdby that timedmore than a quarter of the confirmed cases in the rest of the world (kirby and stewart, ). as the impacts of the coronavirus continued to be felt, there was evidence of an economic downturn in different countries, including in developed economies, where the number of people filing for unemployment claims increased. due to the economic hardships, it became apparent that many countries were trying to ease the lockdown restrictions to allow for reopening of economies, but in a gradual and cautious manner to avoid the reemergence of cases. it is within these days that governments were seen to propose economic stimulus packages to bail out their citizens and economies, including companies that were already struggling due to reduced activities. at the same time, due to the economic and social strives, there was evidence of political tension between countries as they trade blame on responsibilities toward containing the coronavirus before it spread, and become global pandemic (business davidson, a; smith, ) . during these days, it also became clear that the world was a long way before a vaccine could be developed and thus, the demand for personal protective equipment (ppes) would continue, and we see countries and regions formulating policies to control the exportation of ppes and medical supplies to other countries. with the increasing scarcity of ppes and other basic, medical essentials, these were seen to rely on the world health organization (who) and well-wishers for the supplies. within these days, there is also evidence of there was no safe-haven against coronavirus, as even those in cruise ships and aircraft carriers were infected and with cases in such places spreading faster (cna, c; gajanan and mansoor, ; kaneko and kim, ; willsher and sabbagh, ) . it also dawned that even those in positions of power and authority are not immune to the virus, where some even succumbed to their injuries. within these days, it also became apparent that every single sector is highly dependent on the health sector, as those like sports and entertainment, religious sectors and others remained "grounded" with some high profile events such as professional football leagues, olympics, and wrestling being canceled, postponed, or suspended indefinitely (bbc sport, ; cacciola and deb, ; schad, ) . during this period also, it becomes apparent that it is possible for technology companies to set aside their competition and come together for the common goal of humanity (apple, ) . therefore, even as events of these third days had been devastating and heartbreaking, there is much that humanity can learn, and have learned, and going forward, even after the covid- is finally phased out, as people, governments, regions, and economies embark on rebuilding, some of the positives that have been learned will need to be kept alive. the following sections document the unfolding of the pandemic. during this month, every effort counted in the fight against the spread of covid- , and this was emphasized by the events of march . on this day, finally, the who conceded that without a doubt, coronavirus amounted to a global pandemic (who, ad) . the build-up to this global pandemic announcement saw a national wide lockdown declared in italy on th following an uncontrollable and astronomic increase in the number of new cases and deaths in the country (bbc, c) . following this, the country was beginning to experience unprecedented abandonment by its neighbors and country members of the eu who had continued to issue a travel advisory to their citizens against traveling into or from italy (gov.uk, a) . unsurprisingly, by th, all eu member states had experienced the outbreak of the covid- disease, and most of the first cases were related to travelers fleeing italy after the situation therein started to worsen (who, ad) . in north america, the situation in the united states was also getting out of hand, with over states including arizona, washington d.c., michigan, colorado, vermont and rhode island, and others declaring states of emergency (razek, ) . here, on march , the united nations headquarters in new york closed its doors to the public for fear of spreading the virus (krisel, ). as the situation escalated, with over confirmed cases in the country, and over deaths from the virus, the national basketball association (nba), one of the most popular and fancied sporting activity in north america abruptly suspended its season, as of march , when a player of the utah jazz tested positive for coronavirus, just before their game with oklahoma city began (cacciola and deb, ) . these unfolding attracted a host of intervention measures in the country to ensure people would observe the health guidelines, especially by staying at home and keeping social distancing. first, on march , vice president pence announced that medical insurance companies had agreed to waive all copayments on covid- testing and also extended their coverage for the treatment of the disease (office of the president, b). similarly, the country, through homeland security, announced a level travel advisory and subsequently temporarily restricting entry to all foreign travelers from china, iran, and certain countries of europe. the restrictions also demanded that all american citizens and legal permanent residents and their immediate families returning from countries already affected by the virus must undergo a self-quarantine for a minimum of days upon arrival (homeland security, ) . this announcement was affirmed by the oval office address by president trump stating that travel advisory applied to all the countries in the schengen area (collinson, ) . the decision by trump was disapproved by the eu leaders (gaouette et al., ) . elsewhere, to control and reduce the spread of the virus, the schooling system in different countries was seen to be disrupted. as of march , a un report indicated that about % of students across the globe were out of school and this included countries like italy, czech republic, part of spain (madrid region), greece, and austria among many others that took the decision of closing the school to protect students and their families, as a mean to comply with who's health guidelines (who, p) . surprisingly, as countries hastened to close down schoolsdhighlighting the worsening of this situation, reports from china indicated that normalcy was returning to a point that some schools were reopening especially in qinghai province (cgtn, ) . in regard to financing efforts against this disease and supporting technological advancement in the development of test kits and vaccine development, on march , the bill & melinda gates foundation, mastercard, and wellcome together committed approximately $ million (bill and melinda gates foundation, ). on the same date, the coalition for epidemic preparedness innovations on its part committed an extra $ . million to render the organization's total investment in vaccine development to $ . million, with the funds expected to help both the company novavax and the university of oxford to research and develop a vaccine for this disease (kff, ). furthermore, on march , the united kingdom announced more funding ($ . million) , this time from its national budget to aid vulnerable countries in their efforts against covid- (gov.uk, b) . two days after declaring the coronavirus a global pandemic, circumstances in the western part of the globe have led the who to make another declaration; this time, the new epicenter of the outbreak of coronavirus was europe (who, ae). this announcement was not surprising as of then, italy was already overwhelmed ( , cases and deaths already) (snuggs, ) , and spain had in the day declared a state of emergency (cnbc, ) . things in other member countries of the union were also worsening, with the region recording over deaths in a span of h from the disease, and over new cases in the same period (who, c) . and surprisingly, from the situation report by the who (who, c), all the cases in each of these countries were of local transmission; thus, warranting the decision different countries were making to restrict movements, and where possible, instituting total lockdowns like the case of italy. on the western side of the globe, more states in the united states were declaring a state of emergencies, restricting the number of people in gatherings, closing all learning institutions, and restricting movements among other things. these happenings were more pronounced on march , and when the worse came to worst, present donald trump, under the robert t. stafford disaster relief and emergency assistance act (stanford act), declared a state of national emergency (office of the president, a). by then, the number of cases in the united states had increased to and those who died from the disease reached deaths, with transmission happening locally (who, j) . in total, the global number of confirmed cases had reached a high of , cases, with of those reported in the past h. of the sum, , had been confirmed from countries, of which were reporting their first cases. the remaining cases were reported in china, where situations were coming back to normal, with only new cases reported in the populous country, and deaths were reported in the -h period. wuhan, the former epicenter only recorded five confirmed cases (reuters, c) . outside china, the deaths increased by , raising the total tally to cases (who, c). following these unprecedented unfolding globally, economies were facing numerous challenges, as most economic activities had stalled or were nonexistent. for instance, in the united states, the stock exchange recorded the lowest point, only reminiscence with situations of (mccabe and ostroff, ). for this reason, different agencies introduced financial packages to offer some support. for instance, the adb announced a $ million package that could be accessed by companies to supply critical essentials for combating covid- (adb, ) . in europe, the european bank for reconstruction and development is reported to have approved a $ . billion financial package to help companies in the region to remain afloat during this period the region was experiencing the most trying moment in the recent history (williams, ) . amid the challenges of covid- and its impacts, some countries like taiwan found some solace in the use of technology to track and instill the mandatory quarantine, especially for those coming from certain areas. with technology, enforcement officers were able to know those who were flaunting rules and their whereabouts, and this helped reduce the spread of the virus, despite it being just kilometers from china where things were worse some days ago (yun, ) . in europe, there was some use of technology, especially mobile apps, that helped in mapping and tracking cases, and to bolster this even further, the european commission (ec) was offering funding to a tune of v m ($ . ) for start-ups or small medium enterprises (smes) developing technologies with capacities to treat, test, monitor, or offer other aspects that could help in the fight against covid- (euroean commission, a). in the past month since the first case was confirmed in africa, the number of countries affected in the continent increased to by march , with seven reporting their first case in a span of h. also, a week prior, the number of cases in the continent was only , but they increased to with six deaths reported to have been imported, except for south africa, algeria, senegal, and cameroon (who, k) . in europe, most countries were receiving unprecedented numbers of new cases, especially in italy, spain, france, and germany, which recorded , , , , and new cases, respectively, and almost all cases in most of these eu countries were locally transmitted (who, k). the number of deaths in the region was also rising with italy losing people in a single day (snuggs, ) , while spain lost , france , and the united kingdom lost lives. in germany, which was reported to have embarked on mass testing as early as the situation warranted so, the number of deaths was relatively low (only two reported by th) (who, k) . following the dire state in the region, the european commission published guidelines (euroean commission, b) on the exportation of ppes out of the region. among such guidelines were the restriction of exportation of the said equipment unless with express green light from the eu member states. however, the eu was categorical that the measures taken were only within a specified period, especially during that period when those ppes were greatly needed locally; and thus, it was not a total ban on export, which would contravene the region's international obligations in matters of trade (euroean commission, b) . in the middle east, the severity of the disease was still present in iran, which until th had a total of , confirmed cases and deaths, with a high of deaths having been reported in a period of h. the situation in other countries within the region was controlled with only deaths reported ( in iraq, in lebanon, and in bahrain). in the american region, only a few confirmed cases were reported, and only deaths were reported in ecuador. however, the government there continued to institute proactive response measures to ensure the spread would be contained. for instance, the cdc announced that no gathering would be allowed in the united states that have more than people, thus putting into disarray functions such as weddings, concerts, and sporting events among others that are known to attract a large crowd (the new york times, a). more states declared a state of emergencies, while more schools in different states (more than states), including new york city with over . students (shapiro, ) calling for the closure of schools. one major news in the united states on that day was the negative test results for the country's president, who a few days ago had some contact with a brazilian official who turns positive after the testdprompting president trump to undergo testing (education week, ) . in other places, country borders were being closed. for instance, after confirming their first covid- cases, kazakhstan and uzbekistan closed their borders (reuters, j) . colombia also closed its border with venezuela, while turkey, with one of the leading airline services globally, suspended flights to nine european countries (liptak, ) . lebanon reported to have called for a -day lockdown in the entire country to curb the spread of the virus, which for the past week had claimed the lives of three people (france , b). the other goods news of the day came from south korea, which had shown a great resolve in bringing down the number of new cases, and this was bearing fruits after it implemented a number of strategies that involved the use of advanced technologies. first, it adopted the use of drive-thru clinics where people could be tested within min and receive their results the following day. this allowed them to test over people per hour, as there were such clinics countrywide, where six people were being tested in an hour per clinic (choon, ) . the strategy also reduced local transmissions as contacts were greatly reduced. the country also implemented the use of mobile apps to enforce quarantines and track the spread of the virus (park, ) . the success of the drive-thru clinics and apps were later adopted by the united states and germany (yamey, on th, the health landscape in different regions changed even further, with the western pacific region having the highest number of confirmed cases, mostly because of china. the european region was on its knees, health-wise, with , confirmed cases, with of these being reported in a single day. the number of deaths in this region had also increased by to take the region's tally to deaths. both north and south american regions had cases, and a total of deaths ( deaths reported in a day). the african and the south-east asia regions were relatively saved until then, with only and confirmed cases, respectively, and total deaths for both regions being (who, l). following the dire need in the european region, the eu closed its borders except for essential travels. russia also closed its borders, only allowing its citizens and legal permanent residents to travel back. spain was also reported to have instituted border restrictions for all noncitizens and residents. in france, besides instituting border restrictions like a majority of its eu counterparts, it also announced a countrywide lockdown, which meant that no gathering of any size would be allowed, with people expected to remain at home with some exceptions (onishi and méheut, ) . similar events of widespread lockdowns and border restrictions were also observed in latin america, with countries such as venezuela and peru leading the cue in countrywide lockdowns. colombia and costa rica also instituted border restrictions and control. however, brazil, which by then (march ) had the most confirmed cases in the region, overlooked all the measures that the rest of the world were implementing, and had a section of its population (supporters of their president; jair bolsonaro) demonstrate against his opponents (harris and schipani, ) . in iran, the government was forced to release over , prisoners as a way of curbing the spread of the virus in the country, which was already at alarming levels (hawkins, ) . as the global social fabric was being dismantled by the disease, its impacts were being felt in the economic sphere. for instance, on th, the airline industry in the united states was seeking government financial assistance of up to $ billion to help them remain afloat (sider and mann, ) . the dow jones industry also recorded its historical low after dropping . points; the worst day crash since the "black monday" crash (millhiser, ) . following those uncertainties and the threat covid- posed to the global fabric, a number of well-wishers and philanthropists were seen to be in the frontline of helping countries win this war. on th, the jack ma foundation donated assorted ppes and testing kits to the united states , which greatly needed these following the increasing demand, and the disruption of supply chain following the slow activities in china. on th, the world bank group committed another $ billion to help in the fight against the diseases (the world bank, b), while on the same day, bloomberg philanthropies gave a financial package of $ million, especially to help low-x and middleincome economies (bloomberg philanthropies, ). as the dark crowd of coronavirus continued to spread in italy, its impacts were becoming evident, as in a month, the number of deaths ( ) in the country surpassed those in china ( ) since the onset of the outbreak to march (quinn, b) . its health sector was completely overwhelmed with images of dejected nurses trending on social media, and while that was happening, china reported no new confirmed cases attributable to local infection, as the new cases that it confirmed were suspected to have been imported from other countries (siobhán o'grady et al., b) , as it had started to ease its border restrictions. the number of new cases in italy also increased by cases, bringing their country total to , , becoming the second most affected country after china. as for the european regions, italy recorded a total of over , cases on both th . the number of deaths for both days totaled , far much more than the rest of the regions combined. in the americas, new cases on th were : almost double of what was recorded the previous day ( new cases on th). the eastern mediterranean region recorded new cases to push their region total to , , and the number of deaths in the region reached after ( died on th), with most of these coming from iran. in total, the global confirmed cases had increased to , cases on th after , more cases were reported. the number of total deaths globally increased by a total of to reach a global tally of cases (who, m). on local scenes, the disease affected some prominent people, celebrities, and sports personalities. for instance, in the us nba teams, denver nuggets (wimbish, ), los angele lakers (whitcomb, b) , philadelphia ers (zagoria, ) , and boston celtics (ward-henninger, ) reported that each had some of their players confirmed positive, but they decline to give the names of those players. on the same land, congress representatives, ben mcadams (d-utah) and mario diaz balart of florida, confirmed that they had also contracted the disease (helsel, ) . in washington, two employees of the world bank group tested positive on the th with fears that more could have been affected. on the th, there were reports that prince albert of monaco also tested positive for covid- (romo, ) . another person is the executive director of the world food program, david beasley, who also tested positive after returning from canada (world food program, ) . to respond to the numerous cases and scenarios prompted by the covid- case, different regions, individual countries, and agencies adopted different and diverse measures. for instance, in india, the government was reported to have banned any export of ppes, ventilators, and certain medications and supplements as such were not enough locally (suneja, ) . in addition to this, to reduce further spread, especially from imported cases, it closed its borders for incoming flights (business today, b). in the united states, the number of interventions was observed, for instance, the two june scheduled party primaries in connecticut were postponed (pramuk and dzhanova, ) . president trump also signed into law the family first coronavirus response act that would see most americans receive a family relief of $ . the act also gave $ billion to be accessed by smes (erica werner et al., ) . the university of hong kong received $ , from the coalition for epidemic preparedness innovations to continue with vaccine testing for covid- (galford, ) . on the th, the rockefeller foundation committed a $ million to assist in response to covid- , especially in cities such as nairobi, new york, washington, bangkok, and bellagio (rockefeller foundation, ). since the onset of the coronavirus, there had been a theory that it was mostly affecting older people, but the who debunked this, by indicating that data on those affected in different countries and regions have shown that a significant proportion of those in hospitals are aged below years; hence, calling the younger generation to be also extra cautious. the organization also launched a health alert messaging services through whatsapp and facebook, demystifying the importance of technology in the fight against covid- , especially in sharing data and information (who, d). the organization also reported that it had reached an agreement with different producers in china who were ready to supply the organization with ppes, so that it could continue supporting countries in need of such across the world (schnirring, ) . while that was going on, they delivered an extra . million laboratory test kits for covid- to different parts of the world (watts and simon, ) . there was also news that first vaccine trials had begun, and the who together with its partners was to organize an international study dubbed solidarity trial in different countries aimed at trying different treatments that could be adopted to win over covid- (who, d) . regarding the reports on the spread and impacts of the coronavirus on this day (march ), the situation reported by world health organization indicated that the world was still in great danger of recording even more cases. for instance, italy reported the single largest number of deaths, where people died, and those confirmed increasing to , cases. in the united states, the cdc indicated that it had confirmed a total of , cases (cdc, ). as that was happening, president trump invoked the defense production act, to force general motors (gm) to produce ventilators to fill the gap after the situation in the hospital become dire (haynes, ) . on this, earlier on the day, gm rejected the move, prompting the president to apply his executive authority on them, and the new york governor equated the ventilators to missiles during world war ii (klein and raju, ) . the controversies in the united states were not over as it was reported that canada, through its prime minister, justin trudeau, would return all asylum seekers to the united states (austen, ). elsewhere, cuba invoked border restrictions for all noncitizens and nonresidents. it had delayed this decision to "keep its key tourism industry alive," but the threat of the coronavirus forced the president to take that crucial and bold decision (france , a). as time passes, the spread of the coronavirus virus took hold across the globe. on march , the who declared the virus outbreak as a global pandemic, and days later (on th), the director-general declared that the "pandemic is accelerating" (chappell, ) . and true to his word, in the past days, the number of new confirmed cases each day were averaging , new cases, to push the global total to , confirmed cases. the number of new deaths in those days was also increasing at an average of almost each day, and by rd, the total number of deaths had reached , globally (who, n). of great concern on those numbers is that most of them were coming from the european region, which by rd had reached a high of , confirmed cases and total deaths. the only regions that had shown a lot of resilience were the african region with only total confirmed cases and total reported deaths. the south-east asia region was also relatively spared having confirmed only cases and total deaths. the region of americas was showing worrisome trends, having reported a high of , new cases in a single day (march ) to push its total tally of confirmed cases to , cases and a total tally of deaths ( deaths) reported in a single day (who, n). while a majority of countries, especially in europe writhed in desperation from the impacts of covid- , china reported a third consecutive day with no local new case of coronavirus (the straits times, c). this meant that they could slowly transition back to their previous economic routine, and it also gave hope to those whose situation was worsening. in the other regions, including africa where confirmed cases were low, they were responding to the spread by escalating lockdowns and border restrictions (aljazeera, b) . other countries followed this trend. for instance, on march e , bolivia (reuters, b) , greece (stamouli, ), cuba (oppmann, ) , and the united kingdom (sparrow et al., ) imposed total lockdown in their countries (aljazeera, b) . egypt on the other hand called off all religious activities in mosques and churches for days (mourad, ) . during this period still, other countries including pakistan (reuters, n), vietnam, singapore (benner, ), uae, panama (aljazeera, b) , india, nigeria (reuters, m), and zimbabwe (the citizen, ) closed their borders to all foreign travels and nonresidents and banned international flights to or from their soils for a minimum of days. germany, on the other hand, banned gatherings of more than two persons, as cases in the country started to soar, while on the same day, spain extended the state of emergency for more days, as the situation internally was getting out of hand, with thousands hospitalized, and cases soaring each day (picheta, ) . the decision taken by each individual country was meant for the good of the citizens, but such also had a far-reaching impact on the economy. for instance, the banning of the international flights in these days, and others that had been instituted earlier mean that sectors such as tourism, hospitality industry, and others are grounded, with millions of workers employed in those sectors uncertain of what the future holds. in such circumstances, governments were forced to rely on external organizationsdlike the jack ma foundation, which on nd delivered a consignment of assorted ppes, and test kits to african countries to fight the covid- (meseret and meldrum, ). on rd, the world bank group's president was also pleading with bilateral creditors to extend debt relief to low-income economies to help them build some capacity that could allow them to fight the disease (bank, ) . while this was going on, african finance ministers were pleading for a $ billion economic stimulus in addition to the suspension of external debt to allow their individual countries to fight the coronavirus pandemic (uneca, ). china's progression toward containing the virus received a boost after the province of hubei was freed from the lockdown after almost months since the lockdown was instituted (associated press, ). it was a relief to the residents who, for such a long period, lived in fear and uncertainty of when they would return to their previous routines. the good news was that wuhan, the first epicenter of coronavirus was to open a month later, as the number of new cases had reduced significantly. in the last h, the entire country of china reported on new cases, of which, cases were reported to have been imported (cna, a). the number of deaths had also increased, with seven reported in the city of wuhan (the star, ) . the other good news came from germany where the chancellor's, angela merkel, the first test came back negative for coronavirus, but would undergo the same process a few days later to confidently confirm this result (mischke, ) . the fear that she would have contracted the disease came after a doctor who had attended her turned positive, forcing the chancellor into a safety procedure of self-isolation (mischke, ) . the day however did not present the good news to everyone, especially to governments, health workers, and security forces implementing lockdowns and other measures in different countries and to the general global population. on this, in the past h alone, the number of newly laboratory-confirmed cases neared , and the deaths on a single day accumulated to globally (cna, a). the most unfortunate report on this is that half of the new cases and deaths reported came from european countries ( , cases and deaths), with the american regions also experiencing a high of , new cases and deaths (who, e). regarding the accumulation of confirmed cases, it took at least months for cases to climb to , confirmed, and only days to reach , cases. from here, it only took days for the global total to surpass , confirmed cases, and even more startling, only days for the total to reach almost , confirmed cases. such trends prompted the international olympics committee and japan's olympic authority, led by prime minister shinzo abe, to postpone the olympics scheduled for summer to as more countries had expressed their fears of the virus (ramsay, ) , while others cited lack of preparation and other technicalities (aarons, ) . they also prompted the prime minister of india, narendra modi, to lock down the country for days, only a day after the later declared an immediate grounding of all flights in or out of india (shroff, ) . new zealand also went into lockdown (bbc, e), as australia announced a ban on all overseas travel (whiteman and sharma, ) . while in the united states, a troop of , us national guards was mobilized in states to help in response to the disease (gresik and altman, ), as it had already infected more than , people countrywide. while those were being mobilized, three of their colleagues in the navy (sailors) contracted the virus, when an aircraft carrier they were boardingdtogether with approximately other peopledset sail from vietnam. by now, the situation of covid- globally reached fever-pitch where the u.n. secretary-general antónio guterres argued that the disease was ravaging the whole of humanity, with approximately one-third of the population experiencing one or more covid- -related restriction (unicef, ). following this, there was shortages in all sectors, with the who warning that already, the world was facing a "significant shortage" of assorted medical supplies. on the social sphere, there was a shortage in the health sector prompting the un to launch a $ billion financial package on march targeting global humanitarian responses, especially to be advanced to vulnerable countries (un secretary-general, ). with the funds, those countries would manage to bolster their laboratory equipment, build and increase available sanitation (handwashing) stations, and increase medical supplies among other things. besides the financial package, the who was calling on developed economies to assist african countries with health machines such as ventilators and respirators as the continent cannot satisfy the demand for such, especially if cases of covid- were to increase (ighobor, ). those calls and interventions come at a time when most countries, especially in europe and america, were experiencing one of the darkest moments of their history. for instance, in spain, as of th, the number of reported deaths ( deaths) surpassed those reported in china ( ). but still, italy was leading in the number of people who had died with a total of , with having died in a span of only h. france had also started to lose a significant number of people as a result of the covid- , with already having succumbed in the past h. the islamic state of iran and the united states were also affected with (total deaths ) and (total deaths ) deaths having died in the past h. in regard to the number of confirmed cases, which were averaging , cases per day in the past days, the global total had increased to , by th according to the who data. africa was still showing some resilience despite reports of weak health system, with only deaths reported coming from confirmed cases across the globe (who, o). the economic situation globally was worsening, but even more in the united states where it was reported that by march , over . million american had filed for their employment benefit (casselman et al., ) ; a figure that is thought to be the highest in the history of the country. this could be attributed to the increasing number of people who were contracting the coronavirus especially in new york, which had become the epicenter of the outbreak in the northern american region, with the united states having more cases than any other country (kirby and stewart, ; the new york times, b). but, fortunately, the trump administration's stimulus plandworth $ trilliondwas unanimously passed the senate (carney, ) , thus allowing the government to offer some financial support, especially to those who continued to lose their livelihoods. elsewhere, more countries were responding to the pandemic by instituting lockdowns or other strict measures that would somehow suppress the local transmission. on this, on march , panama was reported to have suspended any form of domestic flights , days after, it had suspended international flights (aljazeera, b) . in thailand, the government declared a state of emergency forcing more areas within the country to shut down (techakitteranun, ) , while iraq and lebanon extended their curfews by days in each country. in russia, moscow shut down all forms of businesses and activities for a week (march to april ), except for essential businesses such as pharmacies and grocery stores (astapkovich, ) . the highlight of the day was the testing positive for coronavirus of uk prime minister boris johnson, which he announced to the world via a video on twitter (bbc, g). he reported that, henceforth, he would be in self-isolation and will continue working from. but, while this was breaking news, the greatest and most unfortunate news came from italy and spain. in spain, it had earlier been reported that it had recorded the highest number of deaths in a single day ( ) (rtve, ), but later only italy released its official report of the day where it indicated that approximately (who later reported (who, f)) people had died within a span of only h. italy had also confirmed new cases while spain reported new cases bringing the total confirmed cases to , and , cases, respectively. however, the united states reported the highest number of new confirmed cases ( , ), taking its total tally to , according to the data by who (who, f) but according to the us cdc data (cdc, ), the total number of cases reported in the country by th had reached , , thus leading globally. in the middle east, iran was reporting the highest numbers of new cases, with cases reported within h and new deaths during the same period (who, f). other countries in the region were relatively calm with no other reporting more than a cases a day. in africa, algeria reported the highest number of deaths ( ) (who, f) while south africa reported the first death from the virus. this death and the increasing number of confirmed cases in the country prompted the government to announce a -week nationwide lockdown (neuman, b) . elsewhere, china reported new cases and new deaths, in what seemed like a signal to a second wave of infection. following this, the government announced a ban on all foreigners, suspecting that they were the cause of this new trend in rise of cases, as out of those new cases, none were from local transmission (bbc, a; mai, ) . on the same date, the african development bank (afdb) provided aid to the continent with a $ billion social bond targeted to economic and social sectors facing stiff challenges from the impacts of covid- (afdb, ). at the same time, the who announced that the vaccine trial dubbed solidarity trialdthat it had announced about on march dwas to begin shortly, with the first trials administered to patients drawn from norway and spain, but overall, the trials would be extended to more than countries that had agreed to be part of the program (who, af). in the united states, the food and drug administration authorized the use of a -min diagnostic kit for coronavirus intended to speed-up the testing process, but a shortage of necessary equipment for collecting specimens was feared to derail the use of this kit (azad, ) . on the same land, donald trump, president of america, signed the $ trillion stimulus that was passed the previous day by the senate (foran et al., ) . even as the month of march came to an end, the incidences related to covid- continued almost unthwarted. for instance, the number of new confirmed cases for the past days has been increasing at an average of above , each day, and the number of deaths occurring each day likewise increased at an average of deaths. within the days, the total number of confirmed cases globally increased from , das captured by the who on march (who, f)dto , by march . another astonishing occurrencedespecially on march dwas the number of people that died in a single day in both spain and italy, which recorded and new deaths, respectively (who, p) . this happened while the number of patients being admitted to different hospitals in both countries exceeded their bed capacity and human resources allocation (cheng, ) . the united states was also going through thick and thin, as the number of new cases in the country continued to soar at alarming rates. even in africad which had shown some levels of resilience against the spread of this pandemicdthe numbers for the past days seemed to increase at an average of almost daily, with egypt, algeria, and south africa being the most affected (who, q) . in fact, the who's director-general highlighted the plight of the global health system and argued that there was a chronic global shortage of medical supplies such as ppes, ventilators, and other basic amenities required to saving lives (who, af). these unfolding events were happening amidst numerous responses and interventions both at local, regional, and international levels by government, international organizations like the who, the world bank, and others. among the new interventions that countries were implementing include the extension of the social distancing guidelines in the united states by president donald trump until the end of the following month (april ), and perhaps with a possible extension to june (shear, ) . the country had also accelerated the testing of individuals, and by th, the president announced that over one million people had been tested despite earlier hiccups in regard to faulty testing kits (tirrell et al., ) . in africa, on th, nigeria was reported to have directed the cessation of movement in two of its most populous cities, lagos and abuja, to reduce the chances of importation of the coronavirus to rural areas (akwagyiram, a) . in mexico, in a bid to reduce the soaring confirmed cases and growing number of deaths as a result of covid- , the government declared a health emergency (reuters, l) . in portugal, the government had resulted in treating everyone including foreigners with pending applications as permanent residents of the country so they could access public health facilities without encountering hitches (reuters, o) . but despite all those negatives, there was good news from the city of wuhan, which after undergoing a "dark moment" in the past months, saw authorities relaxing some quarantine measures, including rail services in and out of the city, meaning that people could eventually access the rest of the country (beaumont, ) . authorities in the province of hubei also announced that they would allow domestic flights to resume in all airports, except tianhe international airport in wuhan (xinhua, c) . the other goods news is that on , the bill & melinda gates foundation, wellcome, and mastercard together granted three institutions (the university of washington, university of oxford, and la jolla institute for immunology) financial support worth $ million to facilitate clinical trials for immunotherapies they were developing (mastercard, ) . in the wake of the new months, the reality of devastation of the covid- in different countries, regions, and globally was becoming clear. for instance, in spain, by april , the number of those affected reached , . but, by then, italy had more than these cases with , confirmed cases, while the united states, which had become the new epicenter, had , confirmed cases, as per the cdc data (cdc, ), while the who reported , (who, r). regionally, cases in europe reached more than half a million people ( , ), where , of those had succumbed to the virus. the region of the americas was the second most affected with a total of , confirmed cases and deaths. the western pacific region was the third hardest hit, with , infected and deaths. the eastern mediterranean regions had , confirmed cases and recorded deaths, while the african region had confirmed cases and reported deaths from the virus. overall, the global total number of confirmed cases had reached , , and an addition of , from the previous reported numbers. the number of deaths had also reached , , with a high of dying in the past h (who, r). by april , the global total exceeded the , , mark as per the john hopkins data, ncov .live, and other websites, but who reported the total numbers at , confirmed cases (who, g). the reality was reflected in the economic sector with the world bank reporting that the impacts of covid- pandemic would force more than million people into poverty (the world bank, a) . the reality of this statement was affirmed in the happenings in the united states, where it was reported that in a period of just week, . million more people filed for unemployment benefits, taking the number of those who had filed for the benefits to over million people (long and dam, a) . the same trends of unemployment were also being experienced in austria where the unemployment levels jumped to % in the country within the months since the onset of the pandemic (reuters, a) . the said reality prompted several unprecedented actions in different countries and organizations. for instance, on april , the un announced the postponement of the climate conference (cop ) scheduled for november due to covid- (un, ) . in the sporting world, the all england club announced that the wimbledon tennis tournament was canceled due to covid- , and this was the first time since world war ii that the championship was called off. on the same day, the health minister in italy announced that the countrywide lockdown would continue to be in force until the th of the month as the number of confirmed cases, and deaths continued to increase (reuters, i). the announcement was also confirmed by the country's prime minister giuseppe conte said that the situation in the country forced him to sign the decree to extend the measures (orihuela et al., ) . the same measures were taken by germany. on april , more actions continued, with saudi arabia extended its curfew to h on its most visited and the holiest cities in islam: mecca and medina (aljazeera, c) . a similar action was taken in thailand involving the entire country, with exception of medical personnel, and those transporting essential products, and for people moving to quarantine or health facilities (the nation, ). peru and panama establish a different strategy for reducing the number of people outside by imposing a gender divide, where certain days were set aside for only men and the others for men. this way, it would be impossible for those living together leaving their homes together (aquino and moreno, ). in the united states, the white house was encouraging people going out to wear masks (sun and dawsey, ) , and this came while most of the citizens were trying to come to terms with stay-at-home orders that had been declared in almost states in the country (nottingham, ) . the highlight of the day is the worsening health status of the uk prime minister boris johnson, prompting him to be moved into intensive care. he was taken to hospital in london the previous day (april ), after the covid- symptoms persisted, days after he tested positive (bbc, g). on the same day, in the same country, new deaths were reported, taking the country's total death toll to while the total number of confirmed cases increased to , after new cases were reported in a period of h. within the european region, the total number of confirmed cases had increased to , after , more cases were reported in a span of h. the number of deaths also had increased by a total of deaths to take the total tally for the region to , , and these were far much more than the total deaths of all other regions combined. on the same day, the united states reported , new cases to take their country's total to , (who, s) and also reported a high of deaths increasing the total deaths recorded in the country to , while other data showed that deaths had reached , (siobhán o'grady et al., a) . in the previous day (april ), it had reported cases and , new cases; the highest reported data in the region since the onset of the pandemic (who, a). as these occurred, president trump reported that hydroxychloroquine, an antimalaria drug, could be used against covid- (crowley et al., ) . in the middle east, the total number of confirmed cases in iran increased to , after more people tested positive. globally, the total confirmed cases stood at , , and the total deaths reported were , (who, s). in africa, where cases had started to increase significantlydreaching and deaths, it was reported that the former libya prime minister mahmoud jibril died of coronavirus the previous day after fighting the covid- disease for approximately weeks (aljazeera, d). in china, which reported new cases and only deaths, fears were that the country would be experiencing asymptomatic transmissions of the virus; hence, the increase in newly reported cases. these were experienced though the country had already introduced border restrictions with other countries, and following the fear of asymptomatic cases, the government vowed to tighten border control measures even further (zhang and munroe, ) . the most astonishing news reported on april was that of the positive testing for coronavirus of four tigers and three lions in the bronx zoo, bringing the total number of cats reported to have contracted the virus to (daly, ) . this raised alarms as no known research had shown that the virus could be passed from humans to animals. this far, a report by the who indicated that more than % (approximately . billion) of students globally have had to remain at home following the closure of school. to offer some intervention on this, the organization, together with unicef and the international publishers association, launched the "read the world" initiative to allow student access learning materials even during the difficult times (who, a). in the sporting sector, to safeguard the lives of participants and to comply with the health guidelines of social distancing and others, the open golf championship was called off; being the second time, it was canceled since during the ww (the open, ). after days of uncertainties, the chinese authorities finally lifted the lockdown on wuhan as promised, after the city successfully saw a reduction in the number of new confirmed cases for the coronavirus (aljazeera, a) . in fact, the report from the entire country was that the new cases that were being reported were all imported ones, and the government had vowed to take extra measures to control its borders (zhang and munroe, ) . the good news on the country is that on the previous day (april ), despite reporting new confirmed casesdwhich were all imported, the country reported zero death for the first time since it started publishing figures of the death related to covid- (who, b) . even on th, the number of new cases was only : all imported and only two deaths. the situation was, however, totally different in other regions, especially in europe where france, on a single day, reported new deaths to push its total death toll to , , while those whose tests turned positive in the past h increased by to take the country's total to , (who, t) . this total was however smaller compared to germany, italy, and spain whose totals had increased to , , , , and , cases, respectively. belgium and the netherlands also witnessed an increase in the number of deaths with and new recorded deaths, respectively (who, b). on this, despite germany having more confirmed cases, it had managed to keep the death toll relatively low, with reports showing that it is due to the mass testing initiative it had embarked on; thus, cases were getting identified before becoming critical (perrigo, ) . until eighth, it had only lost people, while its european counterparts were worse off (who, t) . the other nation that saw the number of casualty increase was the u.s, which, since a few days ago had started to witness numerous deaths, and confirmed cases. on this day, the country lost lives to the disease, and , were the newly confirmed cases taking the country's total to , , according to who data (who, t), but the uscdc reported the total number as , cases (cdc, ), where the difference could be due to difference in reporting time between who on central european time (cet) and us edt time zones. while this was happening, the country's president, donald trump who had frequently attacked the who for failing in its mandate in detecting the virus earlier threatened to withdraw funding to the agency (sevastopulo and manson, ) . he categorically said that the organization had withheld information about the virus and was wrong about the outbreak in china (davidson, a) . but, in a quick rejoinder, the who's director-general warned that it would be disastrous to politicize the fight against the pandemic (wise, ) . following the health situation in france, authorities announced that they were imposing a ban on daytime outdoor exercise in paris, which had allowed its citizens to enjoy despite the country being on lockdown (bbc, f). on the same day (april ), the egyptian authorities announced that the ban on mosques and churches would still continue even during the ramadan period as the country was still facing the challenge of coronavirus, with new cases increasing and more deaths being witnessed (egypt independent, ) . in the asian region, japan joined the list of many other countries who had declared a state of emergency as the number of cases in the country had started to rise in the month (rich et al., ) . in singapore, to contain the spread of the covid- , the health minister gan kim yong announced that the government was banning any form of social gathering whether at home or in public (zhang, ) . the ban came just a day after a motion to outlaw social gathering in the country was rushed and passed to the law in parliament the previous day. elsewhere, as the impacts of the virus continued to be felt, the wellness trust, on april , started an initiative aimed to raise a minimum of $ billion from the private sector by the end of april to fill the financial gap being experienced in search vaccines, drugs, and tests for covid- (wellcome, ) . a similar initiative dubbed "afrochampions initiative" was launched by african union and africa centres for disease control and prevention to raise over $ million for medical responses, with $ million required urgently for the same purpose (africanews, ) . after spending three nights in the intensive care unit, the uk prime minister boris johnson was finally discharged from the unit and transferred to a normal ward where he recovered. in fact, it was reported that he could manage short walks, though he needed some time to feel better (the sun, ) . while the report of his improvement was encouraging, it was not the case for over families in the country, from england who had lost their loved ones as a result of the disease on that particular day. in italy, a total of people lost their lives on th (who, h), while had died the previous day (who, u) . in total, the number of deaths in italy had reached a high of , by th with of these being doctors who had contracted the virus while in line of duty (aljazeera, g) . in spain, hopes of flattening the curve were high after the country saw a decline in the number of deaths for the third consecutive day (landauro and keeley, ) . however, the number of new cases in the country was increasing and had climbed to , cases after more cases were confirmed on th. the renewed hope was also being experienced in china after it continued to witness a reduced number of deaths in the country, as well as more recoveries, which had reached , (regencia et al., ) . while that was happening, the spread of the virus has gone as far as in deep rural areas where a -yearold boy from the indigenous tribe of yanomami found in brazil, amazon forest was confirmed with the coronavirus on t th, and on th, unfortunately, he passed away (phillips, ) . another rare place where the virus was reported was in the cook county jail in chicago where new cases involving inmates and staff were reported (whitcomb, a) . in america still, the number of death from covid- were increasing at an alarming rate, where new deaths were reported on th (who, h) and more had died the previous day (who, u). following these increases, with most of them coming from new york cities, the state had resulted in burials in mass graves as the numbers kept on increasing (anderson, ) , with its confirmed cases being more than any other country globally (bbc, d) . the situation in the united states prompted the german foreign minister to criticize the us handling of the virus (connor, ) . another rare place that was affected by coronavirus is a french navy airplane carrier, where servicemen tested positive to covid- (aljazeera, e) . as the cases globally increased to over . million people, the economic impact of the virus continued to bite. for instance, in the united states, another . million people filed for unemployment claims bringing the total number of those in the same predicaments into almost million in only weeks (long and dam, b) . in vietnam, it was reported that the country was in dire need of almost $ billion to caution its economy against the budget deficit that continued to widen (reuters, r) . albania was also trending on a tight economic path, prompting it to seek financial support from the imf, which extended a loan of $ . million (imf, ) . in zimbabwe, following the ban on all international flights in or out of the country, air zimbabwe sent its employees on leave, which was, unfortunately, unpaid (the herald, ). on the same continent, senegal adopted a directly opposite approach of protecting its workers against being laid off by companies in excuse of the covid- crisis (france-presse, ). on other news, there were reports that google and apple would cooperate to develop a mobile app that would help in tracking coronavirus spread (apple, ) . although that was good news especially coming from the tech world, in singapore, the use of technology faced concerns when online learning platforms that the government had initiated were suspended after the video conferencing zoom platform was hacked during a learning session, and the hackers displayed explicit images to the students (lee, ) . although the death tolls in at least four countries crossed the , mark, others have witnessed significant declines in the number of new cases being reported daily, and thus planning to ease lockdown stances and other strict measures that had been put in place. until april , countries like the united states ( , deaths), spain ( , deaths), italy ( , deaths), and france ( , deaths) were most affected, with the situation in the united kingdom worsening ( , ) (who, w). indeed, a report by the office for national statistics highlighted that uk numbers were underreported by %, the number in the country would be reading over , cases (bruce, ) . on this, it was highlighted that the number of deaths reported did not reflect the actual number represented in over care homes, where most of the elderly population were (mcintyre and duncan). although those numbers are many, there was hope in spain and italy as the number of deaths kept on decreasing each day, and from the report, these were optimistic that they would ease their stand on lockdowndspain by end of june (bbc, h). on this, other more countries including greece (by may ) (tugwell, ) , portugal (by may ), australia (had already started by then), pakistan, and austria (with already thousands of shops reopened (niesner and murphy, )) were considering this move (dw, ). although those countries were eager to lift lockdown measures, germany was considering reintroducing it after community infection cases over the past few days started to rise after the country had cautiously tried to ease the lockdown (mayberry et al., ) . in moscow, president putin strengthened the lockdown measures until may to counter the rising cases of infections (davidson, b) . similar measures were also being taken in china, in the heilongjiang province bordering russia, where cases were reported on april , where chinese nationals who had fled to russia tried to return home (wu, ) . following this, the cases in the province increased to , and chinese authorities in the province promised to reward locals who would report the "illegal migrants" (the straits times, b). georgia, on its part, was planning to lock down four of its largest cities, including its capital tbilisi for days as local transmission started to increase with the county's total cases reaching (who, w), an addition of more confirmed cases (who, v) . on the economic front, the imf warned that the global economy would shrink by approximately % following unprecedented measures like lockdowns, and ban on transportations, and closing down of manufacturing and other industries (rapperport and smialek, ) . in a way to ease the economic pressure, president donald trump started issuing stimulus checks to americans, amid some delays after he realized that his name did not appear on the checks (rein, ) . the situation of the economy is also pointed by activities in heathrow airports where passenger demands were expected to reduce by almost % this month (april), after having plummeted by % last month and cargo volume reduced by . % (rojas, ) . the economy was worsening also for the who after president trump retaliated that he was halting funds to the agency following its mismanagement of the coronavirus (mayberry et al., ) . on the societal fronts, the racial discrimination of blacks in china continued, with the mcdonald outlets in china forced to apologize after the store displayed posters banning black people from accessing the china store (folley, ) . elsewhere, turkey was planning to temporarily release over , inmates, after getting approval from parliament to ease overcrowding; thus, void the risk of coronavirus infection in the facilities (wilks, ) . as of th, covid- had spread to countries and territories across the globe with over , , confirmed cases and , deaths reported. of those cases and deaths, % were reported in europe, while more than % of the remaining cases ( , confirmed cases and , deaths) reported in regions of the americas. the eastern mediterranean region had , confirmed cases and deaths while the south-east asia region had a count of , confirmed cases and deaths. africa, which had started to experience some significant increase in infections, had , confirmed cases with of those newly reported and deaths of which of those occurred in a span of h (who, aa). still in africa, it was noted that out of the countries that had reported cases of covid- were drawn from the western and central part of the continent, and who officials reported that they had teams on the ground to establish the real reason why this was happening (who, ac) . of the total reported deaths, the highest number occurred in the united states with a high of deaths, while the united kingdom had the second tally of the day with cases. france had cases while italy and spain, two countries that had for past days shown remarkable improvement, had and cases, respectively (who, aa). on th, the french navy reported that an airplane carrier had soldiers affected, and in less than a week, on th, the number of those had increased to a total of (willsher and sabbagh, ). although reports in the health sector showed that the world was still unsafe, as had also been warned by the who, other issues were coming up in other sectors. for instance, in japan, whose total confirmed cases tallied to dwhich included three cabinet officialsd and the number of deaths increasing to , the prime minister shinzo abe declared a nationwide state of emergency (mccurry, ) . he also advanced a handout worth u , to every resident of the country regardless of their economic status to caution them during the period of this emergency (the japan times, a). in the united states, on the same day, . million people filed unemployment claims bringing the total number of those in this situation to more than million people in a period of only weeks (long, ) . following this, president donald trump unveiled guidelines aimed to help some economic activities in the country to resume, but he left the final decision of opening the economy, by easing the restrictions on each individual state, to the individual state governors (white house, ). in germany, after experiencing prior issues after easing lockdown measures resulted to increased number of confirmed cases, the government was planning to reopen the economy as from april by allowing some nonessential stores to open and also allowing schools to resume as from may (morris and beck, ). in brazil, president jair bolsonaro fired the minister for health after the minister insisted on strict social isolation guidelines, a move that the president was against. unfortunately, the president had been seen to have regularly downplayed the outbreak of the virus in his country despite the country having , confirmed cases and deaths by april (quinn, a) . in sports, following the situation in france, the tour de france scheduled for june and july was postponed to a tentative date between th august and th september, as the government banned public gatherings to reduce the spread of the coronavirus (tour de france, ). for world wrestling entertainment, the company was planning to lay off some employees including wrestlers and producers such as kurt angle (russell, ) . the move was to caution the company against the financial decline it was facing following the impacts of the pandemic. after months of extreme pressure, anxiety, and uncertainties, wuhan settled and revised its official data relating to the coronavirus. after the review, the death toll from the covid- pandemics increased by % meaning that its number increased from deaths to deaths, pushing the country total by april to deaths. the errors in reporting were attributed to delays, omissions, and incorrect reporting that are understandable following all the many things that are happening during that period (neuman, a) . the number of reported deaths also increased in the african continent after more deaths were reported, taking the total tally to , while new confirmed cases increased by , pushing the continent's total to , , according to africa centres for disease control and prevention (africa cdc) (xinhua, a) , but data by the who for the same period show a total of , cases and deaths (who, x) . death tolls were rising by higher margins in the european regions and had exceeded , deaths, from , , cases reported in the region. this increase, observed throughout spain and italy, however, continued to experience improvements with death rates reducing each day. the united kingdom, france, and belgium still reported increasing numbers of deaths ( , , and , respectively) . however, the united states still leads in the number of confirmed cases ( , on april ) and death tolls ( on the same day) per day for more than two consecutive weeks (who, x) . globally, the total number of cases had increased to a high of over . million, with the number of deaths exceeding , by april (who, x) . despite the risk of the disease being live, the orthodox churches in georgia were observed to flaunt the state of emergency declaration to hold easter masses, where hundreds of congregants attended (antidze, ) . in the united states, a day after the president had outlined a set of rules for reopening the economy, but left the final say on the hands of the governor, some protesters were observed in states of michigan, minnesota, and ohio and others, calling their governors to lift the restrictions in their states (gabbatt, ) . at the same time, texas governor is said to have signed an executive order to allow a reopening as from may (office of the texas governor, ). this was happening, even as the us secretary of defense extended the travel ban for one more month to void the earlier expiry scheduled for may ; thus, showing that the country was still not ready to ease the restrictions it had set. further south, in chile, the government started issuing "immunity cards" for all those who had infected and recovered from the virus. with the card, these could comfortably return to their work stations (thomson, ) . as this was happening, the number of cases in the country rose to , , taking the country as the third most affected in latin america (who, x) . however, the who, through dr. michael ryan, one of the executive directors, warned that there was no evidence that those who were recovering from covid- were developing any immunity that could prevent them from being reinfected (who, ab) . during the same press conference, the director-general emphasized that as chinese authorities allowed the wet market to reopen, they would ensure conformity to food safety and highest levels of hygiene and that the law banning any trade in wildlife for food was to be implemented strictly to save the world from future pandemics like the coronavirus (who, ab). elsewhere, more countries were slowly and cautious easing restrictions, with france allowing visitors to care homes, albeit some conditions (dodman, ). croatia also eased some restrictions allowing people to travel within their districts. in other countries such as the united kingdom and zimbabwe, the lockdown measures were to remain intact until when the government is confident the situations are controlled (today, b) . in saudi arabia, despite the start of ramadan, the top religious authorities of the country were recommending people to pray at home to reduce the spread of the virus among the faithful (reuters, p) . this was necessary, as already, deaths were not sparing countries' leadership. for instance, in nigeria, president buhari's chief of staff, abba kyari became the latest topranking official to die from covid- (akwagyiram, b) . a similar case was reported in guinea where a top official and ally of the president alpha condé also died (afp, a). within a period of h (april e ), the number of infections globally increased from . million cases to over . million, while the number of deaths increased to above , globally (reuters, g) . in europe, the number of those infected increased over this period to over . million, with a daily average increase of approximately , new cases, while the number of new deaths in the areas also increased by an average of above each daydtaking the total deaths in the region to , according to data by the who (who, y). in the american regions, cases increased by an average of , confirmations pushing the total confirmed cases to , cases (who, y). the number of deaths increased to approximately , by april , with a majority of these reported in the united states, which was the new epicenter for the coronavirus. the eastern mediterranean region had its total confirmed cases increase to , cases with people dying from covid- . the western pacific region had a total of , cases after new cases were confirmed while the number of deaths increased to . the south-east asia region and african regions, though have had their cases increase, have shown remarkable levels of resilience despite having some of the weakest health systems. their total confirmed cases increased to , and , cases, respectively, while the number of people who succumbed to the covid- in the regions increased to and deaths, respectively, (who, y) . following the unprecedented increase of infections in the united states, president donald trump had reported on april that he would be signing an executive order to suspend immigration to the united states for the next days. and, true to his word, on st, he signed the order meaning that green card recipients would be blocked from moving into the country, with only workers holding nonimmigrant visas allowed (nick miroff et al., ) . he supported his decision by arguing that the unprecedented effects on covid- had pushed many americans out of jobs, and he would wish to see them access the available job opportunities without having to compete with migrants (nick miroff et al., ) . and to ensure that job opportunities would be available, on the same day, his office and congressional leaders agreed on a $ billion small business and hospitals stimulus package, that now only awaited approval from the house of representatives (roberts, ) . in africa, south africa took a similar approach of bailing out the economy by unveiling a $ billion relief plan that would also aid the most vulnerable in the society during the period that the country was struggling with increasing cases of coronavirus and the lockdown measures (channelstv, ) . the economic struggles saw iran start to reopen its economy with major shopping centers in the capital tehran being the first (press, ) . similar actions were observed in israel, which eased lockdown restrictions to allow small shops and stores to open and allow people to move around, but on condition mask-wearing in public (haaretz, ) . this came as the number of recoveries in those countries started to increase, while the death toll contained (efrati and rabinowitz, ). in the poorest countries in the world, the world bank supported the pandemic bond, launched in , with an amount of $ . million to assist nations from the impacts of covid- (baker, ) . this came as the un world food programme warned that the impacts of covid- would result in the doubling of world hunger, representing a total of million people (anthem, ) . the economy was however not worsening for individuals only, but on this day, it was seen to have particularly worsened for us oil-producing economies and companies, with the prices per barrel going down to $ , a historical event that has never happened (suleymanova, ). the only sector that was seen to be doing well, especially in the united states is the gaming industry, probably due to the "stay-at-home" orders and also due to the closure of schools. but, while the market increased, there were fewer games produced due to the impacts sparked by the coronavirus (schreier, ) . the other sector that was seen to benefit from the impacts of covid- was the environment, where it was reported that following the reduced activities in the manufacturing and transport sector, less emissions ( % drop) are expected during the year (marchand and faigle, ). as over countries continued to fight the spread, and the impacts of covid- in their countries, the united states was the most hit with over , cases and over , reported deaths as up to april . the new cases in the country had increased at an average number of approximately , (cdc, ). as the number of cases continued to increase, and other more "staying-at-home" measures following the lockdowns in different states, the number of those filing for unemployment claims continued to increase with over . million additional claims reported over the past week, which was the fifth consecutive week since this trend started (lambert, ) . these new numbers raised the total of those who had filed for their employment benefits to over million people (chaney and guilford, ) . outside the united states, there were mixed responses to the virus. some were seen to ease and lift the lockdown and subsequent measures they had implemented, while others were seen to be in haste to institute those measures. for instance, in the netherlands, after experiencing some "relative calm" over the past weeks in respect to infections in the country, its number had started to rise with new deaths averaging over each day and reaching a high of deaths and , confirmed cases by april (who, z). to minimize further infection, a stern decision was taken to ban any form of public gather until september ( months extension) the first of such a ban globally. that means that events such as sports, music festivals, and religious grouping would not be resuming anytime soon (reuters, e) . but, it was not the only one extending such measure as in pakistan, the lockdown was extended by two more weeks until may , as the country was still experiencing increasing numbers of local transmission of the virus, and the lockdown extension would somehow reverse these trends (cherian, ) . indonesia also joined the list of those that were strengthening their measures after the government announced that it would be temporarily suspending nonessential domestic and international air and sea travel until the end of may to curtail the spread of the coronavirus in the country (bangkok post, ) . others that extended their lockdown include liberia (garda, ) , lebanon (reuters, k) , and czech, which sought parliamentary intervention to allow the extension of the state of emergency until may (xinhua, b) . on the same breath, some countries and states in the united states started easing restrictions to allow the reopening of their economy. these include states such as georgia, oklahoma, and others in the united states, which took these decisions despite the disapproval of president trump (smith, ) . belgium was ready to start reopening some businesses and schools as from may, but gradually and cautiously (martens, ) . although countries were reacting to covid- situations in different ways, some unfortunate news besides new cases and deaths were also reported. for instance, in the united kingdom, which had seen the confirmed cases increase significantly and the number of deaths rising to beyond , there were reports that among the dead were national health service personnel who had paid the ultimate price in a bid to save their country from the pandemic (express and star, ) . in bangladesh, it was reported that frontline doctors had tested positive for the coronavirus due to strains that the covid-i had put on the healthcare system, with most of those in the frontline experiencing a shortage of ppes, test kits, and hospital beds, among other basic essentials (mahmud, ) . elsewhere in japan, after a dreadful experience with the diamond princess cruise ship, on st, another fateful incidence involving an italian cruise ship (costa atlantica) happened in nagasaki shipyard (the japan times, b). it started when one of the crew members tested positive for coronavirus, while of his colleagues were also showing signs, especially high fever. the following day, after contact tracing from the first confirmed cases, another cases tested positive (the straits times, a). h later, another people tested positive (kaneko and kim, ) and by th, a total of people; all crew members were confirmed as testing positive (cna, b) . following this, the japanese government stated that it would test people, out of the who were on board the cruise ship and those who turned negative would be repatriated back to their home countries. as the fifth month, since the onset of the coronavirus, is almost over, the number of those confirmed to have contracted the virus increased to over million people globally, and at least , were reported to have succumbed to the disease. over the same period, of the million, over , patients had recovered (spotlight, ). one country where success against covid- have, and continued to be celebrated, was in wuhan, hubei province, china, where healthy officials reported that they had treated all cases and those who recovered were discharged from hospital (o'donnell, ) . in fact, as previously reported, the restrictions and lockdown in the provinces were lifted including in wuhan, on april (aljazeera, a) . following this, on rd, china pledged additional funding, amounting to $ million, to the who (shih, ) , as already, it could manage the few cases emerging, and the funds could help other areas that were experiencing high pressure from the pandemic. in the new cases, between th and th, china was reported to have only recorded a total of new cases and asymptomatic cases, but no death was reported in the days (who, i). as cases in china reduced, those in the european region seemed to have continued increasing reaching a high of , , cases after the addition of , new cases on th, and the number of deaths increased to , . in the american region, the number of cases was , , and , deaths reported, according to data by the who (who, i). the eastern mediterranean, western pacific, and south-east asia regions had , , , , and , confirmed cases, respectively. the african region continued to show high levels of resilience with only , confirmed cases and deaths reported (who, i). but as the number of cases continued to increase, reports of more countries planning to ease up the lockdown also increased. as of th, italy and spain, two of the most affected countries by the covid- pandemic, with cases of death in each exceeding , (italy , deaths, spain , ) unveiled plans of how they would open up their country as from may . in italy, according to prime minister giuseppe conte, the manufacturing industry would gradually open as from may , but schools would remain closed for three more months until september (kayali, ) . in spain, people would be allowed to walk out for physical activities, but social distancing will have to be observed, as infections in the country were still real (reuters, q) . saudi arabia is another country that considered lifting the nationwide curfew, except for mecca, which remained under -h curfew (aljazeera, h). in germany, after easing the restrictions a few days ago, it is reported that volkswagen was gearing to resume production in their wolfsburg factory on april (allan, ) , the same decision was also taken by bmw company and other companies such as mercedes, jaguar land rover, and others reopening in a few days (reuters, f) . this came as some protests were witnessed in berlin as people demanded the easing of lockdown measures to allow them to return to work (reuters, d) . in the united states, as some states started reopening businesses, the airline industry, which was yet to resume, received support funds amounting to $ . billion -taking their bailout total from the us treasury to $ . billion, with the first disbursement received on april (landay and shephardson, ) . although those countries were gearing to resume business, others insisted on strict measures as cases continued to rise. for instance, the united kingdom maintained the lockdown as it was still not safe from the virus infections (bbc, i). sri lanka also extended the lockdown in the country to counter the increasing number of cases (afp, b). honduras was even considering extending the lockdown by at least one more week until may (reuters, h) . in india, prime minister modi urged his citizens to piously adhere to the nationwide lockdown to contain the rising cases that came amid the month-long curfew (the straits times, d). by april , it became official that the number of covid- infection cases had exceeded the million (the who reported . million cases and , deaths) people and caused the death of over , people globally. of the confirmed cases, over million were reported in the united states while a quarter of reported deaths from the virus coming from the united states. the number of deaths in the country ( , ) even surpassed the total of those who died during the vietnam war between and , where nearly , people died (woodward, ) . in new york, it was reported that for every four people, one of them had contracted the coronavirus. this is after almost , cases had been confirmed, and more than , deaths were reported in the city alone. these numbers in the united states eclipse those of other reported regions. for instance, as of th, the total number of reported cases in africa ( , ) was far much less than the total number of deaths ( , ) reported in the united states on the same day. in addition, they were more than the total number of deaths ( , ) in italy and the united kingdom, which were leading in terms of reported deaths in europe (worldometer, ) . to reduce these unprecedented trends, some states in the united states started testing for asymptomatic residents such as delivery drivers, rideshare drivers, and others. this came as most of the states were planning to reopen by easing the lockdown restrictions, amidst opposition from president trump, and the latest, judge clay jenkins of dallas county, who mentioned the solution, for now, was to follow science and people to stay at home (holcombe, ) . besides the united states, other countries that are yet to experience some reductions in a number of cases include russia, where president vladimir putin stated that the country was bracing for a new and grueling phase of the pandemic (llyushina, ) . his statement came at a time when the number of confirmed cases had continued to stabilize, and the country performed significantly well to reduce casualties. italy, though determined to ease its lockdown restrictions, was experiencing some new cases, with its numbers reaching beyond the , mark. according to the who, africa, eastern europe, latin america, and parts of asia were still not yet out of risk; hence, caution was required even as some actions such as easing the restriction were being taken. this came as eu experts warned that the world would have to wait longer for the vaccine, which would not be ready until the end of , especially considering the cost implications, and other processes that have to be accomplished (cullen, ) . in relation to this, in new york city, it was reported that medical personnel had started testing famotidine; an over-thecounter heartburn medication could cure covid- (lentile, ) . this came as human trials had also started in germany where biontech, a pharmaceutical company was testing its vaccine on volunteers, with participants already having received the dose as from april (aljazeera, f) . as solutions for the covid- continued to be sought, some diplomatic disharmony was witnessed when india canceled orders for , rapid test kits from china after claiming that they were "faulty," and also went forth to withdraw some of the kits that were already in use in several states (bbc, b) . china responded harshly and claimed that it was unfair and irresponsible for india to label chinese products as "faulty" (business today, a). in sports, following the unseen end for the pandemic, french authorities stated that there was no hope for "big sporting affairs" to come back until september in the years, thus, throwing the french football season in disarray, thus, causing them to be canceled (aarons and lowe, ) . the cancellation came as other countries like germany had already announced that the football season (bundesliga) would return in a date to be confirmed albeit under closed doors (bassell, ) . regarding the olympics, the olympics international committee stated that it would cancel the event coming in the next year if the pandemic would not have ended (schad, ) . olympics must be delayed to ensure french football season will not resume but la liga has new hope of restart adb to provide $ million to support strained supply chains in fight against covid- african development bank launches record breaking $ billion "fight covid- leading member of guinea government dies from coronavirus sri lanka extends virus lockdown coronavirus e africa: african union and african private sector launch covid- response fund nigeria orders -day cessation of movement in lagos, abuja to fight coronavirus nigerian president's chief of staff dies from coronavirus china's wuhan ends coronavirus lockdown but concerns remain coronavirus: travel restrictions, border shutdowns by country curfew in mecca, medina extended to hours over coronavirus former libya prime minister mahmoud jibril dies from coronavirus france reports covid- cases on board aircraft carrier germany company begins human trials of coronavirus vaccine one hundered italian doctors have died of coronavirus saudi arabia partially lifts curfew except in mecca volkswagen restart production as european car factories reopen burials on new york island are not new, but are increasing during pandemic risk of hunger pandemic as covid- set to almost double acute hunger by end of hundreds of parishioners attend orthodox easter vigil in georgia apple and google partner on covid- contact tracing technology ( ) china to end lockdown of coronavirus-hit hubei province; wuhan to open next month moscow shuts down all non-essential shops & restaurants to stop spread of covid- trudeau says canada will return asylum seekers to fda authorizes -minute coronavirus test poorest countries finally set to get world bank pandemic bond funds indonesia bans air, sea travel until june over virus fears world bank group president malpass: remarks to the development committee bundesliga return in may now looks inveitable but fans far from happy coronavirus travel: china bars foreign visitors as imported cases rise coronavirus: india cancels order for "faulty coronavirus: italy extends emergency measures nationwide coronavirus: new york has more cases than any country bbc. ( e) coronavirus: new zealand announces lockdown coronavirus: paris bans daytime outdoor exercise coronavirus: prime minister boris johnson tests positive coronavirus: spain plans return to 'new normal' by end of coronavirus: uk must find 'new normal' to ease lockdown e raab formula e: china race called off amid coronavirus outbreak wuhan eases quarantine as coronavirus cases in us pass , singapore closes borders to keep virus at bay, but no shutdown bill & melinda gates foundation, wellcome, and mastercard launch initiative to speed development and access to therapies for covid- uk coronavirus death toll could be far higher than previously shown coronavirus crisis: china fumes over icmr clampdown on 'faulty' rapid testing kits, calls it 'unfair business today. ( b) coronavirus outbreak: india bans international flights till suspends season after player tests positive for coronavirus senate unanimously passes $ t coronavirus stimulus package it's a wreck': . million file unemployment claims as economy comes apart coronavirus disease : cases in the us china's first batch of schools reopens in qinghai province available at south africa president ramaphosa unveils $ bn covid- relief plan coronavirus: who head says nations must attack as 'pandemic is accelerating europe's hospitals among the best but can't handle pandemic pakistan extends lockdown for days, until may south korea throws up innovative tech solutions in coronavirus fight. available at: straitstimes. com/asia/east-asia/south-korea-throws-up-innovativetech-solutions china's imported covid- cases spike as fears grow of second wave covid- tally rises to on italian cruise ship in japan cruise ship stranded by covid- fears to dock in cambodia spain impose nationwide lockdown due to virus, closes all stores except groceries and pharmacies trump address sparks chaos as coronavirus crisis deepens germany's maas: trump coronavirus response took 'too long ignoring expert opinion, trump again promotes use of hydroxychloroquine coronavirus vaccine won't be ready until end of under "most optimistic seven more big cats test positive for coronavirus at bronx zoo donald trump stokes fresh coronavirus row as wuhan reopens global covid- cases near million as putin warns russia faces 'extraordinary' crisis devil's dilemma': france lifts ban on nursing home visits as some warn against relaxing rules coronavirus: what are the lockdown measures across europe? available at map: coronavirus and school closures israel reverses the trend: more coronavirus recoveries than new cases mosques to remain closed, charity iftar tables banned in ramadan negotiations intensify on capitol hill over massive stimulus legislation as coronavirus fallout worsens applications welcome from startups and smes with innovative solutions to tackle coronavirus outbreak commission publishes guidance on export requirements for personal protective equipment the nhs workers who have died during the coronavirus pandemic mcdonald's apologizes after store in china displayed sign banning black people trump signs historic $ trillion stimulus after congress passes it friday senegal bans layoffs during coronavirus crisis cuba closes borders to non-residents over virus: president lebanon announces two-week lockdown over coronavirus us anti-lockdown rallies could cause surge in covid- cases, experts warn cruise ship docks in mexico, passengers allowed to disembark after being denied entry in jamaica, cayman islands amied coronavirus fears cepi invests $ , into potential covid- vaccine from university of hong kong european union leaders denounce trumps coronavirus travel restrictions liberia: president extends lockdown measures for two weeks from april /update foreign travel advice: italy uk helps world's poorest countries withstand the economic disruption of coronavirus latest guard update: more than , troops mobilised for covid- response a fine for not wearing a mask: these are israel's new coronavirus regulations bolsonaro defies coronavirus to rally against congress coronavirus: iran release , prisoners in bid to tackle spread of virus trump invokes defense production act to force gm to make ventilators dallas county judge opposes governor's plan to reopen and calls for residents to follow science and stay home fact sheet: dhs notice of arrival restrictions on china, iran and certain countries of europe together we can with the war against covid- ) imf executive board approves us$ . million in emergency support to albania to combat italian cruise ship in japan has coronavirus cases italy and spain announce plans to ease coronavirus lockdowns further cepi approves $ . m in additional funding for coronavirus vaccine research, bringing total to $ how new york became the epicenter of america's coronavirus crisis ventilators are to this war what missiles were to world war ii un headquarters closes to public as coronavirus precaution real unemployment rate soars past %dand the u.s. has now lost . million jobs spain sees slowing coronavirus toll, holds virtual easter parades airlines receive extra $ . billion in payroll support singapore stops zoom for home-schooling after hacking report famotidine trial underway in nyc for covid- treatment trump declares national emergency e and denies responsibility for coronavirus testing failures russia will "face a new and grueling phase of the pandemic now has million unemployed, wiping out a decade of job gains america is in a depression. the challenge now is to make it short-lived america is in a depression. the challenge now is to make it short-lived hundreds of doctors in bangladesh infected with coronavirus coronavirus: beijing's ban on foreign travellers comes into force months after it criticised other countries for 'isolating china will coronavirus reduce emissions long term? available at belgium to gradually ease virus lockdown in first half of may covid- therapeutics accelerator awards $ million in initial grants to fund clinical trials coronavirus crisis 'like no other' as cases near m: live updates stocks plunge % in dow's worst day since japan declares state of emergency over coronavirus care homes and coronavirus: why we don't know the true uk death toll as virus spreads, africa gets medical supplies from chinese billionaire the dow jones had its biggest point drop in history monday angela merkel's first coronavirus test result is negative panama suspends domestic flights to curb the spread of coronavirus: civil aviation authority germany to reopen schools, shops after 'fragile' success egypt shuts mosques and churches over coronavirus fears china raises wuhan death stats by half to account for reporting delays and omissions goes into -week lockdown trump to suspend immigration to u.s. for days, citing coronavirus crisis and jobs shortage austria reopens thousands of shops in first loosening of coronavirus lockdown nearly % of americans have been ordered to stay at home office of the president. ( a) letter from president donald remarks by president trump and vice president pence at a coronavirus briefing with health insurers governor abbott issues executive order establishing strike force to open texas coronavirus-press-conference- apr .pdf?sfvrsn¼ bd c cd_ cuba is going under lockdown over coronavirus concerns italy joins germany in prolonging lockdown to quell outbreak covid- : how a phone app is assisting south korea enforce self-quarantine measures why is germany's coronavirus death rate so low? available at first yanomami covid- death raises fears for brazil's indigenous peoples spain to extend coronavirus state of emergency as deaths soar connecticut becomes latest state to postpone primary as coronavirus spreads iran begins to open its economy despite fears of second wave of infection brazil's populist president ousted his respected health minister while continuing to downplay the coronavirus pandemic italy's coronavirus death toll surpasses china's japanese pm and ioc chief agree to postpone olympics until ) i.m.f. predicts worst downturn since the great depression states have declared a state of emergency due to coronavirus global coronavirus death toll exceeds , : live updates unprecedented move, treasury orders trump's name printed on stimulus checks austrian joblessness hits record despite government bit to avoid layoffs bolivia postpones elections, announces nationwide -day quarantine to stem spread of coronavirus china's coronavirus epicenter reports just five cases, beijing tomb-sweepers urged to stay back dozens of protesters were arrested in berlin on saturday for flouting lockdown rules and staging a demonstration against lockdown measures dutch extend ban on major public events until sept europe restarts car factories amid uncertain demand global coronavirus cases pass . million as u.s. tally surpasses , honduras extends coronavirus curfew by one week to may italy's coronavirus lockdown measures to be extended to april : minister kazakhstan, uzbekistan close borders after first coronavirus cases kazakhstan-uzbekistan-close-borders-after-first-coronaviruscases-iduskbn ex lebanon advised to extend coronavirus lockdown to may mexico declares health emergency as coronavirus death toll rises nigeria closes land borders to fight coronavirus spread pakistan suspends internationa flights for two weeks portugal to treat migrants as residents during coronavirus crisis saudi top religious authority recommends home prayers in ramadan amid coronavirus spain to allow outdoor exercise if coronavirus cases contine to fall vietnam in talks to borrow $ billion as budget deficit seen widening japan declared a coronavirus emergency. is it too late? available at us senate approves $ bn funding for small businesses rockefeller foundation. ( ) the rockefeller foundation commits $ million in covid- assistance coronavirus: heathrow passenger demand to fall by more than % in april prince albert ii of monaco test positive for coronavirus the coronavirus map in spain: , dead and more than , infected wwe announces layoffs two days after florida deems company an 'essential business tokyo olympics will be canceled, not delayed, if coronavirus pandemic still poses threat in as italy covid- cases soar, who tackles ppe, test shortages gaming sales are up, but production is down donald trump threatens to freeze funding for who new york city public schools to close to slow spread of coronavirus trump extends social distancing guidelines through end of april china pledges additional $ million funding for world health organization india extends ban on international flights until airlines seek $ billion coronavirus aid package coronavirus deaths surpass , , hhs watchdog says american hospitals face 'severe' shortages of equipment, staff and tests china reports zero new local coronavirus infections; trump signs bill to ensure paid leave, other financial benefits too soon': trump disagrees with georgia governor's decision to reopen businesses coronavirus deaths in italy up by in a day to , global death toll from coronavirus tops greece to go into coronavirus-induced lockdown crash! us crude futures turn negative for first time in history white house expected to urge americans to wear face coverings in public to slow spread of coronavirus government bans exports of certain masks, ventilators, raw material for masks zimbabwe shuts borders after first coronavirus the herald. ( ) breaking: air zim sends workers on unpaid leave japan to declare nationwide state of emergency as virus spreads the japan times. ( b) one crew member tests positive, feverish on cruise ship in japan. available at the nation. ( ) pm announces pm to am nationwide curfew gives new guidelines, new york to close restaurants and schools and italian deaths rise the new york times. ( b) u.s. now leads the world in confirmed cases. available at statement from the r&a/the open in to be cancelled china reports newly imported covid- cases and one in wuhan cases-on-cruise-ship-docked-fo r-repairs. the straits times. ( b) china tightens russian border checks, approves experimental coronavirus vaccine china's imported coronavirus cases soar, no local transmission for third straight day the straits times. ( d) indian pm modi urges citizens to follow lockdown as coronavirus cases rise boris johnson's move from intensive care to a general ward is the lift britain needed world bank group increases covid- response to $ billion to help sustain economies world's first covid- immunity cards are coming to chile more than million people tested for coronavirus in us, but access varies from state to state georgia proposes -day lockdown of four cities including capital uk not thinking of easing virus lockdown measures yet: minister the tour de france greece to gradually start lifting lockdown measures on may . available at: greece to gradually start lifting lockdown measures on key cop climate summit postponed to 'safeguard lives secretary-general's remarks at launch of global humanitarian response plan for covid- african finance ministers call for coordinated covid- response to mitigate adverse impact on economies and society a global approach is the only way to fight covid- , the un says as it launches humanitarian response plan coronavirus: boston celtics guard marcus smart tests positive for covid- chinese businessman to donate , test kits and million masks to the world health organization has distributed . million coronavirus lab tests around the world global covid-zero initiative launched to fill $ bn shortfall for coronavirus response chicago's largest jail reports inmates, staff positive for coronavirus two los angeles lakers players have tested positive for covid- , team says president donald j. trump is beginning the next phase in our fight against coronavirus: guidelines for opening up america again australia bans overseas travel and extends social restrictions situation report - . available at who. ( b) coronavirus disease (covid- ): situation report - . available at who. ( c) coronavirus disease (covid- ): situation report - . available at who. ( d) coronavirus disease (covid- ): situation report - . available at who. ( e) coronavirus disease (covid- ): situation report - . available at who. ( f) coronavirus disease (covid- ): situation report - . available at who. ( g) coronavirus disease (covid- ): situation report - . available at who. ( h) coronavirus disease (covid- ): situation report - . available at who. ( i) coronavirus disease (covid- ): situation report - . available at who. ( j) coronavirus disease (covid- ): situation report - . available at who. ( k) coronavirus disease (covid- ): situation report - . available at who. ( l) coronavirus disease (covid- ): situation report - . available at who. ( m) coronavirus disease (covid- ): situation report - . available at who. ( n) coronavirus disease (covid- ): situation report - . available at who. ( o) coronavirus disease (covid- ): situation report - . available at who. ( p) coronavirus disease (covid- ): situation report - . available at who. ( q) coronavirus disease (covid- ): situation report - . available at who. ( r) coronavirus disease (covid- ): situation report - . available at who. ( s) coronavirus disease (covid- ): situation report - . available at who. ( t) coronavirus disease (covid- ): situation report - . available at situation report - . available at coronavirus disease (covid- ): situation report - who. ( w) coronavirus disease (covid- ): situation report - . available at who. ( x) coronavirus disease (covid- ): situation report - . available at who. ( y) coronavirus disease (covid- ): situation report - . available at who. ( z) coronavirus disease (covid- ): situation report - . available at who. ( aa) coronavirus disease (covid- ): situation report - . available at who. ( ab) covid- virtual press conference. available at who. ( ac) opening statement who director-general's opening remarks at the media briefing on covid- e who director-general's opening remarks at the media briefing on covid- e who director-general's opening remarks at the media briefing on covid turkey to free one-third of its prisoners to curb coronavirus ebrd unveils v billion emergency coronavirus financing package inquiry after of french aircraft carrier's crew catch coronavirus coronavirus: nuggets report member of organization tested positive for covid- who chief warns against 'politicizing' coronavirus unless 'you want to have more body bags world food programme. ( ) statement from wfp executive director david beasley report coronavirus cases remote chinese city hit by coronavirus after weeks of feeling safe africa's covid- death toll hits , , as confirmed cases rise to czech parliament oks extending state of emergency until except wuhan, china's hubei reopens domestic flights what the u.s. needs to do today to follow south korea's model for fighting coronavirus how taiwan is containing coronavirus despite diplomatic isolation by china three members of the philadelphia ers organization test positive for coronavirus china sees rise in asymptomatic coronavirus cases, to tighten controls at land borders key: cord- -qwh inx authors: mendoza, jose luis accini; estrada, victor hugo nieto; lópez, nelly beltrán; bolaños, elisabeth ramos; franco, daniel molano; castell, carmelo dueñas; moreno, albert alexander valencia; amaya, iván camilo alarcón; flórez, john serna; valencia, bladimir alejandro gil; camilo pizarro, g; polo, yulieth maría zabaleta; meza, carmen lucia chica title: actualizacion de la declaraciÓn de consenso en medicina critica para la atenciÓn multidisciplinaria del paciente con sospecha o confirmaciÓn diagnÓstica de covid- date: - - journal: nan doi: . /j.acci. . . sha: doc_id: cord_uid: qwh inx antecedentes y objetivos: la enfermedad por coronavirus de (covid- ) es una enfermedad ocasionada por el nuevo coronavirus del síndrome respiratorio agudo grave (sars-cov- ). se identificó por primera vez en diciembre de en la ciudad de wuhan, en los meses siguientes se expandió rápidamente a todos los continentes y la organización mundial de la salud (oms), la reconoció como una pandemia global el de marzo de . la mayoría de los individuos son asintomáticos pero una baja proporción ingresan a cuidados intensivos con una alta morbilidad y mortalidad. este consenso tiene como objetivo actualizar la declaratoria inicial emitida por la asociación colombiana de medicina crítica (amci) para el manejo del paciente críticamente enfermo con covid- dentro de las áreas críticas de las instituciones de salud. métodos: este estudio utilizó dos técnicas de consenso formal para construir las recomendaciones finales: delphi modificada y grupos nominales. se construyeron preguntas por la estrategia pico. grupos nominales desarrollaron recomendaciones para cada unidad temática. el producto del consenso fue evaluado y calificado en una ronda delphi y se discutió de forma virtual por los relatores de cada núcleo y los representantes de sociedades médicas científicas afines al manejo del paciente con coid- . resultados: expertos nacionales participaron en la actualización del consenso amci, especialistas en medicina critica y cuidados intensivos, nefrología, neurología, neumología, bioeticistas, medicina interna, anestesia, cirugía general, cirugía de cabeza y cuello, cuidados paliativos, enfermeras especialistas en medicina crítica, terapeutas respiratorias especialistas en medicina crítica y fisioterapia, con experiencia clínica en la atención del paciente críticamente enfermo. la declaratoria emite recomendaciones en los ámbitos más relevantes para la atención en salud de los casos de covid- al interior de las unidades de cuidados intensivos en el contexto nacional de colombia. conclusiones: un grupo significativo multidisciplinario de profesionales expertos en medicina crítica emiten mediante técnicas de consenso formal recomendaciones sobre la mejor práctica para la atención del paciente críticamente enfermo con covid- . las recomendaciones deben ser adaptadas a las condiciones específicas, administrativas y estructurales de las distintas unidades de cuidados intensivos del país. background and objectives: the coronavirus disease (covid- ) is caused by the new severe acute respiratory syndrome coronavirus (sars-cov- ). it was first identified in december in wuhan, china. in the following months it spread quickly to all continents and was recognised as a global pandemic by the world health organization (who) on march th, . most cases of infection remain asymptomatic, while a low proportion require intensive care, experiencing high morbidity and mortality. this consensus aims to update the initial statement issued by the colombian association of critical medicine (amci) for the management of the critically ill patient with covid- within the critical areas of health institutions. methods: this study used two formal consensus techniques to construct the final recommendations: modified delphi and nominal groups. questions were constructed using the pico strategy. recommendations for each thematic unit were developed by nominal groups. the consensus product was evaluated and qualified in a delphi round, and was discussed virtually by the speaker of each nucleus, as well as the representatives of scientific medical societies related to the management of the patient with covid- . results: a total of national experts participated in the update of the amci consensus, all specialists in critical and intensive care medicine, nephrologists, neurologists, chest physician, bioethicists, internal medicine specialists, anaesthetists, general surgeons, head and neck surgery, palliative care, nurses specialised in critical medicine, respiratory therapists specialised in critical medicine and physiotherapy, with clinical experience in the care of critically ill patients. this update issues recommendations in the most relevant areas for health care of covid- patients within the intensive care units, contextualised for colombia. conclusions: a significant multidisciplinary group of professionals, who are experts in critical medicine, reviewed and issued recommendations on best practice for the care of critically ill patients with covid- through formal consensus techniques. recommendations must be adapted to the specific, administrative, and structural conditions of the different intensive care units in the country. para la actualización de la declaratoria se utilizaron dos técnicas para el desarrollo de consensos de tipo formal, técnica delphi modificada y grupos nominales. un consenso formal permite integrar las opiniones de un colectivo de expertos que están expuestos a un tema específico (experto afectado) con la mejor evidencia científica disponible, utilizando técnicas que permitan reducir los sesgos de subjetividad. la técnica delphi es una metodología que plantea enviar cuestionarios a un grupo de expertos, para que califiquen una serie de recomendaciones en rondas reiteradas con retroalimentación de los resultados y respuestas anónimas, la técnica delphi empleada fue modificada, variante a la versión original propuesta por la corporación rand en , pero se mantuvo las ventajas de la técnica, la iteración y retroalimentación para reflexión de las propias opiniones. los grupos nominales es una técnica que reúne a un grupo de expertos bajo la coordinación de un facilitador para evaluar y calificar información o preguntas ( , ) . para la actualización se convocó grupos nominales con expertos multidisciplinarios cada uno con un líder o jefe de núcleo. los grupos construyeron las preguntas por metodología pico y desarrollaron progresivamente las recomendaciones hasta las versiones finales. el proyecto se desarrolló en fases, fase : formulación del problema y socialización; fase : elaboración de las preguntas, fase : formulación de las recomendaciones y ronda de calificación. las estrategias de búsqueda se desarrollaron en bases de datos especializadas (medline, embase, lilacs, central), en las circunstancias donde no se encontró evidencia directa, se utilizó y se adaptó evidencia indirecta del tópico relevante en el paciente críticamente enfermo general. expertos con un promedio de años de experiencia en la atención del paciente crítico evaluaron y calificación las recomendaciones en la metodología delphi mediante un cuestionario distribuido por medio de correo electrónico, respetando la política de privacidad de datos vigente. recomendaciÓn se recomienda que los prestadores de servicios de acuerdo con su infraestructura física y la disponibilidad de recursos (tecnológico, humano, de interdependencia y apoyo) definan su modelo de atención para pacientes con covid- en estado crítico basado en principios de factibilidad, efectividad, seguridad y la relación entre la demanda (momento epidemiológico) y capacidad/capacidades de respuesta:  modelo . atención de pacientes con sospecha o confirmación diagnóstica covid- . este enfoque permite concentrar, optimizar y racionalizar recursos y reducir el riesgo potencial de contagio al equipo de atención, de apoyo y de pacientes.  modelo . atención mixta, de pacientes con y sin diagnóstico de covid- , en escenarios que cuentan con unidades de aislamiento normatizados (presión negativa y > -renovaciones completas de aire por hora) soportado en el documento institucional de gestión organizacional y operativo del servicio de cuidados intensivos, descrito en los procesos prioritarios. amci ® menos accidentalidad y violencia). la reducción de procedimientos quirúrgicos complejos electivos es una opción razonable condicionado a las posibilidades del paciente. sin embargo, situaciones como la progresión y descompensación de las patologías crónicas asociadas a las medidas de restricción social puede plantear un efecto bumerang con mayor demanda de camas de uci. con base en las predicciones simuladas de las tasas esperadas de ingreso a uci de pacientes con covid- contrastado con el déficit de servicios y camas de cuidados críticos en el país a partir de la capacidad instalada se han planteado fases de desarrollo cuyas características en términos de servicios, recursos y cronología se aprecian en la ilustración y .  fase (para el gobierno nacional: ampliación de la capacidad instalada*). parte de la liberación de camas de cuidados intensivos destinadas para atención covid- bajo el modelo y/o . la liberación de camas y servicios con mínima adaptación es la fase más inmediata y resolutiva que debe acogerse a la exigencia normativa (resolución de ), en la que se espera menos mortalidad, morbilidad y tasa de complicaciones asociados con la atención de pacientes con covid- en estado crítico.  fase (optimización para el gobierno nacional*) representan el reordenamiento de las camas de cuidados intermedios adultos en camas de cuidados intensivos y de hospitalización en intermedio. de adultos. el gobierno nacional toma en cuenta la ampliación de la capacidad instalada hospitalaria descrita en el plan territorial. para esta fase se necesitan equipos de ventilación mecánica (excluidos por la norma de estos servicios), monitoreo básico y avanzado y un número mayor de talento humano multidisciplinario competente. amci ® acuerdo con las etapas ( - ) y los perfiles requeridos priorizados como primera, segunda y tercera línea de respuesta*. en la ilustración podemos observar que avanzar de las fases a se va a necesitar mayor intervención en términos de organización, planeación operativa, formación por competencias y apoyo por telesalud (teleapoyo o teleexperticia). el personal no especializado o especializado de servicios hospitalarios diferente a urgencia, quirófano o uci pueden constituir grupos de apoyo para la gestión administrativa y de índole humanitaria (líneas de respuesta) la integración de estos requerimientos adaptativos se ha puesto de manifiesto en la experiencia del centro médico new york -presbyterian weill en la ciudad de nueva york, en donde la demanda de camas de unidades de cuidados intensivos (uci) y ventilación mecánica excedió su capacidad.( ) se recurrió a los quirófanos y de recuperación las cuales no estaban en uso porque los procedimientos electivos habían sido pospuestos. se hicieron adecuaciones físicas para garantizar la vigilancia continua de los pacientes y la seguridad del equipo de atención. se capacito a todo el personal de cuidado perioperatorio disponible y fueron distribuidos en las áreas recién configuradas. las enfermeras familiarizadas con las máquinas de anestesia asumieron como terapeutas respiratorios y los intensivistas de anestesia supervisaban estas unidades. recomendaciÓn se recomienda la adopción de un modelo simulado de predicción (basado en el cociente de fatalidad, tasa de ingreso a uci y el número de reproducción ro) para proyectar, de manera anticipada las necesidades de recurso físico, tecnológico y humano de cuidados críticos en fase de preparación de la pandemia por covid- . las tomas de decisiones relacionadas con el fortalecimiento de la capacidad/capacidades de la oferta de cuidados críticos (habilitadas o adaptadas) pueden deducirse mediante la aplicación de modelos matemáticos que intentan, desde la dinámica epidemiológica, establecer el efecto simulado de las medidas de mitigación o supresión adoptadas sobre la tasa de contagio a través del tiempo. con ello se busca planear el uso de recursos e implementar acciones de prevención y de distanciamiento social más eficientes, así como establecer las necesidades en materia de cama de cuidados críticos (intensivos e intermedios) habilitadas o adaptadas en áreas de expansión y con ello los recursos resolutivos como tecnologías, interdependencias y talento humano capacitado. la capacidad predictiva del modelo resulta de establecer: la información en términos de casos proyectados (población susceptible), el modelo de transmisión, el impacto de las amci ® intervenciones no farmacológicas (mitigación y supresión) para lograr disminuir el número de reproducción r (tasa de contagio), la distribución de la gravedad de la enfermedad y con ello el porcentaje esperado de casos críticos el decreto del . . ( ) , por el cual se declara un estado de emergencia económica, social y ecológica en todo el territorio nacional proyectó para una tasa de contagio de . y cerca de millones de casos, la ocurrencia de mil casos de pacientes con covid- en estado crítico ( . %) y la necesidad de incrementar las camas de cuidados intensivos en un % que con una estancia promedio de días tendría un costo de mil millones de pesos. colombia cuenta con cerca de camas de cuidados intensivos ( / parte son intermedio) de las cuales el % podría ser utilizada para la atención de pacientes covid- ( ). con base en el modelo matemático ha proyectado la necesidad de camas de uci indicando por deducción la necesidad de camas a partir de un plan adaptativo de expansión y extensión. colombia reporta a la fecha actual , casos confirmados y nuevos casos de covid- confirmados y cerca del % ocupan una cama de cuidados intensivos (esta cifra es mayor si se tomaran en cuenta los casos sospechosos). de este modo, los modelos matemáticos permiten predecir el comportamiento epidemiológico de la enfermedad y con esto anticiparse a proyectar el plan de fortalecimiento hospitalario (incluyendo camas, tecnologías, talento humano) y los recursos financieros para respaldar la expansión del cuidado críticos. estos modelos deben ser predictivos y no reactivos al comportamiento epidemiológico de la enfermedad y solo debe des escalarse hasta después de reducirse a menos de . el índice ro. ( - ) recomendaciÓn se sugiere la implementación de una estrategia de telesalud (teleapoyo o teleexperticia) en el marco de la pandemia covid- , cuando no se cuente con un intensivista presencial, que, mediante una tecnología adecuada complemente la atención en las áreas de cuidados críticos realizado por personal capacitado. aún cuando es considerada ventajosa sus implicaciones en términos de resultados clínicos, económicos y de riesgos legales no se ha demostrado. en situaciones donde se declara una pandemia los sistemas de salud pueden tener dificultades para hacer frente a una demanda exponencial y fuera de control. esto puede ser así en el marco pandemia covid- que prevé un % de pacientes en condición crítica y que amerita reorganización y/o adaptación de su capacidad de respuesta. incrementar la disponibilidad de camas y servicios de cuidados críticos mediante una estrategia de expansión supone retos asociados a la insuficiencia que se puede presentar en talento humano especializado específicamente de especialistas en medicina crítica y cuidado amci ® intensivo, escenario que se puede complicar en la medida que intensivistas sean separados o aislados en el curso de la epidemia. en este contexto se hace necesaria la implementación de modelos ágiles de telesalud (ts) para el acompañamiento de las unidades de cuidado crítico en expansión y de instituciones prestadoras de servicios de salud de baja y mediana complejidad para la regulación con los equipos de referencia y contrarreferencia de pacientes que pueden necesitar atención en cuidados intensivos. ( ) ( ) ( ) ( ) ( ) ( ) el decreto ley de ( ) plantea la adopción de medidas en el sector salud para garantizar la prestación de los servicios de salud y para facilitar la implementación de modelos de atención que incluyan la telesalud y la prestación de los servicios en la modalidad de telemedicina se determinan algunas medidas temporales para: i) adecuar temporalmente un lugar no destinado a la prestación de servicios de salud, intra o extra mural. ii) prestar servicios en modalidades o complejidades diferentes a las habilitadas dentro de las cuales puede estar la telemedicina iii) prestar servicios de salud no habilitados. en este decreto también se establecen condiciones temporales para la implementación de plataformas tecnológicas para la telesalud. en complemento, la resolución de ( ) (estándares de habilitación) plantea la modalidad de la telemedicina (prestador remisor-prestador de referencia) para las unidades de cuidado intermedio e intensivo. la telesalud se puede prestar de dos maneras: teleapoyo y teleexperticia. tabla . teleapoyo (ta) soporte solicitado por un profesional de la salud a otro profesional de la salud a través de tic siendo responsable de la conducta quién solicita el apoyo. no requiere habilitación y por tanto no requiere autorización transitoria relación a distancia con comunicación sincrónica o asincrónica utilizando tic entre dos profesionales de la salud, uno de los cuales atiende presencialmente al usuario y otro atiende a distancia. el primero es responsable de las decisiones/recomendaciones entregadas al paciente y el segundo es responsable de la calidad de la opinión que entrega y debe especificar las condiciones en las que se da dicha opinión, lo cual debe consignarse en la historia clínica. requiere autorización transitoria (decreto ) ( ) la telesalud y la prestación de servicios de salud en esta modalidad son estrategias seguras y efectivas para guiar, a distancia, el diagnóstico y el tratamiento del paciente hospitalizado y en estado crítico. sus ventajas generales se presentan en la tabla . asociaciÓn colombiana de medicina crÍtica y cuidados intensivos. amci ® tabla . ventajas generales de la telesalud decreto legislativo de .  facilita la viabilidad de aplicación modelos organizativos que favorecen la continuidad y la integridad asistencial y la atención centrada al entorno del paciente, aplicando conceptos de globalidad e interoperabilidad a las organizaciones sanitarias, dando lugar a nuevas formas de organización y trabajo en red.  mejora de la calidad asistencial, ya que facilitan el acceso y la disponibilidad de servicios asistenciales en condiciones de calidad.  mejora calidad de vida del paciente por la disminución de desplazamientos para la atención ya que permite la atención o monitorización remota con tic en su domicilio.  mejora la oportunidad y la resolutividad de la atención.  facilita la equidad en el acceso a los servicios de salud independientemente de la localización geográfica (acerca la atención especializada a toda la población).  mejora la atención integral y seguimiento tanto de los pacientes crónicos, como los de las enfermedades de baja prevalencia.  reduce los tiempos de espera (tanto en la realización del diagnóstico como en el tratamiento), evitando complicaciones por no atención oportuna.  posibilita realizar atención remota de mediana y alta complejidad en la baja complejidad, reduciendo el número de remisiones.  disminuye la posibilidad de infección cruzada entre usuarios de los servicios de salud y el personal de salud.  incide en la formación y competencia del talento humano en salud.  facilita la educación de pacientes en medicina preventiva y salud pública.  descongestiona servicios de urgencias y consulta externa.  contribuye a la reducción de movilidad de personas en la ciudad.  responde a las necesidades inmediatas en salud de la comunidad.  es un medio de racionalización de costos en salud. puede abarcar otros servicios de gestión administrativa como entrega de fórmulas o facturación. amci ® se recomienda la implementación de un modelo de cuidados críticos covid- liderado por intensivistas, en áreas habilitadas o adaptadas, con el beneficio preponderante de disminuir la mortalidad, tiempo de estancia y optimización de recursos. se recomienda una cobertura por intensivistas de al menos horas diarias y un cociente intensivista/paciente cercano a intensivista por cada - pacientes, basado en la alta complejidad de la enfermedad critica covid- con un alto porcentaje de pacientes en ventilación mecánica, largos tiempos de estancia y alto riesgo de mortalidad. fuerte a favor fundamento un intensivista es un profesional médico capacitado en medicina crítica y de cuidados intensivos conforme a los estándares establecidos por una institución de educación superior debidamente reconocida ante el ministerio de salud. este especialista debe liderar y tomar todas las decisiones con respecto al cuidado de los pacientes críticos, incluyendo admisiones y egresos, qué médicos consultar, estándares de atención, gestión de la calidad y seguridad, gestión humana y ética, interacción con la familia e implementación de un programa de investigación y de formación continua para mejorar capacidades y competencias del equipo de atención, control de conflictos, entre otras.( ) existe una enorme validez conceptual y una preponderancia de evidencia que sugiere que ser atendido por un especialista en cuidados críticos (intensivista) es "bueno" para los pacientes de la uci. la mayoría de los estudios demuestran el impacto positivo de un uci dirigida por intensivistas los modelos de personal médico de la uci más ampliamente estudiados difieren en el nivel al cual los intensivistas están involucrados en el manejo de los pacientes. las uci de alta intensidad son aquellas donde un intensivista de tiempo completo u obligatorio maneja a la mayoría de los pacientes diariamente. las uci de baja intensidad no tienen participación intensivista u ofrecen consultas intensivistas electivas. un metaanálisis mostró que un modelo de alta intensidad en comparación con uno de baja intensidad estuvo asociado con una menor mortalidad en la uci, menor mortalidad hospitalaria, y una reducción significativa en la duración de la estancia hospitalaria. un modelo de alta intensidad por la noche se asoció con menor mortalidad solo cuando durante el día era de baja intensidad. ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) asociaciÓn amci ® forzosa" por condición de riesgo siempre en consonancia con los términos establecidos en el decreto ley de ( ). según la normatividad vigente todo miembro del equipo de atención, especialista no intensivista o no especialista (enfermeras, fisioterapeutas/terapeutas respiratorias) y auxiliares de enfermería deben tener constancia de asistencia a acciones de formación continua y/o capacitación en atención covid- en cuidados críticos las cual puede ser parte de un programa institucional de capacitación liderado por el intensivista coordinador o titular del servicio o a partir de cursos respaldados por instituciones académicas acreditadas o los ofrecidos por la asociación colombiana de medicina crítica y cuidados intensivos (amci). las tablas y nos muestra como dentro de este proceso adaptativo por estado de emergencia y atribuido a un desequilibrio entre la oferta y la demanda, otras especialidades, profesionales de la salud y personal en formación pueden hacer parte de los equipos de atención bajo las siguientes premisas: . la supervisión, coordinación y liderazgo del intensivista es necesaria y . el intensivista establece los roles y competencias del th no intensivista y no normatizado, de acuerdo a sus perfiles, y delegada acciones asistenciales (vía aérea, accesos vasculares, reanimación cardiopulmonar, pronación), administrativas (ordenes médicas, notas clínicas) o de naturaleza humanitaria (comunicación con la familia, apoyo emocional al th, etc.). es necesario considerar los roles de las especialidades que formarán parte de la gestión asistencial y/o administrativa de pacientes con covid- en áreas críticas habilitadas o adaptadas de manera transitoria en colombia tabla . integridad de interdependencia (norma / ) integralidad e interdependencia (adaptiva) gfa integridad de interdependencia (norma / ) integralidad e interdependencia (norma / ) integridad de interdependencia (norma / ) obligatorio en gestión asistencial integralidad e interdependencia(norma / ) obligatorio gestión asistencial apoyo a tomas de decisiones(gfa) apoyo a tomas de decisiones (gfa) a:formacion continua + covid- (curso virtual); b: requiere capacitación covid- (curso virtual); c: gfa: grupo focal asistencial, sistema alerta-acción, rcp, pronación, accesos vasculares, ingreso a uci. d: gfad: grupo focal administrativo: consentimiento, notas de evolución. ts: telesalud. se recomienda la aplicación de la escala news- por parte de un equipo de respuesta rápida, para establecer el lugar de atención de pacientes con diagnóstico definitivo o sospecha de infección por covid- que encuentran en los servicios de urgencias o de hospitalización. se recomiendan escalas como el qsofa y el curb- para apoyar la decisión tomada con base en la escala news- . sin embargo, un qsofa mayor o igual a puntos (mínimo / ) y un crb- mayor o igual puntos tienen baja sensibilidad (alta incidencia de falsos negativos) para identificar pacientes que puedan requerir ingreso a uci. se recomienda el score de riesgo covid- -gram para identificar el riesgo de desarrollar un estado de la enfermedad crítico en pacientes con covid- y como herramienta complementaria a la escala news- en escenarios de alta demanda y escasez de recursos, de manera que la decisión de ingreso a uci se haga sobre aquellos pacientes que realmente se beneficiarán de la misma en términos de vidas salvadas y número de años salvados. la escala news fue construida y validada en paciente con infección por el virus de la influenza a/h n y se recomienda como una herramienta objetiva para decidir nivel de atención, incluyendo ingreso a uci o situaciones terminales que requieren acompañamiento familiar y medidas de cuidado paliativo. esta escala incluye variables fisiológicas que son: frecuencia respiratoria, saturación arterial de oxígeno (spo ), uso de oxígeno suplementario, presión arterial sistólica, frecuencia cardiaca (pulso), temperatura y nivel de conciencia. es de mencionar que esta escala no contempla la edad del paciente. en un reporte del acute medicine task force of the royal college, london, uk, recomendó la utilización de la escala news en los servicios de urgencias ( ) . un estudio que evaluó una base de datos con . signos vitales obtenidos de . pacientes demostró que esta escala tiene una buena capacidad para discriminar pacientes en riesgo para un desenlace combinado de paro cardiaco, ingreso no anticipado a uci o muerte dentro de las primeras horas de atención; de esta manera genera una gran oportunidad para el establecimiento temprano de una intervención clínica que cambie el pronóstico del paciente ( ) . la escala news- tampoco contempla la edad, pero sí incluye la presencia de hipercapnia bajo diferentes niveles de spo y oxígeno suplementario. esta escala es la que ha sido estudiada como herramienta para identificar pacientes en riesgo de desarrollar un estado de enfermedad crítica por covid- con un valor ≥ puntos ( / ) ( ) . con base en la escala news- se establece el grado de riesgo, el tipo de alerta, y la intensidad de monitoreo requerido; y de acuerdo con el puntaje arrojado, se define claramente el nivel de atención que requiere el paciente con diagnóstico de infección por covid- , incluso ingreso a uci (tabla ). esto se establece a través de una escala de puntuación así: -score puntos: manejo domiciliario bajo aislamiento y signos de alarma. -score punto: manejo domiciliario y seguimiento clínico en casa. -score - puntos: manejo en salas de hospitalización. -score - puntos: manejo en uci, área covid- . -score ≥ puntos sin condición extremadamente grave o irreversible y con alta posibilidad de recuperación: traslado a uci, área covid- . amci ® -score ≥ puntos con condición extremadamente grave y con datos de irreversibilidad o enfermedad terminal: no ingresa a uci y se traslada a salas de hospitalización con acompañamiento familiar y consulta a experto en bioética y cuidados paliativos. la ilustración establece un flujograma de conductas basado en el puntaje del news- . tabla . news- score. el qsofa con un valor ≥ puntos es otra herramienta recomendada para decidir qué pacientes que ingresan a uci. esta herramienta fue recomendada por la tercera definición de consenso (sepsis- ) para identificar pacientes con alto riesgo de muerte o estadía prolongada en uci entre aquellos con sospecha de infección ( ) . en este score, un punto es asignado para variables así: frecuencia respiratoria ≥ /min, presión arterial sistólica ≤ mmhg y escala de coma de glasgow (ecg) < . el score curb- y su versión simplificada, el crb- se utilizan para evaluar la severidad de enfermedad en personas hospitalizadas con neumonía adquirida en comunidad (nac). ambos scores han sido adoptados por la sociedad británica de tórax para predecir la necesidad de soporte respiratorio o vasopresor intensivo (srvi) en pacientes con covid- ( ) . el score crb- asigna un punto para variables así: confusión de reciente inicio, frecuencia respiratoria ≥ /min, presión arterial sistólica < mmhg o presión arterial diastólica ≤ mmhg y edad ≥ años. pacientes con un score ≥ puntos necesitan hospitalización ( ) . en un estudio clínico observacional realizado sobre los primeros pacientes ingresados en un hospital de noruega con diagnóstico confirmado de covid- , se evaluó la utilización de sistemas de score clínicos al momento del ingreso: news- , qsofa, crb- y sirs, con los puntos de corte previamente mencionados ( ) . la enfermedad se clasificó como enfermedad severa y enfermedad crítica. solo pacientes ( %) se clasificaron como enfermedad crítica. al evaluar los scores con sus puntos de corte, pacientes presentaron un qsofa ≥ [ con enfermedad severa ( %) y con enfermedad crítica ( %)], solo pacientes presentaron un crb- ≥ [ con enfermedad severa ( %) y con enfermedad crítica ( %)] y pacientes presentaron un news- ≥ [( con enfermedad severa ( %) y con enfermedad crítica ( %)]. la mediana del score news- para pacientes con enfermedad severa fue de . [riq: - ] vs . [riq: . - ] para pacientes con enfermedad crítica. los autores concluyen que el qsofa y el crb- se comportan similar y con una baja capacidad para la identificación de enfermedad crónica en pacientes con covid- ; por otro lado, los datos indican que el news- podría ser una herramienta más útil para identificar pacientes con riesgo de un curso más agresivo de la enfermedad ( % vs. %) ( ) . amci ® un estudio de cohorte retrospectivo realizado en un hospital en liverpool (uk), el puntaje qsofa se comportó como el más específico ( %; % ic: % - %) pero el menos sensible ( %; % ic: % - %) en comparación al puntaje sirs y la escala news como predictor de mortalidad hospitalaria en un grupo de paciente admitidos por sepsis al servicio de emergencias ( ) . otro estudio retrospectivo de un único centro comparó el rendimiento de sistemas de score, qsofa, curb- y crb- para predecir la necesidad de soporte vasopresor o respiratorio intensivo (svri) en pacientes ingresados con diagnóstico confirmado de covid- a un hospital de wuhan (china) ( ) . un total de pacientes ( . %) necesitaron svri durante su estadía en el hospital. la tasa de mortalidad hospitalaria en esta cohorte fue de pacientes ( . %). se evalúo el rendimiento de las escalas con análisis de curva roc (auc), puntos de corte óptimo, sensibilidad, especificidad y valores predictivos. el punto de corte óptimo del crb- para predicción de srvi fue de puntos, con una sensibilidad del % y una especificidad del . %. el valor auc del score crb- para predecir la necesidad de svri fue significativamente más alto que el del qsofa ( . ± . vs. . ± . , p= . ). los valores de auc fueron similares entre crb- y curb- para predecir svri ( . ± . vs. . ± . , p= . ). los autores concluyen que el crb- podría ser mejor que el qsofa para identificar paciente con covid- en riesgo de necesitar svri. su et al consideran que fue la inclusión de la edad ≥ años dentro del score crb- lo que le dio un mayor grado de superioridad sobre el qsofa ( ) . el crb- puede ser una herramienta de puntuación útil para covid- debido a su simplicidad en la aplicación, especialmente en emergencias y condiciones de escasez de recursos. finalmente, el score de riesgo covid- -gram fue descrito por un grupo de investigadores en covid- quienes reunieron datos de pacientes en hospitales en china ( ) . esta fue una cohorte retrospectiva multicéntrico en la que se recogieron un total de variables entre demográficas, médicas, clínicas (signos y síntomas), imagenológicas y de resultados de laboratorios. utilizando la metodología de regresión lasso (least absolute shrinkage and selection operator) construyen un modelo de regresión multivariable resultando en un score de riesgo predictivo para desarrollar enfermedad critica en pacientes con covid- confirmado al momento de la admisión. de las variables iniciales fueron predictores independientes estadísticamente significativos para el desarrollo de enfermedad crítica. estas variables fueron: anormalidad en los rx tx (or: . ; %ic: . - . recomendaciÓn se recomienda la aplicación de un algoritmo basado en una evaluación dinámica del score news que involucre una escala de evaluación funcional, para priorizar el ingreso a uci con transparencia científica y ética con equidad social, y de ser posible respaldado por un comité de priorización clínica (cpc) integrado por expertos de cuidado intensivo y un representante del comité de ética hospitalaria durante la pandemia por covid- . se recomienda un modelo determinado por prioridades para definir criterios de ingreso a uci, permite establecer rápidamente qué pacientes se benefician de ingreso uci y qué pacientes deben permanecer en servicios de hospitalización, o con acompañamiento familiar y cuales con medidas de cuidado paliativo. fuerte a favor page amci ® fundamento la pandemia covid- nos ha enseñado que la disponibilidad de camas de uci puede ser insuficiente y el plan estratégico diseñado para ampliar la capacidad de respuesta debe ir de la mano con la implementación rigurosa de un protocolo de triaje y de priorización de ingreso a cuidados intensivos, como medida extraordinaria para optimizar los recursos, mitigar y controlar los efectos de la pandemia sobre el balance oferta (efectiva y resolutiva) y la demanda. los protocolos de triaje y priorización están diseñados para asignar los limitados recursos de una manera justa y transparente donde, por definición, algunas personas serán excluidas del acceso a la atención orientado a aumentar la disponibilidad de camas de cuidados intensivos. sin embargo, es necesario enfatizar que la disponibilidad de camas no es un fin en sí mismo. la intención implícita y explícita de los protocolos de clasificación debiera ser el «bien público» de maximizar la supervivencia de la población. pero es incorrecto suponer que este bien público se logra al maximizar la supervivencia entre los que reciben cuidados intensivos. si bien muchos protocolos de triaje reconocen esto al tratar de excluir a los pacientes que no lo necesitan absolutamente (el «demasiado sanos») y los que tienen menos probabilidades de beneficiarse (él «demasiado enfermo»), no prestan suficiente atención a las diferencias entre grupos en términos de la duración de los cuidados intensivos necesarios para lograr resultados. si el objetivo del triage es mejorar la supervivencia de la población con un recurso escaso, entonces el recurso escaso no son camas, sino días de cama; no son ventiladores, sino tiempo de ventilación. de ello se deduce que el triaje no será efectivo si en la valoración, no se discrimina adecuadamente y se considera de manera equívoca que la gran mayoría de las personas que requieren cuidados intensivos tienen una probabilidad similar de supervivencia y una duración de estadía anticipada similar. ( ) de este modo, el ingreso a uci debe acogerse a los criterios habituales, científicos y éticos, bajo el rigor de "idoneidad clínica" tomando en cuenta parámetros como la gravedad de la enfermedad, la presencia de comorbilidades (severidad, clase funcional), potencial de recuperabilidad, deseo del paciente (o la familia), de equidad distributiva y el uso de las escalas validadas de severidad y de predicción de ingreso a cuidados intensivos. los pacientes con covid- tienden a progresar después del inicio de los síntomas dentro de los a días a una forma grave con síndrome de dificultad respiratoria aguda (sdra) o falla multiorgánica órgano. la identificación temprana y simple de pacientes que requieren respiración intensiva o el soporte vasopresor sería de gran valor durante el brote covid- . ( ) ( ) ( ) ( ) la implementación de un algoritmo "dinámico" que vincule uno o más de las escalas fisiológicas (news con o sin qsofa y/o crb- ≥ ), una escala de predicción de ingreso a uci (covid- -gram) y un puntaje de fragilidad (vipi) puede informarnos sobre el estado actual y evolutivo de la enfermedad y a priorizar el ingreso de pacientes a uci permitiendo un uso óptimo de los recursos y tomar decisiones éticas, transparentes y centradas en la dignidad de los pacientes y el bien público ilustración - . se recomienda no usar escalas de severidad de enfermedad (criterios objetivos) para definir el traslado de pacientes de uci hacia un nivel de menos complejidad de atención, ya que estas escalas no han sido validadas para este uso. se recomienda en la atención por covid- en cuidados intensivos utilizar los mismos criterios de egreso que se emplean para el traslado desde uci hacia una unidad de menor complejidad de pacientes sin infección por covid- . se recomienda contar con áreas de bajo nivel de complejidad asignadas solo a la atención de paciente con infección por covid- , las cuales serán las áreas hacia donde se realiza el de-escalamiento gradual de los pacientes basado en su evolución clínica. cuando se habla de criterios objetivos, se hace referencia a escalas de severidad de enfermedad que ayuden a tomar decisiones más racionales y no basadas en consideraciones tradicionales de resolución de cuadros clínicos. no hay una recomendación definida sobre el uso de escalas de severidad de enfermedad para definir el de-escalamiento de la atención para pacientes críticos. los sistemas de evaluación de severidad de enfermedad generales y específicos pueden identificar una población específica de pacientes en alto riesgo de deterioro clínico luego del traslado fuera de la uci( ); sin embargo, su valor para evaluar que tan preparado está un paciente individual para ser trasladado a un nivel inferior de cuidado no ha sido evaluado( ). los criterios que recomienda el colegio americano de cuidado intensivo( ) para definir el traslado desde uci a un nivel de menor complejidad (unidad de cuidados intermedios o sala de hospitalización) se basan en principios:  cuando el estado fisiológico del paciente se ha estabilizado y ya no es necesario monitoreo y tratamiento en uci.  cuando el paciente cumpla con los criterios de admisión del nivel de menor complejidad, teniendo en cuenta la disponibilidad actual del recurso, el pronóstico del paciente y la presencia de intervenciones activas en curso. específicamente para los pacientes con alto riesgo de muerte y reingreso a uci en quienes se decide no hacer intervenciones adicionales (alta severidad de enfermedad, inestabilidad fisiológica, soporte orgánico), el colegio americano de cuidado intensivo( ) siguiere pasarlos a una unidad de menor nivel de atención o a un hospital de cuidado agudo de largo plazo; siempre con un formato escrito donde se deje claro la decisión para reducir la tasa de reingreso a uci( ). específicamente en situaciones de pandemia y escasez de recursos, la sociedad española de medicina intensiva, crítica y unidades coronarias (semicyuc) recomienda la realización de la escala sofa al menos cada horas para identificar pacientes con evolución tórpida y progresiva a un fallo multiorgánico luego de la iniciación de tratamientos de soporte vital. esto permitirá la adecuación y reorientación de medidas terapéuticas a un objetivo más paliativo, incluyendo la transferencia del paciente a un nivel más bajo de complejidad y la consulta al servicio de cuidado paliativo para que brinde la atención respectiva( ). finalmente, se debe mencionar que no se ha establecido una diferencia en los criterios de egreso de pacientes con covid- para su traslado desde uci hacia una unidad de menos complejidad, con respecto a los utilizados para pacientes sin infección por covid- ( ). todo paciente hospitalizado en uci sea covid- o no, debe ser valorado diariamente para establecer en qué momento su condición clínica permite que sea trasladado fuera de la uci hacia una unidad de menor complejidad. en caso de tratarse de pacientes con sospecha o diagnóstico de covid- , este traslado puede hacerse a una unidad de cuidados intermedios dispuesta como área covid- o una sala de hospitalización con igual asignación( ); esto es lo que se conoce como de-escalamiento gradual de la atención hasta el final egreso del paciente a casa. se recomienda para pacientes con covid- que evolucionan hacia la mejoría, utilizar los criterios clásicos de de-escalamiento del nivel de atención (unidad de cuidados intermedios o sala de hospitalización) que propone el colegio americano de cuidado intensivo( ) . se recomienda aplicar la escala sofa al menos cada horas sumado al criterio de fragilidad y años de vida saludables salvados estos criterios podrían ser válidos en pacientes con fallo terapéutico a las medidas óptimas y orientar decisiones de deescalamiento de medidas y de nivel de complejidad de atención cuando la demanda potencial supera la oferta (capacidad y capacidades), estas decisiones deben ser tomadas idealmente en junta médica. amci ® se recomienda generar procesos administrativos más eficientes para el traslado de pacientes fuera de la uci hacia niveles de menor complejidad, estos ayudarán a liberar recursos para otros pacientes. se recomienda no utilizar el resultado de la rt-pcr positiva para decidir el egreso de la unidad de cuidados intensivos. la literatura no ha definido unos criterios de flexibilidad en uci para el traslado de pacientes con sospecha o diagnóstico confirmado de covid- ; y los criterios que definen la posibilidad de egreso de uci y que aplican a todos los pacientes, incluso aquellos ingresados por una condición crítica en relación con infección por covid- , están claramente definidos por el colegio americano de cuidado intensivo en su documento-guía del .( ). los principios fundamentales han sido revisados en los fundamentos de la pregunta . es importante implementar una estrategia de identificación temprana para aquellos pacientes con soporte vital avanzado que evolucionan progresivamente a fallo multiorgánico y pocas probabilidades de recuperación; el de-escalamiento de medidas y su posterior traslado fuera de la uci, liberará espacio para otros pacientes en situaciones de desborde de la demanda. la sociedad española de medicina intensiva, crítica y unidades coronarias (semicyuc) recomienda que en caso de complicaciones o que se prevea una mala evolución tanto clínica como funcional, se plantee el retiro terapéutico por futilidad y se inicie un manejo con medidas de soporte paliativo, tal como ha sido considerado en los fundamentos de la pregunta ( ) . para el grupo español es claro que, adecuar procesos administrativos más eficientes para traslado de pacientes fuera de la uci a los usualmente utilizados en condiciones normales de práctica clínica, ayudaría a ser más eficientes en la gestión de la demanda ( ) . finalmente, la persistencia de una rt-pcr positiva no es una contraindicación para el traslado del paciente fuera de la uci siempre y cuando se aseguren condiciones de aislamiento por contacto y aerosol en aquellas áreas de menor complejidad de atención; estas incluyen zonas de expansión o área del hospital específicamente acondicionadas para el manejo de pacientes estables o pacientes con limitación de esfuerzo y manejo paliativo de su condición ( ). recomendaciÓn se recomienda que la disposición final de cadáveres de personas con sospecha o diagnóstico de covid- se haga preferiblemente por cremación. en tal caso, las cenizas pueden ser objeto de manipulación sin que suponga ningún riesgo. amci ® se recomienda que la disposición final del cadáver se haga por inhumación en sepultura o bóveda individualizada cuando no se cuente con instalaciones para cremación en el territorio donde ocurrió el deceso o la disponibilidad de esta tecnología desborda la capacidad económica de las personas. se recomienda realizar siempre el aislamiento del cadáver en el lugar del deceso, siguiendo las recomendaciones del ministerio de salud y la protección social (msps). se recomienda que en los casos que se requiera necropsia médico legal y estuviese indicada la cremación, esta deberá contar con la orden del fiscal del caso. se recomienda que la institución establezca en sus procesos prioritarios un protocolo humanizado de despedida bajo estrictos criterios de bioseguridad. no existe una evidencia fuerte que recomiende hacer una disposición de cadáveres de pacientes fallecidos con sospecha o diagnóstico confirmado de covid- con un acto de cremación o con inhumación y sepultura en féretro; sin embargo, siempre y cuando la manipulación y manejo del cadáver hasta su disposición final se haga manteniendo todas las medidas de precaución para evitar la diseminación del virus y siguiendo la normatividad legal vigente, ambas formas son aceptadas. la infección por covid- es una enfermedad con gran variabilidad en presentación clínica, alta tasa de contagio y para la cual no existe en el momento un tratamiento definido. el riesgo de contagio al personal que ejecuta autopsias o procedimientos de tanatopraxia y la probabilidad de diseminación de la enfermedad por la manipulación de cadáveres no se conoce, pero se considera que puede ser alto, teniendo en cuenta que, en ausencia de la aplicación de un método de diagnóstico masivo, todo caso debe considerarse potencialmente positivo. por tanto, el manejo de cuerpos de personas fallecidas con diagnóstico confirmado, sospechoso o probable de sars-cov- (covid- ), debe realizarse con la mínima manipulación posible( ). el cadáver debe ser transferido lo antes posible al depósito y entregado al servicio funerario antes de horas luego del fallecimiento( ). el transporte, la cremación o inhumación, según sea el caso, se efectuará en el menor tiempo posible, con el fin de prevenir la exposición de los trabajadores y comunidad general al virus sars-cov- (covid- ). se debe evitar la realización de rituales fúnebres que conlleven reuniones o aglomeraciones de personas( ). el alistamiento del cadáver será realizado en el ámbito hospitalario del mismo sitio del deceso. las personas que accedan a la habitación donde se encuentre el cadáver, deben tomar las precauciones de transmisión por contacto y gotas, y para ello deben contar con todos los elementos de protección personal (epp) y seguir los procedimientos de amci ® bioseguridad de acuerdo con lo establecido en el protocolo del msps.( ) para hacer el alistamiento del cadáver, se debe cubrir todos los orificios naturales con algodón impregnado de solución desinfectante y se deberá envolver en su totalidad sin retirar catéteres, sondas o tubos que puedan contener los fluidos del cadáver, en tela antifluido o sábana; luego se deberá envolver en dos bolsas plásticas biodegradables que cumplan con las características técnico-sanitarias de impermeabilidad y resistencia a la presión de gases en su interior( ). se debe rociar el interior y el exterior de ambas bolsas con solución desinfectante de hipoclorito sódico que contenga . ppm de cloro activo( ) (exceptuando los casos asociados de covid- y muerte violenta). una vez el cadáver esté adecuadamente dispuesto en las bolsas, se podrá movilizar sin riesgo hacia el depósito de cadáveres siguiendo la ruta intrahospitalaria dispuesta para este traslado. luego el cadáver podrá será entregado al personal del servicio funerario para su depósito en ataúd o contenedor de cremación o inhumación y posterior traslado al sitio de destino final (horno crematorio y/o cementerio), luego de completar toda la documentación necesaria. cuando deba practicarse necropsia médico legal, el cuerpo será entregado a los servidores del sistema judicial quienes asumirán la custodia( ). si se han seguido correctamente todas estas indicaciones, se asume que no hay ninguna diferencia entre disponer del cuerpo enviándolo al crematorio o colocarlo en ataúd para llevarlo al tanatorio y realizar el entierro. si se opta por lo primero, las cenizas pueden ser objeto de manipulación sin que supongan ningún riesgo.( ) se recomienda que el trabajador de la salud conozca a través de la institución donde labora, los riesgos éticos, de salud y seguridad a que se expone por la atención en el paciente covid- , evitando así conflictos e incertidumbres que afecten la atención. se recomienda que las instituciones prestadoras de salud a través de los líderes de atención médica, guíen y orienten a los trabajadores, para ofrecer una mejor atención médica y menor daño emocional durante la pandemia. se recomienda dar a conocer las directrices institucionales sobre el nivel de atención (uci vs. sala médica); inicio del tratamiento de soporte vital (incluyendo rcp y soporte de ventilación); retirada del tratamiento de soporte vital; y derivación a cuidados paliativos (centrados en la comodidad) en la atención médica de los pacientes durante la pandemia, esto genera una atención caracterizada por alivio del sufrimiento, no abandono, respeto a amci ® los derechos y preferencias de los pacientes, igualdad moral de las personas y la equidad en la distribución de riesgos y beneficios en la sociedad. el apoyo de la práctica ética es necesario integrarlo al cuidado de la salud y al bienestar de la fuerza laboral del cuidado en salud. reconociendo los desafíos especiales a que se enfrentan al responder al covid- . esto forma parte del liderazgo en la atención médica y del servicio del deber cívico. berlinger n. el de abril del . en su artículo "respondiendo a covid- como un desafío regional de salud pública pautas preliminares para la colaboración regional que involucra hospitales". refiere que los trabajadores del equipo médico tienen el deber de conocer la gestión asistencial de los "desafíos éticos" previsibles durante la emergencia de salud pública (pandemia covid- ). que los desafíos éticos surgen cuando existe incertidumbre acerca de cómo "hacer lo correcto" es cuando los deberes o valores en los trabajadores entran en conflicto. estos desafíos afectan a la fuerza laboral (carga moral y emocional ante una decisión no prevista) en la atención médica. así como la operatividad en la atención médica (falta de epp y recursos que pueden limitar el buen desempeño por temor a infectarse).( ) los líderes de atención médica tienen el deber de guiar a los trabajadores de atención médica que experimentan condiciones laborales exigentes, mayor riesgo de daños ocupacionales, incertidumbre ética y angustia moral durante una emergencia de salud pública.( ) chih chen a, t. el de abril del . en su editorial ¿cómo deben prepararse los sistemas de salud para la evolución de la pandemia de covid- ? sugiere un apoyo emocional adecuado para el personal y horas razonables de exposición al riesgo para evitar el agotamiento, ya que los profesionales de la salud luchan por cuidar a los pacientes y proteger sus vidas y sus familias. se refiere que a medida que aumenta el número de casos, los médicos y los trabajadores de la salud en la primera línea deben reducir al mínimo su carga de trabajo clínico. las instituciones de atención médica deben reasignar al personal realizar tareas no clínicas, incluidos el papeleo y la recopilación de datos, tanto como sea posible. los hospitales deben tomarse su tiempo para capacitar al personal para implementar eficazmente las precauciones de contacto y los procesos de flujo. ( ) jick j.l. el de marzo del . en relación con la obligación de planificar la atención médica, considera que: los líderes de atención médica tienen el deber de planificar la gestión de los desafíos éticos previsibles durante una emergencia de salud pública. la planificación de los desafíos éticos previsibles incluye la identificación de posibles decisiones de triage, herramientas y procesos. en una emergencia de salud pública que presenta una enfermedad respiratoria grave, es posible que se deban tomar decisiones de clasificación sobre el nivel de atención (uci vs. sala médica); inicio del tratamiento de soporte vital (incluyendo rcp y soporte de ventilación); retirada del tratamiento de soporte vital; y derivación a cuidados paliativos (centrados en la comodidad) si el tratamiento de soporte vital no se iniciará o se suspenderá. es posible que también se deban tomar decisiones de clasificación en relación con la escasez de personal, espacio y suministros. el deber de cuidado fundamental requiere fidelidad al paciente (no abandono como una obligación ética y legal), alivio del sufrimiento y respeto a los derechos y preferencias de los amci ® pacientes. el deber de cuidado y sus ramificaciones son el enfoque principal de la ética clínica, a través de los servicios de consulta de ética clínica a pie de cama, el desarrollo de políticas institucionales y la educación y capacitación en ética para los médicos. deberes de promover la igualdad moral de las personas y la equidad (justicia en relación con la necesidad) en la distribución de riesgos y beneficios en la sociedad. estos deberes generan deberes subsidiarios para promover la seguridad pública, proteger la salud de la comunidad y asignar de manera justa recursos limitados, entre otras actividades. estos deberes y sus ramificaciones son el foco principal de la ética de la salud pública. no se puede emitir una recomendación a favor o en contra acerca del uso de los medicamentos y dispositivos "prototipos" utilizados en el manejo del covid- denominados de uso compasivo o fuera de etiqueta, se considera sin embargo que no pueden ser utilizados por fuera de ensayos clínicos o protocolos institucionales estandarizados de evaluación del perfil de riesgo/beneficio y bajo la aplicación de consentimiento informado. se entiende como uso compasivo la utilización, en pacientes aislados y al margen de un ensayo clínico. dichos medicamentos experimentales no han sido aprobados aún por la fda, ( ) y no se ha demostrado su seguridad y eficacia. es importante recordar que el medicamento médico puede tener efectos secundarios inesperados y graves, y que los pacientes deben considerar los posibles riesgos cuando procuran acceder a un producto médico experimental. hay que tener en cuenta que, para utilizar un medicamento bajo las condiciones de uso compasivo, se requerirá el consentimiento informado por escrito del paciente o de su representante legal, un informe clínico en el que el médico justifique la necesidad de dicho tratamiento. la regulación de la utilización de medicamentos por la vía del uso compasivo se ha realizado dentro de un texto legal sobre la realización de ensayos clínicos. una interpretación común del uso no indicado en la etiqueta y el uso compasivo de medicamentos es que, si el paciente murió, murió de la enfermedad, pero si el paciente sobrevivió, sobrevivió debido al medicamento administrado. recomendaciÓn se recomienda en la comunicación inicial con los familiares del paciente adulto con sospecha o diagnóstico de covid- críticamente enfermo incluir de forma clara y transparente los aspectos relacionados con el derecho al final de la vida que incluye: proporcionalidad en el tratamiento, adecuación del esfuerzo terapéutico, documento de voluntad anticipada, adecuación del esfuerzo terapéutico y la atención paliativa. situaciones estas que se pueden presentar durante la evolución hospitalaria y que requieren de una decisión conjunta entre el médico y el familiar del paciente. se recomienda dar una información específica, y adecuada a los familiares del paciente con sospecha o diagnóstico de covid- , para que firmen el consentimiento informado, generando esta información confianza y comprensión en el familiar. la información del consentimiento que recibe el familiar debe constar dentro de la historia clínica. fundamento el ministerio de salud y protección social del de marzo del a través del documento de "recomendaciones generales para la toma de decisiones éticas en los servicios de salud durante la pandemia covid- ". ante la posible circunstancia de pacientes sin capacidad para la toma de decisiones, por deterioro del estado general o requerimiento de aislamiento, en el cual no se puede contactar a su representante, conduzca la toma de decisiones teniendo en cuenta la prioridad de no hacer daño y la modificación en las condiciones de disponibilidad de los recursos en caso de presentarse deterioro. recuerde que esta situación debe preverse y debe ser informada a los representantes desde la admisión del paciente". durante toda la atención debe darse información sobre la posibilidad de que se presenten limitaciones de acceso a los soportes necesarios incluido al personal de salud , lo anterior puede limitar los derechos individuales o preferencias, esto debe ser informado al paciente y su familia, para que les permita entender que bajo la emergencia, puede presentarse una circunstancia que en condiciones habituales pudiera ser reversible de ser tratada pero en el contexto actual los recursos pueden verse trágicamente limitados, sin que esto implique abandono en el cuidado. el documento se refiere a la información que debe recibir el paciente o su familiar sustituto durante su evolución o fallecimiento. ( )la información durante la evolución también debe incluir: la información sobre el ejercicio de derechos al final de la vida incluyendo la adecuación de los esfuerzos terapéuticos y la suscripción de documentos de voluntad anticipada la consulta y revisión de existencia de este en todos los casos. se recomienda tener un consentimiento informado al ingreso hospitalario del paciente covid- , se deben tener en cuenta las circunstancias del paciente al ingreso hospitalario, si la capacidad para la toma de decisiones está limitada por su estado clínico o incapacidad mental. de ser estas las circunstancias se dará la información al familiar en primera línea de consanguinidad quien asume por el paciente el consentimiento de la información (consentimiento sustituto). se recomienda tener el consentimiento informado en situaciones de excepción o urgencia ante la pandemia por covid- , debe ser universal, en el que se informe el ingreso a la uci, o a cualquier otra área hospitalaria, realización de procedimientos, administración de tratamientos, posibles riesgos, beneficios durante su hospitalización. con esto se respeta el derecho a la autonomía personal en el paciente competente. en caso contrario el familiar tomará la información y asume el consentimiento a la información dada. es importante que el familiar esté informado de las decisiones que se vayan tomando durante la evolución hospitalaria (realización de procedimientos, inicios o cambios de tratamientos, movilización dentro del área hospitalaria. etc.) fuerte a favor fundamento el ministerio de salud y protección social, el de marzo del ha elaborado un formato de "consentimiento informado para acompañante de casos probable/confirmado de covid- ". en que se expresa: "que de manera detallada se me ha suministrado información completa, suficiente, con un lenguaje sencillo y claro. el profesional de la salud me ha explicado la naturaleza de la enfermedad, acerca del significado de caso sospechoso o confirmado del coronavirus covid- en cuanto a su presentación clínica, modo de contagio, medidas para contenerla, posibilidad de sufrir la enfermedad, complicaciones o muerte, mientras permanezca como acompañante del paciente". este documento se firma al ingreso por el acompañante o familiar quien asume las decisiones durante su estancia hospitalaria. ( ) el consentimiento informado en los pacientes covid- será un consentimiento sustituto para su ingreso a la uci y para los procedimientos que en la uci se realicen (colocación de tubo orotraqueal, diálisis, colocación de catéteres, reanimación cardiopulmonar, ecmo, etc.). previa información y autorización del familiar. en circunstancias normales el consentimiento debe ser firmado por el paciente quien en su autonomía acepta la información sobre su manejo y tratamiento. feld ad. recomendaciÓn se sugiere ante la pandemia del covid- , si es posible, que el grupo de expertos en bioética y/o comité de ética institucional sean consultados y estén informados por el médico responsable para la orientación o consejo en la toma de directrices ante decisiones difíciles. se sugiere en lo posible que el médico tratante no asuma solo la responsabilidad moral de la decisión y que la decisión sea institucional y documentada en la historia clínica e informada a los familiares. en caso de no contar con un comité de bioética y/o ética hospitalaria el médico responsable podrá tomar la decisión fundamentada en principios éticos y derechos del paciente o convocar a una junta médica u otro comité relacionado con su dilema o consultar un apoyo externo en bioética. débil a favor fundamento el ministerio de salud y protección social. ( ) el de marzo del en el documento "recomendaciones generales para la toma de decisiones éticas en los servicios de salud durante la pandemia covid- establece: "que en caso de que la institución cuente con un comité de bioética y/o Ética, con el servicio de bioética o Ética clínica, o consultoría clínico-ética, se debe definir una ruta de consulta para los casos que de forma concreta puedan superar las recomendaciones generales. de igual forma establece que en las circunstancias actuales que se viven el actuar ético es parte integral del profesionalismo del cuidado. teniendo en cuenta que los profesionales de la medicina serán los llamados a tomar decisiones de alto estrés moral, al tener que adherirse y promover conductas concretas basados en las circunstancias que les rodean para dar o retirar tratamientos de las personas infectadas, quienes esperan confirmación del diagnóstico y de las personas que acuden a la atención en salud por razones diferentes a la infección por covid- . partiendo de lo antes referenciado, se recomienda que las acciones emprendidas, busquen siempre poder responder a: a. no hacer daño b. beneficiar c. actuar con justicia sobre la persona en el contexto de la emergencia frente a la justicia sanitaria de la población d. mantener la integridad profesional" el comité de bioética y/o comité de ética institucional en tiempos normales o en tiempos de pandemia deberá mantener actualizadas las directrices de toma de decisiones. que apoyaran al médico responsable en la decisión. de no contar el médico con dicho comité o directrices institucionales y deba tomar una decisión que no permite interconsultar, deberá justificar en la historia clínica fundamentado en los principios éticos y derechos del paciente las razones que lo llevaron a tomar la decisión e informar y dialogar con los familiares del hecho. esto es importante que siempre quede documentado en la historia clínica la acción moral y ética de la decisión y el diálogo con la familia. en caso de que el médico responsable no cuente con un comité de bioética y/o comité de ética institucional, ni con el apoyo externo de expertos en bioética. y no quiera tomar la amci ® decisión a título personal podrá consultar a otro médico de la institución su decisión y entre ambos definir la acción a seguir. esta decisión conjunta debe ser documentada en la historia clínica e informada al grupo de trabajo y a los familiares como junta médica. si los familiares después de recibir la información no quedan satisfechos ellos tienen el derecho a la segunda opinión. los comités de bioética y/o comités de ética hospitalaria son entes administrativos, consultores, orientadores, asesores y consejeros de las situaciones que tienen que ver con el respeto y cumplimiento de los principios éticos, deberes y derechos de los pacientes, sus recomendaciones no son vinculantes, apoyan y orientan la decisión médica. aconsejando la mejor decisión ante una situación que genera un dilema moral o ético en el médico responsable. las decisiones médicas son tomadas por el consultor en bioética, quien es médico. los comités institucionales fuera de un comité de bioética y/o ética que podría dar apoyo al médico responsable y que serían otras instancias consultivas serian el comité de humanización, comité de historias clínicas, comité de bioseguridad, comité de infectología, comité de mortalidad hospitalaria, comité de paliativos o un comité de gerencia. pues todos los mencionados tiene que ver con el bienestar del paciente y la seguridad del médico ante una decisión. las decisiones especiales deben ser tomadas inicialmente a través de la realización de un comité (pueden ser los mencionados), en su defecto una junta médica. una vez se tenga la decisión esta debe ser consultada a la familia como una decisión institucional respaldada por el comité o junta médica realizada. se recomienda que todo ensayo clínico que se realice en la institución debe ser presentado, revisado y aceptado por un comité de investigación local o un comité de investigación externo nacional o internacional. se recomienda que todo paciente que se incluya en un ensayo clínico debe contar con un consentimiento informado el cual garantiza la aceptación voluntaria a participar y la comprensión de los objetivos, riesgos, beneficios, derechos y responsabilidades que tiene dentro de la investigación. se recomienda el consentimiento informado en todo ensayo clínico, el cual debe ser debe ser individual en tiempos de normalidad como en tiempos de pandemia por covid- . solo el comité de ética en investigación podrá establecer en tiempos de normalidad o de pandemia las condiciones de dispensa o excepción al requisito de obtener el consentimiento informado. refiere que el consentimiento informado tiene sus raíces en el código de núremberg de y la declaración de helsinki de y ahora es un principio rector para la conducta en la investigación médica. en el consentimiento informado para investigaciones clínicas es claro que los participantes deben entender ampliamente los componentes del consentimiento. ( ) thanh tam, n. et al. el de enero . mediante una revisión sistemática de pubmed, scopus y google scholar y revisando manualmente las listas de referencias para publicaciones hasta octubre de . realizó un metaanálisis de los resultados del estudio utilizando un modelo de efectos aleatorios para tener en cuenta la heterogeneidad. evaluó la proporción de participantes en ensayos clínicos que entienden los diferentes componentes del consentimiento informado. encontrando que los participantes en ensayos clínicos deben comprender los componentes fundamentales del consentimiento informado como: la naturaleza y los beneficios del estudio, la libertad de retirarse en cualquier momento y la naturaleza voluntaria de la participación, así como la comprensión de otros componentes, como la aleatorización y el placebo. la proporción de participantes en ensayos clínicos que comprendieron diferentes componentes del consentimiento informado varió de . % a . %. esto asegura que la toma de decisiones de los participantes es significativa y que sus intereses están protegidos. ( ) la red de américa latina y el caribe de cnb-unesco, ( de marzo de ) que agrupa a las comisiones y consejos nacionales de bioética cuya finalidad es la de asesorar sobre los problemas éticos relativos a las ciencias de la vida y la salud humana expresa su preocupación ante la realización de investigaciones biomédicas en relación con la pandemia de enfermedad infecciosa por coronavirus covid- . reconociendo lo siguiente en relación con el consentimiento informado: que la investigación con seres humanos durante las emergencias debe contar con garantías éticas mayores, no menores, que en las situaciones ordinarias. que en situación de excepción o emergencia los participantes deben seleccionarse en forma justa y proporcionar una justificación adecuada cuando se escogen o excluyen determinadas poblaciones, distribuyendo en forma equitativa las posibles cargas y beneficios de participar en esa investigación. "que se debe obtener el consentimiento informado individual de los participantes incluso en una situación de excepción o alarma, a menos que se cumplan las condiciones para la dispensa del consentimiento informado. las cuales el comité de revisión ética solo puede decidir dar la dispensa al requisito de obtener consentimiento informado: a) si no es factible obtenerlo; y si además los estudios: b) tienen un importante valor social y científico, c) solo suponen riesgos mínimos para los participantes, d) no implican agravio comparativo con otros grupos en situación o no de vulnerabilidad; y si e) se garantiza que no se privará a la población investigada de acceder en forma preferencial al beneficio derivado. de otorgarse un consentimiento informado amplio, éste debería ser única y exclusivamente para los procesos asociados con covid- ".( ) amci ® se recomienda considerar la transición del cuidado intensivo al cuidado paliativo en todo paciente con sospecha o diagnóstico de covid- sin mejoría a pesar de las intervenciones óptimas, con empeoramiento progresivo de su pronóstico vital y ante un evidente deterioro; aplicando medidas generales en control de síntomas ( manejo de secreciones -tratamiento del dolor -tratamiento de la disnea -sedación paliativa), así como apoyo espiritual, siempre acompañando al paciente y nunca abandonarlo en el final de la vida. fuerte a favor fundamento la sociedad española de anestesiología, reanimación y terapéutica del dolor en su documento: "marco Ético pandemia covid- " madrid, de marzo de refiere: la sedación paliativa en pacientes hipóxicos con progresión de la enfermedad no subsidiaria de tratamiento debe considerarse como una expresión de buena práctica clínica y debe seguir las recomendaciones existentes. si se prevé un período agónico no corto, se debe proporcionar una transferencia a un entorno no intensivo.( ) se recomienda la utilización de guías establecidas previamente a la pandemia por el ministerio de salud y sociedades científicas para orientar las decisiones que se tomen al final de la vida en pacientes con sospecha o diagnóstico de covid- . estas guías deben ser divulgadas al equipo de atención y aplicadas en los pacientes en casos de: adecuación del esfuerzo terapéutico (aet), orden de no reanimar (onr), consentimiento sustituto, voluntades anticipadas, cuidados paliativos. se recomienda fundamentar las decisiones del final de la vida individualizadas a cada paciente y a cada situación sin llegar a tomar decisiones apresuradas sin fundamento científico o ético, solicitando de ser posible una valoración por medicina paliativa para el manejo de síntomas. se recomienda indagar durante la hospitalización de todo paciente con sospecha o diagnóstico de covid- , si en tiempos de salud hizo válida su autonomía y realizó un documento de voluntad anticipada, teniendo en cuenta que esta será equivalente al consentimiento informado. amci ® terapéuticos y la suscripción de documentos de voluntad anticipada.( ) el inicio de sedación paliativa con reubicación del pacientede ser necesario el des escalonamiento por deterioro clínico. en situación de pandemia covid- cuando se refiere a situaciones del final de la vida se relaciona a la adecuación del esfuerzo terapéutico, la sedación paliativa la cual será la maniobra terapéutica que se utilizará en pacientes no recuperables y que no son candidatos a cuidados intensivos por covid- ,( ) que evolucionan desfavorablemente y tienen mal pronóstico a corto plazo, así como la disnea refractaria y la limitación del esfuerzo terapéutico. el delirium o síndrome confusional por fallo cerebral agudo, es un problema habitual en situaciones de alteración orgánica severa, y ha sido descrito como uno de los síntomas neurológicos presente en los pacientes que sufren infección por el covid- ( ). wilson c. de abril del . en su artículo "la crisis golpea al final de la vida" se refiere a que el brote de coronavirus está obligando a las personas a enfrentar dilemas en torno a la cantidad de atención médica que se debe brindar al final de la vida y apresurar decisiones controvertidas sobre rechazar ciertos tratamientos. dicen los expertos que esto ha alentado a más personas a tomar decisiones de tratamiento anticipadas relacionadas con la rcp y la ventilación,( ) haesen s. el de mayo de . en su artículo "dirigir a los ciudadanos a crear directivas anticipadas" las voluntades o directrices anticipadas son para las personas que quieran asumir plenamente su papel de ciudadanos responsables tomando decisiones proactivas. la decisión de redactar directivas anticipadas marca un cambio del enfoque actual de "aceptación" a un escenario de "exclusión voluntaria".( )al emitir una directiva de tratamiento anticipado, una persona autónoma puede expresar formalmente qué tipo de tratamiento desea y no desea recibir en caso de que se enferme o se lastime y no pueda decidir de manera autónoma sobre su tratamiento. ( ) ministerio de salud y protección social en su documento de voluntades anticipadas que es el documento en el que toda persona capaz, sana o en estado de enfermedad, en pleno uso de sus facultades legales y mentales y como previsión de no poder tomar decisiones en el futuro, declara, de forma libre, consciente e informada su voluntad sobre las preferencias al final de la vida que sean relevantes para su marco de valores personales.( ) se recomienda que el paciente crítico con covid- que no es candidato para ingresar o continuar recibiendo cuidados intensivos y que presente deterioro rápido con mal pronóstico a corto plazo, se le brinde una adecuación del esfuerzo terapéutico orientada a acompañamiento al final de la vida, alivio del sufrimiento y control de síntomas. dependiendo de la disponibilidad de recursos se sugiere dentro del plan de atención hospitalaria contar con un área destinada a la atención del final de vida con el recurso físico, humano y de procesos necesario. marzo del . refiere: en situación de adecuación terapéutica, retirada de medidas y/o mala evolución es adecuado derivar al paciente a un área de menor complejidad para establecer el plan de cuidados paliativos. consultar al servicio de cuidados paliativos para procurar la continuidad de cuidados de los pacientes en los que se haya acordado la limitación de tratamientos y aliviar su sufrimiento, incluyendo la sedación paliativa en los casos en los que sea precisa.( ) schmidhauser tf. el de abril . considera en su publicación que: los cuidados paliativos durante la pandemia de covid- deben adaptarse a un estilo de" cuidados paliativos de emergencia" ya que los pacientes pueden deteriorarse rápidamente y requieren decisiones rápidas y planes de tratamiento claros. estos deben ser seguidos fácilmente por los miembros del personal de salud que atienden a estos pacientes. además, los cuidados paliativos deben estar a la vanguardia para ayudar a tomar las mejores decisiones, atender a las familias y ofrecer apoyo espiritual.( ) se recomienda como estrategia de protección personal en las unidades de cuidado intensivo sin presión negativa y cubículos abiertos utilizar de forma continua el respirador n o fpp , adicional a otros elementos de protección para prevención del contagio por covid- . la atención segura en áreas crítica para todas las modalidades de atención se fortalece a través de las medidas de precauciones estándar en el manejo de todos los pacientes, establecidos en el "manual de medidas básicas para control de infecciones en prestador servicios de salud" ley de , por la cual se dictan medidas sanitarias. resolución de , numeral y numeral . epp. el respirador, n o fpp , puede utilizarse de manera continua por a horas, o desecharlo antes si está visiblemente contaminada o si está húmeda. luego de colocar la n se debe verificar prueba de ajuste antes de ingresar a la unidad para atención de pacientes con covid- de la siguiente manera: mascarillas sin válvula de exhalación: cubra la totalidad de la mascarilla con ambas manos y exhale con fuerza. si nota fugas de aire por sus bordes, reajuste la posición del respirador. mascarillas con válvula de exhalación: cubra el respirador con ambas manos e inhale con energía. deberá sentir una presión negativa dentro de la mascarilla. si detecta alguna pérdida de presión o entrada de aire, reajuste la posición del respirador. no se puede emitir una recomendación a favor o en contra acerca de la efectividad de bioseguridad del uso extendido, continuo o intermitente de los respiradores n ó ffp . sin embargo, se considera que puede ser una alternativa, bajo la adopción de un protocolo riguroso, cuando se debe optimizar el uso de los epp en el contexto de un acceso limitado. el reúso no está permitido en colombia. la duración máxima del uso continuo de la n es de a horas, siguiendo las recomendaciones del manual de medidas básicas para control de infecciones en ips de minsalud. pero en la vida real, ningún trabajador tolera a horas continuas con un respirador. por esto, su uso continuo en el sitio de trabajo dependerá de la necesidad de pausar para comer, para ir al baño, etc. en este caso, se guardará en una bolsa de papel para su nueva colocación, si tiene menos de horas, o desechará si está visiblemente contaminada o se torna húmeda. el reúso de la n dependerá de la casa del fabricante, de si contiene o no celulosa en su estructura del respirador. por ejemplo, la recomendación de desinfección para los respiradores sin celulosa es con peróxido de hidrógeno vaporizado al % por minutos (tabla y ). los respiradores n de uso industrial tienen mayor contenido de celulosa que los de uso médico por lo tanto para procesos de esterilización, solo los n de uso médico podrán ser esterilizados mediante de peróxido de hidrógeno vaporizado (sterrad®) ( - ) . ¿existe superioridad en términos de protección personal para el personal sanitario y de apoyo dentro de las unidades de cuidados intensivos con la utilización del overol frente a la bata manga larga con antifluido durante la atención del paciente con covid- ? no se puede emitir una recomendación a favor o en contra si los overoles ofrecen mayor protección por cobertura corporal frente a otros elementos como vestidos largos, batas y delantales. resulta intuitivo que su uso genera una mayor protección en especial en servicios cohortizados. sin embargo, su uso está asociado con una mayor dificultad para su colocación y retiro, lo que puede potencializar el contagio del usuario, la utilización debe hacerse bajo un protocolo supervisado y chequeado. las batas modificadas para ajustarse firmemente en el cuello pueden reducir la contaminación. en estudios ya descritos el uso de un respirador eléctrico purificador de aire con overol puede proteger contra el riesgo de contaminación mejor que una máscara n y una bata con un rr: . , intervalo de confianza (ic) del %: . a . pero fue más difícil su retiro con rr . , ic del % . a . . en un eca ( participantes), las personas con una bata larga tenían menos contaminación que aquellas con un overol. las batas pueden proteger mejor contra la contaminación que los delantales.( - ) los epp como batas y overoles deberían estar hechos de un material que cumpla con los requisitos mínimos de la asociación americana de químicos textiles:  tipo a: buena repelencia al agua, resistente a la penetración, pero mala permeabilidad al aire.  tipo b: buena repelencia al agua, buena permeabilidad al aire, pero poca resistencia a la penetración del agua.  tipo c: bata quirúrgica que tiene poca repelencia al agua y resistencia a la penetración de agua.  tipo d: hecho de fibras de polietileno de alta densidad, tela no tejida (tyvek®), tiene buena repelencia y resistencia al agua, mala permeabilidad al aire. no se puede emitir una recomendación a favor o en contra para el uso de respiradores elastoméricos como elementos de protección personal dentro de las unidades de cuidados amci ® intensivos. no hay evidencia que soporte la superioridad de los respiradores elastoméricos frente a los n , son más costosos, difíciles de utilizar y pueden implicar algún riesgo para el paciente. por tanto, su uso sólo debería considerarse frente a un desabastecimiento de los n y bajo la adopción de un protocolo institucional riguroso y bajo chequeo. los respiradores elastoméricos son respiradores ajustados a media cara o cara completa, esta última otorga protección ocular. su filtración está determinada por el filtro que se utilice, estos van desde partículas de nivel n a p . están hechos de material sintético o de goma que les permite desinfectarse, limpiarse y reutilizarse repetidamente. están equipados con cartuchos de filtro reemplazables. al igual que los respiradores n , los respiradores elastoméricos requiere entrenamiento adecuado para su correcta colocación y retiro. por eso es muy importante revisar el manual del usuario antes de su uso. los respiradores elastoméricos no deberían utilizarse en entornos quirúrgicos, debido al riesgo potencial de contaminación del campo quirúrgico, con el aire que sale de la válvula de exhalación. como recomendación de buena práctica, aprobado por la fda, debe colocarse una máscara quirúrgica encima de la válvula de exhalación para evitar este riesgo. solo se debe permitir el uso del respirador elastoméricos por clínica para evitar infecciones cruzadas, esto permitirá una protección esencial contra agentes infecciosos y la auto contaminación. aunque los cartuchos de filtro son finalmente desechables, están destinados a ser reutilizados hasta que ya no se puede respirar o se vuelven visiblemente sucio. generalmente se recomienda, en la mayoría de los casos, hacer recambios cada días. deben tener procedimientos de limpieza/desinfección actualizados y aprobados por su manufacturador.( , - ) recomendaciÓn se recomienda realizar la limpieza y desinfección de equipos biomédicos y de superficies las veces que sean necesarias y en el momento de egreso del paciente siguiendo los protocolos de cada institución. el desinfectante para este proceso debe ser de nivel intermedio o alto para superficies y equipos biomédicos y cumplir con las recomendaciones del fabricante según lo aprobado en el registro sanitario. fuerte a favor fundamento para la desinfección de las superficies ambientales hospitalarias y domiciliarias, la oms recomienda emplear un desinfectante que sea efectivo contra virus cubiertos (el coronavirus pertenece a esta categoría), específicamente, recomienda emplear alcohol etílico para la desinfección de algunos equipos biomédicos reusables (p. ej.: termómetros) y para las superficies, el hipoclorito de sodio o precursores de sodio como el dicloroisocianurato de sodio (nadcc) que tiene la ventaja de la estabilidad, la facilidad en la dilución y que no es corrosivo.( ) (tabla ). page se recomienda que el ingreso de un paciente a uci debe hacerse bajo un procedimiento estandarizado que incluya la coordinación y comunicación de los servicios vinculados, adecuación de la unidad de atención a las necesidades del paciente y la garantía de la bioseguridad del equipo multidisciplinario. se recomienda que cada institución establezca en sus procesos prioritarios el circuito del traslado que incluye el itinerario del traslado, el uso de ascensor, el número y la organización de los intervinientes sanitarios y no sanitarios (celadores, seguridad, limpieza), las medidas de protección empleadas por los mismos (epp, limpieza) y los recursos materiales necesarios durante el traslado. el traslado de pacientes con casos sospechosos o confirmados de covid- se puede presentar entre servicios a nivel hospitalario o entre instituciones con diferentes niveles de atención y deben tenerse las precauciones universales de un traslado seguro. una posición responsable es evitar el traslado de estos pacientes el máximo posible, a menos que sea imprescindible, teniendo en cuenta el riesgo/beneficio. considerar evitar traslados interinstitucionales solo por temas administrativos. el personal sanitario que realice el traslado debe contar con todos los epp, considerando este traslado como de alto riesgo de transmisión vírica. se debe utilizar mascarilla quirúrgica o n- , de acuerdo con el riesgo amci ® de aerosolización. hasta que la rt-pcr para sars-cov- este negativo se podrían retomar las prácticas habituales de traslado de los pacientes . ( ) ( ) ( ) capítulo . abordaje diagnóstico y covid- se recomienda en pacientes con diagnóstico o sospecha de infección por sars-cov- clasificar la enfermedad en leve, severo o paciente crítico, teniendo en cuenta los criterios de la clasificación por las fases y estadios de la enfermedad. se recomienda en pacientes con diagnóstico o sospecha de infección por sars-cov- , clasificados como críticos y que requieren de intubación orotraqueal realizar la clasificación por fenotipos ( o ), con el fin de proyectar una estrategia de ventilación mecánica. el covid- , es una enfermedad con una presentación clínica diversa, desde formas leves hasta presentaciones graves que incluyen el sdra, la mediana del período de incubación desde la exposición hasta el inicio de los síntomas es de aproximadamente a días, y el . % de los pacientes sintomáticos tendrán síntomas dentro de los . días después de la infección ( ) , que incluye fiebre, tos, disfagia, malestar general, mialgias, anorexia, náuseas, diarrea, anosmia y ageusia; la disnea se presentó entre los y días ( ) y puede representar progresión a covid- severo, que se manifiesta con hipoxemia, disfunción orgánica múltiple, documentación de arritmias cardíacas, rabdomiólisis, coagulopatía y choque ( ) . dentro del espectro de enfermedad, siddiki et al, proponen un enfoque estructurado por fases expresados en tres estadios (historia natural de la enfermedad), siendo el primero donde la patogenicidad viral es dominante, se incluye el periodo de incubación, síntomas leves, con multiplicación del sars-cov- centrándose principalmente en el sistema respiratorio gracias a la unión del virus con el receptor de la enzima convertidora de angiotensina (ace ), el hemograma puede revelar linfopenia y neutrofilia sin otras anormalidades significativas. el estadio es la enfermedad pulmonar establecida, neumonía viral, tos, fiebre con progresión en algunos casos a hipoxia con trastorno de los índices de oxigenación (pao /fio menor mmhg), hallazgos en imágenes de tórax (radiografía y/o tomografía) de infiltrados alveolares o vidrio esmerilado, mayor linfopenia y elevación de transaminasas ( a: sin hipoxemia, b: con hipoxemia). el estadio o fase de híper inflamación sistémica extrapulmonar se caracteriza por elevación de biomarcadores inflamatorios y estado protrombótico (il - , il- , il- , ftn -α, proteína c reactiva, ferritina y el dímero d), con presencia en las formas más graves de disfunción orgánica múltiple, lesión miocárdica (troponina y péptido natriurético de tipo b elevados), con fenómenos trombóticos, progresión a sdra y choque ( ) . amci ® la neumonía por sars-cov- , se característica por disociación entre la severidad de la hipoxemia y el mantenimiento relativamente bueno de la mecánica respiratoria, con compliance del sistema respiratorio en promedio de ml / cmh o; gattinoni, marini et al, proponen dos fenotipos de presentación de la insuficiencia respiratoria; el primero (tipo ) con una mecánica pulmonar adecuada, con baja probabilidad de reclutabilidad y con hipoxemia, relacionado al desbalance entre la perfusión y la ventilación; el segundo (tipo ) más acorde a las definiciones de sdra (csdra "covid- patient with sdra"), con una compliance pulmonar baja y reclutabilidad potencial( , ) ( ). se propone la siguiente clasificación clínica del covid- . ( , , y pacientes críticos de %, con tasa global de mortalidad de , %, siendo mayor entre los pacientes de a años con % y entre los mayores de años con . %, dentro del grupo de pacientes clasificado como crítico la mortalidad descrita fue del %( ). recomendaciÓn se recomienda en cuidado intensivo, realizar el diagnóstico de covid- del paciente sospechoso por medio de rt-pcr conociendo su alta especificidad, su variabilidad en relación con el tiempo y pérdida de rendimiento diagnóstico luego de la primera semana de inicio de los síntomas. se recomienda tomar la primera muestra para rt-pcr de hisopo nasofaríngeo o de cornete medio sobre hisopado oro faríngeo o de saliva, de ser negativo se puede repetir la prueba de a horas preferiblemente de tracto respiratorio inferior, esputo no inducido o en aspirado traqueal en paciente intubado. se recomienda el uso conjunto de rt-pcr e igm por elisa en pacientes con sospecha de covid- , primera rt-pcr negativa, que se encuentren entre la segunda y tercera semana desde el inicio de los síntomas, con el objetivo de mejorar la sensibilidad en la identificación de infección por sars-cov- . en cuidado intensivo, el diagnóstico de covid- se fundamenta con base en la presentación clínica compatible y factores epidemiológicos asociados con probabilidad de infección; el diagnóstico definitivo se realiza con pruebas de amplificación de ácido nucleico del virus (naat), la detección del genoma viral del sars-cov- se realiza por medio de reacción en cadena de la polimerasa por transcriptasa reversa (rt-pcr) dado a su especificidad del % ( , ) ; por lo cual todo paciente que cumple con la definición de caso sospechoso se le debe realizar rt-pcr, sars-cov- independientemente de si se encuentra otro patógeno respiratorio ( ) . las muestras para el diagnóstico por rt pcr se recolecta de las vías respiratorias superiores, nasofaringe, cornete medio u orofaringe; todos con alta especificidad. sin embargo, se sugiere recolectar los hisopos nasofaríngeos o de cornete medio por tener mayor sensibilidad ( ( / ) . en pacientes con neumonía severa a quienes se le realizó lavado broncoalveolar (bal) y rt-pcr entre los días y el % de las muestras fueron positivos, en pacientes no intubados con esputo no inducido el % de las muestras fueron positivas ( , ). wang et al, en un estudio de pacientes con covid- , las rt-pcr con tasas positivas más altas fue en muestras extraídas por bal ( %; de muestras) y esputo % ( de muestras) ( ) . para la detección del sars-cov- por rt-pcr en pacientes en cuidado intensivo, teniendo en cuenta la rigurosidad de aspectos de bioseguridad y aerosolización, se debe tomar la primera muestras en nasofaringe o cornete medio, si esta prueba es negativa se puede repetir en a horas, si este es el caso o existe más de días desde el inicio de los síntomas se prefiere una muestra del tracto respiratorio inferior, por esputo no inducido por personal de salud o por aspirado traqueal en pacientes intubados ( , ), aunque el rendimiento diagnóstico del bal es alto por lo general, se debe evitar la broncoscopia para minimizar la exposición de los trabajadores de la salud ( ) . la probabilidad de detección del arn de sars-cov- puede variar según la fase de la enfermedad, si bien una rt-pcr positiva confirma el diagnóstico de covid- , los reportes falsos negativos y la sensibilidad se ve influenciado por el tiempo desde la exposición e inicio de síntomas. kucirka et al, en un análisis de siete estudios evaluaron el rendimiento diagnóstico de la rt-pcr en relación con el tiempo desde el inicio de los síntomas o la exposición, con resultados expresados en tasa estimada de falsos negativos, siendo del % el día de la exposición, del % el día (estimado como primer día de síntomas, ic: % a %), % en el día (día desde el inicio de síntomas, ic: % a %) luego comenzó a aumentar nuevamente de % en el día (ic: a %) a % en el día (ic: a %) ( ) . la precisión y los valores predictivos de rt-pcr para sars-cov- no se han evaluado sistemáticamente, la sensibilidad de las pruebas moleculares está influenciada por múltiples factores como sitio y calidad de la muestra, técnica de procesamiento; probablemente las menores tasas de falsos negativos (sensibilidad entre y %) está entre el día y luego de inicio de los síntomas ( ) . a partir de aquí el rendimiento diagnóstico disminuye, por lo tanto, es importante que el intensivista valore estas consideraciones en el momento de tomar conductas, en cuanto tipo de aislamiento, tratamiento y pronóstico. amci ® las pruebas serológicas detectan anticuerpos contra el sars-cov- y ayudan a identificar pacientes que han tenido la enfermedad y algunos con la enfermedad activa, la seroconversión se ha descrito entre el día y , sin embargo, hay incertidumbre en la incidencia de la seroconversión ( ) . estas pruebas se usan principalmente en tamizaje poblacional y estudios de seroprevalencia; en cuidado intensivo el análisis de la igm por elisa contribuye a la detección de pacientes con infección reciente, además con el análisis conjunto con la igg se clasifica el estado de infección en agudo o convaleciente. las pruebas serológicas se realizan por diferentes técnicas como la inmunocromatográfica de flujo lateral, la inmunofluorescencia indirecta (ifi) y el ensayo de inmunoadsorción ligado a enzima (elisa) ( , ) . las pruebas serológicas no deben usarse como la única prueba para diagnosticar o excluir la infección activa por sars-cov- . la sensibilidad y la especificidad de muchas de estas pruebas serológicas son inciertas, así como su valor predictivo positivo. los anticuerpos detectables generalmente tardan varios días en desarrollarse. guo et al, documenta niveles de anticuerpos por elisa, con una mediana de detección de anticuerpos igm e iga de días (iqr, - ) y de igg de días (iqr, - ) después del inicio de los síntomas, con una probabilidad de resultados positivos de . %, . % y . % respectivamente; es probable que el rendimiento diagnóstico de igm por elisa sea mayor que la de rt-pcr después del quinto día luego de inicio de síntomas; cuando se combinan estas técnicas (elisa igm con rt-pcr) la tasa de detección positiva es del . % ( ) . zaho et al, en un estudio de pacientes con covid- , donde el , % estaba en condición crítica, la mediana del tiempo desde el inicio de los síntomas hasta la detección de anticuerpos (técnica elisa) fue de días para igm y días para igg; dentro de los primeros días desde el inicio de los síntomas solo el . % tenía anticuerpos detectables, entre los días a la sensibilidad de igm fue . % e igg de . %, luego de los días la sensibilidad igm e igg fue de . % y . % respectivamente; el uso combinado de rt-pcr y elisa igm presentó una sensibilidad del % entre los días a y del % entre los días a . ( ) la rt-pcr tiene especificidad del %, con adecuado rendimiento diagnóstico entre los días y luego del inicio de los síntomas con sensibilidad que varía entre el y %, con presencia ascendente de falsos negativos luego del día , por lo cual el diagnóstico debe tener consistencias epidemiológicas y clínicas (síntomas y hallazgos radiológicos compatibles con covid- ) donde una rt pcr negativa no excluye la enfermedad; la precisión y el tiempo para la detección de anticuerpos varían con la técnica utilizada, su uso es limitado en cuidado intensivo, sin embargo su identificación por técnica elisa en conjunto con rt-pcr mejora la sensibilidad y la probabilidad de falsos negativos, especialmente entre los días y desde el inicio de síntomas. faltan estudios que evalúen el rendimiento diagnóstico de las diferentes pruebas. amci ® se recomienda la medición de marcadores de severidad al ingreso a uci del paciente críticamente enfermo por covid- (hemograma, transaminasas, ldh, ferritina, troponina, dímero d y pcr) los cuales se han asociado con peor pronóstico en la enfermedad por covid- , logrando ofrecer intervenciones más tempranas. se recomienda no utilizar una periodicidad de rutina para la medición de seguimiento de biomarcadores de severidad en el paciente con sospecha o diagnóstico de covid- . en un estudio cohorte retrospectivo que evaluó pacientes diagnosticados con covid- desde el de enero de hasta el de marzo de , fang liu y colaboradores encontraron correlación en la elevación de il- y pcr con la gravedad clínica, lo que sugiere podrían usarse como factores independientes para predecir la severidad del cuadro, los pacientes con il- > . pg./ml o pcr> . mg/l tenían más probabilidades de tener complicaciones graves ( ) , así mismo en otro estudio multicéntrico retrospectivo de pacientes infectados se identificó resultados de laboratorio con diferencias significativas con elevación de glóbulos blancos, valores absolutos de linfocitos, plaquetas, albúmina, bilirrubinas, función renal, transaminasas, troponina, proteína c reactiva e interleucina (il ) en el grupo con desenlace de mortalidad contra los dados de alta ( ) . entre otros marcadores la troponina como lesión cardiaca (elevación de troponina por encima del percentil límite de referencia superior) se ha reportado en % a % de los pacientes con covid- en wuhan, china, en dos estudios retrospectivos por xiabo yang y colaboradores ( , ) . en una revisión sistemática de mayo , kermali m. y colaboradores exponen que existe evidencia a favor de los valores bajos de linfocitos y plaquetas y valores elevados de los biomarcadores il- , pcr, troponina, ldh, ferritina, proteína amiloidea a y dímero d, pueden relacionarse con la gravedad de la infección por covid- y su fuerte asociación con la mortalidad ( ) . estos resultados pueden usarse como un complemento en la práctica clínica para guiar a los médicos a identificar pacientes con mal pronóstico y la rápida implementación de medidas de soporte, monitorización y reanimación en la evolución de los pacientes críticos en la unidad de cuidados intensivos. solo en estudio, karmali et al, en , determinan en promedio entre a horas, la periodicidad en el seguimiento de estos, sin embargo, no se discrimina entre pacientes críticos y no críticos. consideramos que el seguimiento de estas pruebas debe estar ajustado al juicio clínico del médico intensivista tratante, según la evolución de los pacientes. se muestran el comportamiento de los biomarcadores mas frecuentes en la tabla . tabla . biomarcadores en pacientes críticos con sospecha o diagnóstico de covid- . tendencia de biomarcador en relación con la gravedad covid- pcr aumentada recomendaciÓn se recomienda la no medición de marcadores de inflamación o de severidad de forma rutinaria solo con el objetivo de iniciar un tratamiento específico o algoritmos terapéuticos en la enfermedad por covid- en pacientes críticos. el síndrome de liberación de citocinas o denominado "tormenta de citocinas" parece asociarse en pacientes con afecciones graves por covid- . la citocina proinflamatoria il- es la citocina mejor documentada en covid- correlacionada con la gravedad, el estado crítico del paciente, la carga viral y el pronóstico ( , , ) . se han descrito mayores niveles de citoquinas proinflamatorias (il- , il- , il- , factor estimulante de colonias de granulocitos, factor de necrosis tumoral e interferón gamma) asociadas a compromiso pulmonar severo en pacientes con infección por coronavirus, determinado por la rápida replicación del virus, infiltración masiva de células inflamatorias y trastorno severo de la inflamación ( , ) . igualmente, está asociada la presencia de linfopenia como biomarcador de mal pronóstico para covid- ( ) . hallazgos similares se encontraron en la pandemia de influenza a (h n ) de sin ser especificó su valor ( ) . las manifestaciones clínicas de la tormenta de citocinas incluyen síndrome de respuesta inflamatoria sistémica, hipotensión, síndrome de fuga capilar, insuficiencia renal, sdra, miocarditis, entre otras ( ) , algunos autores han determinado este cuadro como un síndrome de linfohistiocitosis hemofagocitica secundaria. es razonable pensar que, en pacientes con sospecha de tormenta de citocinas basado en los hallazgos de laboratorio, el manejo con inmunomoduladores puede resultar beneficioso, sin embargo, los resultados del manejo de la hiperinflación basado en pruebas diagnósticas han tenido resultados encontrados en pacientes con covid- . el uso de esteroides, inmunoglobulina endovenosa, inhibidores del receptor de citoquinas (tocilizumab) o inhibidores de janus kinasa, han disminuido los valores de los biomarcadores, días de hospitalización ( ) o necesidad de fracciones elevadas de oxígeno ( ) , sin embargo no han demostrado beneficio sobre la mortalidad y en algunos casos, si un aumento en la incidencia de infecciones bacterianas o fúngicas sobreagregadas ( ) . se recomienda realizar radiografía simple de tórax para todos los pacientes con sospecha o diagnóstico de covid- en uci. se recomienda realizar tac de tórax según disponibilidad de tecnología institucional, ante la incertidumbre diagnostica, teniendo en cuenta las condiciones clínicas, la tolerancia del paciente al traslado y los protocolos administrativos de seguridad. fuerte a favor fundamento se reconoce como el gold estándar diagnóstico de infección pulmonar por covid- a los estudios moleculares, sin embargo, estos presentan limitaciones: a) contaminación de las muestras b) errores en la técnica de la toma, c) muestra insuficiente para ampliación genética favoreciendo falsos negativos d) demora de reporte de los resultados. por lo anterior, se recomienda imágenes diagnósticas en la aproximación de paciente con sospechas de infección pulmonar por covid- ( , ) .  radiografía simple de tórax: ventajas: mayor accesibilidad que la tac de tórax y realización de la prueba a la cabecera del enfermo desventaja: baja sensibilidad en estadio temprano, después del día de inicio de los síntomas presenta aumento en el rendimiento diagnóstico  tac de tórax: ventaja: es ampliamente recomendada. alta sensibilidad en estadios tempranos. permite describir extensión, distribución, localización, densidades parenquimatosas, aplicables en clasificaciones y puntajes diagnósticos, pronósticos y de seguimiento en permanente evolución y mejoría. algunas asociaciones referentes como asociación china de radiología, en su recomendación de expertos propone clasificación tomografía en estadios temprana avanzada severo disipación desventaja: traslado del paciente hasta el tomógrafo (no todos los enfermos toleran el transporte) y tecnología no disponible en todos los niveles de atención page no se puede emitir una recomendación a favor o en contra para el uso de ecografía pulmonar a la cabecera del paciente crítico como herramienta diagnóstica o de pronóstico en con covid- . se puede considerar como una alternativa para la valoración imagenológica pulmonar en el paciente crítico con covid- cuando las condiciones del paciente no permitan su traslado. no se sugiere la utilización de la ecografía pulmonar para el seguimiento de lesiones pulmonares agudas en el enfoque del paciente crítico con covid- . puede utilizarse para determinar complicaciones asociadas a la enfermedad o en la inserción de dispositivos invasivos. en general los estudios de imágenes no representan un papel concluyente para el diagnóstico de covid- . la ultrasonografía en específico requiere estudios de validación, un programa de entrenamiento es operador dependiente, y se le atribuido limitaciones en la capacidad de discriminación en la cronicidad de las lesiones pulmonares. la ultrasonografía pulmonar puede servir como herramienta a la cabecera del paciente para mejorar la evaluación del compromiso pulmonar y reducir el uso de radiografías de tórax y tomografía computarizada ( ) , sin embargo no debe usarse para el diagnóstico inicial, pues éste se compone de criterios clínicos, radiográficos y microbiológicos que actualmente son el estándar de oro; la ecografía no los reemplaza debido a la baja especificidad en relación con el virus, se sugiere su uso como complemento en la valoración diaria del paciente, ojalá realizada por el mismo observador. la ecografía pulmonar es altamente sensible y puede revisar de forma rápida y precisa la condición pulmonar, creando un potencial para evaluar los cambios o la resolución con el tiempo, especialmente en la uci, escenario en el que cada vez se usa más para la detección de múltiples patologías pulmonares que se pueden demostrar junto con covid- , sin embargo, hasta la fecha no hay hallazgos específicos, ni patognomónicos que se relacionen con covid- en el examen ecográfico del paciente ( ) . la adopción de ultrasonido pulmonar puede reducir la necesidad de exposición a la radiación ionizante y, a su vez, reducir la cantidad de radiografías necesarias para la evaluación rutinaria del paciente, disminuyendo también la exposición de personal asistencial adicional como el uso de elementos de protección personal ( ) . es bien conocido el beneficio de la ecografía durante y después de la colocación de accesos venosos centrales para establecer la presencia o no de complicaciones inmediatas como neumotórax. a la fecha no hay publicaciones acerca de la utilidad del ultrasonido como herramienta para establecer pronóstico. se necesitan más estudios para evaluar la utilidad de la ecografía pulmonar en el diagnóstico y manejo de covid- ( ) . se recomienda no establecer un punto de corte en el valor de dímero d para el inicio rutinario de anticoagulación plena en el contexto de infección por covid- . se recomienda la administración de profilaxis antitrombótica según protocolo institucional independiente de niveles de dímero d en el paciente críticamente enfermo por covid- . los fenómenos inflamatorios inherentes a procesos infecciosos son considerados desde décadas previas, factores protrombóticos, no siendo una excepción la infección por covid- . en algunas publicaciones se hallan asociaciones con desenlaces cardiovasculares negativos ( ) y sugieren asociación entre niveles elevados de dímero d ( marcador de estado de trombosis ) y riesgo de embolismo pulmonar con or crecientes or de . a los días hasta . a los días de seguimiento ( ) . de igual manera, zhou et al, reportan asociación de dímero d mayor a mcg/ml y mortalidad ( ) sin embargo los estudios presentan limitaciones en su diseño, a pesar de ello algunos autores proponen anticoagulación como factor de protección en mortalidad sin precisar precisión en la dosis, tipo de heparina y selección de enfermos ( ) . finalmente la european heart journal en su entrega de farmacología cardiovascular desarrolla una propuesta en la cual combina un puntaje previo de riesgo de cid en uci a niveles de fibrinógeno; esta pudiera ser una herramienta para selección de pacientes a recibir anticoagulación sin embargo aún está en proceso de validación ( ) . por estos motivos, hasta el momento, no se tiene suficiente cuerpo de evidencia que permita hacer una recomendación basado en los niveles de dímero d como variable aislada para administración de anticoagulación terapéutica. se recomienda no utilizar de rutina la procalcitonina en un algoritmo diagnóstico, para diferenciar entre neumonía viral vs bacteriana o confirmar la presencia de una sobreinfección bacteriana en el paciente con sospecha o diagnóstico de covid- . se recomienda no medir de forma rutinaria la procalcitonina en pacientes con sospecha o diagnóstico de covid- como factor pronóstico. la procalcitonina es un biomarcador que ha sido incluido en algoritmos de diagnóstico y pronóstico durante los últimos años. schuetz et al, en , concluyen en una revisión sistemática de estudios, que la procalcitonina es segura dentro de un algoritmo, para guiar a los médicos tratantes entre iniciar o suspender antibióticos en neumonía adquirida en la comunidad; sin embargo en una revisión sistemática más reciente, kamat et al, reportaron una sensibilidad % [ic % %- %; i = . %], especificidad % [ % ic, %- %; i = , %]) para el inicio de tratamiento antibiótico para neumonía bacteriana, lo cual nos determina que la prueba es inespecífica para diferenciar entre infecciones virales vs bacterianas. en neumonía por sars-cov- , se han publicado algunos artículos evaluando el uso de la procalcitonina como prueba asociada al pronóstico de los pacientes. liu et al encontraron que la procalcitonina se asoció a mayor severidad de los cuadros de neumonía. hr, . ; % ci, . - . ; p= . . en este estudio también se tuvo un resultado similar con la proteína c reactiva y la il- . plebani et al, publican un metaanálisis, donde sugiere que los niveles elevados de procalcitonina se asocian a mayor severidad de la infección. (or, . ; % ci, . - . ). es importante mencionar, que en estos estudios se evaluaron otros biomarcadores de inflamación como interleucina , proteína c reactiva y ferritina; presentando todos ellos, aumento en sus valores y asociándose a severidad de la enfermedad; por tanto, se considera que, en particular, la procalcitonina elevada, no representa una diferencia en el pronóstico, comparado con otros biomarcadores de inflamación. hasta el momento no se han publicado estudios en infección por sars-cov- donde se evalué el papel de prueba diagnóstica para confirmar sobreinfección bacteriana o diferenciar entre neumonía viral vs bacteriana. ( , ( ) ( ) ( ) se recomienda no usar de forma rutinaria el uso de pruebas clínicas de laboratorios clínicos para determinar la resolución de la enfermedad crítica por covid- . se recomienda considerar la ausencia de dificultad respiratoria y fiebre por más de horas, requerimiento de oxígeno a baja concentración y bajo flujo, como indicadores clínicos de resolución de la fase crítica de la enfermedad por covid- . se recomienda no utilizar de forma rutinaria el uso de pruebas microbiológicas de erradicación viral, para determinar la resolución de la enfermedad en pacientes en uci con covid- . amci ® enfermedad está asociado tanto a la carga viral como a la respuesta hiperinflamatoria del huésped a la infección viral. en cuanto a la carga viral, en pacientes que tienen un curso leve de infección, el pico de la carga viral en muestras nasales y orofaríngeas ocurre durante los primeros - días tras el inicio de síntomas y prácticamente desaparece al día , mientras que en los que cursan con neumonía severa en uci, la carga viral es veces mayor y puede persistir la excreción viral hasta el día a ( ) . por esta razón, consideramos que en los pacientes en uci no es necesario confirmar la erradicación del virus o su negativización en muestra respiratorias, orina o heces, para determinar la mejoría clínica, curación o para el egreso del paciente crítico ( ) . en el contexto clínico, el pronóstico se ha asociado a la presencia de marcadores bioquímicos elevados, sin embargo, no existe evidencia que el seguimiento con estos marcadores iniciales de inflamación determine el momento exacto de la resolución de la enfermedad. varias organizaciones internacionales como el cdc de usa y el european centre for disease prevention and control ( mar ) ( , ), national centre for infectious diseases (ncid) singapore ( ), world health organization ( de marzo de )( ), han establecido criterios para resolución clínica y egreso hospitalario de los pacientes. estos criterios incluyen: ausencia de fiebre mayor a horas sin antipiréticos, mejoría de los síntomas respiratorios, ausencia de requerimiento de hospitalización por otras patologías, el resultado de dos ( ) rt-pcr para sars-cov- negativas, con intervalo de muestra mayor a horas. la utilidad de dichos criterios no ha sido evaluada en pacientes en cuidado intensivo. en uci, huang et al ( ) , describieron en pacientes a quienes se dio egreso, la ausencia de fiebre por días, mejoría radiológica y evidencia de erradicación viral, como criterios de alta. sin embargo, consideramos que deben primar los criterios clínicos sobre los paraclínicos, en el momento de definir el egreso de un paciente de cuidado intensivo, teniendo como principal indicador la ausencia de dificultad respiratoria y la mejoría en los índices de oxigenación, con requerimiento de oxígeno suplementario a bajos flujos y concentración ( ) . se recomienda la cánula de alto flujo, donde esté disponible, en pacientes con covid- a nivel del mar con hipoxemia leve (pao /fio < y > o sao /fio < y> ). en alturas superiores a los mts por encima del nivel del mar esta terapia se puede considerar en pacientes que no tengan hipoxemia severa (pafi< ). amci ® se recomienda en pacientes críticos por covid- el uso de la cánula de alto flujo en salas de presión negativa, donde estén disponibles, que garanticen la seguridad del recurso humano. si no se dispone de habitación con presión negativa se puede optar por habitación individual cerrada. se debe contar con todo el equipo de protección personal necesario para el personal sanitario y de apoyo. se recomienda colocar mascarilla quirúrgica por encima de la cánula nasal en el paciente con sospecha o diagnóstico de covid- y mantener una distancia mínima de metros con otros pacientes. se recomienda la intubación inmediata en pacientes críticamente enfermos con sospecha o diagnóstico covid- con índice de rox ([spo /fio ] / frecuencia respiratoria) < a las horas de iniciada la oxigenación con cánula de alto flujo teniendo en cuenta que el retraso en la intubación aumenta la mortalidad. se recomienda considerar la cánula de alto flujo en caso de agotamiento de ventiladores mecánicos. la cánula de alto flujo ofrece flujos de hasta litros/minuto, que aportan una fracción inspirada de oxígeno (fio ) constante que reduce el espacio muerto y produce una presión positiva que genera reclutamiento alveolar y puede redistribuir el líquido alveolar ( ) ( ) ( ) . se ha reportado que al generar aerosoles, aumenta el riesgo de contagio para el personal de salud ( , ( ) ( ) ( ) . hasta el punto de que se ha recomendado su uso en salas con presión negativa ( ) . recientes publicaciones han establecido que la cánula de alto flujo genera una corta distancia de dispersión de aerosoles con lo cual las medidas de distanciamiento, un adecuado equipo de protección personal y donde estén disponibles, realizarla en salas de presión negativa darían seguridad al uso de la cánula de alto flujo ( , ) . a pesar de que la experiencia en la actual pandemia ha sido escasa, basada en series de casos, estudios retrospectivos y de metodología limitada, ha resultado ser promisoria en cuanto a la mejoría en la oxigenación y la tolerancia por el paciente ( , , , , , ( ) ( ) ( ) ( ) ( ) . sin embargo, hasta el momento no se ha establecido que la cánula de alto flujo evite la intubación. la caf podría convertirse en un alto riesgo de mortalidad al prolongar la decisión de intubación y al favorecer la lesión pulmonar autoinducida (p-sili) por aumento del esfuerzo inspiratorio. por todo ello es necesario un estricto y estrecho monitoreo del paciente durante una o dos horas para definir si ha habido mejoría o no mientras se realizan estudios que demuestren que evita la intubación y genera desenlaces clínicos importantes como menor estancia en uci, menor estancia hospitalaria y menos días de ventilación mecánica. la terapia de oxígeno de caf podría ser considerada para pacientes atendidos en altitudes mayor a mts, que no tienen hipoxemia severa (pafi < ), la respuesta debe evaluar dentro de los a minutos posteriores a su inicio y los pacientes que no mejoran amci ® significativamente y progresa la dificultad respiratoria no deben mantenerse con esta terapia. el monitoreo del paciente con caf para la toma de decisión de éxito o fracaso de esta estrategia y considerar la posibilidad de intubación incluye la evaluación gasométrica, la oximetría de pulso, así como considerar los criterios para intubación: frecuencia respiratoria > por minuto, deterioro de conciencia, inestabilidad hemodinámica, pao /fio < (a nivel del mar), sao /fio < , índice de rox< , , spo < % ( , - , - , , ) . se recomienda crear o ajustar protocolos institucionales de sedoanalgesia basado en objetivos con escalas validadas. se recomienda el uso de analgesia multimodal que incluya analgésicos opioides, no opioides y bloqueos regionales en el paciente crítico por sospecha o diagnóstico de covid- . se recomienda sedación profunda con agentes como midazolam o propofol para mantener rass entre - y - en pacientes covid- con sdra severo, necesidad de uso de relajantes neuromusculares o posición prona. se puede considerar en planos de sedación superficial agentes como propofol o dexmedetomidina (coadyuvante) para mantener rass entre y - en pacientes seleccionados con sospecha o diagnóstico de covid- con sdra no severo. en la actualidad no se encuentra evidencia de alta calidad proveniente de ensayos clínicos, sino editoriales, series, reportes de casos y artículos de revisión de expertos ( ) ( ) ( ) . la creación y aplicación de protocolos de sedoanalgesia adaptados a cada institución ha mostrado disminución del tiempo en la uci y menores complicaciones ( , ) . es importante definir objetivos guiados por escalas, recomendándose sedación profunda o completa en situaciones especiales como ventilación mecánica invasiva por sdra severo, disincronía ventilatoria persistente, posición prona y bloqueo neuromuscular (bnm), como puede observarse en pacientes covid- con compromiso pulmonar severo. mientras que se debe procurar sedación ligera, cooperativa o no sedación en pacientes en ventilación mecánica invasiva en pacientes con sdra no severo, ventilación no invasiva y en el retiro de la ventilación ( , ) . los opioides han sido el pilar de la analgesia en dolor moderado a severo. el fentanilo es actualmente el más usado; el remifentanilo reduce el tiempo en ventilación en pacientes amci ® renales, hepáticos, ancianos y neurológicos; la hidromorfona se prefiere en el retiro de la ventilación y en pacientes extubados; y la metadona ha mostrado disminuir la tolerancia a opioides ( ) . se propone el uso de estrategias de analgesia multimodal asociando medicamentos no opioides como el paracetamol, ketamina a dosis analgésicas (< , mg/kg) en dolor somático, lidocaína en dolor visceral, y pregabalina en dolor neuropático ( ) . la sedación ligera o cooperativa son mejores con propofol en cuanto a tiempo de despertar y con dexmedetomidina para preservar funciones cognitivas y el impulso respiratorio, con menor desacondicionamiento ( ) . en sedación profunda, el propofol ha mostrado más fácil titulación y menos acumulación que el midazolam; sin embargo, su uso se ve limitado hasta horas y a dosis < , mg/kg/h, ante el riesgo de pris (síndrome relacionado con la infusión de propofol). el midazolam, sin dosis techo ni tiempo límite y de bajo costo, ha sido el más utilizado de los sedantes, disminuyendo su uso por su asociación con delirium y de retraso en los tiempos en ventilación; sin embargo, la pandemia covid- ha vuelto a aumentar su uso. la dexmedetomidina ha sido utilizada como adyuvante en sedación profunda, disminuyendo el consumo de sedantes, con menos efectos secundarios ( , ) . se muestran los medicamentos para sedoanalgesia y relajación neuromuscular que se pueden utilizar en los pacientes con covid- en la tabla . se recomienda iniciar una estrategia individualizada de ventilación mecánica ajustadas a las condiciones específicas de severidad en el paciente crítico con covid- . amci ® se recomienda la ventilación protectora en modos controlados por volumen o por presión que garanticen un volumen corriente < cc/kg de peso predicho teniendo como metas una presión meseta < cm h o y una presión de conducción < cm h o. se recomienda emplear fracciones inspiradas de oxígeno para lograr metas de saturación de acuerdo con la pao /fio entre y % en el paciente con sospecha o diagnóstico de covid- . en la paciente embarazada entre y %. se recomienda en el paciente crítico por covid- iniciar con peep individualizado a la severidad del compromiso pulmonar y ajustar el nivel de peep de acuerdo con la tabla de fio /peep. el estudio arma ( ) demostró que la ventilación con bajos volúmenes corrientes (vt) se asocia con reducción de: mortalidad (p= . ), en días libres de ventilación mecánica (p= . ) y días libres de falla orgánica (p= . ). una revisión sistemática posterior confirmó que el uso de bajos volúmenes se asocia con menor progresión a sdra ( ) . un metaanálisis que revisó estudios y meta-análisis en uci confirmó que la ventilación protectora era una de las tres intervenciones que mejora la sobrevida en pacientes con sdra ( ) . esto fue confirmado por landoni en un análisis de estudios multicéntricos con impacto en mortalidad en uci ( ) . recientes publicaciones han sugerido que en covid- puede haber dos fenotipos que se diferencian en la distensibilidad ( , ) . sin embargo, el mismo estudio arma demostró que "el beneficio de ventilación con vt más bajo fue independiente de la distensibilidad de las vías respiratorias, lo que sugiere que el vt más bajo fue ventajoso independientemente de la distensibilidad pulmonar". más aún, el uso de bajos vt se asoció con una reducción en las concentraciones de interleuquina lo cual explicaría el mayor número de días sin falla orgánica múltiple y sugeriría una reducida respuesta inflamatoria asociada a la ventilación protectora ( ) . con el tiempo la evidencia ha demostrado que la ventilación protectora, además de vt y presión meseta bajos, debe incluir presiones de conducción menores de cm h o ( ) ( ) ( ) . existe suficiente evidencia que demuestra que fio y pao altas se asocian con aumento en la morbimortalidad ( ) ( ) ( ) . en sdra el estudio arma y una más reciente publicación demostraron que el tener metas conservadoras de pao se asocia con mayor sobrevida ( , ) . hasta el momento, la literatura en ventilación mecánica ha demostrado que la mejor estrategia para ajustar el nivel de peep en sdra es la tabla de fio /peep ( , ) . amci ® se recomienda la ventilación mecánica protectora en sdra por covid- independiente del fenotipo de presentación. se recomienda la clasificación de fenotipos en sdra para pacientes con covid- para ajustar la toma de decisiones de manera individualizada en ventilación mecánica. el manejo ventilatorio en covid- tiene los mismos principios generales de los pacientes con sdra ( ) . sin embargo, la identificación de fenotipos podría impactar en la evolución y pronóstico ( ) . gattinoni ha postulado el desarrollo de un sdra típico (fenotipo h: con alta elastancia, alto cortocircuito, alto peso pulmonar) o una presentación atípica (fenotipo l: caracterizado por baja elastancia, bajo shunt, bajo peso pulmonar). ( ) . pelosi et al sugiere clasificar los pacientes con tres fenotipos similares ( ) . con base en tales fenotipos se han propuesto estrategias ventilatorias diferenciales para minimizar el daño inducido por el ventilador (vili) ( ): . el primer paso, en el fenotipo l, es revertir la hipoxemia aumentando la fio . . en el tipo l, hay varias opciones no invasivas: cánula nasal de flujo alto, presión positiva continua en la vía aérea (cpap) o ventilación no invasiva (niv). se debe evaluar el esfuerzo inspiratorio y, de estar disponible, medir la presión esofágica. la peep alta puede disminuir los cambios de presión pleural y detener el ciclo vicioso que exacerba la lesión pulmonar. sin embargo, la peep alta, en pacientes con distensibilidad normal, puede tener efectos hemodinámicos perjudiciales. en cualquier caso, las opciones no invasivas son cuestionables, ya que pueden asociarse con altas tasas de fracaso y retraso de la intubación. . la magnitud de las presiones pleurales inspiratorias puede determinar la transición del tipo l al h. la presión esofágica > cmh o aumenta el riesgo de vili y, por lo tanto, la intubación debe realizarse lo antes posible. los tipo l, si son hipercápnicos, pueden ser ventilados con volúmenes > ml / kg (hasta ml / kg). la posición prona debe ser usada solo en último caso, ya que las condiciones pulmonares son buenas. la peep debe reducirse a - cm h o, dado que la capacidad de reclutamiento es baja y el riesgo de falla hemodinámica aumenta. la intubación puede evitar la transición al fenotipo tipo h. . los pacientes tipo h deben ser tratados como sdra grave, incluyendo mayor peep, si es compatible con la hemodinamia, posición en pronación y soporte extracorpóreo. en el fenotipo se deben aplicar las estrategias de ventilación protectora convencional ( , ) . amci ® se recomienda en paciente con covid- considerar hipoxemia refractaria cuando no se obtienen las metas de oxígeno propuestas, a pesar de las maniobras ventilatorias recomendadas y cumple con los siguientes parámetros: pafi < , fio > , y peep apropiado, considerando la altitud. se recomienda considerar la utilización de ecmo, en sitios donde esté disponible y con alta experiencia para obtener resultados aceptables, en pacientes con hipoxemia refractaria luego de haber implementado ventilación protectora, relajación neuromuscular y posición prona. se recomienda administrar tromboprofilaxis en todos los pacientes con covid- con hipoxemia refractaria que no presenten contraindicaciones. la hipoxemia refractaria no es un concepto estático y absoluto, según la definición de berlÍn del sdra, se clasifica el sdra en leve, moderado y severo de acuerdo con la relación pao y fracción inspirada de oxígeno, con peep mayor de cms de h o. la hipoxemia severa es aquella que cuenta con una pafi menor de ( ) ( ) ( ) . la hipoxemia refractaria hace referencia a un estado de hipoxemia severa que a pesar de las diferentes estrategias ventilatorias no aumenta la pafi y tiene consecuencias en el estado ácido básico y metabolismo celular permitiendo una anaerobiosis ( , ) . para definir la hipoxemia refractaria deben coincidir varios escenarios , una pafi menor de , una fracción inspirada de oxígeno mayor de . , a pesar de un peep apropiado no se tiene en cuenta en la definición el ph ni la paco ni el tiempo transcurrido ( ) . algunas de las medidas terapéuticas no ventilatorias que se han empleado en sdra y covid- con hipoxemia refractarias son la oxigenación con membrana extracorpórea (ecmo) y la tromboprofilaxis o anticoagulación de rutina. la oxigenación extracorpórea a través de una membrana ha sido una estrategia controvertida en pacientes con hipoxemia refractaria de diferentes orígenes, en la epidemia de la influenza por el virus h n fue usada en pacientes con hipoxemia refractaria teniendo resultados aceptables ( ) . en el estudio eolia los resultados no mostraron mejoría en la supervivencia, aunque hay diferentes posiciones y estudios post hoc de este ensayo clínico con beneficios, su uso se limita a casos muy restringidos y en sitios de alta experiencia para obtener resultados aceptables ( ) . en sdra por covid- el ecmo se ha usado en hipoxemia refractaria entre un a . % en diferentes series con resultados variables ( , , ) . un tipo de pacientes hipoxémicos y con ventilación mecánica han presentado cuadros tromboembólicos pulmonares en estos casos la trombólisis de rescate con activador de plasminógeno tisular rtpa (alteplase) se ha recomendado con resultados alentadores en serie de casos, pero su evidencia es muy débil para ser recomendada( - ). dada la alta frecuencia de enfermedad tromboembólica reportada en covid- se ha reportado la utilidad de la tromboprofilaxis, especialmente en casos de dímero d o índice de sic elevado ( ) . amci ® se recomienda monitorizar sistemáticamente la oxigenación con los índices: pao /fio y sao /fio , y en donde esté disponible el monitoreo continuo con capnografía. se recomienda monitorizar de forma rutinaria la presión meseta y la presión de conducción como estrategia al pie de la cama para verificar la ventilación protectora. el sdra y covid- , es una condición dinámica que apenas se está caracterizando, hay varias presentaciones que no cumplen con todos los criterios de berlÍn ( , ) . gattinoni ha caracterizado en dos presentaciones el sdra en los pacientes con neumonía por coronavirus sars-cov- , una con alta compliance, mínima reclutabilidad; la otra con baja compliance, pulmones pesados y reclutabilidad, tal vez esta presentación sea el verdadero sdra ( , , ) . los pacientes que requieren ventilación mecánica por falla ventilatoria en covid- , son los que mayor mortalidad tienen al parecer por la lesión pulmonar inducida por la intubación tardía y el gran esfuerzo respiratorio con presiones transpulmonares oscilantes y muy negativas ( , , ) . la monitoria de estos pacientes soportados con ventilación mecánica tiene dos objetivos: el primero detectar el deterioro clínico para sugerir estrategias más avanzadas como el ecmo, y el segundo es evitar el daño pulmonar inducido por la ventilación mecánica. se debe tener presente la mayor posibilidad de contagio con el número de manipulaciones en el paciente, por esto nunca olvidar el perfecto uso de los elementos de protección personal y disminuir el número de contacto con el paciente. las metas que se buscan con la ventilación mecánica en el paciente con sdra por covid- son mantener una oxigenación adecuada teniendo en cuenta la altura sobre el nivel del mar con pao entre y mmh y metas de saturaciones reportadas entre y % a y % , mantener una ventilación adecuada evitando el espacio muerto , disminuir el trabajo respiratorio y protegiendo el pulmón del daño ocasionado por la ventilación mecánica y las repercusiones hemodinámicas ( ) .  el confort de los pacientes en ventilación mecánica es la principal señal de un uso adecuado del modo ventilatorio y los parámetros ventilatorios apropiados para la patología y demanda del paciente ( ) .  las curvas y bucles son herramientas indispensables para valorar la mecánica respiratoria del paciente soportado con ventilación mecánica, se puede diagnosticar amci ® las asincronías del paciente y el ventilador, el origen, tipo y frecuencia además de la respuesta al manejo. también se evalúa la resistencia de la vía aérea ( ) . variables fisiológicas:  es importante valorar la oxigenación del paciente, la literatura actual sugiere el monitoreo de la pafi es el más representativo y sencillo test para valorar la oxigenación y representa el shunt pulmonar, se debe hacer mínimo diariamente, o cuando se haga una intervención en el ventilador o paciente; en sdra por covid- la hipoxemia se relaciona directamente con mortalidad, debe mejorar con la ventilación mecánica ( , ) .  la medición de la paco indica la de la ventilación, la hipercapnia tiene relación directa con el espacio muerto en el paciente con sdra, y varios estudios la relacionan con la mortalidad. puede evaluarse directamente en los gases arteriales o relacionarla con el pco expirado por medios de la capnografía, gattinoni propone una forma de evaluarla al lado de la cama del paciente relacionando el etco /paco , cuando es < de sugiere un shunt elevado y mayor espacio muerto; áreas de pulmón ventiladas y no aireadas. otras tecnologías incluidas en el ventilador moderno como la capnografía volumétrica se está validando para evaluar el espacio muerto, la reclutabilidad y la titulación de peep ( , ) .  la saturación venosa mixta svo , refleja de manera subrogada la función ventricular, no todos los pacientes tienen catéter de arteria pulmonar para su medición por lo que se está reemplazando con el ultrasonido en la cabecera del paciente; recordar que el % de los pacientes con sdra cursan con falla ventricular derecha ( ) . monitoria de mecánica ventilatoria y protección pulmonar:  para evitar el daño pulmonar debe propender por un volumen corriente bajo ( - ml/kg de peso predicho) y presión plateau menor de cms h , para garantizar la ventilación con protección pulmonar ( , ) .  driving pressure ( presión cambiante de la vía aérea, presión diferencial o presión de conducción) es la presión plateau (presión pico en ventilación controlada por presión) menos peep, debe ser menor de cm h , está relacionado con aumento en la mortalidad en pacientes ventilados por que representa una medición indirecta del strain pulmonar porque relaciona el volumen corriente con la compliance del sistema respiratorio y este a su vez se relaciona con el volumen espiratorio pulmonar final ( ) .  la medición de la compliance del sistema respiratorio es necesaria y nos clasifica el paciente de acuerdo con su fenotipo para trazar el plan de manejo ventilatorio, cuando la compliance es baja, esto se puede hacer al lado de la cama del paciente con los ventiladores modernos ( , ) .  la construcción de la curva presión/volumen aún es una herramienta útil para ubicar el área de ventilación segura del paciente, evitando el atelectrauma y la sobredistensión pulmonar(estrés) , el peep se calcula dos puntos por encima del punto de inflexión inferior y el punto de inflexión superior nos indica hasta dónde podemos aumentar el volumen corriente este punto debe estar por debajo de cms h para evitar la sobre distensión, con los ventiladores modernos se puede construir esta curva ( , ) . amci ®  las curvas presión tiempo en pacientes ventilados con modos volumétricos pueden monitorizar la resistencia de la vía aérea, la compliance pulmonar, el trabajo respiratorio, las curvas de flujo puede también indicar si se presenta autopeep, resistencia aumentada de la vía aérea entre otras ( ) .  presión transpulmonar, en casos más complicados donde es más difícil obtener la meta de oxigenación a pesar del peep en aumento una opción es el catéter esofágico, para medir la presión transpulmonar en la inspiración y espiración y calcular así el stress pulmonar y evitar las presiones oscilatorias y sobre todo negativas para evitar el daño pulmonar. esta herramienta también ayuda a evaluar el trabajo respiratorio, y el diagnóstico de las asincronías que se presenten en el paciente ventilado ( , ) . se recomienda no utilizar de forma rutinaria la relajación neuromuscular en el paciente crítico con covid- con sdra. se recomienda utilizar la relajación neuromuscular en pacientes en posición supino o prono, que están fuera de parámetros de protección pulmonar (presión de conducción mayor y presión plateau mayor a ) con pafi menor y cuando ya no es posible limitar el volumen corriente. se debe considerar la utilización de protocolos estandarizados con el fin de disminuir la variabilidad, y según disponibilidad seleccionar el cisatracurio como primera opción, en caso de escasez se pueden utilizar otras opciones teniendo en cuenta su farmacodinamia y farmacocinética. el de marzo de , la organización mundial de la salud emite una serie de orientaciones para el manejo de la infección respiratoria aguda grave (irag) en pacientes con sospecha o diagnóstico de covid- . en el paciente críticamente enfermo con sdra moderado o grave (pao /fio < ) por covid- no está indicado de forma sistemática el bloqueo neuromuscular mediante infusión continua debido a que no se cuenta con evidencia suficiente que sustente mejoría en la supervivencia con respecto a una estrategia de sedación ligera sin bloqueo neuromuscular, se debe considerar su uso cuando se evidencia asincronía paciente-ventilador a pesar de la sedación, hasta el punto de que no se pueda limitar el volumen corriente de forma fiable, hipoxemia o hipercapnia que no mejoran con el tratamiento ( ) . recomendaciÓn se recomienda no utilizar de forma rutinaria oni en pacientes adultos que presenten sdra e infección por sars-cov- . fuerte en contra fundamento a la fecha (mayo de ) no contamos con estudios sobre el uso de óxido nítrico inhalado (oni) como tratamiento de pacientes con infección covid- . existe evidencia indirecta sobre el uso de oni en el síndrome de dificultad respiratoria aguda (sars-cov), y la infección por coronavirus en el síndrome respiratorio de oriente medio (mers-cov) ( ) . en cochrane realizó una revisión sistemática que incluyó ensayos de calidad moderada con pacientes adultos con sdra tratados con óxido nítrico inhalado. los resultados no mostraron ningún efecto estadísticamente significativo sobre la mortalidad (rr . , % ci . - . ). se mostró mejora transitoria en el índice de oxigenación a las horas (md (diferencia media) - , , ic del % - , a - , ) y mejoría en pao /fio a las horas (md , , ic del % , a , ). no se identificó diferencia significativa en los días libres de ventilación y finalmente se presentó aumento estadísticamente significativo en la incidencia de insuficiencia renal en pacientes con óxido nítrico inhalado (rr , , ic del % , )( ). amci ® en se realizó un estudio observacional que incluyó pacientes tratados de dos hospitales de beijing con oni como tratamiento para sars ( ) . en comparación con ningún tratamiento, oni mejoró la saturación arterial de oxígeno (spo ) de % a % (p< . ); se asoció a menor necesidad de oxígeno suplementario (p< . ) y menor necesidad y retiro de cpap y bial (p < . ). los cambios en radiografía de tórax mejoraron en de los pacientes que recibieron oni. sin embargo, debido a problemas graves de validez por pequeño tamaño de la muestra (n= , oni= , control= ), no aleatorización y no enmascaramiento en la asignación, se considera que este estudio cuenta con baja calidad metodológica, lo cual limita la interpretación de los resultados. en un estudio retrospectivo multicéntrico que incluyó pacientes con mers-cov en condición crítica en arabia saudita, se mostró que el manejo con ventilación no invasiva (niv) tenía mayor probabilidad de requerir óxido nítrico en comparación con los pacientes con ventilación mecánica invasiva ( , % vs , %, p a , ) ( ) . en una serie de casos en la que participaron pacientes con infección por mers-cov confirmada o probable, pacientes recibieron oni debido a hipoxemia refractaria. en el seguimiento a días, cinco de los pacientes continuaron vivos ( ) . los estudios sobre mers-cov se limitaron a una serie de casos y una cohorte retrospectiva con baja calidad de evidencia. en ambos estudios, los pacientes recibieron otras terapias de rescate (relajación neuromuscular, ventilación oscilatoria de alta frecuencia, ecmo y posición en prono), por lo tanto, se desconoce el efecto terapéutico clínico del oni en el tratamiento de la infección por mers-cov. a la fecha ( de mayo de ) tres ensayos clínicos evalúan el papel del óxido nítrico inhalado en pacientes con covid- y sdra leve/moderado, y como profilaxis para los trabajadores de la salud covid- (tabla ). tabla . comparación de ensayos clínicos que evalúan el papel del óxido nítrico inhalado en pacientes con covid- y sdra leve/moderado, y como profilaxis para los trabajadores de la salud covid- . no se cuenta con evidencia por el momento que respalde el uso de óxido nítrico inhalado en pacientes con covid- . los resultados de los ensayos en curso, así como ensayos clínicos de alta calidad son necesarios para apoyar su uso. sólo evidencia indirecta metodológicamente limitada de óxido nítrico en pacientes con sras mostró una mejor oxigenación, una menor necesidad de oxígeno suplementario y mejoría en la radiografía de tórax. en pacientes con sdra y mers-cov, no mostró un beneficio claro e incluso mostró un mayor riesgo de insuficiencia renal ( ) . otros estudios han evaluado el efecto tóxico asociado a su uso documentando metahemoglobinemia( ), inhibición de la agregación plaquetaria y formación de dióxido de nitrógeno ( ) . razones por la cuales guías recientemente publicada no recomienda su uso de forma rutinaria( ). recomendaciÓn se recomienda el uso temprano de la ventilación en posición prona, por al menos horas continuas, en pacientes con sdra por covid- con pao /fio < mmhg. la ventilación en posición prono como estrategia ventilatoria propuesta desde los años ( ), cuenta con evidencia que demuestra resultados positivos en cuanto a mejoría de mortalidad, mejoría en el trastorno de oxigenación y el reclutamiento alveolar en pacientes con sdra. los mecanismos por los cuales la posición prona conduce a la mejoría en el trastorno de oxigenación y del reclutamiento alveolar en los pacientes con sdra, incluyen ( ) ( ) ( ) ( ) : amci ®  mejoría de la relación ventilación/perfusión y mayor homogeneidad en la distribución de aire en los pulmones.  aumento del volumen de fin de espiración.  disminución del efecto compresivo del corazón en los pulmones.  mejoría del drenaje de las secreciones.  optimización del reclutamiento alveolar, con mejoría de la distribución del volumen corriente, a su vez, limita el desarrollo del daño alveolar pulmonar. los estudios coinciden en el efecto benéfico que esta terapia tiene en la mejoría de la oxigenación, el objetivo se centrará en evaluar las recomendaciones con respecto a:  beneficio de la terapia con respecto a la mortalidad al día , al día y a los meses.  beneficio de la terapia según el grado de severidad de sdra con respecto la relación pao /fio .  tiempo de terapia en posición prono con mayor beneficio.  número de sesiones de la terapia en posición prono.  recomendaciones según balance riesgo/beneficio en lo que respecta a los efectos adversos: retiro o desplazamiento no planeado de catéteres, obstrucción de tubo endotraqueal, neumonía asociada a ventilador, lesiones de presión. se eligieron artículos que con las características metodológicas consistentes ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . de estos ocho artículos se excluyó uno por corresponder a pacientes pediátricos ( ) . al evaluar los escritos de forma cronológica, se puede apreciar en los primeros artículos ( , ) , la dificultad para lograr enrolar (reclutar) el suficiente número de pacientes, de tal manera que algunos estudios fueron detenidos de forma prematura ( , , , ) . era entonces esperable que los resultados no fueran concluyentes, y que no lograran ser robustos, al no alcanzar el tamaño de muestra deseado, comprometiéndose la confiabilidad, el poder y corriendo el riesgo de obtener resultados falsamente negativos. sin embargo, se podía percibir en los diferentes estudios, una notoria mejoría en la oxigenación, sin repercusión en la mortalidad ( ) ( ) ( ) ( ) ( ) ( ) . por otro lado, es necesario tener en cuenta que los estudios iniciales ( ) ( ) ( ) ( ) no se realizaron con el uso de ventilación protectora asociada a la pronación. esto es un elemento pertinente, pues la ventilación protectora puede per se, brindar un efecto adicional en la mejoría de la oxigenación. otro efecto importante que debe analizarse es el bloqueo neuromuscular, cuya evidencia hoy sugiere su uso en criterios ya mencionados ( ) . con el tiempo y según la experiencia de cada centro, se fue utilizando con menor dificultad ( ) . sin embargo, no se tenía aún claro qué tipo de pacientes obtenían el mayor beneficio de la terapia, además que el tiempo de la terapia en posición prona, seguía siendo una incógnita. la evidencia reflejaba hasta el momento que los pacientes con sdra más severos y la terapia aplicada por más tiempo se asociaban con una tendencia a la reducción en mortalidad. para dirimir qué tipo de pacientes se beneficiarían más de la terapia, se tomó como base, la severidad del sdra según la relación pao /fio ( ) . a pesar de que los estudios iniciales( - ) enfrentaban el reducido tamaño de muestra, algunos análisis identifican beneficio de la mortalidad ( ) en pacientes con sdra más severo, constituyendo un probable umbral de beneficio cercano y por debajo de - mmhg ( ) . amci ® antes del estudio proseva ( ) en totalidad estudios reportan mortalidad al día ( , ) , un estudio mortalidad al día ( ) , uno estudio mortalidad al día ( )y uno mortalidad al día ( ) . sin embargo, al tomar todos los estudios, aún no se alcanzaba suficiente significancia estadística para reducir la mortalidad a los días y meses. con el estudio proseva -guerin et als -en el año ( ) , se alcanza más poder estadístico, demostrando un beneficio importante en pacientes con pao /fio menor de mmhg, ventilados con bloqueo neuromuscular y ventilación protectora en su totalidad, y logrando una reducción de la mortalidad al día y mantenida hasta el día con respecto al grupo control ( . % ( de participantes) versus . % ( de ) (p< . ). de tal manera que, según la evidencia disponible, en lo que al trastorno de oxigenación se refiere (según la relación pao /fio ), sugiere que el mejor candidato para esta estrategia ventilatoria es el paciente con sdra severo con una pao /fio menor de mmhg. es de primordial importancia detenerse a considerar por otra parte, el número de horas que se implementaría la terapia. el estudio inicial realizado por gattinoni et al. ( ) , llevó a los pacientes a un período corto de horas, sin encontrar resultados positivos en mortalidad. (resultados que no se pueden solamente atribuir a la calidad del estudio, sino también, al reducido número de horas de la ventilación en posición prono). mancebo et als (la abreviación latina para "otros "es et al.), y fernández et al. ( , ) por su parte, optan por ventilar un mayor número de horas ( - horas) obteniendo resultados (que sugieren una reducción en mortalidad) con tendencia a disminuir mortalidad. si bien diferentes metaanálisis sugieren no (la ausencia de beneficio) beneficio de la ventilación en prono ( , ) , los resultados son diferentes cuando se aborda la terapia con períodos mayores a horas ( ) . teniendo en cuenta, que el estudio con más poder estadístico ( ) postula horas de terapia en posición prono, la recomendación es la pronación por un tiempo mayor a horas, contemplando hasta las horas por sesión. otra pregunta que surge con frecuencia es el número de veces que se puede implementar la terapia. existen diferentes estudios en los cuales se indica el número de veces en promedio en que se llevó el paciente a posición prono ( , ) , otro protocolo en donde se estipula un número límite de días en los que se llevó a cabo la terapia( ), y otro estudios en los cuales no se precisó el número de sesiones de la terapia ( , ) . se podría entonces recomendar con respecto a la mayor evidencia disponible ( ) , pronar a los pacientes en varias sesiones ( en promedio) (depende de los criterios para continuar o suspender el prono que deben ser individualizados para cada paciente, en cada zona geográfica y en cada unidad de cuidados intensivos, es difícil saber si es el promedio para todos), y considerarla más veces si es necesario. en lo que respecta a los efectos adversos, tres estudios reportaron barotrauma y neumonía asociada a ventilador ( , , ) ; dos estudios desplazamiento de catéter central ( , ) y siete estudios reportaron extubación ( ) ( ) ( ) ( ) ( ) ( ) ( ) . sin embargo, los efectos adversos no alcanzaron significancia estadística para proscribir la terapia ( ) . recientemente fue publicado el consenso colombiano de sdra( ) en el cual se hace referencia a las recomendaciones para realización de ventilación prono. se presenta la lista de chequeo, y medidas que deben ser realizadas en la maniobra para lo cual se cuenta con la participación de terapia respiratoria, enfermería y médico. se recomienda implementar un protocolo de retiro de ventilación mecánica basado en la prueba de respiración espontánea y articulado con un protocolo de sedación y analgesia en el paciente críticamente enfermo por sospecha o diagnóstico de covid- . desde diciembre de , un número de casos de neumonía por síndrome respiratorio agudo severo sars-cov /covid- en wuhan china se identificaron, como causa de insuficiencia respiratoria aguda( ). el síndrome de dificultad respiratoria aguda (sdra) ocurre en el % de los pacientes hospitalizados y en el % de los pacientes admitidos a la unidad de cuidados intensivos (uci) en wuhan ( ) . mientras la ventilación mecánica es una intervención que potencialmente salva la vida, esta puede llevar a múltiples complicaciones y contribuir a la lesión pulmonar ( ) . es por todo esto que el retraso en el retiro de la ventilación mecánica puede aumentar el riesgo de amci ® infecciones, aumenta la sedación innecesaria, el trauma de la vía aérea y aumento en el costo de la atención de estos pacientes ( ) . el retiro de la ventilación mecánica es un proceso de tres pasos, el primero es conocido como preparación la cual depende de variables fisiológicas, criterios clínicos y predictores de weaning (destete), el segundo paso es el propio weaning, el cual consiste en la disminución del soporte ventilatorio entregado al paciente, con el objetivo de llevar al último paso que es la extubación( ), ilustración . por todo lo anterior, se recomienda realizar un proceso de retiro de ventilación mecánica invasiva adoptando un protocolo, seleccionando adecuadamente a los pacientes, ya que evidencia sugiere que la adecuada selección de los pacientes disminuye los días de ventilación mecánica, disminuye la estancia hospitalaria y la estancia en uci ( ) . se recomienda realizar el retiro de la ventilación mecánica siguiendo los pasos antes mencionados, iniciando con la preparación, la cual consiste en: preparación . asegurarse que la lesión pulmonar que llevó a la falla respiratoria esté resuelta. . adecuado intercambio de gas, definido como adecuados índices de oxigenación con peep (presión positiva al final de la expiración) a cmh o, y fio (fracción inspirada de oxígeno) < . . al igual que el proceso de intubación, es un proceso que genera aerosoles por lo cual se recomienda la aplicación de lidocaína dosis de , a , mg por kilogramo de peso, a minutos antes la extubación con el objetivo de disminuir el reflejo de tos ( ) y la exposición del personal de salud. se recomienda en el paciente con sospecha o diagnóstico de covid- a quien se considera realizar vmni, utilizarla en salas de presión negativa, donde estén disponibles, que garanticen la seguridad del recurso humano, con todo el equipo de protección personal necesario. se recomienda considerar la vmni en pacientes con covid- con hipoxemia leve (pao /fio < y > o sao /fio < y> ) en salas de presión negativas, donde estén disponibles que garanticen la seguridad del recurso humano, con todo el equipo de protección personal necesario. fuerte a favor se recomienda considerar la vmni en pacientes con covid- con hipoxemia leve (pao /fio < y > o sao /fio < y> ) y con historia de epoc o cuadro de edema pulmonar agudo asociado en salas de presión negativas, donde estén disponibles que garanticen la seguridad del recurso humano, con todo el equipo de protección personal necesario. se recomienda colocar doble filtro en el circuito del ventilador para reducir el riesgo de generación de aerosoles en vmni del paciente crítico con sospecha o diagnóstico de covid- . se recomienda la intubación inmediata en pacientes críticamente enfermos por covid- si se evidencia respiración toraco-abdominal, uso de músculos accesorios, frecuencia respiratoria > , hipoxemia (pao /fio < o sao /fio < ), fracaso ventilatorio (ph< . con paco > mmhg), hacor> . existe suficiente evidencia que demuestra que la vmni es una estrategia que reduce la mortalidad en pacientes críticos ( , , ) . además, reduce la necesidad de intubación. los números de casos necesarios a tratar (nnt) son: ocho para salvar una vida y para evitar una intubación ( ) . estos desenlaces son fundamentalmente en pacientes con epoc y edema pulmonar agudo ( ) ( ) ( ) ; también hay evidencia a favor, aunque menos fuerte, en pacientes inmunosuprimidos ( , ) . se ha planteado mayores tasas de éxito con interfaces faciales totales o con helmet ( , ( ) ( ) ( ) ( ) ( ) . por el contrario, en falla respiratoria hipoxémica hay evidencia en contra del uso de vmni ( ) . la experiencia previa con h n , sars y mers no apoya el uso de la vmni en falla respiratoria hipoxémica de origen viral ( ) ( ) ( ) ( ) ( ) ( ) . además, se ha cuestionado el uso de vmni en covid- por el riesgo de contagio al generar aerosoles ( ) . recientemente se demostró que la distancia de dispersión de aerosoles era menor de un metro ( ) . por otro lado, el fracaso de la vmni se ha asociado con alta morbimortalidad ( ) ( ) ( ) . ello obliga a evaluar estrictamente la posibilidad de éxito o fracaso. así, en falla respiratoria amci ® hipoxémica la escala hacor ha sido validada para este fin y un puntaje> contraindicaría la vmni ( ) . adicionalmente si se emplea la vmni el prolongar la decisión de intubación puede aumentar la mortalidad y es por ello necesario monitorizar estrictamente al paciente y evaluarlo para establecer, ojalá antes de dos horas, si el paciente responde a la vmni ( , , ) . las indicaciones para intubación en este caso son respiración toracoabdominal, uso de músculos accesorios, frecuencia respiratoria mayor de , hipoxemia (pao /fio < o sao /fio < ), fracaso ventilatorio (ph< . con paco > mmhg), hacor> o índice de rox (spo /fio )/frecuencia respiratoria) < ( , , , , , ) . recomendaciÓn se sugiere el uso de posición prono en pacientes no ventilados críticamente enfermos por covid- que no responden a la oxigenoterapia convencional de acuerdo con los protocolos institucionales, las condiciones de cada servicio y la tolerancia individual de cada paciente. débil a favor fundamento los pacientes con enfermedad por coronavirus (covid- ) están en riesgo de desarrollar un síndrome de dificultad respiratoria aguda (sdra) ( ) . en pacientes intubados con síndrome de dificultad respiratoria aguda grave, la posición prona (pp) temprana y prolongada (al menos horas diarias) mejora la oxigenación y disminuye la mortalidad ( , ) .debido a que las unidades de cuidados intensivos (uci) están sobrecargadas con pacientes con covid- , la pp en paciente despierto con respiración espontánea puede ser útil para mejorar la oxigenación y prevenir las transferencias hacia uci. un estudio describió la viabilidad del uso de la ventilación no invasiva y la cánula de alto flujo asociado a la pp estableciendo su tolerancia y su seguridad en pacientes con sdra moderado y severo( ); la pronación puede reclutar todas las regiones pulmonares y favorecer el drenaje de secreciones de la vía respiratoria, mejorando el intercambio gaseoso y la supervivencia en el síndrome de dificultad respiratoria (sdra) ( ) . en una comunicación corta proveniente de italia en el cual se incluyeron pacientes que son sometidos al pp asociada con el uso de ventilación no invasiva, se concluye que proporcionar niv en la posición prona a los pacientes con covid- y sdra en salas generales en un hospital en italia era factible. la frecuencia respiratoria disminuyó durante su implementación y la oxigenación mejoró durante una pronación posterior a su línea de base. si la intubación se evitó o se retrasó, queda por determinar ( ) . en otro reporte de caso, publicado recientemente por un grupo francés( ) de pacientes con covid- e insuficiencia respiratoria hipoxémica manejados fuera de la uci, el % amci ® fue capaz de tolerar pp durante más de horas. sin embargo, la oxigenación aumentó durante el pp solo un % y no se mantuvo en la mitad de los pacientes después del regreso a la posición supina. estos resultados son consistentes con los hallazgos de pequeños estudios previos de pp en pacientes no intubados ( ) . un ensayo clínico controlado que evalúe el uso del pp en pacientes no intubados puede ser un mecanismo para seleccionar pacientes que bien puedan beneficiarse de esta estrategia terapéutica. dada la evidencia débil que soporta el uso del pp en pacientes no intubados en términos de la disminución de la necesidad de entubación o ingreso a cuidados intensivos y la duda razonable de aumentar desenlaces deletéreos en aquellos pacientes en los cuales se retarde el tiempo de intubación, no se emite recomendación, a favor o en contra, del empleo de esta estrategia de manera rutinaria. en situaciones en las cuales hay limitación de recursos y de disponibilidad de camas en cuidados intensivos el uso de la pp asociada a vni o cánula de alto flujo podría ser una estrategia útil para mejorar la oxigenación en pacientes infectados con covid- e hipoxemia. se recomienda considerar la elevación de biomarcadores como la troponina i o t y el nt-pro-bnp en el paciente con covid- como indicadores de injuria miocárdica aguda, sin embargo, no reemplazan la ecocardiografía en el enfoque del paciente con sospecha de disfunción miocárdica. fuerte a favor fundamento la injuria miocárdica aguda asociada a covid- se reporta con frecuencia teniendo en cuenta los cambios en biomarcadores como la troponina y cambios electrocardiográficos, pero su impacto en la función cardíaca se desconoce y mucho menos su correlación con los cambios ecocardiográficos. los pacientes con covid- pueden desarrollar una serie de complicaciones cardiacas desde injuria miocárdica, arritmias, infarto, hasta miocarditis fulminante con falla cardiaca aguda y shock cardiogénico ( ) . la troponina i, se ha encontrado más elevada en pacientes con curso fatal por covid- ( ) . los niveles de nt-pro-bnp han sido reportados con elevación severa en pacientes con miocarditis y disfunción sistólica, con una disminución progresiva en relación a la mejoría de los pacientes, pero no parece tener un correlación significativa con el cambio de la fracción de eyección (fevi) ( ) . la evidencia clínica sugiere que la elevación de los biomarcadores es más relacionada al compromiso sistémico que el daño miocárdico directo, q. deng y colaboradores en un análisis retrospectivo de pacientes, reportaron niveles iniciales de troponinas normales casi en la mayoría, en el , % de los casos los niveles incrementaron significativamente, principalmente en los que fallecieron y solo pacientes tenían fevi menor al % y ninguno inferior al %, lo cual no sugiere una asociación entre las dos amci ® pruebas ( ) . en una publicación donde se compara el fenotipo de pacientes con covid- con un histórico de pacientes con sdra por influenza ( ) , se encontró que los primeros tenían mayor elevación de troponinas % vs %, pero en los parámetros ecocardiográficos contrario a lo que se esperaría los índices de rendimiento ventricular fueron mayores para el grupo de covid- : Índice cardiaco . vs . l/m/m ; fevi vs %; tapse vs mm, nuevamente aunque no fue uno de los objetivos del estudio, parece no encontrarse correlación entre los biomarcadores que sugieren injuria miocárdica y los parámetros ecocardiográficos, el cual constituye uno de los pilares de la exploración cardiaca. se recomienda considerar como marcadores iniciales de mal pronóstico en el paciente crítico con covid- con sospecha de disfunción miocárdica aguda la elevación persistente de troponina i, mioglobina o creatin kinasa; independiente de la fracción de eyección del ventrículo izquierdo evaluada mediante ecocardiografía. fundamento los pacientes con covid- admitidos a la unidad de cuidados intensivos presentan con frecuencia disfunción cardiaca primaria, que puede corresponder a cardiomiopatía por estrés o miocarditis viral, pero también pueden ser consecuencia del compromiso sistémico ( , ) . aunque parece que en los fenotipos cardiovasculares estudiados, el compromiso hemodinámico severo de la función sistólica izquierda y derecha es menor ( ) . en el estudio de deng y colaboradores con pacientes con covid- , la fiebre, la disnea, hipoxemia, la obesidad y niveles elevados de cpk, troponina y nt-pro-bnp se relacionaron significativamente con mayor severidad ( ) . en el subgrupo de pacientes con miocarditis frente a controles, el perfil clínico se describe con mayor edad, niveles de temperatura más elevados ( . ± . vs . ± . ; p: . ), mayor proporción de disnea ( , vs %), y de dolor torácico ( , vs , %). en los pacientes fallecidos el % tuvieron picos de elevación de troponina i y de nt-pro-bnp dentro la semana que precedió la muerte, el % presentaron alteraciones electrocardiográficas y solo el % presentaron fracción de eyección menor o igual al % ( ) . shi y colaboradores, enrolaron pacientes para describir el significado clínico del compromiso miocardio de pacientes con covid- en wuhan, pacientes fallecieron, de los cuales el % presentaron injuria miocárdica aguda ( ) . el área bajo la curva (auc) de la troponina i inicial para predecir muerte intrahospitalaria fue de , (ic %, de , - , ) con una sensibilidad y especificidad del %, el auc para mioglobina fue de . y para cpk-mb fue de , ( ). un punto de corte para el pico más alto de troponina i de . , tuvo un hazard ratio para mortalidad de . (ic %, . - . ; p= . ). en un análisis multivariado la edad avanzada, la respuesta inflamatoria y las enfermedades cardiovasculares subyacentes se asociaron con mayor riesgo de lesión miocárdica en pacientes con covid- . con la información disponible parece que los biomarcadores de lesión miocárdica aguda elevados amci ® al ingreso y de forma persistente pueden predecir el riesgo de mortalidad intrahospitalaria en los pacientes con sospecha o diagnóstico de covid- con afectación cardiovascular. se recomienda no realizar de forma rutinaria ecocardiografía en pacientes críticos con covid- . se debe practicar ecocardiografía en pacientes con sospecha o diagnóstico de covid- si presenta alguna de las siguientes condiciones: . síntomas y signos de insuficiencia cardíaca aguda de novo. . shock o deterioro súbito hemodinámico refractario a líquidos y/o vasoactivos con sospecha de origen cardiogénico. . sospecha de infarto agudo de miocardio o embolismo pulmonar para determinar intervenciones terapéuticas con un beneficio clínico. . cambios en el electrocardiograma, arritmias ventriculares o paro cardiorrespiratorio no explicados por otra causa. para nuestro conocimiento, en el momento no existe estudios clínicos que evalúen los criterios para realización de ecocardiograma en el paciente con covid- . las sociedades de ecocardiografía han recomendado realizar el ecocardiograma en el contexto clínico en el cual, la información obtenida proporcione un cambio en la conducta o se espere un beneficio clínico al realizar este procedimiento ( ) ( ) ( ) ( ) . igualmente, se recomienda realizar el examen a la cabecera del paciente y el escaneo debe ser dirigido a contestar preguntas específicas según el contexto clínico del paciente ( ) ( ) ( ) ( ) ( ) . ward et al, en su publicación describe cómo el uso del ecocardiograma limitado (dirigido) en la university of chicago medicine (ucm), aumentó significativamente durante la pandemia ( % frente a %, p < . ), posterior a la implementación de recomendaciones sobre el uso apropiado de la ecocardiografía en tiempos de pandemia ( ) . los pacientes con infección por sars -cov- pueden presentarse con comorbilidades cardiovasculares que potencialmente estén descompensadas y/o compromiso cardiovascular por covid- . en este último, podemos encontrar alguno de los siguientes fenotipos: falla cardiaca aguda en el marco de compromiso directo viral o secundario al estrés metabólico y liberación de citoquinas, síndrome coronario agudo, cor-pulmonar secundario a tep o por compromiso secundario al sdra ( , , , ) . las manifestaciones cardiovascular puede sospecharse en el marco de choque que no esté explicado por causas extracardiacas evidentes que no responde a líquidos, dolor torácico con clínica de síndrome coronario agudo, cambios electrocardiográficos y elevación de biomarcadores de lesión miocárdica, signos de falla cardiaca descompensada, deterioro súbito de la oxigenación, arritmias o paro cardiorrespiratorio ( , , ) . ante estas manifestaciones, el ecocardiograma podría ser útil para entender el origen de la descompensación aguda, al estar enfocado a amci ® responder preguntas acerca de la función ventricular global y segmentaria (en el abordaje de síndrome coronario agudo), compromiso del ventrículo derecho, alteraciones valvulares, derrame pericárdico, si existe una contribución cardiovascular al compromiso pulmonar, si en el marco del choque existe evidencia de componente cardiogénico y cómo podría guiarse/optimizarse el soporte hemodinámico de estos pacientes( - ). se sugiere en pacientes críticamente enfermos con covid- que cursan con shock y sdom, ajustar la monitoria a las condiciones clínicas del paciente y recursos disponibles. se puede considerar el cap para el monitoreo del gasto cardiaco, la valoración de la perfusión y orientar los elementos hemodinámicos del tipo de shock, el cap de gasto cardiaco continuo puede disminuir la exposición del personal de salud frente al catéter de medición convencional. se sugiere la utilización de la tdtp dependiendo de la disponibilidad del recurso para orientar el diagnóstico diferencial del sdra versus edema pulmonar cardiogénico en los pacientes con covid- . fundamento los pacientes con infección severa por sars-cov- , cursan con alto riesgo de falla renal y cardiovascular, con necesidad de un manejo restrictivo de líquidos, lo que justifica la monitoria estricta en uci ( , ) . el catéter venoso central es útil para la monitoria inicial de estos pacientes, sin embargo, su predicción a respuesta a volumen está limitada ( ) ( ) ( ) . la monitoría no invasiva tiene limitaciones en casos severos de inestabilidad hemodinámica, ventilación espontánea y en presencia de peep alto, lo que limita su uso para el cálculo de gasto cardiaco y la predicción de respuesta a líquidos ( , ) . la monitoria con cap puede ser considerada en pacientes con covid- que cursan con choque y doms, con el objetivo de realizar un diagnóstico definitivo de los componentes del choque, valorar la hipoperfusión, la función cardiaca y el estado de volemia ( , ) . igualmente, los pacientes con sospecha tep o compromiso del ventrículo derecho pueden beneficiarse de esta monitoria( ). richard et al, en su estudio determinaron los desenlaces asociados al uso de cap vs cvc en pacientes con shock, sdra, o ambos, sin evidenciar diferencias en mortalidad ( . % vs . % p =. ) o estancia hospitalaria. el uso de cap no garantiza la mejoría de desenlaces en pacientes con covid- , sin embargo, la presencia de una monitoria continua ayudaría a optimizar los recursos y disminuiría la interacción con el paciente, con menor exposición del equipo médico ( ) . la monitoria por tdtp puede utilizarse en pacientes con covid- que cursan con choque, buscando optimizar el manejo hídrico, valorar el agua extravascular pulmonar (evlw) y el índice de permeabilidad vascular pulmonar (pvpi) con el fin de establecer el diagnóstico amci ® definitivo del edema pulmonar: sdra vs cardiogénico ( ) ( ) ( ) . hu et al, en su estudio evaluaron los desenlaces del uso de evlw y la presión de cuña de la arteria pulmonar (pawp) como estrategias para el manejo de líquidos en pacientes sdra, no encontraron diferencias significativas en las tasas de supervivencia (p = , ). no obstante, en el grupo de evlw la duración de la ventilación mecánica y la estancia en la uci fueron significativamente menor (p < , ), al igual que el balance hídrico (p < . ), con mejoría significativa en los índices de oxigenación (p = . )( ). no se puede emitir una recomendación a favor o en contra para la utilización de un protocolo de ultrasonido rutinario a la cabecera del paciente (pocus). sin embargo, se podría considerar el uso en pacientes seleccionados, con los adecuados epp y desinfección de los equipos; donde el pocus pueda tener ventajas sobre otras modalidades de monitoria o en pacientes con limitaciones para monitoria invasiva que requieren evaluación del estado hemodinámico o determinación de severidad del compromiso pulmonar. las recomendaciones sobre la utilidad de pocus en pacientes con covid- están enfocadas principalmente en la evaluación de la severidad/progresión de la lesión pulmonar, diagnóstico de manifestaciones cardiovasculares, monitoria hemodinámica y en la guía de fluidoterapia ( , ( ) ( ) ( ) . en la valoración del compromiso pulmonar por covid- , el pocus ofrece una ventaja sobre otras modalidades de monitoreo, debido a la capacidad de enmarcar el compromiso pulmonar en una línea de tiempo según sus hallazgos: desde la aparición de un patrón de "líneas b", consolidaciones subpleurales con evolución a consolidaciones multilobares, irregularidades en el artefacto de la línea pleural y finalmente aparición de patrón de "líneas a" una vez inicie la recuperación, con adecuada correlación tomográfica ( ) ( ) ( ) ( ) . en la diferenciación del origen del choque, el pocus ha demostrado superioridad versus el concepto clínico al evaluar: función ventricular (incluyendo ventrículo derecho), vena cava inferior, líquido libre abdominal, lesiones aórticas, compromiso pulmonar y búsqueda de trombosis venosa profunda identificando tep ( , ) . en cuanto a la monitoria hemodinámica de pacientes con covid- , adicional a la función y gasto cardíacos, se recomienda variables dinámicas de respuesta a líquidos y ultrasonido pulmonar en el diagnóstico de sobrecarga hídrica ( ) . la variabilidad de gasto cardiaco calculado por pocus durante la elevación pasiva de miembros inferiores, identifica los respondedores a líquidos con sensibilidad del % y un lr (-): . [ %ci, . - . ]) ( ) . la variabilidad de la vena cava inferior muestra limitaciones en pacientes con aumento de presiones de cavidades derechas y respiración espontánea ( ) . en cuanto a otras modalidades de monitoría no invasiva, es importante conocer las limitaciones en el marco de compromiso hemodinámico severo, ventilación espontánea, alteraciones valvulares aórticas, entre otras ( ) . marik ( ) . el ultrasonido tiene limitaciones específicas como la necesidad de un operador experimentado y la adecuada calidad de las imágenes. adicionalmente, en los pacientes con covid- , esta modalidad de monitoreo requiere una mayor interacción con el paciente, mayor uso de epp en comparación con otras modalidades el pac( ). se recomienda perseguir al inicio de la reanimación del paciente críticamente enfermo con covid- , metas clínicas de fácil medición, como la presión arterial media (entre y mmhg) o el gasto urinario (mayor a , cc/k/h) y metas de perfusión como el lactato en sangre arterial (menor a mmol), la saturación venosa central de oxígeno (entre y %) y la diferencia veno arterial de co (menor a mmhg). se han reportado casos de disfunción ventricular como causa de choque asociado a covid- , sin embargo, no se ha descrito un manejo específico o cambios en las metas de reanimación para estos pacientes, las manifestaciones de hipoperfusión tisular son: alteración de la conciencia, oliguria, piel fría y moteada y pulso débil. a nivel de gases sanguíneos las metas de reanimación pueden ser globales como el lactato (en sangre arterial vn< mmol) y la diferencia veno arterial de co (pv-aco vn < mmhg) o regionales como la saturación venosa central de oxígeno medida en la sangre venosa tomada de un catéter central (vn: - %). se puede optimizar la perfusión, interviniendo los principales determinantes: fluidos para aumentar el volumen intravascular, inotrópicos para aumentar la fuerza de contractilidad, vasopresores para recuperar la presión de perfusión y transfusión de glóbulos rojos para aumentar la hemoglobina como transportador de oxígeno ( ) , las recomendaciones dadas en el documento anterior siguen siendo válidas e incluyen entre otras que todo paciente con covid- en estado de shock debe ser ingresado de forma inmediata a la unidad de cuidados intensivos, garantizando el aislamiento indicado, procurando recuperar la presión arterial media a valores > mmhg, para ello la utilización de un catéter venoso central en los pacientes que no responden al manejo inicial y el procedimiento debe ser realizado por el médico con mayor entrenamiento, idealmente guiado por ecografía si hay disponibilidad y las competencias, así mismo las estrategia de control estricto de fluidos para no generar efectos deletéreos relacionados a la sobrecarga de volumen, es lo más indicado. se recomienda en la reanimación inicial de pacientes en estado de shock con sospecha o amci ® diagnóstico de covid- , guiar la fluidoterapia con el uso de índices clínicos como el tiempo de llenado capilar, temperatura de la piel y depuración de lactato; en fases avanzadas donde el monitoreo clínico es insuficiente utilizar medidas dinámicas como la variabilidad de presión de pulso (vpp), la variabilidad de volumen sistólico (vvs), la respuesta a la maniobra de elevación pasiva de piernas o la prueba de oclusión teleespiratoria de acuerdo a los recursos disponibles y la experiencia. fuerte a favor fundamento sobre los objetivos de intervención y el tipo de agente vasoactivo a utilizar en pacientes con covid- y shock no existe una evidencia directa y las recomendaciones se basarán en evidencia indirecta de pacientes críticos con diversos tipos de shock en especial el séptico y vasopléjico. la falla circulatoria aguda asociado a sdra en covid- se presenta con una frecuencia del - % y en la admisión a urgencias la hipotensión y un lactato ≥ es infrecuente( , ). la baja sensibilidad del qsofa y crb- para predecir la severidad del covid- y la necesidad de intervenciones de terapia intensiva refleja lo infrecuente del shock en esta condición. factores como la vasoplejia, fuga capilar asociada al estado hiperinflamatorio, altos requerimientos de peep y disfunción cardiaca pueden ser generadores o contribuyentes del shock y deben ser considerados en el abordaje diagnóstico, en su interpretación para lograr tomas de decisiones adecuadas. en pacientes con sdra, una reanimación óptima de líquidos debe tomar en cuenta aspectos como tiempo (oportunidad), tipo (cristaloides balanceados y/o no balanceados o coloides) y volumen (ni mucho, ni poco) con el objetivo de disminuir la mortalidad, el tiempo de vm y de cuidados intensivos, sin que ello afecte los índices de oxigenación, de perfusión tisular y la morbilidad asociada con su uso inadecuado. la administración agresiva de líquidos puede empeorar la oxigenación y la disfunción ventricular, lo que potencializa un mayor tiempo de ventilación mecánica e incluso la mortalidad. la evidencia ha demostrado que una estrategia conservadora de fluidos (balance - +/- amci ® en una revisión sistemática y un metaanálisis de rct (n = . ) una terapia dirigida al aclaramiento temprano de lactato frente a una terapia guiada por la saturación venosa central de oxígeno (svo ), se asoció con una reducción significativa de la mortalidad (rr , ), menor estadía en la uci (dm , días), y menor duración de la ventilación mecánica (dm - , horas). pero se debe resaltar que un nivel alto de lactato no siempre indica hipovolemia; también puede ser causada por uso de adrenalina, agonistas beta o por disfunción mitocondrial, insuficiencia hepática e isquemia mesentérica ( ) . por otra parte, el llenado capilar (crt), una prueba técnicamente fácil y accesible, realizada cada minutos se asoció con una reducción no significativa de la mortalidad (hr , ) en comparación con la medición de lactato sérico cada horas. dado el potencial beneficio sobre mortalidad, duración de estancia en uci y la duración de la ventilación mecánica, así como su accesibilidad, sugerimos utilizar parámetros dinámicos de temperatura de la piel, tiempo de llenado capilar y / o medición de lactato sobre parámetros estáticos para evaluar la capacidad de respuesta a la fluidoterapia en pacientes con covid- y shock( ). se recomienda en pacientes adultos con covid- y estado de shock, escoger la norepinefrina como el vasopresor de primera línea y a la vasopresina el de segunda. si no se cuenta con norepinefrina el uso de vasopresina o epinefrina serían la primera elección; la dopamina no se recomienda por el mayor riesgo de arritmias. se recomienda iniciar dobutamina frente al aumento de la dosis de norepinefrina en pacientes en estado de shock con evidencia de disfunción cardíaca e hipoperfusión persistente a pesar de la reanimación inicial. fuerte a favor fundamento sobre los objetivos de intervención y el tipo de agente vasoactivo a utilizar en pacientes con covid- y shock no existe una evidencia directa y las recomendaciones solo pueden basarse en evidencia indirecta de pacientes críticos con sepsis y sdra. en pacientes en shock séptico los agentes vasoactivos para alcanzar una pam de - es un objetivo razonable. una presión media más alta puede incrementar . veces el riesgo de arritmias cardiacas y no está exento de riesgo de isquemia en las extremidades ( ) . para aproximarnos a la escogencia de los vasoactivos en shock séptico, basados en su perfil de riesgo/beneficio, la guía scandinavian society of anaesthesiology and intensive care medicine (ssai ) task force for acute circulatory failure( ), la revisión sistemática de cochrane database con rct con un n: ( ) y el ensayo clínico controlado de honarmand k et al con un n: , ( ) amci ®  la noradrenalina es el agente vasoactivo más ampliamente estudiado con el menor riesgo a priori de efectos no deseados, razón por la cual se sugiere usar como el agente vasoactivo de primera línea en pacientes con covid- y shock.  si la noradrenalina no está disponible la vasopresina o epinefrina se muestran como la mejor alternativa. los factores que determinan la elección entre vasopresina y epinefrina pueden incluir disponibilidad y el perfil de seguridad de estos agentes. con la vasopresina, la isquemia digital puede ser una preocupación y con epinefrina, la taquicardia, la isquemia miocárdica y el exceso de producción de lactato.  el uso de dopamina se ha asociado un . veces mayor de riesgo de aparición de arritmias frente a la norepinefrina y un posible aumento del riesgo de mortalidad. por ello la dopamina no debe utilizarse en pacientes con covid- y shock donde haya disponible de norepinefrina o las alternativas señaladas  en shock distributivo la adición de vasopresina a las catecolaminas evidenció baja certeza de reducción de la mortalidad (rr , ; ic del %: , a , ), alta certeza de una reducción de la fibrilación auricular (rr , ; ic del %: , a , ) y certeza moderada de un mayor riesgo de isquemia digital (rr , ; ic del %: , a , ). en vista de estos hallazgos se plantea la vasopresina como un agente vasoactivo de segunda línea a ser utilizado si la pam objetivo no se ha alcanzado con norepinefrina en pacientes con covid- y shock. no existe evidencia directa en pacientes con covid- y shock, para establecer una recomendación sobre cuál es el agente inotrópico óptimo. en una guía de práctica clínica de que evalúa el agente inotrópico óptimo en pacientes con insuficiencia circulatoria aguda (shock), no se identificaron rct que comparen dobutamina versus placebo o ningún tratamiento. con base en una justificación fisiopatológica, sugerimos agregar dobutamina, más que no suministrar ningún tratamiento, en pacientes con covid- y shock con evidencia de disfunción cardíaca e hipoperfusión persistente a pesar de la reanimación con líquidos y altas dosis de norepinefrina. el uso de dobutamina en estado de shock, incluso en pacientes con covid- con shock, debe ser investigado. recomendaciÓn se recomienda no suspender la medicación estándar para falla cardiaca en pacientes con sospecha o diagnóstico de covid- , especialmente los iecas, ara-ii, y b-bloqueadores, si la condición clínica permite continuar el uso de esta medicación, ya que no se ha podido confirmar una asociación nociva. amci ® previos alrededor de la relación independiente de la edad avanzada, enfermedad cardiovascular subyacente (enfermedad coronaria, insuficiencia cardíaca y arritmias), tabaquismo activo y epoc con muerte por covid- ( ) ( ) ( ) ; esos mismos reportes sugieren que las mujeres son proporcionalmente más propensas a sobrevivir a la infección por covid- que los hombre; existen además consideraciones especiales desde el punto de vista cardiovascular, que se deben tener en cuenta al decidir cualquier terapia en paciente afectados por covid- y existe la hipótesis de un efecto nocivo de la terapia estándar para falla cardiaca en estos pacientes ( ) . en un estudio observacional que incluye paciente con infección por covid- , se evaluó la relación entre la enfermedad cardiovascular subyacente, y la asociación entre la terapia farmacológica cardiovascular y la mortalidad ( ); respecto a los factores de riesgo cardiovascular, el . % de los pacientes tenían hiperlipidemia, el . % tenía hipertensión, el . % tenía diabetes mellitus, y en relación a los medicamentos, los sobrevivientes usaron más comúnmente ieca y las estatinas que los no sobrevivientes, mientras que no se encontró asociación entre la supervivencia y el uso de ara ii; respecto a los otros medicamentos incluidos b-bloqueadores, antiplaquetarios e insulina no se encontraron diferencias significativas; sin embargo, y teniendo en cuenta el impacto sobre mortalidad del uso de betabloqueadores en la falla cardiaca, consideremos que la decisión de continuar su uso debe basarse en el análisis clínico de cada paciente y su estabilidad clínica. se recomienda establecer un protocolo de reanimación ajustado al contexto del paciente con covid- con una organización administrativa ajustada a la pandemia que incluya las siguientes estrategias:  desarrollar una estrategia de prevención del paro cardiorrespiratorio en el paciente con sospecha o diagnóstico de covid- basada en la detección oportuna.  formar un equipo multidisciplinar formado en rcp con líderes médicos, de en enfermería y en terapia respiratoria, los cuales deben educar a todo el equipo de trabajo en la identificación de signos de alerta temprana, cambios abruptos de variables clínicas, técnicas de monitoreo, interpretación de paraclínicos y de alarmas de monitoreo.  entrenamiento del personal sanitario a través del uso de la simulación clínica en manejo de crisis, epp, y procesos de atención fundamentales en la atención del paro cardiaco en el paciente con sospecha o diagnóstico de covid-  promover la comunicación asertiva, planeación y retroalimentación de las intervenciones realizadas antes y después de un evento de paro cardiaco (briefing y debriefing), con el fin de establecer modificaciones que conllevarán a mejoras en la atención de futuros eventos. amci ® el pronóstico y sobrevida de un paciente con sospecha o diagnóstico de covid- que presenta paro cardiaco depende de la prevención a través del reconocimiento oportuno de las causas reversibles de éste, la no presencialidad y un ritmo de paro no desfibrilable lo hacen de mal pronóstico. la prevención va a depender del nivel de entrenamiento del equipo previamente, y en época de pico de pandemia cuando el talento humano especializado disminuya, se hace necesario que en los equipos de trabajo estén liderados por especialistas en la disciplina para que puedan guiar al equipo. los nuevos procesos de atención del paciente, la alta contagiosidad del virus, y el uso de nuevos medicamentos hacen que se requiera un entrenamiento del personal para estandarizar los procesos y disminuir el error médico. la crisis de covid- está ejerciendo una presión sin precedentes sobre las personas, los equipos y los sistemas organizacionales, conllevando a errores médicos que van desde la infección cruzada por el personal sanitario con la posibilidad de cometer errores en la atención. cada día trae nuevos desafíos: picos en volumen y gravedad, escasez de equipos y estrés en los médicos sobrecargados, que se manifiesta según la experiencia de wuhan en insomnio y depresión. se propone implementar una estrategia antes, durante y después del trabajo clínico, denominada circle up covid- desarrollada por center of medical simulation dirigida a convertir equipos de trabajo muchas veces insustituibles , en eficientes , seguros, fuertes y que se apoyan mutuamente incluyendo en mejora de la salud psicológica . impactando en el rendimiento del equipo , y promoviendo el bienestar y la resiliencia( - ) se recomienda establecer un protocolo de reanimación ajustado al contexto clínico del paciente con covid- que incluya las siguientes modificaciones:  implementar criterios de selección e inicio de maniobras de rcp en la atención del paro cardíaco basados en la bioética y en el pronóstico de supervivencia a corto y largo plazo de los pacientes.  promover la prevención del paro cardiaco mediante la detección oportuna del riesgo y definir intubaciones programadas.  asegurar la correcta protección con los epp necesarios al abordar el paro cardiaco y la intubación que son procedimientos generadores de aerosoles.  priorizar el manejo de la vía aérea antes del inicio de las compresiones torácicas, haciendo énfasis en la reducción de la exposición de aerosoles (código azul protegido).  utilizar filtro de alta eficiencia contra virus para todas las estrategias de ventilación (bolsa mascarilla con cierre hermético y en el circuito del ventilador).  promover la realización de la intubación por el operador de mayor experticia con uso de videolaringoscopio si está disponible y considerar el acceso supraglótico solo si el intento de intubación es fallido. amci ®  en caso de parada cardiaca en ventilación mecánica iniciar el masaje cardiaco evitando las desconexiones del circuito del respirador.  en caso de paro en posición prono si el paciente se encuentra vigil retornar rápidamente a la posición supino y si está en ventilación mecánica es razonable realizar compresiones en la espalda. fuerte a favor fundamento se hace necesario el entrenamiento en el manejo de los procedimientos generadores de aerosoles y se sugiere que el que realiza la intubación orotraqueal debe ser el más experto. el riesgo de aerosolización es de . en el proceso de intubación orotraqueal, el de compresiones torácicas es de , , ventilación mecánica no invasiva de , , ventilación manual pre-intubación de , , succión después de intubación , . se ha descrito que si no se ha capacitado previamente en el retiro de los epp existe más riesgo de auto contaminación y aumenta ésta sin un líder supervisor al retirarlo. según revisión de cochrane sobre ropa y equipo de protección para los trabajadores sanitarios para evitar que se contagien con el coronavirus y otras enfermedades altamente infecciosas da a conocer que la capacitación presencial, la simulación por ordenador y la capacitación por vídeo dieron lugar a menos errores a la hora de quitarse el epp que la capacitación impartida solo como material escrito o una conferencia tradicional ( ) ( ) ( ) ( ) ( ) ( ) . se recomienda no considerar la existencia de manifestaciones neurológicas específicas o típicas atribuidas a la infección por sars-cov- . se recomienda realizar la valoración neurológica integral del paciente con diagnóstico o sospecha de sars-cov- teniendo en cuenta manifestaciones frecuentes relacionadas a covid- : disgeusia, anosmia, cefalea, vértigo, confusión, delirium, alteración de estado de consciencia, eventos cerebrovasculares, ataxia, polineuropatías inflamatorias y convulsiones. una revisión sistemática realizada por asadi-pooya et al. entre diciembre y marzo de mostró que el % de los pacientes con covid- presentaron sintomatología neurológica. analizaron cinco artículos (n= ) donde eran retrospectivos, y era prospectivo, encontrando cefalea entre el y el %, vértigo entre el y el %, confusión en el %, alteración del estado de consciencia en el %, eventos cerebrovasculares en un %, ataxia en un , % y convulsiones en un , % ( ) . amci ® menor a participantes donde recolectarán información sobre el compromiso neurológico en pacientes con covid- con un seguimiento hasta febrero de ( ) . la hiposmia y la disgeusia de aparición súbita son manifestaciones clínicas muy prevalentes en pacientes con covid- evidentes aun en ausencia de sintomatología respiratoria alta. lechien et al publicaron un estudio multicéntrico que incluyeron hospitales europeos reclutando pacientes infectados con covid- levemoderado donde , % presentaron alteraciones relacionadas con el olfato y , % presentaron alteraciones relacionadas con el gusto, donde la anosmia se presentaba antes que cualquier otro síntoma en el , % de los casos y el , % de los casos no presentaba rinorrea u obstrucción nasal, la recuperación del olfato fue presente en el % de los pacientes y las mujeres fue el grupo poblacional más afectado (p= , ) ( ) . otras manifestaciones clínicas son las alteraciones de la agudeza visual, y dolor tipo neuralgia ( ) . respecto a las patologías psiquiátricas; la serie de mao comenta que el , % de los pacientes tiene clínica de alteración del estado de consciencia, concepto que se aproxima a la defunción de delirium. severance et al. encontraron que pacientes con sintomatología psicótica aguda presentaron niveles elevados de inmunoglobulina g para coronavirus del tipo hku , nl y oc con diferencias estadísticamente significativas respecto a los individuos controles (n= ) (p< , ). donde la respuesta inmune para nl fue asociado con el espectro-esquizofrenia (or: . , ci . - . , p= . ) pero no se correlaciona con desórdenes afectivos ( ) . aún no se ha descrito una correlación directa de este trastorno psicótico con covid- . los síntomas musculares se han observado en pacientes infectados por covid- incluyendo la miopatía del paciente en estado crítico (miopatía difusa no necrotizante con degeneración grasa de fibras musculares), la miopatía necrotizante (ligada a falla orgánica múltiple) y la miopatía de filamentos gruesos( ). se recomienda considerar como predictores clínicos neurológicos de alerta para sospechar covid- : anosmia, disgeusia, delirium y alteraciones neuromusculares inespecíficas sin otra causa aparente de explicación. se recomienda no establecer de rutina predictores neurológicos específicos de mal pronóstico en el paciente críticamente enfermo con covid- . se deben tener en cuenta los factores de riesgos generales de mal pronóstico para la población general como la edad avanzada, las comorbilidades cardiovasculares y el tabaquismo. page la proteína spike (s) del covid- es reconocida por la enzima convertidora de antígenos (eca ) de la célula huésped cuyo papel es el punto de entrada molecular a tejidos pulmonares, gastrointestinales y neuronales ( ) . la forma como el covid- ingresa al sistema nervioso central es desconocido, pero se especula que inicialmente invade terminales nerviosas periféricas y después llega al sistema nervioso central a través de una ruta guiada por sinapsis nerviosas con un patrón ascendente (ruta dada por el coronavirus hev y el oc- ) ( , ) . en modelos de roedores el covid- ingresaría al cerebro a través del nervio olfatorio, atravesando la lámina cribiforme propagándose por el tálamo y el tallo cerebral; explicándose por la expresión de los receptores de la enzima convertidora de antígenos (eca ) en la superficie de las mucosas nasales, las neuronas y la glía ( , , ) . una segunda forma de ingreso es a través de la vía hematológica mediante arterias cerebrales atravesando la barrera hemato-encefálica utilizando las células inflamatorias como un modelo similar al del caballo de troya ( , , ) logrando una ubicación definitiva en células neuronales y endoteliales del lóbulo frontal como lo demostraron en estudios post-mortem descritos por paniz -mondolfi et al, lo que explicaría los cambios comportamentales de paciente ( ) . la tercera forma de acceso al sistema nervioso central es mediante el drenaje del sistema linfático cerebral invadiendo ganglios linfáticos hiliares y mesentéricos con sintomatología gastrointestinal asociada ( ) . una vez ha logrado ingresar tiene la capacidad de infectar macrófagos, microglía, y astroglía los cuales secretan factores proinflamatorios como interleuquina , interleuquina , y factor de necrosis tumoral alfa ( ) . esta condición se exacerba con el desencadenamiento de la tormenta de citoquinas liderada por la interleuquina , interleuquina , interleuquina e interferón gamma ( ) . de esta forma los coronavirus siendo neurotrópicos ocasionan múltiples manifestaciones clínicas ya mencionadas, así como encefalitis, parálisis flácida, incluyendo la asociación con guillain-barré ( ) . los síntomas que harían sospechar la presencia de neurocovid- son la náusea, el vómito y la anorexia, estos síntomas pueden ser el reflejo del compromiso del virus en el área postrema del piso del cuarto ventrículo que hace parte del complejo vagal dorsal de la médula oblonga. sin embargo, estos síntomas pueden enmascararse como una respuesta inespecífica relacionada con un compromiso gastrointestinal ( ) . como se mencionó previamente la anosmia y la disgeusia son síntomas significativos para sospechar en covid- ( ) ; esto es debido a una lesión directa sobre el nervio olfatorio (i par craneal), y la lesión de alguno de los tres nervios encargados de registrar el sentido del gusto como lo son el vii, ix y x pares craneales, así como el compromiso del núcleo solitario y del tálamo como zona de relevo; de hecho el núcleo del tracto solitario es muy cercano al centro respiratorio que podría ocasionar disnea de origen central ( ) , otros núcleos como el núcleo dorsal motor del vago y el núcleo ambiguo están relacionados con funciones cardiovasculares a tener en cuenta ( ) . respecto a los factores de riesgo destaca el tabaquismo el cual aumenta la posibilidad de neuroinfección debido a interacciones funcionales entre el receptor nicotínico de acetilcolina y el receptor eca el cual está sobreexpresado en pacientes fumadores ( ) . amci ® en pacientes con infecciones severas vs infecciones no severas ( . % vs . %, p = . ), incluyendo eventos cerebrovasculares ( , % vs , % p= , ), alteración del estado de consciencia ( . % vs . %; p< . ) y lesiones musculoesqueléticas ( , % vs , % p< ) ( ) . la encefalopatía que se manifiesta como una alteración aguda o subaguda del estado de consciencia presentándose en pacientes con comorbilidades, factores de riesgo cardiovasculares, edad avanzada y deterioro cognitivo previo ( , , ) . así como aquellos individuos con hipoxemia la cual induce metabolitos anaerobios en el sistema nervioso central, edema celular, intersticial e isquemia ( ) . los eventos cerebrovasculares pueden ser desencadenados por cuadros de hipoxia, inmovilización, un incremento de la respuesta proinflamatoria o por predisposición a la hipercoagulabilidad ( ) . respecto a este último rubro tanto la edad (hazard ratio , /por año % ic , - , ) y la coagulopatía definida como como un tiempo de protrombina mayor a segundos, o tiempo de tromboplastina mayor a segundos (hr , % ic , - , ) fueron considerados predictores independientes de complicaciones trombóticas ( ) ; otros trabajos reportan incremento del conteo plaquetario y niveles elevados de dímero d ( ) . de hecho, un scoping review realizado por wilson y jack muestra que la presencia de eventos cerebro vasculares es un factor de riesgo de mal pronóstico para pacientes infectados por covid- ( ) . mao et al. reportaron eventos cerebro vasculares en pacientes con covid- , los factores de riesgo más relevantes fueron los clásicos factores de riesgo cardiovasculares (diabetes, hipertensión y edad avanzada), así como una presentación sistémica severa, teniendo como un denominador común el compromiso estructural de grandes vasos ( ) . la presencia de convulsiones (clínicas o subclínicas) puede ser una manifestación de eventos cerebro vasculares, meningoencefalitis o hipoxia cerebral. siendo los factores de riesgo más importantes en su exacerbación las alteraciones electrolíticas como hipocalcemia, las reacciones adversas a medicamentos y la epilepsia como comorbilidad de base ( , ) . otros tipos de coronavirus como lo son el e, , y oc se han aislado de líquido cefalorraquídeo (lcr) de pacientes con esclerosis múltiple sugiriendo posiblemente sean agentes etiológicos en la exacerbación de brotes de esta patología sin embargo aún no se ha documentado la asociación entre covid- y ésta condición ( ) . otras patologías en las cuales se ha asociado la presencia de esta familia de microorganismos es la enfermedad de parkinson, la esclerosis lateral amiotrofia, la neuritis óptica y la encefalitis aguda diseminada ( , ) . múltiples trabajos han documentado la asociación entre polineuropatía y coronavirus. la mayoría de ellos consideran que existe una estrecha relación entre una polineuropatía autoinmune exacerbada por la infección por coronavirus o bien un compromiso nervioso periférico inducido por bloqueo neuromuscular, alteraciones hidroelectrolíticas o disvitaminosis( ). amci ® se recomienda que todo paciente con acv isquémico se considere sospechoso de infección por covid- si presenta: sintomatología asociada sospechosa de infección por covid- , contacto cercano con individuos con sintomatología infecciosa, allegados con viajes recientes, si la historia clínica es atípica, si la información suministrada no es clara, si presenta deterioro del estado de alerta inexplicable, y si al examen físico presenta hallazgos compatibles con una infección por covid- . se recomienda que todo paciente con acv isquémico de quien no se pueda recibir información se considere sospechoso de covid- ya que el evento cerebro vascular es una complicación que se ha reportado en pacientes con infección por covid- . hay una gran evidencia que correlaciona la presencia de infección por covid- con factores de riesgo cardiovasculares. esto se demostró en un metaanálisis que incluyó estudios de china (n= ) donde las comorbilidades más frecuentes fueron hipertensión ( , %, % ic: - , %), diabetes ( , %, % ic , - , %), enfermedad cardiovascular ( . %, % ic: . - . ) y patologías respiratorias ( . %, % ic: . - . %). al comparar severidad vs no severidad la presencia de hipertensión tuvo un or de . ( % ci: . - . ), y la enfermedad cardiovascular un or de . ( % ci: . - . ) respectivamente ( ) . existieron pocos casos de hipercoagulabilidad en pacientes sin factores de riesgo cardiovasculares ( ) . la cohorte de wuhan (n= ) publicada por wang et al. mostró otros factores de riesgo que podrían eventualmente estar asociados a estado de embolia y trombosis como shock en , %, arritmias , % y miocarditis en un , %. situaciones que conllevarían a hipercoagulabilidad, lesión endotelial y eventualmente la aparición de acv. ( ) . en este orden de ideas existe una estrecha correlación entre la presencia de factores de riesgo cardiovasculares que ocasionarían acv y que podrían eventualmente estar relacionados con la patogenia de covid- . ante esta inquietud khosravani et al. publicaron en stroke un informe especial donde realizan ciertas recomendaciones para el abordaje de los pacientes con acv en el contexto de la pandemia por covid- de una forma rápida, eficaz y segura para los diferentes profesionales de la salud. surge así el código stroke protegido el cual consiste en:  usar elementos de protección personal y una mascarilla al paciente  ejecutar protocolo de aislamiento de contacto y gotas  ejecutar protocolo de aerosoles si el paciente está sometido a ventilación mecánica no invasiva, manejo de aspiración de secreciones o maniobras de reanimación cardiopulmonar básica y avanzada  si el paciente presenta deterioro del estado de alerta con necesidad de soporte ventilatorio alto con fracción inspirada de o mayor a % se recomienda intubar temprano y proceder con el transporte. se debe proceder con el código stroke protegido si el paciente presenta alguna de las siguientes condiciones:  si el paciente presenta sintomatología sospechosa de covid- (fiebre, tos, dolor torácico, disnea, cefalea, mialgias, emesis)  si existe algún contacto cercano con sintomatología infecciosa  si el paciente o alguno de sus allegados ha presentado viajes recientes amci ®  si el paciente es covid- positivo  si refiere al interrogatorio una historia clínica atípica o poco clara  si el paciente o alguno de sus acudientes es incapaz de suministrar información  si el paciente presenta deterioro del estado de alerta  si al examen físico se encuentran signos compatibles con patologías diferentes a covid- por último, estas son las recomendaciones en el momento de realizar el traslado a saber:  no apresurarse dentro de la sala de reanimación o dentro de la unidad de cuidados intensivos y mantener la calma  designar un líder para el traslado del paciente y para supervisar el uso adecuado de los elementos de protección personal  limitar el número de personas encargadas del transporte  evitar la contaminación con otras áreas del hospital( ). se recomienda no realizar neuroimagen de rutina en pacientes críticos por covid- con cefalea y anosmia, dado que no existe una evidencia concluyente que demuestre una estrecha correlación entre estos síntomas y hallazgos imagenológicos. fuerte en contra fundamento en la mayoría de los casos la cefalea es un síntoma no específico que no es característico de irritación meníngea la ocurrencia de cefaleas aisladas en ausencia de otros síntomas sugiere un mecanismo benigno más que un compromiso de sistema nervioso central ( ) . sin embargo, el covid- al tener una capacidad neuroinvasiva, se han reportado casos de encefalitis virales con o sin necrosis hemorrágicas de compromiso temporal mesial y talámico que ameritarían estudio de imagen diagnóstica ( ) . un estudio retrospectivo publicado por kandenmirli et al. evaluó pacientes en hospitales infectados con covid- de los cuales requirieron manejo en uci donde el % de ellos (n= ) presentaron sintomatología neurológica. la resonancia magnética cerebral fue realizada en % (n= ) de estos pacientes. el % tuvieron hallazgos agudos, el % tuvieron alteraciones corticales de la captación de señal en el modo flair, pacientes tuvieron anormalidades en la señal flair en la sustancia blanca profunda y subcortical, pacientes con lesiones en el lóbulo frontal, en el lóbulo parietal, en el lóbulo occipital, en el lóbulo temporal, en la corteza de la ínsula, y en el giro cingular ( ) . amci ® un paciente presentó trombosis de seno venoso y otro presentó un infarto en el tercio medio del territorio de la arteria cerebral media. en % de los pacientes no se encontraron hallazgos que sugieran compromiso intracraneal de covid- . una correspondencia escrita por helms et al. reportaron pacientes con sdra y covid- en dos unidades de cuidados intensivos en francia entre marzo y abril del , el % presentaron signos neurológicos como delirium evaluados mediante cam-icu ( %), agitación ( %), signos del tracto cortico espinal ( %), síndrome disejecutivo ( %). de ellos se realiza resonancia magnética en pacientes encontrando alteraciones en la perfusión en un %, un realce de leptomeninges en un %, y un acv isquémico en un %; dos pacientes asintomáticos presentaron áreas isquémicas con hiperintensidad focal ( ) . ante estos hallazgos los principales diagnósticos diferenciales son las patologías autoinmunes, encefalitis, convulsiones e hipoglucemia. los pacientes con compromiso frontal bilateral poseen hipoxemia que ocasionan hipoperfusión fronto temporal. las microhemorragias corticales (y no) son consecuentes de la ruptura de la membrana hematoencefálica resultando en este patrón mencionado. el estado postictal muestra un compromiso simétrico de la sustancia blanca. de esta forma hay que considerar otras condiciones como las comorbilidades cardiovasculares, las reacciones adversas a los medicamentos, e hipoxia inducida por sdra que ocasionarían patrones imagenológicos de confusión, que ponen en duda la estrecha relación entre covid- y hallazgos de resonancia magnética ( ) . en este orden de ideas necesitamos más datos para determinar cuáles son los hallazgos imagenológicos relacionados con neurotropismo y qué patrones pueden encontrarse directamente relacionados con la presencia de convulsiones, hipoxia o el desencadenamiento de una tormenta de citoquinas( , , ). se recomienda la valoración neurológica completa en los pacientes con sospecha o infección por covid- . se recomienda la monitorización electroencefalográfica continua por al menos h o según la consideración del especialista en neurociencias en el paciente en estado crítico con sospecha o infección por covid- en quien se sospeche crisis epilépticas o estatus no convulsivo. las manifestaciones neurológicas en pacientes con infección por covid- pueden estar presentes en el % de los casos ( , , ) . en el paciente en estado crítico con infección por covid- se han observado complicaciones vasculares que puede causar ataque cerebrovascular agudo isquémico o hemorrágico con tazas de entre el al % por lo que el examen neurológico debe realizarse para documentar la presencia de déficit amci ® neurológico focal que haga sospechar esta patología ( , , ) . es conocido que los pacientes en unidades de cuidado crítico tienen patologías que aumenta el riesgo de crisis o estado epiléptico, entre las cuales se encuentran ( ) ( ) ( ) ( ) :  pacientes sin patologías neurológicas hospitalizados en unidad de cuidado intensivo  hemorragia subaracnoidea  hemorragia intracraneal  trauma cráneo encefálico moderado a severo  infección del sistema nervioso central  tumor cerebral  encefalopatía hipóxico-isquémica algunas de estas patologías se presentan más frecuentemente en pacientes por covid- por lo que la monitorización electroencefalográfica continuar es requerida en este grupo de pacientes. el virus puede producir descompensación de paciente con epilepsia conocida, crisis por fiebre, crisis producidas por el estado crítico del paciente o las patologías subsecuentes que se han observado en esta infección ( ) . el tiempo de monitorización requerido debe ser entre a horas para lograr una sensibilidad de a %( , ). se recomienda realizar tomografía cerebral simple ante las manifestaciones neurológicas focales que nos hagan sospechar ataque cerebrovascular isquémico o hemorrágico. la resonancia cerebral puede ser necesaria como estudio complementario para determinar otros diagnósticos diferenciales en los pacientes con sospecha o infección por covid- . las manifestaciones neurológicas en pacientes con infección por covid- pueden estar presentes en el % de los casos ( , , ) . en el paciente en estado crítico con infección por covid- se han observado complicaciones vasculares que puede causar ataque cerebrovascular agudo isquémico o hemorrágico con tazas de entre el al % por lo que el examen neurológico debe realizarse para documentar la presencia de déficit neurológico focal que haga sospechar esta patología ( , , ) . la tomografía cerebral hace parte de la valoración inicial del ataque cerebrovascular isquémico y del estudio para determinar la presencia de otros diagnósticos diferenciales como ataque cerebro vascular hemorrágico en paciente con dicha patología puede ser necesario realizar angiotac con extensión a tórax en caso de sospecha de oclusión proximal o estudios endovasculares en pacientes que sea indicado ( ) . la realización de resonancia cerebral usualmente documenta alteraciones en los pacientes con covid- en el - % de los casos evaluados no relacionada con el acv. se recomienda la realización de punción lumbar en el paciente con sospecha o diagnóstico de covid- con base en los reportes de casos disponibles:  paciente con crisis epilépticas de novo.  paciente con alteración del estado de conciencia persistente a pesar de encontrarse metabólicamente compensado, descartado ataque cerebrovascular u otra causa de encefalopatía.  paciente con manifestaciones como mielitis, neuropatía craneal múltiple o sospecha de polineuropatía desmielinizante aguda. las capacidades neurotrópicas de los coronavirus en general han sido expuestas desde la infección por sarscov. en cuanto al sars-cov- , asadi-pooya y colaboradores( ), han descrito, la posibilidad de ingreso al sistema nervioso central tras el ingreso por la mucosa nasal o por una gran viremia en el torrente sanguíneo. se han descrito procesos inflamatorios asociados (encefalitis) y en previamente con el sars y el mers hasta lesiones desmielinizantes (encefalomielitis aguda diseminada). estas primeras manifestaciones en con el sars fueron presencia de crisis epilépticas de novo, en quienes excluyendo otras causas tanto por neuroimagen además de pruebas microbiológicas en lcr, les fue descubierto el sars cov mediante pcr rt. en la presente pandemia, takeshi moriguchi y colaboradores ( ) describieron el primer caso de encefalitis asociado a sars-cov- , en un hombre joven en japón, que, tras días de clínica respiratoria, desarrollo crisis epilépticas y alteración del estado de conciencia, sin antecedente conocido de epilepsia. se realizo imagen por resonancia cerebral, demostrando hiperintensidades a nivel temporal y lcr que mostró pleocitosis linfocitaria, se descartaron otros virus ( herpes, herpes zoster) y se le realizó pcr rt para sars-cov- siendo positiva. inclusive en este paciente los primeros hisopados faríngeos fueron negativos, pero los hallazgos en tomografía de tórax hicieron sospechar la infección por sars-cov- . otro caso descrito de encefalitis hemorrágica aguda, fue también descrito en la revisión de ahmad y colaboradores ( ) . donde una mujer joven presentó cuadro respiratorio de fiebre de días de evolución y compromiso del estado de conciencia. en esta paciente se aisló el sars-cov- en hisopado faríngeo y ante el compromiso severo del estado de conciencia, se realizó resonancia que mostró compromiso hemorrágico bitalámico, en regiones temporales e ínsula, apoyando que se tratara de una diseminación tras neuronal probablemente con puerta de entrada mucosa olfatoria y siguiendo la diseminación por el los tractos del primer nervio hasta la corteza entorrinal, que es la vía propuesta de infección descrita inclusive por grupos como el de montalvan ( ) y natoli ( ) . amci ® precisamente, en la revisión sistemática de montalvan ( ) se describen caso de mielitis en contexto de paciente con infección por sars-cov- , en quien se documentó la infección en lcr. se recomienda la medición de ácidos nucleicos por rt-pcr para sars-cov- en líquido cefalorraquídeo en los pacientes con sospecha o confirmación de infección por sars-cov- que realice crisis epilépticas de novo, en quien se descarte otras causas de estructuralidad (acv, tumores) o causas metabólicas (alteraciones hidroelectrolíticas, hipoglicemia, uremia etc.). se recomienda la medición de ácidos nucleicos por rt-pcr para sars-cov- en líquido cefalorraquídeo en pacientes con sospecha o confirmación de infección por sars-cov- con alteración franca del estado de conciencia, en quien se haya descartado como causante hipoxia, ataque cerebrovascular, alteración hidroelectrolítica o estatus no convulsivo mediante imágenes y electroencefalograma. se recomienda la medición de ácidos nucleicos por rt-pcr para sars-cov- en líquido cefalorraquídeo en pacientes con sospecha de encefalitis, mielitis o síndrome de guillain barré. en pacientes críticos, se ha recomendado búsqueda activa de compromiso del snc por sars-cov- , sobre todo en pacientes con crisis epilépticas que no sean sintomáticas a trastornos metabólicos, además de hallazgos imagenológicos y curso clínico. las descripciones hechas por asadi y takeshi ( , ) , muestran pacientes con cursos tórpidos, en los que el común denominador es una alteración del estado de conciencia persistente a pesar que otras variables (metabólicas, vasculares e infecciosas diferentes al sars-cov- ). de igual forma pacientes que realicen en contexto de la enfermedad, un cuadro de debilidad generalizada aguda, con arreflexia e incluso compromiso de nervios craneales como los descritos por zahra sedaghat( ). page amci ® se recomienda en los pacientes críticos con compromiso pulmonar por covid- , un manejo orientado de fluidos frente a una estrategia liberal, ajustando el balance de fluidos de acuerdo con la evaluación clínica y/o a la capacidad de respuesta a volumen para garantizar la perfusión renal. se recomienda ajustar la intensidad de la monitoria en el paciente crítico con covid- al grado de severidad de la enfermedad para alcanzar tempranamente metas de reanimación que se reflejen en menor riesgo de lesión renal aguda. se recomienda evitar el uso de medicamentos nefrotóxicos teniendo en cuenta la farmacocinética y farmacodinamia individual, así como las interacciones farmacológicas en el paciente crítico con covid- . el manejo de la volemia en los pacientes críticos ha cambiado considerablemente en las últimas décadas orientándose a un manejo titulado, evitando la administración empírica de altos volúmenes de líquidos durante la fase de reanimación de los pacientes siendo el flujo sanguíneo el determinante primordial del aporte tisular de oxígeno; los principales componentes de este deben optimizarse y balancearse para evitar la disoxia tisular. en estados de bajo flujo, los mecanismos compensadores neurohumorales producen una redistribución del flujo a lechos no esplácnicos y a nivel renal una redistribución corticomedular convirtiendo el tejido medular renal en una zona vulnerable a la lesión. de igual forma, el flujo sanguíneo renal se ve reducido de forma refleja en presencia de hipoxemia y/o hipercapnia. diversas fuentes de información nos han indicado cómo orientar adecuadamente el manejo del estado de perfusión tisular en los pacientes críticos con o sin una condición de shock, siendo la estimación aproximada del estado de volumen del paciente el pilar fundamental sobre el cual se basará toda la estrategia de restablecimiento o mantenimiento de la volemia del paciente con el fin de mantener la perfusión adecuada. aunque históricamente se prioriza la normalización del volumen en la reanimación de un paciente inestable, hemos comprendido la importancia que tiene el tiempo para lograr las metas en el pronóstico general del paciente y evidencias como el trabajo de ospina y cols. soportan el uso temprano de vasopresores para lograr de forma temprana metas de perfusión mientras buscamos la normovolemia. los pacientes con enfermedad pulmonar asociada a covid- deben mantenerse normovolémicos para preservar el flujo sanguíneo renal siendo la evaluación del estado de volumen un verdadero reto clínico. la fiebre, el aumento de pérdidas insensibles, la baja ingesta o las pérdidas por el tracto digestivo, pueden hacer que un paciente con covid- tenga hipovolemia, situación que puede desencadenar daño renal de no ser revertida apropiadamente y a tiempo. del otro lado del espectro, la administración liberal de líquidos además del potencial de empeorar la lesión pulmonar en presencia de una membrana alveolo capilar seguramente alterada, puede producir por sí misma un incremento en el riesgo de desarrollar lesión renal como lo demostró el estudio de grissom. desde el punto de vista de las metas amci ® hemodinámicas que se deben tener con un paciente con covid- , se recomienda seguir los lineamientos de la campaña sobreviviendo a la sepsis, orientadas a mantener un óptimo estado de volumen, unas presiones de perfusión en un rango que permita la regulación de los flujos regionales en los distintos órganos y un gasto cardíaco dentro de unos rangos establecidos para una perfusión sistémica óptima. el examen clínico sigue teniendo vigencia absoluta para una adecuada aproximación al paciente, por ello debemos buscar los indicadores clínicos tradicionales de hidratación (piel, mucosas, enoftalmos, edema, etc.), el llenado capilar como lo describe hernández y cols en el estudio andrómeda-shock, el estado de alerta, las funciones cognitivas y la rata urinaria son entre otros unos marcadores aceptables para hacernos una idea del estado de adecuación de la perfusión periférica. la oliguria como marcador de perfusión renal está presente en / parte de los pacientes al ingreso a uci sin tener en sí sola una implicación pronóstica, sin embargo, la persistencia de esta en el tiempo es un indicador de alerta y obliga a una evaluación más detallada de las diversas variables que pudieran ocasionarla. debemos recordar que la administración de cargas de líquidos solamente está justificada cuando hay una respuesta cardiovascular a dicha administración, situación que se puede prever con una prueba de elevación pasiva de las piernas o con métodos más invasivos como la variabilidad de la onda de pulso, del volumen sistólico y/o del gasto cardíaco, entre otros. el esfuerzo respiratorio del paciente, los volúmenes utilizados en las estrategias de ventilación protectora y las arritmias frecuentemente presentes en los pacientes con compromiso pulmonar limitan el rendimiento diagnóstico de diversos dispositivos utilizados para la evaluación del estado de volumen y el gasto cardíaco, situación que debemos conocer y manejar( , - ). se recomienda no utilizar de forma rutinaria la administración de tratamientos específicos antivirales para el paciente crítico con covid- , con lesión renal aguda o crónica se recomienda no utilizar de rutina remdesivir en los pacientes con falla renal crónica y debe suspenderse en los pacientes que desarrollan lesión renal aguda con tfg < ml/min. las intervenciones farmacológicas en los ensayos clínicos deben ajustarse a la farmacocinética y farmacodinamia específicas de cada molécula. la incidencia de falla renal reportada por criterios de kdigo, en los estudios chinos fue de . % de los pacientes críticamente enfermos y de . % en los pacientes con covid- y amci ® sdra. sin embargo, otros estudios han demostrado que hasta un %de pacientes con covid- que ingresan a la uci pueden presentar falla renal aguda. la falla renal en los pacientes con covid- es multifactorial como se ha descrito en preguntas anteriores por lo que se recomienda la toma diaria de creatinina sérica y el seguimiento continuo del gasto urinario y otros parámetros de la función renal como hematuria, proteinuria, tasa de filtrado glomerular, nitrógeno ureico en sangre, dímero d. los medicamentos que se emplean en el manejo de la infección covid- que actualmente incluyen oseltamivir, lopinavir/ritonavir, ribavirina, y la cloroquina o hidroxicloroquina son metabolizados principalmente en el hígado, aunque en la orina se encuentran metabolitos derivados de oseltamivir, ribavirina y de la hidroxicloroquina. por esto en ninguno de los estudios realizados en torno a la infección por sars-cov- se ha realizado ninguna recomendación en cuanto a la modificación de su dosis. la hidroxicloroquina por su parte se metaboliza a cloroquina, que a su vez se metaboliza a monodesetilcloroquina y a bisdesetilcloroquina. este medicamento no es dializable en las diálisis intermitentes y la única recomendación en los pacientes con falla renal, es hacer seguimiento electrocardiográfico estrecho para vigilar la prolongación del qtc. el favipiravir es un inhibidor de la polimerasa dependiente de rna que se encuentra en fase experimental para el tratamiento de la infección por sars-cov- . la eliminación de este medicamento se realiza por vía renal y en los pacientes con falla renal en estadios leves a moderados se ha encontrado una concentración dos veces mayor en el riñón que sus niveles en sangre; sin embargo, esto no se ha asociado con ningún evento adverso por lo que la recomendación actual es no disminuir la dosis en pacientes con falla renal. el remdesivir se elimina por vía renal por lo cual no se recomienda administrar en pacientes con falla renal y los pacientes que desarrollan falla renal con el medicamento durante los estudios han sido retirados de los ensayos clínicos. no se cuenta con estudios que evalúen el remdesivir en una tfg < ml/min. en la tabla se describen algunas intervenciones farmacológicas propuestas en medio de la pandemia para el manejo del covid- y su relación con la tasa de filtración según tfg. recientemente , izzedine et al publicaron una carta editorial en el kidney international may , donde alertan sobre el posible efecto nocivo de la hidroxicloroquina en la aparición de falla renal aguda al inhibir la autofagia celular que es un proceso importante en la remodelación de los túbulos renales, siendo estas células de alto recambio, pudiendo todo esto contribuir a la aparición de falla renal aguda( , , - ) se recomienda aplicar las indicaciones tradicionales de terapia de soporte renal en pacientes críticamente enfermos con covid- . se recomienda el inicio de terapia de soporte renal en pacientes críticos con covid- con hipercalemia severa o acidosis metabólica severa, refractarias a pesar del manejo médico óptimo o cuando el balance positivo de fluidos es deletéreo, con mayor requerimiento de oxígeno suplementario y que no responde a diuréticos. se recomienda el inicio temprano de terapia de soporte renal dentro de las primeras horas de una indicación absoluta, asegurando previamente una adecuada reanimación de la perfusión tisular. en ausencia de trastornos hidro-electrolíticos y severa sobrecarga de volumen, el tiempo de inicio de diálisis es controversial. amci ® se recomienda en pacientes críticos con covid- que requieren soporte renal, las modalidades de terapia continua o extendida si cursa con inestabilidad cardiovascular, de acuerdo con la disponibilidad institucional. se debe considerar en pacientes críticos con covid- , que requieren inicio de soporte renal preferir la vía femoral para inicio de la terapia para disminuir el riesgo de contaminación por proximidad, la siguiente vía se establecerá de acuerdo con la evolución y condiciones del paciente. en pacientes diagnosticados con covid- se puede presentar la insuficiencia renal aguda como parte de su enfermedad. en estudios observacionales de usa y china la ira se reportó entre un y % de los pacientes. la enfermedad renal en pacientes con covid- se puede manifestar como ira, hematuria o proteinuria, y conllevan un mayor riesgo de mortalidad. la ira se asocia con cambios hemodinámicos y liberación de citocinas, pero no se descarta citotoxicidad directa por el virus. en un estudio realizado en nueva york con pacientes covid- positivos se diagnosticó lesión renal aguda en % de ellos, siendo leve con aumento de creatinina dos veces por encima del nivel basal en % de los pacientes, moderada en % de los pacientes, y severa con más del triple de la creatinina basal en %. hubo hematuria en el % de los pacientes y proteinuria en el %. se requirió terapia dialítica en el % de todos los pacientes con diagnóstico de ira, y el % de los pacientes que requirieron diálisis estaban en ventilación mecánica. la ira fue notada dentro de las primeras horas de admisión a uci en el % de los pacientes y se relaciona con la severidad de la enfermedad. existen además predictores independientes: edad, raza negra, diabetes, hipertensión, enfermedad cardiovascular, ventilación mecánica, y uso de vasopresores. la terapia dialítica debe instaurarse precozmente una vez realizado el diagnóstico, idealmente dentro de las primeras horas, después de asegurado que se ha completado el proceso de reanimación correspondiente. las indicaciones te trr en pacientes críticos con ira en covid- no difieren del paciente crítico general y se debe considerar ante: manifestaciones severas de uremia, sobrecarga de volumen, trastornos ácidos básico, refractarios, hipercalemia severa con manifestaciones cardiovasculares. pero no hay datos clínicos que respalden el inicio temprano vs tardío en esta población particular. pero un planteamiento válido es que la sobrecarga de volumen en pacientes que desarrollan sdra es perjudicial, dificultando el soporte ventilatorio óptimo, por lo cual se puede considerar un umbral más bajo para el inicio de trr con esta indicación específica: sdra + sobrecarga de volumen + infección covid- ( ) . amci ® el paciente debe ser dializado en el cubículo de cuidado intensivo o en la habitación de aislamiento en los casos en que esté disponible y siempre evitar traslado a unidades con otros pacientes. la crrt es la modalidad preferida para este tipo de pacientes, pero debe quedar claro que esto depende de las facilidades de la institución que albergue al paciente y de la experticia de los profesionales. el acceso vascular en el paciente crítico general debe ser en su orden: vena yugular interna derecha, venas femorales comunes, vena yugular interna izquierda, y debe ser colocado por el médico encargado del paciente si está capacitado para ello, para evitar exposiciones innecesarias del personal de la salud. sin embargo, por precaución por el riesgo de contaminación, recomendaciones de expertos basadas en seguridad sugieren la utilización el catéter femoral. el tipo de catéter recomendado es un catéter doble lumen transitorio. sería ideal el monitoreo a través de cámaras del procedimiento para evitar el contacto prolongado del personal de enfermería durante el procedimiento de diálisis. en algunos casos específicos y de acuerdo con la disponibilidad, la diálisis peritoneal puede ser una alternativa. en los casos de crrt el líquido efluente no es contaminante para el personal de la salud. para terminar, es importante hacer énfasis en que en algunos hospitales ha habido escasez de insumos y esto puede llegar a convertirse en un serio problema. se recomienda para casos de fuerza mayor:  un litro de solución salina al . % con cloruro de potasio a necesidad  un litro de dextrosa al % en agua con meq de bicarbonato de sodio  un litro de solución salina al . % con gr de cloruro de magnesio  un litro de solución salina al . % con gr de cloruro de calcio esto nos da una solución de cuatro litros que contienen: meq/l de sodio, . meq/l de bicarbonato, . mmol/l de magnesio y . mmol/l de calcio, más una cantidad variable de potasio. esta solución se puede usar como líquido dializante en pacientes en terapias de reemplazo renal continuo. especial cuidado se debe tener en el proceso de anticoagulación, pudiéndose usar heparina no fraccionada, hbpm, y citrato en los centros donde se tenga experiencia ( , , ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . se sugiere no utilizar de rutina la trrc más hemoperfusión en el paciente crítico con covid- . débil en contra page amci ® se puede considerar en el paciente crítico con covid- con lesión renal aguda en quien se considere inicio de trrc, considerar la utilización de filtros de fibra hueca con propiedades adsortivas o asociado con cartuchos para hemoperfusión directa. el síndrome de liberación de citocinas (tormenta de citocinas) es un importante determinante en la transformación de infección por covid- de leve a moderado y progresión de la lesión de un órgano como el pulmón con neumonía y sdra a compromiso sistémico con inestabilidad hemodinámica, cid y fom. los pacientes afectados de tormenta de citocinas se encuentran con niveles altos de il- especialmente, además de il- , tnf, que se relacionan con pobres pronósticos y mayor mortalidad. la asociación entre la lesión alveolar y renal (eje pulmón-riñón) es evidenciada en estudio del por panitchote y cols con pacientes con sdra secundaria a neumonía y sin enfermedad renal preexistente que desarrollaron lesión renal aguda en el % con aki en el % de ellos. recientemente en estudio en china zhou, con pacientes afectados de covid- se encontraron como indicadores de mal pronóstico pacientes con altos niveles de dímero d, il- , troponina i, dhl, ferritina y choque séptico. las terapias de depuración extracorpórea han sido utilizadas como tratamiento en pacientes con lesión severa por covid- ; dentro de estas se cuentan la crrt, hemoperfusión aislada, intercambio plasmático (tpe), plasmafiltración y adsorción (cpfa) y crrt + hemoperfusión. dentro de los beneficios de la crrt se cuentan la estabilidad hemodinámica, estabilidad del medio interno, depuración de toxinas pequeñas y medianas, incluidos mediadores inflamatorios, cuando se utiliza terapia convectiva, además de permitir soporte nutricional. la asociación de este procedimiento con membranas especiales (an + metilsulfonato y polietilamina oxiris) permiten hacer adsorción de citocinas (il- ) y endotoxinas, por periodos de h por días consecutivos para manejo de tormenta de citocinas. la hemoperfusión aislada o asociada a crrt, también permite la remoción de il- , utilizando cartuchos ha , con procedimientos de a horas de duración por días consecutivos ( , ( ) ( ) ( ) ( ) ( ) ( ) . no se puede emitir una recomendación a favor o en contra sobre el uso rutinario de la plasmaféresis como opción terapéutica en la fase de inflamación del paciente con covid- . amci ® el coronavirus covid- puede inducir el síndrome respiratorio agudo severo (sars), que conduce a la disfunción inmune, la liberación excesiva de citoquinas inflamatorias, y a una serie de reacciones en cascada de activación de citoquinas, que resultan en lesiones alveolares difusas, formación de membrana hialina, exudación de fibrina y otras manifestaciones de lesión del pulmón. en casos severos, la tormenta de citoquinas sistémicas invade el sistema circulatorio, lo que lleva a una inestabilidad hemodinámica, shock y mods ( ) . los niveles de il- , il- , tnf-a y otras citoquinas inflamatorias en pacientes con covid- grave son significativamente más altos, lo que puede estar relacionado con un mal pronóstico ( ) . por lo tanto, la plasmaféresis se puede usar con seguridad y efectividad en pacientes con covid- grave, para eliminar mediadores inflamatorios de gran peso molecular. la seguridad depende como todas las terapias extracorpóreas de un personal de la uci entrenado, preparado y capacitado para aplicar las intervenciones en forma óptimas ( ) . las terapias extracorpóreas de soporte de órganos pueden representar una parte importante de la respuesta y los médicos y otros profesionales de la salud deben estar familiarizados con estas terapias sofisticadas. se debe hacer un llamado a la acción, para crear conciencia sobre las diferentes técnicas extracorpóreas, cada una con criterios específicos y modalidades de prescripción, entrega y monitoreo( , ). se recomienda no utilizar de forma rutinaria el uso de un tratamiento específico dirigido a pacientes con infección por sars-cov- /covid- comparado con el manejo estándar para mejorar desenlaces clínicos fuertes. actualmente no existe una terapia dirigida que se a efectiva para el manejo del virus; un número alto de estudios han surgido en los últimos dos meses, la mayoría sin el rigor metodológico suficiente para tomar decisiones adecuadas con respecto al manejo del amci ® paciente con infección por sars-cov- . el conocimiento en la estructura del virus y el mejor entendimiento en la fisiopatología de la enfermedad genera un sinnúmero de potenciales fármacos que han sido ensayados para el manejo de la enfermedad. en tiempos de pandemia, con una patología catastrófica en términos de vidas humanas y costos hospitalarios; es importante encontrar soluciones a desenlaces importantes como mortalidad, días de estancia en uci y en el hospital, aumento en los días libres del ventilador, disminución de complicaciones mayores debido a la enfermedad entre otros. hasta el momento no se ha documentado ninguna terapia específica que pueda impactar sobre estos desenlaces; pero la calidad de los trabajos, tampoco dejan claro sin él no usar ningún tratamiento específico mejora los desenlaces al menos al disminuir el número de complicaciones. este nuevo beta-coronavirus es similar al coronavirus del síndrome respiratorio agudo severa (sars-cov) y del síndrome respiratorio del medio este (mers-cov); por lo tanto, varias moléculas que habían sido evaluadas en este tipo de enfermedad rápidamente se abrieron paso a ensayos clínicos en paciente con covid- . estos ensayos principalmente observacionales, aleatorios pero abiertos con un número pequeño de pacientes no han permitido sacar adecuadas conclusiones y es frecuente como ver las diferentes guías de las principales sociedades del mundo cambiar de forma frecuente sus recomendaciones; no existes evidencia de estudios clínicos aleatorios y controlados que midan desenlaces fuertes, la premura de un tratamiento efectivo ha sacrificado el rigor metodológico que una investigación requiere. una estructura viral y replicación conocidas generan posibles dianas para que diferentes fármacos puedan ser investigados, antivirales tipo arbidol el cual inhibe la fusión de la membrana en la envoltura viral a algunos receptores; antimaláricos como la hidroxicloroquina y la cloroquina, las cuales inhiben la entrada viral y endocitosis por múltiples mecanismos, así como los efectos inmunomoduladores demostrados en el huésped; antivirales que impiden la replicación como el lopinavir o darunavir inhibiendo las proteasas o la ribavirina, el remdesivir o el favipiravir que actúan como análogos de nucleótidos o fármacos que actúan modulando la respuesta específica del huésped como el tocilizumab el cual se une al receptor de la il- inhibiendo el punto de acción de esta; los corticosteroides con múltiples efectos en la modulación del sistema inmunológico del paciente o los fármacos para evitar la respuesta secundaria a esta cascada inflamatoria como son los anticoagulantes. por último, se han buscado estrategias con el fin de mejorar la inmunización pasiva del huésped en el uso del plasma de pacientes convalecientes o el uso de inmunoglobulinas enriquecidas entre otros tratamientos propuestos para esta enfermedad. como vamos a ver más adelante, actualmente no existe un tratamiento específico con el nivel de evidencia suficiente para recomendar de manera generalizada; tampoco existe suficiente evidencia del manejo del soporte básico sin el uso de fármacos dirigidos, que demuestre que esta estrategia se deba implementar de manera sistemática en todos los pacientes; por lo tanto, a continuación trataremos de resolver las inquietudes con respecto a los diferentes medicamentos que han sido usados en la pandemia del sars-cov- /covid- . se recomienda no utilizar antimaláricos tipo hidroxicloroquina (hcq) o cloroquina (cq) para el manejo de pacientes con infección por sars-cov- /covid- . para la fecha no hay un adecuado sustento bibliográfico que soporte el uso de antimaláricos en la prevención o manejo de pacientes con infección por sars-cov- tanto leve, moderada como severa. los mayores estudios no muestran utilidad clínica y tendencia a mayores eventos cardiovasculares con el uso de antimaláricos en pacientes con infección por covid- comparado con no darlo. su utilidad se deriva principalmente de resultados en estudios preclínicos e in vitro; como los presentados por wang y cols donde evaluaron medicamentos de manera in vitro contra el covid- , siendo el remdesivir y la cq efectivos de manera in vitro contra el nuevo coronavirus( ); liu y cols, donde la hcq fue efectiva en inhibir la infección por sars-cov- in vitro que junto con su potencial antiinflamatorio tenía potencial para el uso clínico ( ) y yao y cols, donde la hcq fue más potente que la cq para inhibir el sars-cov- in vitro y fue recomendado para el uso en humanos en dosis de mg dos veces al día por el primer día, seguido de mg dos veces al día por días más mantendría la concentración efectiva del fármaco en el tejido pulmonar ( ) . los pocos estudios clínicos, son de baja calidad y no han mostrado mejoría ni eficacia en el uso de antimaláricos para el manejo de paciente adultos con covid- , algunos estudios iniciales con pocos pacientes con resultados favorables ( ) e incluso con recomendaciones para uso en las primeras versiones de guías internacionales para la amci ® hcq y cq, encontrando superioridad en estudios observacionales, de pocos pacientes, sin comparadores para inhibir la exacerbación de la neumonía, hallazgos de las imágenes pulmonares, promover una conversión negativa al virus y acortar el curso de la enfermedad; la cq tuvo un efecto notable tanto en términos de resultado clínico como de eliminación viral ( ) ; considerando la hcq y la cq como un tratamiento costo efectivo ( ) . estudios posteriores con un mayor número de pacientes no han logrado reproducir los estudios preclínicos iniciales; mahévas y cols, evaluaron la efectividad de la hcq en pacientes admitidos a cuatro hospitales en francia, con neumonía por covid- quienes requieren oxígeno, pero no se encontraban en uci, comparado con una población con manejo estándar; la hcq se usó a dosis de mg día en las primeras horas a la admisión, este estudio no soporte el uso de la hcq en pacientes admitidos al hospital con covid- que requieren oxígeno al no reducir de forma significativa la admisión a la uci, el sdra o muerte en el día después del ingreso ( ) ; por el contrario, se han reportado efectos secundarios frecuentes (prolongación del intervalo qt, hipoglucemia, cambios en el estado mental, alteraciones gastrointestinales y retinopatía); silvia borda y cols, evaluó la seguridad y eficacia de dos dosis de cq en pacientes con covid- severo en un estudio aleatorizado, doble ciego fase iib en pacientes adultos hospitalizados con infección por sars-cov- , los pacientes fueron expuestos a dosis altas de cq ( mg dos veces al día por días) o dosis bajas ( mg dos veces al día en el día y una vez al día por días), los hallazgos preliminares de este estudio sugieren que la dosis más alta de cq no debe recomendarse para pacientes críticos con covid- debido a sus posibles riesgos de seguridad, especialmente cuando se toman simultáneamente con azitromicina y oseltamivir; estos hallazgos no pueden extrapolarse a pacientes con covid- no severo ( ); tang y cols, evaluaron la eficacia y seguridad de la hcq con el manejo estándar en un estudio multicéntrico, abierto, aleatorio y controlado en china, pacientes con covid- positivo se incluyeron en el análisis de intención a tratar ( en el grupo de hcq y en el grupo estándar), la hcq fue administrada a dosis de mg día por tres días y mantenimiento con dosis de mg día (duración del tratamiento: dos a tres semanas en pacientes con enfermedad leve a moderada o enfermedad severa respectivamente); la administración de hcq no resultó en una significativa mayor probabilidad de conversión negativa comparado con el tratamiento estándar, los efectos adversos fueron mayores en el grupo de hcq ( ) . con todo esto la hcq y la cq, si se usan deberá ser bajo estudios experimentales aprobados con una estricta monitorización y vigilancia clínica de la frecuencia cardíaca y el intervalo qt, los niveles de glucosa, la función hepática y renal, y el cribado clínico de trastornos mentales y visuales en pacientes que reciben estos fármacos. debe evitarse hcq/cq en pacientes con enfermedades cardiovasculares subyacentes. nuevas evidencias con un mayor número de pacientes podrían sacar la hcq y la cq inclusive de estudios clínicos; barbosa y cols, evaluaron en un estudio cuasialeatorio comparativo el uso fuera de registro de la hcq en pacientes positivos por el sars-cov- , el pronóstico primario fue la necesidad de escalar el soporte ventilatorio, cambio en el conteo de linfocitos o cambio en el índice de neutrófilos/linfocitos, un total de pacientes fueron incluidos, en el brazo de hcq. la administración de hcq fue asociada con la necesidad de aumentar el nivel del soporte ventilatorio comparado con aquellos que no recibieron hcq al día del estudio, no hubo beneficios en la mortalidad, reconstitución inmunológica y riesgo de intubación ( ) . el estudio con un mayor número de pacientes proviene de la ciudad de new york; geleris y cols, examinaron la asociación entre el uso hcq y la intubación o muerte en un centro médico de ny, se analizaron . amci ® estaban más enfermos en términos de oxigenación, en este estudio observacional la administración de hcq no fue asociada con una disminución en el riesgo compuesto de intubación o muerte ( ) . se recomienda no utilizar antimaláricos tipo hidroxicloroquina (hcq) o cloroquina (cq) en combinación con azitromicina (az) para el manejo de pacientes con infección por sars -cov- /covid- . fundamento para la fecha la evidencia no favorece el uso combinado de los antimaláricos en combinación con la azitromicina; por el contrario, la combinación de estos dos medicamentos puede ser deletérea, inclusive con un aumento reportado en la mortalidad y la aparición de arritmias ventriculares de novo; estudios iniciales fueron promisorios, gautret y cols, evaluaron inicialmente el efecto de la hcq en la carga viral respiratoria en conjunto con el uso de azitromicina, la presencia del virus al día fue el pronóstico primario; pacientes con tratamiento mostraron una significativa reducción en la carga viral al día de la inclusión comparado con los controles; la azitromicina adicionada a la hcq fue significativamente más eficiente en la eliminación viral ( ) ; nuevamente gautret y cols, realizaron un estudio observacional, no controlado, no comparativo de pacientes tratados con la combinación de hcq más azitromicina, presentando una mejoría significativa en disminución de la carga nasofaríngea del virus y una menor tiempo de enfermedad ( ) ; luego million y cols, evaluaron la combinación de hcq y az en un estudio retrospectivo de . pacientes con sars-cov- tratados con hcq ( mg tres veces al día por días) + az ( mg en el día , seguido de mg al día por los próximos días), el pronóstico fue mortalidad, empeoramiento clínico (ingreso a uci) o persistencia viral; la administración de hcq+az en combinación antes de que aparecieran las complicaciones del covid- es segura y asociada a una baja mortalidad en los pacientes ( ) ; soportado además por estudios in vitro que demuestran que la combinación de hcq y az tienen efectos sinérgicos para el sars-cov- a concentraciones compatibles con las que se obtienen en pulmones humanos ( ) . otros estudios por el contrario no han encontrado resultados positivos, es así como, magagnoli y cols, en un análisis retrospectivo de pacientes confirmados con infección por sars-cov- en centros de veteranos de los eeuu, un total de pacientes fueron evaluados (hcq, n= ; hcq+az, n= ; no hcq, n= ), en este estudio no hubo evidencia que el uso de la hcq tanto sola o en combinación con la az, redujo el riesgo de ventilación mecánica en pacientes hospitalizados con covid- ; una asociación con un aumento en la mortalidad fue identificada en pacientes tratados con hcq sola ( ) . nuevamente los estudios con un mayor número de pacientes se encuentran en la ciudad de new york; rosenberg y col, describieron la asociación entre hcq, con o sin az en el pronóstico de pacientes hospitalizados con covid- ; un estudio de cohorte multicéntrico retrospectivo en pacientes hospitalizados con covid- en hospitales de ny, los pacientes recibieron ; en pacientes hospitalizados en el área metropolitana de ny con covid- , el tratamiento con hcq, az o ambos, comparado con ningún tratamiento, fue no significativamente asociado con diferencias en la mortalidad hospitalaria ( ) . recomendaciÓn se recomienda no utilizar de forma rutinaria el uso rutinario del lopinavir/ritonavir para el manejo de pacientes con infección por sars-cov- /covid- . en la actualidad no existe evidencia a favor o en contra en el uso del tratamiento con antirretrovirales con lopinavir/ritonavir en el manejo de pacientes adultos hospitalizados con covid- ; no se observó ningún beneficio con lopinavir/ritonavir más allá de la atención estándar. se está en espera de cierre de diferentes ensayos futuros que confirme o excluyan el uso de lopinavir/ritonavir en el paciente covid- . en diciembre de , un nuevo coronavirus, designado sars-cov- , ha causado una pandemia ( , , , ) ; cuando hablamos de enfermedad producida por covid- hablamos de enfermedades que van desde las enfermedades leves autolimitantes del tracto respiratorio hasta neumonía rápidamente progresiva, neumonía grave, falla multiorgánica y muerte. hasta este momento no existen agentes terapéuticos específicos para las infecciones por coronavirus. después de la aparición del síndrome respiratorio agudo grave (sars) en , entre los fármacos aprobados se identificó lopinavir, un inhibidor del aspartato proteasa tipo del virus de inmunodeficiencia humana (vih), que tiene actividad inhibitoria in vitro contra el sras-cov, el virus que causa el sars en los seres humanos y el ritonavir combinado con lopinavir para aumentar su vida media plasmática a través de la inhibición del citocromo p ( ) . se comenzaron estudios evaluando la respuesta antiviral in vitro de la combinación de lopinavir/ritonavir y ribavirina en pacientes con sars; comparados con pacientes tratados con ribavirina sola, que sirvieron como controles históricos; el pronóstico adverso (sdra o muerte) fue significativamente más bajo en el grupo de tratamiento comparado con los controles históricos ( . % vs . %, p = . ) al día del inicio de los síntomas; una reducción adicional en el uso de esteroides y de infecciones nosocomiales fue vista en el grupo de tratamiento con una disminución en la carga viral y aumento en el conteo de linfocitos ( ) ; del mismo modo, el lopinavir tiene actividad, tanto in vitro como en modelo animal, contra el coronavirus del síndrome respiratorio de oriente medio (mers-cov) ( ) . estos estudios previos son el soporte inicial para el uso del lopinavir/ritonavir en la epidemia del covid- ; cao y cols, en mayo de publicaron en china, un estudio controlado, aleatorizado en pacientes hospitalizados con prueba ; los efectos adversos gastrointestinales fueron más comunes con el lopinavir-ritonavir, pero los eventos adversos serios fueron más común con el grupo control; el tratamiento con lopinavir-ritonavir fue suspendido en pacientes ( . %) secundario a los eventos adversos ( ) . otro estudio hung y cols, en hong kong, evaluaron en un trabajo multicéntrico, prospectivo, aleatorizado, fase la eficacia y seguridad de la terapia combinada por días de lopinavir mg y ritonavir mg cada h, ribavirina mg cada h y tres dosis de millones de ui de interferón beta- b en días alternos en pacientes con covid- comparado con lopinavir/ritonavir cada h (grupo control); el resultado primario fue tiempo en la negativización de la pcr viral en el hisopado nasofaríngeo en paciente con covid- ; pacientes fueron ingresados, en el grupo de combinación y en el grupo control; en el grupo de intervención de forma significativa se negativizo la prueba de pcr de forma más rápida ( días [iqr - ]) que el grupo control ( días [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ; hr . [ic % . - . ], p = . ); los eventos adversos fueron similares entre los grupos; ningún paciente murió durante el estudio ( ) . por último, un pequeño estudio de zhu y cols en china, con pacientes con sars-cov- ; evaluaron de forma retrospectiva los efectos antivirales y seguridad del lopinavir/ritonavir y el arbidol (antiviral aprobado en china y rusia para el sasr y la influenza), pacientes en el grupo de lopinavir/ritonavir y en el grupo de arbidol; los pacientes lopinavir/ritonavir presentaron un mayor tiempo para la negativización de la prueba de pcr viral (p < . )( ). se recomienda no utilizar de forma rutinaria remdesivir como antiviral para el manejo de pacientes con infección por sars-cov- /covid- . se debe considerar su uso en escenarios de estudios de investigación clínica aprobados. actualmente no hay disponibilidad del medicamento en el país (colombia) por lo cual no se incluye en los protocolos de manejo de paciente con covid- . en estados unidos el primer paciente con covid- mostró una mejoría significativa de sus síntomas con horas de tratamiento con remdesivir ( ) , lo que abrió la puerta a un nuevo tratamiento para el sars-cov- ; el remdesivir (gs- ) es un análogo de los nucleótidos que inhibe la rna polimerasa; con un amplio espectro antiviral, puede inhibir la replicación de múltiples coronavirus en las células epiteliales del sistema respiratorio ( ) ; estudiado ( ) . por último, un estudio publicado por antinori y cols, en milán, italia; de manera prospectiva (compasional) incluyó pacientes con neumonía por sars-cov- mayores a años bajo ventilación mecánica o con una saturación de oxígeno ≤ % al aire ambiente o un puntaje del national early warning score ≥ ; el pronóstico primario en cambio en el estado clínico en una escala ordinal de categorías ( = no hospitalizado de regreso a sus actividades diarias normales; = muerte); de los paciente ingresados, se encontraban en uci y en un piso de hospitalización de enfermedades infecciosas; un curso de días de remdesivir fue completado por pacientes ( %) y suspendido en , de os cuales ( . %) se descontinuo por eventos adversos; a los días, ( . %) pacientes de piso fueron egresados, permanecían hospitalizados y uno murió ( . %), en la icu ( . %) fueron egresados, ( . %) pacientes murieron, ( . %) aún se encontraban en ventilación mecánica y ( . %) estaba con mejoría pero aún hospitalizado; la hipertransaminasemia y la injuria renal aguda fueron los eventos adversos más frecuentes reportados ( . % y . %, respectivamente); los datos sugieren que el remdesivir puede beneficiar a pacientes con neumonía por sars-cov- hospitalizados por fuera de la unidad de cuidado intensivo ( ). page se recomienda no utilizar de rutina la ivermectina para el manejo de pacientes con infección por sars-cov- /covid- . para la fecha no se cuenta con la suficiente evidencia para emitir una recomendación para el uso de la ivermectina en pacientes con covid- , en estudios iniciales in vitro, caly y cols, demostró como la ivermectina, una droga autorizada por la fda como antiparasitario tiene un efecto antiviral de amplio espectro de manera in vitro, con una reducción significativa de la replicación viral en modelos experimentales ( ) , un estudio aún sin publicar, observacional multicéntrico de casos y controles (n: casos y n: controles), realizado entre el de enero y de marzo de , incluyó pacientes diagnosticados con covid- confirmados por laboratorio, la dosis fue de mcg/kg de ivermectina más la terapia médica de soporte en comparación con terapia médica sin ivermectina, el resultado principal fue la medición de supervivencia; en pacientes que requirieron ventilación mecánica, la mortalidad fue menor en el grupo de ivermectina ( , % y , % respectivamente) y las tasas de mortalidad global fueron más bajas con ivermectina ( no se puede emitir una recomendación a favor o en contra sobre el uso compasivo o rutinario de tocilizumab en pacientes con infección por sars-cov- /covid- . en pacientes individualizados se ha reportado desenlaces clínicos favorables. se puede considerar su uso en pacientes que cumplan con todos los siguientes criterios: ver tabla . el tocilizumab (tcz) un anticuerpo monoclonal humanizado igg k, el cual se puede unir de manera específica a los receptores solubles de membrana para la il- (sil- r and mil- r) y ha sido ampliamente usado en el tratamiento de enfermedades autoinmunes, tales como la artritis reumatoide, la enfermedad de still del adulto o vasculitis de grandes vasos ( ) . un primer estudio de xiaoling xu y cols, describió en china, pacientes tratados con tocilizumab, se documentó una mejoría en los síntomas, en los requerimientos de oxígeno y en los hallazgos imagenológicos de la tomografía de tórax; los niveles promedio de il- antes de la terapia fueron de . pg./ml; todos los pacientes recibieron lopinavir y metilprednisolona antes de la terapia. se trata de una serie con una muestra pequeña de pacientes en donde solo ( %) pacientes estaban en condición crítica ( ) . posteriormente luo y cols, en china, reportan el uso de tocilizumab en pacientes, con mejoría en el aumento de la pcr en todos los pacientes, excepto uno, y una disminución de la il . el nivel sérico de il- tendió a aumentar inicialmente y luego disminuyó en pacientes. los niveles medios de il- antes de la terapia fueron de . pg./ml; % de los pacientes recibieron metilprednisolona; el % fallecieron. es otra serie pequeña, con pacientes ( , %) en condición crítica ( ) . roumier y cols, en francia, estudiaron pacientes que recibieron tcz, observando que se redujo la necesidad de ventilación mecánica en comparación con los controles ( amci ® . ); en este estudio, no hubo diferencias en la reducción de la mortalidad y pacientes ( %) se encontraban en uci ( ) . klopfenstein y cols, también en francia, en un estudio retrospectivo de casos y controles, encontraron que pacientes que recibieron tcz (n= ), a pesar de tener más requerimiento de oxígeno, con resultados biológicos más pobres (mayor linfopenia y un nivel de pcr superior) al inicio del estudio que los pacientes sin tcz (n = ), presentaron el objetivo combinado (ingreso a uci y mortalidad) menor que los pacientes sin la terapia ( % vs %, p = . ); es otra serie, que disminuye la necesidad de ventilación mecánica ( % vs %, p = . ) de manera significativa ( ) . luego rimland ca y cols informan los primeros datos de pacientes con covid- tratados con tcz en los estados unidos, de ellos en ventilación mecánica; la pcr y el fibrinógeno mejoraron rápidamente, pero no hubo mejoría en otros marcadores o resultados clínicos. sólo a seis pacientes les tomaron niveles previos de il y de ellos dos tenían niveles bajos ( ) . en otro estudio mikulska y cols, próximo a salir en jama, en pacientes con sdra moderado a severo, hay mayor disminución de la mortalidad con el tratamiento combinado de tocilizumab y esteroides, en relación con cada una de estas terapias. por último, no todos los estudios han mostrado resultados positivos; kimmig y cols, de chicago (eeuu), en de los pacientes críticos con covid- , que recibieron tcz, se asoció con una mayor incidencia de infecciones bacterianas secundarias, incluida la neumonía asociada al ventilador ( . % vs. . % p = . ) ( ) . posterior a la recomendación hay nueva evidencia publicada y estudios aún sin publicar que puede soportar el uso de los inhibidores de la il- en pacientes con sars-cov- /covid- ; morena y col, en un estudio de tocilizumab como uso "off-label" en el tratamiento de neumonía por sars-cov- en milán, italia, este estudio abierto, prospectivo, describe las características clínicas y el pronóstico de pacientes con covid- confirmado y severo tratados con tcz iv, todos los pacientes, presentan niveles plasmáticos elevados de il- (> pg/ml) y saturación de oxígeno < % al aire ambiente, pacientes ( %) se encontraban con sistema de alto flujo de oxígeno y en ventilación invasiva, a los días luego del tratamiento se observa una caída dramática en la temperatura corporal y la pcr, con un incremento significativo en el conteo de linfocitos (p < . ); a los días del tratamiento, pacientes ( %) mostraron una mejoría en la severidad del cuadro; fueron dados de alta; ( %) mostraron empeoramiento de su cuadro clínico y de estos, murieron ( %). la mortalidad fue significativamente asociada con el uso de ventilación mecánica al inicio ( . % vs % de los pacientes en soporte de oxígeno no invasivo, p = . ), el efecto adverso más frecuente reportado fue la elevación de las enzimas hepáticas ( %), trombocitopenia ( %) e infecciones bacterianas serias e infecciones fúngicas en un ( %); los autores concluyen que el tcz ejerce un rápido beneficio sobre los marcadores inflamatorios y la fiebre, aunque no se consiguió un impacto clínico sobre el pronóstico, el riesgo aumentado de infecciones severas no es despreciable ( ) . capra y col, describieron pacientes en un hospital de italia con neumonía por covid- y falla respiratoria sin soporte ventilatorio y al menos uno de los siguientes: frecuencia respiratoria ≥ respiraciones/min, saturación ≤ % o pao /fio <= mmhg, los pacientes recibieron la terapia estándar para el momento (hidroxicloroquina, lopinavir y ritonavir) y fueron considerados el control; pacientes recibieron tzc con días de la admisión más el manejo estándar, los pacientes en el grupo de tratamiento mostraron de manera significativa una mayor sobrevida comparado con los pacientes control (hr para muerte, . ; % ic], . a . ; p = . ), ajustado para las características clínicas de base; de pacientes en el grupo de tcz y de en el grupo control murieron; % y . % de los pacientes que se dieron de alta en el grupo de tcz y en el control se recuperaron; la función respiratoria mejoró en el . % de los amci ® pacientes con tcz que aún se mantenía hospitalizados, donde el % de los controles empeoro y requirieron ventilación mecánica, dando al tcz un espectro positivo en términos de curso clínico y sobrevida en pacientes con covid ( ). guaraldi y col; evaluaron el papel del tcz en reducir el riesgo de ventilación mecánica invasiva en pacientes con neumonía severa por covid- quienes recibían tratamiento estándar para el momento (hidroxicloroquina, azitromicina, antirretrovirales y heparinas de bajo peso molecular) en un estudio retrospectivo, observacional en bologna, reggio emilia y módena, italia; el tcz fue dado a dosis de mg/kg de peso corporal de forma iv (con un máximo de mg) en dos infusiones separadas h o mg sc administradas en dos dosis simultáneas, una en cada muslo ( mg en total), cuando la formulación iv no se encontraba disponible; el pronóstico primario fue la combinación de ventilación mecánica invasiva o muerte; de pacientes ingresados, ( %) tenían neumonía severa por covid- y fueron incluidos, ( %) de pacientes en el grupo estándar requirieron ventilación mecánica, comparados con ( %) de pacientes tratados con tcz (p = · ; [ %] de pacientes tratados iv y [ %] de pacientes tratados sc); ( %) pacientes en el grupo estándar murieron, comparado con ( %; p < . ) pacientes con tcz ( [ %] del grupo iv y [ %] sc); luego de ajustar para sexo, edad, centro de reclutamiento, duración de los síntomas y puntaje de sofa, el tratamiento con tcz fue asociado con una reducción en el riesgo de ventilación mecánica invasiva o muerte (hr . , % ic . - . ; p = . ); ( %) de pacientes tratados con tcz fueron diagnosticados con nuevas infecciones en comparación con ( %) de pacientes en el grupo estándar (p < . ) ( ) . campochiaro y col, en un solo centro evaluó la eficacia y seguridad del tcz en pacientes con covid- severo, se diseñó un estudio retrospectivo en pacientes con características de hiper-inflamación (definida como una elevación tanto en la pcr, ≥ mg/l, normal < mg/l o ferritina ≥ ng/ml, normal < ng/ml en presencia de un incremento en la dhl > u/l), acompañado de un compromiso respiratorio severo, definido como hallazgos típicos en la radiografía y/o tomografía, la presencia de una saturación de oxígeno ≤ % al aire ambiente o una pao :fio ≤ mmhg ingresados a la uci, comparando pacientes con tcz iv al manejo estándar, pacientes fueron incluidos de los cuales fueron tratados con tcz; los pacientes se encontraban con alto flujo o ventilación mecánica no invasiva, a días de seguimiento, % de los pacientes con tcz experimentaron mejoría clínica comparado con un %del tratamiento estándar (p = . ); la mortalidad fue % en el grupo de tcz y % en el grupo estándar (p = . ); la incidencia de infección y trombosis pulmonar fue similar en ambos grupos ( ); somers y col, evaluaron un estudio observacional en pacientes con neumonía por covid- severo que se encontraban en ventilación mecánica, evaluando como pronóstico la probabilidad de sobrevida posterior a la extubación; pacientes fueron incluidos, recibieron tcz y no; en los modelos ajustados, el tcz, fue asociado con una reducción del % en el riesgo de muerte [hr . % ic . a . ]; aunque el tcz, fue asociado con un incremento en la proporción de pacientes con superinfecciones ( % vs. %; p < . ), no hubo diferencias en la mortalidad a días entre los pacientes tratados con tcz con o sin superinfecciones [ % vs. %; p= . ] ( ). price y col, también publicaron un estudio observacional de pacientes hospitalizados con covid- , los pacientes recibieron tcz si cumplían criterios del síndrome de liberación de citoquinas, se evaluaron pacientes; de los cuales ( %) recibieron tcz, estos pacientes que recibieron ventilación mecánica la sobrevida fue del % ( % ic, - ), luego del tcz pocos eventos adversos fueron reportados y tanto la oxigenación como los biomarcadores de inflamación mejoraron ( ) y por último, en un estudio preliminar con datos aún sin publicar perrone y col, evaluaron la eficacia del tcz en pacientes con neumonía por covid- , en un estudio amci ® multicéntrico fase en italia; se utilizó tcz, a dosis de mg/kg iv, una o dos administraciones con horas de diferencia; y casos fueron disponibles para un análisis de intención a tratar, pacientes murieron; las tasas de letalidad fueron de . % ( . % ic, . - . , p = . ) y . % ( . % ic, . - . , p < . ) a y días; el tcz redujo la tasa de letalidad a días pero no a días comparado con las esperadas sin presentar una toxicidad significativa; la eficacia fue más evidente en los paciente que no requerían ventilación mecánica ( ). recomendaciÓn se recomienda no utilizar de rutina bloqueadores de interleuquina- (anakinra) en pacientes con infección por sars-cov- /covid- . aunque su ventaja está en el perfil de seguridad, su vida media corta ( horas) y porque las infecciones oportunistas son raras ,no hay suficiente evidencia para emitir una recomendación sobre el uso de este medicamento; cavalli y cols, de milán, italia, realizaron un estudio de cohorte retrospectivo en pacientes con sdra moderado a severo con hiperinflamación (pcr ≥ mg/dl, ferritina ≥ ng/ml o ambos), manejados con ventilación mecánica no invasiva fuera de la uci y que recibieron tratamiento con hidroxicloroquina y lopinavir, los pacientes que recibieron anakinra, mg/kg dos veces al día intravenosa (n= , dosis alta) o mg dos veces al día subcutánea (n= pacientes, dosis baja) fueron comparados con una cohorte retrospectiva que no recibió anakinra (tratamiento estándar); la duración del tratamiento se prolongó hasta el beneficio clínico sostenido (reducción del % en la pcr, y una pafi > , durante al menos días consecutivos) o hasta la muerte, bacteriemia, o efectos secundarios (alt > veces valores de referencia); el tratamiento con anakinra a bajas dosis se interrumpió después de días debido a la escasez de efectos sobre la pcr y el estado clínico. a los días, el tratamiento con dosis altas de anakinra se asoció con una reducción en la pcr y mejoría en la función respiratoria en de pacientes ( %); en el grupo estándar, ocho de pacientes ( %) mostraron mejoría respiratoria a los días. en días de seguimiento, la sobrevida fue del % en el grupo de dosis altas de anakinra y del % en el grupo estándar (p = . ). se trata del primer estudio que demuestra seguridad y mejoría en los pacientes covid- , pero en el contexto fuera de la uci ( ) . huet y cols, de parís, francia, realizaron el estudio llamado ana-covid- en el que compararon pacientes tratados con anakinra subcutánea mg dos veces al día durante h, luego mg diarios durante días, con pacientes históricos; su criterio de inclusión fue tener una saturación de oxígeno del % o menos con un soporte de mínimo de l / min de oxígeno. la admisión a la uci por ventilación mecánica invasiva o muerte se produjo en ( %) pacientes en el grupo de anakinra y ( %) pacientes en el grupo histórico (hr . amci ® pacientes en el grupo histórico tuvieron un aumento en las aminotransferasas hepáticas ( ). recomendaciÓn se sugiere que la terapia con interferón sólo sea considerada en pacientes con formas graves de infección por covid- en el marco de un estudio clínico. estudios preliminares muestran que el virus del covid- induce una expresión muy débil de interferones en las células infectadas, lo que obstaculiza la respuesta inmune innata temprana a la infección y sugiere que el uso de interferón (ifn) exógeno para estimular la inmunidad antiviral ( ) . zhou q y col, en china, en un estudio observacional de pacientes con covid- con gravedad mixta proporcionó evidencia de muy baja calidad que la adición de interferón-α a la terapia con umifenovir no afecta el tiempo de eliminación viral o la duración en la estancia hospitalaria cuando se comparó con el umifenovir solo ( ) . hung if y cols, de hong kong, realizaron un ensayo multicéntrico, en adultos con covid- , en los que pacientes recibieron una combinación de lopinavir/ritonavir y tres dosis de millones de unidades internacionales ( · mg) de interferón beta- b en días alternos (grupo de combinación) y pacientes recibieron lopinavir/ritonavir (grupo control); la terapia de combinación fue segura y superior al control, para aliviar los síntomas y acortar la duración de la eliminación del virus y la estancia hospitalaria; se trata de un estudio fase , en pacientes con covid- leve a moderado (ningún paciente con ventilación en el grupo de combinación), en el que el ifn se administró en los primeros días de inicio de los síntomas y con el uso de un análogo de nucleósido oral (ribavirina), que no está en nuestras guías ( ) . se necesitan estudios de ifn solo o combinado en pacientes críticos con covid- . los efectos adversos de los ifn tipo i pueden limitar su uso para una intervención generalizada, como se propone en el brazo ifn-β con lopinavir/ritonavir del ensayo solidaridad de la oms. la administración por inhalación de vapor que se realiza actualmente en china ofrece la ventaja de acceso rápido al tracto respiratorio; sin embargo, la farmacodinamia y la farmacocinética de este modo de administración nunca se han evaluado. se sugiere no utilizar de rutina corticoides en el tratamiento de pacientes con sospecha o diagnóstico de covid- . no se puede considerar su uso profiláctico ni en pacientes con enfermedad leve sin requerimiento de oxígeno. débil en contra page en diciembre de , una serie de casos de neumonía de causa desconocida surgió en wuhan, hubei, china, con presentaciones clínicas muy parecidas a una neumonía viral; los análisis de secuenciación profunda de muestras del tracto respiratorio inferior indicaron un nuevo coronavirus, que se denominó novel coronavirus (covid- - ) ( ) . en la actualidad, en ausencia de terapia preventiva para sars-cov- , la piedra angular de atención para pacientes con covid- sigue siendo el manejo de apoyo, que va desde el tratamiento ambulatorio sintomático hasta el tratamiento intensivo completo con medidas de soporte en cuidados intensivos ( ) . dentro del manejo farmacológico se ha planteado la opción del uso de corticoides, la justificación estaría basada en la disminución de la respuesta inflamatoria del huésped a nivel pulmonar; es decir, un efecto inmunomodulador, ya que esta infección puede conducir a un síndrome de distrés respiratorio agudo (sdra); sin embargo, el beneficio puede verse superado por los efectos adversos, incluido el retraso en el aclaramiento viral y mayor riesgo de infección secundaria. a pesar de que la evidencia directa de corticoides en covid- es limitada, revisiones de los resultados en otras neumonías virales nos podrían orientar en principio en esta actual situación ( ) . teniendo en cuenta lo anterior; stockman y cols, en el . , realizaron una revisión sistemática sobre ensayos en pacientes con sars; quince ensayos examinan el uso de corticoides con diez o más pacientes en tratamiento; ensayos también recibían ribavirina; trece de estos estudios no fueron concluyentes; dos estudios describen un daño potencial con el uso de esteroides; en la literatura china estos autores encontraron catorce estudios con uso de esteroides en sars; doce fueron suspendidos por posible daño, la mayoría de estos ensayos se realizaron con muestras pequeñas de pacientes y de manera retrospectiva ( ) . arabi y cols, en noviembre de . , realizaron un estudio multicéntrico de cohorte retrospectivo en hospitales de atención terciaria de arabia saudita, donde se incluyeron pacientes; el uso de corticoides en pacientes con mers no se asoció con un cambio significativo a los días en la mortalidad y se documentó un retraso en la eliminación del arn de mers-cov ( ) . en cuanto hace referencia a la situación actual de pandemia por sars-cov- y compromiso pulmonar; wu y cols, en marzo de . realizaron un estudio retrospectivo de pacientes con covid- en china; para aquellos pacientes que desarrollaron sdra, el tratamiento con metilprednisolona estuvo asociado con una disminución del riesgo de muerte ( / [ %] con esteroides vs / [ %] sin esteroides; hr, . [ic %, . - . ]), con las limitaciones de los estudios retrospectivo, de un solo centro, con un limitado número de pacientes ( ). zha y cols, en marzo de . , describen el uso de corticosteroides en el tratamiento de pacientes con covid- ; no hallaron asociación entre la terapia con esteroides y el pronóstico de los pacientes sin sdra, siendo un estudio con una serie muy pequeña de pacientes ( ) . yang y cols, en marzo de . , en una revisión sistemática y meta-análisis que incluyó . pacientes de estudios, describen como el tratamiento con corticoides estuvo asociado con una mayor mortalidad (rr = . , ic % = . - . , p = , ), mayor estancia (wmd = . , ic % . - . , p = < , ) y una mayor tasa de infección bacteriana (rr = . , ic % . - . , p = < . ); con algunas limitaciones en este metaanálisis, la mayoría de los estudios incluidos son estudios de cohorte retrospectivos, controles históricos, con un bajo nivel de evidencia y una falta de ensayos controlados aleatorizados con buen diseño, sin un estándar uniforme para el tiempo y la dosis de los corticoides utilizado en los estudios; los efectos de los corticosteroides pueden ser influenciado también por otras opciones terapéuticas, como los medicamentos antivirales ( ) . por último, li y cols, en mayo de . , en otra revisión sistemática y metaanálisis, con respecto al uso de corticosteroides en sujetos con amci ® infecciones por sars-cov- , sars cov y mers-cov, se determinó que hubo retraso en la eliminación del virus sin mejoría en la supervivencia, reducción en la duración de la hospitalización o tasa de admisión en la uci y/o uso de ventilación mecánica; presentándose varios efectos adversos. debido a la preponderancia de los estudios observacionales en el conjunto de datos y los sesgos de selección y publicación, se concluye especialmente con respecto al sars-cov- , que se necesita mayor investigación con ensayos clínicos aleatorizados. internamente en este meta-análisis sugiere precaución al usar esteroides en pacientes con covid- ( ). horby y col en una rama del ensayo de evaluación aleatorizada de la terapia covid- (recovery), estudio aleatorizado, controlado, abierto que compara una gama de posibles tratamientos con la atención habitual en pacientes hospitalizados con covid- , compararon el uso de la dexametasona a dosis de mg día (oral o intravenosa) una vez al día por días o el alta según lo que ocurriera primero contra el manejo habitual; en pacientes aleatorizados que recibieron dexametasona se compararon con pacientes en manejo estándar; ( . %) pacientes en el grupo de dexametasona y ( . %) pacientes en el grupo control murieron a los días, con un riesgo relativo ajustado para la edad (rr . ; % ic . a . ; p < . ). la mortalidad relativa y absoluta variaron significativamente en relación al soporte ventilatorio al momento de la aleatorización; la dexametasona redujo las muertes en una tercera parte de los pacientes que recibieron ventilación mecánica invasiva ( . % vs. . %, rr . , % ic . a . ; p < . ), y una quinta parte en los pacientes que reciben oxígeno sin ventilación mecánica invasiva ( . % vs. . %, rr . , % ic . a . ; p = . ), pero sin reducir la mortalidad en paciente que no recibieron soporte respiratorio al momento de la aleatorización ( . % vs. . %, rr . , % ic . a . ]; p = . ) ( ). se recomienda no utilizar plasma convaleciente como tratamiento de rutina en paciente con sars-cov -covid- . se debe considerar su uso en el marco de un ensayo clínico y con alguno de los dos escenarios siguientes: escenario a (enfermedad severa), definida como uno o más de los siguientes: disnea, frecuencia respiratoria > /min, spo < %, pao /fio < o empeoramiento radiológico con aumento > % de los infiltrados pulmonares en - horas. escenario b (enfermedad que amenaza la vida), definida como uno o más de los siguientes: falla respiratoria, choque séptico, o disfunción multiorgánica. se recomienda no utilizar plasma convaleciente para profilaxis clínica de rutina contra la infección por sars-cov- , solo se debe considerar en el marco de un ensayo clínico. ( ) . una revisión sistemática y meta-análisis exploratorio realizado en identificó estudios de infección por coronavirus sars e influenza severa, el estudio reveló una reducción de la mortalidad, especialmente si el plasma convaleciente se emplea en la fase temprana de la enfermedad cuando se comparó con placebo o no tratamiento (or . ; ic del % . - . ); sin embargo, hay que tener presente que los estudios son de baja calidad, carecen de grupos control y puede tener riesgo moderado a alto de sesgo ( ) . se ha sugerido que el plasma convaleciente de pacientes que se han recuperado de covid- puede ser una terapia potencial, proporcionando inmunidad pasiva de los anticuerpos específicos contra sars-cov- y podría servir para prevenir y tratar la enfermedad ( ) . las personas que se han recuperado de la infección por sars-cov- pueden generar anticuerpos neutralizantes ( , ) que podrían tener aplicación en la prevención de infección en ciertos escenarios, como las personas con comorbilidades subyacentes que predisponen a enfermedad grave y aquellas con exposición de alto riesgo como los trabajadores de la salud y los expuestos a casos confirmados de covid- . existen algunos riesgos asociados con el uso de plasma convaleciente, unos conocidos y otros teóricos; los riesgos conocidos son aquellos asociados con la transfusión de hemocomponentes, incluida la transmisión de virus (ej. vih, vhb, vhc, entre otros) ( ); riesgo muy bajo, con los estándares de calidad actuales de los bancos de sangre; también se pueden presentar complicaciones no infecciosas, como las reacciones alérgicas, anafilaxia, reacción febril a la transfusión, lesión pulmonar aguda relacionada con la transfusión (trali), sobrecarga cardiaca asociada a transfusión (taco) y hemólisis si se administra plasma abo incompatible ( ) . los riesgos teóricos incluyen el empeoramiento de la infección dependiente de anticuerpos (antibody-dependent enhancement of infection -ade); el ade puede ocurrir en varias enfermedades virales e implica una respuesta inflamatoria exagerada ante la presencia de ciertos anticuerpos ( ) . otro riesgo teórico es que la administración de anticuerpos a las personas expuestas al sars-cov- puede evitar la enfermedad, pero modifica la respuesta inmune de tal manera que esos individuos monten respuestas inmunes atenuadas, lo que los haría vulnerables a la reinfección posterior, si se comprueba que este riesgo es real estos individuos podrían ser vacunados contra covid- cuando exista una vacuna disponible ( ) . durante el brote actual en china, se utilizó plasma convaleciente en algunos pacientes con covid- ( ), desde esta publicación se identificaron publicaciones relacionadas con el tema, entre todos los estudios fueron tratados con plasma convaleciente un total de pacientes( - ) (tabla ). shen y cols en marzo describieron en china el primer reporte en el cual el plasma convaleciente puede ser una opción de tratamiento en pacientes con covid- ; reportaron una serie de casos de pacientes críticamente enfermos con covid- y síndrome de dificultad respiratoria aguda (sdra), todos en ventilación mecánica, a quienes se les administró plasma convaleciente con anticuerpos neutralizantes [ a días después del inicio de la enfermedad (ddie)], todos ellos posteriormente mostraron mejoría clínica, la carga viral de los pacientes disminuyó y fueron negativas en los días posteriores a la intervención ( ) . de forma similar, duan y cols en mazo en china reportaron mejoría clínica en una serie prospectiva de casos de paciente severamente enfermos con covid- , que recibieron plasma convaleciente con un tiempo medio de . ddie ( a días) después del inicio de los síntomas, e hicieron amci ® una comparación con un grupo control histórico comparables en edad, género y severidad de la enfermedad ( ) . zhang y cols en mazo , en china reportaron una serie de casos de pacientes con covid- críticamente enfermos, en falla respiratoria con ventilación mecánica y dos de ellos con ecmo (membrana de oxigenación extracorpórea), a quienes se les dio tratamiento con plasma convaleciente en un tiempo medio . ddie, posteriormente todos tuvieron mejoría clínica ( ) . posteriormente ahn y cols en abril en corea, describieron una serie de dos casos de paciente con covid- severamente enfermos, en falla respiratoria y con ventilación mecánica, quienes además de recibir hidroxicloroquina, lopinavir/ritonavir y metilprednisolona, fueron tratados con plasma convaleciente entre - ddie, ambos pacientes se recuperaron y fueron liberados de la ventilación mecánica, uno fue dado de alta al momento del reporte ( ) . ye y cols en abril en china, describieron una serie de pacientes con covid- con anormalidades imagenológicas y deterioro clínico a pesar del tratamiento estándar y con pcr para sars -cov- persistentemente positiva, aunque no estuvieron en falla respiratoria o con ventilación mecánica, de hecho, una de las pacientes era portadora asintomática; todos recibieron plasma convaleciente entre a ddie, en todos los pacientes, excepto , hubo resolución de los cambios de vidrio esmerilado y consolidación, todos mejoraron y fueron dados de alta ( ) . zeng y cols en abril en china, reportaron una serie de casos con covid- en falla respiratoria y se compararon con controles que no recibieron plasma convaleciente por limitación en la disponibilidad y compatibilidad abo; a este grupo de paciente, se les administró plasma convaleciente en promedio . ddie, en todos los casos se negativizó la pcr para sars-cov- a los días después del tratamiento; sin embargo, contrario a los reportes de los estudios previos, en este grupo se murieron pacientes ( % vs %, p = . ), pero tuvieron mayor porcentaje de aclaramiento del virus (pcr sars-cov- negativa % vs . %, p = . ) antes de la muerte e incluso el tiempo de sobrevida fue mayor en el grupo de tratamiento (p = . ) ( ) . salazar y cols en mayo , en houston, texas, reportaron una serie de pacientes con covid- severa o amenazante para la vida, el desenlace primario fue seguridad y el secundario fue el estado clínico de los pacientes al día luego de la transfusión; al día posttransfusión, pacientes ( %) mejoraron con relación a su estado clínico basal, ( %) no tuvieron cambios y pacientes tuvieron deterioro clínico. siete de los nueve pacientes que mejoraron ( %) habían sido dados de alta; para el día post-transfusión, ( %) de los pacientes presentaron mejoría y pacientes más, habían sido dados de alta; tres pacientes permanecían sin cambios, pacientes se deterioraron y uno murió por una condición no relacionada con el plasma; el promedio de estancia hospitalaria fue de . días y la estancia hospitalaria luego de la transfusión fue en promedio días; hubo una disminución de los valores promedio de pcr desde . mg/dl el día , a , mg/dl y . mg/dl los días y respectivamente; al momento de la publicación del artículo, solo permanecían intubados pacientes; todos los pacientes que requirieron ecmo ya se habían liberado y ( %) fueron dados de alta ( ) . también en texas, estados unidos, ramachandruni y col en mayo , reportaron una serie de casos con covid- severa, falla respiratoria y en ventilación mecánica o pao /fio < , todos con comorbilidades; a los cuales les administraron metilprednisolona y posteriormente plasma convaleciente; compararon los valores basales de pao /fio y posterior a la intervención; encontrando, mejoría de la pao /fio en % luego del tratamiento con esteroides y en % luego de la administración de plasma convaleciente ( ) . finalmente, en respuesta al brote de covid- en los eeuu y las tasas de mortalidad reportadas, la fda en colaboración con la mayo clinic y la comunidad nacional de bancos de sangre desarrollaron un programa nacional de acceso ampliado para recolectar y distribuir plasma convaleciente donado por amci ® individuos que se han recuperado de covid- ; entre abril y mayo , ; fueron incluidos . pacientes con covid- severa o potencialmente mortal o con riesgo alto de progresión a covid- severa o potencialmente mortal en el programa nacional de acceso ampliado; en ese tiempo, un total de . pacientes inscritos recibieron transfusión de plasma convaleciente covid- . en una publicación reciente, joyner y cols en mayo , en estados unidos, hicieron un análisis de seguridad después de la transfusión de plasma convaleciente covid- humano con compatibilidad abo en . adultos hospitalizados con covid- grave o potencialmente mortal, % de los cuales se encontraban en uci; la incidencia de eventos adversos serios (eas) durante las horas siguientes a la transfusión de plasma convaleciente fue < %, incluyendo mortalidad ( . %); de los eas reportados, hubo incidentes reportados como eas relacionados, incluyendo muertes, eventos de taco, trali y reacciones alérgicas graves asociadas a la transfusión; sin embargo, solo (de ) eas fueron considerados definitivamente relacionados con la transfusión de plasma convaleciente por el médico tratante; en este grupo de pacientes, la tasa de mortalidad a los siete días luego de la administración del plasma convaleciente, fue del , % ( ) . a pesar que la tasa general de letalidad para la covid- parece ser aproximadamente . % ( ), la tasa de mortalidad reportada parece no ser excesiva si la comparamos con los informes de wuhan que sugieren tasas de letalidad del % para los pacientes hospitalizados ( ) y % entre los pacientes en unidad de cuidados intensivos ( ) . los nueve estudios mostraron mejoría en muchos aspectos, incluyendo el aclaramiento del virus, la disminución del suplemento de oxígeno y la ventilación mecánica, la normalización de los valores de laboratorio, y la recuperación en los hallazgos pulmonares radiológicos. todos los estudios, reportaron que no se presentaron eventos de seguridad o reacciones adversas serias relacionadas con la administración de plasma convaleciente en pacientes con covid- , excepto en casos relacionados, según criterio de los médicos tratantes, en el estudio publicado por joyner y cols ( ) . esta serie de estudios son alentadores; sin embargo, la mayoría de los reportes de casos tienen limitaciones significativas: carecen de los ajustes para factores de confusión críticos, incluidos los co-tratamientos, las características basales, la gravedad de la enfermedad y el momento de administración del plasma y deben ser seguidas de investigaciones adicionales. para establecer mejor el papel del plasma convaleciente es necesario realizar estudios dirigidos a los siguientes escenarios: . el uso como profilaxis post-exposición . evaluar si el plasma convaleciente es útil en paciente con enfermedad leve . el efecto del plasma convaleciente en pacientes con enfermedad moderada . el tratamiento de rescate con plasma convaleciente en pacientes que requieren ventilación mecánica debido a covid- . finalmente, trabajos que evalúen la seguridad y farmacocinética del plasma convaleciente en los pacientes pediátricos con alto riesgo. actualmente están en curso varios estudios para evaluar el tratamiento de pacientes infectados con sars-cov- con plasma convaleciente. una búsqueda realizada el de mayo de en clinicaltrials.gov con los términos "plasma convaleciente y covid- " mostró ensayos en curso sobre el uso de plasma convaleciente en pacientes con amci ® covid- , que nos ayudarán a resolver las inquietudes relacionadas con esta intervención ( ) . page se recomienda no utilizar de rutina las las inmunoglobulinas hiperinmunes en pacientes con infección por sars-cov- /covid- . la inmunoglobulina hiperinmune (h-igiv) se deriva de individuos con altos títulos de anticuerpos contra patógenos específicos y se ha utilizado con éxito en el tratamiento de infecciones, como el citomegalovirus y la gripe h n ( ) . se propone que la inmunoglobulina hiperinmune combinada con medicamentos antivirales puede ser efectiva en el tratamiento de pacientes con covid- , estos anticuerpos (ac) recogidos de los pacientes recuperados serán específicos contra covid- al aumentar la respuesta inmune en pacientes recién infectados ( ) . existe evidencia más sólida para el uso de h-igiv en el tratamiento de enfermedades virales. cheng y cols en enero de , realizaron una revisión retrospectiva en hong kong, que reveló que el plasma convaleciente de los sobrevivientes de sars-cov administrados a pacientes con sars-cov que tenían enfermedad progresiva resultó en tasas de alta significativamente más altas en el día y tasas de mortalidad más bajas, en comparación con los controles históricos ( ) . hung y cols en febrero de , realizaron un estudio de cohorte prospectivo sobre la efectividad del plasma convaleciente de los sobrevivientes de h n con un título de ≥ : ofrecido a pacientes de la uci con infección grave por h n ; los pacientes que rechazaron las infusiones de plasma convalecientes fueron controles; veinte de los pacientes recibieron sueros convalecientes, el tratamiento con plasma convaleciente condujo a una reducción significativa de la carga viral respiratoria, los niveles séricos de citocinas (il- , il- , tnfα) y la mortalidad ( ) . posteriormente hung y cols en agosto de , publicaron un estudio multicéntrico prospectivo, doble ciego, aleatorizado y controlado en el que compararon la efectividad de la inmunoglobulina hiperinmune (h-igiv) del plasma convaleciente de los sobrevivientes de h n versus la inmunoglobulina iv (igiv) normal, en pacientes con h n en uci con soporte respiratorio y recibiendo oseltamivir; este estudio mostró, una reducción de la carga viral y una mayor supervivencia en el grupo que recibió h-igiv dentro de los días posteriores al inicio de los síntomas, demostrando la superioridad de la inmunoglobulina hiperinmune sobre la igiv en el tratamiento de la infección grave por h n ( ). el uso de inmunoglobulina hiperinmune ha demostrado una clara efectividad en el tratamiento de la gripe y el sars-cov; sin embargo, el plasma se debe recolectar y procesar de pacientes convalecientes y verificar que tenga títulos adecuados. según la experiencia con el sars-cov, lo ideal es recolectar plasma de pacientes con un curso de enfermedad más leve ( ) . poco se sabe sobre la seguridad de la inmunoglobulina hiperinmune cuando se usa para el tratamiento de infecciones por coronavirus, los riesgos incluyen la exacerbación de la infección dependiente de anticuerpos (antibody-dependent enhancement of infection -ade)( ); el ade puede ocurrir en varias enfermedades virales, e implica una respuesta inflamatoria exagerada ante la presencia de ciertos anticuerpos; sin embargo, los estudios en sars y mers no proveen información suficiente para extrapolarse a la infección por sars-cov- . no se encontraron estudios con inmunoglobulina hiperinmune en el tratamiento de pacientes con covid- . no se puede emitir una recomendación a favor o en contra para el uso de la inmunoglobulina intravenosa como tratamiento adyuvante en pacientes con covid- severo. se debe considerar la inmunoglobulina intravenosa como tratamiento adyuvante en pacientes con covid- severo, en el contexto de estudios clínicos en los siguientes escenarios. escenario a (enfermedad severa), definida como uno o más de los siguientes: disnea, frecuencia respiratoria > /min, spo < %, pao /fio < o empeoramiento radiológico con aumento > % de los infiltrados pulmonares en - horas. escenario b (enfermedad que amenaza la vida), definida como uno o más de los siguientes: falla respiratoria, choque séptico, o disfunción multiorgánica. en las enfermedades virales, los anticuerpos ejercen su efecto por neutralización viral (bloqueo de la entrada de células virales y, por lo tanto, replicación), activación del complemento, opsonización y mediación de citotoxicidad celular dependiente de anticuerpos. la neutralización viral es específica de antígeno; otras actividades antivirales son antígeno-inespecíficas y se realizan en parte a través de interacciones fc: fc receptor. en la infección por sars-cov- , el principal antígeno objetivo asociado con la neutralización es la proteína spike, que es responsable de la unión del sars-cov- a las células epiteliales, incluidos los neumocitos; los anticuerpos en las inmunoterapias pasivas covid- son de naturaleza policlonal, con múltiples epítopos contra los paratopes de sars-cov- , incluido el dominio de unión al receptor en la proteína spike ( ) . la inmunoglobulina intravenosa (igiv) es un producto derivado del plasma de miles de donantes utilizados para el tratamiento de inmunodeficiencias primarias y secundarias, afecciones autoinmunes/inflamatorias, trastornos neuroinmunológicos y secuelas relacionadas con infecciones; la igiv proporciona protección inmune pasiva contra una amplia gama de patógenos; actualmente, la experiencia con el uso de igiv en el tratamiento de la infección por sars-cov- es muy limitada; sin embargo, la justificación del uso de ivig en la infección por sars-cov- es la modulación de la inflamación ( ) . la igiv se ha usado en el tratamiento de otros coronavirus, incluido el sars cov. stockam y cols, en septiembre de , en respuesta a una petición de "the world health organization -who", realizaron una revisión sistemática de los efectos del tratamiento en los pacientes con síndrome respiratorio agudo, incluida la igiv o el plasma convaleciente; se evaluaron cinco estudios sobre el uso de igiv o plasma convaleciente administrado además de corticosteroides y ribavirina, se consideró que estos estudios no fueron concluyentes ya que los efectos de la igiv o el plasma convaleciente no podían distinguirse de otros factores que incluían comorbilidades, estadio de la enfermedad o el efecto de otros tratamientos ( ) . wnag y cols, en mayo , hicieron un estudio prospectivo, en un solo centro, de infección por sars en taiwán, se administró igiv si el paciente tenía leucopenia amci ® o trombocitopenia, o si había progresión rápida de la enfermedad en la radiografía; un total de pacientes recibieron igiv, de los cuales tenían citopenias graves, uno de ellos tenía evidencia de síndrome hemofagocítico y paciente tuvieron progresión radiológica de la enfermedad; el estudio sugiere que la igiv condujo a una mejora significativa en el recuento de leucocitos y plaquetas, pero reconoce que no había un grupo de control para evaluar objetivamente las respuestas ( ) . lew y cols, en julio , reportaron un estudio retrospectivo de un solo centro en singapur, se encontró que los pacientes adultos con sars tratados con un régimen de pulso de metilprednisolona ( mg) e igiv ( . mg/kg) diariamente durante tres días consecutivos tuvieron una hazard ratio ajustada de . para mortalidad en comparación con el grupo no tratado, con una tendencia hacia una recuperación más temprana; sin embargo, este hallazgo no fue estadísticamente significativo (ic del %: . a . ; p = . ); además, este resultado tuvo como factor de confusión el uso concurrente de esteroides ( ) . aunque algunas de las preparaciones de igiv comercializadas actualmente (gamunex-c y flebogamma) contienen anticuerpos que reaccionan de forma cruzada contra el sars-cov- y otros antígenos de virus, in vitro( ), hasta la fecha, ningún ensayo clínico de alta calidad ha demostrado eficacia y seguridad convincentes de igiv en epidemias de coronavirus. a pesar de que los datos para el uso de igiv en la infección por sars y mers son débiles, la dosis alta de ivig puede ser útil en la infección grave por sars-cov- a través de la modulación inmune, saturando fcγr y reduciendo ade ( ) . en general, la inmunoglobulina intravenosa es bien tolerada y el perfil de seguridad es bien conocido. las reacciones adversas comunes son leves y autolimitadas, pero se sabe que en pacientes de alto riesgo se producen efectos adversos graves, como trombosis, disfunción renal y muerte. en cuanto la evidencia (tabla ); xie y cols en abril, en wuhan, china, realizaron un estudio retrospectivo, revisando casos de covid- severa (disnea, fr > /min, spo < % en reposo, pao /fio < , progresión imagenológica > % en - horas) o críticamente enfermos (falla respiratoria con ventilación mecánica, choque, disfunción orgánica múltiple) en el cual evaluaron la mortalidad a días como desenlace primario y como desenlace secundario evaluaron la mortalidad a días, días de estancia hospitalaria, de uci y la necesidad de ventilación mecánica; reportaron que el tratamiento con igiv dentro de las horas posteriores al ingreso no sólo redujo el uso de la ventilación mecánica comparado con el tratamiento luego de horas del ingreso ( . % vs . %, p = . ), sino que también redujo la duración de la estancia en el hospital ( . ± . vs . ± . días, p = . ) y la uci ( . ± . vs . ± . días, p = . ); mejorando en última instancia la mortalidad a los días (p = . ); concluyen, que el estudio demostró que el tratamiento con igiv en pacientes con covid- con neumonía grave puede mejorar los indicadores en poco tiempo y mejorar la eficiencia del tratamiento de los pacientes con alta efectividad ( ) . el tratamiento con dosis altas de igiv ( g/día durante días) al inicio del distrés respiratorio, sumado al tratamiento de soporte y en un caso combinados con antivirales (lopinavir/ritonavir) y metilprednisolona en covid- grave publicado por cao y cols en marzo, en wuhan, china ( ), demostró la elevación de los recuentos de linfocitos, disminución de los marcadores inflamatorios, recuperación de la oxigenación, resolución parcial/completa de las alteraciones radiológicas pulmonares y las pruebas de hisopos nasales y orofaríngeos negativos dentro de unos pocos días después del inicio tratamiento (< días). lanza y cols en mayo , reportaron en nápoles, italia, el caso de una mujer de años que tenía covid- severa y que venía con deterioro clínico a la cual se le venía dando tratamiento con hidroxicloroquina más azitromicina, no se le administraron amci ® esteroides por el riesgo de disminuir la depuración de la viremia, a quién se le administró igiv el día después de iniciados los síntomas con mejoría clínica rápida, normalización de los gases arteriales y disminución marcada de los infiltrados pulmonares al día y respectivamente; como evento adverso, reportaron hipotensión durante el inicio de la infusión que se mejoró al disminuir la velocidad de infusión. la paciente finalmente se recuperó, negativizó rt-pcr sars-cov- y fue dada de alta ( ) . se recomienda la tromboprofilaxis farmacológica en todos los pacientes confirmados o sospechosos de covid- severo, a menos que está contraindicada, en cuyo caso es razonable la implementación de profilaxis no farmacológica. en términos generales se reconoce que los pacientes hospitalizados con enfermedad médica aguda, incluidas infecciones como la neumonía, tienen un mayor riesgo de eventos tromboembólicos ( ) . tang y cols, en china describieron múltiples trastornos de la coagulación en pacientes con covid- , aquellos pacientes que no sobrevivieron tenían significativamente mayores niveles de dímero-d y productos de degradación de la fibrina y con tiempos de coagulación convencionales más alargados al ingreso (p < . ); . % de los no sobrevivientes y . % de los sobrevivientes cumplían criterios para coagulación intravascular diseminada( ); este mismo grupo realizó un estudio con pacientes con covid- severo, pacientes con coagulopatía asociada a covid- (cac), definida por un sic score ≥ la utilización de tromboprofilaxis redujo de manera significativa la mortalidad a días ( . % vs . %, p = . ) así como también en aquellos con un se recomienda no utilizar de rutina antiagregación en pacientes con covid- severo con el fin de prevenir desenlaces neurológicos adversos. no se encuentran estudios en la literatura para el uso de antiagregantes para el manejo específico del covid- ; el manejo de los eventos cardiovasculares en pacientes covid- no difiere de la población general sin la enfermedad. no se establecen diferencias en los estudios descritos, ni en las publicaciones hasta la fecha de la revisión ( ) . no se puede emitir una recomendación a favor o en contra sobre el uso de la anticoagulación terapéutica de rutina con heparinas de bajo peso molecular o heparina no fraccionada en pacientes con bajo riesgo de sangrado y con un curso clínico grave o crítico, que además tengan elevación del dímero d mayor a mcg/ml ( ng/ml) y/o fibrinógeno mayor a mg/dl. diferentes publicaciones describen como una estrategia de tratamiento basada en profilaxis con heparina de bajo peso molecular (hbpm) para tratar la coagulopatía grave por covid- podría no ser suficiente. especialmente porque estos pacientes tienen dentro de su coagulopatía, una predisposición mayor a la presencia de trombosis que al sangrado. además, los bajos niveles de antitrombina que se han descrito en estos pacientes, los hace más resistentes a la heparina, lo que sugiere que las dosis profilácticas ya sea de heparina no fraccionada o hbpm pueden ser inadecuadas( - ). asociaciÓn colombiana de medicina crÍtica y cuidados intensivos. amci ® no se puede emitir una recomendación a favor o en contra sobre la anticoagulación terapéutica de rutina con heparinas de bajo peso molecular en pacientes con covid- en estado crítico, que presenten elevación del dímero d mayor a mcg/ml ( ng/ml). tang y cols, en china con un estudio retrospectivo donde se incluyeron pacientes con covid- severo, se evaluó la presencia de trombosis como desenlace asociado. este estudio describe como niveles de dímero d por encima de ng/ml estaban asociados a una mayor probabilidad de muerte y en estos pacientes el tratamiento anticoagulante reduce de manera significativa la mortalidad ( . , ic % . - . ) ( , ) . no se puede emitir una recomendación a favor o en contra para la medición rutinaria de niveles de anti xa en pacientes con covid- en los que se decide hacer anticoagulación terapéutica con hbpm. se puede considerar la medición de niveles anti xa si se cuenta con la disponibilidad del recurso. harr y cols, en un estudio en donde se incluyeron pacientes con hiperfibrinogenemia relacionada a trauma, se evidenció como los niveles de fibrinógeno se correlacionaron significativamente con la consistencia del coágulo y adicionalmente como se genera una relación inversa entre los niveles de fibrinógeno y la actividad de las hbpm, lo que sugeriría una potencial resistencia a la heparina. basados en que los pacientes covid- presentan niveles de fibrinógeno en muchas ocasiones con niveles > mg/dl e incluso > mg/dl lo que hace razonable considerar que aquellos pacientes covid- que requieren dosis terapéuticas de hbpm y es posible evaluar los niveles de anti xa, hacer ajustes y monitoreo del nivel de anticoagulación sería una opción razonable ( ) . se recomienda el uso de hbpm o hnf para la anticoagulación terapéutica en pacientes con una indicación específica con diagnóstico de covid- . amci ® como previamente se describió, una revisión sistemática comparó las dosis fijas de hbpm subcutánea con dosis ajustadas de hnf intravenosa o subcutánea en personas con clínica sugestiva de tep, esta revisión demostró que la incidencia de tep recurrente fue menor con hbpm que en los participantes con hnf (or . , ic % . a , ), también se asoció con una reducción en el tamaño del trombo (or . , ic % . a . ), evidencia de baja calidad. sin embargo, no hubo diferencias en la mortalidad general entre los participantes tratados con hbpm y los tratados con ufh (or . , ic % . a . ). por otra parte, los protocolos de manejo en escenarios de coagulación intravascular diseminada (cid), proponen el uso de hnf por encima de la hbpm en pacientes en los que se indica la anticoagulación. más aún, la presencia de falla renal aguda es común en los pacientes con covid- , por lo que la opción de tratamiento con hnf tiene también escenarios en donde podrían ser de elección ( , ) . capítulo . procedimientos y covid- recomendaciÓn se recomienda realizar la preoxigenación en pacientes con sospecha o diagnóstico de covid- , cuando estén disponibles, en áreas de presión negativa con mínimo recambios de aire por hora o en instalaciones con ventilación natural o que tengan un recambio de aire de mínimo l/seg si están disponibles. se recomienda como complemento opcional durante la preoxigenación en el paciente crítico con diagnóstico o sospecha de covid- la caja de acrílico para protección durante la intubación, la caja no protege contra la generación de aerosoles fuera de esta y requiere para su uso, entrenamiento previo. si es difícil su uso retírela inmediatamente. se recomienda utilizar en la mascarilla quirúrgica sobre la mascarilla de oxigenación en el paciente crítico con sospecha o diagnóstico de covid- . se recomienda utilizar filtros hpfa entre la máscara y el dispositivo disponible para la preoxigenación en el paciente crítico con sospecha o diagnóstico de covid- . se recomienda en el paciente con sospecha o diagnóstico de covid- preoxigenación por a min, si el paciente luego de minutos no tiene incremento en la mejoría inicie la administración de medicamentos. se recomienda en caso de compromiso hemodinámico considerar ventilación a dos manos con cierre hermético de la máscara sobre la cara del paciente con frecuencias altas (> por minuto y baja presión). amci ® fundamento el manejo de la vía aérea es un procedimiento considerado generador de aerosoles, la enfermedad covid- tiene una alta tasa de transmisión y el personal de salud requiere el uso estricto del epp ( , ) , revise el enunciado para epp recomendado en esta guía. la posibilidad de permanencia del virus en algunos ambientes puede durar hasta horas, por esto una estrategia para proteger al equipo de salud y otros pacientes podrías ser estar en áreas con presión negativa, lo cual no es fácil de encontrar en nuestro contexto o que tenga un adecuado recambio de aire( ). como medidas complementarias se pueden utilizar opciones como las cajas acrílicas para intubación, esta disminuye el riesgo de contaminación por gotas, pero no elimina los aerosoles, es necesario previo entrenamiento. en caso de que la caja sea una limitante retírela inmediatamente ( ) . los pacientes covid- , clásicamente se presentan con tos, esto es un factor de riesgo para quienes manipulan la vía aérea, la utilización de mascarilla por parte del paciente debajo del dispositivo bolsa mascarilla , la cual también deberá tener un filtro de alta eficiencia para disminuir el número de partículas que pueden estar en el ambiente durante la preoxigenación y posible ventilación, ésta última la cual será evitada al máximo ( , , ) . la preoxigenación es una técnica que pretende barrer el nitrógeno y aumentar la disponibilidad de oxígeno para que cuando el paciente presente apnea por los medicamentos para la intubación o por su condición clínica, se disponga de un tiempo mayor sin desaturación crítica y riesgo de colapso cardio-respiratorio. considere que los pacientes con formas moderadas y severas de covid- , pueden tener más comprometida esta reserva respiratoria y puede no ser efectiva la preoxigenación y cuando inicia la apnea, la desaturación será más precoz. si después de minutos de preoxigenación no hay mejoría de la saturación arterial, considere fallida esta maniobra y considere mayor riesgo de hipoxemia severa con probabilidad de bradicardia extrema y paro cardiorrespiratorio. en caso de requerir ventilación por disminución rápida de la saturación de oxígeno arterial y considere necesario ventilación manual bolsa mascarilla a dos manos no debe ser vigorosa y debe utilizar filtros hpfa, estos reducirán los aerosoles en el ambiente( , ). se recomienda la utilización de cajas de acrílico para intubación del paciente con sospecha o diagnóstico de covid- como complemento durante la intubación para disminuir el riesgo de contaminación por gotas, sin embargo, no protege % la generación de aerosoles y si ésta hace más difícil la intubación retírela inmediatamente. amci ® se recomienda minimizar los intentos de intubación orotraqueal en el paciente con sospecha o diagnóstico de covid- , el primer intento debe procurar ser realizado por el más experimentado en el manejo de la vía aérea. se recomienda la intubación con videolaringoscopio en pacientes con covid- teniendo en cuenta disponibilidad y entrenamiento); esta alternativa puede ofrecer ventajas frente a la laringoscopia tradicional. se recomienda administrar medicamentos para asegurar la vía aérea en secuencia de inducción rápida, para obtener en el menor tiempo posible condiciones para la intubación ( a s). se recomienda en caso de intubación fallida por personal experto, considerar dispositivos supraglóticos como las máscaras laríngeas como medida de rescate con el riesgo de generación de aerosoles. se recomienda contar con disponibilidad de vasopresor y atropina en el sitio donde se realizará la intubación. en caso de contar con lidocaína se recomienda utilizar a dosis de mg/kg sin epinefrina. administrada minutos antes de la intubación. como se describió en el aparte de preoxigenación, se deben garantizar todas las medidas basadas en bioseguridad y protección adecuada para el personal de la salud, ubicación en áreas que cuenten con presión negativa o salas con un óptimo recambio de aire pueden ayudar a disminuir el riesgo de contagio. las medidas complementarias como la caja de taiwán o caja de intubación puede complementar de forma opcional estas medidas durante el proceso de aseguramiento definitivo de la vía aérea pero no garantiza % la eliminación de aerosoles, pudiendo ser un obstáculo para quien realiza la intubación, de ser así, se deberá retirar inmediatamente, por eso sólo es un complemento al epp, que es la verdadera protección en estos escenarios (se debe incluir máscaras n o ffp fpp ) ( , ) . el paciente críticamente enfermo puede tener comprometida de forma significativa su reserva respiratoria y hemodinámica por su cuadro clínico y puede empeorar por los medicamentos utilizados durante la intubación orotraqueal. las complicaciones en el manejo de la vía aérea se presentan cuando se realiza más de un intento dentro de los cuales están el traumatismo, desaturación e hipoxemia ( ) . es por esto por lo que se debe procurar que el primer intento sea realizado por el más experimentado en el manejo de la vía aérea e idealmente se logre la intubación en el primer intento con la menor hipoxemia secundaria ( , , ( ) ( ) ( ) . basado en el planteamiento anterior y considerando la ventaja de intubar pacientes críticamente enfermos en el primer intento dadas sus condiciones clínicas, la revisión de amci ® demandas asociadas a manejo de vía aérea en los estados unidos sigue siendo preocupante al considerar posibles causas la falta de entrenamiento y falta de aplicación de las guías y recomendaciones de manejo así como en la utilización de equipos adecuados para pacientes específicos ( ) ; se ha planteado especialmente en los pacientes covid- los cuales tienen un importante compromiso pulmonar y alto riesgo de desaturación, la posibilidad de encontrar una vía aérea difícil no predicha y dificultades en su manejo( , ). es por esto que se requiere del mejor dispositivo para manejo de vía aérea invasiva disponible, siempre y cuando se cuente con el adecuado entrenamiento previo en su uso, la ventaja de los videolaringoscopio se debe a la superioridad al compararla con la laringoscopia convencional, siendo en algunos grupos la primera opción para intubaciones electivas ( , ) . como se ha mencionado, el riesgo de una rápida desaturación en pacientes con enfermedad pulmonar, así como en pacientes con covid- , se debe utilizar la inducción de secuencia rápida la cual se utiliza para pacientes con estómago lleno en los cuales se quiere lograr condiciones de inconciencia y de intubación óptimas en el menor tiempo posible para disminuir el riesgo de broncoaspiración. en estos casos de falla respiratoria con tan mala reserva se quiere aprovechar la ventaja que ofrece esa técnica para tener en poco tiempo al paciente intubado con menor riesgo de desaturación. es así como los medicamentos en una inducción de secuencia rápida incluyen el opioide, hipnótico y relajante, estos dos últimos administrados simultáneamente y lavados con un bolo de cc. la opción del opioide en nuestro contexto suele ser fentanilo a dosis de a mcg / kg iv, dando a minutos de latencia para su efecto, luego el hipnótico que puede ser propofol entre y , mg / kg si la estabilidad hemodinámica lo permite o considera usar vasopresor simultáneo. en caso de preferir evitar la hipotensión la ketamina a dosis de a , mg / kg es una opción más estable hemodinámicamente. con relación al relajante neuromuscular la succinilcolina es la clásicamente utilizada dosis de a , mg/kg pero debido a sus efectos secundarios como hiperpotasemia, fasciculaciones, mialgias y un importante riesgo de hipertermia maligna algunos grupos no lo consideran, el rocuronio a dosis de , mg/kg ha demostrado lograr tiempos y condiciones de intubación similar a la succinilcolina sin los efectos secundarios de esta ( , ) algunos grupos han considerado no utilizarlos si la condición clínica del paciente es crítica pues éste período de latencia puede ser acompañado de una hipoxemia severa y paro cardíaco, por lo tanto sólo usan hipnótico y relajante neuromuscular. ante una vía aérea difícil no predicha en la cual no se logre la intubación, considere los dispositivos supraglóticos como las máscaras laríngeas los cuales son más fáciles de insertar en comparación con la técnica de intubación orotraqueal, y deben estar dentro del planeamiento y organización de elementos para manejo de la vía aérea invasiva. al lograr ventilar con este dispositivo se logrará una recuperación del paciente, pero se pueden generar aerosoles pues este mecanismo de cierre puede permitir escape de aire y macropartículas durante el ciclo respiratorio ya sea manual o mecánico ( , ) . el cuadro clínico de pacientes críticos y particularmente covid- , puede asociarse a inestabilidad hemodinámica y requerimiento de soporte vasopresor. la adición de medicamentos como los opioides o hipnóticos pueden asociarse a hipotensión la cual puede no responder a volumen, es necesario evitar episodios de hipotensión en especial en pacientes ancianos, con enfermedades cardiovasculares de base las cuales pueden tolerar menos estos cuadros de hipotensión, así como también pueden favorecer amci ® desbalance en la relación ventilación/perfusión a nivel pulmonar empeorando los cuadros de hipoxemia. la hipoxemia puede acompañarse de bradicardia y si no se corrige la ventilación o la bradicardia es muy probable que el paciente presente paro cardiorrespiratorio, por lo cual se recomienda utilizar una dosis de atropina para corregir la bradicardia, no mejorará la oxigenación, pero tendrá un tiempo adicional para recuperar la oxigenación y ventilación del paciente. en estos casos debe tener disponibles vasopresores y atropina desde el planeamiento de los medicamentos necesarios para el manejo de la vía aérea ( ) . se recomienda la intubación orotraqueal oportuna y no retrasar el inicio de la ventilación mecánica invasiva en los pacientes con sdra severo por covid- debido a mayor riesgo de desenlaces adversos. fundamento definir el momento de la intubación en esta población es un reto. la mayoría de los autores recomiendan el inicio "temprano" de la ventilación mecánica, sin embargo, la definición de cuando es temprano no es clara. este punto es motivo de análisis dado que a la luz de la evidencia actual la utilización de métodos no invasivos como la ventilación no invasiva y la cánula de alto flujo, para manejo inicial de pacientes con algún grado de hipoxemia es controvertido entre otras por el riesgo que supone al personal sanitario al ser un procedimiento generador de aerosoles. en el un estudio mostró que la intubación retrasada después de la falla al utilizar cánula de alto flujo o la ventilación no invasiva para pacientes con insuficiencia respiratoria moderada y grave se asoció con una mayor mortalidad. publicaciones recientes muestran que solo la quinta parte de los pacientes que murieron por covid- recibieron ventilación mecánica invasiva y soporte respiratorio más agresivo antes de la muerte, lo que indica que en muchos pacientes se habría retrasado la intubación. de los pacientes fallecidos solo el % recibieron tratamiento de oxígeno nasal o con mascarilla facial antes de su muerte. esta baja proporción puede tener varias explicaciones. primero, algunos pacientes con hipoxemia severa no tenían otros síntomas, como dificultad para respirar o disnea, es decir, desarrollaron una especie de hipoxemia silenciosa. en segundo lugar, la falta de suficientes ventiladores mecánicos invasivos es una razón importante que evitaría que los pacientes reciban intubación. tercero, el manejo de estos pacientes por un equipo de médicos no intensivistas; por lo tanto, pueden no estar seguros del momento en que un paciente requiere intubación. la serie de casos de la epidemia de covid- en wuhan mostró que la intubación tardía era común en la etapa inicial de la epidemia, mostrando que una de esas posibles razones del retraso incluía falta de ventiladores mecánicos invasivos y falta de capacitación clínica específica para el soporte respiratorio. recomendaciÓn se recomienda tomar la decisión de intubación orotraqueal en el paciente crítico con sospecha o diagnóstico de covid- utilizando una combinación de variables clínicas, gasométricas y hemodinámicas. tabla la intubación orotraqueal (iot) efectiva y segura, programada debe prevenir el colapso respiratorio y hemodinámico. siempre es necesario asegurar la escena del procedimiento de intubación con las consideraciones técnicas y de protección personal adecuadas. conocer los pasos para la realización del procedimiento de intubación orotraqueal (iot) contextualizados al paciente covid- , reduce los riesgos innecesarios. la iot es un procedimiento generador de aerosoles por lo tanto lo ideal es realizarlo en una habitación con presión negativa, sin embargo, la baja disponibilidad en el país obliga a utilizar otras alternativas de seguridad. una habitación de presión negativa es un cuarto que tiene una presión más baja que las áreas adyacentes, lo que mantiene el flujo de aire fuera de la habitación y hacía habitaciones o áreas contiguas. las puertas de la sala deben mantenerse cerradas, excepto al entrar o salir de la sala, y la entrada y la salida deben minimizarse. la intubación en el paciente crítico con covid- es de los procedimientos que mayor riesgo de aerosolización tiene, por lo tanto, se debe adoptar una posición de intervención oportuna, pero también segura, para evitar desenlaces desfavorables en el paciente y disminuir el riesgo de contaminación en el personal de salud, se recomienda individualizar cada caso mediante la combinación y análisis de los criterios clínicos, gasométricos y hemodinámicos de cada paciente. ( , ( ) ( ) ( ) se recomienda no realizar de rutina broncoscopia en los pacientes con sospecha o diagnóstico de covid- , debido al riesgo de generación de aerosoles. se puede considerar en atelectasias masivas con compromiso significativo de la oxigenación adicional a la lesión pulmonar per sé y la hemorragia alveolar para control local directo. en general la realización de broncoscopia en pacientes con sospecha o confirmación de covid- debe ser evitada y realizarse sólo con indicación de emergencia como cuerpo extraño en la vía aérea, hemoptisis masiva, obstrucción grave de la vía aérea central o atelectasia lobar o pulmonar completa( ). esto debido a la alta carga viral en la mucosa nasal y faríngea de los pacientes con infección por sars-cov- ( ) y la alta producción de aerosoles infecciosos que se generan durante este procedimiento. en caso de ser necesaria su realización, deberá ser llevada a cabo por el operador con mayor experiencia amci ® minimizando el tiempo de exploración y el personal expuesto en la sala. es mandatorio utilizar epp completo que incluya respirador fpp o fpp , bajo protocolo supervisado de donning y doffing ( ) . son de elección los broncoscopios desechables de un solo uso, pero de no ser posible se prefiere el uso de un broncoscopio flexible por encima de uno rígido por la más fácil manipulación de este. idealmente el procedimiento se llevará a cabo en el mismo cubículo del paciente que deberá contar con presión negativa y recambio de aire de a veces por hora. recomendaciÓn se recomienda no realizar de rutina la broncoscopia para la recolección de muestras para el diagnóstico de covid- en el paciente críticamente enfermo. la broncoscopia es una prueba de segunda elección para la toma de muestras respiratorias en los pacientes con sospecha o confirmación de covid- ( ) . la toma de muestras del tracto respiratorio superior por hisopado nasofaríngeo u orofaríngeo es el método primario y de elección para determinar la infección por sars-cov- . solo si resultaran dos pruebas negativas y persistiera una alta sospecha diagnóstica estaría indicado tomar muestras del tracto respiratorio inferior por broncoscopia, ya sea aspirado endotraqueal (bas) o lavado bronco alveolar (bal) ( ), prefiriendo la realización de minibal para la recolección de muestras ( ). las muestras deberán ser recogidas en un recipiente estéril, e introducidas en una bolsa con autocierre. deben manejarse con cuidado extremo evitando manipulaciones innecesarias y bajo protocolos de protección para el personal que las maneja, y trasladarse al laboratorio para su análisis. pueden almacenarse a - ºc las primeras h de su recolección; si se demorara más el análisis, precisa almacenarse a temperatura de - ºc ( ) . en una serie china la sensibilidad del bal fue de % frente a % en muestra de esputo (no recomendada) y % en hisopado nasofaríngeo ( ) por lo que el especialista que realiza el procedimiento deberá sopesar el riesgo de este procedimiento en cada caso, valorando que se beneficiarán aquellos pacientes que tengan una indicación adicional para su realización. se recomienda la realización de la traqueostomía cuando está indicada, en los pacientes covid- sospechosos y confirmados con pronóstico razonable de vida, después del o día de ventilación , previa valoración y consenso por el equipo quirúrgico y de cuidado intensivo, asegurando que las condiciones clínicas, ventilatorias y hemodinámicas se encuentran controlada. en el contexto de pacientes hospitalizados en cuidado intensivo, la traqueostomía se realiza para facilitar el destete de la ventilación mecánica, mejorar la limpieza de la vía aérea y el manejo de las secreciones, aumentar la comodidad de los pacientes y la movilización y disminuir la probabilidad de complicaciones como la estenosis traqueal; sin embargo no hay una clara disminución en la mortalidad ( ) ( ) ( ) . la infección actual por sars-cov , tiene diferentes estadios de gravedad, uno de ellos es el compromiso pulmonar el cual se caracteriza por un síndrome de dificultad respiratorio agudo (sdra). de acuerdo con el comportamiento de la covid- , entre un % a un % de los pacientes requieren ventilación mecánica ( , ) , este grupo de pacientes con manifestación grave del compromiso pulmonar requiere estrategias de protección pulmonar en la ventilación mecánica, sedación profunda y posiblemente parálisis muscular y puede tener una mortalidad entre el % y el % ( , ) . una de las principales características en éste grupo de pacientes es la mortalidad temprana, definida ésta como aquella que se produce en menos de días; de acuerdo a la experiencia en wuhan, china; leung ( ), reporta que la mortalidad se presenta en los primeros cinco días luego de la admisión hospitalaria y de acuerdo a lo referido por graselli et al ( ) , en la región de lombardía, italia, la mediana de mortalidad se presenta al día siete después del ingreso. con estas consideraciones, al principio de la pandemia y en las aproximaciones iniciales no se recomendaba realizar la traqueostomía en los primeros días posteriores a la intubación orotraqueal. sin embargo, con el conocimiento de la fisiopatología y las experiencias en otras series, como medida para facilitar la liberación de la ventilación mecánica, se ha podido realizar el procedimiento después de la primera semana de inicio de la ventilación. de acuerdo con el curso natural de la enfermedad, el paciente en promedio se intuba al día a de iniciado los síntomas, una semana posterior a la intubación para la traqueostomía, estaríamos alrededor del día de la enfermedad, donde los pacientes ya tendrán una disminución de la carga viral. esto sin embargo no evita la utilización de los epp necesarios. esta medida en específico fue discutida y consensuada entre la sociedad de medicina critica amci y la asociación colombiana de cirugía. no existe evidencia que permita evaluar el riesgo real de infección del personal asistencial de los pacientes con sospecha o diagnóstico de covid- en la realización de traqueostomías. se debe considerar en la traqueostomía y la realización de ésta como un procedimiento generador de aerosoles (organización mundial de la salud). se recomienda que los epp requeridos para la realización del procedimiento, deben incluir máscaras ffp o n , protección ocular, vestido antifluido idealmente desechable y amci ® guantes; este nivel de protección representa el mayor nivel de seguridad para realizar el procedimiento en el paciente con sospecha o diagnóstico de covid- . no existe actualmente artículos que permitan evaluar cual es el riesgo real de infección del personal asistencial en la realización de traqueostomías en pacientes con covid- ; quizás el ejemplo más cercano, es una serie de casos, reportada durante la epidemia del síndrome respiratorio agudo grave en el ( ), en el cual se realizaron traqueostomías sin ninguna infección del personal, en este reporte se aseguró un adecuado uso del equipo de protección personal (epp), el cual incluía las medidas de barrera, máscaras ffp y cuando existía la disponibilidad, respiradores con suministro de aire purificado. la traqueostomía y la realización de ésta es considerada por la organización mundial de la salud (oms) un procedimiento generador de aerosoles, bajo esta perspectiva, el epp requerido para la realización del procedimiento, debe incluir máscaras ffp o n , protección ocular, vestido antifluido idealmente desechable y guantes; este nivel de protección representa el mayor nivel de seguridad para realizar el procedimiento mencionado. es obligatorio, que todo el personal reciba el entrenamiento para la postura, el uso y el retiro de los epp, si estos pasos no se realizan de la forma adecuada, representan una fuente de contaminación( ). se recomiendan no esperar la negativización de la pcr para sars-cov para realizar la traqueostomía en el paciente con diagnóstico de covid- . fuerte en contra fundamento los estudios de zou et al y lescure et al ( , ) , muestran que la carga viral de los hisopados nasales y faríngeos es elevada en la primera fase de la enfermedad, con una disminución entre el día nueve al quince, pero esta puede permanecer detectable hasta por tres semanas ( ) . existen recomendaciones acerca de la necesidad de realizar la traqueostomía una vez la pcr para sars-cov sea negativa ( , ) ;aunque este esquema suena lógico, es importante tener presentes las siguientes consideraciones. la sensibilidad de una sola muestra para ruta-pcr puede ser sólo del %( ) y es posible que sea necesario realizar una segunda prueba para minimizar el riesgo para quien realiza el procedimiento, aunque esta aproximación no siempre puede ser viable desde el punto de vista clínico, epidemiológico y administrativo. amci ® recomendamos que la mejor estrategia es diferir la realización de la traqueostomía hasta días luego de la intubación cuando esta indicada, con el conocimiento acerca de la evolución natural de la enfermedad, en ese momento en la mayoría de los pacientes, lo más probable es que la condición ya se encuentre en la tercera semana desde el inicio de los síntomas, en cuyo caso lo más probable es que ya exista una disminución de la carga viral; este hecho no evita que se deba utilizar de la forma correcta los epp. recomendaciÓn se recomienda escoger la técnica teniendo en cuenta la experticia que tenga en el grupo tratante y la anatomía del paciente para la decisión de la técnica. se recomienda la guía ecográfica para disminuir la probabilidad de complicaciones del procedimiento si la anatomía es desfavorable para la realización de traqueostomía percutánea. se recomienda la traqueostomía quirúrgica en pacientes de riesgo elevado de complicaciones donde se requiere un control más rápido y seguro de la vía aérea. se recomienda no utilizar de forma rutinaria la utilización de broncoscopia para la realización de traqueostomía por vía percutánea. no hay evidencia directa hasta la fecha de publicación del consenso si existe superioridad entre las dos técnicas en el paciente con sospecha o diagnóstico covid- . en pacientes críticos no existen diferencia en los desenlaces cuando se evalúa el rendimiento de la técnica percutánea y la técnica quirúrgica, la elección de uno u otro método está dado por la anatomía del paciente, el entrenamiento de los profesionales y la disponibilidad de los diferentes insumos y técnicas. tampoco se ha logrado hasta la fecha evaluar durante la pandemia de covid- si existe una diferencia entre las dos técnicas y por lo tanto no es posible acercarse a una recomendación basada en la literatura. sin embargo, es importante que para la decisión de la técnica a utilizar se considere la anatomía del paciente y los siguientes aspectos:  no se recomienda la utilización de broncoscopia para la realización de traqueostomía por vía percutánea, ésta aumenta la generación de aerosoles y el número de personas expuestas a estos ( , ) . amci ®  si la anatomía es desfavorable para la realización de traqueostomía percutánea, la guía ecográfica puede disminuir la probabilidad de complicaciones del procedimiento ( ) .  la traqueostomía quirúrgica es una alternativa para la realización del procedimiento en las unidades de cuidado intensivo en momentos de sobrecarga laboral y adicionalmente puede tener un mejor y más rápido control de la vía aérea, especialmente en pacientes con riesgo elevado de complicaciones ( ) . recomendaciÓn se recomienda el uso de la terapia ecmo en sdra severo refractario por covid- (pao /fio < , posición prona, requerimiento de relajantes neuromusculares en algunos casos vasodilatadores pulmonares y maniobras de reclutamientos) sin respuesta clínica manifestado por:  pao /fio < mmhg por mas de horas  pao /fio < mmhg por mas de horas  ph < . + paco > mmhg por mas de horas además del criterio anterior, se recomienda tener en cuenta la edad, las comorbilidades y la expectativa de sobrevida del paciente con buena calidad de vida y en circunstancias donde no exista limitación de recursos. no hay estudios clínicos aleatorizados sobre el uso del ecmo en pacientes con covid- ( , ) . existe el estudio eolia ( ) , el cual fue detenido durante su realización, y de acuerdo a un análisis bayesiano posterior puede interpretarse como una disminución de la mortalidad en los pacientes en ecmo con sdra severo ( , , ( ) ( ) ( ) ( ) . de igual manera debe considerarse la racionalización de los recursos y el estado de prevalencia de la pandemia en un lugar determinado. el inicio de la terapia puede evaluarse en función de la cantidad de pacientes en falla respiratoria y la disponibilidad de personal y otros recursos; si el hospital debe comprometer todos los recursos en proveer medidas básicas de cuidado intensivo no debe utilizar el ecmo ( , ) . los pacientes jóvenes sin comorbilidades son considerados de alta prioridad al igual que los trabajadores de la salud ( , ) . amci ® se recomienda no desarrollar nuevos centros de ecmo en época de pandemia, sobre todo en situaciones con limitación de recursos. fuerte en contra fundamento actualmente se recomienda el uso del ecmo con las mismas indicaciones para sdra basado en la capacidad de las instituciones de salud para iniciar éste tipo de terapias ( ) . en épocas de crisis la capacidad de los hospitales está saturada y obliga a la reubicación y optimización de los recursos ( , ) . los centros que ofrecen la terapia en ecmo deben ser centros con resultados favorables y tiempos de soporte de pacientes relativamente cortos ( ) . cuando estamos en tiempos de capacidad hospitalaria convencional y existe disponibilidad de camas de cuidado intensivo se pueden ofrecer los servicios de ecmo vv, va, e-cpr inclusive a pacientes no covid- , cuando estamos en contingencia y capacidad nivel se debe hacer un triage respecto a pacientes jóvenes y ofrecer ecmo vv, va, escoger muy bien los casos para pacientes no covid- y no ofrecer e-cpr, cuando estamos en contingencia y capacidad nivel es porque ya se están usando sitios de expansión y están casi saturados se restringe el ecmo a todas las indicaciones y se prioriza a pacientes con indicaciones no covid- con mayor riesgo de sobrevida, el ecmo vv queda para pacientes jóvenes, con disfunción de órgano y covid- positivo, no se ofrecerá ecmo va o e-cpr y cuando estamos en capacidad de crisis es porque la capacidad total hospitalaria está sobresaturada y no es posible realizar ecmo tanto en pacientes covid- como en los no covid- ( , ) . se recomienda practicar e implementar medidas de capacitación y vigilancia continua para mejorar la higiene de manos, evaluando la adherencia a protocolos establecidos en los trabajadores de la salud mediante listas de chequeo y supervisión para evitar infecciones cruzadas en el entorno del paciente con sospecha o diagnóstico de covid- . se recomienda establecer protocolos específicos para reducir el riesgo de infecciones que se deriven de la interacción y el cuidado del paciente crítico con sospecha o diagnóstico de covid- . amci ® se recomienda implementar prácticas de cuidado para la prevención de contagio de covid- . se debe utilizar el equipo de protección personal (epp) para la prevención de enfermedades de componente infeccioso asociado a exposición con fluidos corporales derivados del paciente crítico con sospecha o diagnóstico de covid- . las infecciones relacionadas con la atención sanitaria (iras) son definidas por la organización mundial de la salud como aquellas "infecciones que se presentan en un paciente durante el proceso de atención en un hospital u otro centro sanitario que no estaban presentes o no se estaban incubando en el momento del ingreso; se incluyen las infecciones contraídas en el hospital pero que se manifiestan tras el alta hospitalaria y también las infecciones profesionales entre el personal del centro sanitario". las iras representan una importante carga de enfermedad que se asocia a un impacto negativo en la economía del paciente y del sistema sanitario. la organización mundial de la salud plantea la higiene de manos como la principal medida necesaria para reducir y prevenir las iras; por esta razón establece directrices sobre la higiene de manos en la atención sanitaria y basada en esta propone la estrategia multimodal para la mejora de higiene de manos. las estrategias mencionadas anteriormente han demostrado el incremento en el cumplimiento de higiene de manos y disminución en las infecciones relacionadas con la atención en salud. la estrategia multimodal se articula a través de cinco componentes: cambio del sistema, formación, evaluación/ retroalimentación, recordatorios en el lugar de trabajo clima institucional. a través de estos componentes, se garantiza que el centro sanitario cuenta con la infraestructura necesaria para practicar adecuadamente el lavado de manos incluyendo dentro de este el acceso a un suministro seguro continuo de agua, jabón, preparado alcohólico y toallas; a su vez se proporciona educación, evaluación y retroalimentación con regularidad a todos los profesionales sanitarios ( se recomienda realizar un plan de cuidados organizado y específico en paciente crítico con sospecha o diagnóstico de covid- , ofreciendo el uso óptimo de recursos e intervenciones. se recomienda evitar el uso de excesivo de papelería relacionada con los registros usados para gestión de insumos y atención de los pacientes. se recomienda realizar intervenciones educativas enfocadas a mejorar la adherencia y adecuado uso de los epp. se debe procurar el cuidado de los elementos de protección personal bajo un protocolo que conserve las condiciones de integridad de estos. la actual reserva de elementos de protección personal (epp) es insuficiente debido al aumento de la demanda global, por el incremento de casos de covid- y por la información errónea que ha conllevado a compras de pánico y almacenamiento. por esta razón la organización mundial de la salud a través de su guía: uso racional del equipo de protección personal para la enfermedad por covid- ha implementado las siguientes estrategias para optimizar la disponibilidad de (epp): usar los (epp) adecuadamente, minimizar la necesidad de (epp) y coordinar el suministro adecuado de (epp). ( ) la duración máxima del uso continuo de la n es de a horas, siguiendo las recomendaciones del manual de medidas básicas para control de infecciones en ips de minsalud. pero en lo cotidiano, ningún trabajador tolera a horas continuas con un respirador. por esto, su uso continuo en el sitio de trabajo dependerá de la necesidad de pausar para comer, para ir al baño, etc. en este caso, se guardará en una bolsa de papel para su nueva colocación, si tiene menos de horas, se desechará si está visiblemente contaminada o se torna húmeda. el reusó de la n dependerá de la casa del fabricante, de si contiene o no celulosa en su estructura del respirador. por ejemplo, la recomendación del consenso colombiano acin sobre la desinfección para los respiradores sin celulosa es con peróxido de hidrógeno vaporizado al % por minutos. los respiradores n de uso industrial tienen mayor contenido de celulosa que los de uso médico por lo tanto para procesos de esterilización, solo los n de uso médico podrán ser esterilizados mediante de peróxido de hidrógeno vaporizado (sterrad®)( - ). amci ® se recomienda elaborar el protocolo de pronación del paciente críticamente enfermo por covid- , garantizando el entrenamiento al personal de salud, organizando el recurso humano, dispositivos de apoyo y tiempo establecido para cambios de posición para prevenir las lesiones por presión en el paciente. fuerte a favor fundamento la estrategia de pronación es una alternativa eficiente en el manejo del síndrome de dificultad respiratoria en pacientes críticos y es fundamental la gestión del profesional de enfermería en la prevención de complicaciones y eventos adversos, lo cual aportará significativamente a la calidad del cuidado ofrecido favoreciendo las mejoras en la oxigenación. es importante optimizar los cuidados de enfermería en torno de los cuidados de piel en los pacientes en ventilación mecánica en decúbito prono, los estudios han demostrado como principal complicación las lesiones de presión con una incidencia hasta de . %, siendo las más frecuentes las grado y ( ). una lesión se puede producir si se supera una presión en el tejido capilar arterial de mmhg denominándose interfaz de presión. basándose en lo anteriormente mencionado, el cambio de posición es un componente integral de la prevención y el tratamiento de las upp, con una justificación sólida y de amplia recomendación en la práctica de enfermería ( ) . el uso de superficies especiales para el manejo de la presión (semp) a partir del estudio de defloor ( ), se determinó un antes y un después en el uso de las semp en conjunción de los cambios posturales. este realizo un importante aporte para reducir la incidencia de lesiones por presión comparado con los colchones de estándar. se recomienda promover actividades para controlar el nivel de estrés en el personal durante las jornadas de trabajo: identificar y reconocer los propios límites, buscar o proponer ayuda psicológica profesional cuando sea requerido, promover estilos de vida saludables, y organizar los turnos de trabajo asegurando periodos de descanso. se recomienda compartir las emociones con pares y superiores, analizar objetivamente las situaciones adversas, manejar fuentes de información objetivas y científicas, realizar pausas activas durante el turno y brindar espacios grupales para expresar emociones, miedos e incentivar al equipo de trabajo reconociendo su labor. amci ® se recomienda utilizar recursos de salud mental ocupacional, apoyo por enfermedad y licencia familiar, además de garantizar una adecuada dotación de personal. los estilos de superación personal y el crecimiento psicológico desempeñan un papel importante en el mantenimiento de la salud mental de las enfermeras. es razonable suponer que los niveles de ansiedad y estrés entre los profesionales de la salud son proporcionalmente más altos que los de la población general debido al contacto directo con pacientes infectados. esto puede explicar por qué las enfermeras de primera línea son excepcionalmente vulnerables a la fatiga y al agotamiento (wang, okoli, et al. ) , agotamiento mental, falta de moral del personal, control / autonomía de decisión, menor calidad de vida y baja satisfacción laboral (cheung y yip, ). ( ) . una investigación reciente realizada en china continental menciona el impacto negativo de la pandemia de covid- en los trabajadores de atención médica de primera línea, incluidos los mayores niveles de ansiedad (shanafelt, ripp y trockel, ), depresión (xiang et al. ), estrés postraumático síntomas, soledad e impotencia (xiang et al. ) ( , ) . los aspectos traumáticos y estresantes de la participación en una pandemia también ponen en riesgo el daño psicológico a los médicos ( ) . la experiencia psicológica de las enfermeras que atienden a pacientes con covid- se puede resumir en temas: primero, las emociones negativas presentes en la etapa inicial consisten en fatiga, incomodidad e impotencia que fue causado por el trabajo de alta intensidad, el miedo y la ansiedad, y la preocupación por los pacientes y sus familiares. segundo, los estilos de auto afrontamiento incluyeron ajustes psicológicos y de vida, actos altruistas, apoyo de equipo y coordinación racional. tercero, encontramos crecimiento bajo presión, que incluía un mayor afecto y agradecimiento, desarrollo de posición de responsabilidad profesional y autorreflexión. finalmente, encontraron que las emociones positivas ocurrieron simultáneamente con emociones negativas( ). se recomienda ofrecer mecanismos de apoyo para amortiguar el estrés relacionado con la pandemia por covid- . esto incluye intervenciones para pacientes y familias ofreciendo recursos de salud mental y educación al egreso, previo a este reforzar visitas virtuales. se recomienda anticipar las necesidades de salud mental de los pacientes, el personal y las familias para ofrecer una respuesta integral de salud pública. se debe incluir atención psicológica en la hospitalización para pacientes, familiares y personal afectado por covid- . se recomienda proporcionar atención de salud mental en las comunidades, mientras que se requiere distanciamiento social y los recursos del sistema de salud son limitados. amci ® se recomienda mantener una estrategia de comunicación asertiva con la familia, teniendo en cuenta la formación del personal sobre las estrategias para comunicar malas noticias. ser solidarios con el duelo de las familias y acompañar el proceso de afrontamiento aún en la distancia, identificando factores de riesgo para patología mental o duelo complicado, utilizando los recursos institucionales de salud mental para mejorar las intervenciones. la pandemia tiene el potencial de crear una crisis secundaria de angustia psicológica y desbordamiento del sistema de salud mental. los miembros de la familia pueden experimentar angustia, miedo o ansiedad por la hospitalización de un ser querido, particularmente cuando las medidas de control de infecciones restringen las visitas. la telesalud (incluida la cobertura de seguro para la telesalud), el suministro extendido de medicamentos, el aumento de la capacitación en salud mental del proveedor, el apoyo virtual de pares y los grupos virtuales de apoyo al uso de sustancias pueden ayudar a garantizar que se satisfagan las necesidades de salud mental de la comunidad ( ). el sistema de salud y los líderes de enfermería deben asegurarse de que su personal de enfermería clínica esté protegido y respaldado para que puedan proporcionar esta dimensión crucial de la atención de covid- . se recomienda crear grupos centralizados y definidos para atención de pacientes con sospecha o diagnóstico de covid- que se encarguen de elaboración, socialización e implementación de protocolos. estos deben incluir los aspectos de infraestructura, áreas delimitadas, utilización de epp, listas de chequeo, observadores, insumos y recursos que permitan atención integral. se recomienda organizar el plan de atención del paciente con sospecha o diagnóstico de covid- de enfermería con la asignación de actividades, número de personas según escalas que midan escalas de carga laboral para definir el número adecuado de los miembros del equipo de trabajo, tiempo de atención, gestión de recursos, gestión de riesgo y un líder por turno que garantice el cumplimiento fuerte a favor fundamento la implementación de estrategias de gestión en contingencias genera un trabajo organizado, enfocado en la prevención y tratamiento centralizado, elaboración y socialización de protocolos claros, áreas específicas, delimitadas y asignadas, con un uso racional del recurso humano que se despliega en fases, desde el inicio de la emergencia considerado como detección temprana hasta la atención directa de pacientes con sospecha amci ® o confirmación de sars-cov- . dentro de las fases tempranas, se busca la gestión de los recursos necesarios para la atención de estos pacientes, con una asignación de zonas o servicios y unas condiciones particulares, tratamientos específicos y actividades de atención especiales para las cuales se discriminan medicamentos, dispositivos e insumos necesarios para el cuidado de enfermería. los grupos de atención deben contar con capacitación, gestión y supervisión, apoyo logístico, apoyo psicológico y retroalimentación ( , ) . el plan de atención de enfermería debe tener presente la minimización de exposición, la prevención de infecciones en el personal y cuidados especiales derivados de la condición clínica de los pacientes con esta infección, altamente contagiosa y con síntomas o necesidades que rompe el modo operacional convencional y que requiere implementación basada en la práctica clínica. por lo tanto, el plan debe ser centralizado oportuno, ordenado, seguro y eficiente e incluye: relación enfermería/paciente de acuerdo a criticidad, capacitaciones y entrenamiento al personal de enfermería de línea de frente en el área crítica de aislamiento mediante videos, infografías y procesos prácticos (el contenido de capacitación incluye el uso de elementos de protección personal, higiene de manos, desinfección de áreas, manejo de residuos y esterilización de dispositivos de atención al paciente y manejo de exposición ocupacional), asignación de actividades clínicas (atención directa) y administrativas (supervisión, observador, líderes, gestión de recurso humano y medicamentos), soporte y contratación de personal adicional ante la contingencia con preparación académica o inducción, asignación de turnos razonables con períodos de descanso (alimentación, eliminación), coordinación con otros departamentos y optimización de flujos de trabajo, estrategias de control de infecciones y trabajo en equipo ( , ) . se recomienda que las muestras clínicas tomadas para el diagnóstico de covid- deben conservarse a temperatura entre - a °c, y luego de las horas deben permanecer congeladas a una temperatura de - °c. se recomienda que se realice el envío al laboratorio de salud pública de referencia dentro de las horas posteriores a la toma de la muestra del paciente. se recomienda que el transporte de las muestras debe realizarse con geles o pilas congeladas. se recomienda considerar que las muestras del tracto respiratorio bajo presentan la mejor certeza diagnóstica en pacientes con neumonía para adultos intubados y ventilados mecánicamente con sospecha de covid- . se recomienda contar con elementos de protección personal de acuerdo con las precauciones establecidas para el paciente con sospecha o diagnóstico por covid- para evitar la transmisión a profesionales de la salud. se debe evitar perder el circuito cerrado en los pacientes ventilados mecánicamente y valorar el riesgo de las acciones en pacientes con peep alta. se recomienda realizar la toma de muestra post mortem no invasiva por hisopado nasofaríngeo dentro de las primeras seis ( ) horas posteriores al fallecimiento, para que esta sea útil para su análisis. las muestras clínicas tomadas para el diagnóstico de coronavirus deben conservarse a temperatura entre - a °c, y luego de las horas deben permanecer congeladas a una temperatura de - °c. sin embargo, la muestra puede conservarse en un tiempo máximo de refrigeración por horas. no obstante, se sugiere que se realice el envío al laboratorio de salud pública de referencia dentro de las horas posteriores a la toma. si no se conserva la cadena de frío adecuada, la muestra puede ser inviable. el transporte de las muestras debe realizarse con geles o pilas congeladas ( , , ) .se debe tener en cuenta que no conservar la cadena de frío durante el transporte de la muestra, degradan la partícula viral, obteniéndose falsos negativos ( ) . las muestras del tracto respiratorio bajo presentan la mejor certeza diagnóstica en pacientes con neumonía. para adultos intubados y ventilados mecánicamente con sospecha de covid- en comparación al tracto respiratorio superior (nasofaríngeo u orofaríngeo). en el caso de aspirado traqueal, es importante considerar que para la obtención de las muestras para el diagnóstico de covid- se deben contar con elementos de protección personal de acuerdo a las precauciones estándar para evitar la transmisión a profesionales de la salud, circuito cerrado y valorar su realización en aquellos pacientes con peep alta ( ) . la toma de muestra post mortem no invasiva por hisopado nasofaríngeo se debe hacer antes de seis ( ) horas post mortem, para que esta sea útil para su análisis( , - ). se recomienda en los pacientes con diagnóstico covid- , monitorizar continuamente la oxigenación mediante saturación arterial de oxígeno con pulso oxímetro y la aparición temprana de signos clínicos de dificultad respiratoria durante la monitorización (aleteo nasal, cianosis, tirajes intercostales). se recomienda no suministrar de forma rutinaria suministrar oxígeno si la saturación de oxígeno (spo ) está por encima de %, y no se evidencian signos clínicos de dificultad respiratoria durante la monitorización continua del patrón respiratorio. se recomienda como parámetro importante para evaluar la oxigenación y guiar el suministro de oxígeno mediante los diferentes dispositivos la transferencia de oxígeno, medida por la pao / fio o sao /fio . se propone iniciar la oxigenoterapia por cánulas de bajo flujo y ajustar el flujo (máximo l) hasta alcanzar la spo objetivo ≥ %; si el paciente se encuentra en estado crítico iniciar con mascarilla con bolsa de reserva (a - l / min). una vez que el paciente esté estable, el objetivo de oxigenación es mantener niveles de spo entre y % en pacientes no embarazadas y entre - % en pacientes embarazadas. se recomienda no utilizar de forma rutinaria el uso de dispositivos que generan aerosoles durante la administración de oxígeno (dispositivos venturi o nebulizador de alto flujo o jet) en pacientes con sospecha o diagnóstico covid- . en las diferentes guías publicadas para manejo de pacientes positivos para covid- las metas de oxigenación durante la terapia de oxígeno en adultos recomiendan iniciar la oxigenoterapia a l / min y ajustar el flujo hasta alcanzar la spo objetivo ≥ % durante la reanimación; o use mascarilla con bolsa de reserva (a - l / min) si el paciente está en estado crítico. una vez que el paciente esté estable, el objetivo de oxigenación es > % de spo en pacientes, no embarazadas y ≥ - % en pacientes embarazadas( ). los dispositivos para la oxigenoterapia se pueden dividir en dos grupos, dependiendo de si cubren la totalidad o una parte de los requerimientos respiratorios del paciente. unos son de bajo flujo o para esfuerzos mínimos del paciente, estos dispositivos completan su ventilación con aire ambiente y los sistemas de alto flujo cubren la totalidad de los requerimientos inspiratorios del paciente. escalones terapéuticos: oxigenoterapia convencional a diferentes concentraciones de bajo flujo (son las cánulas nasales, las mascarillas simples y las mascarillas con reservorio), es el primer escalón terapéutico ante cualquier paciente que presente una situación de hipoxemia (spo ) < % respirando aire ambiente. el objetivo debe ser ajustar la fio (hasta . ) para mantener un nivel de oxigenación adecuado, considerado este como una spo > %. la administración de oxígeno se considera un procedimiento generador de aerosoles de riesgo bajo y por lo tanto es adecuado para pacientes covid- positivos( ). b. en adultos con signos de emergencia (respiración obstruida o ausente, dificultad respiratoria severa, cianosis central, shock, coma y / o convulsiones) deben recibir vía aérea amci ® de emergencia manejo y oxigenoterapia durante la reanimación para apuntar a spo ≥ %. una vez el paciente está estable, objetivo> % de spo en adultos no embarazadas y ≥ - % en mujeres embarazadas. c. para el manejo del paciente con covid- la máscara de no re inhalación se considera como la opción de preferencia para escalar el paciente antes de la intubación y considerar la transferencia a uci; esto se debe a que puede proporcionar altas fracciones inspiradas de oxígeno ( ) . d. los dispositivos que generan aerosoles durante la administración de oxígeno (dispositivos venturi o nebulizador de alto flujo o jet), no están indicados para manejo de covid- ( ). se recomienda aplicar las estrategias de retiro de la ventilación mecánica habituales para pacientes adultos críticos en general, hasta el momento no se ha construido una evidencia contundente para el destete en covid- . se recomienda en el paciente críticamente enfermo por covid- un descenso de la presión de soporte (psv) según tolerancia clínica, de esta forma el paciente podrá ser sometido a la realización de prueba de respiración espontánea con una presión de soporte de entre - cm h o. se recomienda que el destete automatizado puede ser considerado como una herramienta útil según disponibilidad de equipos para realizarlo. se recomienda no utilizar las maniobras que incrementan la aerosolización como la prueba de respiración espontánea en pieza en t o el cuff-leak test en el momento de realizar la medición de los predictores de éxito en el destete. fuerte en contra fundamento la realización de las pruebas de respiración espontánea sigue siendo un factor predictor importante en el éxito en el retiro del soporte ventilatorio mecánico y la indicación de tiempo de duración sigue siendo de a minutos debido a que las intubaciones realizadas en el mismo periodo de tiempo no han tenido diferencias significativas en el éxito del destete ( , ) . en los pacientes que han sido ventilados por más de horas y que el motivo por el cual fueron llevados a ventilación mecánica ya ha sido superado se debe establecer un protocolo de destete que debe incluir una prueba diaria de respiración espontánea y la minimización o retiro de la sedación (si no existe alguna contraindicación)( , ). la movilización temprana como factor coadyuvante en el éxito de la liberación mecánica ya se ha documentado en otros escenarios similares, razón por la cual la implementación amci ® temprana de este tipo de estrategias será un punto de vital importancia para recuperar la funcionalidad de los pacientes con covid- ( ) . se recomienda que la extubación de los pacientes críticamente enfermos por covid- se debe realizar con los elementos de protección personal requeridos para el riesgo de aerosoles. se recomienda no estimular la tos y el esputo inducido en los pacientes con sospecha o diagnóstico de covid- posterior a la extubación inmediata. se recomienda no utilizar de forma rutinaria la vmni en la falla respiratoria post extubación en pacientes críticos que no tengan una enfermedad concomitante que sea respondedora a la vmni como el epoc o edema pulmonar de origen cardiogénico en pacientes con sospecha o diagnóstico de covid- . fuerte en contra se recomienda mantener un umbral bajo para decidir intubación en caso de sospecha de fallo en la extubación en el paciente con sospecha o diagnóstico de covid- . la estricta monitoria y manejo del paciente posterior a la extubación surgen como un reto insoslayable para el personal de cuidado intensivo, enfocando todos sus esfuerzos en evitar la re-intubación, lo que se traducirá en un descenso significativo de la morbilidad y la mortalidad que supone una re-intubación ( ), la cual se puede definir como el no requerimiento de re intubación en las primeras horas post extubación ( , ) . en los últimos años la cánula nasal de alto flujo (caf) se ha convertido en una herramienta útil en el soporte de oxigenoterapia en los pacientes extubados que presenten riesgo de reintubación ( , ), y a la vez no presenten hipercapnia ( ) . la utilización de ventilación mecánica no invasiva de manera profiláctica en la falla respiratoria post extubación no ha demostrado tener éxito evitando la re-intubación en las primeras horas ( , ) excepto en las situaciones donde el paciente presente una enfermedad pulmonar o alteración cardiaca concomitante que sea respondedora a el manejo con vmni como lo son la enfermedad pulmonar obstructiva crónica (epoc) y el edema pulmonar de origen cardiogénico ( , ) . los pacientes extubados en los que se halla documentado epoc, se sugiere posterior a la extubación la implementación de una estrategia de niv de manera protocolaria ( , ), con una intensidad de hora cada horas durante un período mínimo de horas ( ). se recomienda utilizar en los pacientes con extubación reciente que no expresen predictores de riesgo de fracaso, sistemas de oxigenoterapia convencionales de bajo flujo que generen menos riesgo de aerosolización, fuerte a favor se podría considerar cánulas de alto flujo de oxígeno y/o la ventilación mecánica no invasiva (con una máscara facial adecuadamente ajustada y ramas inspiratorias y espiratorias separadas) como terapia de puente después de la extubación, pero se deben brindar las condiciones estructurales necesarias (habitaciones de presión negativa o habitaciones aisladas de puertas cerradas) y con epp estrictos para el personal sanitario. fuerte a favor fundamento las pautas de anzics establecen que la caf y/o la ventilación no invasiva (con una máscara facial bien ajustada y ramas inspiratorias y espiratorias separadas) pueden considerarse como terapia de puente después de la extubación, pero deben proporcionarse epp estricto en el aire. la terapia cpap o bipap (con alta presión espiratoria final) podría ser útil para prevenir la eliminación del reclutamiento en estos pacientes. en el momento de la extubación, los pacientes a menudo han estado enfermos durante más de una semana. es probable que su carga viral disminuya en ese punto, por lo que el riesgo de transmisión del virus puede ser menor (en comparación con la intubación inicial) ( ) . de no contar con predictores de que nos indiquen que podría fracasar la extubación se deben utilizar entonces sistemas de oxigenoterapia convencionales de bajo flujo que generen menos riesgo de aerosolización( ). se recomienda limpiar y desinfectar con frecuencia el área de retiro de epp, incluso después de que se haya completado cada procedimiento de eliminación. se debe limpiar esta zona, pasando de las áreas más limpias a las más sucias, antes de ingresar a la habitación del paciente y realizar el manejo y disposición final de residuos. se recomienda realizar la limpieza de superficies con un desinfectante adecuado o con una solución de hipoclorito sódico que contenga ppm de cloro activo (por ejemplo, un producto con hipoclorito en una concentración de - gr/litro, se hará una dilución : en el momento de su utilización). amci ® se recomienda que los recipientes que contengan los residuos deberán quedar en el lugar designado a tal efecto, que permanecerá cerrado hasta que, según el procedimiento de gestión de residuos de la institución sean retirados. los circuitos, filtros, succión cerrada y tot deben ser dispuestos en bolsas de color rojo las cuales deben ser de polietileno de alta densidad de . milésimas de pulgada y deben contar con un rótulo donde se indiquen: el nombre del generador, las palabras residuos biolÓgicos (covid- ) . una vez dispuesto, apretar y asegurar con nudo la bolsa de residuos y remover la bolsa de residuos del recipiente de residuos. posteriormente, desinfectar el exterior de la bolsa con solución desinfectante. luego colocar la bolsa de residuos en otra bolsa adicional de residuos y apretar y asegurar con nudo la bolsa de residuo. finalmente desinfectar la exterior bolsa de residuos con solución desinfectante. una vez terminada la disposición de los residuos de extubación, desinfectar los guantes con que manipuló los residuos con solución desinfectante y ubicar la bolsa de residuos dentro del vehículo de recolección interna de residuos. finalmente desinfectar el exterior de la bolsa de residuos con solución desinfectante. una vez terminada la disposición de los residuos de extubación, desinfectar los guantes con que manipuló los residuos con solución desinfectante y ubicar la bolsa dentro del vehículo de recolección interna. acogerse a la ruta sanitaria que asegure el menor riesgo de contaminación en el traslado interno de los residuos en la habitación del paciente (zona limpia) y zona sucia, se debe garantizar la ubicación de recipiente plástico de color rojo, liviano, resistente a los golpes, en material rígido impermeable, de fácil limpieza, y resistentes a la corrosión. los recipientes deberán ser lavados y desinfectados de acuerdo con los procedimientos establecidos por el prestador de servicios de salud( - ). se recomienda utilizar un ajuste de peep del paciente crítico por covid- , basado adicional a la tabla de peep, en las condiciones clínicas del paciente, en los índices de oxigenación, en la mecánica respiratoria del paciente y en los métodos de monitoreo disponibles. se recomienda titular la peep más alta que mantenga o mejore la relación safi y permita una presión plateau ≤ cmh o. se recomienda utilizar otras estrategias de titulación de peep probadas y con las cuales el equipo de trabajo esté familiarizado, dependiendo de la disponibilidad del recurso: ensayo peep decremental precedido por una maniobra de reclutamiento; titulación mediante la amci ® estimación de la presión transpulmonar con catéter esofágico o tomografía de impedancia eléctrica. fuerte a favor fundamento la titulación de la peep debe hacerse en función de la distensibilidad, oxigenación, espacio muerto y estado hemodinámico. puede titularse la peep mediante la estimación de la presión transpulmonar con catéter esofágico o tomografía de impedancia eléctrica. podría también titularse a partir de la fórmula (dp=plateau-peep) teniendo en cuenta que sea lógico el acoplamiento matemático fisiológico (lo que resultaría en una peep de cmh o si la presión plateau es de cmh o). la titulación de la peep requiere consideración de los beneficios (reducción de atelectrauma y mejora del reclutamiento alveolar) frente a los riesgos (sobre distensión inspiratoria final que conduce a lesión pulmonar y mayor resistencia vascular pulmonar)( , , ). se recomienda aplicar los protocolos de rehabilitación física como estrategia beneficiosa en el tratamiento respiratorio y físico de pacientes críticamente enfermos por covid- . se recomienda realizar la movilización precoz del paciente críticamente enfermo por covid- durante el curso de la enfermedad siempre que sea posible hacerlo de forma segura, asegurando la protección personal del personal sanitario. derivado del tratamiento médico intensivo para algunos pacientes con covid- , incluida la ventilación pulmonar protectora prolongada, la sedación y el uso de agentes bloqueantes neuromusculares, los pacientes con covid- que ingresan en la uci pueden presentar un elevado riesgo de desarrollar debilidad adquirida en la uci empeorando su morbilidad y mortalidad. por lo tanto, es esencial la rehabilitación temprana después de la fase aguda del síndrome de distrés respiratorio agudo (sdra) para limitar la gravedad de la debilidad adquirida en uci y promover la recuperación funcional. según la guía de la oms y la ops, enfatizan extremar el uso de los elementos de protección personal (epp) durante las intervenciones de rehabilitación física. la rehabilitación física proporciona intervenciones a través de movilizaciones, ejercicio terapéutico y programas individualizados a las personas que superan la enfermedad crítica asociada con covid- durante la ventilación mecánica y luego de esta, con el fin de permitir un retorno al hogar con funcionalidad. la prescripción de la movilización y ejercicio terapéutico debe de ser considera cuidadosamente en función del estado del paciente teniendo en cuenta, la estabilidad hemodinámica y clínica de la función respiratoria. cuando las movilizaciones, ejercicio terapéutico o programas de rehabilitación están indicados, debe realizarse una correcta planeación teniendo en cuenta amci ® la identificación/uso del personal mínimo necesario para realizar la actividad de manera segura. y el aseguramiento de todo el material que requerido esté a la mano y funcione correctamente y esté perfectamente limpio y desinfectado. si el material/equipo tiene que ser compartido con otros pacientes, límpielo y desinféctelo después de cada uso, entre paciente y paciente. se requiere personal entrenado específicamente para la limpieza y desinfección de los equipos, en una habitación aislada. y siempre que sea posible, evitar el traslado del material entre las áreas infectadas y no infectadas del hospital, manteniendo el equipamiento en las zonas aisladas ( ) ( ) ( ) ( ) ( ) . ( basados en un estudio preliminar aún sin publicar, se podría sugerir el uso de dexametasona a dosis de mg (oral o venosos) por días o hasta el alta si ocurre primero en pacientes hospitalizados con sospecha o diagnóstico de covid- que requieren suplencia de oxígeno, incluyendo aquellos con ventilación mecánica, que sean menores de años y con más de días de síntomas. amci ® actualmente no existe una terapia dirigida que se a efectiva para el manejo del virus; un número alto de estudios han surgido en los últimos dos meses, la mayoría sin el rigor metodológico suficiente para tomar decisiones adecuadas con respecto al manejo del paciente con infección por sars-cov- . el conocimiento en la estructura del virus y el mejor entendimiento en la fisiopatología de la enfermedad genera un sinnúmero de potenciales fármacos que han sido ensayados para el manejo de la enfermedad. en tiempos de pandemia, con una patología catastrófica en términos de vidas humanas y costos hospitalarios; es importante encontrar soluciones a desenlaces importantes como mortalidad, días de estancia en uci y en el hospital, aumento en los días libres del ventilador, disminución de complicaciones mayores debido a la enfermedad entre otros. hasta el momento no se ha documentado ninguna terapia específica que pueda impactar sobre estos desenlaces; pero la calidad de los trabajos, tampoco dejan claro sin él no usar ningún tratamiento específico mejora los desenlaces al menos al disminuir el número de complicaciones. este nuevo beta-coronavirus es similar al coronavirus del síndrome respiratorio agudo severa (sars-cov) y del síndrome respiratorio del medio este (mers-cov); por lo tanto, varias moléculas que habían sido evaluadas en este tipo de enfermedad rápidamente se abrieron paso a ensayos clínicos en paciente con covid- . estos ensayos principalmente observacionales, aleatorios pero abiertos con un número pequeño de pacientes no han permitido sacar adecuadas conclusiones y es frecuente como ver las diferentes guías de las principales sociedades del mundo cambiar de forma frecuente sus recomendaciones; no existes evidencia de estudios clínicos aleatorios y controlados que midan desenlaces fuertes, la premura de un tratamiento efectivo ha sacrificado el rigor metodológico que una investigación requiere. una estructura viral y replicación conocidas generan posibles dianas para que diferentes fármacos puedan ser investigados, antivirales tipo arbidol el cual inhibe la fusión de la membrana en la envoltura viral a algunos receptores; antimaláricos como la hidroxicloroquina y la cloroquina, las cuales inhiben la entrada viral y endocitosis por múltiples mecanismos, así como los efectos inmunomoduladores demostrados en el huésped; antivirales que impiden la replicación como el lopinavir o darunavir inhibiendo las proteasas o la ribavirina, el remdesivir o el favipiravir que actúan como análogos de nucleótidos o fármacos que actúan modulando la respuesta específica del huésped como el tocilizumab el cual se une al receptor de la il- inhibiendo el punto de acción de esta; los corticosteroides con múltiples efectos en la modulación del sistema inmunológico del paciente o los fármacos para evitar la respuesta secundaria a esta cascada inflamatoria como son los anticoagulantes. por último, se han buscado estrategias con el fin de mejorar la inmunización pasiva del huésped en el uso del plasma de pacientes convalecientes o el uso de inmunoglobulinas enriquecidas entre otros tratamientos propuestos para esta enfermedad. amci ® a los diferentes medicamentos que han sido usados en la pandemia del sars-cov- /covid- . de manera reciente en datos preliminares aún sin publicar horby y col en una rama del ensayo de evaluación aleatorizada de la terapia covid- (recovery), estudio aleatorizado, controlado, abierto que compara una gama de posibles tratamientos con la atención habitual en pacientes hospitalizados con covid- , compararon el uso de la dexametasona a dosis de mg día (oral o intravenosa) una vez al día por días o el alta según lo que ocurriera primero contra el manejo habitual; en pacientes aleatorizados que recibieron dexametasona se compararon con pacientes en manejo estándar; ( . %) pacientes en el grupo de dexametasona y ( . %) pacientes en el grupo control murieron a los días, con un riesgo relativo ajustado para la edad (rr . ; % ic . a . ; p < . ). la mortalidad relativa y absoluta variaron significativamente en relación al soporte ventilatorio al momento de la aleatorización; la dexametasona redujo las muertes en una tercera parte de los pacientes que recibieron ventilación mecánica invasiva ( . % vs. . %, rr . , % ic . a . ; p < . ), y una quinta parte en los pacientes que reciben oxígeno sin ventilación mecánica invasiva ( . % vs. . %, rr . , % ic . a . ; p = . ), pero sin reducir la mortalidad en paciente que no recibieron soporte respiratorio al momento de la aleatorización ( . % vs. . %, rr . , % ic . a . ]; p = . ) ( ) . no se emite recomendación a favor ni en contra para el inhibidor de la janus quinasa (baricitinib) en los pacientes con sospecha clínica o diagnóstico de covid- severo. uno de los reguladores conocidos de la endocitosis es la proteína quinasa asociada a ap (aak ); la interrupción de aak podría, a su vez, interrumpir el paso del virus a las células y también el ensamblaje intracelular de partículas del virus. uno de los seis fármacos de unión a aak de alta afinidad es el inhibidor de la janus quinasa (jak y jak ), llamado baricitinib, que también se une a la quinasa asociada a la ciclina g, otro regulador de la endocitosis ( ) . el baricitinib alcanza concentraciones plasmáticas suficientes para inhibir aak con mg o mg una vez al día; por su baja unión a proteínas plasmáticas y a su mínima interacción con las enzimas cyp, permite combinarlo con los antivirales. sin embargo, algunos piensan que el bloqueo de la señal jak-stat por baricitinib puede producir un deterioro de la respuesta antiviral mediada por interferón, con un posible efecto facilitador sobre la evolución de la infección por sars-cov- ; otras limitantes son la linfopenia (no dar si < cel./ mm ) y el aumento de la cpk. ( , ) . cantini y cols, en abril , en italia, administraron baricitinib a mg/día vía oral por semanas a pacientes con covid- moderado y los compararon con un grupo control; la terapia mejoró significativamente los parámetros clínicos, respiratorios y de laboratorio (pcr); ninguno de los pacientes requirió uci vs % del grupo control, sin eventos adversos. se amci ® trata de un estudio piloto de seguridad e impacto clínico en pacientes que no estaban en uci ( ) . ¿en pacientes hospitalizados con sospecha o diagnóstico de covid- el uso de n-acetil cisteína modifica el curso clínico de la enfermedad o genera beneficios en desenlaces clínicos de interés? basados en evidencia indirecta para el manejo del sdra y resultados observaciones en covid- , se podría utilizar el uso de n-acetil cisteina a dosis de mg/kg/día durante los primeros cinco días del sdra, aunque no se ha demostrado impacto en la mortalidad, su utilización parece relacionarse con una disminución significativa en la estancia en la unidad de cuidados intensivos y con disminución de los marcadores inflamatorios en pacientes con covid- . la severidad de la infección en covid- , en gran parte depende de la respuesta inmunológica de cada persona, sin embargo, se encuentran mecanismos fisiopatológicos de relevancia. sobreproducción de moco en vía aérea superior e inferior, que en parte explica la dificultad en la mecánica ventilatoria y los retos de ventilación en estos pacientes, la descarga desmedida de citoquinas proinflamatorias que se asocian a la falla multiorgánica y la coagulopatía asociada a la disfunción endotelial. esto mecanismos fisiopatológicos son comunes en el sdra, incluido los casos asociados a covid- ( ). amci ® enfermo con falla respiratoria aguda, la cual engloba falla respiratoria hipóxica (tipo ), falla respiratoria hipercápnica aguda (tipo ), sdra y lesión pulmonar aguda, se revisaron ensayos clínicos, más de pacientes. el análisis del grupo de n acetilcisteína intravenoso mostró una reducción de estancia en uci, de . días, con una heterogeneidad muy baja del %, con valoración de la evidencia calificada como de alta calidad y baja probabilidad de sesgo ( ) . en covid- , fue utilizada con recuperación completa en un caso severo de un paciente con déficit de glucosa fosfato deshidrogenasa (g pd), con control de la hemolisis y resolución del compromiso pulmonar. en pacientes sin déficit de g pd, también ha sido asociada a mejoría clínica y disminución significativa de los niveles de pcr y ferritina ( ) . en una revisión de costo efectividad nacional, se identificaron referencias, de ellos era revisiones sistemáticas de la literatura, dos de las cuales incluían metaanálisis (lu y zhang ), y fueron incluidos en la evaluación. estos estudios incluyeron información de ensayos clínicos que comparaban la aplicación de nac intravenosa frente a placebo o cuidado usual en pacientes con sdra. los tres estudios reportan como resultado de mortalidad rr de . con ic al % de . a . (lu ), rr de . con ic al % de . a . (lewis ) y rr de . con ic al % de . a . (zhang ) . para el tiempo de estancia en uci solo las revisiones con metaanálisis reportaron resultados, encontrando una diferencia de promedio de días de estancia de - . días con ic al % de - . a - . (lu ) y de - . días con ic al % de - . a - . (zhang ). una de las revisiones reportó que en ninguno de los estudios analizados se presentaron eventos adversos. no se encontraron resultados para los desenlaces de infección, sobreinfección, ni uso y tipo de antibiótico utilizado. en el análisis se encontró una reducción estadísticamente significativa de los días de estancia en uci de los pacientes que recibieron tratamiento con n-acetilcisteína intravenosa con dosis entre y mg/kg/día durante los primeros cinco días del sdra, en comparación con los pacientes que recibieron placebo o manejo usual. no se reportó diferencia estadísticamente significativa en la reducción de la mortalidad de los pacientes que recibieron nac. ( ) calidad de vida . ¿cómo podemos medir la calidad de vida, en los pacientes con covid- que egresan de la uci? se recomienda utilizar los marcadores disponibles de severidad y del riesgo de mortalidad por covid- en los pacientes internados en la uci. amci ® las secuelas inmediatas en los pacientes víctimas del devastador ataque sistémico del covid- durante su estancia en la uci son valorables, pero no se dispone de herramientas que permita medir el grado de afectación de la calidad de vida de estos pacientes posterior al egreso de la uci o de alta hospitalaria, por lo tanto, se sugiere realizar estudios de creación, validación y utilización de instrumentos de valoración de la calidad de vida en pacientes con covid- posteriores al alta hospitalaria. parte importante de los pacientes con diagnóstico de covid- que ingresan a la uci, evolucionan tórpidamente presentando deterioro progresivo de los diferentes órganos llegando en pocos días a una falla multiorgánica ( ) , estos pacientes presentan características clínicas y de laboratorio que se relacionan de manera significativa con mayor severidad y riesgo de mortalidad ( , ) . a pesar de conocer con alguna precisión el riesgo de severidad y mortalidad de los pacientes que ingresan a la uci, no disponemos de un score que nos permita evaluar y predecir el grado de afectación en la calidad de vida de los pacientes que logran sobrevivir. aproximadamente un , % del total de pacientes con enfermedad por covid- ingresan a uci, y de estos , % sometidos a ventilación mecánica ( ); lamentablemente los pacientes con enfermedad severa que logran sobrevivir y recuperarse han sido sometidos a una larga estancia en la uci y a ventilación mecánica invasiva con una intubación prolongada, que puede producir disfunción en la deglución impidiendo a la persona alimentarse de forma correcta y segura. es importante diagnosticar esta disfagia en los pacientes que se están recuperando del covid- y tratarla correctamente desde el principio para evitar complicaciones importantes como la malnutrición y la deshidratación, así como el riesgo de neumonía aspirativa. además de la disfagia, la fibrosis pulmonar y el riesgo de trombos son los problemas más frecuentes, pero no los únicos. una de las características de la enfermedad severa por covid- es que el virus provoca una enfermedad multiorgánica, con un amplio y heterogéneo abanico de secuelas cuyo alcance todavía se desconoce y aunque el órgano más afectado es el pulmón, puede afectar también otros órganos o sistemas incluido el snc, que en los casos más graves puede presentar encefalitis, delirios, desorientación y confusión, síntomas que pueden persistir tras el alta de la uci. otra secuela frecuente son las polineuropatías, esta afectación suele comenzar con una sensación de hormigueo en las extremidades y en los pacientes con covid- se presenta además con un cuadro de miositis que provoca debilidad y cansancio al caminar, a veces incluso en reposo; en algunos pacientes se presenta tal debilidad que dificulta llevar el alimento a la boca e incluso deglutirlo. sin embargo, la primera y más frecuente de las manifestaciones neurológicas del covid- es la pérdida del olfato, que a veces perdura como secuela tiempo después del alta. un estudio en pacientes ingresados en el hospital clínico san carlos de madrid revela que el % había sufrido anosmia en mayor o menor grado. la importancia de este síntoma radica en que las fosas nasales pueden ser la vía de acceso del virus al sistema nervioso central. amci ® otras posibles secuelas neurológicas asociadas a la infección por covid- son la ageusia, la cefalea y amnesia a corto y mediano plazo. también son importantes las secuelas que afectan al sistema cardiovascular. un estudio publicado en la journal o the american medical association advierte que un % de los pacientes presenta una elevación de las enzimas que indican daño en el miocardio. la inflamación que provoca el virus puede provocar directamente ese daño y también puede agravar el estado de pacientes que ya tengan una patología cardiovascular de base, muchas miocarditis son reversibles, pero hay una parte importante que deja como secuela una pérdida de la función contráctil. todavía se desconoce el alcance y es difícil medir el impacto de la enfermedad sobre el corazón porque en algunos casos, los síntomas de insuficiencia cardíaca se confunden con los de la neumonía. otra de las complicaciones más frecuentes, y potencialmente más grave, afecta al mecanismo de coagulación de la sangre. durante el ingreso hospitalario se han visto numerosos casos de ictus. la secuela más importante es el riesgo de que se formen trombos, que pueden ir al pulmón o al cerebro, y si se producen en las arterias, pueden dar lugar a un infarto, aunque este efecto es mucho menos frecuente. eso explica que algunos pacientes de covid- dados de alta hayan tenido que volver a ingresar por trombosis. finalmente es importante tener presente que a las afectaciones que haya podido producir el virus, hay que sumar las secuelas neurológicas propias de una estancia prolongada en una unidad de cuidados intensivos que también pueden ser graves y a veces no se distinguen bien unas de otras. debilidad muscular, desorientación, depresión y problemas psicológicos son secuelas muy habituales entre los pacientes que salen de la uci por enfermedades diferentes. por la anterior razón es difícil, por ahora, saber qué es efecto directo del virus y que puede derivarse del proceso de hospitalización. aún es difícil decir si los daños a largo plazo dependen del propio virus o de los efectos adversos del proceso tratante. sin embargo, este análisis de las posibles secuelas del covid- en el cuerpo, se presenta con más dudas que certezas. como es habitual en medicina, las causas pueden ser múltiples y muchas veces reflejan la participación de varias complicaciones que se han podido dar durante el proceso infeccioso directo o por la hospitalización, la información sobre los mecanismos de invasión del sars-cov- en todos los órganos sigue siendo, por ahora, escasa. y también lo es nuestro conocimiento sobre los efectos adversos de los medicamentos, muchos de ellos experimentales, que se han utilizado durante esta crisis. gran parte de lo que conocemos actualmente sobre los efectos de este virus proviene de la experiencia clínica de otros colegas y de las historias de pacientes que han sufrido la enfermedad, quedando todavía mucho por descubrir. dado el actual panorama, diferentes hospitales e instituciones de salud se preparan en torno a la rehabilitación, habilitando ya unidades multidisciplinares poscovid- para el seguimiento de estos pacientes y algunos centros están contactando con los pacientes dados de alta para evaluar su estado y hacer un seguimiento a su salud. también están en marcha varios estudios multicéntricos para evaluar el alcance de las secuelas, prácticamente todos los centros sanitarios deberán tener pautas de seguimiento y control para los pacientes ya dados de alta, creándose necesario la utilización simultánea de amci ® instrumentos de medición de calidad de vida, que en nuestro país colombia, ya se han utilizado previamente con este fin ( , ) . con este instrumento de medición de la calidad de vida se realizaron algunos estudios piloto tanto en pacientes crónicos como en la población general con el fin de determinar la comprensión del instrumento y factibilidad de aplicación del mismo en cuanto a la consistencia interna, la revisión realizada por vilagut y cols demostró que la aplicación de la escala arrojó en diversos estudios un alfa de cronbach igual o superior a . en todas las escalas excepto en función social ( ) . y aunque un número cada vez mayor de estudios mide los resultados físicos, cognitivos, de salud mental y de calidad de vida relacionada con la salud (cvrs) en los sobrevivientes adultos de la uci, los datos sobre las propiedades de medición de tales instrumentos son escasos y, en general, de calidad deficiente a justa. se necesitan análisis empíricos que evalúen el rendimiento de los instrumentos en adultos sobrevivientes de la uci para avanzar en la investigación en este campo ( ) . finalmente, el conocimiento de las secuelas y complicaciones dejadas por la infección del covid- , permitirá identificar importantes variables clínicas que acompañan a esta enfermedad y que afectan de manera importante la calidad de vida de los pacientes que padecen la enfermedad severa en la unidad de cuidados intensivos. en la actualidad no existen estudios para evaluar el riesgo de malnutrición aguda en pacientes hospitalizados por sars-cov- . experiencias con otras infecciones virales por influenza, se han identificado como factores asociados con mortalidad, la presencia de malnutrición, la adquisición de infección intrahospitalarias, la falla respiratoria y la presencia de infiltrados en la radiografía de tórax ( ) . las guías espen recomiendan utilizar el must o el nrs- ( ), para la tamización del riesgo nutricional, estos puntajes de tamización previamente han sido validados en múltiples patologías y contextos clínicos; sin embargo, existen otros puntajes útiles desde la perspectiva clínica como la valoración global subjetiva, mini-nutritional asessment( ), puntaje nutric ( ) y la global leadership initiative on malnutrition (glim) ( ) . el proceso de diagnóstico nutricional debe involucrar, dos componentes: la identificación del riesgo con la utilización de alguno de los puntajes previamente validados en otros contextos y posteriormente el diagnóstico de los pacientes con malnutrición y la valoración de la gravedad de ésta; en este último paso es importante la valoración del índice de masa corporal, los hábitos de consumo calórico y proteico, la presencia de inflamación, los trastornos gastrointestinales, las enfermedades de base y siempre que sea factible el cálculo de la masa muscular. tabla . en vista del riesgo de infección al personal de salud, no siempre será necesario la visita nutricional al paciente, ésta podría ayudarse con entrevista al familiar, interrogatorio vía amci ® telefónica y sólo en caso necesario el examen del paciente para lo cual se requiere el uso de equipo de protección personal completo. esta estrategia de interrogatorio al familiar o al paciente por vía remota o telefónica puede ayudar a identificar los patrones de consumo y los hábitos nutricionales de riesgo y en caso de ser necesario la valoración nutricional disminuye el tiempo de exposición a un ambiente contaminado. para la atención presencial de pacientes en el ámbito de cuidado intensivo, es necesario definir cuál es el riesgo que existe de infección para el personal de salud, para aclarar esta pregunta se debe definir si hay un riesgo de generación de aerosoles( ). aunque no existen pautas específicas para la nutrición en pacientes con covid- , las diferentes sociedades científicas han desarrollado guías de pauta clínica para la nutrición de pacientes con esta enfermedad ( , ) . idealmente la nutrición debe ser iniciada de forma temprana, esto se refiere al inicio en las primeras a horas del ingreso a cuidado intensivo o en las primeras horas luego de la intubación y el inicio de la ventilación mecánica( ) y se prefiere la vía enteral. aunque no existen estudios para evaluar el momento del inicio de la nutrición en pacientes con infección por sars-cov , el inicio temprano de la nutrición ha mostrado beneficios en términos de mortalidad y reducción de infecciones con dicha estrategia ( , ) . adicionalmente es importante, evaluar el riesgo de morbilidad y mortalidad asociado a la malnutrición aguda en el ámbito del paciente crítico, en los pacientes que no se alcance la meta de aporte calórico y proteico por vía enteral o que exista contraindicación para ésta, se debe considerar el inicio de nutrición por vía parenteral, especialmente cuando su riesgo nutricional agudo sea elevado (puntaje nutric ≥ , nrs ≥ ) ( ) ( ) . el choque no es una contraindicación para la utilización de nutrición enteral ( ) y no es una indicación para el uso de nutrición parenteral, quizás la mejor estrategia, es vigilar la presencia de disfunción gastrointestinal, en combinación con la presencia de intolerancia a la nutrición enteral, especialmente en pacientes con acidosis láctica en progreso y cuando sea necesario escalar la dosis de vasopresores o exista incapacidad para la reducción de éstos. no es necesario medir el residuo gástrico de rutina, es preferible iniciar procinéticos de forma rutinaria. la sonda debe colocarse con cuidado de evitar riesgo de contaminación, preferiblemente al entubar al paciente. algunos pacientes pueden presentar diarrea, ya que se ha descubierto la presencia de la proteína ace (receptor del virus sars-cov- ) en células del esófago, estómago, duodeno y recto. no existe evidencia que indique que la nutrición enteral durante la posición prono aumente el riesgo de complicaciones. sugerimos no suspender nutrición enteral al durante la pronación, se debe iniciar con dosis trófica de ml/h. amci ® se recomienda una estrecha monitorización de la tolerancia a la nutrición enteral para pacientes en posición prono. se recomienda para aumentar la tolerancia de la ne a los pacientes en posición prona, una elevación del tórax entre - º (posición de trendelenburg inversa) no realizar endoscopias digestivas para ubicación de sondas avanzadas recomendaciones de nutrición parenteral los pacientes con covid- pueden requerir niveles significativos de sedación y bloqueo neuromuscular, lo que puede aumentar la incidencia de intolerancia gastrointestinal. la nutrición parenteral (np) debe utilizarse donde la alimentación enteral no está disponible o no logra completar el % de los requerimientos. si existen limitaciones para la ruta enteral, se podría recomendar nutrición parenteral periférica (npp) en la población que no alcanza el objetivo proteico energético por nutrición oral o enteral. la np temprana debe iniciarse lo antes posible en el paciente de alto riesgo para el cual la ne gástrica o yeyunal temprana no es factible. los pacientes de alto riesgo incluyen aquellos con sepsis o shock que requieren múltiples vasopresores o en aumento, o cuando se requiere soporte respiratorio de alta presión (niv, cpap o peep). metodología de calificación y resumen de las opiniones dentro de consensos formales how to use the nominal group and delphi techniques transforming ors into icus decreto del de marzo impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand how will countrybased mitigation measures influence the course of the covid- epidemic? incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia pattern of early human-to-human transmission of wuhan estimates of the severity of coronavirus disease : a model-based analysis global telemedicine implementation and integration within health systems to fight the covid- pandemic: a call to action telemedicina durante la epidemia de covid- en chile: guía de buenas prácticas y recomendaciones evaluating tele-icu cost--an imperfect science amci ® . colombia pdlr an international survey of training in adult intensive care medicine do intensivist staffing patterns influence hospital mortality following icu admission? a systematic review and meta-analyses nighttime physician staffing improves patient outcomes: no impact of critical care physician staffing on patients with septic shock in a university hospital medical intensive care unit on-site physician staffing in a community hospital intensive care unit. impact on test and procedure use and on patient outcome effect on icu mortality of a full-time critical care specialist intensive care unit physician staffing: seven days a week, hours a day intensivist-to-bed ratio: association with outcomes in the medical icu the effect of multidisciplinary care teams on intensive care unit mortality potential reduction in mortality rates using an intensivist model to manage intensive care units physician staffing patterns and clinical outcomes in critically ill patients: a systematic review association between critical care physician management and patient mortality in the intensive care unit variation in intensive care unit outcomes: a search for the evidence on organizational factors variation in critical care services across north america and western europe benchmark data from more than , adults that reflect the current practice of critical care in the united states impact of telemedicine intensive care unit coverage on patient outcomes: a systematic review and meta-analysis the use of nonphysician providers in adult intensive care units clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the new york city area comparison of crb- and quick sepsis-related organ failure assessment for predicting the need for intensive respiratory or vasopressor support in patients with covid- acute medical care. the right person, in the right setting--first time: how does practice match the report recommendations the ability of the national early warning score (news) to discriminate patients at risk of early cardiac arrest, unanticipated intensive care unit admission, and death covid- : symptoms, course of illness and use of clinical scoring systems for the first patients admitted to a norwegian local hospital the third international consensus definitions for sepsis and septic shock sirs and news for predicting inhospital mortality and icu admission in emergency admissions treated as sepsis development and validation of a clinical risk score to predict the occurrence of critical illness in hospitalized patients with covid- triage: care of the critically ill and injured during pandemics and disasters: chest consensus statement intensive care during the -coronavirus epidemic therapeutic and triage strategies for novel coronavirus disease in fever clinics critical care utilization for the covid- early experience and forecast during an emergency response icu admission, discharge, and triage guidelines: a framework to enhance clinical operations, development of institutional policies, and further research amci ® . swiss society of intensive care medicine. recommendations for the admission of patients with covid- to intensive care and intermediate care units manual de bioseguridad para prestadores de servicios de salud que brinden atención en salud ante la eventual ethical framework for health care institutions & guidelines for institutional ethics services responding to the coronavirus pandemic how should health systems prepare for the evolving covid- pandemic? reflections from the perspective of a tertiary cancer center compassionate use of remdesivir for patients with severe covid- recomendaciones generales para la toma de decisiones éticas en los servicios de salud durante la pandemia covid- col dsyps. resolución de para los suscritos después de junio col dsyps. consentimiento informado para acompañante de casos probable/confirmado de covid- informed consent: not just for procedures anymore palliative-end-of-life-and-bereavement-care- -march- .pdf [ . asedp. guía práctica de cuidados paliativos en situación de pandemia covid- directing citizens to create advance directives who guidelines on hand hygiene in health care: first global patient safety challenge clean care is safer care pdf;jsessionid =bd d b c b b aa b c?sequence= [ . standardization ecf. protective clothing-performance requirements and tests methods for protective clothing against infective agents cdc. guidance for the selection and use of personal protective equipment (ppe) in healthcare settings filtering facepiece respirators in healthcare settings n -respirators-surgical-masks-and-face-masks [ . anvisa. guidelines for health services: prevention and control measures that should be adopted when assisting suspected or confirmed cases of infection with the new coronavirus personal protective equipment for the ebola virus disease: a comparison of training programs effect of single-versus doublegloving on virus transfer to health care workers' skin and clothing during removal of personal protective equipment assessment of self-contamination during removal of personal protective equipment for ebola patient care equipment-infection-control/n -respirators-surgical-masks-and-face-masks [ . cdc. interim domestic guidance on the use of respirators to prevent transmission of sars infection control measures for operative procedures in severe acute respiratory syndrome-related patients commentary: protecting health workers from airborne mers-cov-learning from sars safety recommendations for evaluation and surgery of the head and neck during the covid- pandemic aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review minimally invasive surgery and the novel coronavirus outbreak: lessons learned in china and italy sars-cov- viral load in upper respiratory specimens of infected patients covid- and the otolaryngologist: preliminary evidence-based review what we do when a covid- patient needs an operation: operating room preparation and guidance a retrospective study of success, failure, and time needed to perform awake intubation detection of sars-associated coronavirus in throat wash and saliva in early diagnosis the infection evidence of sars-cov- in ocular surface： a singlecenter cross-sectional study ophthalmologic evidence against the interpersonal transmission of review article: gastrointestinal features in covid- and the possibility of faecal transmission liver injury in covid- : management and challenges plan de contingencia para los servicios de medicina intensiva frente a la pandemia covid- plan de contingencia para los servicios de medicina intensiva frente a la pandemia covid- seeiuc. plan de contingencia para los servicios de medicina intensiva frente a la pandemia covid- the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application clinical features of patients infected with novel coronavirus in wuhan covid- : consider cytokine storm syndromes and immunosuppression covid- illness in native and immunosuppressed states: a clinical-therapeutic staging proposal covid- pneumonia: ards or not? management of covid- respiratory distress stages or phenotypes? a critical look at covid- pathophysiology characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention sars-cov- rna, qualitative real-time rtpcr interim guidelines for collecting, handling, and testing clinical specimens for evaluating the accuracy of different respiratory specimens in the laboratory diagnosis and monitoring the viral shedding of comparative accuracy of oropharyngeal and nasopharyngeal swabs for diagnosis of covid- detection of sars-cov- in different types of clinical specimens global surveillance for covid- caused by human infection with covid- virus intensive care management of coronavirus disease (covid- ): challenges and recommendations variation in false-negative rate of reverse transcriptase polymerase chain reaction-based sars-cov- tests by time since exposure severe acute respiratory syndrome coronavirus -specific antibody responses in coronavirus disease serology for sars-cov- : apprehensions, opportunities, and the path forward profile of igg and igm antibodies against severe acute respiratory syndrome coronavirus (sars-cov- ) profiling early humoral response to diagnose novel coronavirus disease (covid- ) antibody responses to sars-cov- in patients of novel coronavirus disease prognostic value of interleukin- , c-reactive protein correction to: clinical predictors of mortality due to covid- based on an analysis of data of patients from wuhan clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study the role of biomarkers in diagnosis of covid- -a systematic review cytokine release syndrome in severe covid- epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology analysis of serum cytokines in patients with severe acute respiratory syndrome covid- infection: the perspectives on immune responses pneumonia and respiratory failure from swine-origin influenza a (h n ) in mexico tocilizumab treatment in covid- : a single center experience effective treatment of severe covid- patients with tocilizumab diagnosis and treatment of novel coronavirus pneumonia based on the theory of traditional chinese medicine a rapid advice guideline for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (standard version) our italian experience using lung ultrasound for identification, grading and serial follow-up of severity of lung involvement for management of patients with covid- point of care and intensive care lung ultrasound: a reference guide for practitioners during covid- . radiography (lond) point-of-care lung ultrasound findings in patients with covid- pneumonia cardiovascular considerations for patients, health care workers, and health systems during the covid- pandemic d-dimer in patients infected with covid- and suspected pulmonary embolism anticoagulant treatment is associated with decreased mortality in severe coronavirus disease patients with coagulopathy anticoagulation in covid- procalcitonin to initiate or discontinue antibiotics in acute respiratory tract infections procalcitonin to distinguish viral from bacterial pneumonia: a systematic review and meta-analysis procalcitonin in patients with severe coronavirus disease (covid- ): a meta-analysis viral load of sars-cov- in clinical samples discharge criteria for confirmed covid- cases -when is it safe to discharge covid- cases from the hospital or end home isolation? epidemiologic features and clinical course of patients infected with sars-cov- in singapore. jama. . . who. clinical management of severe acute respiratory infection when novel coronavirus ( -ncov) infection is suspected: interim guidance surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease (covid- ) clinical consensus recommendations regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to sars-cov- infection current evidence for the effectiveness of heated and humidified high flow nasal cannula supportive therapy in adult patients with respiratory failure high-flow nasal cannula oxygen therapy is superior to conventional oxygen therapy but not to noninvasive mechanical ventilation on intubation rate: a systematic review and meta-analysis comparison of high-flow nasal cannula versus oxygen face mask for environmental bacterial contamination in critically ill pneumonia patients: a randomized controlled crossover trial covid- ): protecting hospitals from the invisible high-flow nasal cannula may be no safer than noninvasive positive pressure ventilation for covid- patients high-flow nasal cannula for covid- patients: low risk of bio-aerosol dispersion hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china the use of high-flow nasal oxygen in covid- high-flow nasal cannula oxygenation revisited in covid- high flow nasal cannula is a good treatment option for covid- . heart lung patient selfproning with high-flow nasal cannula improves oxygenation in covid- pneumonia expert recommendations for tracheal intubation in critically ill patients with noval coronavirus disease intubation and ventilation amid the covid- outbreak: wuhan's experience sedation for critically ill patients with covid- : which specificities? one size does not fit all covid- : icu delirium management during sars-cov- pandemic protocolized intensive care unit management of analgesia, sedation, and delirium improves analgesia and subsyndromal delirium rates changing sedation practices in the intensive care unit--protocol implementation, multifaceted multidisciplinary approach and teamwork effects of neuromuscular blockers on transpulmonary pressures in moderate to severe acute respiratory distress syndrome early deep sedation is associated with decreased in-hospital and two-year follow-up survival pain management protocol implementation and opioid consumption in critical care: an interrupted time series analysis. rev bras ter intensiva ketamine added to morphine or hydromorphone patient-controlled analgesia for acute postoperative pain in adults: a systematic review and meta-analysis of randomized trials dexmedetomidine vs midazolam for sedation of critically ill patients: a randomized trial a randomized, double-blind pilot study of dexmedetomidine versus midazolam for intensive care unit sedation: patient recall of their experiences and short-term psychological outcomes effect of dexmedetomidine added to standard care on ventilator-free time in patients with agitated delirium: a randomized clinical trial ventilation with lower tidal volumes as compared with traditional tidal volumes for acute lung injury and the acute respiratory distress syndrome lower tidal volume at initiation of mechanical ventilation may reduce progression to acute respiratory distress syndrome: a systematic review effects of interventions on survival in acute respiratory distress syndrome: an umbrella review of published randomized trials and meta-analyses mortality in multicenter critical care trials: an analysis of interventions with a significant effect covid- pneumonia: different respiratory treatment for different phenotypes? incidence, clinical course, and outcome in patients with acute respiratory distress syndrome driving pressure and survival in the acute respiratory distress syndrome driving pressure: a marker of severity, a safety limit, or a goal for mechanical ventilation? arterial hyperoxia and mortality in critically ill patients: a systematic review and meta-analysis association between administered oxygen, arterial partial oxygen pressure and mortality in mechanically ventilated intensive care unit patients oxygen exposure resulting in arterial oxygen tensions above the protocol goal was associated with worse clinical outcomes in acute respiratory distress syndrome documento de rionegro surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease (covid- ) covid- pneumonia: different respiratory treatments for different phenotypes? intensive care medicine subphenotyping ards in covid- patients: consequences for ventilator management distinct phenotypes require distinct respiratory management strategies in severe covid- acute respiratory distress syndrome: advances in diagnosis and treatment acute respiratory distress syndrome the berlin definition an official american thoracic society/european society of intensive care medicine/society of critical care medicine clinical practice guideline: mechanical ventilation in adult patients with acute respiratory distress syndrome covid- pandemic: overview of protective-ventilation strategy in ards patients respiratory support for adult patients with covid- respiratory monitoring in adult intensive care unit extracorporeal membrane oxygenation for ards in adults extracorporeal membrane oxygenation for severe acute respiratory distress syndrome extracorporeal membrane oxygenation as treatment of severe covid- infection: a case report optimizing provision of extracorporeal life support during the covid- pandemic: practical considerations for canadian jurisdictions rescue therapy for severe covid- associated acute respiratory distress syndrome (ards) with tissue plasminogen activator (tpa): a case series early outcomes with utilization of tissue plasminogen activator in covid- associated respiratory distress: a series of five cases tissue plasminogen activator (tpa) treatment for covid- associated acute respiratory distress syndrome (ards): a case series inhaled nitric oxide for acute respiratory distress syndrome (ards) and acute lung injury in children and adults outpatient inhaled nitric oxide in a patient with vasoreactive ipah and covid- infection lung recruitability in covid- -associated acute respiratory distress syndrome: a single-center observational study acute respiratory failure in covid- : is it "typical respiratory failure in patients infected with sars-cov- association between hypoxemia and mortality in patients with covid- ventilatory ratio in hypercapnic mechanically ventilated patients with covid- -associated acute respiratory distress syndrome ventilator-induced lung injury esophageal pressure monitoring: why, when and how? manejo clínico de la infección respiratoria aguda grave (irag) en caso de sospecha de covid- early neuromuscular blockade in the acute respiratory distress syndrome inhaled nitric oxide in acute respiratory distress syndrome: from bench to bedside inhaled nitric oxide for acute respiratory distress syndrome (ards) in children and adults inhalation of nitric oxide in the treatment of severe acute respiratory syndrome: a rescue trial in beijing noninvasive ventilation in critically ill patients with the middle east respiratory syndrome. influenza other respir viruses clinical course and outcomes of critically ill patients with middle east respiratory syndrome coronavirus infection effect of nitric oxide on oxygenation and mortality in acute lung injury: systematic review and metaanalysis the toxicology of inhaled nitric oxide the pathophysiology of nitrogen dioxide during inhaled nitric oxide therapy use of extreme position changes in acute respiratory failure effects of the prone position on respiratory mechanics and gas exchange during acute lung injury the prone position eliminates compression of the lungs by the heart effects of prone positioning on lung protection in patients with acute respiratory distress syndrome body position changes redistribute lung computed-tomographic density in patients with acute respiratory failure: impact and clinical fallout through the following years effect of prone positioning on the survival of patients with acute respiratory failure effects of systematic prone positioning in hypoxemic acute respiratory failure: a randomized controlled trial prone positioning improves oxygenation in post-traumatic lung injury--a prospective randomized trial a multicenter trial of prolonged prone ventilation in severe acute respiratory distress syndrome prone positioning in acute respiratory distress syndrome: a multicenter randomized clinical trial prone positioning in patients with moderate and severe acute respiratory distress syndrome: a randomized controlled trial prone positioning in severe acute respiratory distress syndrome effect of prone positioning on clinical outcomes in children with acute lung injury: a randomized controlled trial neuromuscular blockers in early acute respiratory distress syndrome the efficacy and safety of prone positional ventilation in acute respiratory distress syndrome: updated study-level meta-analysis of randomized controlled trials prone ventilation reduces mortality in patients with acute respiratory failure and severe hypoxemia: systematic review and meta-analysis an updated study-level meta-analysis of randomised controlled trials on proning in ards and acute lung injury noninvasive versus invasive mechanical ventilation for immunocompromised patients with acute respiratory failure: a systematic review and meta-analysis discontinuing mechanical ventilatory support the ventilator discontinuation process: an expanding evidence base delayed weaning in mechanically ventilated patients: a call for implementation of weaning protocols in low-and middle-income countries effect of pressure support vs t-piece ventilation strategies during spontaneous breathing trials on successful extubation among patients receiving mechanical ventilation: a randomized clinical trial mechanical ventilation weaning issues can be reconnection to mechanical ventilation for h after a successful spontaneous breathing trial reduces reintubation in critically ill patients: a multicenter randomized controlled trial lidocaine during intubation and extubation in patients with coronavirus disease (covid- ) official ers/ats clinical practice guidelines: noninvasive ventilation for acute respiratory failure non-invasive positive pressure ventilation to treat respiratory failure resulting from exacerbations of chronic obstructive pulmonary disease: cochrane systematic review and meta-analysis meta-analysis: noninvasive ventilation in acute cardiogenic pulmonary edema noninvasive ventilation in acute heart failure noninvasive ventilation in immunosuppressed patients with pulmonary infiltrates, fever, and acute respiratory failure is there a role for noninvasive ventilation in acute respiratory distress syndrome? a meta-analysis pandemic influenza a in argentina: a study of patients on mechanical ventilation early noninvasive ventilation treatment for severe influenza pneumonia critically ill patients with influenza a(h n ) infection in canada clinical characteristics and outcomes of patients with influenza a(h n ) virus infection with respiratory failure requiring mechanical ventilation the sars, mers and novel coronavirus (covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? more awareness is needed for severe acute respiratory syndrome coronavirus transmission through exhaled air during noninvasive respiratory support: experience from china covid- pandemic and non invasive respiratory management: every goliath needs a david. an evidence based evaluation of problems clinical outcomes of patients requiring ventilatory support in brazilian intensive care units: a multicenter, prospective, cohort study comparative effectiveness of noninvasive and invasive ventilation in critically ill patients with acute exacerbation of chronic obstructive pulmonary disease assessment of heart rate, acidosis, consciousness, oxygenation, and respiratory rate to predict noninvasive ventilation failure in hypoxemic patients an index combining respiratory rate and oxygenation to predict outcome of nasal high-flow therapy british thoracic society/intensive care society guideline for the ventilatory management of acute hypercapnic respiratory failure in adults baseline characteristics and outcomes of patients infected with sars-cov- admitted to icus of the lombardy region prone position for acute respiratory distress syndrome. a systematic review and meta-analysis efficacy and safety of early prone positioning combined with hfnc or niv in moderate to severe ards: a multi-center prospective cohort study respiratory parameters in patients with covid- after using noninvasive ventilation in the prone position outside the intensive care unit use of prone positioning in nonintubated patients with covid- and hypoxemic acute respiratory failure first case of covid- complicated with fulminant myocarditis: a case report and insights. infection cardiac involvement in a patient with coronavirus disease (covid- ) suspected myocardial injury in patients with covid- : evidence from front-line clinical observation in wuhan, china cardiovascular phenotypes in ventilated patients with covid- acute respiratory distress syndrome covid- and acute heart failure: screening the critically ill -a position statement of the cardiac society of australia and new zealand (csanz) characteristics and clinical significance of myocardial injury in patients with severe coronavirus disease ase statement on protection of patients and echocardiography service providers during the novel coronavirus outbreak clinical guidance regarding provision of echocardiography during the covid- pandemic guidance for the diagnosis and management of cv disease during the covid- pandemic echocardiography during the coronavirus disease (covid- ) pandemic: expert opinion of the working group on echocardiography of the polish cardiac society echocardiography in the time of covid- utilization and appropriateness of transthoracic echocardiography in response to the covid- pandemic covid- illness and heart failure: a missing link? covid- clinical guidance for the cardiovascular care team surviving sepsis campaign: international guidelines for management of sepsis and septic shock hemodynamic monitoring options in covid- advanced pulmonary and cardiac support of covid- patients: emerging recommendations from asaio hemodynamic assessment in the contemporary intensive care unit: a review of circulatory monitoring devices early use of the pulmonary artery catheter and outcomes in patients with shock and acute respiratory distress syndrome: a randomized controlled trial experts' opinion on management of hemodynamics in ards patients: focus on the effects of mechanical ventilation the clinical usefulness of extravascular lung water and pulmonary vascular permeability index to diagnose and characterize pulmonary edema: a prospective multicenter study on the quantitative differential diagnostic definition for acute lung injury/acute respiratory distress syndrome extravascular lung water and pulmonary arterial wedge pressure for fluid management in patients with acute respiratory distress syndrome recommendations for echocardiography laboratories participating in cardiac point of care cardiac ultrasound (pocus) and critical care echocardiography training: report from the american society of echocardiography bedside focused cardiac ultrasound in covid- from the wuhan epicenter: the role of cardiac point-of-care ultrasound, limited transthoracic echocardiography, and critical care echocardiography echocardiography in pandemic: front-line perspective, expanding role of ultrasound, and ethics of resource allocation can lung us help critical care clinicians in the early diagnosis of novel coronavirus (covid- ) pneumonia? ccusg) cccusg. findings of lung ultrasonography of novel corona virus pneumonia during the - epidemic ultrasound in covid- : a timeline of ultrasound findings in relation to ct a preliminary study on the ultrasonic manifestations of peripulmonary lesions of non-critical novel coronavirus pneumonia effect of focused bedside ultrasonography in hypotensive patients on the clinical decision of emergency physicians accuracy of point-of-care multiorgan ultrasonography for the diagnosis of pulmonary embolism will this hemodynamically unstable patient respond to a bolus of intravenous fluids? predict) priedic. does respiratory variation in inferior vena cava diameter predict fluid responsiveness: a systematic review and meta-analysis does central venous pressure predict fluid responsiveness? a systematic review of the literature and the tale of seven mares clinical characteristics of coronavirus disease in china comparison of two fluid-management strategies in acute lung injury the surviving sepsis campaign bundle: update incorporating dynamic assessment of fluid responsiveness into goal-directed therapy: a systematic review and meta-analysis relative efficacy and safety of early lactate clearance-guided therapy resuscitation in patients with sepsis: a meta-analysis effect of a resuscitation strategy targeting peripheral perfusion status vs serum lactate levels on -day mortality among patients with septic shock: the andromeda-shock randomized clinical trial pooled analysis of higher versus lower blood pressure targets for vasopressor therapy septic and vasodilatory shock scandinavian ssai clinical practice guideline on choice of first-line vasopressor for patients with acute circulatory failure vasopressors for hypotensive shock canadian critical care society clinical practice guideline: the use of vasopressin and vasopressin analogues in critically ill adults with distributive shock cardiovascular disease, drug therapy, and mortality in covid- cardiovascular considerations in treating patients with coronavirus disease (covid- ) clinical characteristics of deceased patients with coronavirus disease : retrospective study inclusion of high-fidelity simulation training in a critical care nursing internship high-fidelity simulation in a clinical care unit is feasible and safe interim guidance for basic and advanced life support in adults, children, and neonates with suspected or confirmed covid- ropa y equipo de protección para los trabajadores sanitarios para evitar que se contagien con el coronavirus y otras enfermedades altamente infecciosas adult advanced life support for covid- covid- reverse cpr: a pilot study of cpr in the prone position central nervous system manifestations of covid- : a systematic review an italian multicenter retrospective-prospective observational study on neurological manifestations of covid- (neurocovid) olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (covid- ): a multicenter european study update on the neurology of covid- coronavirus immunoreactivity in individuals with a recent onset of psychotic symptoms potential neurological impact of coronaviruses: implications for the novel sars-cov- neurological insights of covid- pandemic neurological manifestations of covid- and other coronavirus infections: a systematic review human coronaviruses and other respiratory viruses: underestimated opportunistic pathogens of the central nervous system? viruses neurological manifestations in covid- caused by sars-cov- cns penetration of potential anti-covid- drugs central nervous system involvement by severe acute respiratory syndrome coronavirus- (sars-cov- ) neurological manifestations of patients with covid- : potential routes of sars-cov- neuroinvasion from the periphery to the brain neurological complications of coronavirus and covid- autonomic brain centers and pathophysiology of covid- neuropathologists play a key role in establishing the extent of covid- in human patients does covid infect the brain? if so, smokers might be at a higher risk neurologic manifestations of hospitalized patients with coronavirus disease neurological complications of coronavirus disease (covid- ): encephalopathy. cureus coronavirus disease (covid- ) in neurology and neurosurgery: a scoping review of the early literature prevalence of comorbidities and its effects in patients infected with sars-cov- : a systematic review and metaanalysis protected code stroke: hyperacute stroke management during the coronavirus disease brain mri findings in patients in the intensive care unit with covid- infection neurologic features in severe sars-cov- infection evidence of the covid- virus targeting the cns: tissue distribution, host-virus interaction, and proposed neurotropic mechanisms epidemiology of covid- in a long-term care facility in king county, washington acute cerebrovascular disease following covid- : a single center neurological manifestations of hospitalized patients with covid- in wuhan, china: a retrospective case series study improved epileptic seizure detection combining dynamic feature normalization with eeg novelty detection acute systemic complications of convulsive status epilepticus-a systematic review outcome predictors for status epilepticus--what really counts tratamiento del estado epiléptico, consenso de expertos consensus for prevention and management of coronavirus disease (covid- ) for neurologists. stroke vasc neurol recomendaciones de diagnóstico y tratamiento del ataque cerebrovascular isquémico agudo durante la contingencia por covid- seizures associated with coronavirus infections a first case of meningitis/encephalitis associated with sars-coronavirus- neurological manifestations and complications of covid- : a literature review does sars-cov- invade the brain? translational lessons from animal models guillain barre syndrome associated with covid- infection: a case report lung-kidney interactions in critically ill patients: consensus report of the acute disease quality initiative (adqi) workgroup intravascular volume assessment in the critically ill patient the dose response multicentre investigation on fluid assessment (doremifa) in critically ill patients fluid management with a simplified conservative protocol for the acute respiratory distress syndrome* surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease (covid- ) effects of very early start of norepinephrine in patients with septic shock: a propensity score-based analysis the clinical relevance of oliguria in the critically ill patient: analysis of a large observational database clinical characteristics of coronavirus disease (covid- ) in china: a systematic review and meta-analysis management of acute kidney injury in patients with covid- liver and kidney injuries in covid- and their effects on drug therapy clinical characteristics of risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease mitigating risk of covid- in dialysis facilities additional guidance for infection prevention and control recommendations for patients with suspected or confirmed covid- in outpatient hemodialysis facilities sars-cov- in the peritoneal waste in a patient treated with peritoneal dialysis antibody response and viraemia during the course of severe acute respiratory syndrome (sars)-associated coronavirus infection kidney disease is associated with in-hospital death of patients with covid- acute kidney injury in patients hospitalized with covid- acute kidney injury in hospitalized patients with coronavirus disease (covid- ): a meta-analysis collapsing glomerulopathy in a patient with coronavirus disease (covid- ) renal histopathological analysis of postmortem findings of patients with covid- in china collapsing glomerulopathy in a covid- patient renal involvement and early prognosis in patients with covid- pneumonia expert consensus on the application of special blood purification technology in severe covid- pneumonia kidney involvement in covid- and rationale for extracorporeal therapies factors associated with acute kidney injury in acute respiratory distress syndrome effect on extrapulmonary sepsis-induced acute lung injury by hemoperfusion with neutral microporous resin column kdigo guidelines:modality of renal replacement therapy for patients with aki potential effect of blood purification therapy in reducing cytokine storm as a late complication of critically ill covid- new fronts emerge in the influenza cytokine storm coronavirus epidemic: preparing for extracorporeal organ support in intensive care diagnosis and treatment novel coronavirus pneumonia (covid (covid- ): international expert opinions and coronavirus epidemic and extracorporeal therapies in intensive care: si vis pacem para bellum group rc. effect of dexamethasone in hospitalized patients with covid- : preliminary report remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) zhejiang da xue xue bao yi xue ban breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies treating covid- with chloroquine clinical efficacy of hydroxychloroquine in patients with covid- pneumonia who require oxygen: observational comparative study using routine care data effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus (sars-cov- ) infection: a randomized clinical trial hydroxychloroquine in patients with mainly mild to moderate coronavirus disease : open label, randomised controlled trial clinical outcomes of amci ® patients with covid- : a quasi-randomized comparative study observational study of hydroxychloroquine in hospitalized patients with covid- hydroxychloroquine and azithromycin as a treatment of covid- : results of an openlabel non-randomized clinical trial clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in covid- patients with at least a six-day follow up: a pilot observational study early treatment of covid- patients with hydroxychloroquine and azithromycin: a retrospective analysis of cases in marseille, france in vitro testing of combined hydroxychloroquine and azithromycin on sars-cov- shows synergistic effect outcomes of hydroxychloroquine usage in united states veterans hospitalized with covid- . medrxiv association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in new york state treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture a trial of lopinavir-ritonavir in adults hospitalized with severe covid- triple combination of interferon beta- b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with covid- : an open-label, randomised, phase trial arbidol monotherapy is superior to lopinavir/ritonavir in treating covid- first case of novel coronavirus in the united states remdesivir for severe acute respiratory syndrome coronavirus causing covid- : an evaluation of the evidence remdesivir: review of pharmacology, preclinical data and emerging clinical experience for covid- remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial compassionate remdesivir treatment of severe covid- pneumonia in intensive care unit (icu) and non-icu patients: clinical outcome and differences in post-treatment hospitalisation status the fda-approved drug ivermectin inhibits the replication of sars-cov- in vitro usefulness of ivermectin in covid- illness icon (ivermectin in covid nineteen) study: use of ivermectin is associated with lower mortality in hospitalized patients with covid adult haemophagocytic syndrome macrophage activation-like syndrome: a distinct entity leading to early death in sepsis development and validation of the hscore, a score for the diagnosis of reactive hemophagocytic syndrome coronavirus disease (covid- ): a clinical update interleukin- blockade for severe tocilizumab therapy reduced intensive care unit admissions and/or mortality in covid- patients clinical characteristics and early outcomes in patients with covid- treated with tocilizumab at a united states il inhibition in critically ill covid- patients is associated with increased secondary infections off-label use of tocilizumab for the treatment of sars-cov- pneumonia in impact of low dose tocilizumab on mortality rate in patients with covid- related pneumonia tocilizumab in patients with severe covid- : a retrospective cohort study efficacy and safety of tocilizumab in severe covid- patients: a single-centre retrospective cohort study tocilizumab for treatment of mechanically ventilated patients with covid- . medrxiv tocilizumab treatment for cytokine release syndrome in hospitalized covid- patients: survival and clinical outcomes interleukin- blockade with high-dose anakinra in patients with covid- , acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study anakinra for severe forms of covid- : a cohort study baricitinib therapy in covid- : a pilot study on safety and clinical impact weak induction of interferon expression by sars-cov- supports clinical trials of interferon lambda to treat early covid- pharmacologic treatments for coronavirus disease (covid- ): a review clinical evidence does not support corticosteroid treatment for -ncov lung injury sars: systematic review of treatment effects corticosteroid therapy for critically ill patients with middle east respiratory syndrome corticosteroid treatment of patients with coronavirus disease (covid- ) the effect of corticosteroid treatment on patients with coronavirus infection: a systematic review and meta-analysis impact of corticosteroid therapy on outcomes of persons with sars-cov- , sars-cov, or mers-cov infection: a systematic review and meta-analysis group rc. effect of dexamethasone in hospitalized patients with covid- : preliminary report meta-analysis: convalescent blood products for spanish influenza pneumonia: a future h n treatment? convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (h n ) virus infection use of convalescent plasma therapy in sars patients in hong kong the effectiveness of convalescent plasma and hyperimmune immunoglobulin for the treatment of severe acute respiratory infections of viral etiology: a systematic review and exploratory meta-analysis the convalescent sera option for containing covid- characterization of spike glycoprotein of sars-cov- on virus entry and its immune cross-reactivity with sars-cov establishment and validation of a pseudovirus neutralization assay for sars-cov- prevention of transfusion-transmitted infections noninfectious serious hazards of transfusion molecular mechanism for antibody-dependent enhancement of coronavirus entry treatment of critically ill patients with covid- with convalescent plasma effectiveness of convalescent plasma therapy in severe covid- patients treatment with convalescent plasma for critically ill patients with severe acute respiratory syndrome coronavirus infection use of convalescent plasma therapy in two covid- patients with acute respiratory distress syndrome in korea treatment with convalescent plasma for covid- patients in wuhan effect of convalescent plasma therapy on viral shedding and survival in patients with coronavirus disease treatment of covid- patients with convalescent plasma in efficacy of convalescent plasma and short course of corticosteroids in patients with covid- early safety indicators of covid- convalescent plasma in -day mortality and associated risk factors for hospitalized patients with covid- in wuhan, china: an ambispective observational cohort study immunoglobulins in the treatment of covid- infection: proceed with caution! could intravenous immunoglobulin collected from recovered coronavirus patients protect against covid- and strengthen the immune system of new patients? hyperimmune iv immunoglobulin treatment: a multicenter double-blind randomized controlled trial for patients with severe influenza a(h n ) infection active therapy with passive immunotherapy may be effective in the fight against covid- clinical manifestations, laboratory findings, and treatment outcomes of sars patients acute respiratory distress syndrome in critically ill patients with severe acute respiratory syndrome currently available intravenous immunoglobulin contains antibodies reacting against severe acute respiratory syndrome coronavirus antigens effect of regular intravenous immunoglobulin therapy on prognosis of severe pneumonia in patients with covid- high-dose intravenous immunoglobulin as a therapeutic option for deteriorating patients with coronavirus disease successful intravenous immunoglobulin treatment in severe covid- pneumonia esc guidelines for the diagnosis and management of acute pulmonary embolism developed in collaboration with the european respiratory society (ers) abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia covid- and thrombotic or thromboembolic disease: implications for prevention, antithrombotic therapy, and follow-up: jacc state-of-the-art review isth interim guidance on recognition and management of coagulopathy in covid- isth interim guidance on recognition and management of coagulopathy in covid- : a comment thromboembolic risk and anticoagulant therapy in covid- patients: emerging evidence and call for action postinjury hyperfibrinogenemia compromises efficacy of heparin-based venous thromboembolism prophylaxis fixed dose subcutaneous low molecular weight heparins versus adjusted dose unfractionated heparin for the initial treatment of venous thromboembolism perioperative management of patients infected with the novel coronavirus: recommendation from the joint task force of the chinese society of anesthesiology and the chinese association of anesthesiologists outbreak of a new coronavirus: what anaesthetists should know barrier enclosure during endotracheal intubation exhaled air dispersion during bag-mask ventilation and sputum suctioning -implications for infection control optimizing preoxygenation in adults a model to describe the rate of oxyhaemoglobin desaturation during apnoea first-attempt success is associated with fewer complications related to intubation in the intensive care unit complications of endotracheal intubation in the critically ill consensus guidelines for managing the airway in patients with covid- : guidelines from the difficult airway society, the association of anaesthetists the intensive care society, the faculty of intensive care medicine and the royal college of anaesthetists management of difficult tracheal intubation: a closed claims analysis difficult airway society guidelines for management of unanticipated difficult intubation in adults incidence and predictors of difficult mask ventilation and intubation practical recommendations for critical care and anesthesiology teams caring for novel coronavirus ( -ncov) patients disease jot. society for advanced bronchoscopy consensus statement and guidelines for bronchoscopy and airway management amid the covid- pandemic lack of sars transmission among public hospital workers american association for bronchology and interventional pulmonology (aabip) statement on the use of bronchoscopy and respiratory specimen collection in patients with suspected or confirmed covid- infection updated guidance on evaluating and testing persons for coronavirus disease early tracheotomy versus prolonged endotracheal intubation in unselected severely ill icu patients risk factors for posttracheostomy tracheal stenosis systematic review and meta-analysis of studies of the timing of tracheostomy in adult patients undergoing artificial ventilation outcomes and prognostic factors in patients with severe acute respiratory syndrome in hong kong clinical features of deaths in the novel coronavirus epidemic in china surgical considerations for tracheostomy during the covid- pandemic: lessons learned from the severe acute respiratory syndrome outbreak ) he. covid- : guidance for infection prevention and control in healthcare settings clinical and virological data of the first cases of covid- in europe: a case series aao position statement: tracheotomy recommendations during the covid- pandemic recommendations from the cso-hns taskforce on performance of tracheotomy during the covid- sensitivity of chest ct for covid- : comparison to rt-pcr performing tracheostomy during the covid- pandemic: guidance and recommendations from the critical care and acute care surgery committees of the american association for the surgery of trauma recommendation of a practical guideline for safe tracheostomy during the covid- pandemic tracheotomy in the intensive care unit: guidelines from a french expert panel. ann intensive care venovenous extracorporeal membrane oxygenation for acute respiratory distress syndrome: a systematic review and meta-analysis extracorporeal membrane oxygenation for severe acute respiratory distress syndrome and posterior probability of mortality benefit in a post hoc bayesian analysis of a randomized clinical trial surviving sepsis campaign international guidelines for the management of septic shock and sepsis-associated organ dysfunction in children use of ecmo in ards: does the eolia trial really help? mechanical ventilation management during extracorporeal membrane oxygenation for acute respiratory distress syndrome. an international multicenter prospective cohort treatment limitations in the era of ecmo initial elso guidance document: ecmo for covid- patients with severe cardiopulmonary failure extracorporeal life support for adults with respiratory failure and related indications: a review preparing for the most critically ill patients with covid- : the potential role of extracorporeal membrane oxygenation research in extracorporeal life support: a call to planning and provision of ecmo services for severe ards during the covid- pandemic and other outbreaks of emerging infectious diseases association of hospital-level volume of extracorporeal membrane oxygenation cases and mortality. analysis of the extracorporeal life support organization registry position paper for the organization of extracorporeal membrane oxygenation programs for acute respiratory failure in adult patients guía de aplicación de la estrategia multimodal de la oms para la mejora de la higiene de las manos special attention to nurses' protection during the covid- epidemic initiation of a new infection control system for the covid- outbreak preparing your intensive care unit for the covid- pandemic: practical considerations and strategies practical recommendations for the perioperative management of the patient with suspection or serious infection by coronavirus sars-cov covid- under the sars cloud: mental health nursing during the pandemic in hong kong kilinc balci fs. ersonal protective equipment for preventing highly infectious diseases due to exposure to contaminated body fluids in healthcare staff what are the effects of multimodal campaigns to improve hand hygiene of healthcare workers? orientaciones para el manejo, traslado y disposición final de cadáveres por covid- guía para el cuidado crítico de pacientes adultos graves con coronavirus (covid- ) en las américas guia para toma de muestras respiratorias en pacientes con sospecha de infeccion por coronavirus detection of novel coronavirus ( -ncov) by real-time rt-pcr soporte respiratorio en pacientes covid- dispersal of respiratory droplets with open vs closed oxygen delivery masks: implications for the transmission of severe acute respiratory syndrome regarding non-invasive respiratory support in the adult patient with acute respiratory failure secondary to sars-cov- infection desconexión de la ventilación mecánica . ¿ por qué seguimos buscando métodos alternativos ? a comparison of four methods of weaning patients from mechanical ventilation. spanish lung failure collaborative group use of weaning protocols for reducing duration of mechanical ventilation in critically ill adult patients: cochrane systematic review and meta-analysis epidemiology of weaning outcome according to a new definition. the wind study the decision to extubate in the intensive care unit factores de riesgo asociados con la extubación fallida en pacientes adultos de una unidad de cuidados intensivos de la ciudad de cali respiratory support after extubation: noninvasive ventilation or high-flow nasal cannula, as appropriate. ann intensive care effect of postextubation high-flow nasal cannula vs noninvasive ventilation on reintubation and postextubation respiratory failure in high-risk patients: a randomized clinical trial high-flow nasal cannula to prevent postextubation respiratory failure in high-risk nonhypercapnic patients: a randomized multicenter trial noninvasive positive-pressure ventilation for respiratory failure after extubation noninvasive positive-pressure ventilation for postextubation respiratory distress: a randomized controlled trial the japanese respiratory society noninvasive positive pressure ventilation (nppv) guidelines (second revised edition) weaning from mechanical ventilation intermittent noninvasive ventilation after extubation in patients with chronic respiratory disorders: a multicenter randomized controlled trial (vhyper) anzics). dcidaynz. pautas covid- hispaflow) endgemdtdscafea. respiratory support therapy after extubation: who and how? orientaciones para el uso adecuado de los elementos de protección personal por parte de los trabajadores de la salud expuestos a covid- en el trabajo y en su domicilio orientaciones para el m anejo de residuos generados en la atención en salud ante la eventual introducción del virus covid- a colombia orientaciones para el manejo de residuos generados en la atención en salud ante la eventual introducción del virus covid- a colombia ministerio de sanidad. documento técnico manejo en atención primaria del covid- gobierno de españa mds. documento técnico manejo clínico del covid- : unidades de cuidados intensivos ventilacion mecanica en covid- . una aproximación práctica expert consensus and recommendations on safety criteria for active mobilization of mechanically ventilated critically ill adults melbourne: anzics mobilization of intensive care patients: a multidisciplinary practical guide for clinicians fisioterapia en el manejo del paciente covid en fase aguda hospitalaria extrapulmonary manifestations of covid- cytokine storms: understanding covid- postulated adjuvant therapeutic strategies for covid- war to the knife" against thromboinflammation to protect endothelial function of covid- patients effects of n-acetylcysteine treatment in acute respiratory distress syndrome: a meta-analysis mucoactive agents for acute respiratory failure in the critically ill: a systematic review and meta-analysis therapeutic blockade of inflammation in severe covid- infection with intravenous n-acetylcysteine eficacia y seguridad del uso de n-acetilcisteína parenteral en el manejo de los pacientes con síndrome de dificultad respiratoria del adulto (sdra) analysis of factors associated with disease outcomes in hospitalized patients with novel coronavirus disease confiabilidad del cuestionario de calidad de vida en salud sf- en the spanish version of the short form health survey: a decade of experience and new developments a systematic review finds limited data on measurement properties of instruments measuring outcomes in adult intensive care unit survivors population-based surveillance for pandemic influenza a (h n ) virus in guatemala association between malnutrition and clinical outcomes in the intensive care unit: a systematic review identifying critically ill patients who benefit the most from nutrition therapy: the development and initial validation of a novel risk assessment tool glim criteria for the diagnosis of malnutrition -a consensus report from the global clinical nutrition community espen expert statements and practical guidance for nutritional management of individuals with sars-cov- infection nutrition therapy in the patient with covid- disease requiring icu care guidelines for the provision and assessment of nutrition support therapy in the adult critically ill patient: society of critical care medicine (sccm) and american society for parenteral and enteral nutrition guidelines for the provision and assessment of nutrition support therapy in the adult critically ill patient: society of critical care medicine (sccm) and american society for parenteral and enteral nutrition espen guideline on clinical nutrition in the intensive care unit safety and outcomes of early enteral nutrition in circulatory shock gastrointestinal function in intensive care patients: terminology, definitions and management. recommendations of the esicm working group on abdominal problems key: cord- -j hnldk authors: saadat, saeida; rawtani, deepak; hussain, chaudhery mustansar title: environmental perspective of covid- date: - - journal: sci total environ doi: . /j.scitotenv. . sha: doc_id: cord_uid: j hnldk the outbreak of covid- has caused concerns globally. on january who has declared it as a global health emergency. the easy spread of this virus made people to wear a mask as precautionary route, use gloves and hand sanitizer on a daily basis that resulted in generation of a massive amount of medical wastes in the environment. millions of people have been put on lockdown in order to reduce the transmission of the virus. this epidemic has also changed the people's life style; caused extensive job losses and threatened the sustenance of millions of people, as businesses have shut down to control the spread of virus. all over the world, flights have been canceled and transport systems have been closed. overall, the economic activities have been stopped and stock markets dropped along with the falling carbon emission. however, the lock down of the covid- pandemic caused the air quality in many cities across the globe to improve and drop in water pollutions in some parts of the world. on late december in a hospital in wuhan city, in china an unusual pneumonia was noticed with a link to an animal market that sells poultry, fish and other animals to the public (xu et al., ) . this event was soon reported to the world health organization (who). in a month ( january), the causal microorganism had been identified as a novel coronavirus that was named covid- . genome sequencing and reverse transcription polymerase chain reactions tests of this virus had been done. who r&d had been started to quicken diagnostics, therapeutics and vaccine development and a candidate vaccine was prepared for initial laboratory testing . the emergency committee of who declared a global health emergency on january based of growing case notification rates at chines and international locations. the case detection rate is changing on a daily basis and could be tracked in nearly real time on the developed website by johns hopkins university and other media. in the middle of february , china suffered the huge burden of morbidity and mortality, whereas the incidence in other asian countries, in europe and north america remains low so far (velavan and meyer, ) . coronaviruses are single-stranded rna viruses that can infect not only humans, but also a huge variety of animals as well (kooraki et al., ) . these viruses were first studied by tyrell and bynoe in who cultured them from patients with common cold. due to their spherical virions morphology along with a shell and surface projections like a solar corona, these viruses were named coronaviruses. in latin corona means crown and there are four different subfamilies including alpha, beta, gamma and delta coronaviruses identified so far. alpha and beta-coronaviruses have been originated from mammalians, particularly from bats, gamma-and delta-coronaviruses originated from pigs and birds (ather et al., ) . the genome of these viruses differs between kb and kb. the beta-coronaviruses could cause severe disease and fatalities among the other seven subtypes of these viruses. alpha-coronaviruses cause mildly symptomatic or even asymptomatic infections. sarscov- is a beta-coronavirus and is related to the sars-cov virus. there are four structural genes encoding the nucleocapsid protein (n), the spike protein (s), a small membrane protein (sm) and the membrane glycoprotein (m) with an extra membrane glycoprotein (he) occurring in the hcov-oc and hku betacoronaviruses. the whole genome of sars-cov- is % identical to that of a bat coronavirus cao et al., ) . sars-cov- seemingly had made its transition from animals on an animal market in wuhan city in china. although, the efforts to identify potential intermediate hosts seem to have been neglected in wuhan and the exact transmission route have to be clarified. the primary clinical symptoms of the sars-cov- -linked disease covid- which permitted the case detection as pneumonia. recently literatures report the description of gastrointestinal symptoms and asymptomatic infections, especially among young children. the average incubation period is ranging from to days zhou et al., ) . as we are writing these lines, the pandemic affects countries and territories, with around , , infected subjects, more than , deaths and . recovered patients, according to the johns hopkins university. as who has declared the fast spreading of covid- as an epidemic, the citizens around the globe hastened to go home. for instance, in the case of wuhan city in china which has been the epicenter of the pandemic with over than million people, is shown to have produced tons of clinical trash on a single day exactly february/ which is four times the amount the city's only dedicated facility can incinerate per day. as coronavirus is spreading rapidly to other parts of the world, very soon the medical waste management could be a big issue. medical health organizations waste management companies have already taken step in coronavirus decontamination services, it is becoming very crucial for governments to find solutions soon. at the meantime, it is every individual's duty to follow the regulations while discarding of their face masks and other medical wastes (luan and ching, ) . to the end, it is possible only by mutual understanding and willingness and world will emerge stronger than this epidemic. some people are at higher risk of adverse effects from contact to medical wastes as well, including cleaners, trash collectors and some other people who have to spend a great amount of time in public places. all over the world governments stopped students to go to schools and universities, and a lot of employees are being asked to work from home, only those who are maintaining the cleanliness of cities have to go to their jobs daily, that makes them among the most vulnerable groups and one that is highly susceptible to the virus from respiratory shed droplets on the masks. they may also be infected by other pathogens existing in the discarded pieces of garbage, for instance meningitis and hepatitis b. the masks are made up of plastic based materials that are liquid-resistant and are long lasting after they are discarded, ending up in ocean or landfill. the surgical masks should not be worn longer than one day, discarding them and empty bottles of hand sanitizer along with solid tissue papers are ending up to a huge trail of medical waste in the environment. for instance, in hong kong, where covid- infection started in late january/ the medical wastes have already polluted the environment. recently, an environmental ngo ocean asia in soko islands took a survey, according to it, in hong kong a large amount of discarded single-use masks washed up to a -meter stretch of beach. gary stokes the director of the ocean asia ngo, who has been monitoring the ocean surface trash, his team has seen a few masks over the years, but now they were spotted all along the high tide line and seashore with new deposits coming with each current. while this recent covid- outbreak, the general public have started wearing surgical masks in order to take precautionary measures. when million people suddenly start wearing one or a couple of masks daily, single use gloves and hand sanitizers, the amount of trash created is going to be substantial. the contrary impacts of such medical wastes are far-reaching. when these are remained discarded in an animal's natural habitat in both land and ocean this could cause animals to mistakenly eat this as food and lead in their death (hellewell et al., ) . the diagram below illustrates the problems of polluting the environment by medical wastes while covid- pandemic (fig. ). covid- does not affect everyone in the same way. there are several reasons that's why different socioeconomic groups are affected by this pandemic in different ways. to understand the consequences, and to predict how this pandemic affects differently with various socioeconomic groups is not easy and good data is the key to it. these socioeconomic factors include population density, urban and rural settings, education level, lifestyle, the size of household and homeowners & tenants. sometimes only a single block distance neighborhood household within the socioeconomic spectrum can make a huge difference in one's life (demonstrate form the us in club vita's us longevity map). therefore, sometimes it is very unfortunate that people who are feeling the effects of covid- very severely, are probably in your neighbors (messner, ) . majority of the countries are now trying different tactics to stop the spreading of the disease and trying to limit only a subset of the people would catch the disease. it has been indicated that groups with lower socioeconomic status could be more at danger from the spread of the covid- , based on the analysis of new york showing that poor neighborhoods have been affected highly. covid- spreads by droplets shed of the respiratory system by someone with the virus, which means it would spread with higher proximity of people, larger contact networks and lower levels of hygiene. there are some factors, which increase the risk of catching the virus. -population density: close contact among people is very high in urban areas rather than rural areas. -household size: a big household will have a higher chance to bring the virus home, while in household where one person lives alone; he/she will have to catch the virus outside the household. in sweden, social-distancing regulations are not taken very strictly due to the high proportion of single person household. whereas in italy based on the multi-generational homes apparently contributed to the multiplication of the coronavirus. -social distancing level: social distancing is very effective to stop the spread of the disease, but several reasons that various groups might show dissimilar levels of social distancing: -official advice might be dependable between regions, for instance, guidance in the us has varied even between neighboring towns. access to local guidance might be different between socioeconomic groups, for instance guidance might be provided online or in particular languages. -working from home might reduce social contact, but can only be available to some people focused in jobs linked to higher socioeconomic status. -stay at home regulations would be more than a challenge for those who live in smaller and crowded houses or without outside space. -some groups would be obedient to social distancing regulations not all. -not all who are infected by the covid- will react severely to it. there are some factors that contribute to the risk of covid- but they are probably felt differently by different socioeconomic groups (lipsitch et al., ) -people who have had medical problems of diabetes, chronic respiratory disease, cardiovascular disease, or even high blood pressure and cancer are at higher risk from coronavirus (giannis et al., ; fang et al., ; zheng et al., ) . -who has warned the smokers that they might be highly at risk because to the obvious effects of smoking on the lungs and smoking is common in lower socioeconomic groups. -different socioeconomic groups do not have access to the same level of healthcare services. this would particularly common in countries like us where the huge number of uninsured population is concentrated in certain industries not to universal health care system. therefore, some socioeconomic groups are more likely at risk compared to others. so, logically higher numbers of deaths can be expected from certain parts of society. this can be highly related for pension plans using analysis of this experience of the population to predict future mortality rates. the post pandemic population may look more different compared to the start point of this outbreak. the annual percentage change in gross domestic products is shown in table. . the short-term scenarios of the covid- environmental aspects raise many questions. china is struggling to rebound from the epidemic and has to limit the re-entry of covid- to its region by put a check on travelers coming from abroad (bogoch et al., ) . in a country with such a high population, where the majority of its population has not yet experienced covid- , and has no immunological contact with this virus, the possibility of second wave is a big risk. european and north american countries has not yet reached to the peak of the epidemiological curve. one crucial aspect seems obvious: the fast control of the outbreak done by china could not be implemented to democratic countries where rights of individuals are very high. therefore, outside china no leader has the capability to enforce these measures at the level of china (bai et al., ) . the question is: what will happen in countries of indian sub-continent, the middle-east and south america, where they live in crowded forms traditionally, big gatherings are common, and the public health systems are insufficient. the possibility of secondary peak appearance could not be estimated. in the mid-term, the scenario in the southern hemisphere should be considered. not almost all south american and african countries have access to national health systems and sufficient health care services. many of these nations decided to close the borders, however very late, when they already had patients of covid- inside. all these indications show that the southern hemisphere would not escape from this pandemic. the outbreak is widening in the southern hemisphere now, and this is happening while the higher income nations are struggling over their own problems in (i) applying control actions (ii) trying to recuperate from the massive social and economic impacts, and (iii) focusing in preventing re-entry of covid- by foreign travelers (chinazzi et al., ) . the long-term scenario of probable secondary waves of outbreak is concerning as well. a second wave might be devastating more than the first one, based on other pandemics in history. economists have shown serious concerns about the economic effects of control measures taken during this crisis (hemida and abduallah, ) . however, there are many models that show the economic impacts of the disease and majority of the economists are challenged by the social and economic depth of the pandemic. they are trying to understand the control as soon as possible. although the economic losses are obvious, but still economists are not able to grasped the extending nature of the outbreak that is causing far more economic damage compared to drastic measures taken to end the pandemic globally as soon as possible (meo et al., ; anderson et al., . the covid- pandemic will have severe impact on socioeconomic growth across the globe as shown in table. . general actions to decrease person to person transmission of coronavirus are needed to control the present outbreak. special restrictions strategies and efforts should be applied to protect the highly vulnerable populations such as children, health care workers, and older aged people . a guideline has been already published for the medical employees, health care providers, and public health individuals and researchers who are interested in working in the coronavirus (mossa-basha et al., ) . the major death cases of coronavirus outbreak are happening mainly in old people probably because of a poor immune system that allows rapid growth of viral infections. the public services must provide in decontaminating reagents for sanitizing hands multiple times on a daily basis (luan and ching, ) . physical contact with contaminated and wet things must be counted in dealing with the coronavirus, particularly agents which could be a possible rout of transmission. china and some other countries such as the us applied travel screening that could control and prevent the spread of the virus. epidemiological alterations in coronavirus infections must be observed. the probable routes of transmission and subclinical infections, adaptation, progression must be taken into consideration and spreading of virus among people and potential intermediate animals and reservoirs should perceived. moreover, still there are significant numbers of questions that need to ponder. these are, but not limited to, details about how many people have been tested, how many of them turned positive and whether this range stays constant or fluctuating. additionally, only fewer pediatric cases have been reported to date; that could be due to lack of testing and not due to true infection (rothan and byrareddy, ) . only in a period of few months, the world has changed. thousands of people have been deceased, and hundreds of thousands have been infected by covid- . and the rest of people who are not infected, their entire life has been changed by this virus. in italy, the most massive travel restrictions are being placed since second world war. in london, the normal busy bars, theatres, and other public places have been closed and people are asked to stay in their homes. the flights are being canceled in all over the world. majority of people are staying at home, practicing social distancing and working remotely (harapan et al., ) . it is all happening to control the spread of coronavirus, and to decrease the death rate. however, all these changes have led some unexpected consequences. as industries, transportation systems and all other bossiness have shut down; it has caused a sudden drop in carbon emission. compared to this time last year, levels of air pollution in new york have dropped at almost % due to measures that have been to restrict the spread of virus. in china, emissions data shows a % decrease at the starting point of the year as people were told to stay at home, factories closed and coal use feel by % at china's largest power plants since the last three months of . according to the ministry of ecology and environment, the amount of good quality air was around . % compared with the same time last year in more than cities all over china. in europe, nitrogen dioxide (no ) emission dropped over northern italy, spain and uk, as shown in satellite images (ficetola and rubolini, ) . this epidemic has also caused extensive job losses and threatened the sustenance of millions of people as businesses are struggling and are shut down to control the spread of virus. economic activities have been stopped and stock markets dropped along with the falling carbon another unexpected environmental impact of coronavirus has been observed in venice, italy. as the tourist's numbers culled due to the coronavirus, the waters in venice's canals are cleaner compared to the past. while motorboats, sediment churning and other water pollutants have been dropped efficiently, residents got amazed by seeing the clear water and the fish could be seen once again in the canals. one of the other effects of coronavirus on environment is the noticeable drop in coal consumption. this contributed in a large scale drop in air pollutants in china. the number of airborne pollutants like co , co and nitrous oxides has fallen too. as millions of people are holding on lockdown across the globe, energy consumption profiles in buildings are being disturbed. as many people working from home nowadays, domestic energy consumption is predicted to rise very quickly. the predictions data showed that this has risen around to % in the us. this pandemic would ultimately save energy and also might have an effect on reducing the consumption of polluting fuels in power stations as the demand has been dropped (lau et al., ) . the covid- pandemic has changed the air quality in many cities across the world as shown in the fig. . the covid- pandemic is spreading very quickly every day, and the number of people putting on lockdown is increasing, to date more than , people have died across the globe and there is a direct loss to the world economy. however, many think that there is a good side; that the spread of virus has been decreasing air and water pollution and probably even saved lives in this process. nevertheless, this epidemic which is taking people's lives certainly should not be seen as a way of bringing about positive environmental change. first of all, it is not certain for how long this dip in emission will be. when the epidemic finally subside, then carbon and other pollutant emissions get back then it would be as if this clear sky view never happened and the changes we see today will not have lasting impact. general actions to reduce person to person transmission of covid- are required to control the current outbreak. special attention and labors should be applied to save the highly vulnerable populations including children, health care workers, and old people. there is already published guideline available for the medial employees, health care providers, and public health individuals and researchers who are interested in working in the coronavirus. most of death cases of coronavirus outbreak are happening largely in old people possibly due to a weak immune system that permits rapid growth of viral infections. the public services must provide decontaminating reagents for sanitizing hands multiple times on a routine basis. physical contact with contaminated and wet things must be taken into count while dealing with coronavirus, particularly agents that could be a possible route of transmission. epidemiological alterations in coronavirus infections must be observed taking into consideration the probable routes of transmission and subclinical infections, furthermore to the adaptation, progression, and spreading of virus among people and potential intermediate animals and reservoirs. there are still some remaining doubts that have to be considered. the most important thing is about the details of how many people have been tested, how much of them turned positive and whether this range stays constant or variable. a less number of pediatric cases have been reported to date; that could be due to lack of testing and not due to true infection. how will country-based mitigation measures influence the course of the covid- epidemic? coronavirus disease (covid- ): implications for clinical dental care presumed asymptomatic carrier transmission of covid- pneumonia of unknown aetiology in wuhan, china: potential for international spread via commercial air travel remdesivir for severe acute respiratory syndrome coronavirus causing covid- : an evaluation of the evidence the effect of travel restrictions on the spread of the novel coronavirus (covid- ) outbreak are patients with hypertension and diabetes mellitus at increased risk for covid- infection? comparison of air quality in some of the biggest cities around the world before the covid- pandemic and while the lockdown climate affects global patterns of covid- early outbreak dynamics coagulation disorders in coronavirus infected patients: covid- , sars-cov- , mers-cov and lessons from the past coronavirus disease (covid- ): a literature review feasibility of controlling covid- outbreaks by isolation of cases and contacts the sars-cov- outbreak from a one health perspective coronavirus (covid- ) outbreak: what the department of radiology should know early dynamics of transmission and control of covid- : a mathematical modelling study the positive impact of lockdown in wuhan on containing the covid- outbreak in china coronavirus disease (covid- ): spectrum of ct findings and temporal progression of the disease defining the epidemiology of covid- -studies needed a reusable mask for coronavirus disease sars to novel coronavirus-old lessons and new lessons biological and epidemiological trends in the prevalence and mortality due to outbreaks of novel coronavirus covid- the institutional and cultural context of cross-national variation in covid- outbreaks policies and guidelines for covid- preparedness: experiences from the university of washington the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak trop med int health, . the covid- epidemic clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china pathological findings of covid- associated with acute respiratory distress syndrome covid- and the cardiovascular system a pneumonia outbreak associated with a new coronavirus of probable bat origin key: cord- -ea a xfl authors: dhama, kuldeep; patel, shailesh kumar; sharun, khan; pathak, mamta; tiwari, ruchi; yatoo, mohd iqbal; malik, yashpal singh; sah, ranjit; rabaan, ali a.; panwar, parmod kumar; singh, karam pal; michalak, izabela; chaicumpa, wanpen; martinez-pulgarin, dayron f.; bonilla-aldana, d. katterine; rodriguez-morales, alfonso j. title: sars-cov- jumping the species barrier: zoonotic lessons from sars, mers and recent advances to combat this pandemic virus date: - - journal: travel med infect dis doi: . /j.tmaid. . sha: doc_id: cord_uid: ea a xfl coronavirus disease (covid- ), caused by sars-cov- (severe acute respiratory syndrome - coronavirus- ) of the family coronaviridae, appeared in china in december . this disease was declared as posing public health international emergency by world health organization on january , , attained the status of a very high-risk category on february , and now having a pandemic status (march ). covid- has presently spread to more than countries/territories while killing nearly . million humans out of cumulative confirmed infected asymptomatic or symptomatic cases accounting to almost million as of july , , within a short period of just a few months. researchers worldwide are pacing with high efforts to counter the spread of this virus and to design effective vaccines and therapeutics/drugs. few of the studies have shown the potential of the animal-human interface and zoonotic links in the origin of sars-cov- . exploring the possible zoonosis and revealing the factors responsible for its initial transmission from animals to humans will pave ways to design and implement effective preventive and control strategies to counter the covid- . the present review presents a comprehensive overview of covid- and sars-cov- , with emphasis on the role of animals and their jumping the cross-species barriers, experiences learned from sars- and mers-covs, zoonotic links, and spillover events, transmission to humans and rapid spread, and highlights the new advances in diagnosis, vaccine and therapies, preventive and control measures, one health concept along with recent research developments to counter this pandemic disease. in the st century, we have faced a few deadly disease outbreaks caused by pathogenic viruses such as bird flu caused by avian influenza virus h n , swine flu caused by reassorted influenza virus h n pandemic (h n pdm ), severe acute respiratory syndrome (sars) caused by sars-cov (coronavirus), the middle east respiratory syndrome (mers) caused by mers-cov [ ] [ ] [ ] , ebola [ ] , zika [ , ] , nipah virus infections, and the most recent threat [ ] , coronavirus disease (covid- ) that has been posed by severe acute respiratory syndrome coronavirus (sars-cov- ) of the family coronaviridae, genus betacoronavirus [ ] [ ] [ ] [ ] [ ] [ ] [ ] . the sars-cov- virus emerged from the city of wuhan, hubei province, china, during december , was declared as public health international emergency by the world health organization (who) on january , . consequently, it was categorized in a high-risk category on february , , and gained the pandemic status on march , . the disease emerged from wuhan, china, as its epicentre, which moved later to italy, then the usa, and brazil. subsequently, within a short time interval of six months, it has affected nearly countries/territories and claimed near to . million human deaths out of cumulative confirmed infected asymptomatic or symptomatic cases accounting to almost million. sars-cov- has very adversely affected the usa, brazil, india, russia, south africa, peru, mexico, chile, spain, the united kingdom (uk), iran, pakistan, saudi arabia, italy and other countries. the disease incidences are lower in children than adults but exhibit all symptoms of a disease like adults [ ] . the lessons learned from earlier threats of sars, mers and the present covid- pandemic situations warrants designing and implementing some modified plans and strategies to combat emerging and zoonotic pathogens that could pose pandemic threats/risks while taking away many human lives [ , [ ] [ ] [ ] [ ] [ ] [ ] [ ] . researchers and health agencies across the world are putting high efforts to contain/restrain the spread of this deadly disease. they are pacing to develop potential vaccines and therapeutics/drugs [ , ] . evidence from the initial outbreak indicates earlier cases had links to huanan wholesale seafood market in china [ ] and further isolation of sars-cov- from different samples of the area (people, animals, birds, discharges, soil, structures) suggests the involvement of intermediate hosts [ ] . recently, a literature of review has pointed out the possible potential role of the animal-human interface, zoonotic links and spillover events towards the origin of sars-cov- / covid- [ , , [ ] [ ] [ ] [ ] [ ] . in the past couple of decade's animal origin viral diseases, especially bats-linked, have increased many folds in humans with noted cross-species transmissions. although many of the illnesses are linked with bats still information on their ecological behaviour, molecular aspects are limited, which could lead to more viral outbreaks shortly [ ] . the ongoing covid- pandemic has emphasized the importance of understanding the evolution of natural hosts in response to viral pathogens. in a recent study on ace receptors, the gene was found under intense selection pressure in bats and positive selection in other selected mammalian hosts [ ] . the sars-cov- is also thought to have originated from bats, just like sars-cov and mers-cov. civets and dromedary camels are considered as the intermediate host of sars-and mers-cov, respectively, from where they were transmitted to humans [ ] . the understanding of genomic signatures of sars-cov- with other covs is must for strategic planning through identifying natural or intermediate hosts. using genomic and protein data in a natural vector method (alignment-free approach), phylogenetic analysis revealed the possible transmission path originates from bats to pangolins to humans [ ] . however, the likely source of virus origin and the intermediate host of sars-cov- are yet to be identified. initially, when the novel virus emerged in china, a hypothesis was put forward, claiming the recent recombination event as the cause of the sars-cov- emergence . nevertheless, the phylogenetic and recombination analysis performed within the subgenus of sarbecovirus demonstrated that the novel virus shows discordant clustering with bat-sars-like coronavirus (ratg ) sequences thus rejecting the possibility of a recent recombination event [ ] . previously, it was found that the continuous passaging of mers-cov in non-susceptible cells that express viral receptors led to the accumulation of mutations in the spike protein gene. this paid attention to the potential of coronaviruses like mers-cov to undergo mutations that enhance viral entry into novel animal species, thus resulting in cross-species transmission [ ] . the covid- outbreak is still associated with several unanswered questions like the possibility of shedding of the virus before the onset of clinical signs, whether the transmission is limited to only through respiratory droplets, the possibility of an intermediate host that is responsible for zoonotic spillover, and the possible transmission characteristics [ , ] . hitherto studies report that the spillover risk remains high from zoonotic viruses and on the same lines a study from north america proposed a hypothesized conceptual model demonstrating sars-cov- spillover from humans to naive wildlife host species through the gastrointestinal route where stool from covid- infected patient contaminates water bodies and reaches to wildlife hosts [ ] . besides, the pandemic imposed a massive blow on the chinese economy, which is not going to heal soon [ ] . instead of the current situation, singapore's prime minister lee hsien loong rightly said that the virus might have started in china. however, it does not respect nationality or race. it does not check your passport before it goes into your body, and anybody can be infected. hence, all suspected people need to be tested and quarantined [ ] . further research exploring the sars-cov- associated zoonosis and mechanisms accounting for its initial transmission from animals to humans, will lead to sort out the spread of this virus as well as design and develop appropriate prevention and control strategies to counter covid- . the present comprehensive manuscript presents an overview on covid- , an emerging sars-cov- infectious disease while focusing mainly on the events and circumstantial evidences with regards to this virus jumping the species barriers, sharing a few lessons learned from sars-and mers-covs, zoonotic spillover events (zoonosis), acquiring transmission ability to infect humans, and adopting appropriate preventive and control measures [ ] . it also highlights the recent advances in sars-cov- diagnosis (see supplement material s ), vaccine, drugs and therapies (see supplement material s ), which could aid to counter and restrain this emerging virus at the face of pandemic situations, as well as prevention and control (see supplement material s ). sars-cov- is an enveloped virus measuring approximately - nm in diameter with a single strand positive-sense rna genome ranging from to kilobases in length [ , ] . it has club-shaped glycoprotein spikes in the envelope, giving it a crown-like or coronal appearance [ ] . the genome sars-cov- is comprised of ′ untranslated region ( ′ utr) that includes ′ leader sequence, open reading frame (orf) a/b (replicase genes), spike (s) protein, envelop (e) protein, membrane/matrix (m) protein, and accessory proteins (orf , , a, b, and b), nucleoprotein (n), and ′ untranslated region ( ′ utr) in their sequence [ ] . it has a % genetic identity to mers-cov and % to sars-cov [ , ] . the receptor-binding domain (rbd) of virus spikes helps in binding to cellular receptor angiotensin-converting enzyme (ace- ) [ , ] . orf and rbd of sars-cov- may have a role in elucidating cellular interactions and cross-species transmission mechanisms [ ] . receptor binding motifs (rbm) have a role in interaction with human receptors, human to human transmission, and cross-species transmission as gln provides favourable interaction, and asn shows compatibility with human ace- [ ] . besides, sars-cov- has superior transmission competence in comparison to the sars-cov, leading to a continuously increasing number of confirmed cases [ ] . sars-cov- has the potential to survive in the environment for several days [ ] . though believed to be sensitive to environmental factors and alcohol-based sanitizers, bleach, and chloroform, the sars-cov- can survive in wet surroundings for days and in closed air conditions up to hours [ , ] . survival of sars-cov- varies with the nature of the surface (glass, fabric, metal, plastic, or paper), environment, and virus load. it can survive on surfaces for hours to several days. it can survive in aerosols for up to hours and on plastic for up to hours [ , ] . the initial clinical picture of the covid- was pneumonia of unknown origin as the first clinical cases were presented with signs of pneumonia [ ] . later it was diagnosed as sars-cov- infection that was associated with severe pneumonia. hence, initially named as novel coronavirus pneumonia (ncp) [ ] . as the outbreak proceeded, a series of cases were produced, developing a wide range of clinical signs with few remaining asymptomatic being in the early incubation stage of the disease. thus covid- is characterized by three major patterns of the clinical course of infection, including mild illness producing upper respiratory signs, non-life-threatening pneumonia, and severe pneumonia with acute respiratory distress syndrome (ards) [ , ] . initially, mild signs appear for - days, followed by rapid deterioration and ards. it can be mild to moderate in % of affected cases, including pneumonia and non-pneumonia cases. in comparison, . % are severe cases, including dyspnea, respiratory distress, hemoptysis, gastrointestinal infection, liver, central nervous system, and lung damage cases [ , ] . critical cases account for . % and include respiratory failure, septic shock, and multiple organ failure/dysfunction cases. few cases remain asymptomatic and include cases that can become any of the above during infection [ ] . thus, the symptoms can be nonspecific and can range from no symptoms (asymptomatic) to severe pneumonia [ ] . in this context, a study concluded that the covid- is probably overestimated, as around . million people succumb to respiratory diseases every year in comparison to approximately , deaths due to the sars-cov- infection [ ] . the typical clinical signs of covid- are fever, chills, cough, fatigue, and chest distress [ , ] . fever and cough are considered as the most common symptoms in covid- patients [ ] , followed by headache, dyspnea, sore throat, hemoptysis, myalgia, diarrhoea, nausea, and vomiting are also observed [ , ] . some patients have shown rhinorrhea, chest pain [ ] , nasal congestion [ ] , anorexia, pharyngalgia, and abdominal pain [ ] . furthermore, neurological symptoms like anosmia and ageusia are also reported as significant clinical symptoms of covid- [ ] . the characteristic of covid- is attacking the lower respiratory tract and producing signs of upper respiratory distress, including rhinorrhea, sneezing, and sore throat [ ] . the clinical presentation of individuals infected with sars-cov- revealed upper respiratory tract infection, viremia, viral shedding from the nasopharynx, and stool along with the development of nausea, vomiting or diarrhoea after antiviral treatment [ ] . on diagnostic imaging using computed tomography (ct scan) and radiography (x-ray) bilateral pneumonia, ground-glass opacity, multiple mottling, pneumothorax, infiltration, consolidation or bronchoinflation sign has been noted in many cases of covid- [ , , ] . previously, sars-cov was found to infect the brainstem heavily [ ] . even though fever is considered as the most common symptom associated with covid- infection, a large proportion of the patients do not express fever during the initial hospital admission [ ] . the different transmission routes of sars-cov- infections have not yet been entirely ascertained, and are still under investigation. both direct and indirect pathways of transmission are being explored [ ] . similar to sars and mers, sars-cov- is predominantly spread via the respiratory route [ ] . person to person transmission is the main reason for community and global spread. the initial estimated reproduction number (rovalue) of covid- was assessed to be from . to . in december , which later has been increased to a mean value of . (range . - . ) [ ] . human-to-human transmission is by face-to-face contact with a sneeze or cough, or from contact with secretions of infected people [ , ] . nevertheless, the infectivity of other secretions and excretions are not fully understood and may require further study [ ] . aerosol and plastic surfaces can sustain virus for hours to days [ ] . travelling of infected people is considered as the main reason for the global spread of covid- [ , ] . although the asymptomatic and mild cases are the major hurdle in the evaluation of the real number of infected people, the genuine data on travellers returning from affected countries or areas may prove crucial in estimating the disease incidence [ ] . the possible occurrence of super-spreading events is very high at large gatherings, and suspension of gathering during a pandemic may prove crucial in reducing the overall transmission [ ] . close contact with any person within feet of the covid- patient or anyone having direct contact with secretions of covid- patients [ ] may set up the infection. unlike sars-cov, most transmissions in covid- are during the prodromal period when the infected individuals produce large quantities of virus in the upper respiratory tract, move/travel, and usually work thus spreading virus before illness develops [ ] . the rapid spread of covid- among the susceptible population can be due to the wide variation in illness degrees that results in a missed diagnosis. heavy viral load in asymptomatic cases and nosocomial transmission is spreading covid- unknowingly [ ] . recently, high viral load was detected in the sputum of convalescent patients, pointing out the possibility of prolonged shedding of sars-cov- even after recovery. this finding, along with the fact that asymptomatic persons can also act as the potential source of infection, may warrant a reassessment in the transmission dynamics of the covid- outbreak [ ] . the presence of viral nucleic acids in faeces is an important finding, thereby increasing the possibility of faecal-oral transmission. however, symptoms may or may not be manifested [ ] . this was found to be the unique feature of covid- and was lacking in the previous sars and mers outbreaks. in a study conducted by the chinese cdc, it was found that the majority of patients ( . %) infected with covid- infection were either asymptomatic or had mild pneumonia [ , ] . furthermore, all forms of sexual contacts have been reported to pose a significantly high risk of disease transmission through respiratory aerosols and fomites. however, to date, no evidence of sexual transmission is available, and further investigation is required in this direction [ ] . disease severity is higher in older individuals, especially males with immunocompromised conditions and comorbidities like diabetes, asthma, or cardiovascular diseases [ , ] . these are considered to be vulnerable to the sars-cov- infection. predisposition increases under risk environments where transmission of the virus from affected persons or contaminated fomites to unaffected ones becomes feasible. it was earlier noted that covs are not common to affect immunocompromised patients like other some viral infections (influenza, rhinovirus, adenoviruses, to name a few). the current pandemic has shown sars-cov- to affect more lethally than young patients, mainly destroying the lung tissues [ ] . till now, evidence regarding the higher susceptibility of pregnant women in comparison to non-pregnant women lacks in covid- . also, there is no evidence of vertical transmission (mother to fetus/baby transmission) of covid- infection [ ] . a case study reporting the birth of a healthy infant by a sars-cov- infected woman suggests that mother-to-child transmission is unlikely in the case of covid- . the study also pointed out that on the delivery day, all the samples tested negative except for sputum, which proved positive [ ] . however, as per one most recent report, neonates have been found positive for sars-cov- , indicating the possibility of vertical transmission from infected mothers to their progeny, thus rendering newborns into a high-risk group owing to their immature immune system [ ] . individuals harbouring sars-cov- may remain asymptomatic for the incubation period [ ] . different from sars-cov and mers-cov infection, the median incubation period of covid- was found to be four days [ ] . the median period from the development of signs to death was days [ ] . the case fatality rate (cfr) of covid- was found to be lower than mers and sars [ ] . however, current disease dynamics with the involvement of many more countries or areas may change the future mortality rate. the recent analysis suggests that the total fatality rate of covid- is calculated at . % [ ] . however, italy experienced the worst cfr of more than % with older people and males suffering from multiple comorbidities as primary victims [ ] . sars-cov- has shown characteristics of efficient replication in the upper respiratory tract, causing the less abrupt onset of clinical signs just like the common cold and unlike sars-cov [ ] . it can also replicate in the lower respiratory tract as has been noted in cases without pneumonia but having lesions in the lungs on radiological examination [ ] . the pathogenesis mechanisms of covid- are yet to be fully elucidated. however, both cellular and humoral immune responses against sars-cov- or its antigenic structures like spike protein (s) are believed to be of importance [ , ] with disturbed levels of inflammatory mediators playing a mediating role [ ] . following receptor binding with angiotensin-converting enzyme (ace ) through receptor binding motif (rbm) of the receptor-binding domain (rbd) of s subunit of the sars-cov- spike glycoprotein (s), virus gains entry in host cells [ , , ] . s subunit helps in the fusion of viral and hosts cell membranes [ , ] . sars-cov- produces cytopathic effects in respiratory and gastrointestinal surface epithelial cells [ ] . these include multinucleated syncytial cells, abnormally enlarged pulmonary cells, infiltration with mononuclear cells, lymphocytes infiltration in pulmonary organs, fibrinous exudation, and hyaline deposition [ ] . cytokine storm is believed to be involved in this inflammatory pathophysiology of the covid- patients producing lung lesions and systemic symptoms [ ] . elevated levels of tnf-α, il b, ifnγ, ip , gcsf, mip a, and mcp , may have stimulated t-helper- (th ) cells leading to this inflammatory cascade [ ] . however, levels of anti-inflammatory mediators (il , il ) were also increased, indicating t-helper- (th ) stimulation, which suppresses inflammation, unlike what happens in sars [ ] . a study documented that the nucleic acid of sars-cov- detected in the faecal samples was as accurate as of that of pharyngeal samples obtained from infected patients. moreover, the patients tested positive for sars-cov- in stool showed no gastrointestinal symptoms and had no relation to the severity of lung infections [ ] . one of the significant clinical signs of covid- patients during the initial presentations was gastrointestinal symptoms. hence, the involvement of git in pathogenesis needs to be explored. the significant laboratory findings include lymphopenia, increased values of erythrocyte sedimentation rate, c-reactive protein, lactate dehydrogenase, and decreased oxygenation index [ ] . an increase in proinflammatory cytokine and a decrease in antiinflammatory cytokines have also been noted [ ] . viral isolation has been achieved from bronchoalveolar lavage of affected persons; however, in the case of pregnant women, serum, faeces, urine, breast milk, umbilical cord blood, placenta, and amniotic fluid were found to be negative for sars-cov- [ ] . at the same time, the sputum was tested positive [ ] . the presence of abnormal coagulation parameters in patients with severe novel coronavirus pneumonia was associated with poor prognosis. the non-survivor patients had higher levels of d-dimer, and fibrin degradation product (fdp) along with longer activated partial thromboplastin time and prothrombin time compared to survivors at the time of admission [ ] . though clinical manifestations, pathological changes, and diagnostic laboratory findings can unravel the disease nature helping in devising therapeutic modalities, however, for epidemiological aspects and future prevention and control, simultaneous tracing of the origin and explaining the spillover events can prove beneficial. the sars-cov- has first been reported from the pneumonia patients of the wuhan city in hubei province of china. these patients were involved in trading at a wet animal market in the huanan area. it is believed that sars-cov- is introduced from the animal kingdom to human populations during november or december , as revealed from the phylogeny of the genomic sequences from the initially reported cases [ ] . the spillover of sars-cov- from animals to humans took place at the beginning of december [ ] , and the clinical cases appeared around ending december [ , ] . genetic analysis showed that this novel virus is closely related to bat covs and is similar but distinct from the sars virus [ ] . several evidences based on genome sequences, the homology of the ace receptor, and the presence of single intact orf on gene indicate bats as a natural reservoir of these viruses. however, an unknown animal is yet to be unravelled as an intermediate host [ , , , , ] . initial investigations on animal source origin of sars-cov- have inconclusively revealed snakes [ ] , pangolins, and turtles [ ] . the rapid spread of covid- followed the initial animal to human spillover through human-to-human transmission. genetic epidemiology had revealed that the spread from the beginning of december when the first cases were retrospectively traced in wuhan was mainly by a human-to-human transmission and not due to continued spillover [ ] . these species cross jumping, spillover, and rapid transmission events are linked to viral characteristics, host diversity, and environmental feasibility. coronaviruses being rna viruses have high mutation rates that, besides creating new strains, enable them to adapt to a wide range of hosts. hence, based on genome sequences, all known human covs have emerged from animal sources [ ] . this seventh member of the human cov has also been isolated initially from the pneumonia patients who were having direct or indirect links to the huanan seafood market in wuhan china, wherein other animals were also being sold [ ] . these include a -year-old lady retailer in this wet animal market, a -year-old frequent visitor to this market, and a -year-old man [ , ] . further, isolation of the sars-cov- from the environmental samples around this market, including people, animals, soil, discharges, or structures, strengthens the claims of involvement of hosts either as a reservoir or intermediate [ , , ] . recently, a pomeranian dog as a probable intermediate host was identified; however, such reports are yet to be validated, and research is underway to explore the emergence of this infectious disease at the animal-human interface [ , ] . multiple substitutions were observed in ace receptors of a dog [ ] . in this context, the pomeranian dog of the infected owner found positive for covid- suggest the permissiveness of the species for sars-cov- as a result of species jumping [ , ] . among the fifteen dogs tested from different households with confirmed human covid- cases in hong kong sar, two dogs were found to be infected with sars-cov- . the diagnosis was made using quantitative rt-pcr, serology, and viral genome sequencing. virus isolation was also done from the samples obtained from one dog. the genetic sequences of viruses obtained from the two dogs were identical to the ones that were detected from their human cases indicating human-to-dog transmission [ ] . moreover, a study reported that the sars-cov- might infect the cats and further transmitted by the infected cat to other cats [ ] . one cat was tested positive for sars-cov- in france that showed mild respiratory and digestive signs. the cat was tested positive by rt-qpcr on the rectal swab, and serological analysis identified the presence of antibodies against sars-cov- . genome analysis further confirmed that the sars-cov- isolated from the cat belongs to the phylogenetic clade a a seen in french human indicating humanto-animal transmission [ ] . this is not the first time that a domestic cat has been found susceptible to zoonotic coronavirus. during the sars-cov outbreak, domestic cats were tested positive for sars-cov that were living near sars infected humans [ , ] . even though experimental evidence indicates the possibility of sars-cov- transmission from infected to a susceptible cat close, sars-cov- transmission between cats or cat-tohumans are not reported under natural conditions [ ] . furthermore, along with dogs and cats, the zoo animals like tigers and lions were also reported to get the sars-cov- infection and exhibit clinical signs such as vomiting, diarrhoea, dry cough, breathing difficulty and wheezing [ , ] . spillover of sars-cov- was also reported in mink farms of netherlands, further increasing the concern of transmission to humans. outbreaks of sars-cov- were reported in two mink farms holding , and animals. the virus is suspected to be introduced by a farmworker having covid- [ , ] . host-pathogen interactions and pathogenesis determine the severity and expression of disease [ , [ ] [ ] [ ] . adaptation over time reduces the severity of infection as happened with hcovs; however, the emergence of novel viruses or strains due to genetic alterations or recombinations can enhance hardness producing novel diseases like covid- [ , ] . evolutionarily, the balance of viral-human interaction and immune response against virus enables adaptation, thereby persistence in a host without severe or symptomatic disease when the aggravated pathogenesis results in mortality. hence, loss of sustainable hosts and transmission to novel hosts becomes inevitable for future sustainability [ , ] . a pathogen cannot kill all its hosts, and for future sustainability, it adapts to some suitable host or spills over to a new host. sars-cov- has been implicated to be originated from animals, and associated with animal linkages, spillover events, cross-species barrier jumping and zoonosis [ , , , [ ] [ ] [ ] ] . since the beginning of till the end of , three coronaviruses viz. sars-cov, mers-cov, and sars-cov- have caused havoc in the human population globally and will continue to do so. earlier identified betacoronaviruses (sars-cov and mers-cov) were reported in guangdong province of china in november and saudi arabia in , respectively [ ] . sars-cov- is the third zoonotic betacoronaviruses recognized in this century. however, the cfr of the sars-cov- is lower to date when compared with sars and mers. it should not be overlooked as many asymptomatic cases may remain undiagnosed due to the unavailability of diagnostic kits in china. with nearly . million deaths till the preparation of the manuscript, sars-cov- is proven to be deadliest as far as the number of deaths is concerned in comparison with sars-cov and mers-cov with and associated deaths, respectively [ , ] . earlier, covid- was linked with the exposure to the huanan seafood market. however, individuals with no history of exposure above were also diagnosed with the illness, further supporting the human to human spread through droplets produced by cough and sneeze [ ] . the spread of covid- that occurred with a high pace and lack of transparency in reporting the disease by the chinese health ministry and failure in the timely implementation of preventive measures has been considered as the primary contributor as stated earlier in sars [ , ] . both sars-cov and sars-cov- showed prominent similarities in their pathogenesis and epidemics. in both cases, bats were considered as the natural host, and the cold temperature and low humidity in cold, dry winter provided conducive environmental conditions that promoted the survival of the virus in the environment [ ] . further, moriyama et al. [ ] assessed the significance of the environmental factor on host immune system targeting innate and adaptive both responses in the respiratory tract. zoonotic spillover is the transmission of pathogens to humans from vertebrate animals [ ] . at present, these spillovers are of significant concern as in the past, many spillovers in the form of nipah, hendra, ebola, sars, mers, and ongoing covid- involving many animal species like pigs, horses, monkeys, camels, civets, among others, were documented. bovine covs have been reported to infect children and thus possess zoonotic potential [ , , , ] . spillover is governed by the interaction of viral-specific proteins like s protein and host ace receptor [ , , , ] . these s proteins have rbd in covs, which contain receptor binding motifs (rbm) that help in specific binding to host ace receptors [ , ] . mutations in amino acid sequences of rbds results in a change in specificity of a receptor, interaction and binding, hence alteration in transmissibility, pathogenicity and cross-species jumping with a predisposition to novel and more severe diseases [ , ] . in the case of sars-cov- , rbd of s protein has - times affinity ace r [ , ] . it has furin recognition sequence "rrar" at the s -s cleaving site that represents a functional site for the cellular serine protease tmprss thus increasing the efficiency of transmission and contagiousness [ , , ] . in addition to enhanced binding affinity, electrostatic complementarity and hydrophobic interactions are critical to enhancing receptor binding and escaping antibody recognition by the rbd of sars-cov- , thereby further increasing transmission capability and contagiousness [ ] . a detailed investigation regarding the emergence of new coronavirus, host range, and transmissibility is crucial to understand such pandemics shortly. the literature revealed that before the appearance of sars-cov and mers-cov, human coronavirus (hcov) strains like hcov-nl , hcov- e, hcov-oc , and hcov-hku were the covs strains producing mild infections in humans. however, their natural ancestral hosts were of animal origin, like bats for hcov-nl , and hcov- e and rodents were natural hosts for hcov-oc and hku . these four hcovs were initially of low pathogenicity. to enhance the pathogenicity, they used intermediate hosts such as cattle for hcov-oc (natural host was rodent), and alpacas for hcov- e (bats were natural host) and this way acquired the ability to infect human beings with serious health hazards [ ] . added to the involvement of bats and pangolins, the recent reports revealing sars-cov- infection in cats, dogs, tigers, lions and minks have raised concerns over this virus affecting multiple animal species, and also points out towards the incidences of reverse zoonosis [ , , , , , ] . the ferrets, cats, and primates are suggested to be good candidates for susceptibility to sars-cov- [ , ] . covid- research and surveillance in companion and pet animals, livestock animals, zoo animal species, wildlife animal species as well as their handlers, veterinarians, and owners need to be enhanced during the pandemic, which would help to follow better integrated one health strategies [ ] and appropriate preventive and mitigation to counter sars-cov- effectively [ , , [ ] [ ] [ ] [ ] [ ] . significance of covid- monitoring and implementation of suitable public health measures among workers involved in meat and poultry processing facilities/industries has been emphasized, which would protect them as well as aid in preserving the critical meat and poultry production infrastructure and the meat products [ ] . the involvement of intermediate hosts in maintaining and transmitting the virus to susceptible host predisposes humans to novel covs leading to the emergence of new diseases in humans. the currently ongoing sars-cov- / covid- pandemic has put on hold the entire world [ , ] . the covs have frequently been associated with animal and human diseases and have a zoonotic interface [ , ] . usually, one or more types of animal hosts are involved in the transmission cycle of covs to humans [ , ] . that can be natural host, reservoir host, intermediate host or definitive host [ ] . bats have been the natural hosts for human covs of alphacoronavirus (hcov-nl , hcov- e) and betacoronavirus (sars-cov, mers-cov, sars-cov- ) genera whereas for betacoronavirus members hcov-oc and hcov-hku , rodents are the natural hosts. genome sequence analysis has revealed bats as a natural host for sars-cov- [ , ] . in natural or reservoir hosts, covs adapts well, however, being unstable rna viruses, they keep multiplying continuously without producing disease thereby enabling persistence or survivability and accumulation of mutations over the time resulting in the emergence of newer and novel strains of viruses [ , , ] . these unique strains or viruses occasionally spill over to other species including animals or humans, adapting to their body systems and hence broaden the biological host range for evolutionary sustainability; however, results in epidemiological widening of disease sphere as well [ , ] . this transmission and adaptation scenario initiates a host-pathogen response resulting in the novel usually severe diseases that can at times be fatal in initial stages or over extended periods until virus pathogen adapts to host or the host develops sufficient immune defence [ , ] . it has been reported that almost all hcovs have originated from animals like bats (sars-cov, mers-cov, hcov-nl , and hcov- e) and rodents (hcov-oc and hku ) [ , ] . additionally, covs have been reported to infect several species of domestic and wild animals either clinically or subclinically [ , , , ] . cattle, horses, camels, swine, dogs, cats, birds, rabbits, rodents, ferrets, mink, bats, snakes, frogs, marmots, hedgehogs, malayan pangolin along with other wild animals may serve as a reservoir host of coronavirus [ , , , , [ ] [ ] [ ] [ ] [ ] [ ] . in the context of sars-cov- , snakes, pangolins and bats have been suspected as intermediate hosts since the first cases of covid- had links to huanan sea food market where different animals, birds, and wild animals were being sold along with seafood items [ , , , , , ] . coronaviruses have been reported to cause salivary, enteric and respiratory infections in laboratory animals (mice, rat, guinea pig, and rabbit) and urinary tract infection, respiratory illness and reproductive disorder in poultry [ , ] . in bovine, canine, feline and swine covs infections have resulted in diarrhoea, enteritis, respiratory illness, gastro-intestinal affections and nervous symptoms [ , , [ ] [ ] [ ] . coronavirus, namely-sw , has been reported in captive beluga whale using a panviral microarray method [ ] . among all the assumptions on animal hosts as the intermediate host, genomic and evolutionary information from pangolins reveals the highest closeness to the sars-cov- than any other host covs isolates [ ] . the spike protein, the main target of many studies searching for a cure of covid- , has been found highly similar to sars-cov- and, thus, could serve as a surrogate system for further evaluations [ ] . bats are the natural reservoir host of many covs. as reported earlier, out of alphacoronaviruses and out of betacoronaviruses as per the international committee on taxonomy of viruses (ictv) classification were solely originated from bats [ , ] . according to the literature, bats have been regarded as a potential wildlife reservoir whereas civets and dromedary camels as intermediate hosts of sars-cov and mers-cov, respectively [ , ] . the bat coronavirus, batcov ratg , has shown higher relatedness to sars-cov- at the whole genome level and spike gene in particular [ ] . coexistence and frequent recombination between highly diversified and prevalent bat sars-related coronaviruses (sarsr-cov) and coronaviruses may suggest the probable emergence of novel viruses shortly [ , ] . benvenuto et al. [ ] analyzed the whole genome sequences of different covs using fast unconstrained bayesian approximation (fubar) to understand the evolutionary and molecular epidemiology of sars-cov- . the authors concluded that sars-cov- clustered with sequences of bat sars-like covs with a few mutations in nucleocapsid and spike glycoprotein, suggesting its probable transmission from the bats [ ] . bats, especially horseshoe bats (rhinolophus spp.), are considered to be the known reservoirs of sars-related covs. since the bat origin, covs have always caused outbreaks in humans, studying the diversity and distribution of coronavirus populations in the bats will help to mitigate future outbreaks in humans and animals [ ] . interestingly, bats play a crucial role in all the spillovers mentioned above, indicating their importance in the emergence of new viruses. the reason behind the emergence and broad host range of covs in the past and present might be due to unstable rna-dependent rna polymerase (rdrp), lack of proof-reading ability, high frequency of mutations in the receptor-binding domain of spike gene and genetic recombination [ , , ] . bat covs have high diversity and great potential of spillover in different animal species, as reported earlier in civet cat and dromedary camel, leading to well-known pandemics sars and mers, respectively along with the recent spillover in pigs resulted in swine acute diarrhoea syndrome (sads). however, spillover resulted in the emergence of sads-cov, which showed a % genomic identity with bat coronavirus, which led to severe mortality with , deaths in neonatal piglets [ ] . fortunately, it did not excel in the form of the third pandemic, and no human cases were reported till date. the spillover responsible for ongoing covid- is still under investigation and a matter of great concern for the researchers all around the globe. based on resampling similarity codon usage (rscu), snakes (bungarus multicinctus and naja atra) were suggested as wildlife reservoirs of sars-cov- and reported to be associated with the cross-species transmission [ ] and later it was disapproved by other researchers [ , ] . unfortunately, to date, the intermediate host of the sars-cov- is abstruse what results in its escalation in the human population around the globe. in this context, analyzing the interaction between the asn site in rbd of spike glycoprotein of sars-cov- and the residue at sites of ace receptor of different hosts (pangolins, turtle, mouse, dog, cat, hamster and bat) revealed that tyrosine has higher receptor binding affinity than histidine suggesting pangolins and turtle be closer than bats to humans and maybe the probable intermediate hosts of sars-cov- [ ] . however, this hypothesis was also contradicted by li et al. [ ] based on an insertion of the unique peptide (prra) in the sars-cov- virus, which was lacking in covs from pangolins. moreover, sars-cov- showed higher similarity to the betacov/bat/yunnan/ratg / compared to the ones that were isolated from the pangolins, thereby denied the direct link of the virus from pangolins. however, further studies are required to confirm the role of pangolins in sars-cov- spread to humans. the receptor-binding domain of the spike protein of sars-cov interacts with the host receptor ace facilitating its potential of cross-species, as well as human-to-human transmission [ ] . similarly, the spike protein of sars-cov- was reported to recognize ace receptors expressed in fish, amphibians, reptiles, birds, and mammals and has a more robust binding capacity (affinity) in comparison to sars-cov [ ] . this suggests their involvement as probable natural and intermediate hosts [ ] , which may further help in the selection of animal models for epidemic investigation and preventing its spread [ ] . bat origin covs have been found to cross the species barrier that favoured their transmission via recombination/mutations in the rbd. the evidence of a virus outbreak that occurred in chinese pig farms suggests its possible cross-species [ , ] . also, murine cells were found permissive for sars-cov after substitution of his with lys in the ace receptor of a mouse, which suggests the role of residue changes in the cross-species and human-to-human transmission [ ] . mutation in residues at position and of receptor binding motif (rbm) of sars-cov was reported to play a role in civet-to-human and human-to-human transmission, respectively [ , ] . the covs are more prone to recombination and mutations leading to variable host range, and resemblance of receptors in various hosts results in cross-species jumping [ , , ] . genetic divergence due to these genetic alterations results in the evolution of newer viral strains having altered virulence, tissue tropism, and host range [ , ] . moreover, the presence of threonine at position was reported to enhance the binding affinity of rbm for the ace receptor of civet and humans [ ] . however, many sarsrelated coronaviruses (sarsr-cov) have been reported in bats and used ace receptors for entry into a host cell, which showed its potential to infect humans directly without any intermediate host [ ] . in addition to this, no direct transmission of sarsr-cov is reported from bats to humans to date. however, seropositivity on a serological investigation of individuals without prior exposure to sars-cov residing near bat caves in china revealed likely infection of humans by bat sarsr-cov and related viruses [ ] . besides, the interspecies transmission potential of sarsr-covs is due to the orf gene [ ] . as per reports, the sars-cov emerged via recombination of bat sarsr-covs, was transmitted to farmed civets along with other mammals, and these infected civets spread the virus to market civets. the virus was reported to undergo mutations in infected market civets before its spillover to humans. similarly, the mers-cov circulated for years in camels before the pandemic [ , ] supporting the hypothesis that after species jumping the exogenous viruses opted for adaptation to the environment and host before spillover to humans [ ] . moreover, the possible spillover of other circulating bat sarsr-covs to humans from mammalian hosts soon is highly anticipated. the cross-species jumping and adaptation are determined by the presence of specific receptors on host tissues (like ace receptor for hcov-nl , sars-cov and sars-cov- , dipeptidyl peptidase- for mers-cov, human aminopeptidase n for hcov- e, -oacetylsialic acids for hcov-oc , hcov-hku ) which help in binding and entry of the virus into host cells [ , ] . these receptors are present in various body systems in animals and humans, including respiratory and gastrointestinal systems [ ] . reservoir host animals including bats and rodents possess these receptors which are similar to those present in camels, masked palm civets (paguma larvata), or bovines, that act as an intermediate host for different covs [ , , ] . presence of some of these receptors in humans like ace or dpp makes them vulnerable to cov infection like sars-cov and mers-cov causing sars and mers infections, respectively [ , ] . the mers-cov spike was found to possess the capacity for adapting to species variation in the host receptor dpp [ ] . the mechanism expressed by mers-cov in adapting to infect cells of new species might be present in the other coronaviruses. ace has also been found as a binding receptor for sars-cov- [ ] . the species-specific variations in the host receptors limit the interaction with cov spike protein, and this is responsible for the development of the species barrier that prevents spillover infection. snakes, civets, and pangolins are considered as the potential intermediate hosts of covid- . however, further confirmation is required by tracking the origin of the virus. this is critical for preventing additional exposure to this fatal virus [ ] . the probability of the sars-cov- spread during incubation and convalescent period has been suggested [ ] . as per reports, presence of covs has been observed in respiratory droplets, body fluids and inanimate objects with the ability to remain infectious for nine days on contaminated surfaces resulting in its risk of self-inoculation via mucous membranes of the eyes, mouth or nose [ ] [ ] [ ] . nosocomial, as well as human-to-human transmission, have been reported to occur via virus-laden aerosols, contaminated hands or surfaces, and close community contact with an infected person [ , , ] . the ocular route has been reported in the human-to-human transmission of sars-cov- , as observed in sars-cov, suggesting the involvement of different ways other than the respiratory tract [ , ] . later on, the probability of the faecal-oral route for potential transmission of the virus was also suggested [ ] . the metatranscriptome sequencing of sars-cov- in the bronchoalveolar lavage fluid (balf) of infected individuals resulted in polymorphism in few intra-hosts variants, suggesting the in vivo evolution of the virus thereby affecting its virulence, transmissibility, and infectivity [ ] . an overview of coronaviruses jumping the cross-species barriers, zoonotic covs transmitted from bats to animals before spillover to humans, and possible prospects for further transmission to mammalian hosts is depicted in figure . the first two decades ( - ) of st century have proven a nightmare for the countries around the globe considering the coronavirus zoonosis, including the ongoing crisis of covid- which has involved entire fields of global [ , ] . the countries affected severely by previous covs were even not evolved entirely from the effects of sars and mers when the covid- struck almost the entire world. novel coronavirus sars-cov- has shaken all the sectors of the countries irrespective of being developed or underdeveloped including healthcare system, economics, trade, infrastructure, service and production sectors [ , ] . being a zoonotic disease with still unknown intermediate host, undisclosed features of a novel viral pathogen, unclear modes of transmission and ecological aspects, less explored pathogenesis and substantial morbidity and considerable mortality, the safety of all is a matter of great concern, and thus the involvement of various authorities was sought since the inception of disease [ , , , ] . the first time the need for one health concept has risen to a level that authorities in various countries implemented coordinated approaches between medical, veterinary, public health, wildlife, food safety, environmental departments and so on [ ] [ ] [ ] . that involved acquiring suggestions, diagnosis and prevention and treatment measures and their implementation in collaboration. non-medical staff in association with the medical staff was employed for initial screening, quarantine, contact tracing when the expertise of molecular biologists or technicians from various disciplines was used in the laboratory diagnosis. medical staff provided the cure and management of the patients when the public health departments, including public health engineering, municipality, food and supplies ensured sanitation, hygiene, food supply and safety. imposing of lockdown was provided by security personnel's and the transport department facilitated the movement of stranded people. thus, this crises management strategy involved various agencies directly or indirectly. however, as the animal, human and environmental health is linked to one another, the prime and future efforts should primarily focus on all these aspects. in addition to regular hand hygiene, respiratory etiquette, social/physical distancing, use of personnel protective equipment (ppe) and food safety recommendations, one health approach encompasses the role of veterinary, medical and environmental specialists for the prevention and control of current covid- crises and investigating the animal origin of covid- , regulating and limiting the sale and farming of wildlife species for food and taking a one health approach to food systems feeding the world for the prevention of future pandemics [ , , ] . considering the contagiousness of the virus, discouraging the working of affected individuals, public health hygiene strategies, and social distancing has been recommended as preventive measures [ , ] . food hygiene and safety, as recommended by oie [ ] and usda [ ] , should be followed. as the viral survivability has been demonstrated on various surfaces [ ] hence disinfection by using recommended disinfectants is necessary [ ] . environmental hygiene and cleanliness are also essential [ ] . interaction with animals and improper utilization of animal products during an outbreak should be avoided [ ] . though the one health involves mainly public health, animal health and environmental experts, however, for the successful management of current crises and future prevention and control requires the participation of all concerned sectors having a role in public health measures, identifying clinical cases, diagnosis, contact tracing, proper infection control in various settings, isolation, quarantine, cure and management, public awareness, facilitation of infrastructure and other facilities through local administrations [ , ] . as the human covid- cases are on the rise due to efficient human-to-human transmission, there is a subsequent rise in the natural infections of covid- among the companion and wild animal species owing to the spillover. this is mainly because of the specific biological and virological characteristics of coronaviruses that gives them the ability to easily cross-species barriers [ ] . even though animal-to-human transmission is not reported in covid- , 'one health' approach is necessary to control this pandemic virus a schematic illustration of covid- clinical signs, modes of transmission, important diagnostic methods, and advances in vaccine development along with salient prevention and control strategies are presented in figure . with the rising number and worldwide spread of covid- , the need for global efforts rely heavily on the investigations carried out at infection sites to trace different aspects of this novel coronavirus outbreak. one of the critical facets and the earliest research must involve determining the root cause, origin, and source of this emerging infectious disease. shreds of evidence have revealed various cross-species jumping or spillover from animals to humans of these zoonotic coronaviruses. detailed serological investigation of all domestic and wild animals residing in the proximity to humans is of utmost necessity to know and prevent likely spillover of many other bat-related covs in the future. rapid detection of spillovers above will only be possible by the implementation of an effective and robust surveillance system for circulating viruses with high zoonotic potential in animals. besides, detection of a pathogen while crossing the species barrier to start circulation among humans and prevention of human-to-human transmission in early-stage may prove crucial in termination of a probable epidemic or pandemic. application of 'one health' concept involving medical, veterinary, wildlife, public health, and other related professionals may help in infection tracing, exploring risk factors and predisposition, minimizing risk to susceptible ones, and finally devising better prevention and control strategies. in the initial stages of the covid- outbreak, the steps taken for implementing stringent control and preventive measures have bought us some time. this time has to be efficiently utilized for developing sars-cov-specific therapeutic drugs and vaccines that can prevent the further spread of this fatal pathogen. for the time being early detection, isolation, and management of covid- infected cases and for the immediate future awareness and implementation of the necessary steps of prevention and control to under risk and predisposed groups may help in long term prevention and control goals. however, it is clearly understood that relying exclusively on public health measures will not resolve the threat caused by covid- . hence efforts to curb this emerging zoonosis at all levels need to be enforced under the one health approach. a systematic review of therapeutic agents for the treatment of the middle east respiratory syndrome coronavirus (mers-cov) mers-cov as an emerging respiratory illness: a review of prevention methods clinical predictors of mortality of middle east respiratory syndrome coronavirus (mers-cov) infection: a cohort study ebola virus disease: an emerging zoonosis with importance for travel medicine preliminary estimation of the basic reproduction number of zika virus infection during colombia epidemic zika and microcephaly in latin america: an emerging threat for pregnant travelers fatal zika virus disease in adults: a critical reappraisal of an under-recognized clinical entity advances in designing and developing vaccines, drugs, and therapies to counter ebola virus swine flu is back again: a review emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments advances in developing therapies to combat zika virus: current knowledge and future perspectives nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies -a comprehensive review the coronavirus: learning curves, lessons, and the weakest link spectrum of covid- in children novel coronavirus: a crown jewel of pandemics strategies shift as coronavirus pandemic looms novel coronavirus, poor quarantine, and the risk of pandemic the sars, mers and novel coronavirus (covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? history is repeating itself: probable zoonotic spillover as the cause of the novel coronavirus epidemic susceptibility of felids to coronaviruses coronavirus: global solutions to prevent a pandemic covid- , an emerging coronavirus infection: advances and prospects in designing and developing vaccines, immunotherapeutics, and therapeutics coronavirus disease pandemic (covid- ): challenges and a global perspective epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study report of the who-china joint mission on coronavirus disease cross-species transmission of the newly identified coronavirus -ncov evolutionary history, potential intermediate animal host, and cross-species analyses of sars-cov- covid- : another infectious disease emerging at the animal-human interface. the new zealand medical journal coronaviruses: a paradigm of new emerging zoonotic diseases. pathogens and disease covid- : animals, veterinary and zoonotic links bat-borne virus diversity, spillover and emergence exceptional diversity and selection pressure on sars-cov and sars-cov- host receptor in bats compared to other mammals covid- : lessons from sars and mers analysis of the hosts and transmission paths of sars-cov- in the covid- outbreak full-genome evolutionary analysis of the novel corona virus ( -ncov) rejects the hypothesis of emergence as a result of a recent recombination event adaptive evolution of mers-cov to species variation in dpp outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle spillover of sars-cov- into novel wild hosts in north america: a conceptual model for perpetuation of the pathogen economic impacts of wuhan -ncov on china and the world fear can be more harmful than the severe acute respiratory syndrome coronavirus in controlling the corona virus disease epidemic the arrival of sars-cov- in venezuela genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission coronavirus -ncov: a brief perspective from the front line identification of a novel coronavirus causing severe pneumonia in human: a descriptive study receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in wuhan, china, as at the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak zhonghua yu fang yi xue za zhi [chinese journal of preventive medicine interim guidance for environmental cleaning in non-healthcare facilities exposed to sars-cov- aerosol and surface stability of sars-cov- as compared with sars-cov- clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by sars-cov- an update on sars-cov- /covid- with particular reference to its clinical pathology, pathogenesis, immunopathology and mitigation strategies technical advisory group for infectious h. covid- : what is next for public health? the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak -an update on the status systematic comparison of two animal-to-human transmitted human coronaviruses: sars-cov- and sars-cov sars-cov- : fear versus data the first novel coronavirus case in nepal zhonghua jie he he hu xi za zhi = zhonghua jiehe he huxi zazhi = chinese journal of tuberculosis and respiratory diseases clinical characteristics of patients with -ncov infection clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan anosmia in a healthcare worker with covid- in madrid, spain for the singapore novel coronavirus outbreak research t. epidemiologic features and clinical course of patients infected with sars-cov- in clinical features of patients infected with novel coronavirus in wuhan the neuroinvasive potential of sars-cov may play a role in the respiratory failure of covid- patients clinical characteristics of coronavirus disease in china indirect virus transmission in cluster a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster early phylogenetic estimate of the effective reproduction number of sars-cov- evidence of sars-cov- infection in returning travelers from wuhan, china secondary attack rate and superspreading events for sars-cov- novel coronavirus (covid- ): emergence and implications for emergency care unique epidemiological and clinical features of the emerging novel coronavirus pneumonia (covid- ) implicate special control measures transmission of -ncov infection from an asymptomatic contact in germany novel coronavirus infection and gastrointestinal tract sexual health in the sars-cov- era coronaviruses and immunosuppressed patients: the facts during the third epidemic novel coronavirus infection and pregnancy lack of vertical transmission of severe acute respiratory syndrome coronavirus working committee on p, neonatal management for the p, control of the novel coronavirus i the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application ct imaging of the novel coronavirus ( -ncov) pneumonia case-fatality rate and characteristics of patients dying in relation to covid- in italy preliminary identification of potential vaccine targets for the covid- coronavirus (sars-cov- ) based on sars-cov immunological studies is covid- receiving ade from other coronaviruses? microbes and infection the novel coronavirus ( -ncov) uses the sars-coronavirus receptor ace and the cellular protease tmprss for entry into target cells cryo-em structure of the -ncov spike in the prefusion conformation the spike glycoprotein of the new coronavirus -ncov contains a furin-like cleavage site absent in cov of the same clade the novel coronavirus: a bird's eye view fecal specimen diagnosis novel coronavirus-infected pneumonia abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia genomic epidemiology of betacov outbreak of a novel coronavirus composition and divergence of coronavirus spike proteins and host ace receptors predict potential intermediate hosts of sars-cov- origin and evolution of pathogenic coronaviruses a novel coronavirus from patients with pneumonia in china oie. animal and environmental investigations to identify the zoonotic source of the covid- virus. . . diseases pisfi. coronavirus disease update ( ): companion animal, dog suspected, request for information infection of dogs with sars-cov- coronavirus can infect cats -dogs, not so much first detection and genome sequencing of sars-cov- in an infected cat in france virology: sars virus infection of cats and ferrets belgian cat infected by owner. the brussels times a tiger at bronx zoo tests positive for covid- ; the tiger and the zoo's other cats are doing well at this time coronavirus rips through dutch mink farms, triggering culls sars-cov infection in farmed mink updated understanding of the outbreak of novel coronavirus ( -ncov) in wuhan enhanced receptor binding of sars-cov- through networks of hydrogenbonding and hydrophobic interactions zoonotic origins of human coronaviruses jumping species-a mechanism for coronavirus persistence and survival. current opinion in virology emerging coronavirus disease (covid- ), a pandemic public health emergency with animal linkages: current status update. the indian journal of animal sciences mers-cov and now the -novel cov: have we investigated enough about coronaviruses? -a bibliometric analysis middle east respiratory syndrome coronavirus (mers-cov) bats, civets and the emergence of sars responding to global infectious disease outbreaks: lessons from sars on the role of risk perception, communication and management seasonality of respiratory viral infections. annual review of virology pathways to zoonotic spillover genomic characterization and phylogenetic classification of bovine coronaviruses through whole genome sequence analysis biological and genetic characterization of a hemagglutinating coronavirus isolated from a diarrhoeic child receptor recognition mechanisms of coronaviruses: a decade of structural studies discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin novel coronavirus (sars-cov- ) epidemic: a veterinary perspective susceptibility of ferrets, cats, dogs, and other domesticated animals to sars-coronavirus coronavirus sars-cov- (covid- ) and companion animal pets is covid- the first pandemic that evolves into a panzootic? importance of the one health approach to study the sars-cov- in latin america need for integrated surveillance at human-animal interface for rapid detection & response to emerging coronavirus infections using one health approach the risk of sars-cov- transmission to pets and other wild and domestic animals strongly mandates a one-health strategy to control the covid- pandemic. one health a critical needs assessment for research in companion animals and livestock following the pandemic of covid- in humans. vector borne and zoonotic diseases mitigating the impacts of covid- on the livestock sector guidelines to mitigate the impact of the covid- pandemic on livestock production and animal health among workers in meat and poultry processing facilities - states cov- : an emerging coronavirus that causes a global threat viral genetics accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence covid- and emerging viral diseases: the journey from animals to humans molecular evolution of human coronavirus genomes epidemiology, genetic recombination, and pathogenesis of coronaviruses bat origin of a new human coronavirus: there and back again coronavirus infection in equines: a review emergence of avian infectious bronchitis virus and its variants need better diagnosis, prevention and control strategies: a global perspective synanthropic rodents as virus reservoirs and transmitters. revista da sociedade brasileira de medicina tropical identification of alpha and beta coronavirus in wildlife species in france: bats, rodents, rabbits, and hedgehogs consensus document on the epidemiology of severe acute respiratory syndrome (sars). geneva: world health organization isolation and characterization of -ncov-like coronavirus from malayan pangolins first respiratory transmitted food borne outbreak? canine respiratory coronavirus: an emerging pathogen in the canine infectious respiratory disease complex. the veterinary clinics of north america: small animal practice canine enteric coronaviruses: emerging viral pathogens with distinct recombinant spike proteins feline coronaviruses: pathogenesis of feline infectious peritonitis identification of a novel coronavirus from a beluga whale by using a panviral microarray probable pangolin origin of sars-cov- associated with the covid- discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus evidence for camel-to-human transmission of mers coronavirus isolation and characterization of viruses related to the sars coronavirus from animals in southern china new insights into the mechanisms of rna recombination generation of coronavirus spike deletion variants by high-frequency recombination at regions of predicted rna secondary structure the -new coronavirus epidemic: evidence for virus evolution fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin structure analysis of the receptor binding of -ncov initial public health response and interim clinical guidance for the novel coronavirus outbreak -united states evolutionary origins of the sars-cov- sarbecovirus lineage responsible for the covid- pandemic china coronavirus: six questions scientists are asking complete genome sequence of bat coronavirus hku from chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome structure of sars coronavirus spike receptor-binding domain complexed with receptor structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human the outbreak of sars-cov- pneumonia calls for viral vaccines what can animal coronaviruses tell us about emerging human coronaviruses? veterinary record potential host range of multiple sars-like coronaviruses and an improved ace -fc variant that is potent against both sars-cov- and sars-cov- receptor and viral determinants of sars-coronavirus adaptation to human ace isolation and characterization of a bat sars-like coronavirus that uses the ace receptor serological evidence of bat sars-related coronavirus infection in humans bat coronaviruses in china mers coronavirus neutralizing antibodies in camels zoonotic spillover and emerging viral diseases time to intensify zoonoses surveillance in brazil outbreak of novel coronavirus (sars-cov- ): first evidences from international scientific literature and pending questions severe acute respiratory syndrome coronavirus on hospital surfaces avian influenza and sialic acid receptors: more than meets the eye? the lancet infectious diseases transmission of sars and mers coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents emerging threats from zoonotic coronaviruses-from sars and mers to -ncov ocular tropism of respiratory viruses. microbiology and molecular biology reviews -ncov transmission through the ocular surface must not be ignored first case of novel coronavirus in the united states genomic diversity of sars-cov- in coronavirus disease patients emerging zoonoses: a one health challenge covid- : first severe pandemic of the st century coronavirus outbreak will set back india's growth recovery covid- : a look into the modern age pandemic biosafety and biosecurity approaches to restrain/contain and counter sars-cov- /covid- pandemic: a rapid-review oie. questions and answers on the covid- calling for a covid- one health research coalition from sars to covid- : a previously unknown sars-related coronavirus (sars-cov- ) of pandemic potential infecting humans -call for a one health approach ohc. covid- and one health steps to help prevent another animal-to-human virus pandemic prevention cfdca. covid- and animals usda ensures food safety during covid- outbreak disinfectants for use against sars-cov none. key: cord- -b f z r authors: allam, zaheer title: underlining the role of data science and technology in supporting supply chains, political stability and health networks during pandemics date: - - journal: surveying the covid- pandemic and its implications doi: . /b - - - - . - sha: doc_id: cord_uid: b f z r this concluding chapter explores how data science and technology has been key in fighting covid- through early detection and in the devising of tools for containing the spread. interestingly, two precedence constraints are seen to emerge. first, data-driven modeling is the leading policy at an urban and national level, and second, legislations, which are being passed at record speed, will remain as a legacy postvirus. it is expected that those will accelerate the digital transition of communities for decades to come and lead to a resurgence of the smart cities concept which peaked in . this chapter thus outlines the increasing role of data science in health sciences, the need for more robust digital infrastructures, and the role of technology in supporting livability of communities and world order. in a period of just months, the global landscape had been overturned by the coronavirus, which was not seen as a threat in the initial stages when reports from started trickling from wuhan, china. in fact, for almost weeks after it was reported on december , , it had only affected people and had not spread to any other regions, or outside the city of wuhan. for this reason, even the world health organization hesitated to identify it as a public health emergency of international concern (pheic) (who, c) and as global pandemic (branswell, ) . but when it started to spread, first to neighboring regions, and to more parts of the china, and finally, to regions far and wide, it caused unprecedented panic and fears. worse still, the number of infections started to increase exponentially, with substantial numbers of deaths in different parts of the world. by the end of months, the disease, which was later renamed to covid- , had infected over million people and killed over , , with most of the deaths witnessed in the most developed regions and countries (sullivan et al., ) . worse still, it had sparked fear and panic on governments prompting them to institute some measures with far-reaching impacts on societies, economies, the political sphere, and also the environment. for the first time in history, numerous countries had instituted lockdowns in their countries (barry and jordans, ; bermingham, ) , imposed border restrictions, banned noncitizens or permanent residents from their countries, and grounded transportation networks. there have been also total suspension of flights, on both domestically and internationally (pham, ) , and unprecedented use of security forces in different countries to impose those measures. economies across the globe have been halted, with only a few sectors, more so those providing essential services allowed to perform. the measures have also been accused of disrupting of supply chain (cohen, ; oecd, ; shwartz, ) , thus prompting wide-scale scarcity of basic things including medical supplies that have been in great demand in different parts of the globe. socially, the emergence of covid- brought unprecedented pains, fears, agony, and disarray as people, in their thousands, and millions are hospitalized, others separated with their loved ones forever. in worse-case scenarios, in areas with high daily death rates, deaths from hospitals were buried in mass graves with relatives void of the opportunity to say good bye. the devastation has been even worse on those who traveled outside their countries, and with lockdowns and restricted transportation, people have had to remain displaced until such measures are eased or lifted. the measures that have been imposed in different countries have also seen unprecedented impacts on livability, especially in urban areas where people are forced to remain indoors, with limited supplies (nkengasong and mankoula, ; wearden and jolly, ) , with no social interactions, and with pressures from loss of jobs and source of their livelihoods. such have prompted social strives, where in different parts of the globe such as in india, the united states, and germany, residents of some towns called for lifting of lockdowns and other restrictions. such issues were arising when the united nations' world food programme had warned that the effects of covid- would result into increase in the number of acute hunger, affecting more than million people globally (anthem, ) . politically, as the covid- situation escalated, more political tensions were built. for instance, countries have been seen trading accusations as to the responsibility that each has played in escalating the situation. others such as china have been accused by countries such as the united states, germany, the united kingdom, spain, and even france of having mishandled the situation and failing to share conclusive information and data in time to allow others to prepare (bronstad, ; pleasance, ) . on other occasions, the united states has been blamed for instituting measures such as banning european travelers into the united states, also for banning exportation of medical supplies and other issues (larsen and gramer, ). in fact, with no immediate end on sight for this pandemic, there were fears that the tension may even escalate to dangerous heights, warranting interventions of international bodies. while the emergence of covid- had severely impaired the global systems, it however, exposed the importance and power of modern technologies in helping address events such as pandemics. for instance, in the first stages of the outbreak of this virus, when the chinese scientists and authorities and the who were trying to identify the virus (who, d), and whether it could have impacts beyond wuhan, a tech startup named bluedot was able to detect that the world was facing an outbreak, which may end up having global impact. using real-time data from different sources such as airlines ticketing and numerous news outlets, it made the prediction days earlier, before the who made the announcement (allam et al., ; bowles, ) . on the same, allam et al. ( ) highlighted that there was also another startup named metabiota that correctly predicted that the outbreak would spread to the neighboring regions in a matter of time, and a week later, the prediction came true as japan, thailand, singapore, and others that had been noted as potential target for the outbreak confirmed their first cases. besides those, even when countries went on lockdown, the use of technology became even more apparent, as devices such as drones, robots, sensors, smart helmets, and thermal detectors were widely used for different purposes such as delivery, identifying potential coronavirus virus cases and other purposes (who, b) . technologies such as artificial intelligence (ai), machine learning, natural language processing, and big data have also been instrumental in some countries in implementing quarantines, in search for vaccines and drugs and in helping reduce further spread of the virus. after such success on the use technology, it is incumbent upon different stakeholders in the global sphere to invest more resources in ensuring widespread of the same in different sectors; as going forward, the global systems will require a concerted effort to restore. for instance, in the economic front, there are signs that the world may be headed for a recession and that would have far-reaching impacts not only on the economies (africa renewal, ; statista, a statista, , b stephanie and gerstel, ; wang, ; wearden and jolly, ) but also on the environment. on this, with the use of technologies in sectors such as agriculture, manufacturing, energy production, and building and construction, it would be possible not only to revive the economies but also to void impacts on the environments. by ensuring continuity of the strides already made in different sectors, more so the environmental, the world may escape the dangers posed by climate change and others that are related to environmental sustainability (allam and jones, ) . with that background, this chapter will concentrate on discussing the role of technology and data science in supporting supply chains, economies, and political sustainabilities. the occasional occurrence of pandemics in the world is not unusual from a historical perspective. since time immemorial, humans have had to contend with these, but, fortunately, most of those remained local, especially due to a number of factors. first, the global population has been played a significant part in the spread of pandemics, and in earlier days, population were relatively smaller and people were sparsely distributed. secondly, the interaction between different groups of people from different countries and regions was limited as transportation infrastructures were not well developed, until recently. also, urbanization was not as pronounced as it is today, and this played a key role in preventing widespread. today, things are extremely different, as the population has already increased to . billion people, and it is projected to reach a high of . billion by and to . billion by (un, ). furthermore, technological advancement is at all-time high, and this has made interactions, communication, transportation, and research among other things more robust and efficient. these modern facts have made it possible for pandemics to be widespread and devastating. therefore, in the case of infectious diseases like the covid- , it is not surprising that they spread quite fast and impact numerous people and sectors in a short period of time. for instance, by the time of writing this chapter, the coronavirus had spread to over countries, infecting over million people and killed over people. it had also started to spark some political and economic tensions, besides impacting greatly the social aspects in every part of the globe. the technological advancement, however, cannot be overlooked on the lens of facilitating spread, but its greatest strength has been in controlling and preventing further spread and devastations. for instance, during the spanish flu outbreak ( e ), where technology was rudimentary, over million people lost their lives (martini et al., ) . however, as technology continued to advanced, including in the medical fields, the succeeding pandemic such as the e severe acute respiratory syndrome (sars) spread was effectively contained, and it only spread into countries and only infected people over that period. even other outbreaks such as the middle east respiratory syndrome (mers) (cdc, ), ebola (wojda et al., ) , zika (kazmi et al., ) , and influenza like the swine flu (aris-brosou et al., ) that have broken out did not have devastating impacts as compared with the spanish flu. in fact, even the hiv that emerged in the s, and is still present to date, has well been managed due to availability of technologies (the, ) . despite that, these have had some significant impacts on social and economic frontiers, which cannot be overlooked and which demand even further advancement in the medical field to help with the identification of outbreaks before they spread. one of the most novel ways of ensuring that future outbreaks can be contained is widespread application of data computation and analysis (allam and jones, ) , which already, as discussed in the previous section, was instrumental in making predictions about the outbreak and spread of covid- by bluedot and metabiota. in other fields such as climate change, the application of predictive technologies has been widely used, and these have had significant impacts in helping promote discourses on climate sustainability, emissions reduction, and the need to adopt alternative energy production (allam, a (allam, , b . while the use of technology is being promoted, it is not meant to debase the role of other players in the medical world, but such would supplement the efforts, by making the work of investigators, pharmacists, researchers, and others even more pronounced and with far-reaching outcomes. it would also help in hastening processes, making decisions, collecting data, and reducing human errors in interpretation of said data, thus reducing misdiagnosis and other such issues that have occasionally been witnessed in the medical field . such benefits are made even more robust by the availability of diverse data sources, data collecting technologies, and different data sharing platforms. for instance, with the increase of internet infrastructures, now supporting even g in some regions (o'mahony et al., ) , and with the availability of numerous smart, mobile devices such as phones, drone, wearable technologies, and cameras, data generation and sharing is becoming pronounced. similarly, the increase in number of social media platforms (cinnamon et al., ) , increased online news outlets, and mobile apps among others are helping in generating unprecedented amounts of data (allam, b) . the use of such apps has earlier been used, especially during the haiti earthquake and the cholera outbreak in the same country where health professionals collaborated with telecom companies such as digicel (largest telecompany in the country) to track the movement of people. this allowed for optimal resource management and also in deployment efforts of those offering different forms of assistance (bengtsson et al., ; lu et al., ) . even in the current pandemic, there is evidence of widespread use of technologies, besides what bluedot and metabiota did. in different parts of the globe, governments, telecoms, and startups have been seen to develop different apps and online tools such as trackers that have helped in tracking and mapping the spread of the disease (porterfield, ; voa student union, ; wakefield, b) . for instance, in south korea, it is reported that they developed a platform that allowed security and health personnel effectively impose quarantine and would warn them whenever individuals were flaunting such measures (park, ) . computation technologies were also widely used in china to combat the spread of covid- (chaturvedi, ) , and even as it continued to spread in other countries, we have seen rival tech companies such as apple and google collaborating to make tracking tools to aid in effective mapping and tracking of the spread of the virus (apple, ) . by tapping on these technologies, there are possibilities of enriching the available database such that even in the future, it would be easier to address emergencies of whatever nature. on this, the most promising thing with the use of data computation technologies is that data from different spheres could be collated and analyzed to reach an informed conclusion. this is how bluedot company made the prediction through the use of a wide expertise network as it hosts a rich expertise base comprising of meteorologists, software developers, data scientists, ecologists, geographers, epidemiologists, veterinarians, and others, thus allowing them to make informed conclusion, which are inspired by insights from the diverse backgrounds (bluedot, a (bluedot, , b . going further, even post-covid- , the role of computation technologies will continue, especially in reevaluating the policy responses, and hence help different stakeholders to identify areas of weakness and how such could be strengthened in case of similar future major disruptive events. following the numerous technological interventions initiated to combat the covid- pandemic, it is now evident that technology, especially related to data storage, data processing and sharing is part of the backbone of the health industry. this has been given the impetus by the happening in the technological sphere where much effort has been made in improving data collection methodologies, with the use of smart devices gaining traction. in regard to data storage, developments have been made significantly, where research is being performed to see whether it could be possible to store such in human genomes or proteins such that, in the future, unlimited amounts of data could be stored. in regard to data processing, as noted earlier, the medical field would benefit even further through the upcoming advancements in ai-driven tools, the advancement in machine learning technologies, and also the improvement in big data technologies. with these technologies, it will be possible to process vast amount of data, in real time and from diverse sources as noted earlier; hence, the insights and conclusion drawn from such will have far-reaching impacts. this far, in the medical field, with such technologies, there is evidence that it is now possible to perform noninvasive surgeries that reduce fatalities and also reduce healing time for patients, and such have proven beneficial (elrod, ) , especially during this period of covid- . others such as the d printing are gaining traction, especially in address complex medical issues, especially those requiring implantation of biomedical devices. according to javaid and haleem ( ), d printing is offering the possibility to have relatively smaller implant devices at the comfort of patients. in the case of covid- , already, with the available data, researchers have estimated and predicted the various case scenarios that different countries would face, especially in terms of fatality and recoveries, and infection, hence allowing all involved parties to prepare (giordano et al., ; tokars et al., ) . for instance, in the united states, using such computation, it was estimated that country may have an approximate death toll of , and have millions affected. and already, the number of infections in the country has clocked over million (cole et al., ) . when those technologies and many others are complemented by data computation, the medical field can be made to benefit even further, and already, market of those devices and the number of companies investing in the medical fields are increasing. in particular, with the notable achievements and recognition that data processing startups have gained over this period of covid- following the correct predictions made, the market for smart devices will continue to grow even further. on this, before the emergence of the pandemic, it had been projected that the number of internet of things (iot)e supported devices in the health industry would reach a total of billion devices by and billion devices by (digital information world, ), thus pushing the device market to us$ . billion (fortune business insight, ). mordo intelligence ( ) undervalues the market and argues that it will increase to a high of us$ . billion by from a high of us$ . billion report in . but in both predictions, it is true that the growth in the market is relatively high, at a compounded annual growth rate (cagr) of more than % each year. mordo intelligence ( ) credits such increase in number to factors such as the improvement in accuracy and connectivity that such devices have made possible in the healthcare sector and also the emergence of big data in healthcare such that any amount of data that such could generate would be stored and processed without fear of lack of storage. with the world focusing on statistical modeling for data gathering from the increasing covid- cases, and solutions driven from processing that data, it means that solutions derived may also be technologically driven. in fact, even as governments, scientists, agencies, individuals, and other stakeholders intensify the search for a vaccine and drug for this disease, already, as noted earlier, technological processes have managed to assist in reducing the spread of the virus. for instance, the example cited in the previous section about the use of mobile platforms in the republic of south korea to enforce quarantine is proof that technology holds a sizable share in bringing to an end the coronavirus menace and that of future pandemics. it is worth noting that using technology, the chinese authorities managed to identify the coronavirus genome sequence and posted the same on a public database where it could be accessed by all accredited researchers (ecdc, ). within no time, labs across the world had access to this, and they managed to clone it (scott et al., ) . through such public platforms, those labs shared information and data on all the experiments that failed, helping reduce repetition, and they are also helping researchers on areas to focus (ramiah, ) . in other cases, through statistical modeling, organizations, including the who and others, have been able to develop dashboards that are helping to track the spread of coronavirus, and these are providing people with real-time updates on what is happening across the globe (who, a). similarly, using these modeling, especially those that are ai driven, china managed to diagnose thousands of coronavirus cases, as these could read through thousands of ct scans in a record time with an accuracy level of over % (ramiah, ). this helped reduce time and also ease the pressure on the radiologists who were already overwhelmed due to the fast rates at which cases were being confirmed and hospitalized. an article posted in the university of copenhagen website (uoc, ) explains that ai will, in such cases, go ahead to predict the patients who may urgently be in need of ventilators, depending on severity of their case. ai-based machine learning and natural language processing have also been employed in health facilities in other countries with huge success rates (wright, ) , thus providing hope in the fight against the spread of the virus, and finally, finding a cure for the disease. but its most promising use, in respect to fighting the covid- pandemic, is its ability to crawl through the data pertaining to the , approved drugs already on the market and make predictions from over million possible pairs or over . billion triple-drug combinations. but with ai-powered technologies, researchers predict that possible combination of drugs; whether a part or triple that could go to human trials would take only few weeks. and, already, companies such as healx (earley, ) , exscientia (exscientia, ) , scipher medicine (wakefield, a) , and others are also in advanced stages of proposing possible drugs that could be repurposed and be tried as cures for covid- . outside the hospital environment, as noted in the previous chapters, giant corporations such as apple, google, alibaba, tencent, and others have been seen to develop apps and platforms that provide data sharing platforms, and such have helped in mapping areas where cases were spreading faster and where people could get help and get tested. all the data collected from these platforms and numerous others that are actively being used elsewhere across the globe would remain its usefulness, even post-covid- , but this will require a superior statistical modeling tools to manage the increasing magnitude of such data. in this case, therefore, it will not be farfetched to employ the services of ai-driven technologies such as machine learning, natural language processing, and others such as big data that have already proven capable of delivering quality statistical results in real time and with high levels of reliability. during the period where c vid- has engulfed the world and brought almost everything at a standstill, the role of data processing and sharing is not only being hailed in the health sector but also seen to be critical in other spheres such as the economy, society, and the environment. in the economic sector, there is much that the emergence of the coronavirus has prompted, especially with restriction on movements, grounding of transportation and lockdowns. firsts, as noted by the international labour organization (ilo, ), these measures meant to assist the health sector have transformed the way a majority of people work. on this, a portion of the workforce has managed to continue working from home via teleworking, or through other means. but a majority of the population, especially those in the informal sector, have had their routines greatly disrupted, with a majority globally already filling for unemployment claims. for instance, in the united states, in about weeks, from march to april , over million people filled unemployment claims (jones, ) , higher than the december recession where . million people filed similar claims (department of labor, ). such happenings have increased economic pressures on families, forcing them toward seeking family relief, and other social support systems to see them through the period of aforementioned restrictions. with the disruptions in the labor market, mahler et al. ( ) used data processing to showcase that the estimation on issues such as global poverty will tilt upward, whereas, in the absence of the coronavirus, this year ( ), the global poverty rate would have followed the projected historical trend that showed that it could decrease. but now, with the available data from over countries on those locked down, those losing their jobs and the disruption on other economic areas, it shows that the pandemic will push the poverty by around . % higher from rate, and . % higher from what had been predicted earlier (mahler et al., ) . data processing has also been used during this period to predict that the current health crisis could lead to a recession, where some experts argue that already, the recession has already started in the united states (stewart, ) . the disruptions in the economic sectors have not only prompted challenges on the economic front butalso raised concerns on the security sector, especially with countries seen to short-circuit and ban the exportation of health equipment of other countries. these have raised fears of lack of transparency, thus affecting global collaboration on the fight against the virus. in particular, the issue of data on infections, deaths, and medical supplies has sparked political tensions between different countries, even prompting accusations on independent bodies such as the who (sevastopulo and manson, ) . the need for transparency on data sharing on covid- has thus been emphasized by different global organizations like the united nations (un), world bank, and others (the world bank, ) . according to the world bank ( ), data transparency not only would help in reducing political tension and win over the coronavirus but is also prerequisite in weathering down the economic shocks affecting the global economy, especially by helping enhancing trust in governments, hence promoting investments especially post-covid- . in a bid to ensure that the issue of transparency, especially on the origin and the outbreak of the virus, is established, countries such as the united states have been seen to establish fact-finding committees, whereas others such as germany, sweden, and australia are considering doing the same in due course (amaro, ) . the need for reverse engineering as reported in an article posted in nature medicine (oppmann, ) is warranted by the lack of collaboration, especially by the chinese, whom the european union (eu) chief, ursula von der leyen, said need to be involved in the investigation of the origin of the virus, so that more understanding on the origins can be uncovered, leading to better preparations for future pandemics (amaro, ) . the first such reverse engineering was performed by researchers at peter doherty institute for infection and immunity in collaboration with royal melbourne hospital and university of melbourne where a copy of virus was grown in the lab from samples from an infected patient (reuters, ) . the need for participation of as many parties as possible is to elucidate the real origin of the virus, and issues that have raised numerous theories, where the united states claimed that it may have originated from a virology laboratory in wuhan, china (stanway, ; borger, ; law, ) . china strongly rejected this theory and is also backed by the who, which warned against blaming individual countries for the virus outbreak and spread since this would jeopardize the steps already in place to stop its spread (pérez-peña and mcneil, ) . the availability of diverse institutions, governments, and laboratories and hospitals participating in the fact finding about the coronavirus does not only offer hope and possibilities of gathering data across a diversity array of networks and regions, but also their findings would facilitate efforts of finding a cure for the virus. the identification of the genome sequencing of the virus, for instance, is a positive in the search for vaccines, and drugs, especially noting that these genome sequences are deposited in the public databases, where all researchers can access them. the same are also submitted to the "global initiative on sharing all influenza data" (gisaid) platform. as noted earlier, despite the controversies that are associated with the source of the virus, knowing the actual source would not only hasten in the development of the vaccine and cure but also help in winning back confidence of numerous stakeholders, whom, to this far, have shown dissatisfaction on how the whole issue of the pandemic has been managed. winning the confidence of everyone will help in further collaboration efforts in eliminating the virus, unlike the scenario where individual country is seen to be looking inwardly and applying their own policies, trials, and test, and treating information from other countries with suspicion. while the exploding demand for data-driven solutions at this particular period is all geared toward overcoming the spread and impacts of the coronavirus, this may spark and reignite the need for smart cities concepts, which peaked in (allam and newman, ; allam, ) . in the current dispensations, most of the digital solutions that cities across the world have been observed to be concentrating on is the health sector with the aim of containing any incidence of coronavirus, especially to prevent further spread (allam et al., ; allam and jones, ) . on this front, numerous devices and technologies, such as state-ofthe-art thermal imaging sensors, smart helmets with sensors, use of drones, robots, and mobile phone applications have been in use in this period to help in screening and providing contactless diagnosis against the virus. even postcoronavirus, such technologies will still remain relevant, as they also will be part of numerous other iot devices that are seen to be increasing, as the demand for smart solutions increases. on this, even before the emergence of coronavirus, the demand for smart cities, as expressed by mordor intelligence ( ), was growing, and this had catalyzed the demand for iot devices, which, by , were only . billion devices and had been projected to reach a high of . billion devices by , as the application of smart cities concept continued. besides this, the global market for the iot solutions had reached a high of over us$ billion by , and the projections were that it would cross us$ . trillion by (liu, ) . according to horwitz ( ) from cisco, currently, the number of iot-connected devices globally is over billion, and she also predicts that they would increase to over billion devices by , especially due to improvement in areas such as internet connectivity where many cities will have the g services by then. as those devices increase, the smart cities market will also continue to grow, and as smart cities association ( ) report showcases, it will improve from the $ billion valuation to over us$ . billion valuation by . on the above, though the outbreak of covid- may have somehow halted the attention on application of the smart cities concepts that different cities were piously pursuing, its management is seen to be prompting new legislations aimed at enhancing tech solutions to contain the spread, and most of these will survive postvirus. their enactment, therefore, does not only address the virus, but in the future, they will also add to the existing ones on urban livability, and ultimately, they will lead to better urban and policy decisions. in particular, those policies have formulated to guide in restricting movements, instituting guidelines, and containing the transport sectors, and others will have a positive bearing in the future in ensuring issues such as traffic congestion, supply of basic services, and provision of securities and other issues are maintained. this will be based on the increasing data that different cities are generating those measures that have been placed to contain covid- . for instance, das (philip james) explains how the university of newcastle is using smart technologies to track the adherence to social distancing measures in newcastle, and after analyzing the massive data (capturing over . billion individual events), the conclusion is that the sensors being used were able to give real-time data on how people were responding and also identified areas and issues prompting bottlenecks. on this, as noted by allam and jones ( ) , one of the issues that has appeared prominently in the course of containing the spread of covid- is the nationalistic approach, in decision-making where each country has been observed to look inward, with little regard to the plight of its neighbors. such an approach would be counterproductive in a smart cities concept, as the devices installed need to communicate with others within the network to ensure synchronization of data and information, hence reading to informed decisions and insight drawn after data analysis. with lockdowns, it has been evident that urban livelihood was to be negatively impacted, and in no time, this came to pass, with citizens in a number of cities in different countries protesting. this situation in cities is largely blamed on the haphazardly formulated policies that were mechanically enacted with little consideration of the negative impact that they would draw on locals. in most cities, despite the high population and density, government was seen to delay in implementing measures that would allow them to manage early detection, which would eventually help to reduce the number of local transmissions that prompted the lockdown. however, the blame is not all on government, for it also took time before it was established that the virus could be transmitted from one person to the other. therefore, in most cities, the lockdown came when local transmission had already spread. but while that is the case, local governments had the capacity to learn, especially by analyzing data of cities such as wuhan, which was affected first, and see how cases were spreading quickly and thus prepare effectively, especially by formulating restrictions measures that are more flexible, while being effective, for locals. such would have sufficed, as most urban cities are characterized of high-density and high-rise buildings, where during total lockdown, people would feel trapped, where grant ( ) supports that the planning of such leaves only a little or no open spaces where people could move out for recreation. but with prior planning, as was observed in france, people had opportunities to walk out, albeit under very strict conditions. but while things have been complicated by lockdowns, one take-home after the covid- is the need for intelligent urban planning principles, and this could be achieved by promoting decentralization, of some services, especially those that could be done achieved remotely as advised by shenker ( ) . already, this has been happening in this era of covid- , where some people have been able to work from home via live telecommunicating. there has also been a widespread use of digital transactions such as use of mobile money transactions, which could help in decentralizing the financial services. while the future postcovid is still uncertain, there are clear indications that the technological revolutions that were brought about to address it will remain as a legacy. there will be calls, soon enough, for communities, cities, and regions will use this momentum to craft more resilient fabrics while keeping in mind societal and economic equity in the process. eca estimates billions worth of losses in africa due to covid- impact redefining the smart city: culture, metabolism and governance. case study of port louis biotechnology to render future cities as living and intelligent organisms data as the new driving gears of urbanization artificial intelligence (ai) provided early detection of the coronavirus (covid- ) in china and will influence future urban health policy internationally climate change and economic resilience through urban and cultural heritage: the case of emerging small island developing states economies on the coronavirus (covid- ) outbreak and the smart city network: universal data sharing standards coupled with artificial intelligence (ai) to benefit urban health monitoring and management redefining the smart city: culture, metabolism and governance redefining the use of big data in urban health for increased liveability in smart cities eu chief backs investigation into coronavirus origin and says china should be involved risk of hunger pandemic as covid- set to almost double acute hunger by end of apple and google partner on covid- contact tracing technology viral outbreaks involve destabilized evolutionary networks: evidence from ebola virus death tolls soar in us, italy, iran as global lockdown intensifies improved response to disasters and outbreaks by tracking population movements with mobile phone network data: a post-earthquake geospatial study in haiti coronavirus: world faces 'similar economic shocks' to china as the global lockdowns escalate better public health surveillance for infectious diseases bluedot protects people around the world from infectious diseases with human and artificial intelligence enormous evidence" coronavirus came from chinese lab how canadian ai start-up bluedot spotted coronavirus before anyone else had a clue who says coronavirus is not yet a pandemic but urges countries to prepare class action filed against china over covid- outbreak middle east respiratory syndrome (mers) the china way: use of technology to combat covid- evidence and future potential of mobile phone data for disease disaster management oil markets brace for who's global health emergency declaration us could see millions of coronavirus cases and , or more deaths this is how smart city technology can be used to tell if social distancing is working iot in healthcare expectations for healx will use ai to seek combination therapies to treat covid- event background covid- acute care handbook for physical therapists (fourth edition) partnerships: exscientia announces joint initiative to identify covid- drugs with diamond light source and scripps research iot in bfsi market size to reach usd . billion by ; growing utilization of iot solutions in the banking sector will support growth modelling the covid- epidemic and implementation of population-wide interventions in italy what cities can learn from lockdown about planning for life after the coronavirus pandemic the future of iot miniguide: the burgeoning iot market continues covid- impact on the collection of labour market statistics significant advancements of d printing in the field of jobless claims climb to million in six weeks as covid- layoffs continue to rise a review on zika virus outbreak, epidemiology, transmission and infection dynamics china casts itself as global savior while u.s. and eu focus on virus at home. available at coronavirus origin: few leads, many theories in hunt for source global iot market size predictability of population displacement after the haiti earthquake. proceedings of the national academy of sciences of the united states of america the impact of covid- (coronavirus) on global poverty: why sub-saharan africa might be the region hardest hit the spanish influenza pandemic: a lesson from history years after smart cities market size, share e segmented by solution (smart mobility management looming threat of covid- infection in africa: act collectively, and fast mobile nation : the g future coronavirus: the world economy at risk. oecd. oppmann p. ( ) cuba is going under lockdown over coronavirus concerns covid- : how a phone app is assisting south korea enforce self-quarantine measures now trump's scapegoat, warned about coronavirus early and often airlines around the world are suspending flights to china as the coronavirus spreads angela merkel becomes latest world leader to hint china has mislead the world over coronavirus and urges beijing to be "more transparent surge of smartphone apps promise coronavirus tracking, but raise privacy concerns ways technology is helping to fight the coronavirus australia scientists to share lab-grown coronavirus to hasten vaccine efforts australian lab first outside of china to copy coronavirus, helping vaccine push donald trump threatens to freeze funding for who cities after coronavirus: how covid- could radically alter urban life coronavirus recession looms, its course 'unrecognizable global smart cities market to reach a whopping $ . trillion by china lab rejects covid- conspiracy claims, but virus origins still a mystery coronavirus (c vid- ) impact on gdp growth in france statista. ( b) forecasted impact of coronavirus (covid- ) on gdp in italy q -q the global economic impacts of covid- the coronavirus recession is already here known global covid- deaths pass , e as it happened the global hiv/aids epidemic-progress and challenges transparency is key to weathering shocks, investing in growth, and enhancing trust in government the changing face of surveillance for health caredassociated infections world population prospects artificial intelligence to predict corona-patients' risk of needing ventilators phone apps in china track coronavirus coronavirus: ai steps up in battle against covid- coronavirus: tracking app aims for one million downloads china may adjust gdp growth target due to coronavirus imf: global economy faces worst recession since the great depression who. ( a) coronavirus disease (covid- ): situation report e who. ( b) novel coronavirus ( -ncov): situation report- . available at emergency committee regarding the outbreak of novel coronavirus ( -ncov) who timeline -covid- the ebola outbreak of e : from coordinated multilateral action to effective disease containment, vaccine development, and beyond ai becomes an ally in the fight against covid- key: cord- -odtue a authors: comandatore, francesco; chiodi, alice; gabrieli, paolo; biffignandi, gherard batisti; perini, matteo; ricagno, stefano; mascolo, elia; petazzoni, greta; ramazzotti, matteo; rimoldi, sara giordana; gismondo, maria rita; micheli, valeria; sassera, davide; gaiarsa, stefano; bandi, claudio; brilli, matteo title: insurgence and worldwide diffusion of genomic variants in sars-cov- genomes date: - - journal: biorxiv doi: . / . . . sha: doc_id: cord_uid: odtue a the sars-cov- pandemic that we are currently experiencing is exerting a massive toll both in human lives and economic impact. one of the challenges we must face is to try to understand if and how different variants of the virus emerge and change their frequency in time. such information can be extremely valuable as it may indicate shifts in aggressiveness, and it could provide useful information to trace the spread of the virus in the population. in this work we identified and traced over time amino acid variants that are present with high frequency in italy and europe, but that were absent or present at very low frequencies during the first stages of the epidemic in china and the initial reports in europe. the analysis of these variants helps defining phylogenetic clades that are currently spreading throughout the world with changes in frequency that are sometimes very fast and dramatic. in the absence of conclusive data at the time of writing, we discuss whether the spread of the variants may be due to a prominent founder effect or if it indicates an adaptive advantage. the worldwide fast spread of sars-cov- virus during the first months of this year has caused , deaths with more than , , confirmed cases since the first reports of novel pneumonia in wuhan, hubei province, china (zhou et al. ; wu et al. ) up to may (who b . the virus belongs to the beta-coronavirus, and it is the seventh coronavirus known to infect humans, causing severe respiratory and systemic disorders (rothan and byrareddy ) , with a basic r index estimated to range from . to over . the closest known relatives of sars-cov- circulate in animals, specifically bats or pangolins (zhang, wu, and zhang ) , suggesting that an animal virus crossed species boundaries to efficiently infect humans, possibly through multiple passages in intermediate animal hosts, even though the transmission route has not been yet identified to date (andersen et al. ). traces of the history of the spread are present in the viral genome and comparative genomics approaches can therefore be used to understand how viruses can adapt to multiple hosts, uncovering key signatures of this adaptation (andersen et al. ; wan et al. ) , and to trace the infection routes of the virus. at the same time, genomic studies can help tracing viral variants that may be geographically restricted and/or may account for different levels of infectivity and mortality in humans. these variants might arise during the spread of the epidemic, as viruses are known for their high frequency of mutation, particularly in single stranded rna viruses -as in the case of sars-cov- (sanjuán and domingo-calap ) , which has a single, positive-strand rna genome. randomly generated variants can then spread in the population, due to stochastic reasons (i.e. founder effect, drift) or as a consequence of positive selection exerted by intrinsic biological features (such as the level of virus infectivity and its transmission rate), or extrinsic factors such as use of antivirals or reactions by the immune system or other defence mechanisms put in place by the host (di giorgio et al. ) . therefore, haplotype(s) present at the beginning of the epidemic spread can change in time; sometimes novel variants can overcome ancestral ones, and this can be a consequence of different levels of aggressiveness but also of mechanisms beyond selection. if the different variants are identical in terms of their ability to infect and replicate in the host, country-specific switches in haplotype frequency with respect to the most common haplotypes can depend on the very first haplotype(s) arriving in the country (provine ) . instead, when haplotype frequency changes globally, then the hypothesis of differential aggressiveness becomes more probable, indicating that the novel variants may be better adapted to infect human hosts; however, even in this case, the complexity of global human mobility or sampling bias, may originate patterns that may seem causal but are not. here, we present a comprehensive study of the coding sequences from sars-cov- genome sequences isolated since the beginning of the epidemic. italy was the first european country registering non-imported covid- cases requiring hospitalization. the first registered case of covid- was on february , , a young man in the lombardy region in northern italy, diagnosed with atypical pneumonia (livingston and bucher ) . in the next hours more cases were detected, and as of april th , italy registered , cases with , deaths, one of the highest toll in europe and in the world. who classifies the spreading occurring in italy as community transmission, indicating that the country is experiencing large outbreaks of local transmission with no possibility to trace transmission chains between the cases, and with multiple and unrelated clusters of transmission. the high mortality rate observed in italy, especially at the beginning of the epidemic raised the question whether italian strain(s) might have increased aggressiveness. while the increased mortality observed in italy could be explained by the fact that, at the beginning of the epidemic, swabs were performed only on individuals showing up at a hospital, distorting the sampling toward a group of symptomatic individuals devoid of healthy carriers, we cannot exclude that italian haplotype frequency are partially different, at least genetically. to have a better insight on the history and spread of the covid- pandemic in italy and thanks to the sequences deposited in the gisaid database, we identified non synonymous mutations that are differentially frequent in italian sars-cov- strains respect to strains circulating globally. these mutations are enriched in italy, but present in strains from other countries as well, as shown by tracing their relative frequency in time both globally and in different countries, therefore we traced their distribution worldwide and complemented with a phylogenetic analysis to understand how the variants are related. genomes were downloaded from the gisaid.org repository on april, , , and a second time on april, , , and are listed, together with reference to the submitting laboratories, in supplementary table . we extracted coding sequences using a strategy based on tblastn (camacho et al. ) comparisons using as queries all the proteins from the sars-cov- reference sequence deposited in ncbi (accession mn ). after the comparison, the coordinates of the blast alignments on each genome were used to extract the coding sequence. nucleotide sequences were then aligned and translated, and the alignments were manually checked for the presence of frameshifts, and manually edited. alignments were manually edited to remove partial and poorly aligned sequences, resulting in a variable number of sequences per alignment. this manual curation resulted in alignments containing a minimum number of sequences for orf a and a maximum of sequences for the nucleocapsid protein, with an average of sequences per alignment. we are aware that by removing sequences with gaps we are likely removing part of the genuine variability present (i.e. indels), however, we observed indels with such a low frequency that we attributed them mostly to sequencing/assembly errors and decided that the clear advantage of a stronger signal outweighs the possible disadvantages deriving from information loss. additional analysis with high quality genome sequences will be necessary to evaluate whether indels represent an important source of variation. regardless, this does not change the results of our analysis as the target of this work are point mutations. sequences from the alignments were used to build amino acid frequency profiles by using the r-package seqinr (charif and jr ) . basically, for each protein encoded in the sars-cov- we obtained two profiles, one for italian strains and one for the entire set of sequences. as the positions in the alignments for the two groups under examination are congruent, we can then calculate: that is the maximum log ratio of the frequency (f) of all amino acids at a certain position i in the alignment in italian ( it ) and total ( all ) sequences. then we identify positions with s> . that corresponds to the identification of positions where there is a frequency change in one of the residues of at least x. variability in multi-alignments was quantified by calculating entropy = − ∑ # - # : -# at each position of each manually curated protein multi-alignment. mutual information was calculated based on (buck and atchley ) to assess whether variants tend to co-occur frequently. to build updated time profiles of the identified variants, sequences were downloaded a second time from gisaid.org on april, , ( sequences, only high quality and high coverage). sampling dates were retrieved from the database and can be found in the gisaid sequence acknowledgment table (supplementary table ). sequences for which the geographic origin and/or the data were not correctly defined (supplementary table ), were removed, to obtain a database of about sequences, with some per-site variability due to the variable presence of ns in the sequences. we calculated two different time series, one for the entire set of sequences available up to the moment of sequence download, and one by considering only sequences taken from predefined groups of countries (hereinafter the time series by country). in the latter, we merged nearby countries to increase the precision of the estimation of the relative frequency of variants within predefined time intervals. the total time range since the first sequence available ( days) was split into ( for the analysis by country, as the number of sequences per interval is smaller) non-overlapping intervals of about days (~ days for the time series by country). interval duration was selected looking for a compromise among the number of sequences available on average per interval in the different groups and the time resolution of the time series. for each interval we calculated the frequency of the observed variants and the shannon diversity index considering all concatenated coding sequences (not limited to the positions considered in this work). in supplementary table we show the number of sequences used for each country for each interval. we performed a phylogenetic analysis by concatenating nucleotide aligned on the basis of the manually curated amino acid alignments. we selected the best phylogenetic model for our alignment using modeltest-ng (darriba et al. ) (gtr+i+ model) and then we performed maximum likelihood phylogenetic estimation in raxml (stamatakis ) . the obtained phylogenetic tree was then visualized and integrated with additional information about variants and geographical origin using figtree (https://github.com/rambaut/figtree/). our analysis allowed us to identify positions in four proteins that present drastic changes in amino acid frequencies when comparing italian sequences with worldwide sequences available on gisaid.org on april, , ( figure ). however, we discovered that residues found at these positions are not peculiar of italy and, as a matter of fact, they are the most variable genomic positions across available sars-cov- sequences (supplementary figure ) . therefore, we decided to proceed with a worldwide analysis. the sites that we identified are: . position in the spike protein, where an aspartate residue is found in high frequency in sequences obtained at the beginning of the pandemic. a variant, with a glycine residue at the same position is however now very common in europe, italy in particular. during the preparation of this manuscript, we realized that some of the variants are also the topic of other papers and preprints predating this work e.g. (korber et al. ; banerjee et al. ; somasundaram, mondal, and lawarde ; begum et al. ; bai et al. ; yang et al. ; pachetti et al. ) . the fact that we identify some of the previously known mutations by using a different approach indicates that they represent a genuine signal rather than artefacts; however, this does not necessarily mean that their increase in time (see below) is a consequence of a correspondingly increased transmissibility rate or aggressiveness in general -for which at the moment there is no conclusive data as stated in most of the available preprints. in the following, we summarize a thorough bibliographical analysis looking for functional information associated with these positions or the domains they belong to. however, we stress once more that virus spreading is characterized by haplotype shifts that are not necessarily related to the performances of the haplotypes themselves -for instance genetic drift or founder effect -therefore without targeted functional studies on the variants it is difficult to ascertain whether one or the other explanation is more probable. figure for a confirmation of the variability of these positions in the entire set of sequences. note that to cope with zeros when taking the logarithm of the ratio of amino acid frequencies, we add a small number to every frequency that depends on the number of sequences in the two groups (italian and world). this makes so that positions with identical amino acid frequencies in the two groups do not get an s exactly equal to zero. d is located in the sd domain of the spike protein. it is positioned in a loop right after a beta-strand and close to a completely solvent exposed disordered region outside and downstream the ace interaction domain (wrapp et al. ; walls et al. ) . the resolution of the three available structures is not high enough to thoroughly discuss h-bond network. it is likely that d side chain does not establish close interactions with neighboring residues. conformationally, d lies in the region of left-handed helices. thus, from the structural point of view, the mutation d g is likely to be neutral (no particularly strong interactions lost from the missing carboxylate group). on the other hand, the mutation might even be beneficial for overall protein stability: given the increased conformational freedom of glycine, it is indeed a perfect residue in turns following beta structures. other authors suggest a positive effect of d g on the virus efficiency in binding the ace receptor. korber and colleagues (unpublished, (korber et al. ) ) suggest the possibility of structural changes in the protein or even an improved antibody-dependent enhancement effect. in coronaviruses, orf is translated to yield the polyprotein that is processed by proteolysis with the production of intermediate and mature nonstructural proteins (nsps). in figure we highlight the position of the variant sites on the polyprotein with respect to known domains, as defined by the conserved domain database ). position corresponds to residue of the non-structural protein (nsp ) which is characterized by four transmembrane helices (th) (angeletti et al. ) , whose role is still unknown. more in detail, position lies at the n-terminal, which protrudes from the external face of the membrane. interaction analysis of the corresponding protein from sars virus shows that nsp can form dimeric or multimeric complexes that can also involve additional viral proteins (nsp , nsp , nsp , nsp , nsp , nsp , orf a) (von brunn et al. ) suggesting that nsp might be involved in the viral life cycle. sars nsp also interact with host proteins, such as prohibitin and (cornillez-ty et al. ), that are involved in cell cycle progression, migration, differentiation, apoptosis and mitochondrial biogenesis (fusaro et al. ; merkwirth and langer ; rajalingam et al. ; sun et al. ) suggesting it might be important to manipulate prominent host functions. murine hepatitis virus and sars-cov strains deleted in this portion of the polyprotein (graham et al. ) have a strongly reduced viral growth and rna synthesis, but are not affected at the level of protein processing. ectopic expression of the nucleotide sequence coding for nsp in murine cells infected by strains missing nsp , allowed to detect its recruitment in viral complexes. it is therefore possible that nsp is involved in global rna synthesis, interaction with host proteins and pathogenesis (von brunn et al. ). in infected cells, nsp seems to be present in small vesicular foci, but in absence of additional viral proteins it localizes in cytoplasmic or nuclear membranes, without a specific target (prentice et al. ; von brunn et al. ). unfortunately, mutagenesis experiments are still not available for sars-cov , and therefore we still do not know whether the variant observed at this site has any effect on in vivo virus properties. position belongs to nsp , a protein that induces the formation of autophagosomes, which is a sign of starvation in uninfected cells (cottam, whelband, and wileman ) . autophagosomes can act as an innate defense against viral infection but they can be hijacked and support the assembly of coronavirus replicase proteins (orvedahl et al. ; suhy, giddings, and kirkegaard ; wileman ). together with nsp and nsp , nsp moreover promotes the formation of the double membrane vesicles typically observed in sars disease (angelini et al. ). nsp is a protein with transmembrane domains (oostra et al. ) and position lays in the luminal loop between the first and second hydrophobic transmembrane domains. in the wild type sars-cov- sequence, we find phenylalanine residues just before l . instead, some of the variants in this paper have a stretch of phenylalanine, keeping this region highly hydrophobic. position belongs instead to the n-terminal domain of the rna-directed rna polymerase (rdrp, also known as nsp ). by inspecting its three-dimensional structure, sars-cov- rdrp displays a n-terminal nidovirus-like rdrp-associated nucleotidyltransferase domain (niran) followed by an interface domain and then by the canonical palm and finger domain structure (gao et al. ) . p (p according to nsp numbering) is located in the alpha-beta interface domain which bridges niran with the finger domain. specifically, p sits on a solvent exposed loop region in the groove formed between niran and the finger domain. the mutation p l mutation does not change the non-polar nature of the side chain and from the conformational point of view the substitution from p to l should not result in specific structural adjustment of the loop. thus, despite no information concerning mutations at the specific sites identified in this work, the three variant sites in the polyprotein belong to important functional regions of the sequence. orf codes for a secreted accessory protein not directly involved in viral replication (dediego et al. ; yount et al. ; tan et al., ) . homologs have been found in some beta-coronavirus, named orf a (tan et al., ) . orf a of sars codes for a protein with a structure similar to immunoglobulin superfamily proteins, specifically the metazoan ig involved in adhesion (nelson et al. ; hänel et al. ) . the function of this protein is not entirely clear, but could be related to the modulation of the immune system. studies have demonstrated that sars-orf a protein localizes mainly in the perinuclear region of the host cell, where it interacts with bst- (bone marrow stromal antigen ) preventing the glycosylation of bst- needed for functioning (taylor et al. ) . bst- inhibits the release of the virus, as observed in hiv- (taylor et al. ) likely at the level of the endoplasmic reticulum-golgi where it binds budding virions. orf has a structure composed of a beta-sandwich fold with seven beta-stands, which highly resembles orf a's structure, but it lacks the c-terminal transmembrane region and has an additional long insert between strands and which is supposed to be involved in peptide binding (tan et al., ) . orf is a fast-evolving gene which, together with the absence of the transmembrane region and the presence of the insertion may suggest some functional divergence with respect to its ancestor (tan et al., ) . it has been proposed that orf may have acquired a function similar to the adenoviral cr protein, which interferes with mhc molecules to attenuate the antigen presentation and therefore the capability of the host immune system to detect the virus. in this context, we notice that l lays within the orf insert, indicating it may represent a further adaptation. because direct functional information on this site is lacking at the moment, it is not possible to ascribe a functional adaptation to these variants; however, variability at this site might counteract mhc interference function, as a fast-evolving region in the insert may have been selected positively to facilitate the interaction with a fast-evolving host molecule (tan et al., ) . after having identified variant sites, we explored the time profile of the seven variable sites across all sequences (figure ) evidencing haplotype frequency changes for all of them between february and march, with five changes being moderate (nucleocapsid r g and g r, orf l s, polyprotein t i and l f) and two more drastic, now representing the most common haplotypes of non-chinese recent sequences (spike d g and polyprotein p l). the spike variant, in particular, was sequenced only few times in china since the beginning of the epidemy, the first time in zhejiang on january ; however, in this country it never reached a significant frequency. conversely, after the first sequencing of this variant in germany on january this variant started at very low-frequency and then became the most common haplotype at this position outside china. a similar situation is true for the haplotype with a leucine in position of the polyprotein -that rapidly increases since the beginning of march. these patterns seem indicative of a functional role for at least some of the variants that undergo an increase in frequency, but in the absence of any functional test or experimental data, we cannot rule out that the observed frequency changes are a consequence of a founder effect in europe followed by a spreading wave from europe to countries where the epidemic started later. a founder effect, however, implies that the founder arrives first, while this is not always the case, at least for some of the variants and part of the countries. at the same time some data both reviewed and unreviewed start to be available, suggesting that d g on the spike might provide some advantage to the virus. bai (bai et al. ) and brufsky (brufsky ) observed a correlation of g with increased mortality, while korber and coworkers (korber et al. ) found a correlation between the presence of the mutation and a higher viral load in patients. in the legend, we indicate the reference residue with an asterisk, and the variant on which we are focusing with an exclamation mark. additional variants were identified in the sequence dataset downloaded on april, , but they never reach significant percentages, at least at the moment. position on the spike and position on the polyprotein covary in a significant way (data not shown). the most likely explanation for this is the rapid sequential fixation of both mutations in the same strain, together with the absence of recombinations in between the two. the two adjacent sites in the nucleocapsid sequences show a perfect agreement in the time profiles, strongly suggesting that they happened together or within a short time. these two mutations respectively remove and add an arginine (passing from rg to kr); by considering the overall frequencies of the possible amino acid pairs at these positions, we suggest that the second arginine may complement the loss of the first one. indeed, rr is never observed, kg is extremely rare (relative frequency, r.f.= . ), while most genomes either present the original pair rg (r.f.= . ) or kr (r.f.= . ). we speculate that this could indeed be a consequence of the non-neutrality of configurations with no arginine at both positions, an information still not giving hints on the fitness of the fixed variant. next,we reasoned that grouping all the sequences uploaded from different countries may provide a picture averaged over variable and more complicated situations that might characterize the evolution of the virus within different countries or geographical areas. we therefore explored the time profiles of the variants in different geographical macro-regions ( figure and figure ) highlighting a highly heterogeneous situation. we also provide a movie illustrating the changes taking place in variant frequencies across overlapping time windows in macro-regions (supplementary movie ), which provides a dynamical view of the time profiles of the variants. figure shows that d g in china never reaches significant frequency while it increased quite rapidly in several areas where it arrived and where it often started at very low frequency with respect to the original haplotype. if a functional role for this mutation will be demonstrated, this pattern seems to indicate that different variants might have different fitness when interacting with different host's haplotypes, i.e. in case asian and european have different haplotypes concerning some of the proteins interacting with the spike, like for instance furin. to conclude, it is clear that since the first appearance of d g and other of the above variants, their relative frequency underwent a significant increase in several countries, most of the time overcoming in prevalence the original variant(s), except for china, south asia, south america and africa. in figure we summarize the most recent situation, by using sequences from the interval april to , . the best phylogenetic model selected according to aic and bic was gtr+i+g, for which the estimated substitution rate matrix contains the following rates, relative to the g<->t rate, taken as unity: a<->c= . , a<->g= . , a<->t= . , c<->t= . the extremely high rate for c to t (or better u, considering we are dealing with an rna virus) is in agreement with the involvement of host apobec-like editing mechanisms, as proposed in recent works (di giorgio et al. ) . besides not being the focus of this paper, these rates provide further evidence that host's mutagen systems may play an important role in the evolution of sars-cov- and its detection by the immune system. the phylogenetic tree integrated with additional information is reported in figure , with different coloring schemes and together with an evolutionary model summarizing how the different variants configurations are likely related to each other. when considering the information about the residues found at the seven positions on which we are focusing (hereinafter variants configurations, vcs), as in figure a , we find that the phylogenetic clades correspond to the six most frequent ones (accounting for over . % of the sequences), that is rgtlpdl, rgtlpds, rgtfpdl, krtllgl, rgtllgl, rgillgl -obtained by linking the variant residues in the order: protein nucleocapsid sites , and , polyprotein sites , and , spike site and orf site ; for this reason hereinafter we will use clades a to f interchangeably with the vcs written above. we are aware that the correlation is not perfect, as can be seen by the presence of additional but low frequency variants within each clade, or the presence of vc misplaced with respect to their major clade. misplaced sequences can be a consequence of insufficient phylogenetic signal or of convergent evolution. for instance, as anticipated above one of the chinese sequences carrying spike variant g (vc: rgtlpgs), is indeed contained within clade b (rgtlpds), indicating convergent evolution with the spike d g variant in clades d, e, f, or maybe an artifact. however, the limited number of similar cases supports our simplification and the correspondence among clades in the tree and vcs. our multi-alignment contains one sequence annotated as bat coronavirus (epi_isl_ ), which provides a rooting of the phylogenetic tree that falls in clade b and indeed contains most of the sequences obtained in china at the beginning of the epidemy ( figure , panel b) . the tree has two main "radiations", one corresponding to variants configurations rgtlpdl, rgtlpds, rgtfpdl and one to krtllgl, rgtllgl, rgillgl, therefore the main partition of the tree corresponds to the identity of residues at position of the spike and of the polyprotein. the two radiations are present at different frequencies in the same countries, with the notable exception of chinese sequences within radiation , except for epi_isl_ , the only sequence with a rgtllgl pattern sequenced in china that is also present in the phylogenetic tree (indicated in figure a ). this suggests that while most of the diversification of radiation took place in china and was then exported outside, the ancestor of radiation travelled outside china early to start a diversification in the countries where it arrived. this hypothesis is in agreement with the fact that epi_isl_ is placed very close to the root of the branch leading to radiation , indicating it may indeed represent a strain closely related to the true radiation ancestor. these observations raise important questions ( ) about the identity and movements of the first individual carrying the ancestral radiation variant outside china ( ) on the timing of the epidemic, but most importantly ( ) the reason why it did not increase in frequency in china but elsewhere. following the topology of the tree we propose an evolutionary model (figure c ) whereby the ancestral bat variants configuration (rgtvpds or any other present in the presently unknown animal host) evolved into rgtlpds and from this to rgtlpdl. we stress that this likely took place through unobserved states/hosts as the root branch length is close to the total length of the tree and therefore we do not consider mutation v l in the polyprotein full sequence as an adaptation to the human host. the latter originated rgtfpdl on one side, and the ancestor of radiation (rgtllgl) that originated both krtllgl (through kg unfit strains?) and later rgillgl. given the almost perfect agreement of the tree with the variants configurations, we analysed the geographical distribution and the time profiles of the seven sites at once, similar to what is done for mlst-based classification of pathogens. in figure a we show the time profiles of the relative abundance of sequences belonging to the clades, clearly showing not only the appearance and increase of the novel clades, but most importantly the gradual disappearance of sequences belonging to clade a (see also supplementary movies and ). when focusing on single clades across all macro-regions previously defined, we find a heterogeneous situation with different variants increasing in time in different countries. however, we can see that all vcs with a proline at position of the polyprotein and an aspartate at position of the spike almost disappear in time, remaining abundant only in south asia and oceania; in the rest of the world, only vcs with a leucine and a glycine at those positions remain in the last interval of our time range, after replacing the existing vcs. this is indeed clear from figure c showing that vc for clade a (rgtlpdl) is no more present in the interval april to , . south asia is particular because it is the only area where vcs of radiation (rgtllgl,krtllgl,rgillgl) are present for some time but then disappear with a re-increase of clade c (rgtfpdl). this may suggest these variants have equal phenotypic characteristics, but as written above, we cannot exclude differential fitness depending on host's haplotypes. by calculating the shannon index for sequences within the same intervals of times used to track the changes in frequency of the variants, we were able to trace the evolution of diversity in different places. peaks indicate the emergence (from outside or by evolution of pre-existing strains) of variants and their increase in frequency. values maintaining a high shannon index correspond to situations where different variants coexist at comparable frequencies, while a decrease after a peak means that after the appearance of one or more new variants / clades, one of them (novel or old) takes over -reducing the variability. we also indicate the first sampled sequence for each of the six clades. variability increases when a new variant appears, then it stays more or less stable when the existing variants maintain their relative frequencies. however, if one of the variants becomes dominant, then variability decreases again after a peak. increasing variability in time means that the arrival of novel variants continues steadily, or that the existing ones become more homogeneous in frequency. in this work, we identified seven positions in coding sequences of the sars-cov- genome that are characterized by a different pattern of amino acids when comparing italian sequences with the global trends around the world. further analysis revealed that these sites are not peculiar of italian strains, and that different combinations of these variants are present at varying relative frequencies in different geographic areas. we found that the combination of these residues identifies six abundant configurations that corresponds to phylogenetic clades and that cover over % of all sequences. this suggests that the characterization of these positions can represent a fast and portable method for the sars-cov- typing, but novel variants are emerging that might eventually take over the old ones through mutations at additional sites. using this approach we were able to follow the evolution of the virus over time among continents, showing that the different clades evolved in different moments and that their frequencies vary among continents. these sites are also the most variable among all available sars-cov- sequences, raising intriguing questions about their functional effects. variants with a leucine at position of the polyprotein together with a glycine at position of the spike, underwent an increase in frequency since the end of january in most countries, overcoming the original haplotypes. mutations that might affect the structure of the spike protein are of primary interest, since many vaccine candidates and serological tests rely on the conformation of this protein (who a). this and other works also explore the hypothesis that the variants may indeed provide a selective advantage to the virus. clade prevalence in different countries could be used to check for mortality rate differences and association with variants, but as the rates depend on many other factors (different screening strategies, different ways to define an individual infected and so on), we feel premature discussing such correlations. once the numbers will be standardized for different countries, this kind of associations, if present, will clearly emerge. moreover, to really clarify these issues, experimental data is required, such as for instance in the form of tninsertion mutagenesis, as performed on other viruses in the past (fulton et al. ) followed by competition experiments in in vitro cultures or the design of genomes carrying well-defined changes. this would allow to understand how the virus tolerate mutations at different sites and might provide information on the importance of different genomic regions for different stages of the infection. query seq. the proximal origin of sars-cov- covid- : the role of the nsp and nsp in its pathogenesis severe acute respiratory syndrome coronavirus nonstructural proteins , , and induce double-membrane vesicles evolution and molecular characteristics of sars-cov- genome mutational spectra of sars-cov- orf ab polyprotein and signature mutations in the united states of america analyses of spike protein from first deposited sequences of sars-cov from west bengal, india distinct viral clades of sars-cov- : implications for modeling of viral spread analysis of intraviral protein-protein interactions of the sars coronavirus orfeome networks of coevolving sites in structural and functional domains of serpin proteins blast+: architecture and applications seqinr . - : a contributed package to the r project for statistical computing devoted to biological sequences retrieval and analysis severe acute respiratory syndrome coronavirus nonstructural protein interacts with a host protein complex involved in mitochondrial biogenesis and intracellular signaling coronavirus nsp restricts autophagosome expansion modeltest-ng: a new and scalable tool for the selection of dna and protein evolutionary models pathogenicity of severe acute respiratory coronavirus deletion mutants in hace- transgenic mice evidence for host-dependent rna editing in the transcriptome of sars-cov- transposon mutagenesis of the zika virus genome highlights regions essential for rna replication and restricted for immune evasion prohibitin induces the transcriptional activity of p and is exported from the nucleus upon apoptotic signaling structure of the rna-dependent rna polymerase from covid- virus the nsp replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication solution structure of the x protein coded by the sars related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin i domains spike mutation pipeline reveals the emergence of a more transmissible form of sars-cov- coronavirus disease (covid- ) in italy genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding cdd/sparcle: the conserved domain database in the coronavirus nucleocapsid is a multifunctional protein prohibitin function within mitochondria: essential roles for cell proliferation and cristae morphogenesis structure and intracellular targeting of the sars-coronavirus orf a accessory protein topology and membrane anchoring of the coronavirus replication complex: not all hydrophobic domains of nsp and nsp are membrane spanning hsv- icp . confers neurovirulence by targeting the beclin autophagy protein emerging sars-cov- mutation hot spots include a novel rna-dependent-rna polymerase variant identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins ernst mayr: genetics and speciation prohibitin is required for ras-induced raf-mek-erk activation and epithelial cell migration the epidemiology and pathogenesis of coronavirus disease (covid- ) outbreak mechanisms of viral mutation genomics of indian sars-cov- : implications in genetic diversity, possible origin and spread of virus raxml version : a tool for phylogenetic analysis and post-analysis of large phylogenies remodeling the endoplasmic reticulum by poliovirus infection and by individual viral proteins: an autophagy-like origin for virus-induced vesicles akt binds prohibitin and relieves its repression of myod and muscle differentiation novel immunoglobulin domain proteins provide insights into evolution and pathogenesis mechanisms of sars-related coronaviruses severe acute respiratory syndrome coronavirus orf a inhibits bone marrow stromal antigen virion tethering through a novel mechanism of glycosylation interference structure, function, and antigenicity of the sars-cov- spike glycoprotein receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus who, coronavirus disease (covid- ) situation report aggresomes and autophagy generate sites for virus replication cryo-em structure of the -ncov spike in the prefusion conformation a new coronavirus associated with human respiratory disease in china genomic, geographic and temporal distributions of sars-cov- mutations severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice probable pangolin origin of sars-cov- associated with the covid- outbreak a pneumonia outbreak associated with a new coronavirus of probable bat origin all authors wish to thank the www.gisaid.org and all the researchers that contributed their sequences to the database for sharing fundamental data for research. we think collaboration is the only approach to counteract the spread of sars-cov- and other similar endeavors. references for all sequences used in this work are in supplementary key: cord- - at euqm authors: rokohl, alexander c.; loreck, niklas; wawer matos, philomena a.; mor, joel m.; zwingelberg, sarah; grajewski, rafael s.; cursiefen, claus; heindl, ludwig m. title: die rolle der augenheilkunde in der covid- -pandemie date: - - journal: ophthalmologe doi: . /s - - - sha: doc_id: cord_uid: at euqm the severe acute respiratory syndrome coronavirus (sars-cov- ) causing coronavirus disease (covid- ) has led to a worldwide pandemic. this pandemic presents a huge challenge for the healthcare system and also for ophthalmologists. previous studies and case reports indicated that sars-cov‑ also infects the conjunctiva resulting in conjunctivitis. in addition, infectious virus particles in the tear fluid can be potential sources of infection; however, the detection of sars-cov‑ rna in the tear fluid has rarely been successful. although isolated conjunctival involvement is highly unlikely, at the current point in time of the covid- pandemic, practically every patient examined by an ophthalmologist could be infected with sars-cov‑ . therefore, protective and hygiene measures should currently be consistently followed to minimize the risk of spreading the virus. currently, there are no treatment recommendations for conjunctivitis associated with covid- . tear substitutes might be helpful for symptom relief but there is no evidence for a topical antiviral therapy. in the future ophthalmologists could play a decisive role in the screening of maculopathies that might occur during covid- treatment using chloroquine or hydroxychloroquine. im dezember wurde dr. li wenliang, ein augenarzt aus der volksrepublik china, in seinem krankenhaus auf patienten, die alle unter einem schweren akuten atemnotsyndrom litten und vorher einen großmarkt in wuhan besuchten, aufmerksam. später wurde diese krankheit corona-virus-disease- (covid- ) getauft, da dieses erstmals beschrieben wurde [ ] . das covid- auslösende severe-acute-respiratory-syndrome-related coronavirus- (sars-cov- ) wurde durch die coronavirus-studiengruppe des internationalen komitees zur taxonomie von viren (international committee on taxonomy of viruses) aufgrund der sehr engen verwandtschaft zum sars-virus (sars-cov), an dem / hunderte menschen gestorben waren, benannt. sars-cov- verbreitete sich innerhalb weniger wochen und verursachte eine weltweite pandemie. an covid- verstarb nicht nur dr. li wenliang, sondern auch weitere zehntausende menschen. die ganze welt steht daher vor neuen und gewaltigen herausforderungen. neben sozialen und wirtschaftlichen auswirkungen steht natürlich die medizinische versorgung im vordergrund, die auch die augenheilkunde betrifft [ , , , ] . eines der hauptziele in deutschland ist die vermeidung von hohen infektionszahlen, die das gesundheitssystem überlasten und damit zu noch höheren mortalitätsraten führen könnten [ ] . frühzeitig sind deshalb deutschlandweit vorbereitungen und umstrukturierungen getroffen worden, um patienten und mitarbeiter trotz eines mangels an benötigter ausrüstung möglichst effektiv zu schützen und um eine adäquate versorgung aufrechtzuerhalten. das elektive routineprogramm in kliniken wurde dazu weitestgehend für einige wochen gestoppt, ambulante vorstellungen von patienten wurden entsprechend den empfehlungen auf nichtverschiebbare, dringliche und notfallmäßige fälle beschränkt [ , ] . da der schwerpunkt in der regel auf epidemiologischen, infektiologischen und intensivmedizinischen themen liegt, soll dieser beitrag einen Überblick über die ophthalmologischen implikationen während der covid- -pandemie geben. neben der okulären beteiligung durch die covid- soll auch auf die gefährdung von augenärztinnen und augenärzten eingegangen werden. zudem soll die rolle der ophthalmologie bei der therapie von covid- erörtert werden. das verständnis darüber, wie sich co-vid- aus epidemiologischer sicht verbreitet, beruht bisher noch weitgehend auf erfahrungsberichten und dem, was über andere, ähnliche coronaviren bekannt ist. bisherige studien legen eine hohe infektiosität von sars-cov- nahe. aktuell geht man davon aus, dass die viren v. a. über aerosole, die beim husten oder niesen einer infizierten person entstehen, von menschen zu menschen übertragen werden [ , [ ] [ ] [ ] [ ] . auch Übertragungen über die tränenflüssigkeit sind möglich. virale rna wurde beispielsweise auch in stuhlproben von infizierten patienten gefunden, was eine fäkal-orale Übertragung oder auch eine schmierinfektion vorstellbar macht [ ] . die vorliegenden erkenntnisse deuten jedoch auch darauf hin, dass sars-cov- häufig durch asymptomatische patienten verbreitet wird [ ] . insbesondere kinder waren meist asymptomatisch und hatten kaum schwere verläufe [ ] . allerdings gibt es hinweise, dass gerade bei infizierten kindern die virusausscheidung länger andauert als bei erwachsenen [ ] . kinder könnten dabei eine entscheidende rolle bei der Übertragung von sars-cov- spielen [ ] . auch dr. li wenliang, der augenarzt, der die covid- als einer der ersten entdeckte und später auch an der krankheit verstarb, könnte von einem asymptomatischen patienten infiziert worden sein [ ] . die inkubationszeit betrug im median tage [ ] , während die mediane dauer der virusausscheidung von infizierten patienten ca. tage beträgt. die patienten leiden typischerweise an fieber, trockenem husten und kurzatmigkeit [ ] . auch diarrhöen, kopf-und gliederschmerzen, abgeschlagenheit sowie geruchs-und geschmacksveränderungen sowie weitere neurologische komplikationen (wie zentrale atemdepression, ischämische zerebrale insulte, meningitis) können vorkommen [ , , [ ] [ ] [ ] ] . zu den komplikationen in schweren fällen gehören v. a. eine lungenentzündung, ggf. mit akutem lungenversagen bis hin zum multiorganversagen [ ] . schwere verläufe mit relativ hohen sterblichkeitsraten kommen insbesondere bei älteren menschen und bei menschen mit komorbiditäten wie immunsuppression, atemwegserkrankungen und diabetes mellitus vor, jedoch sind diese auch bei allgemeinmedizinisch ansonsten als gesund befunde- abb. ophthalmologische untersuchung einer patientin an der spaltlampe. die patientin trägt einen mundschutz. die augenärztin ist durch eine schutzbrille, eine n -atemschutzmaske und einen spaltlampenschutz geschützt nen personen aufgetreten, und zwar in jedem alter [ ] . mittlerweile liegen diverse fallberichte und einige, meist kleinere ophthalmologische studien über eine okuläre beteiligung bei covid- , überwiegend aus china, vor [ - , , , , , ] . diese deuten darauf hin, dass sars-cov- meist eine milde follikuläre bindehautentzündung verursacht, die ansonsten nicht von anderen viralen konjunktivitiden zu unterscheiden ist [ , ] . aber auch das auftreten einer keratokonjunktivitis mit visusminderung ist möglich [ ] . die okuläre beteiligung kann möglicherweise durch aerosolkontakt oder hand-zu-augen-kontakt mit der bindehaut ausgelöst werden. da das virus möglicherweise auch via neurale bahnen sich ausbreiten kann, sind auch infektionswege über zentrale hirnnerven denkbar [ ] . die (kerato-)konjunktivitis scheint entweder als sehr frühes anzeichen einer milden infektion oder während eines krankenhausaufenthaltes aufgrund einer schweren covid- -erkrankung im späteren verlauf aufzutreten [ ] . die genaue inzidenz einer konjunktivitis scheint aktuell noch unklar zu sein. eine retrospektive, chinesische studie, die im new england journal of medicine veröffentlicht wurde und sich v. a. mit nichtophthalmologischen symptomen befasst hat, zeigt lediglich bei von ( , %) hospitalisierten patienten mit laborbestätigter covid- eine klinische bindehautbeteiligung [ ] . jedoch wurde hier keine ophthalmologische untersuchung dokumentiert, und es wurden keine tränenflüssigkeitsproben oder bindehautabstriche entnommen. in weiteren, kleineren studien betrug die inzidenz jedoch bis zu % bei hospitalisierten patienten [ ] . zudem konnte in mehreren studien mit hospitalisierten covid- -patienten sars-cov- -rna in der tränenflüssigkeit nachgewiesen werden [ , , , ] . insgesamt deuten die ergebnisse darauf hin, dass sars-cov- die bindehaut infizieren, eine bindehautentzündung verursachen kann und dass infektiöse viruspartikel in tränenflüssigkeit potenzielle infektionsherde darstellen können. der nachweis von sars-cov- -rna in der tränenflüssigkeit gelang jedoch sehr selten [ , , , ] . allerdings sind die gründe dafür ebenfalls noch unklar. es ist bisher beispielsweise nicht untersucht, wie hoch die sensitivität dieser bindehautabstriche überhaupt ist. eine relativ geringe sensitivität könnte eine erklärung für den seltenen virusnachweis bei den konjunktivitiden sein. aktuell gibt es keinerlei therapieempfehlungen einer covid- -assoziierten konjunktivitis. tränenersatzmittel könnten zur symptomlinderung hilfreich sein. zudem liegen einzelfallberichte über eine erfolgreiche antivirale therapie mit topischer anwendung von valaciclovir und ganciclovir vor [ , ] the severe acute respiratory syndrome coronavirus (sars-cov- ) causing coronavirus disease (covid- ) has led to a worldwide pandemic. this pandemic presents a huge challenge for the healthcare system and also for ophthalmologists. previous studies and case reports indicated that sars-cov- also infects the conjunctiva resulting in conjunctivitis. in addition, infectious virus particles in the tear fluid can be potential sources of infection; however, the detection of sars-cov- rna in the tear fluid has rarely been successful. although isolated conjunctival involvement is highly unlikely, at the current point in time of the covid- pandemic, practically every patient examined by an ophthalmologist could be infected with sars-cov- . therefore, protective and hygiene measures should currently be consistently followed to minimize the risk of spreading the virus. currently, there are no treatment recommendations for conjunctivitis associated with covid- . tear substitutes might be helpful for symptom relief but there is no evidence for a topical antiviral therapy. in the future ophthalmologists could play a decisive role in the screening of maculopathies that might occur during covid- treatment using chloroquine or hydroxychloroquine. weiterhin müssen bereits im vorfeld wechselzeiten bei ophthalmologischen operationen wie insbesondere bei intravitrealen operativen medikamenteneingaben angepasst und auch operationsplanungen und -volumina verändert werden, da die abstands-und hygieneregeln selbstverständlich nicht nur in wartebereichen, sondern auch im operationstrakt und im aufwachraum eingehalten werden müssen. um den zukünftigen bedarf an elektiven, ambulanten konsultationen zu decken und gleichzeitig die ansteckungsgefahr zu reduzieren, halten wir die etablierung von video-und telefonsprechstunden, wie vielerorts bereits geschehen, für ratsam. wie lange all diese maßnahmen und in welchem umfang sie aufrechterhalten werden müssen, wird sich jedoch erst im verlauf zeigen. entscheidend scheinen hier die zulassung von impfstoffen und/oder die einführung einer adäquaten antiviralen therapie zu sein. da die okulären symptome inklusive einer konjunktivitis im rahmen der co-vid- meist mild zu verlaufen scheinen, wird dem augenarzt hier vermutlich keine große rolle zukommen. jedoch ist bisher noch nicht untersucht, ob eine infektion mit sars-cov- nicht zu okulären immunreaktionen oder langzeitfolgen führen kann. allerdings ophthalmologic considerations and testing in patients receiving long-term antimalarial therapy keratoconjunctivitis as the initial medical presentationofthenovelcoronavirusdisease (covid- ) selfreported olfactory and taste disorders in sars-cov- patients: a cross-sectional study clinical characteristics of coronavirus disease in china covid- in children: more than meets the eye sars-cov- -a challenge for all of us assessing viral shedding and infectivity of tears in coronavirus disease (covid- ) patients novel coronavirus disease (covid- ): the importance of recognising possible early ocular manifestation and using protective eyewear there may be virus in conjunctival secretion of patients with covid covid- : face masks and human-to-human transmission. influenza other respir viruses jiazf( ) -ncovtransmission through the ocular surface must not be ignored the covid- pandemic and otolaryngology: what it comes down to? laryngorhinootologie olfactory and gustatory dysfunction in coronavirus disease (covid- ) neurologic manifestations of hospitalized patients with coronavirus disease in wuhan, china recommendations on screening for chloroquine and hydroxychloroquine retinopathy ( revision) a first case of meningitis/encephalitis associated with sars-coronavirus- ophthalmologists are more than eye doctors-in memoriam li wenliang isnovelcoronavirusdisease (covid- ) transmitted through conjunctiva? jmedvirol transmission of -ncov infection from an asymptomatic contact in germany can the coronavirus disease (covid- ) affect the eyes? a review of coronaviruses and ocular implications in humans and animals aerosol and surface stability of sars-cov- as compared with sars-cov- characteristics of ocular findings of patients with coronavirus disease (covid- ) in hubei province evaluation of coronavirus in tears and conjunctival secretions of patients with sars-cov- infection a comprehensive chinese experience against sars-cov- in ophthalmology the use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease (covid- ): the perspectives of clinical immunologists from china the evidence of sars-cov- infection on ocular surface key: cord- -ufcvecwo authors: qiu, ruijin; wei, xuxu; zhao, mengzhu; zhong, changming; zhao, chen; hu, jiayuan; li, min; huang, ya; han, songjie; he, tianmai; chen, jing; shang, hongcai title: outcome reporting from protocols of clinical trials of coronavirus disease (covid- ): a review date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: ufcvecwo objectives: to examine heterogeneity of outcomes in protocols of clinical trials of coronavirus disease (covid- ) and to identify outcomes for prioritization in developing a core outcome set (cos) in this field. design: this study is a review. data sources: databases of icmje-accepted clinical trial registry platform were searched on february , . eligibility criteria: randomized controlled trials (rcts) and non-rcts of covid- were considered.conditions of patients include common type, severe type or critical type. interventions include traditional chinese medicine (tcm) and western medicine. we excluded trials that for discharged patients, psychological intervention and complications of covid- . data extraction and synthesis: the general information and outcomes, outcome measurement instruments and measurement times were extracted. the results were analysed by descriptive analysis. results: registry platforms were searched. a total of protocols were included from protocols. for protocols of tcm clinical trials, outcomes from outcome domains were reported, and almost half ( / , . %) of outcomes were reported only once; the most frequently reported outcome was time of sars-cov- rna turns to negative. ( / , . %) outcomes were provided one or more outcome measurement instruments. outcomes were provided one or more measurement time frame. for protocols of western medicine clinical trials, outcomes from outcome domains were reported; almost half ( / , . %) of outcomes were reported only once; the most frequently reported outcome was proportion of patients with negative sars-cov- . outcomes were provided one or more outcome measurement instruments. ( / , . %) outcomes were provided one or more measurement time frame. conclusion: outcome reporting in protocols of clinical trials of covid- is inconsistent. thus, developing a core outcome set is necessary. keywords: outcomes; clinical trials, covid- ; review. . this review is the first to describe variation in outcomes, outcome measurement instruments and outcome measurement time reporting in clinical trials for coronavirus disease (covid- ). . all the database of icmje-accepted clinical trial registry platform were searched, and randomized controlled trials and observational studies were considered. . the aim of this review was to provide a list of outcomes for clinical trials of covid- , both interventions of traditional chinese medicine and western medicine were considered. . when the searching was conducted, no clinical trials were registered by countries out of china, so all of included protocols were from china. shown in figure . figure . all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . in the outcome domains of protocols of western medicine clinical trials, outcome domains (adverse events/effects, delivery of care, economic, metabolism and nutrition outcomes, mortality/survival) consisted of only one outcome. these outcomes are reported between and times, and the median outcome reporting time is . respiratory, thoracic and mediastinal outcomes included the largest number of outcomes, which includes outcomes; chest imaging is reported more frequently than other outcomes. the number of outcomes in different outcome domains in protocols of western medicine clinical trials is shown in figure . this review is the first to evaluate the outcome reporting of protocols of tcm and western medicine clinical trials for treating covid- . the results showed variations in the outcome reporting. for outcome measurement instruments/outcome definitions and outcome measurement time, there is also heterogeneity. however, many primary investigators did not provide outcome measurement instruments/outcome definitions or outcome measurement time. it is difficult to predict results of clinical trials now. but it is obvious that these problems may result in the exclusion of some studies from systematic reviews/meta-analyses due to the heterogeneity of outcomes or outcome measurements. it is a waste. in this review, we find that there are more than duplicated outcomes between protocols of tcm and western medicine clinical trials. no matter for clinical trials of tcm or western medicine, etiological test, chest imaging, respiratory symptoms, temperature, mortality/survival and adverse events are very important. these outcomes are relevant to the prognosis of disease and safety of therapy. because of no specific therapy can be used in the treatment of covid- , it is necessary and urgent to conduct clinical trials, no matter what the interventions are. we believe that it is important to develop a cos for clinical trials of tcm and western medicine for treating covid- , so that the efficacy of different interventions can be compared and merged in systematic review/meta-analysis. all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/ . / . . . doi: medrxiv preprint author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. . wu c. nasal high-fow preoxygenation assisted fibre-optic bronchoscope intubation in patients with critical all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the all rights reserved. no reuse allowed without permission. author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/ . / . . . doi: medrxiv preprint author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/ . / . . . doi: medrxiv preprint a taxonomy has been developed for outcomes in medical research to help improve knowledge discovery a prospective comparative study for xue-bi-jing injection in the treatment of novel coronavirus pneumonia (covid- ) clinical controlled trial for traditional chinese medicine in the treatment of novel coronavirus pneumonia chinese herbal medicine for severe nevel coronavirus pneumonia (covid- ): a randomized controlled trial a randomized controlled trial of integrated tcm and western medicine in the treatment of severe novel coronavirus pneumonia a single arm study for combination of traditional chinese and western medicine in the treatment of novel coronavirus pneumonia (covid- ) combination of traditional chinese medicine and western medicine in the treatment of common type novel coronavirus pneumonia (covid- ) a single arm study for evaluation of integrated traditional chinese and western medicine in the treatment of novel coronavirus pneumonia a randomized, open-label study to evaluate the efficacy and safety of low-dose corticosteroids in hospitalized patients with novel coronavirus pneumonia clinical study of arbidol hydrochloride tablets in the treatment of novel coronavirus pneumonia glucocorticoid therapy for critically ill patients with severe acute respiratory infections caused by noval coronovirus -ncov: a prospective efficacy and safety of darunavir and cobicistat for treatment of pneumonia caused by -ncov (daco-ncov randomized controlled clinical study of interferon atomization in the -ncov pneumonia randomized controlled clinical study of antiviral therapy in the -ncov pneumonia mild/moderate -ncov remdesivir rct severe -ncov remdesivir rct clinical study of arbidol hydrochloride tablets in the treatment of pneumonia caused by novel coronavirus open,controlled clinical study to evaluate the efficacy of asc f and ritonavir for -ncov pneumonia the efficacy of intravenous immunoglobulin therapy for severe -ncov infected pneumonia efficacy and safety of hydroxychloroquine for treatment of pneumonia caused by -ncov ( hc-ncov efficacy of therapeutic effects of hydroxycholoroquine in novel coronavirus pneumonia . qin n. the efficacy of different hormone doses in -ncov severe pneumonia evaluating and comparing the safety and efficiency of asc /ritonavir and lopinavir/ritonavir for novel coronavirus infection the efficacy of lopinavir plus ritonavir and arbidol against novel coronavirus infection (elacoi) patients infected with novel coronavirus washed microbiota transplantation for patients with -ncov infection vitamin c infusion for the treatment of severe -ncov infected pneumonia treatment of acute severe -ncov pneumonia with immunoglobulin from cured patients clinical study of nebulized xiyanping injection in the treatment of novel coronavirus pneumonia convalescent plasma for the treatment of severe novel coronavirus pneumonia (covid- ): a prospective randomized controlled trial cohort study of novel coronavirus pneumonia (covid- ) critical ill patients a multicenter, randomized, open label, controlled trial for the efficacy and safety of asc / ritonavir compound tablets and lopinavir/ ritonavir (kaletra) and arbidol tablets in the treatm ent of novel coronavirus pneumonia (covid- ) a study for the efficacy of hydroxychloroquine for mild and moderate covid- infectious combined with vitamin c tablets in the treatment of common novel coronavirus pneumonia (covid- ) in the basic of clinical standard antiviral treatment to evaluate the safety and efficiency a randomized, open-label, blank-controlled, multicenter trial for polyinosinic-polycytidylic acid injection in the treatment of novel coronavirus pneumonia clinical application of ecmo in the treatment of patients with very serious respiratory failure due to novel coronavirus pneumonia (covid- ) immunomodulatory therapy for severe novel coronavirus pneumonia (covid- ) clinical study for anti-aging active freeze-dried powder granules in the treatment of acute novel coronavirus pneumonia (covid- ) clinical study for umbilical cord blood mononuclear cells in the treatment of acute novel coronavirus pneumonia (covid- ) clinical study for cord blood mesenchymal stem cells in the treatment of acute novel coronavirus pneumonia (covid- ) clinical study of cord blood nk cells combined with cord blood mesenchymal stem cells in the treatment of acute novel coronavirus pneumonia immunoregulatory therapy for umbilical cord(uc)-derived mesenchymal stem cells(mscs) treatment for the -novel not required. the data is from public database and does not include identifiable patient data. key: cord- -io f kn authors: killeen, g.; kiware, s. title: why lockdown? simplified arithmetic tools for decision-makers, health professionals, journalists and the general public to explore containment options for the novel coronavirus date: - - journal: nan doi: . / . . . sha: doc_id: cord_uid: io f kn half the world's population is already under lock-down and the remainder will have to follow if the ongoing novel coronavirus (covid- ) virus pandemic is to be contained. faced with such brutally difficult decisions, it is essential that as many people as possible understand ( ) why lock-down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes, ( ) why these need to be implemented so early, so aggressively and for such extended periods, and ( ) why international co-operation to conditionally re-open trade and travel between countries that have successfully eliminated local transmission represents the only way to contain the pandemic at global level. here we present simplified arithmetic models of covid- transmission, control and elimination in user-friendly shiny and excel formats that allow non-specialists to explore, query, critique and understand the containment decisions facing their country and the world at large. based on parameter values representative of the united republic of tanzania, which is still early enough in its epidemic cycle and response to avert a national catastrophe, national containment and elimination with less than deaths is predicted for highly rigorous lock down within weeks of the first confirmed cases and maintained for weeks. however, elimination may only be sustained if case importation from outside the country is comprehensively contained by isolating for three weeks all incoming travellers, except those from countries certified as covid-free in the future. any substantive relaxation of these assumptions, specifically shortening the lock-down period, less rigorous lock-down or imperfect importation containment, may facilitate epidemic re-initiation, resulting in over half a million deaths unless rigorously contained a second time. removing contact tracing and isolation has minimal impact on successful containment trajectories because high incidence of similar mild symptoms caused by other common pathogens attenuates detection success of covid- testing. nevertheless, contact tracing is recommended as an invaluable epidemiological surveillance platform for monitoring and characterizing the epidemic, and for understanding the influence of interventions on transmission dynamics. for all but the most expert specialists, the silent early phase of an epidemic, when there is still time to contain it, is often imperceptible and difficult to grasp the significance of. this is especially true for pathogens like novel coronavirus- (covid- ) that largely exhibit only mild symptoms, if any, - that are non-specific and difficult to distinguish from other, more common illnesses. currently, half the world's population is already under lock-down of some kind, meaning vertically enforced and severe restrictions of movement, and the remainder will have to follow if the ongoing covid- virus pandemic is to be contained. faced with such brutally difficult decisions, it is essential for policy-makers, health professionals, journalists and the general public that as many people as possible understand ( ) why lock-down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes, ( ) why these need to be implemented so early, so aggressively and for such extended periods, and ( ) why international co-operation to conditionally re-open trade and travel between countries that have successfully eliminated local transmission represents the only way to contain the pandemic at global level. here we introduce a simplified arithmetic modelling tool for predicting covid- transmission dynamics and how it is likely to respond to different containment, delay or mitigation strategies. we coin the term arithmetic modelling, as distinct from the ubiquitously used term mathematical modelling, to convey the fact that it uses only addition, subtraction, multiplication, division, rounding off, a few conditional statements (eg. if, less than/greater than, and/or), and two unavoidable power terms, to make the necessary calculations. this tool includes no differential equations, calculus, limits, distributions, stochastic simulations or agent-based approaches that would render it opaque to most non-specialist readers, such as medical and public health practitioners, decision-makers, journalists and the general public. the model is presented in userfriendly excel® and shiny® formats that allow non-specialists to explore, query, critique and understand the containment decisions facing their country and the world at large. for those who wish to satisfy themselves that the calculations make intuitive sense, the excel® version provides a complementary spreadsheet format in which the formula for each cell can be critically examined. for those content to accept the underlying arithmetic, the shiny® format provides a convenient interactive web application that can be used on any device. while a formal mathematical description of this model has been critically reviewed by specialist experts, it is provided only as an online supplement because none of the principles, assumptions or predictions are entirely new, and because in our experience nothing deters non-specialists from reading an article faster than equations do. we caution readers not to expect too much from any predictive model in terms of exact numerical reliability, [ ] [ ] [ ] and note that this one is no different. we specifically advise against interpreting the exact numbers this tool generates at face value: any predictive model is, by definition, a deliberately simplified representation of complex real-world processes, the usefulness of which is largely subjective. [ ] [ ] [ ] the exact numerical predictions should therefore not be used to confidently define precise operational timelines for introducing and sustaining interventions, or set effectiveness thresholds required of specific containment measures. instead, the purpose of this tool is to help users broadly understand the inevitable consequences of an uncontained epidemic, explore the likely outcomes a wide range of different possible containment strategies, identify those which could plausibly succeed and understand the failures of those which seem unlikely to do so. prospectively and will be too late to quantify retrospectively. they should therefore factor such unknown levels of uncertainty into their response plans by allowing for wide margins for error when planning the timing, intensity and duration of new interventions, always being more ambitious and cautious whenever in any doubt. assumed input parameters values were chosen to be representative of the united republic of tanzania (table ) , because it has experienced relatively modest inbound air traffic from china , and is still early enough in its epidemic cycle and response for a national catastrophe to be averted. tanzania has also had more opportunity to learn from ongoing experiences in asia, europe and north america, and prepare by establishing testing capacity at the outset of the national epidemic, more consistent with that simplifying assumption of the model than asian and european countries affected earlier in the pandemic would be. tanzania is also a typically vulnerable, low-income african country, - which had only icu beds in all four national referral hospitals combined in , and is representative of the pandemic that is now imminent all across africa. , the simplified model predicts that national containment and elimination may be achieved and sustained, without ever exceeding national icu capacity, by using a full, timely package of interventions. the national epidemic may be contained with only cases and deaths by highly rigorous -week lockdown ( % effective exposure prevention behaviours by % of the population) as soon the first cases are confirmed, weeks into the epidemic, complemented by % effective tracing and isolation of all contacts for confirmed cases (figure ). in this simulation, a rigorous -week lock down was initiated from week onwards and complemented by complete containment of imported cases, as well as contact tracing and isolation of confirmed cases. rigorous lock down was assumed to achieve % reduction of exposure behaviours by % of the population. complete % containment of imported cases assumes that all inbound international visitors are fully isolated for three weeks, , , , , , , except those coming from countries that may be certified as free of local transmission by who in the future. contact tracing and isolation follow up from confirmed cases was assumed to be % effective at preventing onward transmission from entire contact clusters. as points of reference against which ongoing national containment campaigns may benchmark themselves, the epidemic was predicted to grow % bigger each week at the outset and shrink by % each week once rigorous lock down had been in place for several weeks. note, however, that even these alarming projections for the rate of expansion of the epidemic and the rate of contraction required to contain it may under-represent the scale of the challenge in real epidemics. for example, at the outset of the epidemic in china, numbers of confirmed cases doubled every week. , furthermore, subsequent analyses allowing for frequent carriage without overt symptoms indicate much higher viral reproduction rates than assumed in table , and suggest true doubling time for all cases may be less than days. , interesting, almost exactly the same containment trajectory is predicted even if contact tracing and isolation is completely removed from the intervention package (supplementary figure ) , resulting in only more cases and one more death. the explanation for this becomes apparent when one examines the trajectories of confirmed versus all cases: even though the number of real cases never approaches an optimistically-assumed full testing capacity of , patients per week, half of all cases are never tested because they are asymptomatic and most of the remainder are only mildly symptomatic, so they get lost in the mass of other people who appear equally sick for unrelated to is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint covid- . as illustrated in figure d , the background noise of similar mild symptoms caused by other common pathogens dwarfs the mild coid- cases, so almost all of them go untested and undetected. less than one in every tests is conducted on a mildly symptomatic case of covid- , so even though we assume all severe cases are tested, only % of cases predicted to occur were confirmed. with contact tracing and isolation only being possible for this very small fraction of cases, there are obvious limits to how much it can achieve as a containment intervention in its own right. however, successful containment ( figure ) does requires that the lock down intervention is maintained for the full weeks (figure a and b) to eliminate the virus. delaying a -week lockdown by only weeks, the duration of one generation of viral infection, also allows the virus to persist and the epidemic resumes soon afterwards ( figure c and d). a slightly less rigorous lock down of the same duration, which nevertheless achieves % coverage with % reductions of personal exposure behaviours, also fails to eliminate the epidemic with tragic consequences ( figure e and f). furthermore, elimination may only be sustained by comprehensively containing case importation from outside the country ( figure g and h). preventing reintroduction requires isolation of all incoming travellers, except those coming from countries that may be certified as free of local transmission by who in the future, to achieve % prevention of onward local transmission ( figure ). even % containment of imported cases seems unlikely to protect the country against reintroduction of the virus and re-initiation of the epidemic ( figure g and h). tanzania therefore did the right thing by isolating all inbound travelers since march rd (over so far) for two weeks following their arrival). however, for such importation containment measures to effectively exclude new cases from a covid-free tanzania in the future, isolation periods may need to be extended to three weeks. , , , , , , however, it is also notable that all the scenarios in figure two, except for panels g and h, assume % effective containment of imported cases. it is therefore clear that local transmission must be eliminated before such rigorous control of inbound travellers can usefully protect the country against reintroduction. all these delays, truncations or inadequacies of lock down, or imperfections of importation containment, result in failure to eliminate local transmission that then rebounds and rapidly spirals out of control without a second full containment campaign ( figure ). the implications of such an uncontained rebound scenario are essentially identical to doing nothing in the first place: in all cases, % of the population is expected to become infected over about a year, resulting in approximately , deaths and icu demand exceeding capacity about times over. it is also worth noting that total national hospital inpatient capacity of approximately , beds would be overwhelmed by cases of severe coid- disease peaking at . million over a three-week period. under such conditions of a full-blown public health catastrophe, the mitigating effect of stronger health systems in high income countries are largely negated, so our predictions of over half a million deaths in tanzania compare well with those of others for the united kingdom, which has a similar population size. considering also the travel distances and household costs of hospital attendance in tanzania [ ] [ ] [ ] [ ] , it also raises the question as to whether severe covid patients should be cared for in hospitals and other health facilities [ ] [ ] [ ] [ ] which are already % understaffed or at home [ ] [ ] [ ] [ ] with support from a rapidly mobilized cadre of community health workers, for which well-characterized curricula and training platforms already exist. [ ] [ ] [ ] . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . ( ) shortening the lock down period by weeks, from to weeks (panels a and b), ( ) reducing importation containment from % to %, ( ) delaying the lock down by weeks (panels c and d), starting on week rather than week (panels e and f), and ( ) reducing the coverage and protective effectiveness of exposure behaviour reduction from % to % (panels g and h). is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint the mirage of flattening the curve to steadily acquire population-wide herd immunity the best-case scenario we could identify for "flattening the curve", as advocated by many national and international authorities, required removing all importation controls to ensure steady reseeding of the epidemic with a small number of cases and relaxing lock down assumptions to exactly % effective reduction of exposure behaviours among % of the population ( figure c and d) . under such precisely assumed conditions, the epidemic proceeds steadily with between and icu cases per week over a decade, at the end of which national icu capacity has never been exceeded and only deaths will have occurred. however, at the end of such a -year campaign, with no end in sight for at least several decades, only . % of the population would have acquired hard-won immunity through prior infection, so the remainder of the population would remain just as vulnerable to a resurgent epidemic. , intended to flatten the curve enough for national health system capacity to cope while herd immunity is acquired over the long term. all these simulations have identical input parameters to figure except that no importation containment is assumed and the coverage and protective effectiveness of exposure behaviour reduction is assumed to be lower, at % (panels a and b), % (panels c and d) or % (panels e and f). is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint however, such precise control over real epidemics with such sensitive and extremely curved trajectories, will be unachievable in practice. even lowering the assumed lock down coverage and effectiveness parameters for a simulated epidemic by only % to % results in a long drawn out peak that completely overwhelms icu capacity within years and continues to do so after a decade ( figure a and b) , nevertheless leaving % of the population lacking acquired immunity. on the other hand, raising assumed lock down coverage and effectiveness by only % to % results in a long-drawn out containment trajectory that never reaches the elimination end-game ( figure e and f) because the steady trickle of imported cases sustains transmission. re-introducing complete containment of imported cases merely results in a more extended version of figure e and f, with elimination taking over years to achieve (supplementary figure ) . perhaps more to the point, simply expressing icu capacity as a proportion of overall population size pragmatically puts suggestions that countries should aim to merely slow and mitigate their covid- epidemics into stark perspective. even if tanzania can build its icu capacity from to beds in the coming weeks, and even if the whole population could be somehow perfectly queued up for covid- exposure to make full sequential use of that capacity, assuming each patient needs only week in the icu and all regular causes of icu admission magically disappeared, it would take almost two centuries to care for the . million covid- cases expected. readjusting such hypothetical calculations to represent higher capacity countries like ireland or the uk shortens these timeline to decades rather than years, so "flattening the curve" to achieve population-wide "herd immunity" is clearly an infeasible and unwise choice. if a lock down is delayed by three weeks, approximately the duration of one viral infection, the epidemic may still be contained be extending it by the same length of time, from weeks to weeks ( figure a and b) . note, however, that the epidemic peaks at an almost four-fold higher incidence of cases, resulting in , cases and deaths overall. although icu capacity is not expected to be overwhelmed, timely access will clearly represent a challenge for many patients in country with a surface area of almost a million square kilometres and only four national referral hospitals. longer delays of , and weeks necessitate prolonged lock downs ( weeks for the latter) to contain epidemics of rapidly expanding scale: , and then cases, exceeding icu capacity by , and patients, and resulting in , and fatalities, respectively. note, however, that none of this will be obvious during the silent early phase of the epidemic, during which time the number of undetected cases snowballs: even if the lock down response is initiated after only weeks post-initiation, immediately after the first cases are confirmed in this simulation, the epidemic has already quietly progressed much further than most members of the public would guess. indeed, far enough that another people are already actively infected and almost new cases are predicted to occur in the subsequent -week period, out of which only ( %) will be detected. infectious carriers who exhibit little or no symptoms at the time - clearly contribute to the cryptic nature of an early-stage covid- epidemic: in this case we assumed this accounts for % of cases lacking symptoms overt enough to consider self-reporting and seeking a test (table ) . however, a much more important factor is the sheer volume of background noise arising from similar symptoms caused by more common pathogens, such as the common cold and malaria. even though these simulations assume that capacity for conducting , covid- tests per week would have been established in tanzania before the outbreak began, total confirmed cases are only expected to exceed about weeks after the lock down is introduced. most of these confirmed cases are . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint accounted by the clinically severe fraction we assume will all be tested. only % ( / ) of predicted mild or asymptomatic cases are expected to be confirmed because the relatively small number of covid- cases are so easy to miss in a population of million people, out of whom we assume % or , will experience a fever, cough or stomach pains in any given week for unrelated reasons ( figure b and d) . note, however, that that even this is a very conservative assumption about background rates of illness with similar symptoms to covid- : in the first contact-tracing study in the usa, over % of all carefully-followed contacts became symptomatic within weeks, even though none of them became infected with covid- . events . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint these simulations are nevertheless useful in that they illustrate how no perceptible increase in the incidence of such common symptoms may be obvious to the general population unless containment efforts fail and a full-scale, resurgent epidemic sweeps through the country (figure ). tanzania therefore did exactly the right thing by reacting fast during the silent earliest phase of the epidemic, announcing school closures within a day of the first confirmed case report and introducing additional restrictions immediately afterwards. note, however, that the quiet tail of a fading epidemic may be just as dangerous as the it's silent onset. three of the four scenarios in figure include periods of two month or more when few if any confirmed cases are expected, but some mild cases persist that can re-seed the whole epidemic afresh. the predicted persistence of the epidemic despite total predicted cases dropping below zero is an artefact of the simplified deterministic form of the model, which calculates case numbers as a continuous decimal outcome until it drops below . , at which point it is set to because the probability of elimination is % or better. the take-home message is nevertheless clear: persist with rigorous lock-down until one can be sure that elimination has been achieved, drawing on statistical approaches used by veterinary epidemiologists to certify elimination with imperfect surveillance systems. [ ] [ ] [ ] [ ] [ ] [ ] the vital importance of ambition and rigour to lockdown outcome: who dares loses least! as illustrated by figure c and d, it is now crucial that tanzania urgently builds on that early momentum to ramp up lock down efforts to the most rigorous level practically attainable. the implications of even a slightly less rigorous lock down appear less daunting in epidemiological terms but far more severe in practical and economic terms, because it greatly prolongs the lockdown period required: even reducing coverage and effectiveness of personal protection measures by only %, from % to % requires that the lock down period is extended by more than %, from weeks to weeks ( figure c and d) . the practical social and economic sustainability of such a protracted lock down period is very questionable, but much can be learned from the predicted benefits of getting such an imperfect lock down started in good time: the , cases and deaths predicted over the course of such a "slow burn" containment campaign are only marginally higher than for the best case scenario illustrated in figure . it is therefore important to get some form of reasonably rigorous lock down in place as early as possible, and then intensify it as rapidly as possible. like any race, it is critical to get an early head-start by any means possible, but then build up speed towards a strong finish. while compliance and enforcement is of great importance to lock down effectiveness, so is acceptability and socio-economic feasibility. while high income countries move to facilitate population-wide compliance with direct financial support and augmented social services, different tactics will be required in low income countries like tanzania. although tanzania is urbanizing very rapidly, most of the population still resides in rural areas where propagation of directly-transmitted diseases like covid- is always less intense. fortunately, tanzania is currently in the midst of this year's farming season, during which many rural families are out in the fields where social distancing is relatively easy. while farming season also conveniently brings a lull in trading activity at commercial hubs in rural towns and villages, it also represents a seasonal low point in the domestic food reserves of many rural households, so selective food support may be invaluable for enabling the most vulnerable families to comply effectively with self-quarantine and self-isolation directives. however, the growing urban population represents a much larger challenge, because far fewer people rely on farming for their livelihoods. many live in crowded informal settlements where lack of shelter, water, sanitation and space, relying on unreliable, informal sources of income to survive on a day-to-day basis. informal livelihoods and settlements in the busiest urban centres of the country will therefore require particularly urgent attention and creativity, to support daily food, water and hygiene needs. it may also be useful to consider providing safe transport with managed social distancing (to be followed by self-isolation) for those with options to sit out the epidemic with family and friends in rural areas. . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint as is the case for elimination of other diseases, such as malaria for example , it may be more useful to think about gaps in coverage and effectiveness to understand how such apparently minor deficiencies can make all the difference between success and failure: while a shift from % to % lock down coverage and effectiveness might seems small in relative terms, a % shortfall relative to perfect containment is twice as big as %. and the difference between % prevention of onward local transmission from imported cases contrasts starkly with even such high targets as %: when you need to achieve zero new cases in a country, any other number simply isn't good enough. in practical terms, we should first think of most the vulnerable, such those lacking homes, shelter, security, citizenship or family support, [ ] [ ] [ ] especially those in the low income countries at greatest risk. , , , , beyond these long-neglected population groups, the most important lock down coverage and effectiveness gaps will be accounted for by the most important exceptions to restrictions and those exceptional individuals most determined to evade them. unfortunately, the most obvious exceptions to lock down restrictions who will facilitate continued transmission will be health service personnel, [ ] [ ] [ ] [ ] notably those caring for those most vulnerable to the disease. however, all other essential workers in shops, markets, kitchens, food processing facilities, factories, banks, post offices, transport services and law enforcement agencies will also inevitably mediate more transmission than they would if they stayed at home. indeed, it the crew that enabled self-sustaining levels of covid- transmission to persist aboard the quarantined diamond princess cruise ship. it is also worth remembering that the anti-hero of infectious disease epidemiology, the infamous typhoid mary (real name mary mallon) was a cook by profession who infected at least people, three of whom died. like many covid- cases, - mary was a silent carrier of the disease: she herself lived to a ripe old age and died of a stroke rather than typhoid. this is not to say that such essential services should necessarily be suspended, but rather that the roles and working practices of these personnel should be scrutinized particularly carefully. how essential is essential? what is the minimum level of service needed to facilitate extended lock down while mitigating indirect effects on health, well-being and economic welfare that are even worse than covid- ? what procedures, behaviours and protective equipment could most effectively minimize persistent workplace transmission? and with so many people's livelihoods on the lines, we may be asking too much of human nature by expecting everyone to do the right thing voluntarily. many of the greatest public health campaigns in history have necessitated an authoritarian style, and it may be necessary for people all over the world to temporarily embrace and accept new restriction measures they would otherwise justifiably describe as draconian. perhaps the single most important take-home message of the widelyaccepted - rule of epidemiology (less than % of people cause more than % of transmission) is that the extremes of human circumstances and behaviour, especially during mass gatherings and population movements, are more important to the survival of pathogens than the average. it inevitably follows that such exceptions are vitally important to target if one wishes to eliminate covid- . [ ] [ ] [ ] [ ] again, it is worth remembering typhoid mary , who resisted repeated efforts to get her out of the kitchen and did nothing to disprove stereotypes about the stubborn irish. she repeatedly returned to working as a cook because it paid better and frequently changed jobs as people fell ill around her, even changing her name to evade more than years of quarantines imposed on her. it took policemen over three hours to apprehend her despite a stealthy approach and forced entry to her home. eventually mary was found hiding in an outside closet at the rear of a neighbour's house, and things remained spicy following her arrest: "she fought and struggled and cursed. i tried to explain to her that i only wanted the specimens and that then she could go back home. she again refused and i told the policemen to pick her up and put her in the ambulance. this we did and the ride down to the hospital was quite a wild one." . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint when we read about the ongoing "coronavirus challenge" game mediated through social media, we are inclined to think the spirit of mary mallon is alive and well and needs to be curbed. the experiences of those who knew mary mallon seem extreme but are difficult to disregard completely in the context of a pandemic threatening a global population of over billion people with more eccentric characters, miscreants and outright criminals than we would wish in the circumstances: "mary was now about forty-eight years of age and a good deal heavier than she was when she slipped through a kitchen full of servants, jumped the back fence and put up a fight with strong young policemen. she was as strong as ever, but she had lost something of that remarkable energy and activity which had characterized her young days and urged her forward to meet undaunted whatever situation the world presented to her. in these eight years since she was first arrested, she had learned what it was to yield to other wills than her own and to know pain." as for the full the full, timely intervention package simulated in figure (compare with figure s ), removing contact tracing from the less rigorous but extended lock down intervention package has only a modest effect on the overall containment trajectory ( figure e and f), with only more cases and additional fatalities. under a the far more extreme conditions of a failed containment campaign, followed by a resurgent, full-blown epidemic, contact tracing becomes a rather pointless exercise, even for targeting clinical disease management. at the peak of the epidemic, when over million new symptomatic cases may occur per week and even mortality rate may outstrip testing capacity (figure ), so case confirmation success rates may plummet to below . %. however, such spectacular containment failures are to be avoided at all costs and this simplified model only accounts for the direct preventative effects of follow up on subsequent transmission, so none of these simulations should be used to in any way imply that contact tracing and isolation should be de-prioritized. in particular, it does not account for the invaluable functions of contact tracing for monitoring and characterizing an epidemic, , , , , , and for understanding the influence of interventions on transmission dynamics. for example, the tracing of transmission to a relatively small number of clusters in korea, and especially the incrimination of venues like the shincheonji church provide invaluable insights that guide more rigorous, effective follow up on lock down measures. in ireland, early observations that mean size of close contact clusters had shrunk from to were reported to the public as an encouraging early sign that behavioural interventions were impacting risks of onward transmission. without such essential detailed information about how transmission persists, as well as the strengths and weakness of ongoing intervention efforts, national containment programmes would be flying blind. it should be noted, however, that testing, contact tracing and isolation of known contacts is only useful as part of a deliberate containment strategy that keeps an epidemic manageably small, and may be particularly useful for extinguishing the remaining embers of an effectivley-contained epidemic. while testing is always useful for clinical management of severe cases, once % or more of the population has been infected even this important subset of cases alone overwhelms testing capacity ( figure b , d, e and f) and the fraction of non-severe cases confirmed plummets to negligible levels. in any case, population-wide testing of mildly symptomatic cases becomes unhelpful as a guide to targeting containment measures: how does one selectively target those at immediate risk when that means everyone? and how would we attempt contract tracing if we allowed the epidemic to grow to tens or hundreds of thousands of new cases each week? note, however, that the expected failure of contact tracing, and indeed testing generally, is just one more good reason to contain national covid- epidemics before they progress from emergencies (figures and ) into outright catastrophes (figure ). . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . like other recent models of covid- , our simplified formulation does not attempt to predict complex indirect effects of the pandemic upon morbidity and mortality from other causes that will be exacerbated by the expected pressures on a health system that is already overstretched. nor does it attempt to anticipate the extent of economic and social damage that will arise from different epidemic containment scenarios, partly because doing so would defeat the purpose of developing a simplified arithmetic formulation. despite its limitations as a relatively simple and untested model, the predictions described above are consistent with those of most other process-explicit models using more sophisticated mathematical formulations and specialist software, as well as recent reports of heroic , success from china. , , , , in fact, perhaps the most useful new lessons to be learned come from a few studies that reach substantively different conclusions based on markedly different underlying assumptions. our predictions that contact tracing and isolation will play only a minor role in successful containment contrast with those of others which assumed asymptomatic carriage by only % of cases or less, and which do not account for the detection dilution effect of similar mild symptoms caused by other common pathogens ( figure b , d, f, h). on the other hand, the predictions presented here appear relatively optimistic when compared with recent reports suggesting viral reproduction rates are higher than generally thought , because previous analyses failed to consider the likelihood that large fractions of cases may go undetected [ ] [ ] [ ] [ ] [ ] [ ] because they exhibit only mild, non-specific symptoms, if any - , , , [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] as underlined right at the outset of the global response, , the most important remaining question that needs to be answered to reduce the uncertainties of model predictions is the extent of asymptomatic carriage and infectiousness. learning lessons from other diseases like endemic malaria, which is primarily a chronic illness transmitted by semi-immune adult carriers, the term asymptomatic may well be a misnomer not only because some individuals become infectious before exhibiting symptoms, , , , , , , , but also because it is often applied to those who shrug off mild symptoms to get on with their daily lives. , , a particularly important caveat arising from current uncertainty about the role of cryptic carriers is that it also has a major influence on estimation of fatality rate for infections rather than clinical cases. the latest analyses allowing for this phenomenon suggest that fatality rates are may be to times lower per infection than per confirmed case, , consistent with our conclusion that the vast majority of cases are never confirmed. while fatality rates are difficult to estimate directly, , these modelling analyses support the conclusions of the most controlled empirical epidemiological studies, indicating that the covid- fatality rates may be comfortably below %. the surge of severe cases and fatalities in an uncontained epidemic may therefore peak at a far lower level than those predicted in figure . however, much of the variation between fatality rate estimates appears related to geographic differences in health system capacity and burden, , so low income countries will be much more vulnerable. even if the best worst-case scenario proves to be less catastrophic than previously projected, , it will nevertheless overwhelm critical care capacity several times over and should be avoided if at all possible. the current global health emergency demands immediate, bold, pre-emptive decisions in the absence of unambiguous evidence, , based on our best understanding of covid- epidemiology as it stands today. , , the three key sequential actions every country needs to embrace as early and emphatically as possible are contain, eliminate and exclude. even when faced with the prospect of lock downs lasting months or more, there is no place for more timid terms like slow, flatten or mitigate when faced with an epidemic capable of overwhelming icu capacity hundreds of times over . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint or taking several years of restrictions to slowly burn through an entire population at rates that icus can cope with. and tackling this pandemic will rely overwhelmingly upon widespread understanding and mass participation by the entire global public, rather than just the health professionals and high-level decision makers who will lead the response. currently, half the world's population is already under lock down of some kind, meaning vertically enforced and severe restrictions of movement and physical interaction, and the remainder will have to follow if the ongoing covid- virus pandemic is to be contained. faced with such brutally difficult decisions, it is essential to policy-makers, health professionals and the general public that as many people as possible understand why lock down interventions represent the only realistic way for individual countries to contain their national-level epidemics before they turn into public health catastrophes. it also vital for as many people as possible to understand why these need to be implemented so early, so aggressively and for such extended periods. over the medium-to-long term, it will also be vital for us all to understand why widespread national action and international co-operation , will be required to conditionally re-open trade and travel between countries that have successfully eliminated local transmission. as explained by the simplified simulations presented here, this appears to be the only means by which national elimination efforts can be sustained, following which pandemic eradication may be pursued at global level. supplementary figure . the predicted trajectory of a successfully contained national covid- epidemic in the united republic of tanzania, achieved without any contact tracing and isolation. in this simulation, a rigorous -week lock down was initiated from week onwards and complemented by complete containment of imported cases, as well as contact tracing and isolation of confirmed cases. rigorous lock down was assumed to achieve % reduction of exposure behaviours by % of the population. complete % containment of imported cases assumes that all inbound international visitors are fully isolated for three weeks, , , , , , , except those coming from countries that may be certified as free of local transmission by who in the future. however, these simulations differ from figure in that absolutely no contact tracing and isolation was assumed. predicted successful national containment and elimination though prompt, rigorous lockdown, and then sustained with complete containment of imported cases, despite lack of contact tracing and isolation . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted april , . . cc-by . international license it is made available under a is the author/funder, who has granted medrxiv a license to display the preprint in perpetuity. (which was not certified by peer review) the copyright holder for this preprint this version posted april , . . https://doi.org/ . / . . . doi: medrxiv preprint a familial cluster of infection associated with the novel coronavirus indicating potential person-to-person transmission during the incubation period a well infant with coronavirus disease (covid- ) with high viral load clinical characteristics of asymptomatic infections with covid- screened among close contacts in nanjing alert for non-respiratory symptoms of coronavirus disease (covid- ) patients in epidemic period: a case report of familial cluster with three asymptomatic covid- patients transmission of -ncov infection from an asymptomatic contact in germany asymptomatic and human-to-human transmission of sars-cov- in a -family cluster electronic pubication ahead of print sars-cov- viral load in upper respiratory specimens of infected patients evolving epidemiology and impact of non-pharmaceutical interventions on the outbreak of coronavirus disease the different clinical characteristics of corona virus disease cases eleven faces of coronavirus disease electronic pubication ahead of print asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus (sars-cov- ): facts and myths detection of novel coronavirus by rt-pcr in stool specimen from asymptomatic child case management team kcfdc, prevention. early epidemiological and clinical characteristics of cases of coronavirus disease in south korea electronic pubication ahead of print characteristics of covid- infection in beijing radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study evidence of sars-cov- infection in returning travelers from wuhan, china epidemiologic characteristics of early cases with novel coronavirus ( -ncov) disease in korea the rate of underascertainment of novel coronavirus ( -ncov) infection: estimation using japanese passengers data on evacuation flights transmission of covid- in the terminal stage of incubation period: a familial cluster serial interval of covid- among publicly reported confirmed cases electronic pubication ahead of print first known person-to-person transmission of severe acute respiratory syndrome coronavirus (sars-cov- ) in the usa substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov ) the effect of control strategies to reduce social mixing on outcomes of the covid- epidemic in wuhan, china: a modelling study electronic pubication ahead of print modeling the epidemic dynamics and control of covid- outbreak in china prudent public health intervention strategies to control the coronavirus disease transmission in india: a mathematical model-based approach impact of non-pharmaceutical interventions (npis) to reduce covid- mortality and healthcare demand: who collaborating centre for infectious disease modelling, mrc centre for global infectious disease analysis interventions to mitigate early spread of sars-cov- in singapore: a modelling study nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china: a modelling study real-time forecasts of the covid- epidemic in china from short-term forecasts of the covid- epidemic in guangdong and zhejiang electronic pubication ahead of print real-time monitoring the transmission potential of covid- in singapore how will country-based mitigation measures influence the course of the covid- epidemic? the global impact of covid- and strategies for mitigation and suppression: who collaborating centre for infectious disease modelling, mrc centre for global infectious disease analysis identifying locations with possible undetected imported severe acute respiratory syndrome coronavirus cases by using importation predictions analysis of covid- infection spread in japan based on stochastic transition model prediction of the epidemic peak of coronavirus disease in japan, potential impact of seasonal forcing on a sars-cov- pandemic the effectiveness of quarantine and isolation determine the trend of the covid- epidemics in the final phase of the current outbreak in china early dynamics of transmission and control of covid- : a mathematical modelling study estimating the reproductive number and the outbreak size of novel coronavirus disease (covid- ) using mathematical model in republic of korea a conceptual model for the coronavirus disease (covid- ) outbreak in wuhan, china with individual reaction and governmental action transmission dynamics of the covid- outbreak and effectiveness of government interventions: a data-driven analysis phase-adjusted estimation of the number of coronavirus disease risk assessment of novel coronavirus covid- outbreaks outside china electronic pubication ahead of print an updated estimation of the risk of transmission of the novel coronavirus ( -ncov) estimation of the transmission risk of the -ncov and its implication for public health interventions electronic pubication ahead of print uncertainty in epidemiology and health risk and impact assessment wrong, but useful": negotiating uncertainty in infectious disease modelling with covid- , modeling takes on life and death importance passengers' destinations from china: low risk of novel coronavirus ( -ncov) transmission into africa and south america preparedness and vulnerability of african countries against importations of covid- : a modelling study will covid- be a litmus test for post-ebola sub-saharan africa africa prepares for coronavirus bearing the brunt of covid- : older people in low and middle income countries preparedness is essential for malaria-endemic regions during the covid- pandemic referral and admission to intensive care: a qualitative study of doctors' practices in a tanzanian university hospital projection of early spread of covid in africa as of data-based analysis, modelling and forecasting of the covid- outbreak transmission potential and severity of covid- in south korea early epidemiological assessment of the transmission potential and virulence of coronavirus disease (covid- ) in wuhan city: china novel coronavirus -ncov: early estimation of epidemiological parameters and epidemic predictions the novel coronavirus, -ncov, is highly contagious and more infectious than initially estimated a mathematical model for simulating the phase-based transmissibility of a novel coronavirus incubation period and other epidemiological characteristics of novel coronavirus infections with right truncation: a statistical analysis of publicly available case data electronic pubication ahead of print electronic pubication ahead of print. . national bureau of statistics & ministry of finance and planning dar es salaam and the office of the chief government statistician & ministry of finance and planning zanzibar. national population projections: united republic of tanzania estimated effectiveness of symptom and risk screening to prevent the spread of covid- . elife ; serial interval of novel coronavirus (covid- ) infections clinical characteristics of coronavirus disease in china early estimation of the case fatality rate of covid- in mainland china: a data-driven analysis investigation of three clusters of covid- in singapore: implications for surveillance and response measures persistence and clearance of viral rna in novel coronavirus disease rehabilitation patients electronic pubication ahead of print. . ministry of health, community development, gender, elderly and children. health statistical tables and figures for women's determinant factors for preferred place of delivery in dodoma region tanzania: a cross sectional study reasons for delay in seeking treatment among women with obstetric fistula in tanzania: a qualitative study costs of dental care and its financial impacts on patients in a population with low availability of services pathways and associated costs of care in patients with confirmed and presumptive tuberculosis in tanzania: a cross-sectional study a novel approach for a novel pathogen: using a home assessment team to evaluate patients for novel coronavirus (sars-cov- ) proposed protocol to keep covid- out of hospitals coronavirus: home testing pilot launched in london to cut hospital visits and ambulance use ministry of health, community development, gender, elderly and children. mid-term review of the health sector strategic plan iv for an exploration of the feasibility, acceptability, and effectiveness of professional, multitasked community health workers in tanzania quality of sick child-care delivered by community health workers in tanzania factors associated with retention of community health workers in maternal, newborn and child health programme in simiyu region freedom from infection: confirming interruption of malaria transmission two-stage sampling in surveys to substantiate freedom from disease a new probability formula for surveys to substantiate freedom from disease demonstrating freedom from disease using multiple complex data sources : case study--classical swine fever in denmark demonstrating freedom from disease using multiple complex data sources : a new methodology based on scenario trees risk-based disease surveillance: a manual for veterinarians on the design and analysis of surveillance for demonstration of freedom from disease: food and agriculture organization of the united nations eliminating malaria vectors why inequality could spread covid- responding to the covid- pandemic in complex humanitarian crises the neglected health of international migrant workers in the covid- epidemic protecting healthcare personnel from -ncov infection risks: lessons and suggestions am i part of the cure or am i part of the disease? keeping coronavirus out when a doctor comes home covid- : towards controlling of a pandemic coronavirus: hospitals must learn from past pandemics transmission potential of the novel coronavirus (covid- ) onboard the diamond princess cruises ship the curious career of typhoid mary heterogeneities in the transmission of infectious agents: implications for the design of control programs covid- control in china during mass population movements at new year identifying and interrupting superspreading events-implications for control of severe acute respiratory syndrome coronavirus electronic pubication ahead of print covid- : preparing for superspreader potential among umrah pilgrims to saudi arabia secondary attack rate and superspreading events for sars-cov- statement in support of the scientists, public health professionals, and medical professionals of china combatting covid- covid- containment: china provides important lessons for global response china's local governments are combating covid- with unprecedented responses -from a wenzhou governance perspective feasibility of controlling covid- outbreaks by isolation of cases and contacts a novel coronavirus emerging in china -key questions for impact assessment relationships of host infectivity to mosquitoes and asexual parasite density in plasmodium falciparum asymptomatic" malaria: a chronic and debilitating infection that should be treated asymptomatic only at first sight: malaria infection among schoolchildren in highland rwanda communicating the risk of death from novel coronavirus disease (covid- ) electronic pubication ahead of print -novel coronavirus ( -ncov): estimating the case fatality rate -a word of caution potential association between covid- mortality and health-care resource availability parachute use to prevent death and major trauma related to gravitational challenge: systematic review of randomised controlled trials offline: apostasy against the public health elites covid- -navigating the uncharted offline: covid- and the nhs-"a national scandal key: cord- -xhp abg authors: allam, zaheer title: the first days of covid- : a detailed chronological timeline and extensive review of literature documenting the pandemic date: - - journal: surveying the covid- pandemic and its implications doi: . /b - - - - . - sha: doc_id: cord_uid: xhp abg this chapter surveys the global unfolding of events during the first days of the covid- pandemic in china. an extensive review of literature from both academic and popular sources provides a daily overview of the situation covering health, economic, political, and social perspectives and outlines the major course of actions. this chapter surveys, and lays, the chronological timeline of the outbreak, health policy, deaths, recovery, and socioeconomic measures and provides a factual narrative on the unfolding of the pandemic and, while doing so, underlines major milestones and contradictory findings and beliefs on the subject. this supports the perception that data collection varied between research groups, organizations, and national bodies, which later fueled differing viewpoints and policies for combatting the outbreak. the covid- pandemic took the world by surprise and unfolded extremely rapidly. it began relatively slower, and only a little is documented on its actual first case, with claims as from november, while others links it to on december . besides not knowing when it began, there was also very little known on the many issues about the virus, including its mode of transmission, its incubation time, and the medication the vaccination, among many other elements. even to date, at the time of writing, there still remain some gray areas about the virus including its origin and whether it could have permanent impacts on patients, and whether it is possible for patients to develop immunity, among many other areas that are still being looked into. following these uncertainties, there had been numerous health policies with a number of those being rendered ineffective as more knowledge about the virus is revealed. for instance, at the beginning, the world health organization (who) advised that masks should only be worn by health professionals or patients while in hospital, but later on, after it established that there were possibilities of human-to-human transmission, it became apparent that everyone need to wear a mask while in public to prevent transmitting or contracting the virus. however, while the impacts of the virus in the first days were still relatively smaller, and the spread as per the available information was still slower, there were already confirmed cases reported in china, wuhan region ( cases), thailand ( cases), and japan ( case). from the reported cases in wuhan, people had succumbed to the unknown disease, whereas are said to have recovered and discharged. interestingly, on this pandemic, though it took health official approximately days to identify that they were dealing with a new kind of coronavirus, an artificial intelligence (ai)epowered algorithm developed by bluedot, a canadian startup tech company, provided early warnings that the world might be experiencing a new virus outbreak (bowles, ) . the warning came days earlier before the chinese scientist identified the virus (huang et al., ) , and days before they notified the who, which then made the official announcement to the world (who, e). this early warning supports that computer predictions could be relied upon in predicting future pandemics before they arise, hence saving allowing for early preparations the challenges of future pandemic. in these first days of the covid- pandemic, despite the virus having spread to two more countries outside china, most of the global community were not particularly worried, as the perception was that only those who had come into contact with the wuhan seafood market had the highest probability of being infected. therefore, even with the help of technologies like that of bluedot, the countries that were seen to be at risk of the -ncov outbreak (the temporary name previously given to the virus) were those neighboring china and those directly linked to wuhan via airlines. for this reason, some of the countries that were flagged to be at risk included taiwan, australia, united arab emirates, hong kong, japan, and thailand. this chapter documents the outbreak over the first days through the sections in the following. the earliest date of symptoms for covid- , according to a study performed by huang et al. ( ) and published in the lancet journal, was december , . however, there are other sources (bryner, ; davidson, ) claiming that individuals with similar symptoms may have presented themselves to hospital as early as november. according to the report, by south china morning post (ma, ) , the first person who presented similar cases was a male patient of -year old from the province of hubei. however, chinese doctors only came to realize that they were dealing with a new and serious virus late december, when similar symptoms continued to increase every day, and mostly originating from wuhan. according to the article in lancet, the first patient, and whom they insist may be the first case, was reported on december , , and whom did not have direct link with the wuhan seafood market that has been associated with the origin of the virus. this finding interestingly matches with ma ( ) who also argues that the november case was not from wuhan. the story as to the origin of the virus has fueled much political and social divides and is expected to evolve as further efforts are poured into understanding this crisis. the number of new patients voluntarily presenting themselves to hospital continued to increase (bryner, ) . hospitals report new one to five cases with similar symptoms on average each day. however, this being a new virus, some sources quoted december as the first day where the first patient in the city of wuhan sought medical help for pneumonia-like symptoms. at this time, the european centre for disease prevention and control (ecdc, c) contended that many dimensions, which were known today, like the need for social distancing, human-to-human infections, lack of vaccine or cure, and many such issues, were unknown, and the precautionary measures taken then were routinely delivered. also, during these early stages of the onset of the virus, there was no clear evidence of how many people were affected. for this reason, information from chinese authorities (wuhan city health committee, ) and those of the who (who, a) stated that the december , , marked the onset of the first cases that were tested and which were later confirmed positive with covid- , then known as " -ncov." as hospitals continued to receive more patients with unknown "pneumonia-like symptoms," fear of the outbreak is already spreading, especially among the social media (wechat) use within china, more so wuhan (secon, ) . li et al. ( ) explained that during the period beginning december , , the recurrence of the words "sars" and "shortness of breath" in the social media started to increase, and by december , it had peaked. meanwhile, in the hospitals, doctors were observed to concede that there might be a new virus of unknown etymology in wuhan, presenting symptoms of acute respiratory syndrome. the reporting is affirmed by availability of the first four cases officially confirmed. all the four cases were linked to the huanan (southern china) seafood wholesale market, which has been highly linked to have been the source of the virus. while only four cases had been pointed, by this date, bryner ( ) reports that already, over people in wuhan had been infected, but since doctors had not earmarked them as suspected cases noting that there were no suspicion of this "unknown" disease. the cases were only identified after doctors cross-verified records. the suspicion after reporting the four cases was that they were not suffering from sars (severe acute respiratory syndrome), which was still in surveillance since it broke in . with the possibility of an unknown outbreak, at this time, the concern was to establish the transmissibility, severity, and other issues that may be related to this new virus (adhikari et al., ) . the situation unfolded rapidly on this day. first, the chinese officially reported to the who of the possibility of a new virus with symptoms of pneumonia, but of unknown etymology. the information to who officials based in china was that this disease had been detected in wuhan, from the hubei province. by the time of this reporting, the ecdc supported that wuhan municipal health commission was already handling pneumonia cases with of those in critical conditions (ecdc, b) . while reporting, the officials did not have the information about how the disease was transmitted, and in some sources (who, e), they have ruled out human-to-human infection. while that is the case, all patients with the said symptoms who had been received so far in hospitals in wuhan were placed under quarantine, as work to establish and identify the type of the virus and its origin began (safi, ) . while this marked the first official day that the covid- pandemic gained and attracted attention from the international body (who), and the centers for disease control and prevention (cdc), as noted in the previous dates, different cases had been reported. with ambiguity on this, there are contradictory figures from different sources denoting cases with varying dates. but the following part a chronological account of the pandemic: the first days days succeeding the event, reporting has been taken over by international organization and by the who, leading to more coordinated and reliable figures. on january , , the wuhan's huanan seafood wholesale market was indefinitely closed following its associated link with the virus outbreak (juan, ) . the role and link of the market in this story was not only made by the wuhan municipal officials but also by the uscdc (patel and jernigan, ) . while workers in the market, under the watchful eyes of the police, proceeded to close their businesses, health officials were collecting samples from surfaces in the market and sealing them in plastic bags to be analyzed further. the closure included banning of live animals from this market and any other wet markets (who, e). sale of wild animals to restaurants, via online markets or in any other such market, was also banned. besides preventing further spread of the virus, the other intention of the closure of the market was to allow for environmental sanitation and disinfection of the same. there were also some levels of public awareness performed, especially to farmers who reared animals, where emphasis on sanitation was being stressed upon (who, c). outside the market, chinese social media were amassed with different messages pointing to the fact that wuhan, an industrial city of over million people, was experiencing an outbreak of an unknown disease. according to safi ( ) , the fears being spread in those social media platforms were catalyzed by leakage of some medical documents from a hospital in wuhan showing that some people with the virus had been reportedly transferred there. since uncertainties revolved around the virus, panic was building up around the perception that sars backer-emerged. following the spread of this fear, eight individuals accused of spreading rumors were arrested and imprisoned by the public security bureau (tardáguila and chen, ) . outside china, its neighbors were starting to take caution. taiwan was reported to immediately take the issue seriously and demanded the screening for any signs of pneumonia-like or flu symptoms for all individuals coming from china. until this date, the number of those reported to have shown the signs of the disease in question still remains unknown, but consensus builds around the number of cases to be (zhao et al., ) . after rigorous probes, tests, analysis, and other medical practices, the chinese authorities made a global announcement (huang et al., ) that they have successfully identified the virus as a novel coronavirus, similar to the one associated with sars and the middle east respiratory syndrome (mars). prior to this ground breaking discovery, the officials had days earlier, on january , ruled out that the virus they were dealing with was either sars or mars, hence concluding that it was indeed a new type of virus. upon its successful identification, it was tentatively named as " -ncov." the identification came after chinese scientists successfully isolated the virus from one of the patients quarantined in a hospital in wuhan (huang et al., ) . according to an article by singhal ( ), the identified virus had greater than % (> %) homology with the bat coronavirus and was also greater than % similarity with the virus responsible for causing sars (sars-cov). as the identification occurred, it was also reported that the samples previously collected from the wuhan market tested positive, thus confirming the fears that the virus could have originated from there. even after identification of the virus, it was still not clear of how it could be transmitted. but the executive director of the who's health emergencies programme, dr. mike ryan, argued that the virus being a respiratory pathogen could possibly be transmitted from human to human (who, e). at this stage, it is reported that approximately people had contracted the disease and were still under quarantine as reported earlier. beyond china, as report by the who (who, a), neighboring countries were stepping up their health precautions. for instance, japan began to institute comprehensive screening of all travelers coming from wuhan, and anyone with signs of fever or flu were placed under quarantine. in the united states, the country's cdc created a -ncov incident management structure that would help the country as it prepares for upcoming cases. on january , , chinese officials reported to the who that they have finally identified the virus, and subsequently, the who made the official announcement (who, e) of the same to the world. on january , the chinese health officials share unfortunate news that a -year-old man who had been admitted in one of the hospitals in wuhan had died. from the report (ravelo and jerving, ), the man had other underlying health conditions such as chronic liver disease and abdominal tumors, but the cause of his death was attributed to -ncov. by the time of his death, he was reported to have suffered from issues such as respiratory failure and severe pneumonia, septic shock, and multiple organ failure. he was also observed chapter the first days of covid- : a detailed chronological timeline to have suffered from severe acid-based metabolism disorder and cirrhosis. his hospital treatment included antiinfection, ventilator-assisted breathing, life support, and other treatments, but with no positive results. his death was marked as the first known death from this new virus. in regard to new cases, health officials did not record any other case except the cases that had been received up to january . they also expressed that according to an epidemiological survey (who, e), there was no clear evidence that the disease could be transmitted from human to human. however, they affirmed that all the cases in hospital were of people who had been exposed to the wuhan seafood market. on this day, the first -ncov virus genome sequence was deposited in the genbnk (the nih database that where all public genetic sequences are stored) and shared with virologist.org (an online hub for prepublication of data, where the public can freely access for public healtherelated activities and research) and also uploaded to the platform "global initiative on sharing all influenza data" (gisaid) (ecdc, b), through a collaboration of a number of organizations including the shanghai public health clinic centre, the central hospital of wuhan, huazhong university of science and technology, and wuhan center for disease control and prevention among others. all this happened before the information on discovery of the genome sequence was officially shared with the who. however, the details were to be shared with the who the following day together with other viral sequences that were to be shared with gisaid (holmes, ) . in parallel, chinese health officials were considering to temporarily close down the chinese laboratory that was the first to share the coronavirus genome with the world. the laboratory was closed on the following day (hjanuary ) (pinghui, ) . the who was briefed of the availability of the first viral genome sequence of coronavirus, and other five other genomes, which were subsequently deposited in the gisaid platform (holmes, ) . a lab in china, which was first to share genome, publicly closed down "for rectification" as ordered in the previous day, but still there was no clarification of what this "rectification" was supposed to mean. in addition, on this closure, as reported by pinghui ( ) , the laboratory was not given notice as to why they were asked to be closed down, even after relentless permission applications to reopen without any success. but it is assumed the "rectification" here is all about the lab releasing their genome sequence publicly before the officials could publish theirs. despite this bad blood between the laboratory and the officials from the shanghai public health clinic centre and other agencies involved in establishing and depositing the viral genome sequencing, the information is said to be critical in assisting scientists from different parts of the globe in the development of the testing and diagnostic kits and also in search for vaccine and cure for the disease. another major happening of the day is the publishing of interim guidelines by the who on issues pertaining to travel advice, testing in laboratories and medical investigations. these targeted to help countries across the globe to prepare for any eventuality that may arise from the ncov spread. the guidelines also targeted to urge the travellers, especially from or in wuhan to practice extra health caution. also, the guidelines insisted on the need for countries not to impose any travel restrictions on the international travelers (schnirring, ) . while no new cases were reported in wuhan, or in any other parts of china, beyond its border, thailand confirmed their first case, which was also thought to be the first international -ncov one. this first case was a woman, noted to have frequented local fresh market in wuhan, but did not visit the condemned huanan south china seafood market. the -year-old chinese citizen was intercepted at the bangkok airport by the thermal surveillance scanners that detected her high temperature (fever). the identification of this case occurred on january , where she was hospitalized immediately and samples were taken from her, but the healthy officials delayed reporting the case until january . when the samples were subjected to a number of medical tests such aa the reverse transcriptase polymerase chain reaction test and subjected to genetic sequencing, they came back positive for the -ncov. during the travel, she and five family members were in a tour group of members who traveled directly from wuhan to bangkok. before the tests were done, the woman reported to have had experienced fever, chills, sore throat, and headaches. of all those in her company, no one had shown any similar signs (schnirring, ) ; thus, she is the only one who was isolated. with the patient having insisted she did not visit the suspected seafood market in wuhan, the hypothesis of the origin of the virus was put into disarray, and the who insisted that the scope for the investigation of the source of the virus needs to be extended beyond the seafood market to other local markets that are part a chronological account of the pandemic: the first days observed to have also been involved in selling of live animals, including bats, which have been linked with the origin of the virus. another issue that came up from the history of this patient is the incubation period of the virus. according to her, her last visit to the markets was on january . therefore, since then, to the time she was detected to have symptoms, a number of days had passed. this also led to further question of the incubation period of the -ncov. following the identification of the first case outside china, a research group (bluedot developed an aibased system to track the virus spread as from december , (bowles, ) ) from toronto embarked to map out top destinations that would be at high risk following the airline travel history from wuhan. from the research, those flagged as top destinations included thailand, hong kong, japan, taiwan, australia, and the united arab emirates. following the confirmation in thailand, health officials from the country declared that they were tracing and monitoring over contacts that may have interacted with the woman patient (who, b). from january , a number of happenings have been reported. on january , for instance, following the first confirmation outside china, wuhan embarked on a concerted effort of screening all passengers traveling out of the city either via the air, the rail, or buses. the screening was performed at the points of departure (airports, railway stations, ferry terminals, and bus stations) through the help of infrared thermometers that were installed in those key points (who, d) . on this day still, the who, after consultation with chinese officials, reported that there were no clear evidences to conclude that the -ncov virus could be transmitted from person to person, but the option could not be excluded (who, e) . but, while that was going on, of the quarantined cases, of the cases were confirmed to be a married couple, thus watering down the argument that the virus could not involve human-to-human transmission. on january , a major event happened in wuhan, china, where a -year-old man died from the virus (siu et al., ) . like the first reported death, this man also had some other underlying health conditions such as myocarditis, abnormal renal function, and multiple organ failure (ravelo and jerving, ). outside china, japan confirmed their first case, a man in his s who had lived in wuhan and traveled back to japan on january . while in wuhan, he reported to have developed a high fever (january ) (sim, ), but it was only days later, in japan that he was confirmed to be coronavirus positive, as reported by the japanese ministry of health, labor and welfare (gan, ) . the man, who had not visited the huanan seafood market, was taken in hospital in japan as from january where he stayed up to january , where, though he tested positive, he recovered and was dismissed from hospital. on january , vietnam isolated two chinese travelers coming from the chinese city, and though they had not been found positive, this was done as a preventive measure following the news of the spread of the virus outside china. in germany, a team of researchers from german centre for infection research (dzif), berlin, are noted to have successfully developed a prototype of the first diagnostic test that could help in identifying the coronavirus. the laboratory assay was approved and published by the who as a guideline for diagnostic detection, and it became the first test kit in the world (drosten, ) . a second case was reported in thailand. this time, it was a -year-old woman who had traveled from wuhan and arrived at bangkok suvarnabhumi airport on january . upon arrival and screening, she was found to have fever and was isolated into a local medical institute where the coronavirus testing was performed and come back positive (the government of the hong kong specia administrative region, ). the confirmation of the case was made by the ministry of public health of thailand. following this case, thailand was put on a high alert, since in the following weeks was the beginning of the lunar new year holidays, and during such times, millions of chinese travelers usually travel to the country. the alert involved intensifying surveillance in all the country's (four) airports, especially in respect to flights coming from wuhan. but amid such alerts, the country's top officials insisted that there was no outbreak of the virus (promchertchoo, ). in the united states, the uscdc was noted to have dispatched a team of a people to three of its airports in san francisco (sfo), new york (jfk), and los angeles (lax) to complement the existing staff in conducting screening for all individuals entering the country from wuhan, china. the medical team would cooperate with officials from homeland security and customs and border protection (cbp) to ensure total compliance with the screening requirements (uscdc, ). in regard to new infections, the medical research council (mrc) centre for global infectious disease analysis (mrc gida) at imperial college argued that it had made some estimations, which showed that cases in wuhan would likely have increased to almost (imai et al., ) . they argued that such numbers could be ascertained if pneumonia or related cases within wuhan and other connected cities within china could be investigated. the calculations were based on flight and population data, following the fact that cases in thailand and japan had already been detected, and there were possibilities that there could be new cases not yet reported in other destinations that had originated from wuhan since the period that the coronavirus was reported. however, despite availability of those estimates, a summary report capturing happenings up to january was published by ecdc ( a) highlighting that the number of confirmed cases after successful laboratory testing still remained at ( in wuhan, china, in thailand, and in japan). of these, had died, had been discharged from hospital, and were reported as severe cases. after the confirmation of the cases, health officials to this date had managed to trace, identify, and monitor close contacts. of those, were given a clean bill of health, whereas were still under close medical observation, although none of them had tested positive to the virus (wuhan municipal health commission, ). epidemiology, causes, clinical manifestation and diagnosis, prevention and control of coronavirus disease (covid- ) during the early outbreak period: a scoping review how canadian ai start-up bluedot spotted coronavirus before anyone else had a clue ) st known case of coronavirus traced back to november in china first covid- case happened in november researchers develop first diagnostic test for novel coronavirus in china cluster of pneumonia cases caused by a novel coronavirus event background covid- update: cluster of pneumonia cases associated with novel coronavirus e wuhan, china - china's new sars-like virus has spread to japan, but we still know very little about it clinical features of patients infected with novel coronavirus in wuhan report : estimating the potential total number of novel coronavirus cases in wuhan city wuhan wet market closes amid pneumonia outbreak early transmission dynamics in wuhan, china, of novel coronaviruseinfected pneumonia coronavirus: china's first confirmed covid- initial public health response and interim clinical guidance for the novel coronavirus outbreak d united states chinese laboratory that first shared coronavirus genome with world ordered to close for 'rectification', hindering its covid- research wuhan virus: more cases confirmed in thailand covid- e a timeline of the coronavirus outbreak days that changed the world china release genetic data on new coronavirus, now deadly part a chronological account of the pandemic: the first days chinese social-media platform wechat saw spikes in the terms 'sars,' 'coronavirus,' and 'shortness of breath japan confirms first case of infection from wuhan coronavirus; vietnam quarantines two tourists a review of coronavirus disease- (covid- ) china says second person dies in wuhan pneumonia outbreak china arrested for spreading 'hoaxes' about what is now known as coronavirus. what happened to them? available at the government of the hong kong specia administrative region. ( ) chp closely monitors additional confirmed public health screening to begin at u.s. airports for novel coronavirus who. ( a) emergencies preparedness, response: novel coronavirus e china novel coronavirus e thailand (ex-china) who. ( c) novel coronavirus ( -ncov) situation report- . world health organization. who. ( d) novel coronavirus ( -ncov) situation report- . available at who timeline e covid- wuhan municipal health commission on unexplained viral pneumonia wuhan municipal health commission on pneumonia infect by new coronavirus estimating the unreported number of novel coronavirus ( -ncov) cases in china in the first half of key: cord- -g onkjt authors: dey, anusree; das, rituparna; misra, hari sharan; uppal, sheetal title: covid- : scientific overview of the global pandemic date: - - journal: new microbes new infect doi: . /j.nmni. . sha: doc_id: cord_uid: g onkjt covid- (coronavirus disease ) is the disease caused by the novel coronavirus, sars-cov- . genome sequence of the virus revealed that it’s a new zoonotic virus which might have evolved by jumping from bats to humans with one or more intermediate hosts. the immediate availability of the sequence information in public domain has accelerated development of quantitative-reverse-transcription pcr based diagnostics. besides, numbers of clinical trials have been prioritized globally for testing new vaccines and treatments against this disease. this review gives a broad insight into different aspects of the covid- disease, introduction to sars-cov- , mitigation strategies, present status of diagnostics and therapeutics. in december, , a cluster of patients, linked to a local sea food market in wuhan city of hubei province, china, were diagnosed with a viral pneumonia having sars (severe acute respiratory syndrome) like symptoms of unknown etiology [ ] . initial denials of human-to- human transmission of the virus, which were later refuted in january , led to a rapid spread of the disease throughout china within a short span of time. following this, the virus spread like wildfire both within china and across the globe with more than countries affected. in january , the first genome sequence of the virus was released by prof. yong-zhen zhang [genbank accession: mn ]. based on its genome sequence similarity to sars coronaviruses, it was identified as a novel coronavirus and was named sars-cov- . coronaviruses (covs) refer to the largest group of viruses characterized by a spherical morphology with a single-stranded rna surrounded by an outer envelope (fig. ) . j o u r n a l p r e -p r o o f cov- belongs to the genus betacoronaviruses, one of four genera of coronaviruses, which also include sars-cov- and mers (middle east respiratory syndrome)-cov etc. (fig. ) [ , ] . the genome sequence of the novel coronavirus revealed that, similar to other coronaviruses, sars-cov- has a zoonotic origin and mainly thought to have jumped from bats to humans with one or more intermediate hosts ( the disease caused by the novel coronavirus, sars-cov- , was referred to as coronavirus disease of covid- associated coagulopathy has also gained significant prominence, following exhibition of multifarious neurological manifestations by a significant proportion of the patients. ischemic stroke, cerebral hemorrhage and thrombosis are some of the more common symptoms [ ]. however, mortality to a larger extent is also determined by access to quality healthcare. according to the global data as well as the early estimates from china, both old j o u r n a l p r e -p r o o f age and comorbidities may render the patients at higher risk of developing severe disease or death due to covid- infection, perhaps due to a weaker immune functioning [ , ] . the duration between the onset of infection and appearance of the first symptom of the disease in an individual is defined as incubation period. sars-cov- incubation period is typically around - days (ranging from - days) [ , ] , which is similar to its distant cousin, sars-cov- ( - days and upto days in some cases) found to have more severe symptoms [ ] . a virus genome may accumulate mutations while it replicates inside the host cell thereby generating genomic variants across the globe. sars-cov- mutates, albeit at a slow rate j o u r n a l p r e -p r o o f [ ] . characterization of these variants may be helpful in understanding the disease mechanism, how the virus evades the immune system or develops resistance to drugs. having stated that, it will be premature to infer from the currently available data that a particular mutation makes the virus more virulent than others. a recent study found two major versions of the sars-cov- coronavirus, called clade i and clade ii, based on the genome sequence analysis of more than sequences [ ] . the two clades were not found to be any different in terms of contagiousness or disease severity. the disease severity largely depended on host factors such as age, lymphocytopenia, and its associated cytokine storm, not so much on the viral genetic variation [ ] . interestingly, in an independent study, researchers have found three blood based biomarkers which can predict disease severity at least ten days in advance with more than % accuracy, based on a database of infected patients from wuhan, china. based on these results, the disease severity was found to be associated with high level week for igm and - weeks for igg). therefore, it can be used for initial screening of the population followed by a more confirmatory test like qrt-pcr. apart from its use for rapid detection of infection during symptomatic period, the serological test could be used even after the infection has receded, as the antibodies may remain in blood for longer period. this will make it a perfect tool for population studies to get more accurate transmission data world- remdesivir has shown positive outcome, a modestly speed recovery of the treated patients, in the nih funded randomized placebo control clinical trials [ ] . remdesivir will also be tested although lesser in number, there have been instances of serious illness and even deaths in young and healthy individuals. fever in % of infected cases, often accompanied by fatigue, nausea or diarrhea. fever with dry cough and muscle pain. day - + breathing difficulties recovery for some patients, however, hospitalization may be needed for patients with severe conditions (~ %), may develop acute respiratory distress syndrome (ards) due to fluid accumulation in the lungs. some cases may worsen needing admission to the intensive care unit (icu). for most of the people fever ends while coughing may still persist day - for patients headed towards recovery, breathing problems may end at this stage. day - full recovery, however, in some cases ( %), it may lead to death. j o u r n a l p r e -p r o o f strict precautionary measures therefore, it is essential for every individual to take precaution irrespective of their age and health covid- can be detected by thermal scanners thermal scanners cannot detect covid- the prolonged use of medical masks may cause co intoxication or oxygen deficiency the prolonged use of medical masks when properly worn, does not cause co intoxication nor oxygen deficiency exposure of self to uv light may kill the virus uv radiation is extremely harmful for eyes and skin, should not be used to should not be used to disinfect hands or other areas of your skin. consumption or injection of disinfectants will kill the virus in the body disinfectants are effective in killing the virus on inanimate surfaces. however, they are extremely toxic for ingestion. a novel coronavirus from patients with pneumonia in china evolutionary trajectory for the emergence of novel coronavirus sars-cov- a pneumonia outbreak associated with a new coronavirus of probable bat origin covid- disease due to sars-cov- (novel coronavirus) clinical characteristics and differential clinical diagnosis of novel coronavirus disease coronavirus disease (covid- ) coronavirus disease and stroke: clinical manifestations and pathophysiological comorbidity and its impact on patients with covid- in china: a nationwide analysis covid- ) from publicly reported confirmed cases: estimation and application evidence supporting transmission of severe acute respiratory syndrome coronavirus while presymptomatic or asymptomatic receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus covid- infection: origin the trinity of covid- : immunity, inflammation and intervention viral and host factors related to the clinical outcome of covid- geographic and genomic distribution of sars-cov- an interpretable mortality prediction model for covid- patients large scale genomic analysis of sars-cov- genomes reveals a clonal geo- distribution and a rich genetic variations of hotspots mutations cas -based detection of sars-cov- laboratory diagnosis of covid- : current issues and challenges development and clinical application of a rapid igm igg combined antibody test for sars cov infection diagnosis drug targets for corona virus: a systematic review remdesivir for the treatment of covid- -preliminary report tocilizumab among patients with covid- in the intensive care unit: a multicentre observational study adults hospitalized with severe covid- an updated systematic review of the therapeutic role of hydroxychloroquine in coronavirus disease- (covid- ) regalado ep. vaccines for sars-cov- : lessons from other coronavirus strains herd immunity: understanding covid- the authors declare that they have no competing interest. key: cord- - z yli authors: humar, atul; mcgilvray, ian; phillips, murray j.; levy, gary a. title: severe acute respiratory syndrome and the liver date: - - journal: hepatology doi: . /hep. sha: doc_id: cord_uid: z yli nan s evere acute respiratory syndrome (sars) is an emerging novel infectious disorder that was first diagnosed in guangdong province in china in november and subsequently spread worldwide. [ ] [ ] [ ] [ ] [ ] spread of sars is via airborne droplets, and infection results in acute pulmonary inflammation and epithelial damage. during the initial outbreak, sars was documented in approximately , persons globally, resulting in more than deaths. a growing body of evidence has proven that a novel coronavirus is the etiologic agent in sars. electron microscopic analysis of affected lung tissues revealed the distinctive structure of a coronavirus (fig. ). genomic rna of the sars coronavirus (scov) has been isolated from sputum and tissue samples of sars patients. [ ] [ ] [ ] koch's postulates were fulfilled with the demonstration that infection of primates with scov resulted in a similar clinical syndrome as observed in humans. evidence suggests that sars may have originated from an animal reservoir: viruses similar to the scov have been found in himalayan palm civets sold in live-animal markets in guangdong, china. the clinical severity of sars can vary considerably, presumably because of the genetic diversity of host immune responses. clinically, sars is characterized by fever ( %), productive cough and shortness of breath ( %- %), myalgia ( %), and diarrhea ( %- %). in some cases, rapid progression of lung consolidation occurs, leading to respiratory failure and death. , laboratory abnormalities include elevated lactate dehydrogenase ( %), lymphopenia ( %- %), thrombocytopenia ( %), and hypocalcemia ( %). liver enzyme abnormalities are common in sars patients, although hepatic impair-ment has not been reported to be a prominent feature of this illness. coronaviruses are a diverse group of large, enveloped, positive-stranded rna viruses that cause a broad spectrum of diseases, including pneumonitis, hepatitis, nephritis, enteritis, and encephalitis in animals, and several of these viruses are significant veterinary pathogens. in humans, coronaviruses usually cause upper respiratory and enteric infections, and lower respiratory tract disease is rare. there are three groups of coronaviruses; each group is classified based on host range and genomic organization. coronaviruses typically have narrow host ranges. human coronaviruses belong to group (hcov- e) and group (hcov-oc ). although the scov does not strictly fall into any of the three groups of known coronaviruses, it bears closest resemblance to the group coronaviruses, which also contain mouse hepatitis virus (mhv). the type of disease incited by a given coronavirus is influenced by the age and genetic background of the host, the route of infection, and the biologic properties of the coronavirus serotype. the coronaviridae share replicative and transcriptional features. the coronavirus genome is a single, nonsegmented rna strand with an estimated molecular weight of to million da. coronaviruses contain an rna-dependent rna polymerase that transcribes the positive template to synthesize both full-length and subgenomic negative stranded rnas that then serve as templates for mrna synthesis. the polymerase is error prone, and rna recombination occurs at a high frequency, with recombination sites observed throughout the genome, both in translated and untranslated regions, resulting in a very adaptable, mutable viral family. the three major structural proteins of coronaviruses are the nucleocapsid protein, the transmembrane protein, and the surface or spike glycoprotein. coronaviruses of group also have a hemagglutinin esterase protein. the spike glycoprotein binds to receptors on host cells and fuses the viral envelope with host cell membranes. individual coronaviruses use different cellular receptors. whereas the group coronavirus (mhv) uses murine carcinoembryonic antigen-related cell adhesion molecules, which are members of the immunoglobulin superfamily of receptors, a number of group coronaviruses such as human coronavirus e require the zinc metalloprotease aminopeptidase nucleocapsid protein for entry into their target cells. recently, the putative cell receptor for the sars coronavirus has been identified as the metallopeptidase, angiotensin-converting enzyme . in this issue of hepatology, chau et al. describe the clinical course and liver pathologic features in three sars patients with liver impairment. all patients had moderate to marked elevation in serum alanine transaminase and underwent liver biopsy. examination of these biopsy specimens suggested that liver impairment in sars is the result of scov infection of the liver rather than other factors such as drug toxicity, superimposed bacterial sepsis, or a systemic inflammatory response. all three liver biopsies demonstrated hepatocyte apoptosis, and two of three had marked accumulation of cells in mitosis. common pathologic features included ballooning of hepatocytes and mild to moderate lobular lymphocytic infiltration. reverse transcriptase polymerase chain reaction (rt-pcr) was positive for sars coronavirus in liver tissue from all three patients, although virions could not be detected either by plaque assay on vero cells or by electron microscopy. the finding of a significant number of cells in the mitotic phase is interesting, and the authors raise the possibility of cell cycle disruption resulting from the scov, which has been reported in animal experimental models of mhv infection. in other studies, liver enzyme abnormalities have been reported commonly in sars patients with an elevated alanine transaminase being the most common abnormality described. in an analysis of cases of sars, alanine transaminase was elevated in . % of patients. because the scov can be detected in many different types of tissues in infected patients, it is not surprising that direct infection of the liver with the virus can lead to liver enzyme abnormalities. however, this is the first report to associate hepatic scov infection and liver pathologic features. available data about mhv may have relevance to sars and specifically to hepatic injury resulting from sars. although mhv replicates in all mice, certain strains develop a fulminant hepatitis and die, whereas others have little or no liver pathologic features and live. within hours of infection with mhv, livers from susceptible mice had focal necrotic lesions consisting of acidophilic degenerating hepatocytes and nuclear debris with a sparse inflammatory infiltrate. by days after infection, these lesions became larger, more numerous, and were associated with an infiltrate of polymorphonuclear leukocytes ( fig. a) . at days, confluent necrosis was evident, and by day to days, the lesions were densely infiltrated with mononuclear cells and the adjoining liver parenchyma underwent hepatocyte regeneration as evidenced by many mitotic figures (fig. b) . early in the course of the disease, virions could be detected by both plaque assay and electron microscopy, but by day , virions could not be detected by either assay, which may be relevant to the report by chau et al. (fig. ) . defining the basis for susceptibility to severe inflammatory outcomes after coronavirus infection has obvious implications for the study and treatment of clinical sars. although the exact mechanisms for resistance and susceptibility to mhv coronavirus infection have not be determined, studies have shown that in resistant mice, infection leads to a t helper type (th )-dominant response that, through the production of interferon, neutralizing antibodies, and cytotoxic t cells, results in viral clearance. in susceptible mice, viral infection results in a marked inflammatory response, with increased production of tumor necrosis factor, interleukin , and interferon-␥ associated with a t helper type (th ) cellular immune response and production of nonneutralizing antibodies. this response fails to control viral infection and results in endothelial cell activation, recruitment of inflammatory cells, vasoconstriction, intravascular thrombosis, and liver necrosis. interestingly, fibrin thrombi and intimal swelling of pulmonary vessels have been described in autopsy samples of lung from sars patients, and transcripts of a potent prothrombotic, fgl / fibroleukin, have been detected. however, in the paper by chau et al., similar pathologic changes were not noted in the liver biopsies. this may reflect factors such as tropism of the scov agent for the lung, distribution and density of the receptor for scov in liver compared with lung tissue, as well as host genetic factors yet to be determined. the fact that a possible receptor for scov has recently been identified-angiotensin converting enzyme -will help in clarifying organ susceptibility to infection by sars. at present, no effective therapeutic strategy has been developed for patients with sars. treatments that were used commonly in the last outbreak of sars included ribavirin and corticosteroids. ribavirin was chosen be-cause of its broad spectrum of activity against rna viruses and steroids for their antiinflammatory properties. it is currently uncertain whether this treatment regimen had any positive impact on the outcomes. furthermore, use of ribavirin is associated with significant toxicity, including hemolysis resulting in discontinuation of its use. kaletra is a combination of lopinavir and ritonavir, two human immunodeficiency virus protease inhibitors, that has been used in some patients with sars. again, efficacy of this medication against sars is largely unknown. immunoglobulin, interferons, and scov-specific protease inhibitors and fusion inhibitors represent alternative therapeutic options for treating sars patients. interferon has in vitro activity against the sars virus, and recent studies suggest this may be an effective agent, as has been shown for mhv infection in rodents. , currently, it is unknown whether sars will recur. a global infection control effort was effective in ending the first epidemic of sars. however, if sars behaves in a manner similar to other coronavirus, recurrences may be seasonal. in addition, animal reservoirs may serve as a source for future outbreaks. our knowledge and understanding of sars has progressed at a rapid rate, but much remains unknown about this new infectious threat. coronavirus as a possible cause of severe acute respiratory syndrome a novel coronaviruses associated with severe acute respiratory syndrome identification of a novel coronavirus in patients with severe acute respiratory syndrome a major outbreak of severe acute respiratory syndrome in hong kong identification of severe acute respiratory syndrome in canada epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in hong kong sars-associated coronavirus lung pathology of fatal severe acute respiratory syndrome newly discovered coronavirus as the primary cause of severe acute respiratory syndrome isolation and characterization of viruses related to the sars coronavirus from animals in southern china characterization of a novel coronavirus associated with severe acute respiratory syndrome several members of the mouse carcinoembryonic antigen-related glycoprotein family are functional receptors for the coronavirus mouse hepatitis virus-a human aminopeptidase n is a receptor for human coronavirus e angiotensin-converting enzyme is a functional receptor for the sars coronavirus sars-associated viral hepatitis caused by a novel coronavirus: report of three cases acute and chronic changes in the microcirculation of the liver in inbred strains of mice following infection with mouse hepatitis virus type resistance of naïve mice to murine hepatitis virus strain (mhv- ) requires development of a th , but not th response, whereas pre-existing antibody protects against primary infection pattern of disease after murine hepatitis virus strain (mhv- ) infection correlates with macrophage activation and not viral replication the fgl /fibroleukin prothrombinase contributes to immunologically-mediated thrombosis in experimental and viral hepatitis treatment of sars with human interferons therapeutic potential of interferon alfacon- plus corticosteroids in severe acute respiratory syndrome: a pilot study key: cord- -f uk m authors: fraser, douglas d.; slessarev, marat; martin, claudio m.; daley, mark; patel, maitray a.; miller, michael r.; patterson, eric k.; o’gorman, david b.; gill, sean e.; wishart, david s.; mandal, rupasri; cepinskas, gediminas title: metabolomics profiling of critically ill coronavirus disease patients: identification of diagnostic and prognostic biomarkers date: - - journal: crit care explor doi: . /cce. sha: doc_id: cord_uid: f uk m objectives: coronavirus disease continues to spread rapidly with high mortality. we performed metabolomics profiling of critically ill coronavirus disease patients to understand better the underlying pathologic processes and pathways, and to identify potential diagnostic/prognostic biomarkers. design: blood was collected at predetermined icu days to measure the plasma concentrations of metabolites using both direct injection-liquid chromatography-tandem mass spectrometry and proton nuclear magnetic resonance. setting: tertiary-care icu and academic laboratory. subjects: patients admitted to the icu suspected of being infected with severe acute respiratory syndrome coronavirus , using standardized hospital screening methodologies, had blood samples collected until either testing was confirmed negative on icu day (coronavirus disease negative) or until icu day if the patient tested positive (coronavirus disease positive). interventions: none. measurements and main results: age- and sex-matched healthy controls and icu patients that were either coronavirus disease positive or coronavirus disease negative were enrolled. cohorts were well balanced with the exception that coronavirus disease positive patients suffered bilateral pneumonia more frequently than coronavirus disease negative patients. mortality rate for coronavirus disease positive icu patients was %. feature selection identified the top-performing metabolites for identifying coronavirus disease positive patients from healthy control subjects and was dominated by increased kynurenine and decreased arginine, sarcosine, and lysophosphatidylcholines. arginine/kynurenine ratio alone provided % classification accuracy between coronavirus disease positive patients and healthy control subjects (p = . ). when comparing the metabolomes between coronavirus disease positive and coronavirus disease negative patients, kynurenine was the dominant metabolite and the arginine/kynurenine ratio provided % classification accuracy (p = . ). feature selection identified creatinine as the top metabolite for predicting coronavirus disease -associated mortality on both icu days and , and both creatinine and creatinine/arginine ratio accurately predicted coronavirus disease -associated death with % accuracy (p = . ). conclusions: metabolomics profiling with feature classification easily distinguished both healthy control subjects and coronavirus disease negative patients from coronavirus disease positive patients. arginine/kynurenine ratio accurately identified coronavirus disease status, whereas creatinine/arginine ratio accurately predicted coronavirus disease -associated death. administration of tryptophan (kynurenine precursor), arginine, sarcosine, and/or lysophosphatidylcholines may be considered as potential adjunctive therapies. objectives: coronavirus disease continues to spread rapidly with high mortality. we performed metabolomics profiling of critically ill coronavirus disease patients to understand better the underlying pathologic processes and pathways, and to identify potential diagnostic/prognostic biomarkers. design: blood was collected at predetermined icu days to measure the plasma concentrations of metabolites using both direct injection-liquid chromatography-tandem mass spectrometry and proton nuclear magnetic resonance. setting: tertiary-care icu and academic laboratory. subjects: patients admitted to the icu suspected of being infected with severe acute respiratory syndrome coronavirus , using standardized hospital screening methodologies, had blood samples collected until either testing was confirmed negative on icu day (coronavirus disease negative) or until icu day if the patient tested positive (coronavirus disease positive). interventions: none. measurements and main results: age-and sex-matched healthy controls and icu patients that were either coronavirus disease positive or coronavirus disease negative were enrolled. cohorts were well balanced with the exception that coronavirus disease positive patients suffered bilateral pneumonia more frequently than coronavirus disease negative patients. mortality rate for coronavirus disease positive icu patients was %. feature selection identified the top-performing metabolites for identifying coronavirus disease positive patients from healthy control subjects and was dominated by increased kynurenine and decreased arginine, sarcosine, and lysophosphatidylcholines. arginine/kynurenine ratio alone provided % classification accuracy between coronavirus disease positive patients and healthy control subjects (p = . ). when comparing the metabolomes between coronavirus disease positive and coronavirus disease negative patients, kynurenine was the dominant metabolite and the arginine/kynurenine ratio provided % classification accuracy (p = . ). feature selection identified creatinine as the top metabolite for predicting coronavirus disease -associated mortality on both icu days and , and both creatinine and creatinine/ arginine ratio accurately predicted coronavirus disease -associated death with % accuracy (p = . ). conclusions: metabolomics profiling with feature classification easily distinguished both healthy control subjects and coronavirus disease negative patients from coronavirus disease positive patients. arginine/kynurenine ratio accurately identified coronavirus c oronavirus disease (covid ) is caused by the severe acute respiratory syndrome coronavirus (sars-cov- ), which continues to spread rapidly worldwide ( , ). diagnosis of covid typically requires polymerase chain reaction for sars-cov- genes or immunoassay for sars-cov- antigens. covid primarily affects lungs, but dysfunction of other organs, such as heart and kidneys, has also been reported ( ) ( ) ( ) ( ) . the severity of covid may involve the excessive release of inflammatory mediators ( - ) together with microvascular thrombi formation secondary to endothelial injury/activation and glycocalyx degradation ( ) . critically ill covid patients are admitted to the icu, where the mortality rate is reported to be - % with standardized icu care ( , ) . although a number of protein mediators have been identified that predict covid -associated death ( , ) , a further characterization of covid -associated processes and pathways is essential for the identification of novel diagnostic/prognostic biomarkers and for improving covid patient outcomes. metabolomics measures a person's metabolite profile (chemicals with an molecular weight < , da), including amino acids, organic acids, biogenic amines, acylcarnitines, glycerophospholipids, sphingolipids, sugars, and many other compounds ( ) . metabolites fall downstream of genetic, transcriptomic, proteomic, and environmental events, thus providing a cohesive measure of a subject's recent phenotype. two complementary analytical methods for metabolomics are proton nuclear magnetic resonance ( h nmr; μm range) spectroscopy and mass spectrometry (ms; nm-pm range). previous studies have demonstrated the diagnostic and prognostic potentials of metabolomics profiling in selecting patient populations (e.g., traumatic brain injury [ ] ). metabolomics profiling of critically ill covid patients over the first days of their icu stay was the overall aim of this exploratory study, thereby identifying potential metabolite candidates and/or combinations as diagnostic/prognostic biomarkers. our specific objectives were: ) to determine/compare the metabolomes between covid positive (+) icu patients and either healthy control subjects or covid negative (-) icu patients, ) to determine specific metabolites that most accurately differentiated covid + from either healthy control subjects or covid -icu patients, and ) to determine whether specific metabolites can predict covid outcome shortly after icu admission. this study was approved by the western university, human research ethics board (hreb). given the unprecedented pandemic situation and the restricted hospital access for substitute decision makers, waived consent was approved for a short, issued march , ) . in keeping with the society for critical care medicine statement on "waiver of informed consent in emergency situations" ( ), the following criteria were considered relevant for hreb approval of waived consent: the subjects were admitted to the icu with a life-threatening condition; the subjects had impaired decisional capacity; the research staff encountered significant obstacles and delays when attempting to contact the absent substitute decision makers; the study risk was minimal; the research knowledge gained on this new, lethal disease offered an eventual chance of benefit; and community consultation had been implemented. given the pandemic circumstances and the waived consent model applied, no further attempts were made to contact the surviving patients and/or substitute decision makers. the last patient enrolled under waived consent was may , . we enrolled consecutive patients who were admitted to our level academic icus at the london health sciences centre (london, on, canada) and were suspected of having covid based on standard hospital screening procedures ( ) . blood sampling began on icu admission for up to days in covid -patients or up to days in covid + patients, with an additional blood draw occurring on day for covid + patients who have not been discharged. covid status was confirmed as part of standard hospital testing by nasopharyngeal swab detection of two sars-cov- viral genes on polymerase chain reaction ( ). patient baseline characteristics were recorded at admission and included age, sex, comorbidities, medications, hematologic labs, creatinine, arterial-partial-pressureto-inspired-oxygen ratio, and chest x-ray findings. we calculated multiple organ dysfunction score ( ) and sequential organ failure assessment score ( ) for both covid + and covid patient groups to enable objective comparison of their illness severity. both patient groups were characterized as having confirmed or suspected sepsis diagnosis using sepsis . criteria ( ) . we also recorded clinical interventions received during the observation period including use of antibiotics, antiviral agents, systemic corticosteroids, vasoactive medications, vte prophylaxis, antiplatelet or anticoagulation treatment, renal replacement therapy, high-flow oxygen therapy, and mechanical ventilation (invasive and noninvasive). final participant groups were constructed by age-and sex-matching covid + patients with covid -patients and healthy controls without disease, acute illness, or prescription medications that were previously banked in the translational research centre, london, on, canada (reb id# e; reissued march , ; "repository of control biological specimens from healthy volunteers for future research purposes"; directed by dr. d. d. fraser; https://translationalresearchcentre.com/) ( , ) . standard operating procedures were used to ensure all samples were treated rapidly and equally. blood was obtained from critically ill icu patients via indwelling catheters in the morning and placed immediately on ice. if a venipuncture was required, research blood draws were coordinated with a clinically indicated blood draw. in keeping with accepted research phlebotomy protocols for adult patients, blood draws did not exceed maximal volumes ( ) . once transferred to a negative pressure hood, blood was centrifuged and plasma was isolated, aliquoted at μl, and frozen at - °c. all samples remained frozen until use and freeze/ thaw cycles were avoided. a targeted quantitative metabolomics approach was used to analyze the samples using a combination of direct injection (di) ms with a reverse-phase lc-ms/ms custom assay. this custom assay, in combination with an absciex qtrap (applied biosystems, foster city, ca/mds sciex, foster city, ca) mass spectrometer, can be used for the targeted identification and quantification of up to different endogenous metabolites including amino acids, acylcarnitines, biogenic amines and derivatives, uremic toxins, glycerophospholipids, sphingolipids, and sugars ( , ) . the method combines the derivatization and extraction of analytes, and the selective mass-spectrometric detection using multiple reaction monitoring pairs. isotope-labeled internal standards and other internal standards were used for metabolite quantification. the custom assay contained a -deep-well plate with a filter plate attached with sealing tape, and reagents and solvents used to prepare the plate assay. the first wells were used for one blank, three zero samples, seven standards, and three quality control samples. for all metabolites except organic acid, samples were thawed on ice and subsequently vortexed and centrifuged at , × g; µl of each sample was then loaded onto the center of the filter on the upper -well plate and dried in a stream of nitrogen. subsequently, phenyl-isothiocyanate was added for derivatization. after incubation, the filter spots were dried again using an evaporator. extraction of the metabolites was then achieved by adding µl of extraction solvent. the extracts were obtained by centrifugation into the lower -deep-well plate, followed by a dilution step with the ms running solvent ( . % formic acid in water, . % formic acid in acetonitrile for biogenic amines and amino acids, and . % formic acid in methanol for all other classes of metabolites). for organic acid analysis, µl of ice-cold methanol and µl of isotope-labeled internal standard mixture were added to µl of serum sample for overnight protein precipitation at - °c, followed by centrifugation at , × g for minutes. a total of µl of supernatant was loaded into the center of wells of a -deep-well plate, followed by the addition of -nitrophenylhydrazine reagent. after incubation for hours, butylated hydroxytoluene stabilizer ( mg/ml) and water were added before lc-ms injection. mass spectrometric analysis was performed on an absciex qtrap tandem ms instrument (applied biosystems/mds analytical technologies, foster city, ca) equipped with an agilent series uhplc system (agilent technologies, palo alto, ca). the samples were delivered to the mass spectrometer by an lc method followed by a di method. data analysis was done using analyst . . (foster city, ca). plasma samples contain a significant concentration of large-molecular-weight proteins and lipoproteins, which affects the identification of the small-molecular-weight metabolites by nmr spectroscopy. a deproteinization step, involving ultrafiltration as previously described ( ) , was therefore introduced in the protocol to remove plasma proteins. prior to filtration, -kda cutoff centrifugal filter units (amicon microcon ym- , burlington, ma) were rinsed five times each with . ml of h o and centrifuged ( , × g for min) to remove residual glycerol bound to the filter membranes. aliquots of each plasma sample were then transferred into the centrifuge filter devices and spun ( , × g for min) to remove macromolecules (primarily protein and lipoproteins) from the sample. the filtrates were checked visually for any evidence that the membrane was compromised, and for these samples, the filtration process was repeated with a different filter and the filtrate inspected again. the subsequent filtrates were collected and the volumes were recorded. if the total volume of the sample was under µl, an appropriate amount from a -mm kh po buffer (ph ) was added until the total volume of the sample was . µl. any sample that had to have buffer added to bring the solution volume to . μl was annotated with the dilution factor and metabolite concentrations were corrected in the subsequent analysis. subsequently, . µl of a standard buffer solution ( % d o: % . -mm kh po ph . v/v containing sodium trimethylsilylpropanesulfonate (dss) [ . -mm , -dimethyl- silcepentane- -sulphonate, . -mm -chloropyrimidine- carboxylate, and . % nan in h o]) was added to the sample. the plasma sample ( µl) was then transferred to a -mm samplejet nmr tube for subsequent spectral analysis. all h-nmr spectra were collected on a -mhz avance iii (bruker, billerica, ma) spectrometer equipped with a -mm hydrogen, carbon, nitrogen z-gradient pulsed-field gradient cryoprobe. h-nmr spectra were acquired at °c using the first transient of the nuclear overhauser effect spectroscopy (noesy) presaturation pulse sequence (noesy dpr), chosen for its high degree of quantitative accuracy ( ) . all free induction decays were zero-filled to k data points. the singlet produced by the dss methyl groups was used as an internal standard for chemical shift referencing (set to ppm). for quantification, all h-nmr spectra were processed and analyzed using an in-house version of the magnetic resonance for metabolomics (magmet)-automated analysis software package using a custom metabolite library. magmet allows for qualitative and quantitative analyses of an nmr spectrum by automatically fitting spectral signatures from an internal database to the spectrum. each spectrum was further inspected by an nmr spectroscopist to minimize compound misidentification and misquantification. typically, all of visible peaks were assigned. most of the visible peaks were annotated with a compound name. it has been previously shown that this fitting procedure provides absolute concentration accuracy of % or better ( ) . medians (interquartile ranges [iqrs]) and frequency (%) were used to report icu patient baseline characteristics for continuous and categorical variables, respectively; continuous variables were compared using mann-whitney u tests (or kruskal-wallis tests, as appropriate), and categorical variables were compared using fisher exact chi-square, with p values of less than . considered statistically significant. receiver operating characteristic (roc) curves were conducted to determine sensitivity and specificity of individual metabolite ratios for predicting a binary outcome. area-under-thecurve (auc) was calculated as an aggregate measure of metabolite ratio performance across all possible classification thresholds. all analyses were conducted using spss version (ibm, armonk, ny). covid analyte data were visualized with a nonlinear dimensionality reduction on the full data matrix using the t-distributed stochastic nearest neighbor embedding (t-sne) algorithm ( ). t-sne assumes that the "optimal" representation of the data lies on a manifold with complex geometry, but with low dimension, embedded in the full-dimensional space of the raw data. for feature selection, the raw data for each subject were ingested within each feature, across subjects. a random forest classifier was trained on the variables to predict covid status or covid outcome ("scikit-learn" module for python . . open source). a random forest is a set of decision trees, and consequently, we were able to interrogate this collection of trees to identify the features that have the highest predictive value. feature selection was not performed in preprocessing. during training, the random forest classifier performed an implicit feature selection; the top features are those that appear highest ranked in the most trees. to reduce overfitting, the number of trees and maximum depth of each tree was limited ( ) ; thus, covid status was determined using a six-fold cross validation with a random forest of trees, whereas patient outcome was determined using a three-fold cross validation with a random forest of trees and a maximum depth of . to remain conservative and to limit the risk of overfitting further, no hyperparameters were tuned or optimized by design and intent. furthermore, to validate the results and ensure no overfitting occurred, a simple linear support vector machine classifier was used to compare the predication accuracies with excellent concordance. we investigated covid + patients (median years of age = . , iqr = . - . ), age-and sex-matched covid -patients (median years of age = . , iqr = . - . ), and ageand sex-matched healthy controls (median years of age = . , iqr = . - . ; p = . ). baseline demographic characteristics, comorbidities, laboratory values, and chest x-ray findings are reported in table . the covid -patients had significantly higher unilateral pneumonia, whereas covd + patients were more likely to have bilateral pneumonia. sepsis was "confirmed" by infectious pathogen identification in only % of covid patients, whereas sepsis was "suspected" in the remaining % ( ) . a mortality rate of % was determined for covid + patients. we measured a total of plasma metabolites using both di-lc-ms/ms and h nmr. in the event of metabolite repeats measured with both techniques ( metabolites), the h nmr metabolite repeat measurements were deleted from the combined metabolite database, yielding a final number of metabolites analyzed. figure a shows a t-sne plot illustrating that the icu day covid + patient metabolome was distinct and easily separable from age-and sex-matched healthy control subjects. in fact, classification accuracy was % when comparing the two metabolomes. we then identified the top eight metabolites underlying these differences between the cohorts, which are shown in figure b with their associated % importance. in the covid + cohort, relative to the healthy control subjects, kynurenine increased . fold whereas arginine decreased . -fold, sarcosine decreased . -fold, and lysophosphatidylcholines (lysopcs) all decreased . -fold on average. the least number of metabolites that were required to maintain a % classification accuracy between the cohorts was then determined, with only arginine (cutoff ≤ . μm) and kynurenine (cutoff ≥ . μm) required. the excellent predictive ability of an arginine/kynurenine ratio for discriminating a covid patient from a healthy control subject (cutoff ≤ . ) is shown with roc analysis in figure c (auc = . ; p = . ). a comparison of covid + and covid -patient cohorts revealed distinct metabolomes. feature classification again identified kynurenine as one of the leading metabolites underlying the differences between the covid + and covid -cohorts ( fig. a) . we then determined that an arginine/kynurenine ratio again showed an excellent discriminative ability to determine covid status on icu day (cutoff ≤ . ) via roc analyses (auc = . ; p = . ; fig. b ). figure c shows an arginine/ kynurenine ratio time plot for the covid + and covid patients over icu days. the cohorts' ratios were significantly different on icu days and (p = . ). figure a shows a t-sne plot for covid + patients that either survived or died, and demonstrates that the outcomes were distinct and separable. to optimize outcome prediction in covid + patients, the number of metabolites was narrowed using feature selection (fig. b) . creatinine was the leading metabolite and could predict death with % accuracy on both icu days (cutoff > μmol/l) and (cutoff > μmol/l). to improve the variation in patient creatinine values, we then tested the ability of a creatinine/arginine ratio to predict death; the corresponding time plot is shown in figure c . death could be predicted with % accuracy on both icu days (cutoff ≥ . ) and (cutoff ≥ . ), as the creatinine/arginine ratios were significantly different between the covid patients that lived or died at both time points (p = . ). the creatinine/arginine ratios normalized by icu day , regardless of eventual outcome. there were no deaths during the icu days. in this study, we measured metabolites in plasma obtained from icu patients, both covid + and covid -, as well as age-and sex-matched healthy control subjects. given the number of metabolites measured, we analyzed the data with the stateof-the-art machine learning. our exploratory data indicate the presence of a unique covid plasma metabolome dominated by changes in kynurenine, arginine, sarcosine, and lysopcs. additionally, we identify that either creatinine alone or a creatinine/arginine ratio predicted icu mortality with % accuracy. despite the exploratory nature of our study, the data generated suggest that these three metabolites (kynurenine, arginine, and creatinine) could be considered for further investigation as continuous data are presented as medians (interquartile ranges) and categorical data are presented as n (%). vte prophylaxis represents the number of patients receiving venous thromboembolism prophylaxis with regular-or low-molecular heparin; new antiplatelets represents the number of patients who were started on aspirin or clopidogrel during icu stay; new anticoagulation represents the number of patients who were started on therapeutic anticoagulation with regular-or low-molecular heparin, or novel oral anticoagulants potential diagnostic and prognostic biomarkers for covid and that they may be useful for patient stratification in clinical interventional trials. our covid + icu patients were similar to those reported in earlier cohorts ( ) ( ) ( ) ( ) with respect to demographics, comorbidities, and clinical presentation. in contrast to covid -icu patients, our covid + icu patients had a higher frequency of bilateral pneumonia. previous work by our study group in these same patients has determined a unique inflammatory profile characterized by elevated tumor necrosis factor and serine proteases ( ) , and a thrombotic profile associated with endothelial activation and glycocalyx degradation ( ). by employing targeted proteomics, figure . a, subjects plotted in two dimensions following dimensionality reduction in their respective metabolites by stochastic neighbor embedding. green dots represent healthy control subjects, whereas orange dots represent age-and sex-matched coronavirus disease positive (covid +) icu patients (icu day plasma). the dimensionality reduction shows that based on the plasma metabolites, the two cohorts are distinct and easily separable. the axes are dimensionless. b, feature classification, demonstrating the top eight plasma metabolites that classify covid + status versus healthy control subjects with their % association. c, receiver operating characteristic analysis of healthy control subjects versus covid + patients, using an arginine/kynurenine ratio, demonstrates an area-underthe-curve (auc) of . (p = . ). the cutoff value is . . the diagonal broken blue line represents chance (auc . ). we also identified six novel protein immune biomarkers that accurately predict covid associated death ( ) . taken together with the data from this study, covid represents a severe illness with a unique pathophysiological signature, as well as a high mortality rate. indeed, in our cohort of covid patients, icu death was % with standardized icu care. our study has identified a unique metabolome in covid + icu patients that is hypothesis-generating for future diagnostic/ prognostic studies. not only have we provided a rank order listing of metabolites important for covid status, we also identified metabolites that accurately determined covid icu outcome. the former represents diverse metabolites that influence immune function and survival, whereas the latter represents compromised renal function early in icu care. importantly, the metabolites required for covid diagnosis (arginine/kynurenine ratio) and outcome (either creatinine alone or creatinine/arginine ratio) can be easily measured using only ms or immunoassay, making their use as covid biomarkers affordable and easily available. point-of-care analyses for these metabolites could be rapidly developed, such as a lateral flow immunochromatographic assay. furthermore, our study raises the possibility that dietary supplementation of tryptophan, arginine, sarcosine, and lysopcs as adjunctive therapies may aid covid outcome. covid status relied heavily on increased plasma kynurenine. the essential amino acid tryptophan is metabolized to elevate the energy-producing cofactor nicotinamide adenosine dinucleotide, with kynurenine as the first stable intermediate to be formed ( ) . increased degradation of tryptophan, with a consequential increase in kynurenine, occurs during an immune response and is driven by the release of interferon-gamma from the activated t-cells. covid caused intense t-cell activation ( , ) with an approximate -fold increase in plasma interferon-gamma in critically ill covid patients when compared with healthy control subjects ( ) . although plasma kynurenine effectively discriminated covid + patients from healthy control subjects, determination of covid status in icu patients required further specificity that was optimally provided by an arginine/kynurenine ratio. arginine, an amino acid precursor for nitric oxide, was significantly depressed in covid + patients. arginine depletion is likely secondary to the intense requirement for nitric oxide signaling and antiviral activity ( ) , as well as consumption by the enzyme arginase that represents a macrophage immunoregulatory mechanism ( ) . as arginine is essential for tissue repair ( ) , its depletion could potentially delay and/or compromise icu recovery. sarcosine, an amino acid that helped discriminate covid + patients from healthy control subjects, was also significantly depressed. although not superior to the arginine/kynurenine ratio for diagnosing covid status, sarcosine sequestration may have a critical role in covid pathology. sarcosine enhances the activity of antigen presenting cells ( ) and activates autophagy ( ) , or the body's removal of damaged cells and their immunostimulatory debris. as a protective catabolic process during covid , autophagy is critical to the antiviral response by direct elimination of virus, the presentation of viral antigens, and the inhibition of excessive inflammation ( ) . sarcosine levels decrease with age ( ) , and the elderly are most susceptible to covid morbidity and mortality. depressed plasma lysopcs also helped discriminate covid + patients from healthy control subjects. the partial hydrolysis of the dimensionality reduction shows that based on the plasma metabolites, the two cohorts are distinct and easily separable. the axes are dimensionless. b, feature classification, demonstrating the top eight plasma metabolites that classify covid + icu patient outcome as alive or dead with their % association. plasma creatinine was the leading outcome predictor metabolite. c, a time plot, demonstrating the creatinine/arginine ratio for covid + icu patients over icu days that either survived (blue dots) or died (orange dots). the two cohorts are significantly different on icu days and (**p = . ). healthy control range values are represented by green shading. phosphatidylcholines by phospholipase a produces lysopcs, which are subsequently implicated in endothelial activation ( ) and phagocytosis of cellular debris ( ) . decreased plasma lysopcs has been observed in sepsis ( ) , where lysopcs may aid pathogen elimination, and therapeutic replacement has been suggested to improve sepsis outcome ( ) . acute renal dysfunction is strongly associated with high mortality in icu patients ( ) . plasma creatinine, a marker of renal dysfunction, was an excellent discriminator for covid patients that either lived or died. in our covid + cohort, two patients had chronic kidney disease and two patients required renal replacement therapy. the angiotensin-converting enzyme receptor that is essential for sars-cov- uptake is highly expressed on tubule epithelial cells ( ) . acute kidney injury is reported to occur in up to % of covid patients ( ) and is secondary to acute tubular injury from direct viral infection ( ) . our data suggest that covid diagnosis (arginine/kynurenine ratio) and outcome (creatinine alone or creatinine/arginine ratio) can be determined with point-of-care measurements of kynurenine, arginine, and creatinine, and that this rapid and affordable biomarker approach may be complimentary to the more expensive and time-consuming diagnostic tools currently employed (e.g., polymerase chain reaction and antigen immunoassay). furthermore, our study raises the possibility that dietary supplementation of tryptophan (kynurenine precursor), arginine, sarcosine, and lysopcs may aid covid outcome as adjunctive therapies. despite the novelty of the metabolite biomarkers discovered, our study has several limitations. first, we only studied critically ill patients and we cannot determine the full metabolome changes associated with icu admissions. second, although our covd study population was limited, we still identified strong associations between the individual metabolites and outcomes and we fulfilled an urgent need for exploratory data to focus future hypothesisdriven studies on larger cohorts. third, we report only mortality as our primary clinical outcome. future studies with larger sample sizes can explore whether reported changes in specific metabolites correlate with additional clinical outcomes such as functional status in survivors. finally, our analyses employed a cross-validation methodology in which the classifier was trained multiple times, each time on a different subset of the data, with the remainder of the data withheld for use only in testing. the reported accuracy is the mean accuracy of all such trials. this is a standard, accepted, technique in the machine learning literature, but should be validated on a larger testing set that is used only once. overfitting was minimized by using a very small number of trees with a limited depth ( ) , and the results verified by training a simple linear vector machine and by identifying concordance between the results. in summary, we report a unique metabolome in covid + icu patients, with identification of three metabolites that appear to be accurate diagnostic/prognostic biomarkers for future studies. given the rapid spread of covid and the critical need for rapid and affordable diagnostics, our data may be invaluable for future testing. in addition, our exploratory data may be useful for guiding resource mobilization and/or goals of care discussion, but only after validation in larger covid + cohorts. furthermore, patient stratification is critically important for future covid interventional trials. world health organization: who director-general's opening remarks at the media briefing on covid- - covid- in critically ill patients in the seattle region -case series clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease pneumonia in wuhan, china baseline characteristics and outcomes of patients infected with sars-cov- admitted to icus of the lombardy region into the eye of the cytokine storm uk: covid- : consider cytokine storm syndromes and immunosuppression inflammation profiling of critically ill coronavirus disease patients endothelial injury and glycocalyx degradation in critically ill coronavirus disease patients: implications for microvascular platelet aggregation icu and ventilator mortality among critically ill adults with coronavirus disease novel outcome biomarkers identified with targeted proteomic analyses of plasma from critically ill coronavirus disease patients metabolomics for laboratory diagnostics metabolomics profiling of concussion in adolescent male hockey players: a novel diagnostic method society of critical care medicine: waiver of informed consent in emergency situations centers for disease control and prevention: cdc novel coronavirus (ncov) real-time rt-pcr diagnostic panel -instructions for use external validation of a prognostic model for intensive care unit mortality: a retrospective study using the ontario critical care information system the third international consensus definitions for sepsis and septic shock (sepsis- ) translational research in pediatrics: tissue sampling and biobanking translational research in pediatrics ii: blood collection, processing, shipping, and storage policy: guidelines for limits of blood drawn for research purposes in the clinical center the bovine metabolome chemical composition of commercial cow's milk the human serum metabolome optimization of nmr analysis of biological fluids for quantitative accuracy accurate, fully-automated nmr spectral profiling for metabolomics when do random forests fail? in: proceedings of the nd international conference on neural information processing systems kynurenine pathway metabolites in humans: disease and healthy states marked t cell activation, senescence, exhaustion and skewing towards th in patients with covid- pneumonia e: t cell responses in patients with covid- nitric oxide inhibits the replication cycle of severe acute respiratory syndrome coronavirus immunoregulatory interplay between arginine and tryptophan metabolism in health and disease role of arginine and omega- fatty acids in wound healing and infection sarcosine promotes trafficking of dendritic cells and improves efficacy of anti-tumor dendritic cell vaccines via cxc chemokine family signaling sarcosine is uniquely modulated by aging and dietary restriction in rodents and humans digesting the crisis mitochondrial reactive oxygen species mediate lysophosphatidylcholine-induced endothelial cell activation apoptotic cells induce migration of phagocytes via caspase- -mediated release of a lipid attraction signal lipidomic profiling of plasma and erythrocytes from septic patients reveals potential biomarker candidates product inhibition of secreted phospholipase a may explain lysophosphatidylcholines' unexpected therapeutic properties renal failure in the icu: comparison of the impact of acute renal failure and end-stage renal disease on icu outcomes kidney and lung ace expression after an ace inhibitor or an ang ii receptor blocker: implications for covid- acute kidney injury in patients hospitalized with covid- ultrastructural evidence for direct renal infection with sars-cov- key: cord- -iu flbcl authors: chiotos, kathleen; hayes, molly; kimberlin, david w; jones, sarah b; james, scott h; pinninti, swetha g; yarbrough, april; abzug, mark j; macbrayne, christine e; soma, vijaya l; dulek, daniel e; vora, surabhi b; waghmare, alpana; wolf, joshua; olivero, rosemary; grapentine, steven; wattier, rachel l; bio, laura; cross, shane j; dillman, nicholas o; downes, kevin j; oliveira, carlos r; timberlake, kathryn; young, jennifer; orscheln, rachel c; tamma, pranita d; schwenk, hayden t; zachariah, philip; aldrich, margaret l; goldman, david l; groves, helen e; rajapakse, nipunie s; lamb, gabriella s; tribble, alison c; hersh, adam l; thorell, emily a; denison, mark r; ratner, adam j; newland, jason g; nakamura, mari m title: multicenter interim guidance on use of antivirals for children with covid- /sars-cov- date: - - journal: j pediatric infect dis soc doi: . /jpids/piaa sha: doc_id: cord_uid: iu flbcl background: although coronavirus disease (covid- ) is a mild infection in most children, a small proportion develop severe or critical illness. data evaluating agents with potential antiviral activity continue to expand, such that updated guidance is needed regarding use of these agents in children. methods: a panel of pediatric infectious diseases physicians and pharmacists from geographically diverse north american institutions was convened. through a series of teleconferences and web-based surveys, a set of guidance statements was developed and refined based on review of the best available evidence and expert opinion. results: given the typically mild course of covid- in children, supportive care alone is suggested for most cases. for children with severe illness, defined as a supplemental oxygen requirement without need for non-invasive or invasive mechanical ventilation or extra-corporeal membrane oxygenation (ecmo), remdesivir is suggested, preferably as part of a clinical trial if available. remdesivir should also be considered for critically ill children requiring invasive or non-invasive mechanical ventilation or ecmo. a duration of days is appropriate for most patients. the panel recommends against the use of hydroxychloroquine or lopinavir-ritonavir (or other protease inhibitors) for covid- in children. conclusions: antiviral therapy for covid- is not necessary for the great majority of pediatric patients. for children with severe or critical disease, this guidance offers an approach for decision-making regarding use of remdesivir. in december , the novel coronavirus severe acute respiratory syndrome coronavirus (sars-cov- ) emerged in wuhan, hubei province, china, as the cause of a severe respiratory disease, coronavirus disease (covid- ) . as of august , , over million people worldwide have been infected, including over . million in the united states (us) alone, with over , deaths reported globally ( ) . in light of this public health crisis, there has been significant interest in identifying potentially efficacious antiviral therapies, including novel and "repurposed" medications. to guide pediatric clinicians in the use of these agents, and leveraging the sharing antimicrobial reports for pediatric stewardship (sharps) collaborative, we developed an initial antiviral guidance document, published in april , based on best available evidence and expert consensus ( , ) . in the few months since this initial publication, new evidence has emerged demonstrating the efficacy of the antiviral medication remdesivir in shortening time to clinical recovery in adults with covid- , while several other studies have shown ineffectiveness of hydroxychloroquine and lopinavir-ritonavir ( ) ( ) ( ) ( ) ( ) . based on these data, the us food and drug administration (fda) issued an emergency use authorization (eua) for remdesivir, and the previously issued eua for hydroxychloroquine was revoked ( , ) . further, additional observational studies have provided insight into the clinical epidemiology of covid- in children, demonstrating that while most young patients experience mild illness, a small proportion develop severe illness associated with adverse clinical outcomes, including need for pediatric intensive care unit (picu) admission and mortality ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . finally, in april , a newly recognized hyperinflammatory syndrome seemingly associated with covid- emerged, referred to by the royal college of paediatrics and child health as pediatric inflammatory multisystem syndrome temporally associated with sars-cov- (pims-ts) and by the world health organization and us centers for disease control and prevention as multisystem inflammatory syndrome in children (mis-c) ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) . affected children present with evidence of multisystem inflammation, with variable manifestations that may include fever, cardiovascular shock, gastrointestinal symptoms, or dermatologic or mucocutaneous changes ( ) ( ) ( ) ( ) ( ) . the syndrome, while fortunately rare with an estimated incidence of in , persons < years of age often necessitates picu admission and has resulted in rare mortalities ( ) . considering the rapidly expanding evidence base regarding optimal antiviral therapy for covid- , yet an ongoing paucity of pediatric-specific data, we reconvened the expert panel to update our initial guidance document. we remind the reader that this document is not a guideline, and we emphasize the ongoing importance of critical review of emerging literature to inform treatment decisions. we additionally refer the reader to guidelines published by the infectious diseases society of america and the national institutes of health ( , ) . a panel of pediatric infectious diseases physicians and pharmacists from geographically diverse north american institutions developed and refined a set of consensus guidance statements through a series of teleconferences and web-based surveys. the panel considered three major questions: ) what criteria define the pediatric population in whom remdesivir should be prescribed? ) does the presence of any underlying medical condition or characteristic warrant different criteria for remdesivir use based on an increased risk of covid- -related morbidity or mortality? ) should any other agents with potential antiviral activity be used to treat covid- ? following each consensus statement, we summarize our rationale and the relevant available evidence, prioritizing human studies. given the overall limited nature of pediatric data, a systematic review was not performed, nor was the available evidence formally evaluated using grading of recommendations assessment, development, and evaluation (grade) or other methodology. of note, this panel considered only antiviral use, with use of corticosteroids and other immunomodulatory therapies reviewed elsewhere ( ) . this guidance document has been reviewed and endorsed by the pediatric infectious diseases society. a statement of "recommend" reflects the panel's view that the evidence base for or against a therapy is sufficiently strong that departures from these recommendations could be viewed as outside the range of usual practice. a statement of "suggest" reflects the panel's view that there is weighting towards risk or benefit from the therapy. a statement of "consider" reflects the panel's uncertainty about the risk or benefit from the therapy. guidance statement: the panel recommends remdesivir be used only in children with positive sars-cov- viral testing. rationale: the clinical presentation of covid- in children is heterogeneous and overlaps significantly with other infections. administration of remdesivir without confirmation of sars-cov- infection poses a significant risk of exposing patients to unnecessary harms without the possibility of benefit and may deplete scarce remdesivir supplies. a rare exception might be made for critically ill patients with a high suspicion for covid- (based on a highly consistent clinical presentation combined with high local prevalence or contact with a confirmed case) for whom a significant delay in sars-cov- test results is anticipated. in such a scenario, empiric initiation of remdesivir could be considered while awaiting test results. guidance statement: the panel recommends that clinical criteria, particularly respiratory support requirements, be used to define scenarios in which treatment with remdesivir is considered. rationale: respiratory support requirement has been used to define illness severity categories in the published clinical trials evaluating remdesivir efficacy (table ) . because the potential benefit of remdesivir across illness severities may differ, we suggest respiratory support requirement be the primary determinant of whether remdesivir is used. the panel additionally recognizes that the spectrum of clinical presentations varies in children, and that rapid deterioration in clinical status and/or cardiovascular compromise may be additional considerations. finally, the panel also considered radiographic criteria, but because radiographic infiltrates are common, even among well-appearing, clinically stable children, respiratory support requirement was favored as the more objective and therefore relevant measure ( ) . guidance statement: remdesivir is suggested for children with severe covid- . rationale: we regard covid- cases as "severe" if there is a new requirement for supplemental oxygen (or an increased requirement from baseline) but without the need for new or increased non-invasive or invasive mechanical ventilation or ecmo (table ) . remdesivir is suggested in this population based on a randomized trial demonstrating a shorter time to clinical recovery in hospitalized adults treated with remdesivir, with the greatest benefit in the subgroup requiring supplemental oxygen without need for mechanical ventilation. however, the clinical course of severe covid- may be milder in children, and therefore the benefit of remdesivir is less certain, necessitating continued case-by-case assessments of benefit and risk in children. this assessment should be informed by illness severity, illness trajectory, hypothesized risk factors for poor clinical outcomes as detailed in section ii, and remdesivir availability. when available, patients should be enrolled in clinical trials. guidance statement: remdesivir should be considered for all children with critical covid- , unless there are contraindications. rationale: we regard covid- cases as "critical" if there is a new or increased need for non-invasive or invasive mechanical ventilation, hemodynamic instability requiring vasoactive agents, multisystem organ failure, or a rapidly worsening clinical trajectory ( table ) . the aforementioned randomized trial demonstrated no difference in time to clinical recovery among the subgroup of adults requiring mechanical ventilation or ecmo. the benefit of remdesivir therapy is therefore uncertain in this population. however, given extreme illness severity and lack of pediatric-specific data evaluating efficacy, remdesivir should be considered on a case-by-case basis in all critically ill children. this assessment should be informed by illness severity, illness trajectory, duration of ventilation (with initiation earlier in the intubation course favored), and remdesivir availability. when available, patients should be enrolled in clinical trials. rationale: based on the duration recommended in the fda eua and no difference in outcomes in a randomized trial comparing versus days of therapy in adults, we suggest a duration of up to days for most children with covid- who are treated with remdesivir. for children requiring mechanical ventilation or ecmo, a duration of up to days is recommended in the fda eua and was the duration studied in the placebo-controlled trial establishing remdesivir's efficacy in hospitalized adults. however, given data suggesting no difference in outcomes between versus days of therapy, and uncertainty as to whether remdesivir provides any clinical benefit at all for critically ill patients, we suggest a duration of - days, with up to days considered on a case-by-case basis for those patients not improving after days of therapy (table ) . remdesivir is a nucleoside analog prodrug which, when activated, binds to viral rna polymerase, resulting in premature rna chain termination ( , ) . the fda issued an eua for remdesivir on may , for adults and children with severe or critical covid- , which was subsequently expanded to include all hospitalized patients on august , ( ) . prior to the eua, remdesivir could be obtained through single patient expanded access ("compassionate use") requests through the manufacturer, gilead scientific. in vitro data while other nucleoside analogs (e.g., ribavirin) are ineffective against coronaviruses due to the proofreading capability of a unique '-to- ' exoribonuclease and resultant high-fidelity viral replication, remdesivir maintains activity despite the existence of this exoribonuclease ( , ) . in vitro studies also demonstrate a low likelihood of developing resistance, further supporting use of remdesivir ( ) . halfmaximal effective concentration (ec ) for sars-cov- was low in vero e cells ( . m), while cytotoxic concentration was high, suggesting remdesivir specificity for viral rna polymerase and a wide therapeutic index ( ) . the results of four randomized trials evaluating the efficacy of remdesivir have been published at the time of this guidance document. the adaptive covid- treatment trial (actt) (nct ) was a national institutes of health (nih)-funded, multicenter, double-blind, placebo-controlled trial evaluating the efficacy of a -day course of remdesivir in hospitalized adults with covid- . the primary outcome was time to recovery, defined as either hospital discharge or hospitalized without need for ongoing medical care, and was measured on an eight-point ordinal scale. preliminary results demonstrated that patients treated with remdesivir had a median time to recovery of days as compared to days in the placebo group (rate ratio . , % confidence interval [ci] . - . ). in a subgroup analysis stratified by respiratory support requirement, time to recovery was reduced in the group requiring supplemental oxygen only, with no difference in patients not requiring supplemental oxygen (i.e., patients with moderate disease) or in patients requiring mechanical ventilation (invasive or noninvasive) or ecmo (i.e., patients with critical disease). no statistical difference in mortality was detected ( . % in the remdesivir arm versus . % in the placebo arm). there were no differences in key safety outcomes between treatment groups, including anemia, acute kidney injury, or hepatic transaminase elevations ( ) . additional analysis of these data is ongoing. an industry-sponsored trial compared versus days of remdesivir therapy in a cohort of patients aged ≥ years with severe covid- , defined as pulmonary infiltrates on imaging and an oxygen saturation < % on room air or need for supplemental oxygen at randomization (nct ). the primary outcome was clinical status on day using a -point ordinal scale, similar to the previous study. after adjustment for baseline clinical status, which was more severe in the -day group, no differences in the primary outcome were detected in the two treatment arms ( ) . a second industrysponsored, open-label, non-placebo-controlled randomized trial compared standard care versus a -or up to -day course of remdesivir in hospitalized patients with moderate covid- , defined as pulmonary infiltrates on imaging and an oxygen saturation > % at randomization (nct ). the primary outcome of this study was clinical status score on day following randomization on a -point ordinal scale, with differences in the distribution of scores across treatment groups reported as odds of a better clinical status. relative to patients randomized to standard care, patients randomized to days of remdesivir had a greater odds of a higher clinical status (odds ratio . , % ci . - . ) at day , whereas no statistical difference in clinical status was detected in the -day group. significant limitations to this study include ) the unblinded nature of the trial and ) uncertainty as to how to translate the summary odds ratio presented in the primary analysis into a quantifiable and clinically meaningful difference in outcome ( ) . finally, a double-blind, placebo-controlled randomized trial compared remdesivir to placebo in hospitalized adults with severe covid- , defined as radiographically confirmed pneumonia and oxygen saturation of < % on room air or an arterial partial pressure of oxygen to fractional inspired oxygen of ≤ mmhg. similar to the previous two trials, an ordinal outcome scale was used, with the primary outcome of time to clinical improvement defined as the first day within days of randomization that patients experienced improvement of ≥ ordinal levels. this trial was halted prior to target enrollment due to the decline in covid- cases in china, but there was no statistical difference in the primary outcome between treatment groups. complicating the interpretation of these results, use of additional therapies, including antivirals, immunomodulators and corticosteroids, was permitted ( ) . additional published data describing use of remdesivir for covid- include case reports and case series ( ) ( ) ( ) . there are no comparative clinical data evaluating the efficacy or safety of remdesivir for covid- in pediatric patients. most covid- in children is asymptomatic or of mild or moderate severity ( , , , ( ) ( ) ( ) ( ) ( ) . in a large case series of , confirmed and suspected pediatric covid- cases in china, > % had asymptomatic, mild, or moderate infections ( ). data from the us is consistent with these findings, with the majority of children managed as outpatients ( , ) . children receiving remdesivir have been included in several pediatric case series, though data related to clinical outcomes and adverse events are not specifically reported ( , ( ) ( ) ( ) ) . a multinational european cohort of children demonstrated that ( %) had mild or moderate disease, with patients requiring picu admission and just four mortalities. remdesivir was used in patients, but the impact on clinical outcomes was not reported ( ) . similarly, among a cohort of hospitalized children in the us, . % required icu admission and only one mortality was reported. among the children with data on antiviral medication use, just nine received remdesivir ( ) . finally, among children aged < years enrolled in a randomized trial evaluating the efficacy of remdesivir for ebola, there were no serious adverse events attributed to remdesivir in children ( ). the fda-recommended dosing of remdesivir for children is summarized in table ( ) . these recommendations are based on adult physiologically based pharmacokinetic (pbpk) modeling and reflect those used in the aforementioned ebola trial, as well as those recommended for use under the single-patient expanded access ("compassionate use") program. while these doses are expected to provide similar drug exposure to those observed in healthy adults, there are no published pharmacokinetic studies that validate this approach. pediatric providers should be aware that remdesivir is available as an injectable solution and a lyophilized powder, which differ in their concentration of sulfobutylether-β-cyclodextrin sodium salt (sbecd), a renally cleared excipient. the injection solution contains g sbecd per mg vial, whereas the lyophilized powder formulation contains g sbecd per mg vial. for pediatric patients < kg, remdesivir lyophilized powder is used to limit cyclodextrin exposure to less than mg/kg ( ) . finally, while remdesivir is a substrate for cyp c , cyp d , and cp a in vitro, it has a low potential for drug-drug interactions as its metabolism is likely mediated by hydrolase activity. that said, providers are nevertheless encouraged to check drug interactions prior to use ( ) . the fda has warned of possible antagonism between remdesivir and hydroxychloroquine based on in vitro data, so concomitant use of these drugs is not recommended ( ) . several ongoing clinical trials in the us are evaluating the efficacy of remdesivir alone or in combination with various immunomodulatory agents, including baricitinib (nct , nct ), tocilizumab (nct ), and merimepodib (nct ). additionally, remdesivir is being studied in the who-sponsored solidarity trial (nct ). finally, an industry-sponsored study evaluating the safety, tolerability, pharmacokinetics, and efficacy of remdesivir from birth to years of age is underway to inform optimal pediatric dosing (nct ). evidence summary: the pathogenesis of mis-c remains unknown, but the syndrome is presumed to be post-infectious based on three main observations. first, a region's incidence of mis-c has been reported to peak about month after its peak in acute covid- cases ( , ) . second, some affected children have preceding symptoms consistent with acute covid- ( ) ( ) ( ) . finally, a substantial proportion of affected children have positive sars-cov- serology but negative rt-pcr assays, suggesting that their hyperinflammatory state may reflect a post-infectious phenomenon with an aberrant immune response ( , , ) . however, the sars-cov- testing profile is variable in patients meeting criteria for mis-c, with some patients having positive rt-pcr results, sometimes without sars-cov- antibodies ( ) ( ) ( ) . it is unknown whether rt-pcr positivity in mis-c represents replication-competent virus that may act as an ongoing inflammatory trigger. in addition, the overlap of clinical and laboratory features between acute covid- -associated hyperinflammatory syndrome and mis-c can result in diagnostic uncertainty. until the pathogenesis of mis-c is better understood, we suggest limiting remdesivir use to select patients with mis-c and a positive viral testing, including those with an ambiguous clinical presentation, severe illness, or an rt-pcr cycle threshold result suggestive of a high viral load. another potential consideration for remdesivir use is concurrent use of immunosuppressive therapy -particularly corticosteroids -that may impair virologic control. guidance statement: there are no definitive data to support any specific risk factor for severe in children. rationale: the majority of pediatric data related to covid- remains descriptive in nature, including population-level epidemiologic studies and single-and multi-center case series describing primarily hospitalized and/or critically ill patients. the reported prevalence of any comorbidity in these series varies widely, ranging from % to %. nevertheless, the panel recognizes that pediatric clinicians are likely to consider comorbidities when weighing the risks and benefits of antiviral therapy on a case-bycase basis, and in making these decisions may consider: ) the available, albeit limited, pediatric covid- literature; ) risk factors associated with severe covid- in adults; and ) pre-existing medical conditions in children associated with worse clinical outcomes for other viral infections. we have therefore summarized relevant data and highlighted hypothesized risk factors ( table ) that clinicians may consider in determining whether to administer remdesivir. evidence summary: although there is no standard definition for children with medical complexity (cmc), this term generally refers to children who have multiple chronic health conditions, may be dependent on medical technology, and may have functional limitations (e.g., due to neurologic impairment, developmental delays, or genetic syndromes) ( ) . this group's risk of decompensation with pulmonary infections is likely driven by a combination of factors, including abnormalities in mucociliary clearance, muscle tone, and craniofacial structures, as well as potentially delayed recognition of illness due to impairments in communication ( ) . it would therefore not be unexpected if cmc experienced a more severe course following sars-cov- infections, though empiric data confirming this assumption are lacking, and interpretation of published studies is confounded by inconsistent definitions of cmc. in a cross-sectional study of children admitted to north american picus, ( %) were classified as medically complex, whereas only an estimated . % of children in the us are cmc ( , ) . in a large european study of children, both underlying pulmonary disease and neurologic disease were associated with increased risk of picu admission, though whether children in these categories would have met the definition for cmc based on the severity of the underlying condition was not reported ( ) . similarly, two smaller us case series highlight a numerically higher prevalence of children with underlying genetic and neurologic conditions among patients requiring picu admission, though these differences did not achieve statistical significance ( , ) . collectively, these data support the possibility that cmc may be at risk for severe covid- , and medical complexity therefore could be considered in making antiviral treatment decisions. the pediatric cohort described by dong and colleagues remains the largest to date and included children in the < -year category ( ). of these, % had mild to moderate symptoms or were asymptomatic. a more recent case series of children from italy found that infants < months old were at increased risk of critical disease compared to older children, though no deaths occurred. in this series, % of the children who received icu-level care also had comorbidities, and out of the infants in the icu did not require respiratory support ( ) . similarly, a multinational european study including children identified an association between age < month and icu admission, as compared to outpatient management or management on the general ward. however, the degree of respiratory or inotropic support was not reported, so illness severity cannot be assessed, and as in the prior report, there were no mortalities in this age group ( ) . in the report of covid- in us children described above, among infants < year of age, % required icu-level care, compared with % of the children > year of age, suggesting that young age is not associated with increased risk of severe disease ( ) . likewise, the covid- -associated hospitalization surveillance network (covid-net) recently reported surveillance of children hospitalized in the us with covid- , among whom infants < months of age accounted for . % ( / ) of the pediatric hospitalizations. further analysis of clinical severity in of these hospitalized patients did not separate out infants < year but found that children aged - years did not have increased rates of icu-level care compared to older children ( . % vs %). no children - years of age required invasive mechanical ventilation ( ) . several additional reports have also described infants experiencing only mild infection who frequently improved without any intervention ( ) ( ) ( ) . this includes a case series of hospitalized infants < days, none of whom required supplemental oxygen or intensive care ( ) . overall, data are insufficient to suggest that young age alone is a risk factor for severe covid- . initial reports of covid- in the us suggested that adolescents were not at risk of severe disease ( ) . however, as the pandemic has unfolded, single-center reports on the us experience among hospitalized children have suggested an increased proportion of severe respiratory disease in adolescents compared with younger children and infants ( , , ) . a large multicenter report of north american picu hospitalizations describes that the majority of picu admissions occurred in the -to -year-old age group ( ) . as risk factors among adolescents similar to those identified in adults (e.g., obesity) could contribute to icu admissions, older age could be considered a risk factor for increased covid- severity and therefore could be considered in guiding antiviral treatment decisions. in a cohort of children admitted to picus in new york city with acute covid- , % had hematologic malignancy/immunosuppression listed as a comorbidity ( ) . in a separate cohort from the north american picu collaborative study group, % of patients had malignancies or were otherwise receiving immunosuppression ( ) . outcomes were not stratified by co-morbidity in either study, and it remains unclear whether immunocompromised status is a risk factor for severe disease requiring icu-level care. in a large multinational european study, children with malignancy accounted for % of the cohort requiring picu admission ( ) . cohorts of pediatric cancer patients from new york, madrid, and italy had both low rates of infection and low morbidity when infected ( ) ( ) ( ) ( ) . covid-net reported . % of all hospitalized pediatric patients with underlying disease were immunocompromised ( ) . no cohort studies of pediatric solid organ transplant patients with covid- have been published, though case reports and anecdotal information suggest that severe covid- in this population is rare ( ) ( ) ( ) ( ) . finally, in two electronic registries of pediatric covid- cases, severe disease or death appeared uncommon in children who were immunocompromised or in those receiving treatment for cancer ( , ) . these data suggest that children who are mildly to moderately immunocompromised are not at higher risk of severe covid- ; however, the limited number of studies and lack of comparative data preclude an assessment of risk in severely immunocompromised children (table ) considering the limited available data in sars-cov- -infected children, and extrapolating from other viruses, children with severe t-cell deficiency or dysfunction may be at risk of more severe disease and may exhibit longer viral shedding than non-immunocompromised children. these factors could be considered in deciding whether to prescribe remdesivir (table ). we remind clinicians to consider the potential for drug toxicity and drug-drug-interactions given the numerous medications that immunocompromised patients receive, particularly for patients receiving other experimental agents. adult data suggest that, in addition to older age, presence of underlying cardiovascular disease, including coronary artery disease, cardiomyopathy, and hypertension, and chronic respiratory disease are associated with covid- -related morbidity and mortality ( ) ( ) ( ) ( ) ( ) . however, differing etiologies of cardiopulmonary disease in children make direct application adult data challenging, with congenital heart disease as well as bronchopulmonary dysplasia being additional pediatric considerations (table ) . patients with congenital heart disease have not consistently been reported in series describing severely or critically ill cohorts, though one large european series reported that % of non-picu versus % of picu patients had congenital heart disease ( , ) . limited experience suggests a high prevalence of underlying pulmonary disease among children with severe covid- , including children with chronic respiratory insufficiency or failure resulting in technology dependence (i.e., chronic invasive or noninvasive mechanical ventilation) ( , , , ) . a significant prevalence of asthma among children with sars cov- infection has been described in some reports, although data are insufficient to demonstrate an association between underlying asthma and increased risk of severe covid- ( , ) . however, there is evidence to support more severe outcomes from other respiratory viral infections, such as influenza ( , ) , parainfluenza ( ), rsv ( ) ( ) ( ) ( ) , and non-covid- coronaviruses ( , ) , in children with chronic cardiac and pulmonary conditions. presence of severe underlying cardiac or pulmonary disease could therefore be considered when weighing risks and benefits of potential antiviral therapy ( ) . data from retrospective studies suggest that being overweight (bmi > th - th percentile for age and sex) or obese (bmi ≥ th percentile for age and sex) is an independent risk factor for hospitalization and severe manifestations of covid- in adults ( ) ( ) ( ) ( ) ( ) ( ) . being overweight or obese is common in children ( ) , but unlike adults, comorbid cardiovascular disease (e.g., hypertension, diabetes, or renal disease) less often complicates these conditions. initial reports of hospitalized children with covid- are mixed with regard to disease severity in obese children. for example, a case series of children hospitalized with covid- in new york city indicated that obesity was the most prevalent comorbidity, with a significant association with mechanical ventilation in children ≥ years of age ( ) , whereas other series have not demonstrated this association ( , ) . recognizing the limitations of these small series reporting unadjusted analyses, and considering the growing body of evidence supporting an association between overweight and obesity and covid- severity in younger adults, an elevated bmi could be considered when determining whether to administer remdesivir, particularly when associated with cardiovascular comorbidities ( , ) . based on observational data, adults with diabetes mellitus appear to be at elevated risk for several complications of covid- , including progression to severe disease, development of ards, and death ( , , ( ) ( ) ( ) . however, diabetes mellitus has not emerged thus far as a clear independent risk factor for complications of covid- in children ( , ( ) ( ) ( ) . this may be due in part to limited pediatric data, but may also be due to a higher prevalence of type versus type diabetes in children relative to adults, as well as a higher prevalence of associated comorbidities in adults, including obesity ( ) . based on emerging data that support obesity as a risk factor for severe covid- , obesity may be an important comorbidity modifying risk for complications of covid- in children with diabetes mellitus ( , ) . a related issue is that while use of concomitant medications acting on the renin-angiotensin-aldosterone system has been hypothesized to influence risk for covid- -associated complications, current evidence does not support a detrimental effect of these medications ( ) . when considering remdesivir in a pediatric patient with covid- , diabetes mellitus and associated comorbidities such as obesity could be considered in the decision-making process, but diabetes mellitus should not be the sole rationale for choosing to administer antiviral therapy. exposure to angiotensin-converting inhibitor or angiotensin receptor blocker therapy should not influence risk assessment in decisions to administer remdesivir. the initial human data that led to enthusiasm surrounding use of hydroxychloroquine, with or without azithromycin, included small observational studies and randomized controlled trials early in the pandemic ( ) ( ) ( ) ( ) ( ) this study was terminated prior to target enrollment due to waning of the pandemic in china, but no difference in the primary outcome of virologic clearance at days ( % versus %) or time to virologic clearance ( versus days) was detected ( ) . finally, a brazilian trial compared the impact of hydroxychloroquine plus azithromycin versus hydroxychloroquine alone versus standard therapy on day clinical status using a -point ordinal scale in just over hospitalized patients with mild to moderate covid- . no difference was detected in any treatment arm ( ) . also supporting the lack of efficacy of hydroxychloroquine are the results of a randomized trial comparing hydroxychloroquine to placebo for post-exposure prophylaxis following a moderate-or high-risk exposure to sars-cov- . no difference in sars-cov- rt-pcr positivity or sars-cov- -compatible illness within days was detected ( ) . most observational studies have also demonstrated a lack of benefit of hydroxychloroquine. mahavas and colleagues performed a multicenter study evaluating the impact of hydroxychloroquine compared to standard care on icu-free survival at days in a cohort of hospitalized adults with severe covid- . following inverse probability of treatment weighting (iptw), no difference in icu-free survival was detected ( % versus %; hr . , % confidence interval . - . ) ( ) . similar findings were demonstrated by geleris and colleagues, who found no difference in a composite outcome of intubation or death with hydroxychloroquine versus standard care following iptw in a single-center cohort of patients (hr . , % confidence interval . - . ) ( ) . three large observational studies additionally considered the combination of hydroxychloroquine and azithromycin. the first was a multicenter study comparing hydroxychloroquine alone (n= ), hydroxychloroquine plus azithromycin (n= ), or no hydroxychloroquine (n= ) in a cohort of men admitted to us veterans affairs hospitals. unadjusted mortality was highest in the hydroxychloroquine group ( . % versus . % in the combination therapy group versus . % in the untreated group). following propensity score adjustment, hydroxychloroquine therapy remained associated with mortality (hr . , % confidence interval . - . ), while hydroxychloroquine plus azithromycin was not (hr . , % confidence interval . - . ). cause of death was not reported in this study, and given its observational design, it is possible that the association between hydroxychloroquine use and death is the result of residual confounding ( ) . a second study utilized data from the new york state department of health to compare in-hospital mortality in a cohort of patients, including children. no difference in mortality was detected among patients treated with hydroxychloroquine alone (n= ), azithromycin alone (n= ), hydroxychloroquine plus azithromycin (n= ), or neither drug (n= ). cardiac arrest was more common in the group receiving hydroxychloroquine and azithromycin relative to no treatment, but not in patients receiving either drug alone ( ) . finally, a retrospective study including , hospitalized adults suggested reduced in-hospital mortality among patients treated with hydroxychloroquine (hr . ; % ci . - . ) or the combination of hydroxychloroquine and azithromycin (hr . ; % ci . - . ) relative to neither drug ( ). however, a notable limitation was that the hydroxychloroquine-treated patients more often received steroids, a therapy that has been shown to reduce covid- related mortality. this raises the possibility that the mortality benefit seen in the hydroxychloroquine-treated groups was, in fact, driven by the receipt of steroids, especially when considered in the context of multiple randomized trials demonstrating no benefit with hydroxychloroquine therapy. in addition to the lack of efficacy, several reports have highlighted the potential for qtc prolongation with concomitant hydroxychloroquine and azithromycin therapy, occurring in up to % of treated patients ( , ) . the high-dose arm of a randomized trial comparing high-dose ( mg twice daily for days) to low-dose ( mg twice daily on day , followed by mg daily for a total of days) chloroquine was terminated after detection of higher mortality in the high-dose arm ( ) . there are no comparative observational studies or randomized trials evaluating safety or efficacy of hydroxychloroquine or chloroquine in children. frequency of hydroxychloroquine use has been reported in several pediatric case series and was as high as % in a us cohort of critically ill children ( , ( ) ( ) ( ) ) . several authors have evaluated dosing strategies for hydroxychloroquine and chloroquine in children using pharmacokinetic modeling; however, detailed discussion of these studies is beyond the scope of this review ( ) . lopinavir-ritonavir is a protease inhibitor approved by the fda for treatment of pediatric hiv. the ritonavir component inhibits the cyp a metabolism of lopinavir, increasing plasma levels of lopinavir. it is a preferred therapy for children weeks to years of age who require antiretroviral therapy and is an alternative antiretroviral agent for children > years of age ( ) . it is not fda approved or authorized for use in the treatment of sars-cov- infection. its hypothesized mechanism of action for sars-cov- is inhibition of the viral proteinases papain-like proteinase and c-like proteinase, which are key enzymes in coronavirus polyprotein processing. an in vitro study of the antiviral activity of lopinavir in vero e cells demonstrated an ec of . m, which is well above the trough lopinavir serum concentration with dosing used for hiv and doses used in studies of sars-cov- ( , ) . no animal data exist evaluating lopinavir-ritonavir for sars-cov- . a randomized controlled trial compared lopinavir-ritonavir to usual care in hospitalized adults with severe covid- . there was no difference between the groups in time to clinical improvement, defined as a two-point improvement on a seven-point clinical severity scale between the groups ( days versus days), -day mortality ( . % versus %), or virologic clearance. the lopinavir-ritonavir group did experience shorter icu length of stay ( versus days). concerns about the generalizability of these findings include: ) a relatively small sample size, such that only a large difference in outcome was detectable; ) lopinavir-ritonavir was started late in the disease course (median of days after symptom onset), perhaps beyond the time of peak viral replication; and ) a high mortality rate in this cohort, perhaps limiting ability to extrapolate these data to other, less sick patients ( ) ( ) . two smaller trials have reported consistent findings, with no differences in virologic clearance in hospitalized adults treated with lopinavir-ritonavir or another protease inhibitor, darunavir/cobicistat ( , ) . published observational studies largely do not support use of lopinavir-ritonavir for treatment of covid- and highlight a high prevalence of adverse effects, particularly gastrointestinal effects, as well as potential drug-drug interactions from prolonged cytochrome p a inhibition ( ) ( ) ( ) . there are no comparative observational studies or randomized trials evaluating safety or efficacy of lopinavir-ritonavir or other hiv protease inhibitors for treatment of sars-cov- infection in children. reports of use are sparse and limited to case series, the largest of which included children treated with lopinavir-ritonavir, all of whom recovered ( , ) . fund. md has nih-supported collaboration with gilead sciences (u ai ) but does not receive monetary support from gilead. ar is a prior consultant for pfizer outside the scope of this work. there is insufficient evidence to support young age alone as a risk factor for severe covid- . there is insufficient evidence to definitively support older age (i.e., the adolescent age group) as a risk factor for severe covid- . however, based on the higher prevalence of adolescents in published pediatric cohorts relative to younger children, older age could be considered in making antiviral treatment decisions. there is insufficient evidence to definitively support severe immunocompromise as a risk factor for severe covid- in children. however, given the limited evidence base, and based on adult studies of covid- and extrapolation from other viral infections, severe immunocompromise could be considered in making antiviral treatment decisions. evidence to date suggests that mild/moderate immunocompromise should not be considered a risk factor for severe covid- in children. there is insufficient evidence to definitively support underlying cardiac disease as a risk factor for severe covid- in children. however, based on adult studies of covid- , extrapolation from other viral infections, and limited data in children with covid- , presence of underlying cardiac disease could be considered in making antiviral treatment decisions. there is insufficient evidence to definitively support underlying pulmonary disease as a risk factor for severe covid- in children. based on adult studies of covid- , extrapolation from other viral infections, and limited data in children with covid- , underlying pulmonary disease could be considered in making antiviral treatment decisions. there is insufficient evidence to definitively support isolated overweight or obese as a risk factor for severe covid- in the pediatric population. current reports indicate that obesity is prevalent among pediatric covid- hospitalizations, particularly in critically ill cohorts. obesity could be considered in making antiviral treatment decisions. there is insufficient evidence to definitively support diabetes alone coronavirus covid- global cases by the center for systems science and engineering multicenter initial guidance on use of antivirals for children with coronavirus disease /severe acute respiratory syndrome coronavirus sharing antimicrobial reports for pediatric stewardship (sharps): a quality improvement collaborative remdesivir for the treatment of covid- -preliminary report effect of hydroxychloroquine in hospitalized patients with covid- : preliminary results from a multi-centre, randomized hydroxychloroquine in patients with mainly mild to moderate coronavirus disease : open label, randomised controlled trial hydroxychloroquine with or without azithromycin in mild-to-moderate covid- a trial of lopinavir-ritonavir in adults hospitalized with severe covid- fda emergency use authorization for remdesivir covid- ) update: fda revokes emergency use authorization for chloroquine and hydroxychloroquine cdc covid- response team. coronavirus disease in children -united states clinical characteristics and outcomes of hospitalized and critically ill children and adolescents with coronavirus disease (covid- ) at a tertiary care medical center epidemiology of covid- among children in china covid- in children and adolescents in europe: a multinational, multicentre cohort study characteristics and outcomes of children with coronavirus disease (covid- ) infection admitted to us and canadian pediatric intensive care units clinical features, and disease severity in patients with coronavirus disease (covid- ) in a children's hospital in characteristic of covid- infection in pediatric patients: early findings from two italian pediatric research networks the epidemiology of sars-cov- in a pediatric healthcare network in the united states the epidemiological characteristics of an outbreak of novel coronavirus diseases (covid- )-china coronavirus infections in children including covid- : an overview of the epidemiology, clinical features, diagnosis, treatment and prevention options in children hospitalization rates and characteristics of children aged < years hospitalized with laboratory-confirmed covid- -covid-net, states severe outcomes among patients with coronavirus disease (covid- ) -united states severe covid- in children and young adults in the washington, dc metropolitan region clinical manifestations and outcomes of critically ill children and adolescents with covid- in new york city multisystem inflammatory syndrome in children in new york state multisystem inflammatory syndrome in u.s. children and adolescents kawasaki-like multisystem inflammatory syndrome in children during the covid- pandemic in paris, france: prospective observational study an outbreak of severe kawasaki-like disease at the italian epicentre of the sars-cov- epidemic: an observational cohort study clinical characteristics of children with a pediatric inflammatory multisystem syndrome temporally associated with sars-cov- multisystem inflammatory syndrome in children (mis-c) associated with coronavirus disease (covid- ) multisystem inflammatory syndrome in children and adolescents with covid- guidance-paediatric multisystem inflammatory syndrome temporally associated with covid- (pims) childhood multisystem inflammatory syndrome -a new challenge in the pandemic infectious diseases society of america guidelines on the treatment and management of patients with covid- covid- ) treatment guidelines multidisciplinary guidance regarding the use of immunomodulatory therapies for acute covid- in pediatric patients clinical and ct features in pediatric patients with covid- infection: different points from adults structure of the rna-dependent rna polymerase from covid- virus structural basis for inhibition of the rnadependent rna polymerase from sars-cov- by remdesivir coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro remdesivir for or days in patients with severe covid- effect of remdesivir vs standard care on clinical status at days in patients with moderate covid- : a randomized clinical trial remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial case reports study of the first five patients covid- treated with remdesivir in france compassionate use of remdesivir for patients with severe covid- first case of novel coronavirus in the united states a randomized, controlled trial of ebola virus disease therapeutics fact sheet for healthcare providers: emergency use authorization (eua) of remdesivir (gs- ) covid- drug interactions remdesivir by gilead sciences: fda warns of newly discovered potential drug interaction that may reduce effectiveness of treatment covid- -associated multisystem inflammatory syndrome in children -united states children with medical complexity: an emerging population for clinical and research initiatives management and outcomes of pneumonia among children with complex chronic conditions a national profile of caregiver challenges among more medically complex children with special health care needs novel coronavirus infection in hospitalized infants under year of age in china characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding sars-cov- infection in infants less than days old clinical characteristics and outcome of sars-cov- infection in italian pediatric oncology patients: a study from the infectious diseases working group of the aieop covid- in children with cancer covid- infection in children and adolescents with cancer in madrid flash survey on severe acute respiratory syndrome coronavirus- infections in paediatric patients on anticancer treatment a case of an infant with sars-cov- hepatitis early after liver transplantation child with liver transplant recovers from covid- infection. a case report impact of the sars-cov- outbreak on pediatric liver transplant recipients residing in lombardy covid- in a pediatric heart transplant recipient: emergence of donor-specific antibodies covid- in pediatric cancer global registry clinical impact of covid- on patients with cancer (ccc ): a cohort study covid- mortality in patients with cancer on chemotherapy or other anticancer treatments: a prospective cohort study clinical characteristics of covid- -infected cancer patients: a retrospective case study in three hospitals within wuhan, china characteristics and outcomes of coronavirus infection in children: the role of viral factors and an immunocompromised state a multicenter consortium to define the epidemiology and outcomes of inpatient respiratory viral infections in pediatric hematopoietic stem cell transplant recipients respiratory syncytial virus in hematopoietic cell transplant recipients: factors determining progression to lower respiratory tract disease immunodeficiency scoring index to predict poor outcomes in hematopoietic cell transplant recipients with rsv infections cytomegalovirus (cmv) cell-mediated immunity and cmv infection after allogeneic hematopoietic cell transplantation: the react study parainfluenza virus lower respiratory tract disease after hematopoietic cell transplant: viral detection in the lung predicts outcome respiratory syncytial virus lower respiratory disease in hematopoietic cell transplant recipients: viral rna detection in blood, antiviral treatment, and clinical outcomes coronavirus disease case surveillance -united states clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china unique epidemiological and clinical features of the emerging novel coronavirus pneumonia (covid- ) implicate special control measures prevalence of comorbidities and its effects in patients infected with sars-cov- : a systematic review and meta-analysis clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study coronavirus disease (covid- ) pandemic implications in pediatric and adult congenital heart disease the burden of influenza hospitalizations in infants from influenza in children with special risk medical conditions: a systematic review and meta-analysis parainfluenza virus type : case report and review of the literature rates of hospitalization for respiratory syncytial virus infection among children in medicaid the burden of respiratory syncytial virus infection in young children pediatric investigators collaborative network on infections in canada (picnic) study of admission and management variation in patients hospitalized with respiratory syncytial viral lower respiratory tract infection fatality rates in published reports of rsv hospitalizations among high-risk and otherwise healthy children the differential clinical impact of human coronavirus species in children with cystic fibrosis aha/acc guideline for the management of adults with congenital heart disease: executive summary: a report of the american college of cardiology/american heart association task force on clinical practice guidelines covid- in a long-term care facility -king county obesity in patients younger than years is a risk factor for covid- hospital admission obesity could shift severe covid- disease to younger ages association of obesity with disease severity among patients with coronavirus disease clinical findings of patients with coronavirus disease in jiangsu province, china: a retrospective, multi-center study obesity and covid- severity in a designated hospital prevalence of obesity among youths by household income and education level of head of household -united states clinical characteristics of coronavirus disease in china factors associated with hospital admission and critical illness among people with coronavirus disease risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease the burden of diabetes mellitus among us youth: prevalence estimates from the search for diabetes in youth study renin-angiotensin-aldosterone system inhibitors in patients with covid- chloroquine analogues in drug discovery: new directions of uses, mechanisms of actions and toxic manifestations from malaria to multifarious diseases fda emergency use authorization for use of chloroquine phosphate or hydroxychloroquine sulfate hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial clinical and microbiological effect of a combination of hydroxychloroquine and azithromycin in covid- patients with at least a six-day follow up: a pilot observational study no evidence of rapid antiviral clearance or clinical benefit with the combination of hydroxychloroquine and azithromycin in patients with severe covid- infection efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical trial a pilot study of hydroxychloroquine in treatment of patients with moderate covid- a randomized trial of hydroxychloroquine as postexposure prophylaxis for covid- clinical efficacy of hydroxychloroquine in patients with covid- pneumonia who require oxygen: observational comparative study using routine care data observational study of hydroxychloroquine in hospitalized patients with covid- outcomes of hydroxychloroquine usage in united states veterans hospitalized with covid- association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid- in treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalized with covid- qt interval prolongation and torsade de pointes in patients with covid- treated with hydroxychloroquine/azithromycin risk of qt interval prolongation associated with use of hydroxychloroquine with or without concomitant azithromycin among hospitalized patients testing positive for coronavirus disease effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus (sars-cov- ) infection: a randomized clinical trial chloroquine dosing recommendations for pediatric covid- supported by modeling and simulation available from lopinavir plasma concentrations and virological outcome with lopinavir-ritonavir monotherapy in hiv- -infected patients remdesivir, lopinavir, emetine, and homoharringtonine inhibit sars-cov- replication in vitro no clinical benefit from use of lopinavir-ritonavir in hospitalised covid- patients studied in recovery an exploratory randomized controlled study on the efficacy and safety of lopinavir/ritonavir or arbidol treating adult patients hospitalized with mild/moderate covid- (elacoi) antiviral activity and safety of darunavir/cobicistat for the treatment of covid- comparison of hydroxychloroquine, lopinavir/ritonavir, and standard of care in critically ill patients with sars-cov- pneumonia: an opportunistic retrospective analysis stopping lopinavir/ritonavir in covid- patients: duration of the drug interacting effect clinical characteristics and disease progression in early-stage covid- patients in south korea clinical and epidemiological features of children with coronavirus disease (covid- ) in zhejiang, china: an observational cohort study key: cord- -a xrs jy authors: sahu, kamal kant; mishra, ajay kumar; lal, amos title: novel coronavirus ( -ncov): update on rd coronavirus outbreak of st century date: - - journal: qjm doi: . /qjmed/hcaa sha: doc_id: cord_uid: a xrs jy nan dear editor, we read with great interest the recent article by fang et al on novel coronavirus infection ( -ncov) published in february issue ( ) . it was in early december , when the st case of coronavirus disease- (covid- ) was detected in a patient who was admitted for pneumonia of unknown etiology (figure ). we would like to mention a few additional comments about this deadly virus which has been a matter of health concern worldwide. -ncov has been found to be epidemiologically linked to the huanan seafood wholesale market in wuhan, china which is known for selling exotic animals ( ) . while, the exact host is yet to be determined, but based on the genomic studies done till now it has been postulated that possibly bats may be one of the suspected hosts responsible for transmitting this virus to humans however, when compared to the mers outbreak (mortality rate of - %) and sars outbreak (mortality rate of - %), the mortality rate of -ncov is significantly lower ( - %). the possible reason postulated is the excessive cytokine release with mers and sars as compared to -ncov infection, however, this needs to be confirmed in further studies ( ) ( ) . with regards to the identification, health care professionals should be aware of the diagnostic criteria laid down by who to evaluate any suspected case. hence, detailed travel and sick contact history are of utmost importance to ensure that any suspect gets thoroughly evaluation to rule out -ncov infection. with regards to symptomatology, it has been reported that fever, fatigue, and dry cough are the three most common reported symptoms related to -ncov ( , ) . interesting to note that as compared to previous coronavirus outbreaks, diarrhea is rarely reported with -ncov infection ( - ). in conclusion, the current situation with regards to the -ncov outbreak is alarming as the number of cases is increasing day by day. at an individual level, every attempt should be made to follow all the civic responsibilities and mannerism in order to prevent the spread of this infection. changes of ct findings in a novel coronavirus ( -ncov) pneumonia patient full-genome evolutionary analysis of the novel corona virus ( -ncov) rejects the hypothesis of emergence as a result of a recent recombination event novel coronavirus-important information for clinicians plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome mers-cov infection in humans is associated with a pro-inflammatory th and th cytokine profile clinical features of patients infected with novel coronavirus in wuhan clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china comprehensive update on current outbreak of novel coronavirus infection ( -ncov). annals of translational medicine disseminated herpes zoster following treatment with benralizumab a rare case of hemorrhagic cystitis in allogeneic hematopoietic stem cell transplant patient herpes zoster complicating bortezomib therapy mycobacterium avium complex: a rare cause of pancytopenia in hiv infection philippines india russia spain lebanon nepal cambodia israel belgium finland sweden egypt sri lanka key: cord- -o mrpgvj authors: hemmati-dinarvand, farshad; saedi, samira; hemmati-dinarvand, mohsen; zarei, marzie; seghatoleslam, atefeh title: mysterious virus: a review on behavior and treatment approaches of the novel coronavirus, -ncov date: - - journal: arch med res doi: . /j.arcmed. . . sha: doc_id: cord_uid: o mrpgvj abstract at the end of the year , the novel coronavirus ( -ncov) was spreading in wuhan, china, and the outbreak process has a high speed. it was recognized as a pandemic by the world health organization (who) on march . coronaviruses are enveloped and single-stranded rna that have several families including severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers). the pathogenesis mechanism and disease outcomes of sars and mers are now clear to some extent, but little information is available for -ncov. this newly identified corona virus infection represents flu-like symptoms, but usually the first symptoms are fever and dry cough. there has been no specific treatment against -ncov up to now, and physicians only apply supportive therapy. in the present article, we made an attempt to review the behavior of the virus around the world, epidemiology, a pathway for influx into the host cells, clinical presentation, as well as the treatments currently in use and future approaches; nitazoxanide may be our dream drug. we hope that this review has a positive impact on public knowledge for helping to deal with the -ncov and move one step forward toward its treatment in the near future. in late , the local health authorities in wuhan, china, declared a high load of individuals that had pneumonia with unknown etiology ( ) . subsequently, in early january , numerous medical diagnostic laboratories in china reported that a new coronavirus was the cause of occult pneumonia. the world health organization (who) named this invasive virus briefly as novel coronavirus ( ncov) ( ) . coronaviruses are enveloped, single stranded rna, and belong to the subfamily coronavirinae. it has previously been reported that covs which causes human diseases have six types, and is categorized into two subgroups including gently and extremely pathogenic covs. the e, hku , oc and nl are gently pathogenic covs, leading to - % of upper respiratory tract infections ( , ) . instead, the extremely pathogenic covs, containing severe acute respiratory syndrome (sars) and middle east respiratory syndrome (mers), mostly contaminate lower airways and lead to pneumonia ( ) . given that the clinical signs of ncov, sars cov, and mers cov have some resemblances, it can range from asymptomatic infections to severe respiratory illnesses ( ) . the rapid prevalence of the novel type of cov reminds us that it is a major global health threat. chen y, et al. think that severe prevalence of novel cov in the future is inevitable as climate is changing and human exposure to animals is increasing; therefore, the need for effective treatment modalities and training for covs is necessary ( ) . in the present article, we attempted to review the behavior of the virus around the world, epidemiology, a pathway for influx into the host cells, clinical presentation, as well as the treatments currently in use. we hope that this review could have a positive impact on our knowledge of the new virus and help establish effective ways to combat the novel coronavirus in near future. coronaviruses (covs) form a large and important family of viruses found in nature. covs have a positive-sense single-stranded rna (+ssrna) with a gc content of - % that belongs to the family coronaviridae and the order nidovirales. they contain the largest genome among the recognized rna viruses (genome length is about - kb) ( ) . based on the genomic structure and phylogenetic analysis, the family coronaviridae is currently classified into two subfamilies, sarbecovirus containing sars-cov are two major zoonotic pathogenic coronaviruses (table ) . anew pandemic coronavirus, so called -ncov, has been recently introduced in wuhan, china ( ) . -ncov is still considered as unclassified betacoronavirus, but according to early phylogenetic studies, this virus is related to sars and is over % matched with the bat sars-like cov ( ) . accordingly, the international committee on taxonomy of viruses named it severe acute respiratory syndrome coronavirus (sars-cov- ). the -ncov is an enveloped, spherical, and relatively large (about nm in diameter) particle; the envelope of this virus in electron micrographs emerges as a separated pair of electron-dense shells. the viral envelope contains a lipid bilayer by which the membrane (m), envelope (e) and spike (s) structural proteins are harbored ( figure ) ( , ) . the genome of covs is monopartite, linear, single-stranded positive-sense rna (+ssrna) (~ kb in size), capped at the ' end, and poly adenylated at the ' end with at least six open reading frames (orfs) and other subsidiary genes ( ) . the rna genome includes , nucleotides (gene bank accession number mn ), encoding amino acids. the ' terminal two-thirds of the genome contains two orfs, orf and orf that encodes pp a and pp ab polyproteins, which is further split into and proteins, respectively, which encode non-structural proteins (nsps) ( , ) . these proteins are processed into the viral polymerase (rdrp) and other non-structural proteins involved in rna synthesis ( ) . the structural proteins including spike (s), envelope (e), membrane (m), and nucleocapsid (n) are arranged in the order of one-third ' terminal of the genome ( ) . one of the most important genes that can help researchers to produce vaccine in the future is s gene because this gene product has an effective role in receptor binding and host specificity ( ) . recently reported that between the sars-cov genome sequence and the novel coronavirus exist % similarity, thus, named -ncov by who ( ) . this theory may be indicating that -ncov uses the same sars-cov mechanism i.e. through angiotensin-converting enzyme (ace ) receptor and the tmprss protease to infect the human cells. coronavirus spike (s) protein facilitates virus entry into target cells. the binding of sars to the receptor and its entry into the cell depends on a cellular protease ( ) . sequence analysis has shown that some of the -ncov clusters and bat-associated sars cov viruses (sarsr-cov) can use the ace receptor to enter the host cell. analysis of the receptor-binding motif (rbm) and a part of the receptor-binding domain (rbd) that interacts with ace , revealed that most of the essential amino acid residues were retained at -ncov for ace binding, but in the sarsr-cov s proteins were not observed. it was found that it does not use ace for entry into the cells and need priming the s protein for binding to ace ( ) . it has been reported that entry of sars-cov- to host cells may block via a clinical antagonist of the tmprss , a cellular serine protease, that is recruited via sars-cov- to s protein priming. these new findings have significant implications for our knowledge about the transmission and pathogenesis of sars-cov- and treatment approaches ( ) . shieh w-j, et al., reported that sars-cov might goal a full spectrum of similar cells. the sars-cov in the respiratory system leads to infect mostly pneumocytes and macrophages ( ) . in addition to lung, other tissues can expression of ace . thus, sars-cov may extent to extrapulmonary organs. while the affinity of sars-s and sars- -s to ace receptor has been comparable, therefore we still expect this for sars-cov- . previous studies showed that in the upper airways a mild expression of ace ( , ) may be able to reduce sars-cov spread, given that the high dispersion ability of sars cov- against sars-cov ( ). definitively, it is important to note that the high-level expression of ace can prevent lung damage. however, its downregulated through sars-s, which lead to stimulate sars. to enter the virus into host cells and covers s protein cleavage at the s /s and the s ′ sites, the need to specific proteases in the host cells for priming of coronavirus s proteins ( ) . the cutting site of sars- -s, several arginine residues (multibasic) that shows high sensitivity for cutting. actually, into the host cells, sars- -s was proficiently cleaved, fallowing by cleaved s protein was incorporated into vesicular stomatitis virus (vsv) particles. notably, the area in which the incision has occurred can define the zoonotic potential of coronaviruses ( , ) ; the sars-cov and coronavirus have the most closely associated. sars-cov can use endosomal cysteine protease to priming s-protein in tmprss negative cells. nevertheless, priming of protein s via tmprss protease is required for virus entry into target cells, and the spread of the virus in infected host cells ( ) . after the first reports of -ncov outbreak in wuhan, hubei, china, in december , the virus quickly spread throughout china during several weeks, and then on the other asian countries, the middle east, africa, the americas, oceania, and europe. in accordance with the daily information of the who, the pandemic of ncov till now caused , , positive cases and , deaths in the worldwide by th april ( ) , that lead to a main global health concern (table ) and -ncov infections can be hidden for - d without any symptoms generally, but can display from - d mostly ( ) . after the incubation period of the disease, the presentations are mostly fever, exhaustion and cough, which are probably accompanied by nasal congestion, runny nose, expectoration, and rarely diarrhea and headache. typically, fever can be low to moderate, and even with no fever ( ) . after a week and with progress of displaying the disease, other sings such as dyspnea, cyanosis, and eventually systemic fatal symptoms appear, including malaise or restlessness, poor feeding, bad appetite, less activity, and respiratory failure. the late signs that could occur in severe cases may be accompanied by septic shock, metabolic acidosis, irreversible bleeding and coagulation dysfunction ( , ) . the clinical presentations and reports from several investigations are summarized in table ( , ( ) ( ) ( ) ( ) ( ) . the new virus is diffused through droplets of the respiratory system when patients with infection cough, sneeze, or even during the conversation. furthermore, other ways for transmission of the virus are embracing and close contact (e.g., contact with the mouth, nose or eyes conjunctiva via polluted hands). it has been not recognized so far that spread can happen by mother to infant or breast feeding ( ) . -ncov leads to an acute resolved infection, which could be lethal with a mortality rate of about %. in the case of severe infection, it might lead to expiration of the patients due to severe alveolar injury and advanced respiratory failure ( , ) . however, post-mortem biopsy might be taken from the liver, heart, and lung tissues. in the lung histological studies, bilateral diffuse alveolar damage with cellular fibromyxoid exudate might be seen. patent desquamation of the pneumocytes and hyaline membrane construction in the right lung has also been seen to demonstrate acute respiratory failure ( ) . on the other hand, biopsy assay in the left lung exhibited pulmonary oedema with hyaline membrane construction. in the whole lung tissues, interstitial mononuclear inflammatory infiltrates occur mostly by lymphocytes. furthermore, syncytial cells with abnormal puffy pneumocytes characterized via bulky nuclei, amphophilic granular cytoplasm, and noticeable nucleoli in the intra-alveolar spaces were recognized. these features display viral cytopathic-like variations ( ) . pneumonia patients with initial stage lung x-ray analysis demonstrate several small patchy shadows and interstitial variations significant in the lung periphery ( ) . in patients with severe disease, more progress to bilateral multiple ground-glass opacity, infiltrating shadows, and pulmonary merging, with rare pleural effusion, can be seen. in both lungs of the youngsters with severe disease, multiple lobar lesions may be observed ( ) . moreover, biopsy of the liver indicated modest microvascular steatosis and slight lobular activity; nevertheless, there was no definite proof to support -ncov contamination or drug-induced liver damage as a result. subsequently, biopsy observations showed that no clear histological variations were seen in the heart tissue, proposing that -ncov contamination might not directly damage the heart ( ) . a radiograph of an infected person's chest is shown in figure , as an example. (table ). in addition, different companies are working hard for produce vaccine; experts estimate it could take between - months to develop a vaccine ready for market. supplementary table recommended. certain drugs such as methylprednisolone intravenously ( - mg/kg/d) are suggested for - d, but not for long-term consumption ( , ( ) ( ) ( ) ( ) . in severe patients, immunoglobulin can also be recommended intravenously. the suggested dose is . g/kg/d for d, or mg/kg/d for d ( , , ) . in patients with blood circulation problems, drugs that are vasoactive can be used for recovering microcirculation on the basis of sufficient liquid intake ( ) . cases who had acute renal damage should be given kidney tests function. in children, if intracranial hypertension and convulsion happens, there is a need to decrease the intracranial pressure and control convulsion to be suitable ( , ) . there is speculation that patients with -ncov who are receiving ace inhibitors or angiotensin receptor blockers (arbs) may be at increased risk for adverse outcomes ( , ) . the ace is a receptor for severe acute respiratory syndrome coronavirus (sars-cov- ), and reninangiotensin aldosterone system inhibitors can increase the ace levels ( ) . finally, in the patients who had respiratory complication despite nasal catheter or mask oxygenation, heated humidified high-flow nasal cannula (hhhfnc), non-invasive ventilation such as continuous positive airway pressure (cpap), or non-invasive high-frequency ventilation can be used. if improvement is not possible, mechanical ventilation with endotracheal intubation and a protective lung ventilation strategy should be adopted ( ) . it is worth noting that j. x-x running title: -ncov; behavior and treatment approaches outbreak of pneumonia of unknown etiology in wuhan china: the mystery and the miracle emerging coronaviruses: genome structure, replication, and pathogenesis recent insights into -ncov: a brief but comprehensive review origin and evolution of pathogenic coronaviruses coronavirus infections and immune responses a novel coronavirus from patients with pneumonia in china severe acute respiratory syndrome-related coronavirus-the species and its viruses, a statement of the coronavirus study group years of the international committee on taxonomy of viruses: progress and prospects a new emerging zoonotic virus of concern: the novel coronavirus (covid- ) family coronaviridae a origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in china: phylogenetics and coalescence analysis ultrastructure and origin of membrane vesicles associated with the severe acute respiratory syndrome coronavirus replication complex genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding a pneumonia outbreak associated with a new coronavirus of probable bat origin the molecular biology of coronaviruses emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan angiotensin-converting enzyme is a functional receptor for the sars coronavirus structure of sars coronavirus spike receptor-binding domain complexed with receptor discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin immunohistochemical, in situ hybridization, and ultrastructural localization of sars-associated coronavirus in lung of a fatal case of severe acute respiratory syndrome in taiwan tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis influenza and sars-coronavirus activating proteases tmprss and hat are expressed at multiple sites in human respiratory and gastrointestinal tracts structures of mers-cov spike glycoprotein in complex with sialoside attachment receptors modulation of tnf-α-converting enzyme by the spike protein of sars-cov and ace induces tnf-α production and facilitates viral entry trypsin treatment unlocks barrier for zoonotic bat coronavirus infection two mutations were critical for bat-to-human transmission of middle east respiratory syndrome coronavirus tmprss contributes to virus spread and immunopathology in the airways of murine models after coronavirus infection overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses sars-cov, mers-cov, and -ncov emergence of novel coronavirus -ncov: need for rapid vaccine and biologics development recent apprise on coronavirus and its terrible insinuations characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention diagnosis and treatment recommendations for pediatric respiratory infection caused by the novel coronavirus epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study a familial cluster of infection associated with the novel coronavirus indicating possible person-to-person transmission during the incubation period initial public health response and interim clinical guidance for the novel coronavirus outbreak-united states persons evaluated for novel coronavirus-united states epidemiologic and clinical characteristics of novel coronavirus infections involving patients outside wuhan, china clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records pathological findings of covid- associated with acute respiratory distress syndrome clinical features of patients infected with novel coronavirus in wuhan, china a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster a new coronavirus associated with human respiratory disease in china importation and human-to-human transmission of a novel coronavirus in vietnam a locally transmitted case of sars-cov- infection in taiwan national recommendations for diagnosis and treatment of pneumonia caused by -ncov (the th edition). national health commission and national administrative office of chinese tradition medicine role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings treatment of middle east respiratory syndrome with a combination of lopinavir-ritonavir and interferon-β b (miracle trial): study protocol for a randomized controlled trial another decade, another coronavirus expert consensus on the diagnosis and treatment of viral pneumonia in children corticosteroid therapy for critically ill patients with middle east respiratory syndrome clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected diagnosis and treatment guideline of community acquired pneumonia in children ( the first part) guidelines for the diagnosis and treatment of adenovirus pneumonia in children ( edition) covid- and the cardiovascular system are patients with hypertension and diabetes mellitus at increased risk for covid- infection? receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus nitazoxanide, a new drug candidate for the treatment of middle east respiratory syndrome coronavirus candidate drugs under testing for -ncov treatment candidate vaccines under testing for -ncov treatment proposed a pathway for -ncov influx into the host cells the authors gratefully acknowledge department of biochemistry and clinical laboratories, faculty of medicine, tabriz university of medical sciences, and professor nasser samadi, dcls, phd. none.competing interests none declared. not required. key: cord- -qw qynqv authors: laskar, partha; yallapu, murali m.; chauhan, subhash c. title: “tomorrow never dies”: recent advances in diagnosis, treatment, and prevention modalities against coronavirus (covid- ) amid controversies date: - - journal: diseases doi: . /diseases sha: doc_id: cord_uid: qw qynqv the outbreak of novel coronavirus disease ( -ncov or covid- ) is responsible for severe health emergency throughout the world. the attack of severe acute respiratory syndrome coronavirus (sars-cov- ) is found to be responsible for covid- . the world health organization has declared the ongoing global public health emergency as a pandemic. the whole world fights against this invincible enemy in various capacities to restore economy, lifestyle, and safe life. enormous amount of scientific research work(s), administrative strategies, and economic measurements are in place to create a successful step against covid- . furthermore, differences in opinion, facts, and implementation methods laid additional layers of complexities in this battle against survival. thus, a timely overview of the recent, important, and overall inclusive developments against this pandemic is a pressing need for better understanding and dealing with covid- . in this review, we have systematically summarized the epidemiological studies, clinical features, biological properties, diagnostic methods, treatment modalities, and preventive measurements related to covid- . the emergence and spread of novel coronavirus ( -ncov) or the severe acute respiratory syndrome (sars) coronavirus (sars-cov- ) has threatened global public health. the coronavirus disease (covid- ), which is a transmission of sars-cov- to humans, was reported first in wuhan, hubei province, china in december . later, covid- rapidly spread worldwide creating a pandemic as there have been around , , reported cases and , reported deaths to date ( july ) affecting countries and territories around the world and two international conveyances (https://www.worldometers.info/coronavirus/). north america, south america, and asia are the most affected (maximum number of cases) continents by this pandemic so far (https:// www.worldometers.info/coronavirus/, data accessed on july ) ( figure a ). in spite of rapid development of knowledge, precautionary measurements, and clinical trials, researchers, regulatory bodies, and government administrations are facing a great challenge globally in various aspect to prevent covid- pandemic. the present situation is leading us to a still unknown future and conflicting paradox in the battle against sars-cov- . further, a plethora of documents have been published on "coronavirus" and "coronavirus disease" (year-wise keyword search for last years in pubmed on july ) research, where a maximum and a very large number of results were obtained in on both the keywords in comparison to previous years ( figure b) . nature index has also reported a hugely increasing global research publishing phenomenon on covid- pandemic as evidenced by , articles and , preprints (https://www.natureindex.com/news-blog/thetop-coronavirus-research-articles-by-metrics). a thorough and cumulative scientific knowledge about the progress against covid- amid various conflicts and controversies is the need of the time to set a clear directive in this battle. through this review article, we provide an overview of updated and rapidly evolving progress against covid- pandemic including various conflicts to the readers in a comprehensive manner. considering this, we have summarized diverse research areas covering the current known biological properties of sars-cov- , diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. still unknown future and conflicting paradox in the battle against sars-cov- . further, a plethora of documents have been published on "coronavirus" and "coronavirus disease" (year-wise keyword search for last years in pubmed on july ) research, where a maximum and a very large number of results were obtained in on both the keywords in comparison to previous years ( figure b) . nature index has also reported a hugely increasing global research publishing phenomenon on covid- pandemic as evidenced by , articles and , preprints (https://www.natureindex.com/news-blog/the-top-coronavirus-research-articles-by-metrics). a thorough and cumulative scientific knowledge about the progress against covid- amid various conflicts and controversies is the need of the time to set a clear directive in this battle. through this review article, we provide an overview of updated and rapidly evolving progress against covid- pandemic including various conflicts to the readers in a comprehensive manner. considering this, we have summarized diverse research areas covering the current known biological properties of sars-cov- , diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. coronaviruses (subfamily: coronavirinae, family: coronaviridae, order: nidovirales) are enveloped single stranded positive sense rna genomes that range in size from to kilobases [ , ] . coronavirus consists of four structural proteins: the nucleocapsid, envelope, membrane, and spike forming a core-shell morphology (figure ), whose diameter is in the range from nm to nm with spike like projections on its surface [ ] [ ] [ ] . the name, coronavirus (latin: corona = crown) came out due to the presence of a crown or the sun's corona-like spike (s) glycoprotein on viral surface forming club-shaped protrusions, which is also evidenced through the electron microscope [ ] [ ] [ ] . this transmembrane spike (s) glycoprotein on viral surface mediates the entry into host cells, forming homotrimers protruding from the viral surface [ ] . the receptor binding domain (rbd) in the spike (s) glycoprotein is the most mutable part of the coronavirus genome leading to generation of new properties and ability of virus to infect new cell types or even new species [ ] . based on phylogenetic relationships and genomic structures, the subfamily coronavirinae is divided into four genera (α-cov, β-cov, γ-cov, and δ-cov). α-cov and β-cov only infect mammals, whereas γ-cov and δ-cov infect generally birds and sometimes even infect mammals. β-cov and γ-cov are responsible for respiratory diseases in humans and gastroenteritis in animals [ , ] . presence of four coronaviruses (subfamily: coronavirinae, family: coronaviridae, order: nidovirales) are enveloped single stranded positive sense rna genomes that range in size from to kilobases [ , ] . coronavirus consists of four structural proteins: the nucleocapsid, envelope, membrane, and spike forming a core-shell morphology (figure ), whose diameter is in the range from nm to nm with spike like projections on its surface [ ] [ ] [ ] . the name, coronavirus (latin: corona = crown) came out due to the presence of a crown or the sun's corona-like spike (s) glycoprotein on viral surface forming club-shaped protrusions, which is also evidenced through the electron microscope [ ] [ ] [ ] . this transmembrane spike (s) glycoprotein on viral surface mediates the entry into host cells, forming homotrimers protruding from the viral surface [ ] . the receptor binding domain (rbd) in the spike (s) glycoprotein is the most mutable part of the coronavirus genome leading to generation of new properties and ability of virus to infect new cell types or even new species [ ] . based on phylogenetic relationships and genomic structures, the subfamily coronavirinae is divided into four genera (α-cov, β-cov, γ-cov, and δ-cov). α-cov and β-cov only infect mammals, whereas γ-cov and δ-cov infect generally birds and sometimes even infect mammals. β-cov and γ-cov are responsible for respiratory diseases in humans and gastroenteritis in animals [ , ] . presence of four corona viruses (hku , nl , e and oc ) have been found in human circulation which are generally cause mild respiratory disease [ ] . the -ncov is phylogenetically closely related to bat sars-like coronaviruses, hence name sars-cov- and belongs to β-cov genus lineage b [ ] . regarding pathogenicity and transmissibility, sars-cov- may differ from other known sars-cov due to a significant change in its spike glycoproteins (orf , and orf b) [ ] . doremalen et al. [ ] showed that the sars-cov- virus remained viable in aerosols (< µm) for at least up to h and was more stable on plastic and stainless steel than on copper and cardboard. sars-cov- was first identified from the samples (cultured human airway epithelial cells along with the virus from isolated bronchoalveolar lavage fluid) of adult covid- patients in wuhan, china. its morphology was analyzed by negatively stained sample under transmission electron microscopy (tem) [ ] . zhu et al. [ ] made a conclusion based on tem ultra-structural image of sars-cov- virus particles. this follows as (i) it is generally spherically shaped with a diameter ranges from to nm, (ii) it has an envelope with quite distinctive to nm protein spikes, and (iii) it has genetic material which matched to the genome from lineage b of the genus β-cov-showing more than % identity with a bat sars-like cov (bat-sl-covzc , mg . ). these observations are similar to the overall structure of coronaviridae family viruses. tem image of an isolate from the first united states case of covid- is also evidenced the spherically shaped viral particles (colorized blue) containing cross-sections through the viral genome (black dots) [ ] . the crystal structures of the unliganded sars-cov- main protease (m pro ) and its complex with an α-ketoamide inhibitor was used to provide some knowledge about the drug target for covid- [ ] . this m pro enzyme is essential one along with the papain-like protease(s) for processing the viral rna translated polyproteins. thus, inhibition of this enzyme may block the viral replication. the three-dimensional crystal structure, at . Å resolution, of the sars-cov- m pro is highly similar to the sars-cov m pro , due to the % sequence identity. dimerization (necessary for catalytic activity) of the m pro is regulated by domain iii (residues to ) mainly through a salt-bridge interaction between glu of one protomer and arg of the other. like sars-cov- , world also has seen an outbreak of worldwide pandemic and a large-scale fatal swine disease during the past two decades because of three other zoonotic (transmitted from animals to human) coronaviruses, such as sars in , middle east respiratory syndrome (mers) in , and swine acute diarrhea syndrome (sads) in . surprisingly, these viruses have been originated from bats, a natural source of various other highly lethal zoonotic viruses (such as hendra, nipah, ebola, and marburg viruses). sars and sads viruses were claimed to be originated in china [ , ] . based on these facts, scientists including chinese research group from wuhan (primary epicenter of also warned further possible coronavirus outbreaks from bats and with a high probability that outbreak will occur in china [ ] . both sars-cov and mers-cov bat β-coronaviruses crossed over to humans through an intermediary host, which was palm civet cats in the guangdong province of china (sars-cov, in - , mortality rate %) and dromedary camels in saudi arabia (mers-cov, in , fatality rate %), respectively [ ] . in the case of covid- , the virus was transmitted to human from bats, but the intermediary host animal(s) are not yet known. a study claimed that the intermediary host animal is pangolin due to the following findings on pangolin-cov, sars-cov- , and batcov ratg viruses: (i) at the whole-genome level, both pangolin-cov and sars-cov- share . % similarity among them, (ii) pangolin-cov and sars-cov- are reported to be the second closest relative to each other than to batcov ratg , (iii) in the receptor binding domain (rbd) of spike glycoprotein, five key amino acid residues involved in the interaction with human angiotensin converting enzyme (ace ) of pangolin-cov and sars-cov- are consistent, and (iv) only sars-cov- contains a potential cleavage site for furin proteases unlike both pangolin-cov and ratg [ ] . it was also concluded that the transmission of human sars-cov- virus from bat may include more than one intermediary host including pangolins [ ] . similar to sars-cov, the -ncov is reported to have the capability to transmit efficiently among humans due to familial cluster of pneumonia [ ] . several cases were reported person-to-person transmission of this virus not only through family settings, but were also in hospital and infected travelers [ , ] . person-to-person transmission of the sars-cov- infection is occurred via airborne droplets to the nasal mucosa in closed environments, close contact between people, unwashed hands, and touching contaminated surfaces with less possibilities. within the incubation period ranges from to days in general, sars-cov- may replicate locally in cells of the ciliated epithelium resulting cell damage and inflammation. primarily, respiratory secretions of any infected person are used to diagnose the presence of virus by special molecular tests including normal/low white cell counts with elevated c-reactive protein (crp) [ ] . additionally, abnormal computerized tomographic (ct) chest scan is also proved to be helpful to diagnose any infected person even for those with no symptoms or mild disease [ ] . the sars-cov- showed lower mortality but faster spreading than sars-cov and mers-cov. isolation of sars-cov- from oral swabs, bronchoalveolar lavage fluid, and stool proved them to be highly contagious [ , ] . sars-cov- infects human by interacting with a functional receptor, metallopeptidase named angiotensin converting enzyme (ace ), for its successful cellular entry ( figure ) [ , ] . crystal structure of the c-terminal domain of spike protein in complex with human ace (hace ) revealed an overall similar binding mode as that of sars-cov with hace [ ] . it was determined that -ncov uses ace as a cellular entry receptor in human, chinese horseshoe bats, civets, and pigs but not for mice and cells without ace protein expression capability [ ] . other coronavirus receptors, such as aminopeptidase n and dipeptidyl peptidase do not play any role for cellular entry of -ncov [ ] . previous studies revealed that almost all human organs are known to have ace mrna, though the protein expression of ace mrna was largely unknown. such ace receptor is found to be present in arterial and venous endothelial cells, arterial smooth muscle cells in the lungs, stomach, small intestine, liver bile ducts, colon, skin, kidney parietal epithelial cells, lymph nodes, and in the brain [ ] . the surface of lung alveolar epithelial cells and enterocytes of the small intestine also express ace protein allowing them to be infected by sars-cov- [ ] . the tissues of the upper respiratory tract are not the primary site of entrance for sars-cov, as oral and nasal mucosa and nasopharynx did not show ace expression on the surface of epithelial cells, rather upper respiratory tract might be susceptible to secondary infections from the infected lower respiratory tract. lower lungs may show higher opacity in the ct scans due to its more ace expression [ ] . higher viral loads have been recorded in the nose than the in throat, with similar viral loads seen in asymptomatic and symptomatic patients [ ] . coronaviruses generally are found to cause acute and chronic respiratory, enteric, and central nervous system diseases in humans as well as in other animals. the symptoms of a covid- patient are usually fever, cough, sore throat, breathlessness, fatigue, and feeling of discomfort. for most of the people, it is found mild. for elderly and the patient with comorbidities may develop pneumonia, acute respiratory distress syndrome (ards), and multi-organ dysfunction leading to death. many infected people are found to be asymptomatic causing a problem for early detection and controlling the spread of disease. mortality rate estimated by the world health organization (who) (as of march ) is . % (https://www.worldometers.info/coronavirus/coronavirus-death-rate/). further, speculation about the association of human coronaviruses with more serious human diseases (such as multiple sclerosis, hepatitis, or enteric disease in infants) are still under question due to no proper evidence [ ] . in absence of any approved therapeutics or vaccines for the treatment of covid- , who has promoted "test, isolate, and trace" method as a preventive measure. thus, early, rapid, and accurate diagnosis of covid- patients is becoming very crucial to control the sources of infection and to prevent further community spread. with a gradual understanding of biological properties of sars-cov- , various diagnostic methods and device strategy with point of care facilities have been developed for covid- detection worldwide. a summary of various diagnostic methods (table ) are presented for the covid- detection. various countries approved and implied different testing methods according to the regulation of their own health agencies based on situation and availabilities. below subsections are summarized the recent developments on diagnostic methods based on (i) nucleic acid, (ii) protein, (iii) chest scan and (iv) autopsy. nucleic acid-based detection strategy has been widely used against detection of various diseases, including coronavirus and recent covid- . in this section, we review some nucleic acid-based detection methods that are commonly being employed for the diagnosis of covid- . polymerase chain reaction (pcr) is an enzymatic method widely used in molecular biology to make millions to billions of copies of a specific dna sample [ ] . this method involves following steps in a series or cycles of temperature changes: (i) denaturation: separating the two strands of the dna containing the gene segment with the application of heat, (ii) annealing-marking gene segment of each strand of dna with a primer, (iii) primer extension: using a dna polymerase to assemble a copy alongside each segment, and (iv) repeat: continuously copy the copies [ ] . various pcr-based methods are an indispensable, common, and rapid techniques for scientist to amplify a minute nucleic acid sample to a large enough amount for a number of applications [ ] . due to high sensitivity and high sequence specificity, the pcr-based method has been used as a routine and reliable technique for detecting coronaviruses. coronavirus is a rna virus, so in general reverse transcriptase-pcr (rt-pcr) method is implied as follows: coronavirus rna is transcribed into cdna by reverse transcription, then the pcr is performed on cdna, and finally detection of pcr product through specific detection method(s) (gel visualization and sequencing) [ , ] . real-time: real-time reverse transcriptase-pcr (rt-pcr) detection method is evolved as a common platform for detection of all kinds of coronaviruses due to its low cost per test, less time-consuming process and more sensitive than the conventional rt-pcr assay [ , ] . the whole genome sequence of sars-cov- enabled to develop pcr-based kits to diagnose covid- in laboratory and clinical settings [ ] [ ] [ ] [ ] [ ] [ ] . corman et al. [ ] developed a robust diagnostic methodology considering the sars-related virus sequences available in genbank. a close genetic relatedness to the sars-cov and synthetic nucleic acid technology helped this process to design and validate such strategy without using any virus isolates and samples from infected person. such a technique can successfully discriminate -ncov from sars-cov. this approach provided the first version of the diagnostic protocol to the who from exclusivity testing on clinical samples ( january ). a real-time rt-pcr based test is found to be more sensitive than radiological test for pediatric patients [ ] . pediatric patients with milder symptoms, showed no clear clinical signs or chest x-ray findings but their real-time rt-pcr exhibited positive results. further, in this report, real-time rt-pcr showed positive results in rectal swab-testing but negative results in nasopharyngeal swab-testing for eight out of ten pediatric patients suggesting shedding of virus in the gastrointestinal tract and a possible fecal-oral transmission. wang's group [ ] reported that the rt-pcr based findings using different types of clinical specimens collected from infected individuals. in their study, it was found that viral loads were significantly correlated among pairs of throat swab and sputum samples. overall, real-time rt-pcr based method enables developing a high-throughput testing for rapid, on-demand, low-cost, reliable, quantitative detection technique against covid- in clinical settings [ ] . probe free: a team of indian institute of technology, delhi, india reported first probe-free real time pcr assay for covid- detection (http://www.iitd.ac.in/content/icmr-approves-probe-freecovid- -detection-assay-developed-iit-delhi- ). they have used comparative sequence analyses to identify unique regions (short stretches of rna sequences) in the sars cov- genome, which are not present in other human coronaviruses. in this highly sensitive assay, primers can specifically target unique regions (conserved in over fully sequenced) of covid- genomes, which was reported after extensive optimization using synthetic dna constructs followed by in vitro generated rna fragments. indian council of medical research has approved this technique as it does not require any fluorescent probes (thus low-price) but still useful for high throughput testing. isothermal amplification of nucleic acids is a rapid, efficient, and alternative amplification technique than pcr. this process can be applied at a constant temperature without any thermos-cycling apparatus, unlike in the case of pcr [ , ] . the isothermal amplification technique can be performed in water bath, on the cell surface, or even inside living cells, making it a superior technique over pcr [ , ] . based on reaction kinetics of isothermal nucleic acid amplification, it is divided to exponential amplification, linear amplification, and cascade amplification. these are further sub-divided into transcription mediated amplification, nucleic acid sequence-based amplification, signal mediated amplification of rna technology, strand displacement amplification, rolling circle amplification, loop-mediated isothermal amplification of dna, isothermal multiple displacement amplification, helicase-dependent amplification, single primer isothermal amplification, and circular helicase-dependent amplification, based on the developments in molecular biology of dna/rna synthesis [ , ] . furthermore, the use of microfluidic chips, capillary platforms, and test paper with isothermal amplification technique has been developed for single-cell or single-molecule analysis. among these, loop-mediated isothermal amplification (lamp) has been implied successfully for coronavirus detection [ ] [ ] [ ] [ ] . lamp technique can amplify target nucleic acid sequence using two or three sets of primers and a polymerase at a constant temperature (~ - • c) [ ] [ ] [ ] . in comparison to pcr-based technique, lamp can produce considerably higher amount of dna with high strand displacement and replication activity due to the use of additional pair of "loop primers". park et al. [ ] developed reverse transcription lamp (rt-lamp) assay(s) to detect genomic rna of sars-cov- . these rt-lamp assays (in combination with leuco crystal violet colorimetric detection method) can detect as low as copies of sars-cov- rna within min. these rt-lamp assays were highly specific towards sars-cov- compared to other human coronaviruses (hcov- e, hcovoc , mers-cov, and sars-cov). yu et al. [ ] also developed a rapid and sensitive isothermal lamp based method (ilaco) for the detection of covid- virus rna or cdna samples. in this method, ilaco was used to amplify a fragment of the orf ab gene using primers, which was proved to be specific for sars-cov- species (i.e., low chance for false positives) in comparison to the sequences of related viruses by the help of online tool primer-blast (including similar coronaviruses, influenza viruses and normal coronaviruses). ilaco can detect synthesized rna equivalent to copies of -ncov (performance is comparable to taqman based qpcr detection method), where reaction time varied from - min based on virus load in the collected samples. another lamp-based colorimetric detection method was reported to identify sars-cov- virus rna from purified rna or cell lysis (without an rna purification step) [ ] . the sensitivity of this portable method is equivalent to a commercial rt-qpcr test with only heating and visual inspection. zhu et al. [ ] demonstrated a successful and accurate diagnosis of covid- using one-step rt-lamp coupled with nanoparticles-based biosensor (nbs) assay (rt-lamp-nbs) within approximately h (from sample collection to result interpretation). they have employed two designed lamp primer sets (f ab-rt-lamp and np-rt-lamp), heating block (to maintain a constant temperature at • c), a real-time turbidity (la- c) and visual detection reagents (vdr) in addition to nbs interpretation to simultaneously amplify and detect genes of sars-cov- in a "one-step" and "single-tube" reaction. the sensitivity of sars-cov- rt-lamp-nbs was copies (each of detection target) per reaction, whereas no cross-reactivity was observed for all pathogens of non-sars-cov- (virus, bacteria, and fungi). the rt-lamp-nbs assay showed % the analytical sensitivity of sars-cov- for oropharynx swab samples of clinically diagnosed covid- patients and % specificity for clinical samples collected from non-covid- patients. crispr-cas (clustered regularly interspaced short palindromic repeats-crispr associated) is an adaptive immune system, which was discovered first in escherichia coli in and later also in other bacteria species. these are found predominantly in archaea ( % of genomes) than in bacteria ( % of genomes) [ , ] . being an immune system of archaea and bacteria, crispr and crispr-associated proteins deliver protection against invasive nucleic acids (such as dna, or rna from phages, plasmids, and other exogenous dna elements) [ , ] . scientists later exploited this immune responsive system by reengineering to target parts of genetic material for precise genetic alterations of any particular cellular type, which is the basis of crispr therapeutic and diagnostic platforms for human [ , ] . this adaptive immune system is also widely used as a tool for sars-cov- detection. crispr associated enzyme cas has already been utilized for rapid and portable sensing for successful rna-targeting [ ] . a specific high-sensitivity enzymatic reporter unlocking (sherlock) platform was developed by combining isothermal preamplification with cas to detect single molecules of rna or dna for dengue or zika virus [ ] . an updated sherlock protocol has been reported for multiplexable, portable, rapid, and quantitative covid- detection (https://broad.io/sherlockprotocol), which can target sequences in a range between and am ( - copies per microliter of input). another development of accurate crispr-cas -based lateral flow assay able to detect sars-cov- with % positive predictive agreement and % negative predictive agreement from respiratory swab rna extracts (less than min) [ ] . another newly developed method, sars-cov- dna endonuclease-targeted crispr trans reporter (detectr), was found to perform simultaneous reverse transcription and isothermal amplification by (i) rt-lamp for rna extracted (for nasopharyngeal or oropharyngeal swabs), (ii) cas detection of predefined coronavirus sequences, and (iii) cleavage of a reporter molecule confirms, which detects the virus [ ] . a fncas editor linked uniform detection assay (feluda) was developed for detecting nucleotide sequences, classifying nucleobase identity, and inferring zygosity [ ] . feluda is able to distinguish clear signatures of sars-cov- sequence in synthetic dna within one hour using a specific ribonucleoprotein (rnp) from non-specific rnp (such as h n or hbb). feluda can also clearly distinguish between two sars-cov- and sars-cov- sequences. this approach further can be developed as lateral flow assay on a paper strip to distinguish sars-cov- synthetic dna using sars-cov- specific rnp. protein-based testing has become as an alternative and additive detection strategy in addition to nucleic-acid based testing methods for coronavirus [ ] . in response to any infected viral protein antigens, antibodies (i.e., a blood protein produced in response to and counteracting a specific antigen) are generated in patient's body resulting a very specific antigen-antibody (ag-ab) serological interaction. detection of this specific antibody level(s) due to the sars-cov- infection can be useful for surveillance of covid- pandemic. this indirect serological test opens up wide range of possibilities, such as, (i) successful detection of asymptomatic patients, (ii) creating large a window of testing time even with a gradual decrease of viral load, (iii) protect community transmission due to false negative results by other methods, and (iv) proper guidance for individual quarantine period [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . kwok-yung yuen's group [ ] successfully detected antibodies generated in response to sars-cov- viral proteins at the time when the detection of the viral proteins become difficult due to gradual declining trend of viral load(s). serological test using enzyme-linked immunosorbent assay (elisa) for antibodies (immunoglobulin m, igm and immunoglobulin g, igg) is more confirmatory and unreliable results from oral swabs for -ncov detection [ ] . this test can be applied for respiratory, blood, or fecal samples. guo et al. [ ] conducted a covid- profiling study on early humoral response based on iga, igm, and igg response. this study found that igm and iga antibody were detected days, while igg was detected days after symptom onset, with a positive rate of . %, . %, and . %, respectively [ ] . the detection of igm by elisa was found more efficient than that of qpcr after . days of symptom onset [ ] . a successful immunological field-effect transistor (fet)-based biosensing device was developed for detecting sars-cov- in clinical samples, where the sensor was developed by conjugating a specific antibody against sars-cov- spike protein to graphene sheet coated fet [ ] . this rapid diagnostic device for sars-cov- antigen requires no sample pre-treatment or labelling. this is a highly-sensitive detection method for the sars-cov- spike protein at concentrations of fg/ml in phosphate-buffered saline and fg/ml in clinical transport medium, . × pfu/ml in culture medium and . × copies/ml in clinical samples. the false positive results in serological tests for covid- is a concern due to the presence antibodies generated against other coronaviruses (such as for common cold) irrespective of the presence of sars-cov- antibodies. recently, researchers have got a high frequency of cross-reactivity in plasma samples from covid- patients against the s protein of sars-cov- and sars-cov [ ] . however, more accurate antibody-based detection method can be made with additional features of infected patient in serological test, such as (i) combined (igm and igg) antibody assay rather than a single antibody test, (ii) more number of testing, (iii) report of elevated levels of c-reactive protein, d-dimer, lymphocytes, leukocytes, or blood platelets [ ] . there are growing concerns regarding the covid- testing despite of huge efforts in this direction. due to sudden outbreak and a huge increase of covid- cases, a sufficient number of covid- test kits are unavailable in hospitals and healthcare centers. further, an automatic detection system with a quick diagnostic capability could be an alternative or auxiliary method to prevent community spreading of covid- . in this situation, most countries have recommended the rt-pcr-based methods as the standard technique for covid- diagnosis. serological tests are also considered to be the primary technique for covid- detection. however, small hospitals, health centers in sub-urban and village areas, even private hospitals in sub-urban area may not have an approved rt-pcr testing center or pcr testing infrastructure facilities. on the other hand, chest-scan, a routine technique implied for prominent pneumonia pattern, has been evolved as useful non-invasive technique for covid- detection [ ] . both chest x-ray and computed tomography (ct)-scan were successful to distinguish the manifestations of typical pneumonia in the case of mers-cov and sars-cov infection [ , ] . these scans have helped to diagnoses suspected person to isolate and treat more quickly, even when the rt-pcr based test did not respond properly. such tests have proven lung histology (lung damage or holes/honeycomb-like appearance) of covid- patients [ ] . thus, chest-scan is useful for suspected covid- patients with negative rt-pcr result. . . . x-ray x-rays, a form of high-energy electromagnetic radiation, are shorter wavelengths than uv rays and longer wavelengths than gamma rays. x-ray machines are widely available sophisticated diagnostic imaging technique for body, bone and other dense objects that can block the radiation through a limited exposure to radiation. in addition, x-ray scans can be used for lung infections, pneumonia and tumors. an automatic prediction of covid- was successfully reported using chest x-ray images and a deep convolution neural network based pre-trained transfer models (resnet , inceptionv and inception-resnetv) [ ] . these pre-trained transfer models helped to obtain a higher prediction accuracy for small x-ray dataset. this model has end-to-end structure without manual feature extraction and selection methods, where the resnet is an effective one among all pre-trained models in the small dataset ( covid- vs. normal). computed tomography (ct) scan is a computer-assisted medical imaging device which combines cross-sectional (tomographic) scanned images of specific areas or virtual slices of any organ taken from different angles producing a d view of that particular organ. ct-scan is one of the methods used to diagnose various abnormalities of the chest (such as pneumonia, lung cancer etc.) [ , ] . thus, chest ct-scan is also being used as a fast, painless, non-invasive and accurate auxiliary diagnostic method in addition to the rt-pcr test for the suspected covid- patient [ ] [ ] [ ] . the national health commission of china included the chest ct findings as evidence of clinical diagnosis of covid- for patients in hubei province at the fifth edition of the diagnosis and treatment program of new coronavirus pneumonia due to the false-negative rate of rt-pcr test for covid- patient [ ] . several groups found chest ct scan more sensitive and better diagnostic tool in comparison to rt-pcr for covid- detection [ , ] . recent investigations demonstrated that the ct-scan of covid- patient(s) clearly showed bilateral pulmonary parenchymal ground-glass and consolidative pulmonary opacities, with a rounded morphology, crazy-paving pattern, linear opacities, and peripheral lung distribution [ , ] . in contrast, other study did not find any lung cavitation, discrete pulmonary nodules, pleural effusions, and lymphadenopathy [ ] . further, high-resolution ct (hrct)-scan for the chest is reported to be important tool to help clinicians to diagnose quickly and accurately the effected lung disease [ ] . artificial intelligence (ai) and deep learning-based automated ct image analysis of lung have been also developed to distinguish covid- pneumonia and influenza-a viral pneumonia [ ] [ ] [ ] . these automated deep learning based methods can produce graphical pattern of a particular covid- patient which is helpful for clinician to diagnose prior to pathogenic testing [ ] . in spite of such clinical diagnostic values, ct scan still fails to come at the forefront of covid- diagnosis due to the following reasons: (i) it is expensive, (ii) it requires technical expertise, and (iii) it is incapable of distinguishing sars-cov- pneumonia from other viral pneumonia and hysteresis. an autopsy report, through examination of a corpse by dissection, is an important source of information for research purposes to evaluate any disease causing death. autopsy has been proved to be hugely beneficial to diagnose emerging and reemerging infectious diseases, like covid- [ ] [ ] [ ] . in contrary, several groups raised their concern that the few autopsies have been performed on patients who died with suspected or confirmed covid- infection especially in the primary epicenters of pandemic (such as china and italy) [ , ] . despite the suggestion by who on performing post-mortem examinations for covid- deaths with following recommended safety procedures, many governments including italy discouraged the practice of autopsy during the period of increasing number of death and even some scientific report highlighted that the post-mortem examination does not have any primary diagnostic role, whereas autopsy may still have a clinical role in selected cases [ , ] . though based on autopsies, physicians can determine a profound change of the view of covid- disease not as a pneumonia but a systemic, vascular disease, putatively generated by autoimmunity [ ] . thus, a strong recommendation was urged to perform full autopsies on patients who died with suspected or confirmed covid- infection with recommended exceptional biosafety guidelines to reduce the further spread of potential infection from any corpse. there is currently no clinically proven therapeutic regimen to prevent and eradicate sars-cov- infection [ ] . covid- is being managed by the supportive treatment (oxygenation and ventilation, conservation fluid management). however, the use of broad-spectrum antibiotics [ ] . this section summarizes various treatment modalities for covid- ( figure ). important tool to help clinicians to diagnose quickly and accurately the effected lung disease [ ] . artificial intelligence (ai) and deep learning-based automated ct image analysis of lung have been also developed to distinguish covid- pneumonia and influenza-a viral pneumonia [ ] [ ] [ ] . these automated deep learning based methods can produce graphical pattern of a particular covid- patient which is helpful for clinician to diagnose prior to pathogenic testing [ ] . in spite of such clinical diagnostic values, ct scan still fails to come at the forefront of covid- diagnosis due to the following reasons: (i) it is expensive, (ii) it requires technical expertise, and (iii) it is incapable of distinguishing sars-cov- pneumonia from other viral pneumonia and hysteresis. an autopsy report, through examination of a corpse by dissection, is an important source of information for research purposes to evaluate any disease causing death. autopsy has been proved to be hugely beneficial to diagnose emerging and reemerging infectious diseases, like covid- [ ] [ ] [ ] . in contrary, several groups raised their concern that the few autopsies have been performed on patients who died with suspected or confirmed covid- infection especially in the primary epicenters of pandemic (such as china and italy) [ , ] . despite the suggestion by who on performing post-mortem examinations for covid- deaths with following recommended safety procedures, many governments including italy discouraged the practice of autopsy during the period of increasing number of death and even some scientific report highlighted that the postmortem examination does not have any primary diagnostic role, whereas autopsy may still have a clinical role in selected cases [ , ] . though based on autopsies, physicians can determine a profound change of the view of covid- disease not as a pneumonia but a systemic, vascular disease, putatively generated by autoimmunity [ ] . thus, a strong recommendation was urged to perform full autopsies on patients who died with suspected or confirmed covid- infection with recommended exceptional biosafety guidelines to reduce the further spread of potential infection from any corpse. there is currently no clinically proven therapeutic regimen to prevent and eradicate sars-cov- infection [ ] . covid- is being managed by the supportive treatment (oxygenation and ventilation, conservation fluid management). however, the use of broad-spectrum antibiotics [ ] . this section summarizes various treatment modalities for covid- ( figure ) . viral infection is always a major concern for morbidity and mortality in animals and humans worldwide. development of antiviral drugs have been always a pressing need to treat such viral infections. since the approval of first antiviral drug, idoxuridine in , drugs were clinically approved to treat nine human infectious diseases (human immunodeficiency virus, hiv; hepatitis b virus, hbv; hepatitis c virus, hcv; herpesvirus; influenza virus; human cytomegalovirus; varicella-zoster virus; respiratory syncytial virus; and human papillomavirus) [ ] . the antiviral drugs mostly inhibit the viral development rather than destroying the target pathogen unlike most antibiotics. a broad-spectrum antiviral is found to be effective against a wide range of viruses based on drug repurposing strategy [ ] . drug repurposing or drug repositioning is a cost-effective and time-efficient alternative strategy, which involves the recycle or re-use of clinically approved drugs for new disease instead of searching of new drugs [ , ] . in contrary to in vitro phenotypic screening of known drugs, in silico/computational drug repurposing strategy is a hypothesis-driven approach to identify the drugs for the treatment of any disease using big data analysis [ , ] . the drug-repurposing has been implied for several human diseases including antiviral drug development against coronavirus [ ] . various groups have proposed number of drug candidates through drug-repurposing (in vitro and in silico) for covid- treatment [ ] [ ] [ ] [ ] . who focused and initiated the "solidarity trial" (announced on march ) of four existing antiviral compounds/formulations ( figure ) to assess their clinical benefit against covid- [ , ] . viral infection is always a major concern for morbidity and mortality in animals and humans worldwide. development of antiviral drugs have been always a pressing need to treat such viral infections. since the approval of first antiviral drug, idoxuridine in , drugs were clinically approved to treat nine human infectious diseases (human immunodeficiency virus, hiv; hepatitis b virus, hbv; hepatitis c virus, hcv; herpesvirus; influenza virus; human cytomegalovirus; varicellazoster virus; respiratory syncytial virus; and human papillomavirus) [ ] . the antiviral drugs mostly inhibit the viral development rather than destroying the target pathogen unlike most antibiotics. a broad-spectrum antiviral is found to be effective against a wide range of viruses based on drug repurposing strategy [ ] . drug repurposing or drug repositioning is a cost-effective and time-efficient alternative strategy, which involves the recycle or re-use of clinically approved drugs for new disease instead of searching of new drugs [ , ] . in contrary to in vitro phenotypic screening of known drugs, in silico/computational drug repurposing strategy is a hypothesis-driven approach to identify the drugs for the treatment of any disease using big data analysis [ , ] . the drug-repurposing has been implied for several human diseases including antiviral drug development against coronavirus [ ] . remdesivir, an antiviral compound, which showed activity against multiple variants of ebola virus in cell-based assays and rhesus monkey model. chloroquine (cq) and its derivative hydroxychloroquine (hcq), antiviral compound(s) have been used to treat malaria and amebiasis. a combination of lopinavir and ritonavir, is co-formulated for hiv- treatment. another combination of lopinavir and ritonavir plus interferon-beta (lpv/rtv-ifnb) has been approved for the treatment of relapsing-remitting multiple sclerosis and secondary progressive multiple sclerosis. about clinical trials were identified by belhadi et.al., which includes open-label studies ( %), double-blind ( %), and single blind studies ( %) [ ] . they also classified the number of trials (n) and total numbers of planned inclusions (n) for lopinavir/ritonavir (n = , n = ), chloroquine (n = , n = ), hydroxychloroquine (n = , n = ), and remdesivir (n = , n = ). in contrary, several controversial reports including toxic side effects on these promising candidates under clinical trial(s) raised some challenging questions for researchers. those have been presented below: remdesivir, an antiviral compound, which showed activity against multiple variants of ebola virus in cell-based assays and rhesus monkey model. chloroquine (cq) and its derivative hydroxychloroquine (hcq), antiviral compound(s) have been used to treat malaria and amebiasis. a combination of lopinavir and ritonavir, is co-formulated for hiv- treatment. another combination of lopinavir and ritonavir plus interferon-beta (lpv/rtv-ifnb) has been approved for the treatment of relapsing-remitting multiple sclerosis and secondary progressive multiple sclerosis. about clinical trials were identified by belhadi et.al., which includes open-label studies ( %), double-blind ( %), and single blind studies ( %) [ ] . they also classified the number of trials (n) and total numbers of planned inclusions (n) for lopinavir/ritonavir (n = , n = ), chloroquine (n = , n = ), hydroxychloroquine (n = , n = ), and remdesivir (n = , n = ). in contrary, several controversial reports including toxic side effects on these promising candidates under clinical trial(s) raised some challenging questions for researchers. those have been presented below: a report presents that patients (with symptom duration of days or less) receiving remdesivir showed clinical improvement than those receiving placebo, but it did not make any statistically significant clinical benefits [ ] . an open-label non-randomized clinical trial study demonstrated significant decrease in viral load and carriage duration in covid- patients receiving hydroxychloroquine ( mg/day during ten days). this treatment showed enhanced effects in combination with azithromycin, but it identified serious methodological flaws [ , ] . another randomized clinical study did not make any difference in recovery rates upon hydroxychloroquine treatment in covid patients [ ] . however, a hype on cq and hcq has created drug shortages and affected other potential treatments (such as for patients with lupus). there was no significant benefit (clinical improvement) observed with lopinavir-ritonavir treatment [ ] . mortality and percentages of patients with detectable viral rna at various time points were similar in the lopinavir-ritonavir group and the standard-care group. it was also reported median time to clinical improvement was shorter by one day for lopinavir-ritonavir group than that observed with standard care. vaccination is one of the most effective and preventive medications against various diseases caused by pathogens (such as virus or bacteria). currently there are about approved vaccinations available against various life-threatening diseases, including measles, polio, tetanus, diphtheria, meningitis, influenza, typhoid, and cervical cancer (https://www.who.int/topics/vaccines/en/). a vaccine typically contains an agent (weakened or killed forms of any microbe, its toxins, or one of its surface proteins), which though resembles a disease-causing microorganism, but provides active acquired immunity to that particular infectious disease [ , ] . an antiviral vaccine helps to boost our natural immune response to an invading virus by priming it to recognize viral antigens. in general, antiviral vaccines can be classified as follows: (i) inactive or live-attenuated viruses, (ii) virus-like particle (vlp), (iii) viral vectors, (iv) protein-based, (v) dna-based, and (vi) mrna-based vaccines [ , ] . like many other diseases, the vaccine development is not successful and conclusive for coronavirus disease. until now, there is no proper vaccine is developed or approved for the treatment of human coronavirus diseases (such as sars-cov and mers-cov) [ ] [ ] [ ] . most big pharmaceutical companies also in the race to develop effective vaccines for cov infection [ , ] . the existing knowledge on previous strategies for cov vaccine developments can benefit the ongoing research as sequence analysis of the sars-cov- genome showed close relation to sars ( %) and to one bat ratg sars-like cov ( %) than to mers cov ( %) [ ] . liu et al. [ ] reported that patents (mentioned in cas content collection) are directly associated with anti-sars and anti-mers vaccines ( patents on inactive and live-attenuated virus vaccines, patents on dna vaccines, patents on viral vector vaccines, patents on vlp vaccines, and three patents on mrna vaccines) with a demonstrated immune response, which could be a huge boost for covid- vaccine developers. an accelerated evaluation of next-generation vaccine for covid- has been triggered as soon as the genetic sequence of sars-cov- is published on january [ ] [ ] [ ] [ ] . as of july , vaccine candidates have been identified (https://www.who.int/who-documents-detail/draft-landscape-of-covid- -candidatevaccines), of which candidate vaccines are in clinical evaluation ( table ) and candidate vaccines are in preclinical stages. associated problems and pitfalls are surely a major concern resulting huge roadblock for vaccine discovery against covid- . the pitfalls are many folded, which as follows: (i) antibody-dependent enhancement (ade) of viral replication for vaccinated people in future recurrence due to immune backfiring, (ii) rouge immunization resulting a huge damage on someone's own immune cells (such as neutrophil and basophil), (iii) in addition to immune response malfunctioning, three imperatives of vaccine effort: speed, manufacture and deployment at scale, and (iv) global access for a newly developed vaccine [ , ] . further, new findings and hypotheses stirred up the debate on covid- research making it difficult as well as relevant not only in therapy but also in producing a life-saving vaccine, without any risk of generating immunity-based complications. (i) molecular mimicry: two independent groups (lucchese and flöel; macario and cappello) proposed molecular mimicry as the culprit in determining multi-organ damages (including anosmia, leukopenia, and vascular damage) in covid- patients [ ] [ ] [ ] . indeed, there are confirmations that a number of human proteins share common epitopes with sars-cov- proteins and these epitopes are highly immunogenic. (ii) biphasic infection: due to (a) the ability of human coronaviruses to cause respiratory re-infections, regardless of pre-existing humoral immunity and (b) evidence on circulation of severe acute respiratory syndrome coronavirus type (sars-cov- ) in italy before the detection of first covid- case, an hypothesis was given on biphasic infection, the immunological result of a prior viral infections either by sars-cov- or different strains of coronaviruses, or potentially even other respiratory viruses resulting increased susceptibility to more severe forms of covid- , following a secondary infection with sars-cov- [ ] . this theory is sustained by anecdotal clinical reports of "biphasic infection" and "cytokine storm" through a possible ade immunological mechanism, which was already observed with infections sustained by other coronaviruses (such as sars-cov and mers-cov) or other viruses (such as west nile virus and dengue). convalescent plasma (cp) therapy involves the administration of antibodies to a susceptible person to prevent or treat an infectious disease providing an immediate immunity [ ] . in this therapy, donated blood from the infected person who've recovered from that infection have antibodies in their blood that can fight against the infection. the cp therapies have been tested since s as a possible alternative and/or auxiliary treatment including sars-cov, ebola, influenza a (h n ) etc. viruses [ , ] . additionally, cp therapy did not show any serious and immediate adverse effects in earlier cov treatment [ ] . the plasma with antibodies is prepared after separation of blood cells from the donated blood which can be extended to combat against covid- . cp therapy has been generally approved as experimental treatment for patients with critical conditions. duan et al. [ ] reported potentially improved clinical outcomes for severe covid- patients with a dose of ml of cp (derived from recently recovered donors with the neutralizing antibody titers above : ) with additional use of antiviral agents and maximal supportive care. this study confirmed a number of positive outcomes, including, (i) neutralizing antibody level increased rapidly up to : in five cases, while for other four cases maintained at a high level ( : ), (ii) increased oxyhemoglobin saturation within three days, (iii) increase in lymphocyte counts ( . × /l vs. . × /l), (iv) decreased c-reactive protein ( . mg/l vs. . mg/l), (v) varying degrees of absorption of lung lesions within seven days, (vi) undetectable viral load in seven patients who had previous viremia. additionally, treatment with human immunoglobulin is reported to increase same-day thrombotic event risk significantly ( . to . %) [ ] . transfer of blood substances may include inadvertent infection with another infectious disease agent and react to serum constituents resulting immunological reactions such as serum sickness [ ] . more high-quality studies, adequate selection of donors with high neutralizing antibody titers, central blood banking facilities to process the donated serum, efficient serological and virological assays, production and the use of cp according to precise ethical and controlled conditions are needed for implementing this therapy further. latest studies showed that ace , the key functional receptor of sars-cov- , is highly expressed in kidney (nearly times higher than in lung) resulting it to be a main target organ for sars-cov- attack [ ] . thus, novel coronavirus infections hugely damage the kidney of any severe covid- patient suffering from an immunological damage due to a cytokine storm, the imbalance of pro-inflammatory and anti-inflammatory factors. thus, auxiliary continuous blood purification could be an essential technology to take care of inflammatory factors, cytokine storm, electrolyte imbalance, and acid-base balance for any covid- patient resulting a reduced renal work-load and a possible recovery of renal function [ , ] . at present, extracorporeal blood purification technology is supplied for severely ill patient with novel coronavirus pneumonia as an auxiliary treatment to improve condition [ ] . there is an increasing awareness, tendency, and agenda to use traditional (t) medicine (indigenous health traditions) and complementary and alternative medicine (cam) (methods outside the biomedical mainstream, particularly in industrialized countries). globally, half the population uses t/cam as a preventive measure [ , ] . the national center for complementary and integrative health (nccih) of the national institute of health (nih), usa, has included various medical methods under the umbrella term cam, such as homeopathy, naturopathy, ayurveda, medicinal systems, and products originating from traditional medicine [ ] . further, herbalism, aromatherapy, acupuncture, massage, and reflexology are also various name and forms among the most popular branches of cam [ ] . the potential use of cam (sometimes along with conventional medicine) has been reported to be efficient therapeutic strategy against several virus associated diseases such as influenza, dengue, japanese encephalitis, hepatitis c, zika, and hiv [ ] [ ] [ ] . considering the efficacy of cam against coronaviruses with minimal reported adverse effects on host cells, ministry of ayush (ayurveda, yoga & naturopathy, unani, siddha and homoeopathy), government of india, recommended scientists, researchers and clinicians to pursue research and use of indian herbal drugs on covid- . through a memorandum, government of india is now trying to utilize the ayurveda, siddha, homeopathy, and unani system of medicine including prophylactic measures, intervention during quarantine, asymptomatic and symptomatic cases, public health research, survey, laboratory-based research etc. (https://www.ayush.gov.in/). indian traditional medicinal systems, one of the oldest treatments in human history (existed nearly years ago witnessed and scripted in ancient literature), played a significant role in encountering global health due to its antiviral, anti-inflammatory and antioxidant properties [ , ] . such a traditional branch of science could be a potential option against covid- because of its proved efficacy not only in treatment but also in preventive strategy for several diseases, including respiratory viral infections through immunity boosting, rejuvenating lifestyle, and dietary management [ , ] . ayush recommended selected traditional drugs for covid- as follows: http://ayush.mp.gov.in/sites/default/files/corona% advisory_ .pdf. [ ] . traditional chinese medicine (tcm) is also recently being included as one of the treatment modalities in china for covid- . previous record on efficacious tcm against respiratory tract infectious diseases, such as lianhua qingwen capsules (exerts independent antiviral effects) and shufeng jiedu capsules (synergistic antiviral effects with western medicine) on influenza viruses, has encouragd the practice of tcm against covid- [ , ] . wang et al. [ ] reported massive improvement for four covid- patients as a result of combination therapy including chinese and western antiviral medicine, where they used lopinavir/ritonavir (kaletra®), arbidol, and shufeng jiedu capsule (sfjdc) with necessary supportive care. however, lack of high-quality research, standard clinical trials, sufficient research articles, clear mechanism of action, rigorous population studies, prospective business model are also urgently required to establish the therapeutic effect and implementation of t/cam among mass population. in spite of some emphatic results through traditional, complementary, and integrative products, practices, and practitioners against covid- , north american and european governments are keeping their silence on these practices (https: //www.cdc.gov/coronavirus/ -ncov/prevent-getting-sick/prevention.html) and rather warned of possible harm and overselling (https://www.fda.gov/news-events/press-announcements/coronavirusupdate-fda-and-ftc-warn-seven-companies-selling-fraudulent-products-claim-treat-or). john weeks, editor-in-chief of the journal of alternative and complementary medicine, mentioned this double standard attitude as he pointed out that "no practices have definitive evidence for benefit against covid- , yet providers with other stripes are using experimental practices and off-label drugs every day in their desperate to ease patient suffering and elicit hope" [ ] . prevention is the utmost important strategy to fight against covid- in the present situation. several preventive measurements are taken to reduce the spread and transmission of the covid- infection. this is classified as follows (i) contact tracing, (ii) sharing or proper dissemination of information, (iii) precautionary measurements ( figure ). covid- [ , ] . wang et al. [ ] reported massive improvement for four covid- patients as a result of combination therapy including chinese and western antiviral medicine, where they used lopinavir/ritonavir (kaletra®), arbidol, and shufeng jiedu capsule (sfjdc) with necessary supportive care. however, lack of high-quality research, standard clinical trials, sufficient research articles, clear mechanism of action, rigorous population studies, prospective business model are also urgently required to establish the therapeutic effect and implementation of t/cam among mass population. in spite of some emphatic results through traditional, complementary, and integrative products, practices, and practitioners against covid- , north american and european governments are keeping their silence on these practices (https://www.cdc.gov/coronavirus/ ncov/prevent-getting-sick/prevention.html) and rather warned of possible harm and overselling (https://www.fda.gov/news-events/press-announcements/coronavirus-update-fda-and-ftc-warnseven-companies-selling-fraudulent-products-claim-treat-or). john weeks, editor-in-chief of the journal of alternative and complementary medicine, mentioned this double standard attitude as he pointed out that "no practices have definitive evidence for benefit against covid- , yet providers with other stripes are using experimental practices and off-label drugs every day in their desperate to ease patient suffering and elicit hope" [ ] . prevention is the utmost important strategy to fight against covid- in the present situation. several preventive measurements are taken to reduce the spread and transmission of the covid- infection. this is classified as follows (i) contact tracing, (ii) sharing or proper dissemination of information, (iii) precautionary measurements ( figure ). track, trace, and share of the information on covid- are major preventive steps to stop spreading of sars-cov- . a thorough, quick, and updated report should be always available covering various information (such as number of infected cases, casualties, regions affected in each country etc.) on easily accessible platforms. the promotion of "data science" or big data and data driven interdisciplinary research areas has helped a lot to control such global infectious disease or epidemics through extensive surveillance, sharing of epidemiological data, and patient monitoring [ ] . benefits of big data with technological advancement has facilitated the communication among regional, national and international healthcare agencies to monitor future host adaption, viral evolution, infectivity, transmissibility, morbidity, mortality, mental health impact and psychological effects due to covid- epidemic. here we have mentioned some authentic responsible agencies and tools along with several controversies aroused from the use of data science as follows: who: who is providing a daily "situation report" as an update on covid- pandemic (https://www.who.int/emergencies/diseases/novel-coronavirus- /situation-reports), where who receives the data from national authorities. worldometer: worldometer is a free reference website (managed by an international team of developers, researchers, and volunteers) that provides counters and real-time statistics on various topics such as world population, government, economics, society, media, environment, food, water, energy, and health (https://www.worldometers.info/). now the data in website is currently available in languages and will be available in more languages soon (https://www.worldometers.info/ languages/, accessed on may ). this reference website belongs to a united states of america (usa)-based digital company dadax (http://dadax.com/). presently, this website is being used quite popularly to provide various statistics (graphs, countries, death, symptoms, incubation, transmission, news) on covid- pandemic around the world (https://www.worldometers.info/coronavirus/) and the data is also trusted and used by several agencies including government organization of various countries. the speed and ease of communication is the heart of management to control the spread of any infectious diseases as it helps to build extensive surveillance, share of epidemiological data, and patient monitoring. mobile phone or especially smartphone with the help of various mobile apps (software application) can improve this purpose due to its speedy connectivity, computational power, remote access, electronic reporting, epidemiological data basing, real-time geospatial information, digitized process of contact tracing, more complete and shareable records, enhanced coordination among regional, national and global health agencies [ , ] . a past experience on using smartphones for geospatial tracking of infectious diseases such as hiv, ebola, and tuberculosis has helped to build these devices further to control covid- epidemics by implementing healthcare strategies, and improving general awareness among masses [ ] [ ] [ ] . further, smartphone embedded point-of-care testing and self-reporting facilities has helped to reduce risk of contracting covid- as these help actual and suspected patients with mild symptoms under self-quarantine to report remotely without going to any overcrowded hospital or healthcare centers [ , ] . who launched mobile app (https://github.com/worldhealthorganization/app) to accurately track and trace covid- cases. there are also several official contact tracing apps available for the citizen of various countries to inform a person's own health to help governments in strategic control (e.g., "aarogya setu" in india, "covid watch" in usa, "nhs covid- " in uk, "alipay health code" in china, etc.,). despite huge effort and help from data science, dueling in data caused also deviation, divisive and neglecting attitude regarding covid- . this further facilitates the spread of pandemic, shifting epicenters, more casualties, economic loss and so many other secondary problems created due to pandemic. here we have summarized some problems associated with data handling. reproductive number: the basic reproduction number (r ), an indication of the transmissibility of a virus in infectious disease epidemiology, has been used to represent the average number of new covid- infections generated by an infectious person in a totally naïve population [ ] . it is estimated that (i) the number of infections is likely to increase for r > , and (ii) transmission is likely to die out for r < . thus, a true estimation of r can be beneficial in terms of prevention of any infectious disease. liu et al. estimated higher reproductive number of covid- compared to sars coronavirus and also reported that the average reproductive number for covid- (r ~ . ) is considerably higher than that of who estimate (r = . ) [ ] . they mentioned that the current estimates of r for covid- are possibly biased due to insufficient data and short onset time. "risk of death" measurement: estimation of the case fatality risk or the risk of death among positive cases is a common epidemiological practice to measure the severity of infection for a given disease. kobayashi et al. [ ] mentioned several key epidemiological problems for assessment of the severity of covid- as follows-(i) "division of the cumulative number of deaths by that of cases tends to underestimate the actual risk because deaths that will occur have not yet observed, and so the delay in time from illness onset to death must be addressed"; (ii) "the observed dataset of reported cases represents only a proportion of all infected individuals and there can be a substantial number of asymptomatic and mildly infected individuals who are never diagnosed"; (iii) "ascertainment bias and risk of death among all those infected would be smaller when estimated using shorter virus detection windows and less sensitive diagnostic laboratory tests". they further suspected that the total number of reported covid- infections will be underestimated due to many undetected mild or asymptomatic cases that go. open data source: in this fight against covid- , an open data source is a big step forward in the age of big data. amaro et al. [ ] urged to make an effort through a "community letter" for sharing bimolecular simulation data on covid- to help and improve connection and communication among scientists and investigators working on simulation, experimental and clinical data. they committed to share methods, models, and results of their study openly and quickly to test findings, ensure reproducibility, test significance, eliminate dead-ends, and accelerate discovery on covid- applications. they committed to use preprint servers such as arxiv, biorxiv, and chemrxiv, open access data repositories such as zenodo, an open data sharing platforms for models and trajectories such as the molecular sciences software institute (molssi) sars-cov- biomolecular simulation data and algorithm store, the open science framework, the european open science cloud and several other agencies. they also make an appeal and encourage others for similar best practices on open data efforts in other research areas to prevent covid- . cyber-attack: in this grave situation due to covid- , the revolutionized advancement of information and communications technology is a crucial weapon to control the healthcare infrastructure in addition to businesses, deliveries of food and essential items to remote places, online grocery shopping etc. but there is a growing concern due to an increasing report of malicious attacks on information and communications technology during covid- as attackers find this an opportunity for financial gains and promoting evil intents. a times increase in spam email and % in malicious urls have been reported from february to march , in which the united states is found to be the epicenter for such targets [ ] . healthcare systems, government and media outlets, financial services are some of most important organization and industries, which are identified at the risk of cyber-attack [ ] . this team has identified the top ten such deadly cybersecurity threats amid covid- pandemic, which are as follows-(i) distributed denial of services (ddos) attack, (ii) malicious domains, (iii) malicious websites, (iv) malware, (v) ransomware, (vi) spam emails, (vii) malicious social media messaging, (viii) business email compromise, (ix) mobile threats, and (x) browsing apps. the worldometer website was reported under cyber-attack in march and was then hacked a few days later, resulting in incorrect information (dramatic rise on covid- statistics in vatican city) for approximately min (https://www.euroweeklynews.com/ / / /false-report-of- k-dead-in-vatican-city-lastnight-i-nearly-fell-off-my-chair-reading-it/). use of contact tracing covid- apps also raised some security and privacy concern as it keeps personal database of any individual [ , ] . thus there is a continuous debate on this issue and demand of more reliable apps among mass population, whereas governments are trying to make it a mandatory use as experts shown their confidence about these apps [ ] . social media activism: containment measures are primary guideline to tackle the novel coronavirus (covid- ) pandemic. due to moving out of physical public spaces, people are using online platforms as even more prominent and powerful tools to communicate social discussion and understand the unprecedented global crisis. however, ferrara reported after tracking and studying . m real-time english tweets about covid- (the large-scale data was collected since january , , the day the first covid- case was reported on us soil to the dataset up to march , the day before the united states government announced the state of national emergency due to the covid- pandemic) that the information on social media platforms are populated by bots, automated accounts [ ] . this study provided the evidence that high bot score accounts are used to amplify certain topics of discussion at the expense of others, such as (i) promotion of political conspiracies and divisive hashtags alongside with covid- content, and (ii) enabling participatory activism to shed light on issues that may otherwise be censored in china. thus, this study demands more nuanced and regulated discussion on social media platforms on covid- . behavioral changes and use of protective gears have been prescribed as the first and foremost precautionary step to stop the spread of sars-cov- . gradual understanding of the transmission of this virus and previous experience on successful behavioral imposition to control other epidemics such as aids (changes in sexual behavior, condom promotion, and government interventions) has helped a lot in that direction. though more efficient behavioral changes in daily lifestyle requires better understanding and proper implementation of the rules with time on covid- transmission. awareness on the risks from exposure level to respiratory droplets, airborne virus, contamination level from surfaces, concentration of transmission, incubation period, infectivity even before onset of symptoms in the incubation period, transmission from asymptomatic people will definitely be helpful to understand (i) behavioral changes and precautionary guidelines and (ii) use of protective gears. further use of telemedicine and robot can also play a crucial role as precautionary steps to combat against such infectious diseases. behavioral changes and precautionary guidelines: knowledge on covid- has helped to set precautionary guidelines in our day to day lifestyle. various health agencies such as who, the centers for disease control and prevention (cdc), national public health institute of the united states and many more recommended following general measures to prevent the spread of covid- -(i) complete washing of hands often using an alcohol-based hand sanitizer to kill the sars-cov- , (ii) avoid close contact, (iii) cover mouth and nose with a cloth or mask (e.g., n respirators) in public places, (iv) cover coughs and sneezes, (ii) avoid touching eyes, nose and mouth when outside, (iii) avoid travelling or gathering in crowded places, (iv) clean and disinfect frequently touched surfaces, (v) women with infants are encouraged to breastfeed their babies to enhance their immunity (https://www.cdc.gov/coronavirus/ -ncov/prevent-getting-sick/prevention.html, https://apps.who.int/iris/handle/ / ). in addition to hand hygiene practices, who also has given proper guidelines for . sanitation and plumbing of covid- hospitals, quarantine centers; . toilets and the handling of feces of covid- patients; . safe management of health care waste; . environmental cleaning and laundry at healthcare facilities; . safe disposal of greywater or water from washing personal protective gears, surfaces and floors; . safe management of dead bodies; . management of waste generated at home; . treatment and handling requirements for excreta (https://www.who.int/publications-detail/water-sanitation-hygiene-and-waste-managementfor-the-covid- -virus-interim-guidance). the guidance from national center for complementary and integrative health (nccih), national institutes of health prescribed a "healthy waiting" in life style, which includes social distancing (or physical distancing), mild exercise, stress reduction, restriction on smoking and alcohol (https://www.nccih.nih.gov/health/in-the-news-coronavirus-and-alternativetreatments). to prevent such health crisis and boost immunity with special reference to respiratory health, ministry of ayush, india recommended the following self-care guidelines in daily lifestyle (https://www.mohfw.gov.in/pdf/immunityboostingayushadvisory.pdf): further, home isolation or quarantine of suspected cases and those with mild illnesses have been entailed as prevention to reduce the burden on covid- hospitals for severe cases [ ] . as a preventive measurement, countries have imposed not only inter nation lockdown, but also total or partial lockdown inside their territory to minimize transmission from foreign nationals, social gathering and day to day activity [ ] . lockdown area are also classified based on infection progression and hotspot are also indicated to inform mass about the containment zone. thermal screening has become a common strategy to track the probable symptomatic cases at various juncture of transportation. it is obvious that such changes in daily life of general population and healthcare unit need more time to cope with. implementation of such changes is challenging in short time against rapid infectious nature of covid- . according to the psychiatrists and allied professionals, covid- pandemic and such forceful precautionary guidelines created subsyndromal mental health at multiple levels in the general population, among healthcare workers, and in vulnerable populations resulting the symptoms of anxiety and depression, self-reported stress, insufficient sleep [ ] . also, it is surely very conflicting to maintain balance between economy and public health during such long lockdown [ ] . every section of society specially those belonging to lower socio-economic state is being affected economically sooner or later due to such crisis, which create a desperation to neglect such imposed rules on mass population resulting further increase of covid- cases. protective gears: various protective gears are playing an important role to stop the spread pandemic. frontline healthcare professionals, in addition to healthy mass population are at a huge risk in covid- transmission from patients, suspected cases. as of april , more than healthcare workers including doctors have been infected (https://health.economictimes.indiatimes.com/news/industry/whosays-over- -healthcare-workers-across- -countries-infected-by-covid- / ). in during the sars outbreak, nearly % of those virus-affected were healthcare workers [ ] . this is an even more warning situation as it is important that the healthcare workers should be protected from infection to ensure uninterrupted medical facility and to prevent virus transmission to other patients. thus, use of protective gears such as personal protective equipment (ppe) kits, mask (tested n respirators), gloves and goggles are important accessories for healthcare professionals, whereas for mass population mask (more specifically n mask) is foremost important along with other protective guidelines. suddenly, very high demand of such protective gears resulted a huge shortage worldwide, which needs a huge workforce to support healthcare facilities in this crisis. additive manufacturing (i.e., d printing), an eminent technology for medical device preparation, came out as an innovative solution for covid- protective gears production with the help of other embedded technologies such as-(i) antimicrobial polymers and nanoparticles for making ppe, (ii) angiotensin-converting enzyme coated nanoparticles containing respiratory masks, chewing gums and nasal filters (iii) preparation of recyclable decontaminating nanofiber filtered face masks, etc. [ , ] . these ideas will surely be advantageous to prepare more effective protective gears for managing such pandemic, though further research is needed to implement such efforts to market. telemedicine: with the advancement of telecommunication technology, telemedicine has emerged as medical activity involving a doctor-patient distant interaction through telecommunication, which have been interchangeably known as telehealth (more politically correct term) or online health and e-health (fashionable term) [ ] . such telecommunication-based remote medical health facility is surely advantageous against any infectious disease outbreak and thus it is recommended by various health agencies for covid- as it (i) reduces person-to-person contact by obeying social distancing, (ii) maintain balance in facilities with limited workforce, (iii) evolves as an alternative cost effective health provider in comparison to traditional home visit [ ] [ ] [ ] . in spite of a promising future and willingness to use telehealth among patients, telemedicine suffers from various disadvantageous due to (i) less scope outside of emergency situations, (ii) clinician unwillingness and low acceptance among patients, (iii) problem with reimbursement, (iv) organization of the healthcare system. robotic gesture: robots already shown a huge potential as medical device for diagnosis to surgery including pediatric airway operation, oropharyngeal cancer operation etc. [ , ] . in similar fashion, to combat infectious epidemics like covid- , robots can play pivotal roles due to its abilities as follows-(i) large area cleaning and disinfection of contaminated surfaces (such as using uv light devices), (ii) diagnosis by automated or robot-assisted nasopharyngeal and oropharyngeal swab or blood testing, (iii) patient care by delivering medications and food to infected/suspected persons under quarantine, (iv) measuring vital signs, (v) assisting controls on transportation of mass population (such using thermal sensors and vision algorithms), (vi) help in telemedicine, (vii) facial tracking of any individual already having infection as a process of contact tracing, (viii) navigation in high-risk areas for sample transfer as well as delivery of medicines using autonomous drones or robot-assisted ground vehicles [ , ] . such robot-assisted strategy to control epidemic may speed up the process, reduce the risk of infection specially for frontline health care professionals, and increase workforce ( figure ). though despite such help in clinical care, logistics and reconnaissance, proper deployment of robots may face some problem due to privacy and security, incompatible diagnosis with the mutation of virus. tracing, (viii) navigation in high-risk areas for sample transfer as well as delivery of medicines using autonomous drones or robot-assisted ground vehicles [ , ] . such robot-assisted strategy to control epidemic may speed up the process, reduce the risk of infection specially for frontline health care professionals, and increase workforce ( figure ). though despite such help in clinical care, logistics and reconnaissance, proper deployment of robots may face some problem due to privacy and security, incompatible diagnosis with the mutation of virus. in conclusion, this article presented the current progress of four primary and important sphere of research in the battle against covid- pandemic, which are knowledge of the biological properties of virus, diagnostic modalities, treatment modalities, and prevention modalities. the huge development and deployment of advanced level of research and technology has helped to improve severely affected the global health condition due to covid- . a prior knowledge on previous viral outbreaks and pandemic has really helped researchers, health agencies and administrations a lot in response to covid- . in spite of such a plethora of research, the progress was hampered in many areas due to conflicting views and controversies about covid- . several such grey areas in transmission, best diagnostic methods with no false positive reports, possible treatment outcome, figure . possible preventive methodologies against infectious disease in future. in conclusion, this article presented the current progress of four primary and important sphere of research in the battle against covid- pandemic, which are knowledge of the biological properties of virus, diagnostic modalities, treatment modalities, and prevention modalities. the huge development and deployment of advanced level of research and technology has helped to improve severely affected the global health condition due to covid- . a prior knowledge on previous viral outbreaks and pandemic has really helped researchers, health agencies and administrations a lot in response to covid- . in spite of such a plethora of research, the progress was hampered in many areas due to conflicting views and controversies about covid- . several such grey areas in transmission, best diagnostic methods with no false positive reports, possible treatment outcome, contact tracing, precautionary steps, proper public health management and many other fields has shattered the progress resulting a chaos and crisis in public health and economy. despite the conflict, differences in opinions are an important part of any constant progress. thus, these conflicting views have helped the field to grow and will create unprecedented opportunities further solving several unresolved questions. governments should encourage and endorse innovative research ideas to beat such pandemics, not only in basic research and biomedicine, but also in engineering, information technology and many unknown corners to get a marketable solution in spite of such controversies. in search of proper treatment, comparatively well-structured diagnosis and prevention are two important armors against covid- with the help of knowledge on biological properties of sars-cov- . we hope that with time, more accurate cumulative knowledge will dissipate the ambiguity about covid- and translational research will help to restore the public life to normalcy. in that aspect, our review would be a huge boost to address the progress amid controversies on a single platform against covid- . a comparative review the novel zoonotic covid- pandemic: an expected global health concern coronavirus envelope protein: current knowledge clinical virology structure, function, and antigenicity of the sars-cov- spike glycoprotein the proximal origin of sars-cov- the covid- epidemic coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. microbiol a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan aerosol and surface stability of sars-cov- as compared with sars-cov- a novel coronavirus from patients with pneumonia in china public health image library (phil) crystal structure of sars-cov- main protease provides a basis for design of improved α-ketoamide inhibitors fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin epidemiologic clues to sars origin in china bat coronaviruses in china a review of coronavirus disease- (covid- ) probable pangolin origin of sars-cov- associated with the covid- outbreak evolutionary history, potential intermediate animal host, and cross-species analyses of sars-cov- a pneumonia outbreak associated with a new coronavirus of probable bat origin first case of novel coronavirus in the united states structural and functional basis of sars-cov- entry by using human ace tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis diagnosing covid- : the disease and tools for detection sars-cov- viral load in upper respiratory specimens of infected patients the unusual origin of the polymerase chain reaction primer-directed enzymatic amplification of dna with a thermostable dna polymerase comprehensive detection and identification of human coronaviruses, including the sars-associated coronavirus, with a single rt-pcr assay detection of multiple viral sequences in the respiratory tract samples of suspected middle east respiratory syndrome coronavirus patients in jakarta detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction real-time polymerase chain reaction for detecting sars coronavirus sing, a. rapid establishment of laboratory diagnostics for the novel coronavirus sars-cov- in bavaria characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding viral load of sars-cov- in clinical samples improved molecular diagnosis of covid- by the novel, highly sensitive and specific covid- -rdrp/hel real-time reverse transcription-pcr assay validated in vitro and with clinical specimens evaluation of a quantitative rt-pcr assay for the detection of the emerging coronavirus sars-cov- using a high throughput system isothermal amplification of nucleic acids nucleic acid isothermal amplification technologies: a review recent advances and perspectives of nucleic acid detection for coronavirus rapid detection of the severe acute respiratory syndrome (sars) coronavirus by a loop-mediated isothermal amplification assay development of fluorescent reverse transcription loop-mediated isothermal amplification (rt-lamp) using quenching probes for the detection of the middle east respiratory syndrome coronavirus detection of severe acute respiratory syndrome coronavirus rna in plasma during the course of infection development of reverse transcription loop-mediated isothermal amplification assays targeting severe acute respiratory syndrome coronavirus (sars-cov- ) reverse transcription loop-mediated isothermal amplification combined with nanoparticles-based biosensor for diagnosis of covid- rapid molecular detection of sars-cov- (covid- ) virus rna using colorimetric lamp rapid detection of covid- coronavirus using a reverse transcriptional loop-mediated isothermal amplification (rt-lamp) diagnostic platform an updated evolutionary classification of crispr-cas systems biology and applications of crispr systems: harnessing nature's toolbox for genome engineering the next generation of crispr-cas technologies and applications nucleic acid detection with crispr-cas a/c c programmable inhibition and detection of rna viruses using cas multiplexed and portable nucleic acid detection platform with cas , cas a, and csm crispr-cas -based detection of sars-cov- field-deployable nucleobase detection and identification using fncas . biorxiv detection of coronavirus e antibody by indirect hemagglutination clinical characteristics of asymptomatic infections with covid- screened among close contacts in nanjing development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes profiling early humoral response to diagnose novel coronavirus disease (covid- ) rapid detection of covid- causative virus (sars-cov- ) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor cross-reactive antibody response between sars-cov- and sars-cov infections clinical characteristics of coronavirus disease in china chest radiograph vs. computed tomography scan in the evaluation for pneumonia middle east respiratory syndrome corona virus: can radiology be of help? initial single center experience mining x-ray images of sars patients imaging changes of severe covid- pneumonia in advanced stage automated detection of covid- cases using deep neural networks with x-ray images screening for lung cancer with low-dose helical computed tomography: anti-lung cancer association project early chest computed tomography scan to assist diagnosis and guide treatment decision for suspected community-acquired pneumonia patients with rt-pcr-confirmed covid- and normal chest ct sensitivity of chest ct for covid- : comparison to rt-pcr correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases ct imaging features of novel coronavirus ( -ncov) evolution of ct manifestations in a patient recovered from novel coronavirus ( -ncov) pneumonia in wuhan initial ct findings and temporal changes in patients with the novel coronavirus pneumonia ( -ncov): a study of patients in wuhan, china rapid ai development cycle for the coronavirus (covid- ) pandemic: initial results for automated detection & patient monitoring using lung infection quantification of covid- in ct deep learning system to screen coronavirus disease pneumonia a deep learning algorithm using ct images to screen for corona virus disease (covid- ) the importance of the autopsy in emerging and reemerging infectious diseases autopsies on covid- deaths: a missed opportunity and the lockdown of science autopsy in suspected covid- cases covid- deaths: are we sure it is pneumonia? please, autopsy, autopsy, autopsy! societa italiana di anatomia patologica e citologia-siapec. the autopsy debate during the covid- emergency: the italian experience recent insights into the development of therapeutics against coronavirus diseases by targeting n protein molecular immune pathogenesis and diagnosis of covid- approved antiviral drugs over the past years drug repurposing strategies for covid- drug repurposing: progress, challenges and recommendations repurposing host-based therapeutics to control coronavirus and influenza virus in silico methods for drug repurposing and pharmacology computational/in silico methods in drug target and lead prediction combating devastating covid - by drug repurposing covid- treatment by repurposing drugs until the vaccine is in sight fast identification of possible drug treatment of coronavirus disease- (covid- ) through computational drug repurposing study boosting the arsenal against covid- through computational drug repurposing who launches global megatrial of the four most promising coronavirus treatments generating randomized trial evidence to optimize treatment in the covid- pandemic a brief review of antiviral drugs evaluated in registered clinical trials for covid- remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial use of hydroxychloroquine and chloroquine during the covid- pandemic: what every clinician should know a trial of lopinavir-ritonavir in adults hospitalized with severe covid- recent advances in contraceptive vaccine development: a mini-review a review of vaccine research and development: the human immunodeficiency virus (hiv). vaccine research and development on therapeutic agents and vaccines for covid- and related human coronavirus diseases vaccines for covid- : perspectives, prospects, and challenges based on candidate sars, mers, and animal coronavirus vaccines the spike protein of sars-cov-a target for vaccine and therapeutic development the covid- vaccine development landscape the sars-cov- vaccine pipeline: an overview avoiding pitfalls in the pursuit of a covid- vaccine ensuring global access to covid- vaccines molecular mimicry between sars-cov- and respiratory pacemaker neurons molecular mimicry may explain multi-organ damage in covid- is molecular mimicry the culprit in the autoimmune haemolytic anaemia affecting patients with covid- ? hypothesis to explain the severe form of covid- in northern italy convalescent plasma: new evidence for an old therapeutic tool? use of convalescent plasma therapy in sars patients in hong kong treatment with convalescent plasma for influenza a (h n ) infection treatment of covid- : old tricks for new challenges effectiveness of convalescent plasma therapy in severe covid- patients hyperimmune globulins and same-day thrombotic adverse events as recorded in a large healthcare database during the convalescent sera option for containing covid- review of the novel coronavirus (sars-cov- ) based on current evidence initiating acute dialysis at earlier acute kidney injury network stage in critically ill patients without traditional indications does not improve outcome: a prospective cohort study effect of early vs delayed initiation of renal replacement therapy on mortality in critically ill patients with acute kidney injury: the elain randomized clinical trial diagnosis and treatment of novel coronavirus pneumonia based on the theory of traditional chinese medicine a public health agenda for traditional, complementary, and alternative medicine the role of complementary and alternative medicine therapeutic development and drugs for the treatment of covid- complementary and alternative medicine in alliance with conventional medicine for dengue therapeutics and prevention indian systems of medicine: a brief profile covid- : a promising cure for the global panic medicinal plants of tamil nadu (southern india) are a rich source of antiviral activities traditional chinese medicine in the treatment of patients infected with -new coronavirus (sars-cov- ): a review and perspective updated approaches against sars-cov- clinical characteristics and therapeutic procedure for four cases with novel coronavirus pneumonia receiving combined chinese and western medicine treatment call to action: announcing the traditional, complementary and integrative health and medicine covid- support registry big data opportunities for global infectious disease surveillance taking connected mobile-health diagnostics of infectious diseases to the field point-of-care diagnostics: recent developments in a connected age innovation in sexually transmitted disease and hiv prevention: internet and mobile phone delivery vehicles for global diffusion use of a mobile application for ebola contact tracing and monitoring in northern sierra leone: a proof-of-concept study smartphone applications to support tuberculosis prevention and treatment: review and evaluation. jmir mhealth uhealth , , e real-time tracking of self-reported symptoms to predict potential covid- rapid implementation of mobile technology for real-time epidemiology of covid- estimate of the basic reproduction number for covid- : a systematic review and meta-analysis the reproductive number of covid- is higher compared to sars coronavirus a community letter regarding sharing biomolecular simulation data for covid- ten deadly cyber security threats amid covid- pandemic covid- contact tracing and privacy: studying opinion and preferences. arxiv contact tracing mobile apps for covid- : privacy considerations and related trade-offs. arxiv stiller, b. wetrace-a privacy-preserving mobile covid- tracing approach and application. arxiv #covid- on twitter: bots, conspiracies, and social media activism. arxiv social distancing during the covid- pandemic: staying home save lives inter nation social lockdown versus medical care against covid- , a mild environmental insight with special reference to india covid- and mental health: a review of the existing literature beat covid- through innovation protecting health-care workers from subclinical coronavirus infection the role of additive manufacturing and antimicrobial polymers in the covid- pandemic angiotensin-converting enzyme coated nanoparticles containing respiratory masks, chewing gums and nasal filters may be used for protection against covid- infection telehealth for global emergencies: implications for coronavirus disease (covid- ) lessons for the future telemedicine in the era of covid- artificial intelligence: who is responsible for the diagnosis? robotic-assisted surgery for primary or recurrent oropharyngeal carcinoma evaluation of an ultraviolet room disinfection protocol to decrease nursing home microbial burden, infection and hospitalization rates handling, and testing clinical specimens from persons under investigation (puis) for coronavirus disease this article is an open access article distributed under the terms and conditions of the creative commons attribution (cc by) license the authors declare no conflict of interest.diseases , , key: cord- -rsnzyheu authors: hu, yuli; wang, lan; hu, sanlian; fang, fang title: prevention of fogging of protective eyewear for medical staff during the covid- pandemic date: - - journal: j emerg nurs doi: . /j.jen. . . sha: doc_id: cord_uid: rsnzyheu nan one medical staff member became infected despite wearing protective equipment and an n mask; the initial manifestation was unilateral conjunctivitis, which was followed by fever a few hours later. many studies have noted the importance of wearing goggles to protect the eyes from coronavirus infection when in contact with patients. - through interviews with medical staff at our hospital in wuhan, china, we learnt that fogging of goggles was a problem when caring for covid- patients. fogging impairs vision, thus hindering work efficiency when nurses collect blood, for example. this may lead to failure to collect blood properly, or clinical characteristics of coronavirus disease in china a novel coronavirus from patients with pneumonia in china of novel coronavirus-infected pneumonia world health organization work experience of front line nurses from ) . national health commission's briefing on the pneumonia epidemic situation ocular screening in severe acute respiratory syndrome novel coronavirus disease (covid- ): the importance of recognising possible early ocular manifestation and using protective eyewear world health organization. infection prevention and control during health care when novel coronavirus (ncov) infection is suspected. interim guidance the epidemics of myopia aetiology and prevention lack of middle east respiratory syndrome coronavirus infection in thailand application effect of several anti-fogging methods on medical anti-fog skills for medical goggles during the period of prevention and control of coronavirus disease two simple methods dealing with the problem of fogged goggles during the protection against coronavirus disease ling lie etal. the anti-fogging treatments of medical goggles during the covid- the experience of using goggles the observation of the application and effect of using different anti-fogging methods in the intensive care isolation units during covid- the anti-fogging application of the antibacterial hand gel to the reuse goggles during the protection against covid- not applicable. key: cord- -gyvvcnuf authors: fallahi, hamid reza; keyhan, seied omid; zandian, dana; kim, seong-gon; cheshmi, behzad title: being a front-line dentist during the covid- pandemic: a literature review date: - - journal: maxillofac plast reconstr surg doi: . /s - - - sha: doc_id: cord_uid: gyvvcnuf coronavirus is an enveloped virus with positive-sense single-stranded rna. coronavirus infection in humans mainly affects the upper respiratory tract and to a lesser extent the gastrointestinal tract. clinical symptoms of coronavirus infections can range from relatively mild (similar to the common cold) to severe (bronchitis, pneumonia, and renal involvement). the disease caused by the novel coronavirus ( -ncov) was called covid- by the world health organization in february . face-to-face communication and consistent exposure to body fluids such as blood and saliva predispose dental care workers at serious risk for -ncov infection. as demonstrated by the recent coronavirus outbreak, information is not enough. during dental practice, blood and saliva can be scattered. accordingly, dental practice can be a potential risk for dental staff, and there is a high risk of cross-infection. this article addresses all information collected to date on the virus, in accordance with the guidelines of international health care institutions, and provides a comprehensive protocol for managing possible exposure to patients or those suspected of having coronavirus. since the first reported case in wuhan, china, in december , coronavirus disease- has widely spread to japan, korea, iran, and many european countries [ ] . the world health organization (who) declared a pandemic in march . as saliva is a main tool of spread, dentists are in danger of contracting covid- . although the exact nature of this disease must be clarified in detailed studies, current knowledge of coronavirus infection should be shared without any restrictions. this article was written by an iranian team of oral and maxillofacial surgeons. as iran has many covid- patients, they have significant experience with this disease. maxillofacial plastic and reconstructive surgery is an open-access journal, and this type of important information can be shared via our publication platform without restrictions. coronaviruses are enveloped viruses with a positivesense single-stranded rna genome. their helical symmetry nucleocapsid is approximately - kb in size, making it the largest investigated genome among rna viruses [ , ] . coronaviruses have a fundamental resemblance in their organization and genome expression [ ] . previously, it was thought that coronaviruses only cause enzootic infections in a number of animals, including certain birds and mammals, but recent findings indicate that a variety of these viruses, including antigenic groups ( e and nl ), antigenic groups (oc ), and hku , can infect humans [ , ] . these viruses often lead to upper respiratory tract infection, frequently resulting in common cold symptoms. three specific strains of these viruses that are of zoonotic origin, including severe acute respiratory syndrome coronavirus (sars-cov), middle east respiratory syndrome coronavirus (mers-cov), and novel coronavirus ( -ncov), have recently caused lethal infections in humans [ , , ] . coronavirus infections in humans mainly affect the upper respiratory tract and to a lesser extent the gastrointestinal tract. manifestations of coronavirus infections can range from relatively mild (similar to the common cold) to severe (bronchitis, pneumonia, and renal involvement) [ ] (table ) . the ability to infect humans is mainly due to the infection of peridomestic animals, which are considered intermediate hosts, nurturing recombination and mutation events as well as the development of genetic diversity among coronaviruses [ ] . studies have suggested that the spike glycoprotein (s glycoprotein) plays an important role in host range restriction by attaching virions to the host cell membrane [ ] . generally, coronaviruses primarily replicate in the respiratory and intestinal epithelial cells and subsequently cause cytopathic alterations [ ] . since december , numerous unexplained cases of pneumonia have been reported in china. the disease caused by -ncov was called covid- by the who in february [ ] . limiting the exposure of suspicious cases to the rest of society could be an effective strategy in the early outbreak phases. however, the subsequent worldwide virus spread and person-to-person transmission made the situation more complex and uncontrollable [ ] . no detailed studies have been conducted to expound the pathogenicity of -ncov on a molecular scale. however, exploratory data established via whole-genome sequencing and subsequent bioinformatics analyses revealed that -ncov is phylogenetically related to sars-cov that was isolated for the first time in chinese horseshoe bats between and [ ] [ ] [ ] . to a large extent, the clinical similarities of -ncov infection with sars-cov infection are substantial. the incubation period of -ncov has been estimated to be - days, and it has been shown that asymptomatic individuals may also be involved in the spread of this virus [ ] [ ] [ ] . since the possibility of the transmission from asymptomatic carriers has been raised currently, checking body temperature only may not be enough to screen asymptomatic carriers. according to a recent report, temperature-based screening in the airport can detect only % of -ncov carriers and the others were found during the self-isolation period after immigration [ ] . to suppress the disease spread, a wide range of laboratory tests for immigrants and general population seems to be necessary. however, the infection rate from asymptomatic carriers has not been clarified until now. the primary non-specific reported symptoms of -ncov infection at the prodromal phase are malaise, fever, and dry cough. the most commonly reported signs and symptoms are fever ( %), cough ( %), dyspnea ( %), and myalgia or fatigue ( %) [ , ] . unlike patients with other human coronavirus infections (such as sars-cov), upper respiratory tract and intestinal manifestations such as sore throat, rhinorrhea, and diarrhea in those with -ncov infection are infrequent [ , , ] (fig. ). the patient mean age is generally between and years. studies have shown that males are more likely to have this infection [ , , ] . the lack of serious illness in youngsters is a characteristic of sars-cov infection, which is similarly observed in -ncov infection [ ] . increased exposures to -ncov due to occupational requirements, for instance health care workers, maybe another factor contributing to the higher risk of infection. following the outbreak, the full -ncov genomic sequence was released in public databases [ ] . this facilitates the way for further pcr assays for virus detection. the who recommendations for outpatient cases and patients with more critical conditions respectively include rapid collection and nucleic acid amplification testing (naat) of respiratory samples including nasopharyngeal and oropharyngeal swabs as well as sputum and/or endotracheal aspirate or bronchoalveolar lavage [ ] . table presents recommended instructions that all practitioners in the field of dental care, including dentists, assistants, and others, should consider when treating patients or those suspected of having coronavirus. protocol figure shows a protocol that can organize our approach to managing suspected or infected patients. the purpose of this protocol is to protect the entire dental care team, prevent any cross-infection in the office, inform health authorities active in the field of controlling and managing the disease, and ultimately provide the optimal medical and dental care for patients affected by the virus according to the cdc and the ada guidelines. the two main routes known for -ncov transmission include ( ) direct transmission (through coughing, sneezing, and inhalation of droplets) and ( ) contact transmission (through contact with nasal, oral, and ocular mucosa) [ ] . typical clinical manifestations of covid- do not comprise ocular symptoms. however, conjunctival sample analysis has revealed that the transmission of -ncov is not limited to the respiratory tract route [ ] , but ocular exposure is also an effective method of virus transmission [ ] . moreover, studies have revealed that via direct/indirect contact or course and/or droplets, respiratory viruses such as -ncov may be transmitted from human to human. studies have also shown direct and indirect transmission of -ncov through saliva [ ] . for a comprehensive understanding of the transmission dynamics of -ncov, it is also important to know that this virus is also transmissible through asymptomatic patients [ ] . the remarkable feature of -ncov is that its rna is detectable via quantitative reverse transcriptase polymerase chain reaction (qrt-pcr) in stool samples after the first week of infection [ ] . however, the aerosol and fecal-oral transmission routes, which carry more public concern, still need further investigation and confirmation [ ] (fig. ) . new evidence suggests that -ncov may be transmitted directly from human to human via respiratory secretion containing droplets [ , ] . virus transmission through contact and fomites is also likely [ , ] . to et al. [ ] reported that using the viral culture [ ] . since -ncov effectively uses ace receptor for cell invasion, it can promote human-tohuman transmission [ ] . ace + cells are abundantly present all over the respiratory tract. ace + epithelial cells present in the salivary glands were considered one of the main targets of sars coronavirus infection. similarly, -ncov may also use the same mechanism to induce infection, although definitive judgment regarding this issue needs further study [ ] . due to close face-to-face contact with patients and frequent utilization of sharp devices, dental personnel are repeatedly exposed to respiratory tract secretions, blood, saliva, and other contaminated body fluids and are always at risk for -ncov infection. -ncov transmission in dental settings occurs through four major routes: ( ) direct exposure to respiratory secretions containing droplets, blood, saliva, or other patient materials; ( ) indirect contact with contaminated surfaces and/or instruments; ( ) inhalation of suspending airborne viruses; and ( ) mucosal (nasal, oral, and conjunctival) contact with infection-containing droplets and aerosols that are propelled by coughing and talking without a mask [ ] [ ] [ ] [ ] [ ] (fig. ) . the most important concern in dental clinics is the transmission of -ncov via droplets and aerosol because, despite all of the precautions taken, it is almost impossible to reduce droplet and aerosol production to zero during dental procedures [ ] . dental handpieces utilize high-speed gas to rotate with running water, which leads to the generation of a considerable amount of droplets and aerosol mixed with patients' saliva and/ or blood [ ] . therefore, it can be deduced that -ncov is capable of transmitting through dental practice; this transmission can be from patients to clinic staff or other patients at the clinic [ ] . research has shown that coronaviruses can remain on metal, glass, and plastic surfaces for several days [ , ] . therefore, as surfaces in dental clinics serve as venues for droplets and aerosol mixed with patients' saliva and/ or blood, they can effectively help spread infection. coronaviruses can actively maintain their virulence at room temperature from h up to days. their activity at % humidity was significantly higher than %. therefore, in the dental environment, it seems that keeping surfaces clean and dry will play a significant role in preventing -ncov transmission [ ] . table standard precautions based on cdc and ada guidelines for dentists on the coronavirus disease [ ] [ ] [ ] postponing following the announcement of disease outbreak by international or local authorities, dentists can play a significant role in disrupting the transmission chain, thereby reducing the incidence of the disease by simply postponing all non-emergency dental care for all patients. where to treat all dental care should be provided in an outpatient dental setting with a minimum of six air changes per hour, such as a hospital with dental care services or customized clinics equipped for covid- patients. primary non-specific reported symptoms of -ncov infection at the prodromal phase are malaise, fever, and dry cough. the most commonly reported signs and symptoms are fever ( %), cough ( %), dyspnea ( %), and myalgia or fatigue ( %). they also may have traveled to one of the countries considered disease hotspots in the prior days or have encountered people from those countries or people who have traveled to those countries. some patients may be asymptomatic or have unexpected symptoms such as diarrhea. since it is not possible to know the etiology of each patient's illness, it is crucial to follow the guidelines and precautions at all times during the disease outbreak. be alert, identify patients with respiratory illnesses, and provide them a disposable surgical face mask. isolate them in a room with the door closed. limit their direct contact with others. isolated patients must wear masks outside their room. isolate suspected patients before and during care to minimize their direct contact with other patients and staff and immediately report any cases to local and state public health authorities. to prevent -ncov transmission, dental practices should adhere to the infection control protocol, including hand hygiene, providing tissues and no-touch receptacles, and providing face masks for coughing patients. dental health care personnel should wear white coats, gowns, head caps, goggles, face shields, masks, latex gloves, and impermeable shoe covers to prevent exposure. disposable masks should be substituted between patients or even during treatment if they get wet. since covid- recommendations may change rapidly with increasing information about the disease, the ada recommends checking for updates on the cdc's coronavirus infection control web page for health care professionals. the cdc strongly recommends that all health care staff, including dentists and personnel, should receive the flu vaccine and that staff with influenza must not report to work. since the fecal-oral route is considered one of the -ncov transmission routes, attention to hand hygiene before, during, and after dental practice is important. dentists should exercise extreme caution to avoid contact with their own facial mucosal surfaces including their eyes, mouth, and nose. since transmission of airborne droplet is considered one of the main routes of infection spread, application of personal protective equipment such as masks, protective goggles, gowns, helmet, gloves, caps, face shields, and shoe covers is strongly recommended for all health care personnel. covid- patients should not be treated in a regular dental care setting without special considerations. unexpected circumstances may occur when the dentist cannot delay treatment or refer the patient to the appropriate medical institution. under such circumstances, special protective clothing such as hazardous materials (hazmat) suits are required. if hazmat suits are not available, white coats, gowns, head caps, protective eyewear, face shields, masks, latex gloves, and virus-proof shoe covers should be used [ ] . the effect of chlorhexidine, which is commonly used for pre-procedural mouth washing in dental practice, has not yet been demonstrated to be capable of eliminating -ncov. however, oxidative agents containing mouth rinses with % hydrogen peroxide or . % povidone-iodine are recommended. pre-procedural use of mouthwash, especially in cases of inability to use a rubber dam, can significantly reduce the microbial load of oral cavity fluids [ ] . using rubber dams due to the creation of a barrier in the oral cavity effectively reduces the generation of droplets and aerosol mixed with patient saliva and/or blood in m diameter of the surgical field by % [ ] . following the placement of the dam, extra high-volume suction is also required for maximum prevention of aerosol and spatter from spreading [ ] . if it is not possible to use rubber dams for any reason, manual tools such as carisolvs or hand scalers are preferable. throughout the covid- pandemic, the use of any dental handpieces that do not have an anti-retraction function should be avoided. for emergency treatment, anti-retraction handpieces designed with anti-retractive valves can play an effective role in preventing the diffusion and dispersion of droplets and aerosol [ , ] . since there is still little information available regarding -ncov, relatively similar genetic features between -ncov and sars-cov indicate that the novel coronavirus can be vulnerable to disinfectants such as sodium hypochlorite ( ppm or . % for surfaces and , ppm or % for blood spills), . % hydrogen peroxide, - % ethanol, and phenolic and quaternary ammonium compounds if utilized in accordance with the manufacturer's instructions. studies show that other biocidal agents such as . - . % benzalkonium chloride or . % chlorhexidine digluconate probably have lower efficiency. in addition to the type of disinfectant, paying attention to other factors such as the duration of use, dilution rate, and especially the expiration time following the preparation of the solution according to the manufacturer's instructions is also crucial. prior to any inappropriate accumulation, dental office waste should be routinely transported to the institution's temporary storage facility. reusable tools and equipment must be properly pre-treated, cleaned, sterilized, and properly stored until the next use. dental waste resulting from the treatment of suspected or confirmed -ncov patients is considered medically infectious waste that must be strictly disposed of in accordance with the official instructions using double-layer yellow medical waste package bags and "gooseneck" ligation. following the announcement of the disease outbreak by international or local authorities, dentists can play a significant role in disrupting the transmission chain, thereby reducing the incidence of disease by simply postponing all non-emergency dental care for all patients. dental professionals must be fully aware of -ncov spreading modalities, how to identify patients with this infection, and, most importantly, self-protection considerations. the effect of chlorhexidine, which is commonly used for preprocedural mouth washing in dental practice, has not yet been demonstrated to be capable of eliminating -ncov. however, the prescription of oxidative agents containing mouth rinses such as % hydrogen peroxide or . % povidone is recommended. a higher rate of virus exposure because of occupational commitments in health care workers is considered a key factor associated with the increased risk of infection. yen my et al asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus (sars-cov- ): facts and myths homology-based identification of a mutation in the coronavirus rnadependent rna polymerase that confers resistance to multiple mutagens coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus epidemiology, genetic recombination, and pathogenesis of coronaviruses coronavirus envelope protein: current knowledge the novel coronavirus: a bird's eye view recently discovered human coronaviruses medical reviews coronavirus e-related pneumonia in immunocompromised patients epidemiological and clinical features of human coronavirus infections among different subsets of patients isolation and characterization of current human coronavirus strains in primary human epithelial cell cultures reveal differences in target cell tropism coronavirus as a possible cause of severe acute respiratory syndrome epidemiological, demographic, and clinical characteristics of cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study severe acute respiratory syndrome (sars) multiple organ infection and the pathogenesis of sars a cluster of cases of severe acute respiratory syndrome in hong kong clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study a novel pancoronavirus rt-pcr assay: frequent detection of human coronavirus nl in children hospitalized with respiratory tract infections in belgium human coronavirus nl infection in canada croup is associated with the novel coronavirus nl middle east respiratory syndrome coronavirus: a case-control study of hospitalized patients clinical course and outcomes of critically ill patients with middle east respiratory syndrome coronavirus infection epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan clinical characteristics of coronavirus disease in china incubation period of novel coronavirus ( -ncov) infections among travellers from wuhan, china coronavirus infections-more than just the common cold host factors in coronavirus replication. in: roles of host gene and non-coding rna expression in virus infection understanding of covid- based on current evidence transmission of -ncov infection from an asymptomatic contact in germany a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster genomic characterization and infectivity of a novel sars-like coronavirus in chinese bats risk of hepatitis b virus transmission via dental handpieces and evaluation of an antisuction device for prevention of transmission the severe acute respiratory syndrome chinese researchers reveal draft genome of virus implicated in wuhan pneumonia outbreak laboratory testing of novel coronavirus ( -ncov) in suspected human cases: interim guidance ada releases coronavirus handout for dentists based on cdc guidelines: american dental association cdc reminds clinicians to use standard precautions, recommends isolating patients with coronavirus symptoms: american dental association maxillofacial plastic and reconstructive surgery novel coronavirus: american dental association -ncov transmission through the ocular surface must not be ignored consistent detection of novel coronavirus in saliva ocular tropism of respiratory viruses first case of novel coronavirus in the united states transmission routes of -ncov and controls in dental practice going global-travel and the novel coronavirus functional assessment of cell entry and receptor usage for lineage b β-coronaviruses a pneumonia outbreak associated with a new coronavirus of probable bat origin epithelial cells lining salivary gland ducts are early target cells of severe acute respiratory syndrome coronavirus infection in the upper respiratory tracts of rhesus macaques persistence of coronaviruses on inanimate surfaces and its inactivation with biocidal agents pathogenicity and transmissibility of -ncov-a quick overview and comparison with other emerging viruses transmission of blood-borne pathogens in us dental health care settings: update aerosols and splatter in dentistry: a brief review of the literature and infection control implications transmission routes of -ncov and controls in dental practice transmission of sars and mers coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination transmission routes of -ncov and controls in dental practice office of state administration of traditional chinese medicine. notice on the issuance of a program for the diagnosis and treatment of novel coronavirus ( -ncov) infected pneumonia (trial version ) the efficacy of rubber dam isolation in reducing atmospheric bacterial contamination severe acute respiratory syndrome and dentistry: a retrospective view publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations maxillofacial plastic and reconstructive surgery prof. esmaeil yazdi passed away due to coronavirus infection few days ago. he was one of the iranian society of omfs founder years ago. the authors send sincere condolence to his family and colleagues. the authors also appreciate his great contribution on the progress of maxillofacial surgery. the article was written by hrf and bc. dz collected the data. illustrations were drawn by sok and bc. sok and ksg corrected the article and performed the critical review. the authors read and approved the final manuscript. not applicable.availability of data and materials not applicable.ethics approval and consent to participate not applicable. consent for publication not applicable. the authors declare that the authors have no competing interests as defined by nature research or other interests that might be perceived to influence the results and/or discussion reported in this paper. key: cord- - kq u a authors: keyhan, seied omid; fallahi, hamid reza; cheshmi, behzad title: dysosmia and dysgeusia due to the novel coronavirus; a hypothesis that needs further investigation date: - - journal: maxillofac plast reconstr surg doi: . /s - - - sha: doc_id: cord_uid: kq u a nan dysosmia and dysgeusia due to the novel coronavirus; a hypothesis that needs further investigation seied omid keyhan , , , hamid reza fallahi , and behzad cheshmi * coronaviruses are known as enveloped viruses with a positive-sense single-stranded rna genome that their helical symmetry nucleocapsid is about - kilobases in size, making it the largest investigated genome among rna viruses. the disease caused by new coronavirus ( -ncov) was named coronavirus disease- (covid- ) by the world health organization in february . the -ncov is phylogenetically related to severe acute respiratory syndrome-coronavirus (sars-cov) [ ] . it has been shown that -ncov enters the cell through the ace cell receptor in the same way as the severe acute respiratory syndrome (sars) coronavirus [ ] . -ncov effectively uses angiotensinconverting enzyme receptor (ace ) as a receptor for cell invasion [ ] . primary non-specific reported symptoms of -ncov infection at the prodromal phase are malaise, fever, and dry cough. the most commonly reported signs and symptoms are fever ( %), cough ( %), dyspnea ( %), and myalgia or fatigue ( %) [ ] . our information on the probability and effect of -ncov on the peripheral and central nervous system is still scarce and therefore unreliable. there have been various studies evaluating coronavirus's effects on the central nervous system. these studies suggest that the human central nervous system (cns) may be susceptible to coronavirus infection [ ] . routes intended for central nervous system infection with coronaviruses are peripheral trigeminal or olfactory nerves following intranasal inoculation [ , ] . the findings of studies on rodents show that these viruses cause demyelination and stimulate t cell-mediated autoimmune reactions against cns antigens producing the question about the relation between coronaviruses especially the -ncov and neurologic disorder in humans. given that the peripheral trigeminal or olfactory nerves are pathways of penetration of the coronaviruses into the central nervous system, and based on animal studies, it may be hypothesized that complications such as demyelination and stimulation of t cell-mediated autoimmune reactions may occur in the path of the infection spreading, so the occurrence of dysosmia and dysgeusia can be considered potential consequences of these nerve injuries. numerous reports of loss of sense of smell and taste have been received from iranian people as one of the most heavily involved countries with covid- during the outbreak of the disease [ , ] . significant numbers of people with confirmed covid- also reported a complete or partial loss of their sense of smell and taste in the early stages. initial investigations also indicate that in some cases, if one member of a family has experienced such symptoms, other family members have experienced similar symptoms over a short period of time. another primary point that needs further investigation is that in confirmed covid- patients with reported dysosmia and dysgeusia, often, other manifestations were less severe and the patients frequently recovered more quickly. in addition to what has been said that require further investigations to establish their validity, the timeliness or permanence of these complications, as well as how they are likely to be managed and treated, are of particular importance and require thoughtful scrutiny. although there is not sufficient evidence to make a definitive judgment and need more comprehensive investigations, two scenarios are more likely to be suggested as the cause of such an incident. the appearance of dysosmia and dysgeusia whether can be attributed to olfactory nerve and trigeminal nerve damage caused by the -ncov infection or excessive exposure to chemicals and disinfectants that are more commonly used by people due to the viral epidemic. designing a study to assess the validity of such a hypothesis is important in that it can be considered a relatively acceptable diagnostic criterion for both the individual and the physicians. since the existence of such a relationship is likely, it also seems likely that during the covid- outbreak, those who experience complications such as dysosmia and dysgeusia should be considered potential carriers of the virus and that in addition to necessary hygiene measurements, they must quarantine themselves. the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- functional assessment of cell entry and receptor usage for lineage b β-coronaviruses a pneumonia outbreak associated with a new coronavirus of probable bat origin epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study coronavirus infection of the central nervous system: host-virus stand-off susceptibility of laboratory mice to intranasal and contact infection with coronaviruses of other species effect of olfactory bulb ablation on spread of a neurotropic coronavirus into the mouse brain loss of sense of smell among iranians coinciding with coronavirus epidemic olfactory disorder getting prevalent in iran amid coronavirus outbreak all authors contributed substantially to the conception and design of the paper, the acquisition of data, or the analysis and interpretation. bc as the corresponding author verifies that all individuals who made contributions to this study are included either as authors or are acknowledged at the end of the paper. the authors read and approved the final manuscript. this research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. the author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.author details national advance center for craniomaxillofacial reconstruction, tehran, iran. craniomaxillofacial research center, tehran university of medical sciences, key: cord- -rembksdr authors: talwar, shivangi; sood, shivani; kumar, jayant; chauhan, ritu; sharma, mamta; tuli, hardeep singh title: ayurveda and allopathic therapeutic strategies in coronavirus pandemic treatment date: - - journal: curr pharmacol rep doi: . /s - - - sha: doc_id: cord_uid: rembksdr purpose of review: in the last month of , i.e., december, covid- hit wuhan city in china. since then, it has infected more than countries and nearly about . million people with one million deaths globally. it is a viral disease with flu-like symptoms; hence, prevention and management is the best option to be adopted for its cure. recent findings: many healthcare systems, scientists, and researchers are fighting for the cure of this pandemic. ayurvedic and allopathic treatments have been studied extensively and approached for the cure of covid- . in addition to ayurvedic treatments, the ministry of ayush, india, has also recommended many remedies to boost up immunity. allopathic studies involved several antiviral drugs which were used in different combinations for the treatment of covid- . summary: comparative analysis of ayurveda and allopathic treatment strategies were carried out in the present study. depending upon the patient’s conditions and symptoms, ayurveda is useful for the treatment of covid- . allopathic treatments inhibit viral infection by targeting majorly endocytosis, and angiotensin-converting enzyme (ace) receptor signaling. in this article, we summarize different ayurvedic and allopathic medicines and treatment strategies which have been used for the treatment of covid- , a global pandemic. in the last decade, different strains of coronaviruses had presented with challenging health issues to human society. the most popular viruses in this category are severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov). with an increase in the population, migration, and social life, these viruses showed an increased rate in the recombination of intra-and inter-species which made them adapt to every recent host [ ] . in , sars-cov was one of the most dangerous emergencies in the world for human infection. in its initial stage of infection, it infected nearly humans with major cases. the severe acute respiratory syndrome coronavirus (sars-cov- ) emerged in in the month of december in wuhan city of china, which again made the life of humans miserable with numerous fatal health issues and slowly and gradually this virus entrapped the whole world [ , ] . the crown-shaped coronavirus leads to serious infections which was a brief part of the human sars virus and affected the whole world which leads to a loss in business, tourism, and human life [ ] . by the end of february and the start of march , sars-cov- was declared as an international pandemic by the world health organization (who). the symptoms of this infection were similar to that of normal flu but included different categories like patients with mild symptoms, asymptomatic patients with no symptoms, and high symptomatic patients. before the doctors, scientists, and researchers could study and come up with a cure for treatment, this virus had already infected more than lakhs of people across the world with the human coronavirus pathogens, i.e., hcov- e and hcov-oc , which affects the upper respiratory tract. in , the other novel pathogen of humans which were diagnosed during the sars-cov pandemic in the netherlands included cov-nl and hcov-hku . this cov-nl (group i) infected children suffering from bronchiolitis and the hcov-hku (group ii) virus infected the adults in hong kong with chronic pulmonary infection. in september , the who diagnosed another coronavirus which was mers-cov, which speeded up in a deadly manner in the middle east, south asia, and africa and more than % of cases were diagnosed in saudi arab. it was identified that the family line of this virus is group betacoronavirus, i.e., tylonycteris bat coronavirus hku (bat-cov hku ) whose primary host is bats and hku -covs pathogen whose primary host is pipistrellus bats which are single-stranded positive rna bat viruses which are widely distributed during the coronavirus pandemic and very close to humans for infection [ ] [ ] [ ] [ ] . bats were the primary host and act as a repository for causing infections not only in sars-cov, but were also a causative agent in the mers cov. additionally, camels were also suspected as a source of infection within the crossed species hindrance to contaminate people [ ] . so it was remarked as bats are the significant supplies of various alpha coronaviruses and its ancestry of different beta coronaviruses [ ] . in china, the common repository of the sars viruses was the horseshoe bats, but bats being the definitive cause of the mers virus species were yet to be discovered [ ] . sars-cov virus is a ribonucleic acid-containing infectious agent, which is transferable from vertebrates to animals. sars-cov infection is mainly developed in people through social contact and migration [ ] . the viral genome has a basic protein named replicase which helps in the replication of the genetic genome in the host cell and is methylated at the ′ end and the polyadenylated tail at ′ end because of which the genetic material gets connected to the ribosome's and then replication starts [ ] . on the other hand, there is a non-basic protein known as protease, used for the isolation of the proteins present in the chain [ , ] which helps in the formation of different types of cytokines that leads to the production of lymphocytes. these lymphocytes act as a barrier and prevent viral genome from replicating which results in an increase in the inflammatory reactions [ ] . this coronavirus is an enormous group with severe infections causing the symptoms like regular cold, fever, and respiratory disorders (shortness of breath), which helps the virus to propagate and leads to the replication and transmission. the basic symptom is common cold, which led to the discovery of six wellknown different species of coronaviruses which were first distinguished from the patients in the s [ ] [ ] [ ] [ ] . the incubation period of this virus is around about . days including the range of almost . to . days [ ] . it is recommended by doctors and health organizations that coronavirus lasts for about days which is the maximum time period and special precautions should be taken like social distancing, sanitization, self-quarantine, and wearing of masks and gloves [ ] . the main target site for this crucial pathogenesis of the sars-cov includes the respiratory system and the main diseases which are related to heart injuries and anemia. the data records received from different hospitals across the world observed that by the end of and at the start of june , it was reported that the covid- crisis leads to patients with the higher plasma level of proinflammatory cytokines like interleukin (il- ), il- , il- , il- , il- , interferons gamma (ifnγ), interferons alpha (ifnα), tumor necrosis factor alpha (tnfα), and transforming growth factor beta (tgfβ) [ ] . there are a large number of treatments and therapies available for this antiviral infection. but until now, there is no suitable vaccination for this pandemic but various pharmaceutical companies and researchers are working on it and human trials are going on. this short review summarizes the role of allopathic and ayurveda in coronavirus infections. each field plays an important role in their respective areas and will definitely prove fruitful in the early management of covid- patients. until now, there is no treatment for coronavirus but our government has issued management and precaution guidelines along with a supporting healthcare system which could provide great relief in the outbreak of covid- . many approaches like social distancing, wearing a mask, and medical grounds are used to control the pandemic disease. the main approach to regulate this disease was allopathic and ayurveda. from the last years in the late s, a german physician named dr. samuel hahnemann founded the homeopathy as a therapeutic medicine which helped to treat many epidemics, fearful, and severe diseases like cholera, fever, chikungunya, hepatitis, and malaria. the preventive measures of homeopathy are eminent and undeniable; as homeopathic medicines act remarkably on a health condition and cure the diseases. the scientific literature related to homeopathy is highly witnessed [ ] [ ] [ ] [ ] . there are numerous confirmations that in the year - , when spanish flu emerged, homeopathy had shown amazing results, during which around about million patients died around the world and about , , in the usa alone. a study revealed that there was a difference in the mortality rate among the patients which were treated by homeopathy and physicians, i.e., - % appeared differently as they were treated by homeopathy as compare to - % of patients who were treated by allopathic [ , ] . in homeopathic treatment, every patient after being fully diagnosed and analyzed received medicines. the medical grounds of homeopathy have a clear protocol of sanitation, antibiotics, and vaccinations to control the infections [ ] [ ] [ ] . in diseases like dengue which causes hemorrhagic fever, homeopathy has helped in improving the platelet count and therefore there is a slowdown in the clinical center for about - days [ ] . likewise, there are many diseases in which homeopathy has acted as a buffer or control to decrease the mortality rate by about - % conversely with the people who got simply institutional management. so, by looking at the past history, it can be observed that there are many instances in which homeopathy had shown extraordinary results and it can be equivalently used for the covid patients but no study has shown its effects on covid- . the homeopathic medicines like belladonna c, eupatorium perfoliatum q, grindelia, calcarea carb, chinimum sulph, bryonia, gelsemium, phosph orus, t hymulin, camph ora, influenzinum, antim tart, and a combination of few tinctures and homeopathic drugs prove to have a high rate of frequency to reduce severe pain, ache, and many more ailments in viral diseases [ ] . there were numerous people who were infected by the virus and showed progressive circulation in their history in china's wuhan village in december [ ] . the name of the homeopathic therapies was previously reported to prevent viral infections that are presented henceforth [ ] [ ] [ ] [ ] . arsenicum album is formed when for continuously - days arsenic is heated with distilled water. on the basis of the fact sheet released by the ccrh (central council for research in homeopathy), arsenicum album can be considered as "prophylactic medicine" covid- [ ] . the inflammatory symptoms shown by covid- , arsenic toxicity, and hiv infection are the same and there is a definite synergy between them and may have the suitable potential to aggravate each other. therefore, arsenicum album may be considered as a suitable remedy for covid- treatment. arsenic is one of the constituents in it which showed its enumerating impact on the different macrophage cells as well on tumor cells. also, it showed decreased nf-κβ hyperactivity (nuclear factor kappalight-chain-enhancer of activated b cells; diminished verbalization of reporter quality of green fluorescent protein (gfp) in transfect ht cells) and decreased tnf-α (tumor necrosis factor-alpha) release in macrophages. arsenic album- was advised to be taken once in a day for days. the tincture of album- is arsenic trioxide which is highly diluted and it works to prevent disease [ ] . the proposed mechanism of action of arsenicum is shown in fig. . until now, there is no furthermore, for more than years, ayurveda, a sanskrit word, originated in india. nowadays, it is considered as a traditional system of medicine which helps in the management of infection and maintains the homeostasis of disease. it also helps in building the strength of the mind and soul, and teaches the body to fight against stress. during covid- , ayurveda is also playing an important role as it has enough possibilities and potential for the prevention of infection and treatment for corona victims. the asymptomatic cases in india help in implementing the role of ayurveda, through the regular use of ayurveda medicines and home remedies. but still, the confirmation imagined by traditional chinese medicine (tcm) cannot be disregarded in china [ , ] . this is directly understood that at the time of the pandemic, approximately tcm-related workers had been passed on to the hubei district. tcm was officially accepted by the chinese guideline on end and used as a cure for covid- [ , ] . this is especially important to observe that specific tcm wards were set up, and quarantine centers were developed which had used chinese drugs for treatment using western medication [ ] . with the accomplishment of tcm in controlling an infectious pandemic, it was reasonable and major to examine how ayurveda can help in treating covid- [ , ] . by this time, it was the ministry of ayush which created a standard to change indian social protection [ ] and to show the power of ayush to build up prosperity [ ] . with this ultimate objective of ayush, ayurveda during the covid- pandemic, people were divided into four specific classifications [ ] along with characters and natural herbs for treatment which is tabulated in table . this classification has huge necessary information which was complete and well managed. subsequently, it is advised that genuine information of factors that are important should be done on each case. these variables should incorporate age, sex, manifestations, topography, and contact history which results in a clear prescription and should be recorded. on the other hand, tcm did not control covid- cases. equivalent philosophy was also adopted and has been used in ayurveda and it should pursue its own skill for finding and coming about remedies optional on roga and rogi bala. in the allopathic approach, treatment in coronavirus included intravenous infusion of fluid, oxygen therapy, and life support chloroquine and hydroxychloroquine have a possibility of curing an intestinal disorder, systemic lupus erythematosus (sle), and rheumatoid joint torment (ra) [ ] . chloroquine and hydroxychloroquine obstruct glycosylation of host receptors, proteolytic, and maturation of endosomes. these mechanisms have immunomodulatory shocks to host cells by bringing down the cytokine level and control of autophagy and lysosomal [ , ••] . in vitro studies revealed that in the low micromolar concentration, chloroquine crushes sars-cov- with a halfmaximal credible center (ec ) and hydroxychloroquine with a lower ec for sars-cov- differentiated, i.e., ec = . μm and chloroquine: ec = . μm the treatment of covid- included the oral dosage of chloroquine ( mg) and hydroxychloroquine ( mg) on daily basis [ ] [ ] [ ] . but still, there is a lack of data which proves the mechanism of chloroquine and hydroxychloroquine. pharmacokinetic studies reviewed that the ideal dose of hydroxychloroquine for treating covid- patients should be replaced by mg twice instead of mg on daily basis [ ••] . unusually, elective outlines are made for mg of total dose step by step by dividing reliant on freedom and clinical experience for whipple's disease [ ] . the food and drug administration (fda), usa, recommended and certified lopinavir/ritonavir, an oral drug for hiv, with in vitro activity against other novel coronaviruses through the control of -chymotrypsin-like protease [ , ] . there is no in vitro study data for lopinavir/ritonavir against sars-cov- [ ] but a review on lopinavir/ritonavir was assessed for the treatment of sars and mers which showed clinical observations and analysis of sars with less mortality rate and incubation rates, along with experimental research. the studies revealed that drugs should be used during the early stages of viral replication, i.e., beginning - days; otherwise, late initiation with lopinavir/ritonavir had no effect on clinical outcomes [ , ] . a guanine basic drug named ribavirin handles viral ribonucleic-subordinate and polymerase whose activity against various coronavirus makes it a challenger for the treatment of the covid- outbreak. in vitro studies of this drug proved to show advancement against sars-cov by blocking the replication of the virus. this mechanism required a high dose of this drug, i.e., . to . g orally as expected along with blend treatment. past studies told that the patients got either endogenous or enteral cooperation [ ] and no data exists in its role with the respiratory syncytial disease in covid- [ ] . the trial on patients confessed questionable results in which out of examinations, were re-evaluated, with assessments exhibiting hematologic and liver toxicity [ ] . on the other hand, in the treatment of mers, ribavirin was mixed with interferons and its clinical studies resulted in no observable and remarkable effect on viral clearance [ , ] . due to a lack of clinical data with ribavirin for sars-cov- strategies, its supportive occupation must be extrapolated from other ncov data. remdesivir (other name gs- ) is a prodrug monophosphate which helps in the absorption of cadenosine nucleoside triphosphate. it was studied that the antimicrobial activity of this drug against rna proved to be contagions especially in the family of coronaviridae and flaviviridae. due to its low ec value, it proved to be therapeutic against the emergence of ebola virus disease based on its selectivity against host polymerase of ebola [ •] . because of broad reach, presently, remdesivir and its in vitro studies against coronavirus help in treating sars-cov- with ec and ec estimations of . μm and . μm, respectively, and are proved to be a fruitful expected treatment for covid- [ dexamethasone is a type of chemically derived corticosteroid which acts as an immunosuppressor. it abridged deaths by / in patients getting invasive mechanical ventilation and by / in patients being delivered oxygen without invasive mechanical ventilation. however, therapy did not decrease the death in patients not getting breathing support at randomization. therefore, dexamethasone abridged -day mortality among those getting invasive mechanical ventilation [ ••] . mechanistically, it inhibits the growth of the cytokines which cause infection and is therefore useful in this covid- -related hyperinflammation or cytokine storm. it has a high rate of activity and also lasts for a longer duration as compared to other cortisone [ ] [ ] [ ] [ ] [ ] [ ] . studies have shown that it is only useful in those cases where the condition of the patient is critical and cannot be used for the generalized treatment of all patients [ ] . the mode of action of various allopathic drugs is summarized in fig. . these above-discussed drugs mainly inhibit angiotensin-converting enzyme (ace ), endocytosis, non-structural protein c-like protease, and nonstructural proteins rna-dependent rna polymerase (rdrp) to stop viral infection and growth. covid- is considered as pandemic worldwide and spreading at an alarming rate. therefore, it has been essential to explore various strategies to overcome the effect of this dreadful viral disease. this review summarizes the utility of currently opted therapies for covid- . no suitable medicine is found to exist currently for this virus infection. the rapidly increasing patient's data of covid- is triggering scientific communities to come forward to develop some possible therapy. the most reassuring treatment is considered to be remdesivir. this drug is known to possess strong antiviral activity as proven by several in vitro studies. oseltamivir has not presented with suitability, and corticosteroids are at present not recommended. on the other hand, homeopathy and ayurveda may be promising, but not applicable towards all types of patients. therefore, the present study concludes that covid- infection can be prevented by following government guidelines and opting immune-boosting ayurveda routes. acknowledgments the authors want to thank maharishi markandeshwar (deemed to be university) for providing the requisite facility. we acknowledge dr. vaishali aggarwal, department of pharmaceutical sciences, university of pittsburgh, usa, for her guidance. human and animal rights and informed consent this article does not contain any studies with human or animal subjects performed by any of the authors. coronaviruses: emerging and re-emerging pathogens in humans and animals severe acute respiratory syndrome coronavirus-like virus in chinese horseshoe bats isolation and characterization of a bat sars-like coronavirus that uses the ace receptor isolation of a novel coronavirus from a man with pneumonia in saudi arabia comparative analysis of twelve genomes of three novel group c and group d coronaviruses reveals unique group and subgroup features genetic characterization of betacoronavirus lineage c viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus hku in japanese pipistrelle: implications for the origin of the novel middle east respiratory syndrome coronavirus middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease discovery of seven novel mammalian and avian coronaviruses in deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus bat origin of human coronaviruses origin and evolution of pathogenic coronaviruses homology-based identification of a mutation in the coronavirus rna-dependent rna polymerase that confers resistance to multiple mutagens coronaviruses: an overview of their replication and pathogenesis emergency committee regarding the outbreak of novel coronavirus ( -ncov) the immunopathogenesis of sepsis in elderly patients what's to know about coronaviruses clinical features of patients infected with novel coronavirus in wuhan epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china a descriptive study clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan incubation period of novel coronavirus ( -ncov) infections among travellers from wuhan, china the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application clinical management of covid- historical journey of homoeopathy during epidemic diseases in the light of novel coronavirus pandemic homeopathic prevention and management of epidemic diseases development of homoeopathic genus epidemicus for secondary level prevention of dengue virus infection at kannur, kerala the faces of homśopathy. articles on homeopathy homeopathy in influenza-a chorus of fifty in harmony homeopathic approach to covid- : a review research review of genus epidemicus genus epidemicus: are notions of entanglement relevant to the homeopathic understanding of epidemic disease? complementary medicine research effect of adjuvant homeopathy with usual care in management of thrombocytopenia due to dengue: a comparative cohort study effectiveness of homeopathic medicines as add-on to institutional management protocol for acute encephalitis syndrome in children: an open-label randomized placebo controlled trial first covid- case can be traced back to november in china' hubei province: report. the economic times advisory for corona virus homeopathic treatment of patients with influenza-like illness during the a/h n influenza pandemic in india role of homeopathic strategies to fight against viral infections) effect of individualized homoeopathic treatment in influenza like illness: a multicenter, single blind, randomized, placebo controlled study management of early years of simple and mucopurulent chronic bronchitis with pre-defined homeopathic medicines -a prospective observational study with -years follow-up cell sensitivity, non-linearity and inverse effects traditional chinese medicine for covid- treatment traditional chinese medicine for treatment of coronavirus disease national health commission of the people's republic of china. guidelines on diagnosis and treatment of covid covid- pandemic: a pragmatic plan for ayurveda intervention ayurveda rasayana in prophylaxis of covid- universal health coverage and ayush systems ayush research for new india: vision and strategies studying covid- in light of critical approaches to risk and uncertainty: research pathways, conceptual tools, and some magic from mary douglas activating immunity to fight a foe -a new path validation of environmental disinfection efficiency of traditional ayurvedic fumigation practices clinical effect of suvarna bindu prashan ayurvedic rasayana therapy: a rational understanding necessary for mass benefits chyawanprash: a traditional indian bioactive health supplement adaptogenic properties of six rasayana herbs used in ayurvedic medicine building bridges between ayurveda and modern science antioxidant activity of brahma rasayana charaka samhit chikitshyasthan- / . reprint. varanasi: chaukhambha bharati academy adverse effects of ayurvedic drugs: an overview of causes and possibilities in reference to a case of vatsanabha (aconite) overdosing possible correlates of free radicals and freeradical mediated disorders in ayurveda with special reference to bhutagni vyapara and ama at molecular level samhita: a treatise on ayurveda, madhyam khanda the ayurvedic formulary of india. vati prakarana evaluation of ocimum sanctum and tinospora cordifolia as probable hiv-protease inhibitors evaluation of some medicinal plants as putative hiv-protease inhibitors multi-target β-protease inhibitors from andrographis paniculata: in silico and in vitro studies. plants (basel) chemical characterization of an ayurvedic herbo-mineral preparation-mahalaxmivilas rasa a clinical study to evaluate the efficacy of pippali rasayana in certain respiratory disorders mast cell stabilization potential of sitopaladi churna: an ayurvedic formulation ayurveda in critical care: illustrating ayurvedic intervention in a case of hepatic encephalopathy efficacy of ayurvedic medicine in the treatment of uncomplicated chronic sinusitis nanotechnology in medicine: leads from ayurveda assessment of bioavailability of gold bhasma in human participants -a pilot study systematic review of treatment effects clinical outcomes of current medical approaches for middle east respiratory syndrome: a systematic review and metaanalysis effects of chloroquine on viral infections: an old drug against today's diseases? covid- : a recommendation to examine the effect of hydroxychloroquine in preventing infection and progression new insights on the antiviral effects of chloroquine against coronavirus: what to expect for covid- ? in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) chloroquine and hydroxychloroquine as available weapons to fight covid- national health commission and state administration of traditional chinese medicine. diagnosis and treatment protocol for novel coronavirus pneumonia role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture discovering drugs to treat coronavirus disease (covid- ) a systematic review of lopinavir therapy for sars coronavirus and mers coronavirus-a possible reference for coronavirus disease- treatment option treatment of severe acute respiratory syndrome with lopinavir/ritonavir: a multicentre retrospective matched cohort study sars: systematic review of treatment effects oral versus aerosolized ribavirin for the treatment of respiratory syncytial virus infections in hematopoietic cell transplant recipients ribavirin and interferon therapy for critically ill patients with middle east respiratory syndrome: a multicenter observational study adenine c-nucleoside (gs- ) for the treatment of ebola and emerging viruses remdesivir as a possible therapeutic option for the covid- remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov dexamethasone in hospitalized patients with covid- -preliminary report diabetes mellitus is associated with increased mortality and severity of disease in covid- pneumonia -a systematic review, meta-analysis, and meta-regression: diabetes and covid- hypertension is associated with increased mortality and severity of disease in covid- pneumonia: a systematic review, meta-analysis and meta-regression effect of chronic obstructive pulmonary disease and smoking on the outcome of covid- impact of cerebrovascular and cardiovascular diseases on mortality and severity of covid- -systematic review, meta-analysis, and meta-regression potential role of telemedicine in solving st-segment elevation dilemmas in remote areas during the covid- pandemic lymphopenia in severe coronavirus disease- (covid- ): systematic review and meta-analysis dexamethasone for covid- ? not so fast publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations key: cord- -u t h ri authors: dammeyer, jesper title: an explorative study of the individual differences associated with consumer stockpiling during the early stages of the coronavirus outbreak in europe date: - - journal: pers individ dif doi: . /j.paid. . sha: doc_id: cord_uid: u t h ri there is little existing research on why some people stockpile goods and others do not at a time of crisis. more research on this phenomenon and the individual differences associated with it is needed in order to gain a better understanding of what is a potentially economically and socially disruptive behavior. in this study, adult participants from denmark and from the united kingdom responded to a survey about the activity of extra shopping (stockpiling) during the first weeks of the coronavirus outbreak. questions exploring the “big five” personality traits, social dominance orientation, health literacy, and attitudes to the governmental response to the crisis were included in the survey. the explorative analysis showed that stockpiling was associated with high scores on extraversion and neuroticism, and low scores on conscientiousness and openness to experience. stockpiling was also associated with the view that the government should be doing more to stop the coronavirus epidemic. an explorative factor analysis of reasons for stockpiling identified the two factors “panic” and “action”. during the early stages of the coronavirus pandemic in europe, many countries experienced the phenomenon of consumer stockpiling of goods including food, cleaning and hygiene products, and medicines. this was reported in denmark (weirsøe, ) and the united kingdom (barr, ) , the research contexts of this study. such stockpiling of goods is potentially economically and socially disruptive, risking increased prices and scarcity of goods, with particular consequences for vulnerable groups such as the elderly. the objective of this study was to explore the psychological factors that might explain stockpiling. although stockpiling seems to be a common phenomenon in many countries at a time of crisis, there are only a few published studies on the topic and individual differences. sterman and dogan ( ) used the "beer distribution game" to study stockpiling (referred to as "hoarding" and "phantom ordering"). in the game, stockpiling was an objectively irrational gaming behavior, as there were no mechanisms of capacity constraint, competition, or randomness. nevertheless, they found stockpiling behavior among % of the participants. hori and iwamoto ( ) analyzed consumer data on "panic buying" in tokyo following the tohoku earthquake. of relevance for this study, they investigated the characteristics of the households that engaged in panic buying. they found that households with large number of family members, households in urban areas, and households comprising a middle-aged or older full-time homemaker wife were likely to engage in panic buying. one might think that compulsive buying or hoarding disorder might be related to stockpiling. however, whereas compulsive buying and hoarding are associated with depressive and anxiety disorders and impulse control difficulties (frost et al., ) , stockpiling seems to be different. in a qualitative study, kulemeka ( ) explored consumer habits before and during the hurricane season. it was observed that shoppers who engaged in hoarding and panic buying at this time did not show this behavior in the pre-hurricane season, when they were more organized and willing to assist others. few studies to date have investigated if individual differences explain why some people stockpile and others do not. one can hypothesize that, further to differences of age, gender, and educational level, some of the "big five" personality traits are linked to the tendency to stockpile at a time of crisis. people with high scores on neuroticism might be more likely to stockpile because of a stronger response to, and lower ability to cope with, a crisis situation. further, people who are low on agreeableness might have a stronger tendency to stockpile because of a heightened focus on their own needs rather than on a more co-operative and altruistic concern for others. it can be further hypothesized that people who are high on conscientiousness might stockpile in order to be well-prepared for the difficult situation to come. another individual difference of interest is social dominance orientation (sdo), which concerns attitudes towards hierarchical group relations and the desire to ensure that one's own group is dominant (pratto et al., ) . sdo can be seen on a continuum from high (endorsing hierarchy-enhancing ideologies, such as racism) to low (endorsing hierarchy-attenuating ideologies, such as anarchism) (e.g. perry et al., ) . sdo has mostly been researched in association with right-wing authoritarianism, political orientation, and prejudice (perry et al., ) , but it can also be hypothesized that a high sdo score is associated with a tendency to protect one's social group and therefore to stockpile in a time of crisis. health literacy is another factor of interest. this concerns an individual's health-related knowledge and motivation, and their competences to access, understand, appraise, and apply health information in order to make the best judgments and decisions concerning health (sørensen et al., ) . thus, health literacy is not only about knowledge but also about the emotional resources for motivating health relevant behavior and decisions. health literacy might help explain people's stockpiling behavior and it is hypothesized that low levels of health literacy are linked to stockpiling. people with low levels of health literacy are likely to find it more difficult to process healthrelated information and instructions conveyed through various media to stay home and not stockpile. it is known that, at times of crisis, some people stockpile consumer goods while others do not. the very limited research-based knowledge about the possible psychological factors involved calls for an explorative study on individual differences that might help explain the phenomenon. this study looks not only at gender, age, and educational level but also at personality traits, social dominance orientation, health literacy, attitudes to the government response, attitudes to stockpiling, and reasons for stockpiling. data were collected in the weeks just following the respective announcements by the danish and british governments of country-wide lockdowns due to the coronavirus outbreak and when most of the stockpiling or panic buying was reported. for the danish sample, the data collection period was th of march to th of april , and, for the british sample, the data collection period was th of march to th of april . social media forums including facebook and linkedin groups were used for data collection to generate sufficient responses in a relatively short timeframe. the invitation text invited people to participate in a research survey on behavioral responses to the coronavirus crisis. participants gave their informed consent to participate on the first page of the survey. no compensation was offered. the total number of responses was for the danish survey and for the united kingdom survey. participants who did not respond to the question on stockpiling were excluded, resulting in a danish sample of and a united kingdom sample of . see sample characteristics in table . next to gender, age, and level of educational attainment, participants were asked if they were living alone or with one person or more (see table for details). participants were asked: "how much extra shopping (e.g. for food, medicine, lavatory paper etc.) have you done in connection with the ongoing coronavirus outbreak?". response categories were: a lot ( ); some ( ); a little ( ); none at all ( ). a further question asked about attitudes towards extra shopping: "do you think it is ok for people to do extra shopping (e.g. for food, medicine, etc.) in connection with the ongoing coronavirus outbreak?" possible responses were: yes, it is ok ( ); a little extra is ok/it is ok for people with special needs ( ); no, it is not ok ( ). in preparation for the survey question on reasons for stockpiling, people were individually interviewed. the interviewees were all danish and recruited from a student cohort. they were asked: "please mention all the different reasons you can come up with that people may buy extra or stockpile in a crisis situation? think about yourselves and different people you know". the responses from the interviews were amalgamated, resulting in different statements of reasons that were all included in the survey (see the reasons in table ). the survey participants who reported stockpiling were asked to respond to the reasons on a likert scale from "strongly agree" ( ) to "strongly disagree" ( ). an explorative factor-analysis (fabrigar et al., ) was performed on the responses, which showed factors (eigenvalues > . ). a factor solution was also tested but did not show a simple structure or explain much more of the data variance (an additional . %). varimax rotation was used as factors were uncorrelated (fabrigar et al., ) . the two factors were labeled "panic" and "action" based on content (see table for details). the item "i was afraid that suddenly there would not be enough food, medicine etc." had the highest loading for panic ( . ), and "it felt good to be able to do something active in a crisis situation" had the highest loading for action ( . ). for further analysis in this study, sum scores of panic and action reasons for stockpiling were calculated. range - and low scores indicate agreement with the reason for stockpiling. the bfi- was used to measure the "big five" personality traits of extraversion, agreeableness, conscientiousness, neuroticism, and openness to experience. the bfi- has shown to have acceptable psychometric properties (rammstedt & john, ) . each trait is measured with two items, one reversely scored, on a -point likert scale. scoring for each item is the average of the reserved scored and normal scored item, resulting in a score between and . the sdo (s) measures, through items, an individual's attitudes towards social dominance (sdo-d) and anti-eligalitarism (sdo-e). each item is rated on a likert scale from "strongly oppose" ( ) to "strongly favor" ( ) (ho et al., ) . four items tap into each subscale, two normal scored and two reversed scored. sdo-d, sdo-e, and sdo total scores were used in the analyses. the hls-q was used to measure health literacy (pelikan & ganahl, ) . the items are rated on a scale from very difficult ( ) to very easy ( ). a sample item is: "…decide how you can protect yourself from illness based on information in the media?" a simple sum score is calculated and high scores indicate a high level of health literacy. participants were asked: "what do you think of the government's actions (e.g. closing down pubs) to stop the spread of coronavirus?" responses ranged from "much more is needed" ( ) to "it is far too much" ( ). "how serious do you think the coronavirus outbreak is for danish/uk society as a whole?" responses ranged from "extremely serious" ( ) to "not serious" ( ). a final question was: "do you have confidence in how the government and authorities are managing the coronavirus outbreak?" response categories were on a scale from "yes i have full confidence" ( ) to "no, i do not have confidence at all" ( ). all questions were proposed by the author. firstly, a descriptive analysis of frequency of stockpiling, reasons for stockpiling, and attitudes towards stockpiling were reported for each of the two countries. secondly, pairwise correlations between stockpiling and the individual differences and attitudes measures were analyzed. for all participants (danish and british), four out of ten ( . %) reported that they had not done extra shopping during the coronavirus outbreak crisis (see table for details). another four out of ten reported that they had shopped a little extra ( . %), two out of ten ( . %) reported doing some extra shopping, and . % reported that they done a lot of extra shopping. more of the british participants reported extra shopping; . % reported no extra shopping, whereas the figure for the danish participants was . %. for the total sample, about two out of ten ( . %) reported that it is "not ok" for people to do extra shopping. again, the figures were different for the two countries: . % of the danish sample compared to % of the british sample reported that it was "not ok" to do extra shopping. table shows associations between individual differences and doing extra shopping. a gender difference was found for action reasons for extra shopping, with women more likely to give this reasoning than men. no significant associations were found for age or living alone or with one person or more. high levels of educational attainment were associated with panic reasons for extra shopping. it should be noted here again that only those who reported doing extra shopping responded to the further questions on the reasons. table also shows associations between social dominance orientation and extra shopping. significant associations were found, with high scores on sdo-e and high total sdo scores associated with action reasons for extra shopping. finally, a low score on health literacy was associated with action reasons for extra shopping. table shows correlations between extra shopping and attitudes to the coronavirus outbreak situation. for the danish sample and the total sample, a significant association was found between doing extra shopping and believing that the government's actions to stop the spread of coronavirus were too little. further, believing that the government's actions were too little was associated with panic reasons for extra shopping. one significant association was observed for participants' rating of how serious the coronavirus crisis was. for the total sample, the more seriously the crisis was rated, the more likely was the participant to give action reasons for extra shopping. significant associations were found regarding the participants' confidence in the government's management of the coronavirus outbreak. for the total sample, the less confident the participants were, the more likely they were to do extra shopping, believe that it is ok to do so, and give panic reasons for doing so. for the british sample, there was also a significant association between low confidence in the government's management and panic reasons for extra shopping. this study's findings should be interpreted through consideration of its limitations. these limitations are a small sample size and the overrepresentation of women and people with higher education. while participants were assured of anonymity, social desirability bias cannot be ruled out with respect to the questions on doing extra shopping at a time of crisis. however, one of the strengths of this study is that the data were collected during the crisis, thereby minimizing the risk of recall bias. despise the limitations and preliminary nature of this study, it is the first one of its kind and gives novel insight into who was stockpiling and why at an extraordinary time of crisis. no significant associations were found between stockpiling and gender, age, level of education, and type of living arrangement. this contrasts with hori and iwamoto's ( ) study in tokyo which found that households with a middle-aged or older full-time homemaker wife and households with a large number of family members were more likely to engage in panic buying. the difference between the sociocultural context of the present study and that of the hori and iwamoto's ( ) study might explain this, as domestic gender roles might be less traditional in a north european context in than in japan in . the findings for personality traits were partly as hypothesized. those with high scores on neuroticism reported more extra shopping than people with low scores on neuroticism. this is not a surprising finding, as it is well established that people high on neuroticism are more reactive, overreact to stressors, and have more difficulties coping with stressful situations (mroczek & almeida, ) . one example from existing research regards smoking, where high scores on neuroticism are found to be associated with persistent smoking and a progressive smoking trajectory (zvolensky et al., ) . in this study, a high score on neuroticism was also associated with more positive attitudes towards extra shopping during the coronavirus outbreak. a high score on openness to experience was associated with lower levels of extra shopping. explanations might be found in previous research showing that people with high scores on openness to experience have been found to exhibit greater flexibility in dealing with life changes and reflecting on current events (whitbourne, ) . being flexible and open to reasonable alterations in life conditions (tesch & cameron, ) might check people with high scores on openness to experience from engaging in stockpiling. high scores on conscientiousness were also associated with a lower tendency to engage in extra shopping. this was counter to the hypothesis that people high on conscientiousness might stockpile in order to be well-prepared for the crisis. from the findings here, it might be alternatively posited that people high on conscientiousness are checked from stockpiling because of their typical tendencies of being disciplined, organized, and responsible. in line with this, people low on conscientiousness might be more likely to misjudge situations, engage in impulsive behavior, and break rules. however, it should be noted that this study was not able to analyze separately for those with extremes scores but could only analyze the correlations with the full score. therefore, it cannot be ruled out that those with very high scores on conscientiousness might demonstrate a different association with the tendency to stockpile. it was not hypothesized that high scores on extraversion would be associated with extra shopping. that people high on extraversion are more social and also more excitement-seeking might explain this association. however, this is not supported by the finding that those high on extraversion also reported panic reasons for extra shopping. more research is needed on both the different facets of personality traits and the combination of traits. in order to do so, future research should include thorough measures on personality traits. finally, it was hypothesized that agreeableness would be associated with extra shopping, but this could not be confirmed in this study. further research could investigate if stockpiling is more specifically linked to the degree to which people are altruistic or modest, these being two facets of agreeableness. a novel finding from this study concerns the two reasons for extra shopping that were based on an explorative factor analysis of reasons identified in qualitative interviews. for some people, doing extra shopping appears to be related to social activity and doing something active, whereas for others, it appears to be linked to reasons of panic and worry. the panic reasons here were associated with high scores on extraversion and neuroticism and low scores on openness to experience. as discussed above, the links with neuroticism and openness to experience are not surprising, but it is less clear why high scores on extraversion are linked to panic reasons. the action reason for extra shopping was not associated with any of the personality traits, but it was associated with being female, high scores on sdo-e and sdototal, and a low score on health literacy. that people endorsing antiegalitarian (high scores sdo-e) and social dominance (high total sdo scores) views also endorsed action reasons might be explained by previous research showing that a high sdo score is negatively correlated with empathy, tolerance, communality, and altruism (pratto et al., ) . several of the attitudes to the coronavirus situation, encompassing government actions, seriousness of the crisis, and confidence in the government, were associated with the extra shopping variables. this is not surprising and underlines the significance of society-wide factors. this study's findings also indicated differences in mean level scores for attitudes between denmark and the united kingdom, the british sample reported overall lover levels of trust compared to the danish sample. however, due to the convenience sampling method used, no conclusions should be drawn. more research is needed to explore individual differences and how they are potentially linked with and moderate attitudes to governments and authorities in different countries and at different stages of a crisis situation. the study found that individual differences were significant in explaining stockpiling, attitudes towards stockpiling, and reasons for stockpiling. stockpiling was associated with high scores on extraversion and neuroticism, and low scores on conscientiousness and openness to experience. stockpiling was also associated with the view that the government should be doing more to stop the coronavirus epidemic. the study also identified the two composite reasons of panic and action as explanatory factors for engaging in stockpiling. it found that gender, social dominance orientation, and health literacy were related to action reasons for stockpiling, while level of education, extraversion, and openness to experience were associated with panic reasons for stockpiling. despite the limitations and the preliminary nature of this study, it gives a first look into the individual differences that might explain stockpiling behavior at a time of crisis. no funding and no conflict of interest to report. coronavirus panic-buying: as supermarkets rationalize items, should customers be stockpiling? evaluating the use of exploratory factor analysis in psychological research comorbidity in hoarding disorder the nature of social dominance orientation: theorizing and measuring preferences for intergroup inequality using the new sdo scale the run on daily foods and goods after the tohoku earthquake. the japanese political economy us consumers and disaster: observing "panic buying" during the winter storm and hurricane seasons the effects of daily stress, age, and personality on daily negative affect measuring health literacy in general populations: primary findings from the hls-eu consortium's health literacy assessment effort dangerous and competitive worldviews: a meta-analysis of their associations with social dominance orientation and right-wing authoritarianism social dominance orientation: a personality variable predicting social and political attitudes measuring personality in one minute or less: a -item short version of the big five inventory in english and german health literacy and public health: a systematic review and integration of definitions and models i'm not hoarding, i'm just stocking up before the hoarders get here openness to experience and development of adult identity hamstring i netto: kunder i slagsmål om varer openness to experience, identity flexibility, and life change in adults big five personality factors and cigarette smoking: a -year study among us adults key: cord- -fw deem authors: zhang, guangzhi; li, bin; yoo, dongwan; qin, tong; zhang, xiaodon; jia, yaxiong; cui, shangjin title: animal coronaviruses and sars‐cov‐ date: - - journal: transbound emerg dis doi: . /tbed. sha: doc_id: cord_uid: fw deem covid‐ is a highly contagious disease caused by severe acute respiratory syndrome coronavirus (sars‐cov‐ ). it has rapidly spread to countries and territories since first outbreak in december of , posing a substantial economic losses and extraordinary threats to the public health worldwide. although bats have been suggested as the natural host of sars‐cov‐ , transmission chains of this virus, role of animals during cross‐species transmission, and future concerns remain unclear. diverse animal coronaviruses have extensively been studied since the discovery of avian coronavirus in s. the current article comprehensively reviews and discusses the current understanding about animal coronaviruses and sars‐cov‐ for their emergence, transmission, zoonotic potential, alteration of tissue/host tropism, evolution, status of vaccines, and surveillance. this study aims at providing guidance for control of covid‐ and preventative strategies for possible future outbreaks of zoonotic coronavirus via cross‐species transmission. the coronavirus disease broke out in wuhan, china in december , and spread rapidly across the world. on march th of , world health organization (who) announced covid- a pandemic. as of april , just four months since its first outbreak, more than . million confirmed cases and , deaths have been recorded in countries, areas, and territories, and moreover it seems that severe acute respiratory syndrome coronavirus (sars-cov- ) that causes covid- will probably continue to circulate around the globe (https://www.who.int/emergencies/diseases/novel-coronavirus- /situation-reports/). the health authorities and governments of affected countries have paid attention to current pandemic and have taken immediate measures to block covid- transmission, including utilization of personal protective equipment, quarantine, epidemiological investigation, isolation, clinical data analysis and sharing, public health education, maintaining social distance, the creation of diagnostics, therapeutics, and vaccines, etc (xiao and torok ) . the new information is rapidly accumulating and uncovers the nature of sars-cov- , but many questions remain to be answered. (table ) . these six covs usually cause infections in pigs, but pdcov seems to have the ability to infect other species such as badgers, calves, and cats (li et al. ) . moreover, it was reported our phylogenetic analysis with s protein shows that pedv and tgev share only . %- . % of genome similarity with sars-cov- , and phev and pdcov share . %- . % and . %- . % genome similarity with sars-cov- , respectively (table ) . obviously, porcine covs are unlikely the origin of sars-cov- . however, the rbd of sars-cov- is likely to recognize porcine ace based on the high similarity of critical virus-binding residues between porcine ace and human ace (wan, shang, graham, et al. this article is protected by copyright. all rights reserved the investigation needs to be explored. ibv normally binds to cell receptors via sialic acid for its attachment and entry (shahwan et al. ; toro, van santen, and jackwood ) (table ) . live-attenuated vaccines for ibv are usually adopted by the farms, which are developed by serial passages of virulent strains in embryonated chicken eggs (laconi et al. ; masoudi, pishraft sabet, and shahsavadi ; baron, iqbal, and nair kong. an oie report shows that the antibody in a pet dog living with a receptor for both fecv and fipv (hohdatsu et al. ) ( table ). as shown in table showed that the receptor-binding motif of sars-cov- rbd can engage with ace of humans and cats at similar efficiencies (wan, shang, graham, et al. for neonates through colostrum (nemoto et al. ; kanno et al. ) . as for the receptors utilized by sars-cov- , biophysical and structural data showed that the s protein engages with ace with at least times higher affinity compared to that of sars-cov (wrapp et al. ). in addition to ace , sars-cov- may also invade the cell via another receptor: cd ibrahim et al. accepted article ibrahim et al. ; hao et al. ) . it was reported that furin is involved in the cleavage of sars-cov- s protein and further facilitate viral entry . in principle, tissues with consistently high expression of ace or cd are likely susceptible to sars-cov- , including small intestine, kidney (renal tubular cells), testis (leydig cells and cells in seminiferous ducts), gall bladder, heart, stomach, and liver (fagerberg et al. ). according to a recent report shen et al. phylogenetic analysis by researchers from institut pasteur in paris showed that sars-cov- might already circulated in france prior to first local case (gámbaro et al. ). all of these data undoubtedly showed an intricate situation of this virus. thus, more surveillance needs to be taken to explore the origin and diversity of this virus worldwide. importantly, the careful analyses demonstrate that some of the animal covs have evolved to all data generated or analyzed in this study are included in this manuscript and in the supplementary material. this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved strength of infectivity. survey of sars-cov- for experimental, domestic, companion and wild animals excludes intermediate hosts of different species of animals human kidney is a target for novel severe acute respiratory syndrome coronavirus (sars-cov- ) infection isolation and sequence analysis of canine respiratory coronavirus detection of a group coronavirus in dogs with canine infectious respiratory disease analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics diagnosis of feline infectious peritonitis: a review of the current literature phylogenetic network analysis of sars-cov- genomes evolution of infectious bronchitis virus in the field after homologous vaccination introduction', vet this article is protected by copyright. all rights reserved j. saif feline coronavirus type ii strains - and - originate from a double recombination between feline coronavirus type i and canine coronavirus differences in virus receptor for type i and type ii feline infectious peritonitis virus engineering a live attenuated porcine epidemic diarrhea virus vaccine candidate via inactivation of the viral '-o-methyltransferase and the endocytosis signal of the spike protein coronavirus spike protein and tropism changes' human coronaviruses oc and hku bind to -o-acetylated sialic acids via a conserved receptor-binding site in spike protein domain a covid- spike-host cell receptor grp binding site prediction experimental bovine coronavirus in turkey poults and young chickens tracking changes in sars-cov- spike: evidence that d g increases infectivity of the covid- virus triple-reassortant influenza a virus with h of human seasonal origin, na of swine origin, and internal a(h n ) pandemic genes is established in danish pigs attenuated live infectious bronchitis virus qx vaccine disseminates slowly to target organs distant from the site of inoculation identifying sars-cov- -related coronaviruses in malayan pangolins structure, function, and evolution of coronavirus spike proteins broad receptor engagement of an emerging global coronavirus may potentiate its diverse cross-species transmissibility cats under the shadow of the sars-cov- pandemic emergence of sars-cov- through recombination and strong purifying selection emerging lethal infectious bronchitis coronavirus variants with multiorgan tropism', transbound emerg this article is protected by copyright. all rights reserved ferrets immunogenicity and efficacy of live infectious bronchitis /b. ir vaccine in spf chickens origins of the h n influenza pandemic in swine in mexico contribution of the porcine aminopeptidase n (cd ) receptor density to porcine epidemic diarrhea virus infection antibody response to equine coronavirus in horses inoculated with a bovine coronavirus vaccine emergence and pandemic potential of swine-origin h n influenza virus swine enteric coronavirus disease: a review of years with porcine epidemic diarrhoea virus and porcine deltacoronavirus in the united states and canada mutation of the s and c genes in genomes of feline coronaviruses prevalence of feline coronavirus (fcov) and feline leukemia virus (felv) in turkish cats this article is protected by copyright. all rights reserved antibody-binding epitopes in the spike domain and the nucleocapsid protein of feline infectious peritonitis virus sialic acid binding properties of soluble coronavirus spike (s ) proteins: differences between infectious bronchitis virus and transmissible gastroenteritis virus cell entry mechanisms of sars-cov- pathways of cross-species transmission of synthetically reconstructed zoonotic severe acute respiratory syndrome coronavirus genomic diversity of sars-cov- sars-cov- and sars-cov spike-rbd structure and receptor binding comparison and potential implications on neutralizing antibody and vaccine development canine respiratory coronavirus, bovine coronavirus, and human coronavirus oc : receptors and attachment factors', viruses prevalence of feline coronavirus antibodies in japanese domestic cats during the past decade on the origin and continuing evolution accepted article this article is protected by copyright. all rights reserved of sars-cov- genetic diversity and selection regulates evolution of infectious bronchitis virus structural basis for human coronavirus attachment to sialic acid receptors mutational analysis of aminopeptidase n, a receptor for several group coronaviruses, identifies key determinants of viral host range early death after feline infectious peritonitis virus challenge due to recombinant vaccinia virus immunization feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses pathogenic characteristics of persistent feline enteric coronavirus infection in cats receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus molecular mechanism for antibody-dependent enhancement of coronavirus entry development of an inactivated vaccine candidate sars-cov- invades host cells via a novel route: cd -spike protein importance of neutralizing monoclonal antibodies targeting multiple antigenic sites on the middle east respiratory syndrome coronavirus spike glycoprotein to avoid neutralization escape emerging and re-emerging coronaviruses in pigs an outbreak of feline infectious peritonitis in a taiwanese shelter: epidemiologic and molecular evidence for horizontal transmission of a novel type ii feline coronavirus evidence of recombination in coronaviruses implicating pangolin origins of ncov- discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus cryo-em structure of the -ncov spike in the prefusion conformation wenjie tan, and genhong cheng. . 'mutations evidence for gastrointestinal infection of sars-cov- isolation and characterization of -ncov-like coronavirus from malayan pangolins taking the right measures to control covid- systematic comparison of two animal-to-human transmitted human coronaviruses: sars-cov- and sars-cov clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective broad cross-species infection of cultured cells by bat hku -related swine acute diarrhea syndrome coronavirus and identification of its replication in murine dendritic cells in vivo highlight its potential for diverse interspecies transmission novel coronavirus is undergoing active recombination covid- and veterinarians for one health, zoonotic-and reverse-zoonotic transmissions and team singapore novel coronavirus outbreak research. . 'epidemiologic features and clinical course of patients infected with sars-cov- in sars-cov- spike protein variant d g increases infectivity and retains sensitivity to antibodies that target the receptor binding domain the d g mutation in the sars-cov- spike protein reduces s shedding and increases infectivity sars-cov- neutralizing serum antibodies in cats: a serological investigation probable pangolin origin of sars-cov- associated with the covid- outbreak biological and genetic characterization of a hemagglutinating coronavirus isolated from a diarrhoeic child tissue tropisms opt for transmissible reassortants during avian and swine influenza a virus co-infection in swine a genomic perspective on the origin and emergence of sars-cov- evolution of infectious bronchitis virus in china over the past two decades fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin ophthalmologic evidence against the interpersonal transmission of novel coronavirus through conjunctiva', medrxiv: accepted article this article is protected by copyright immunogenicity and safety of a recombinant adenovirus type- -vectored covid- vaccine in healthy adults aged years or older: a randomised contribution of porcine aminopeptidase n to porcine deltacoronavirus infection virulence factors in porcine coronaviruses and vaccine design this article is protected by copyright. all rights reserved this article is protected by copyright. all rights reserved key: cord- -vn q wc authors: ziebuhr, john title: the coronavirus replicase: insights into a sophisticated enzyme machinery date: journal: the nidoviruses doi: . / - - - - _ sha: doc_id: cord_uid: vn q wc nan gene-encoded proteins, includes several cellular proteins and the viral nucleocapsid protein. [ ] [ ] [ ] ) . translation of the genomic rna gives rise to two replicative polyproteins, pp a and pp ab, that mediate the key functions required for sars-cov genome replication and synthesis of major subgenomic rnas encoding the structural proteins (shown in black) and several sars-cov-specific accessory proteins. expression of orf b sequences requires a programmed ribosomal frameshift into the - reading frame during translation of the genome rna, which occurs just upstream of the orf a translation stop codon. the replicative polyproteins are extensively processed by viral proteases. the processing end-products of pp a are designated nonstructural proteins (nsp) to nsp and those of pp ab are designated nsp to nsp and nsp to nsp . cleavage sites that are processed by the c-like protease ( cl pro ), which is also called main protease (m pro ), are indicated by gray arrowheads, and sites that are processed by the papain-like protease, pl pro , are indicated by black arrowheads. the major replicative domains are shown in dark gray and transmembrane domains predicted to anchor the viral replicase to intracellular membranes are indicated in light gray. appr- "-pase, adp-ribose "-phosphatase; pl pro , papain-like cysteine protease ; cl pro , c-like main protease; rdrp, rna-dependent rna polymerase; exon, '-to- ' exoribonuclease; nendou, nidoviral uridylate-specific endoribonuclease; mt, putative ribose- '-o methyltransferase. activation of the coronavirus replication complex involves extensive proteolytic processing of the replicase polyproteins to produce (in ibv: ) mature products called nonstructural proteins (nsp) to (reviewed in refs. and ). the processing involves two different types of proteases. the key enzyme is the so-called c-like protease ( cl pro ), also called main protease (m pro ), which cleaves the central and c-terminal regions of pp a and pp ab at conserved sites. cl pro is a cysteine protease featuring a cys-his catalytic dyad and a three-domain structure. , the nterminal domains i and ii adopt a two-β-barrel-fold structure that resembles the structures of serine proteases of the chymotrypsin superfamily. the c-terminal entirely α-helical domain iii is critically involved in proteolytic activity and dimerization. it is now generally accepted that the cl pro dimer represents the active form of the protease. , intermolecular interactions within the dimer have been suggested to keep the active center (in particular, the s subsite) in a proteolytically competent conformation. , coronavirus main proteases have conserved substrate specificities [(l,i)-q↓(s,a,g)] and, accordingly, similar substrate-binding pocket structures, as has been shown by crystal structure analyses of main proteases from different coronavirus genetic groups. , [ ] [ ] [ ] based on this information, protease inhibitors have been developed that effectively inhibit a broad range of coronavirus main proteases. potentially, these compounds may be useful for treatment of known or newly emerging coronavirus infections. the n-terminal regions of the coronavirus polyproteins, which are poorly conserved among the coronavirus groups i, ii, and iii, are cleaved at two (in ibv) or three sites (in all other coronaviruses) by one (ibv and sars-cov) or two zinc-finger-containing papain-like cysteine proteases called pl pro and pl pro . - pl pro cleavage sites are usually flanked by small residues (mainly gly and ala). pl pro and pl pro probably evolved by gene duplication in one of the ancestors of the present-day coronaviruses. for mhv, it was recently demonstrated that cleavage of the nsp |nsp site and, even more suprisingly, the c-terminal nsp and the entire nsp sequence are not required for mhv replication in vitro. [ ] [ ] [ ] the coronavirus rdrp has been classified as an outgroup of the rdrp superfamily . it resides in the orf b-encoded nonstructural proteins , as was predicted about years ago and now demonstrated for a bacterially expressed form of the sars-cov nsp . the rdrp catalytic domain occupies the c-terminal two-thirds of nsp , but also the n-terminal part of nsp seems to contribute to activity. based on mhv coimmunoprecipitation data, the n-terminal part of nsp has been suggested to interact with other replicase subunits, specifically with nsp ( cl pro ), nsp , and nsp , which is in line with the recently published crystal structure of an nsp -nsp complex from sars-cov. the x-ray crystallography study by zhai et al. provides first insights into the sophisticated architecture of the coronavirus replicase. it shows that eight molecules of each nsp and nsp assemble into a hexadecameric supercomplex that forms a hollow, cylinder-like structure, which, because of its internal dimensions and electrostatic properties, seems to be capable of encircling rna. this nsp -nsp supercomplex, in turn, interacts with nsp , a small single-stranded rna-binding protein, , and interactions of nsp -nsp (-nsp ) with yet other replicase subunits (including nsp ) are likely. on the basis of structural and functional data, it has been speculated that the nsp -nsp complex might act as an important rdrp cofactor, for example, to increase the rdrp processivity. evidence for a critical involvement of the c-terminal pp a processing products (nsp - ) in viral rna synthesis also comes from work on mhv temperature-sensitive mutants, which has shown that nsp , a cys/his-rich protein, has a distinct role in minus-strand rna synthesis. after the rdrp, helicases are the second best conserved enzymes of plus-strand rna viruses. the coronavirus helicase resides in nsp and has been classified as belonging to the helicase superfamily , (fig. ) . coronavirus helicases and all their nidovirus homologs are linked to an n-terminal zinc-binding domain (zbd) involving - conserved cys/his residues. the conservation of a zbd-associated superfamily helicase is considered one of the major genetic markers of nidoviruses. over the past years, the helicase activities of hcov- e and, to a lesser extent, of sars-cov have been characterized. [ ] [ ] [ ] [ ] [ ] mutagenesis and biochemical data revealed that the zbd is essential for the enzymatic activities of both the coronavirus and arterivirus helicases. coronavirus helicases proved to have multiple enzymatic activities, including nucleic acid-stimulated ntpase, dntpase, and rna (plus dna) duplex-unwinding activities. , , coronavirus (and arterivirus) helicases were demonstrated to unwind double-stranded rna substrates with '-to- ' polarity, that is, they move in a '-to- ' direction along the strand to which they initially bind. , the polarity of coronavirus helicase activities contrasts with that of the helicases of flavi-, pesti-, and hepaciviruses, which all operate in the opposite direction, indicating that the biological functions of helicases from the nidovirales and flaviviridae might differ fundamentally from each other. coronavirus (nidovirus) helicases belong to the few helicases that act on both rna or dna substrates with nearly equal efficacy. given that the helicase is part part of the (cytoplasmic) coronavirus replicase complex, it seems unlikely that the observed dna duplex-unwinding activity is of biological significance. coronavirus helicases are able to unwind up to several hundred base pairs of double-stranded nucleic acid in a processive manner, , supporting a role as a "replicative" helicase that separates regions of doublestranded rna that the polymerase might encounter during rna synthesis. coronavirus helicases are able to hydrolyze essentially all natural nucleotides to fuel their translocation along nucleic acids and concomitant unwinding of duplex rna (and dna) structures. [ ] [ ] [ ] [ ] [ ] besides their ntpase and dntpase activities, coronavirus helicases were shown to possess yet another phosphohydrolyase activity, namely an rna 'triphosphatase activity that employs the active site of the (d)ntpase activity. it is reasonable to believe that the nsp -associated rna '-triphosphatase catalyzes the first reaction in the synthesis of coronavirus ' rna cap structures. , given the multiple enzymatic activities of coronavirus helicases and the previously observed diverse roles of the arterivirus helicase in viral replication, transcription and virion biogenesis, it is reasonable to believe that coronavirus helicases are involved in more than one metabolic pathway in the viral life cycle. a detailed sequence analysis by gorbalenya, snijder and colleagues of the sars-cov genome revealed that the enzymology of coronavirus rna synthesis may be significantly more complex than previously thought. in this seminal study published in , as many as five novel enzymatic activities were identified in the genomes of coronaviruses and, to a varying extent, other nidoviruses (fig. ) . the putative activities included (i) a '-to- ' exonuclease (exon) associated with nsp , (ii) an endoribonuclease (nendou) associated with nsp , (iii) an s-adenosyl methionine-dependent ribose '-omethyltransferase (mt) associated with nsp , (iv) an adp-ribose "-phosphatase (appr- "-pase) associated with the so-called "x domain" of nsp , and (v) a cyclic phosphodiesterase (cpdase), which is only conserved in group ii coronaviruses (excluding sars-cov). four of the activities were found to be conserved in all coronaviruses, suggesting that they have an essential role in the coronaviral life cycle. recently, the predicted exo-and endoribonuclease activities were established and characterized using bacterially expressed forms of the exon from sars-cov (minskaia, hertzig, gorbalenya, campanacci, cambillau, canard, and ziebuhr, unpublished data), and the nendou from hcov- e, sars-cov, and ibv. , we have recently demonstrated by reverse genetics using the hcov- e infectious clone that the exon, nendou, and mt domains are all essential for the production of virus progeny. substitutions of predicted active-site residues resulted in diverse defects in viral rna synthesis and virus production (hertzig, ulferts, schelle, and ziebuhr, unpublished data). the underlying mechanisms for the observed defects are currently being studied in detail. the observed pattern of conservation in different nidovirus families suggests a functional hierarchy for the newly identified rna-processing activities, with the manganese ion-dependent uridylate-specific endoribonuclease, nendou, playing a central role. this enzyme is universally conserved in nidoviruses and, besides the zbdassociated helicase, represents a genetic marker of nidoviruses that is also reflected by its previous designation as "nidovirus-specific conserved domain" , . as mentioned above, nendou has been demonstrated by site-directed mutagenesis of the full-length hcov- e clone to be essential for coronaviral rna synthesis. however, we recently obtained mutagenesis data that argue for a more complex scenario regarding the activities of nendou. thus, for example, we found that several single-residue substitutions that abolished the nendou activity in an in vitro rnase assay gave rise to viable (albeit lowtiter) virus when transferred to the hcov- e infectious clone (hertzig, ulferts and ziebuhr, unpublished data). these data indicate that nendou might have more than one activity and/or cleave more than one substrate that likely differs from that used in our in vitro assays. clearly, more work will be required to elucidate the function(s) of nendou in the nidoviral life cycle. in view of the very similar gene expression and rna synthesis strategies employed by the various nidovirus families and genera, it is intriguing that only one (namely nendou) of the newly identified nidovirus rna-processing activities is conserved in arteriviruses. the basis for this differential conservation pattern of rna-processing enzymes is currently unclear but might indicate that the enzymology involved in viral genome-length and subgenome-length rna synthesis varies to some extent among the nidovirus families. alternatively, members of the various nidovirus families/genera might interact differentially with yet-to-be-defined rna-processing pathways of the host cell. it is also worth remembering that arterivirus genomes are about times smaller than other nidovirus genomes and it is possible that (some of) the extra domains conserved in corona-and toroviruses (and, to a lesser extent, in roniviruses) are required to replicate genomes of this unique size. the coronavirus exon activity was recently shown by sequence analysis and site-sirected mutagenesis to be related to cellular enzymes of the dedd exonuclease superfamily (minskaia, hertzig, gorbalenya, campanacci, cambillau, canard, and ziebuhr, unpublished data). this exonuclease family includes cellular '-to- ' exonucleases involved in proofreading, repair, and/or recombination, and it is tempting to speculate that nidoviruses use their exon domains in similar processes, for example, to keep the error frequency of their low-fidelity rdrp below a critical thereshold. in contrast to the essential rna-processing activities (exon, nendou, and mt), the nsp x domain-associated appr- "-pase activity was found to be dispensable for viral replication in vitro. substitutions of putative active-site residues of the appr- "-pase domain, which have been confirmed to abolish enzymatic activity in vitro, gave rise to viable virus. the virus had no apparent defects in viral rna synthesis and grew to the same titers as the wild-type virus. similarly, mhv reverse genetics data demonstrated that coronaviruses tolerate specific substitutions and even deletions in the replicase gene. for example, cleavage of the nsp |nsp cleavage site was shown to be dispensable for viral replication, and even deletion of the c-terminal part of nsp and the entire nsp , respectively, had only minor effects on viral replication. [ ] [ ] [ ] by contrast, several other mutations/deletions were tolerated in vitro but caused attenuation in the natural host. taken together, the data suggest that coronavirus replicases have evolved to include a number of nonessential functions. the fact that some of the "nonessential" protease cleavages and enzymatic activities are conserved in coronaviruses or in specific coronavirus genetic groups suggests that they provide a selective advantage only in the host. although much has been learned about coronavirus replicase organization, localization, proteolytic processing, and viral replicative enzymes, there are still major gaps in our knowledge. inspired by the sars epidemic in , numerous studies aiming at the development of coronavirus vaccines and antivirals have recently been published, and there is no doubt that coronavirus research has gained momentum over the past few years. given the rapidly accumulating biochemical, structural, and genetic information on coronaviruses, a more detailed understanding of the molecular mechanisms involved in coronaviral rna synthesis can be expected to emerge in the near future. it will be of particular interest to identify those proteins that are involved in the specific mechanisms of coronavirus rna synthesis, such as the production of a nested set of subgenome-length rnas and the replication of rna genomes of unprecedented size. furthermore, studies on coronavirus-encoded rna-processing activities and their cellular homologs might reveal interesting insights into the relationship (or interplay) of coronaviral and cellular rna metabolism pathways. in the long run, the unique structural properties of several conserved coronavirus replicative enzymes may lead to the development of selective enzyme inhibitors and possibly even drugs suitable to treat coronavirus infections of humans and animals. my work is supported by the deutsche forschungsgemeinschaft and the european commission. nidovirales: a new order comprising coronaviridae and arteriviridae a comparative sequence analysis to revise the current taxonomy of the family coronaviridae topley and wilson's microbiology and microbial infections coronavirus mrna synthesis involves fusion of non-contiguous sequences an efficient ribosomal frame-shifting signal in the polymerase-encoding region of the coronavirus ibv coronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis big nidovirus genome. when count and order of domains matter unique and conserved features of genome and proteome of sars-coronavirus, an early split-off from the coronavirus group lineage the coronavirus replicase an 'elaborated' pseudoknot is required for high frequency frameshifting during translation of hcv e polymerase mrna the nucleoprotein is required for efficient coronavirus genome replication selective replication of coronavirus genomes that express nucleocapsid protein viral and cellular proteins involved in coronavirus replication molecular biology of severe acute respiratory syndrome coronavirus virus-encoded proteinases and proteolytic processing in the nidovirales structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain coronavirus main proteinase ( cl pro ) structure: basis for design of anti-sars drugs dissection study on the severe acute respiratory syndrome c-like protease reveals the critical role of the extra domain in dimerization of the enzyme: defining the extra domain as a new target for design of highly specific protease inhibitors critical assessment of important regions in the subunit association and catalytic action of the severe acute respiratory syndrome coronavirus main protease severe acute respiratory syndrome coronavirus c-like proteinase n terminus is indispensable for proteolytic activity but not for enzyme dimerization. biochemical and thermodynamic investigation in conjunction with molecular dynamics simulations conservation of substrate specificities among coronavirus main proteases the crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor design of wide-spectrum inhibitors targeting coronavirus main proteases identification of the catalytic sites of a papain-like cysteine proteinase of murine coronavirus proteolytic processing at the amino terminus of human coronavirus e gene -encoded polyproteins: identification of a papain-like proteinase and its substrate characterization of the two overlapping papain-like proteinase domains encoded in gene of the coronavirus infectious bronchitis virus and determination of the c-terminal cleavage site of an -kda protein identification of mouse hepatitis virus papain-like proteinase activity identification of a novel cleavage activity of the first papain-like proteinase domain encoded by open reading frame a of the coronavirus avian infectious bronchitis virus and characterization of the cleavage products the autocatalytic release of a putative rna virus transcription factor from its polyprotein precursor involves two paralogous papain-like proteases that cleave the same peptide bond mechanisms and enzymes involved in sars coronavirus genome expression identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity papain-like protease (plp ) from severe acute respiratory syndrome coronavirus (sars-cov): expression, purification, characterization, and inhibition cleavage between replicase proteins p and p of mouse hepatitis virus is not required for virus replication mutagenesis of the murine hepatitis virus nsp -coding region identifies residues important for protein processing, viral rna synthesis, and viral replication the nsp replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication the phylogeny of rna-dependent rna polymerases of positive-strand rna viruses expression, purification, and characterization of sars coronavirus rna polymerase characterization of the expression, intracellular localization, and replication complex association of the putative mouse hepatitis virus rnadependent rna polymerase insights into sars-cov transcription and replication from the structure of the nsp -nsp hexadecamer the severe acute respiratory syndrome-coronavirus replicative protein nsp is a single-stranded rna-binding subunit unique in the rna virus world the nsp replicase protein of sars-coronavirus, structure and functional insights identification of the mutations responsible for the phenotype of three mhv rna-negative ts mutants two related superfamilies of putative helicases involved in replication, recombination, repair and expression of dna and rna genomes the human coronavirus e superfamily helicase has rna and dna duplex-unwinding activities with '-to- ' polarity guanosine triphosphatase activity of the human coronavirus helicase the severe acute respiratory syndrome (sars) coronavirus ntpase/helicase belongs to a distinct class of ' to ' viral helicases multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase human coronavirus e nonstructural protein : characterization of duplex-unwinding, nucleoside triphosphatase, and rna '-triphosphatase activities a complex zinc finger controls the enzymatic activities of nidovirus helicases biochemical characterization of the equine arteritis virus helicase suggests a close functional relationship between arterivirus and coronavirus helicases virus-encoded rna helicases the predicted metal-binding region of the arterivirus helicase protein is involved in subgenomic mrna synthesis, genome replication, and virion biogenesis the severe acute respiratory syndrome coronavirus nsp protein is an endoribonuclease that prefers manganese as a cofactor major genetic marker of nidoviruses encodes a replicative endoribonuclease the carboxyl-terminal part of the putative berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro-and coronaviruses are evolutionarily related equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily adp-ribose- "-monophosphatase: a conserved coronavirus enzyme that is dispensable for viral replication in tissue culture single-aminoacid substitutions in open reading frame (orf) b-nsp and orf a proteins of the coronavirus mouse hepatitis virus are attenuating in mice key: cord- -d hi myk authors: kirtipal, nikhil; bharadwaj, shiv; kang, sang gu title: from sars to sars-cov- , insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: - - journal: infection, genetics and evolution doi: . /j.meegid. . sha: doc_id: cord_uid: d hi myk abstract human coronaviruses (hcov), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus- (sars-cov- ) – diseases termed as covid- . current sars-cov- outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. in fact, evidence has now shown that coronaviruses undergoes repaid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. this demands the understanding of phenotypic and genotypic classification, and pathogenesis of sars-cov- for the production of potential therapy. in lack of clear clinical evidences for the pathogenesis of covid- , comparative analysis of previous pandemic hcovs associated immunological responses can provide insights into covid- pathogenesis. in this review, we summarize the possible origin and transmission mode of covs and the current understanding on the viral genome integrity of known pandemic virus against sars-cov- . we also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel covid- pathogenesis; and hence, development of therapeutic against broad spectrum of coronaviruses. previously, the coronaviridae study group (csg) identified sars-cov and mers-cov strains into a new species under the new informal subgroup of betacov genus (van boheemen et al., ) . however, recent introduction of subgenus rank in virus taxonomy have established the two informal subgroups of sars-cov and mers-cov as subgenera sarbecovirus and merbecovirus (de groot et al., ; gorbalenya et al., ) , respectively. remarkably, newly emerged sars-cov- differs from previously reported zoonotic pandemic viruses, viz. sars-cov and mers-cov; and hence, taxonomic position of sars-cov- under subgenera sarbecovirus may be tentative to change based on further evidences (gorbalenya et al., ) ( fig. ) . phylogenetic tree analysis of covs constructed based on s gene using molecular evolutionary genetics analysis software under neighbor-joining method and bootstrap values (biswas et al., ) . before the emergence of sars-cov, construction of phylogenetic tree for covs was based on pol (polymerase) or nucleocapsid (n) gene as standard practice. initially, this method proposed sars-cov as a member of gammacov (rota et al., ) . however, further evidences on amino-terminal domain of sars-cov spike protein discovered that out of cysteine residues were structurally conserved with in betacov group while only conserved residues were matched within alphacov and gammacov group (rota et al., ) . subsequently, whole genome-based phylogenetic analysis indicated sars-cov as member of betacov lineage b. likewise, mers-cov was also identified as novel betacov lineage c with high pathogenicity . remarkably, rna-dependent rna polymerase (rdrp) and spike (s) animal covs have been known since the late s like transmissible gastroenteritis virus of swine (tgev), bovine coronavirus (bcov), feline infectious peritonitis virus (fipv), and infectious bronchitis virus (ibv) transmissible (saif, ) . recent studies associated hcovs evolution with expedited urbanization and poultry farming; these practices permitted frequent interchange of species and simplified crossing of species barrier and genomic recombination in these viruses (jones et al., ) . bats harbored a great diversity of covs; viral sampling conducted by the ecohealth alliance in china alone identified about new strains of covs . besides, study of covs diversity harbored by bats in eastern thailand revealed forty-seven covs (wacharapluesadee et al., ) . moreover, bats were documented with unique immune systems that allowed them to cope with a variety of viruses by comparison to other terrestrial mammal (xie et al., ) . also, a high diversity of zoonotic alphacovs and betacovs were also detected in the circulating bats of western europe (ar gouilh et al., ) . generally, bats harbored rna viruses but can be infected by dna viruses (xie et al., ) . although, clear transmission of covs from bats to humans is not yet fully discovered but transmission by intermediary host to humans via direct contact has been widely suggested as one of the probable modes of transmission. the first sars-cov case was documented in november in foshan, china (ge et al., ) . it became an epidemic, affected countries around the world with , cases and deaths (ge et al., ) . during the sars epidemic, the first indication for the source of sars-cov viral strain was detected in masked palm civets (paguma larvata) and raccoon dog (nyctereutes procyonoides). later discovery of antibodies for virus in chinese ferret badgers (melogale moschata) in a live-animal market in shenzhen, china were suspected as source of human infection (drexler et al., ; guan et al., ; song et al., ) . however, later findings predicted these animals merely as incidental hosts in absence of concrete results to support the motion of sars-cov-like viruses in palm civets among the wild or in the breeding factors endorsing bats as animal reservoirs of mammalian viruses were also defined in terms of their densely packed colonies, longevity, close social interaction, and ability to fly (calisher et al., ; luis et al., ) . likewise, first human case of mers was reported in june in jeddah, saudi arabia (ge et al., ) . as of november , , cases of mers have been reported in countries, resulting in fatalities (who, ) . initially, search for mers-cov reservoir was focused on bats; however, serological survey in dromedary camels (camelus dromedarius) from oman and the canary islands exhibited a significant prevalence of mers-cov-neutralizing antibodies (reusken et al., ) . additionally, dromedary camels were detected with mers-cov rna at a farm in qatar related to two human cases of mers; virus particles were detected from dromedary camels in qatar and saudi arabia (hemida et al., ; raj et al., ) . serological evidence supported that dromedary camels has been harboring mers-cov-like virus in eastern africa and northern africa, and middle east, dating back as far as (muller et al., ) . additionally, in saudi arabia, dromedary camels were detected with various viral genetic lineages (sabir et al., ) , including which crossed the species barrier and caused the outbreaks in humans (omrani et al., ) . collectively, these evidences strongly suggested the contribution of dromedary camels as considerable reservoir to mers-cov; the ancestral virus were predicted to cross the species barrier into dromedary camels from bats more than ≥ years ago as supported by serological evidences (fig. ) . recent sars-cov- outbreak highlights the hidden wild zoonotic reservoir of deadly viruses and possible threat of spillover zoonoses (malik et al., ) . in , a food market that sold live in wuhan, china was linked to the outbreak of sars-cov- . through genetic analyses, bats were again suggested as native host of sars-cov- as it shared % genome to two sars-like covs, viz. bat-sl-covzx and bat-sl-covzx from bats zhou et al., b) . however, intermediate host and route which assisted viral transmission to humans is yet fully understood. initially, ji, et al., proposed snakes as an intermediate host of sars-cov- transmission from bats to humans which involved homologous recombination within the viral spike (s) protein (ji et al., ) . later, pangolins (manis spp.) were suggested as potential intermediate host for sars-cov- as it shared % genetic homology with covs in pangolins ( fig. ) (yi et al., ) . however, % variance all over the two-genome sequence was considered as significant difference; and thus, conclusive and concrete evidences are still under j o u r n a l p r e -p r o o f journal pre-proof investigation (yi et al., ) . moreover, scientists also showed concerned about its validation genetics technique (codon usage bias) (callaway and cyranoski, ) . hence, diversity of covs in bat population needs further investigation in detail along with critical surveillance and monitoring of bats to prevent future outbreaks in animals and public. after infection in human, hcovs are transmitted among the human population by close personto-person contact. for example, close contact with infected person under in feet distance has been concluded as major factor for cov transmission . the pandemic viruses, sars-cov, mers-cov and sars-cov- , transmitted between humans mostly by nosocomial transmission; supported by evidences that health care workers and patients had higher frequency of infection against their relatives (de wit et al., ) . the collected data predicted that only - % of sars and - % of mers transmission occurred between family members. also, sars-cov transmission from infected patients to health care workers was very frequent ( - %) and mers-cov transmission between patients was recorded as the most common course of infection ( - % of cases) (chowell et al., ) . such a predominance of nosocomial transmission was predicted due to significant virus shedding that occurred following the onset of infection when most patients were already under medical care (cowling et al., ; peiris et al., ) . a study on hospital surfaces following treatment of mers-cov infected patients detected with viral rna for several days even after patients no longer detected for viral infection (bin et al., ) . moreover, many patients with sars or mers were infected through super spreaders (korea centers for disease control and prevention, ) (chowell et al., ; kucharski and althaus, ) . in addition, sars-cov was also suspected for transmission through air (airborne spread) or some other unkown transmission routes . (e), nucleocapsid (n) proteins, and hemagglutinin (ha), where s, m, and e proteins are embedded in viral envelop while n protein protects viral rna genome located as core of virus ( fig. ) (zhou et al., b) . s protein is characterized as heavily glycosylated protein and contained the receptor binding domain (rbd), which is the most variable structure in covs (zhou et al., b) ; mediates viral entry into host cells (bosch et al., ) . the two different types of spike proteins have been discovered in covs: spike glycoprotein trimmer (s) that can be found in all covs, and hemagglutinin-esterase (he) that found in specific covs (belouzard et al., ; cui et al., ) . some covs, including sars-cov and sars-cov- , contain polybasic cleavage site (rrar/s) at the junction of two subunits (s and s ) of s protein. this allowed digestion by host furin-like protease during viral replication (bosch et al., ) and contributed in determination of viral infectivity towards host range (nao et al., ) . although function of polybasic cleavage site in sars-cov- is not yet discovered; experimental studies with sars-cov and mers-cov have determined that insertion of a furin cleavage site (fcs) at s -s junction enhanced the cell-cell fusion without affecting viral entry (follis et al., ) and efficient digestion enabled mers-cov like covs from bats to infect human cells (menachery et al., ) . furthermore, m protein exists in higher quantities against e protein in virion structure (nal et al., ) and critically required in orchestrating viral shape, assembly and in generation of mature viral envelopes (siu et al., ) . moreover, it also functions in intracellular virion formation without the requirement of s protein. in some occasions, such as in presence of tunicamycin, covs were reported to generate noninfectious virions without spike but contained m protein in envelop (de haan et al., ) . likewise, structural protein, e protein assisted in mature virions secretion from host cells, in addition to other functions like ion channel activity, inhibit the host cell stress response and implicate pathogenesis in host cell through virus (ruch and machamer, ) . n protein essentially assisted in genomic rna packing during viral particle assembly (chang et al., ; hurst et al., ) . whereas, he, which is a hemagglutinin similar to influenza virus hemagglutinin, conducts the acetyl-esterase activity (klausegger et al., ) . recently, role of he was also logged to catalyst viral invasion across host cell membrane and in pathogenesis (ashour et al., ) . hcovs, including sars-cov, mers-cov, and sars-cov- , contained largest nonsegmented positive-sense single-stranded rna genome of size between . and . kb with varied g+c contents of % to % (mousavizadeh et al., ; yang et al., ) . the genome organization for a cov is ′-leader-utr-replicase/transcriptase-spike (s)-envelope (e)membrane (m)-nucleocapsid (n)- ′utr-poly (a) tail (fig. ) . the ′utr (untranslated region) and ′utr are involved in interand intramolecular interactions, essentially required in rna-rna interactions and for binding of viral and cellular proteins (yang and leibowitz, ) . the orf a and orf b occupied first two-thirds of rna genome and produced replicase/transcriptase polyprotein which undergoes autoproteolytic activity with the aid of papain-like proteinase (plpro) and c-like main protease ( clpro or m pro ) to form nonstructural proteins (nsps) . plpro conducts cleavage at n-terminus of replicase polyprotein to produce nsp , nsp , and nsp , required for viral replication (harcourt et al., ) . however, m pro is first protein which autoproteolytically separates polyprotein replicase ab (~ kda, recognition sequence located at leu-gln↓ser,ala,gly; where ↓marks stand for cleavage site) to produced mature viral enzymes and further cleaved downstream nsps at sites to release nsp -nsp ( fig. ) zhang et al., ) . these events indicated the direct role of m pro to mediate maturation of nsps, which are basically required for virus life cycle in host cells. hence, plpro and mpro have been suggested as potential targets in drug development against hcovs. the later reading frames on the genome encoded the four major structural proteins; s, e, m, and n, which are common proteins among all covs . all the viral structural and accessory proteins are decoded by subgenomic (sg) rnas of covs where accessory proteins are interspersed between orfs stands but their number and functional activities are restricted to cov strains . specifically, sars-cov genome translated accessory gene ( a, b, , a, b, a, b, and b), mers-cov encoded accessory genes ( , a, b, , and b), and though exact number of functional proteins remains to be established in sars-cov- but based on previous study on sars-cov, sars-cov- has been predicted with translation of structural proteins (yoshimoto, ) and at least or accessory proteins ( , , a, b, , b, b, , ) (liu et al., ; wu et al., c; zhou et al., b) . also, orf ab position in sars-cov- genome ( - nt) was noticed with change at starting codon position by comparison to sars-cov j o u r n a l p r e -p r o o f ( - nt) and mers-cov ( - nt) . interestingly, conserved amino acid substitution at positions , , , and were also logged in rbd domain of sars-cov- s protein, which was considered as important in sars-cov . it is important to add that genomic material of hcovs is highly susceptible to frequent recombination process which have been directly associated with establishment of altered virulence in new hcov strains (hilgenfeld, ) . all the sars-like covs exhibits typical streadgy for replication and translation following infection in host cell. this section will briefly summarize sars-cov, mers-cov and sars-cov- , their comparative lifecycle in host cell, which began on attachment of virus with host cell receptor and finished with release of newly generated progeny from infected cells. the binding of hcov to host-cell receptor is the initial step in viral infection which determined the severity of infection and pathogenesis. a better understanding of coupling of viral structural proteins with targeted receptor on host cells and other involved proteins, such as host protease, can help to predict the specific zoonotic covs infection in humans. hcovs infection begins with attachment of viral particle on host cell surface by densely glycosylated s protein, which is a trimeric class i fusion protein and consist of two major subunits; a receptor binding domain (s ; also known as rbd) and a second domain (s ) mediated viral fusion with host cell membrane. the fusion process of viral membrane with host cell membrane is triggered when s domain binds with host-cell receptor; for example, angiotensin-converting enzyme (ace ) for sars-cov and sars-cov- (wu et al., b, c) , also as an alternative receptor cd l (a c-type lectin, also called l-sign) with low affinity for sars-cov (jeffers et al., ) , dipeptidyl peptidase- (dpp , also known as cd ) for mers-cov . thus, cleavage of spike glycoprotein is performed by host cell proteases enables interaction of s domain for virus entry into the cell (de wit et al., ) . in the respiratory tract, ace receptor is widely distributed on the epithelial cells of trachea, bronchi, bronchial serous glands, and alveoli , as well as alveolar monocytes and macrophages ; sars-cov attacked these cells and mature virions are later released to infect other new target cells (zhang et al., ) . ace is also diffusely expressed on endothelial cells of arteries and veins, cerebral neurons and immune cells, tubular epithelial cells of kidneys, mucosal cells of intestines, and epithelial cells of renal tubules, presented as a variety of susceptible targets to sars-cov infection (gu and korteweg, ; guo et al., ) . whereas, mers-cov is known to target respiratory tract, liver small intestines, kidney, prostate and activated leukocytes (widagdo et al., ) . remarkably, unlike sars-cov in vitro studies, mers-cov was found to infect human dendritic cells and macrophages ; therefore, virus disrupted the immune system. besides, t (lymphocyte) cells are another potential target for mers-cov due to presence of high amounts of cd . hence, this cov was predicted to dysregulate antiviral t-cell responses because of stimulation of t-cell apoptosis yeung et al., ) . recent studies suggested that sars-cov- employs ace as main receptor as in sars-cov infection with higher affinity, suggesting the likelihood of same group of host-cells being targeted and infected (zhou et al., b; zou et al., ) . after attachment to host-cell surface, virus entry into cell has been deciphered by two different paths based on availability of host cell protease to activate receptor-attached spike protein (fig. ) (simmons et al., ) . in first path, covs invaded host cell as an endosome which is mediated by clathrin-dependent and-independent endocytosis (fig. ) (kuba et al., ; wang et al., a) . this phenomenon induced conformational changes in viral particle which subsequently fused viral envelope with endosomal wall (simmons et al., ) . alternatively, in second pathway, direct invasion of virus particles into host cell are mediated via proteolytic cleavage of receptor-attached spike protein by host's transmembrane serine protease (tmprss ) or transmembrane serine protease d (tmprss d) on the cell surface (heurich et al., ; zumla et al., ) . herein, s domain of spike protein accomplished direct membrane fusion between virus and plasma membrane as initially observed in sars-cov after virus and host cell membrane fusion event, virus released the nucleocapsid packed genomic rna into cellular cytoplasm under the influence of induced structural conformation changes . then, viral genome acted as a mrna and cell's ribosome translates two-thirds of this rna, crossponds to orf a and orf b into two large overlapping polyproteins (pp): pp a and pp ab. the larger polyprotein pp ab translated from a - ribosomal frame shift triggered by slippery sequence (uuuaaac) and downstream rna pseudo knot at end of orf a (masters, ) . this ribosomal frameshift enabled continuous translation of orf a followed by orf b . the encoded polyproteins possess the proteases; pl pro and m pro which assisted in generation of nsps (nsp -nsp ) from polyprotein pp ab, including several replication proteins such as rdrp, rna helicase, and exoribonuclease (exon) . moreover, multifunction and enzyme activities for specific nsps in the previously reported hcov, i.e. sars-cov and mers-cov have been discovered over the past years and summarized elsewhere (masters, ; ziebuhr, ) . most of the newly translated nsps together with structural protein, i.e. n protein, formed the multi-protein replicase-transcriptase complex (rtc) which further conducted the viral genome replication and transcription . at the site of replicative organelles (knoops et al., ) , rtc complex contained rdrp as main replicase-transcriptase protein for the synthesis of negative-sense subgenomic (sg) rna strands from viral rna and transcription of negative-sense subgenomic rna molecules from corresponding positive-sense mrnas . the newly produced minus strands of genomic and sgrnas are subsequently employed as templates for production of positive sense strands (mrnas), j o u r n a l p r e -p r o o f specifically in generation of genomic rna (genome replication) and sg mrnas (transcription). these newly synthesized rna strands acted as genome for generated new viral progeny. also, several smaller mrnas are produced from viral last third of genome which tracks reading frames orf a and orf b, interpreted into viral four structural proteins (s, e, m, and n) and along with accessory proteins (orf a to orf b) become part of viral progeny . besides, other nsps in rtc complex also assist in viral replication and transcription process . for instance, nsp protein, a '- ' exoribonuclease, provides an extra fidelity to rtc complex via proofreading function in rna replication, which lacked in rdrp. likewise, nsp and nsp proteins generated a hexadecameric sliding clamp for rtc complex to catalyst the processivity of rdrp . this increased fidelity and processivity is essentially required in covs during rna synthesis because of their relatively bulky rna genome by comparison to other rna viruses (sexton et al., ) . the viral rna translation process occurred inside host cells' endoplasmic reticulum lead to formation of structural proteins, viz. s, e and m, which moved along the secretory pathway into golgi intermediate compartment. herein, n protein packed the newly produced rna genome and thereby shaped into a helical nucleocapsid. following, virion assembly is triggered by m protein via multiple protein-protein interactions which assisted in incorporation of nucleocapsid, envelope, and spike proteins into virus particles . later, viral progeny germinated into endoplasmic reticulum-golgi intermediate compartment (ergic) and released as secretory vesicles which fused with plasma membrane and secrete from host cell by exocytosis (fig. ) lim et al., ) . generally, human population lacks immunity against covs and hence, susceptible to novel cov infections such as sars-cov- . since, immune response against sars-cov- is not fully j o u r n a l p r e -p r o o f deciphered, recent studies suggested to refer the previous reports on other hcovs, especially sars-cov and mers-cov (fig. ) (yi et al., ) . thus, tlrs mainly mediated the detection of viral rna in mdcs (such as tlrs and some tlr ) and pdcs by tlr (and tlr in human pdcs) (schreibelt et al., ) . based on a specific prr, various-partially cross-talking-signaling pathways resulted in promoters transactivation of antiviral genes (o'neill et al., ) . for instance, a prototypical pamp relevant for covs is dsrna, a by-product from genome replication and transcription (weber et al., ; zielecki et al., ) . dsrna can also be detected by tlr in the endosome while sensed by rna helicases rig-i, mda and kinase pkr in the cytoplasm (rasmussen et al., ; yim and williams, ; yoneyama et al., ) . also, specific ssrnas are presented as pamps, either if they displayed particular features or in the wrong location; for example, tlr detects gu-rich ssrna in the endosome (heil et al., ) . thus, numerous types of prrs are regularly surveying the intracellular and extracellular space to sense virus infections in a sensitive and timely manner. the detection of viral infection triggers complex signaling cascades such as myd that induced manufacture of type i ifns and stimulation of transcription factor nuclear factor-κb (nf-κb). in turn, active nf-κb induced transcription of pro-inflammatory cytokines (fig. ) . moreover, type i ifns signal by ifnα/β receptor (ifnar) and following downstream signal activators and transducers of transcription (stat) proteins triggered the manufacture of antiviral proteins that are programmed by interferon-stimulated genes (isgs) like ifn-induced protein j o u r n a l p r e -p r o o f with tetratricopeptide repeats (ifit ). altogether, this launches an antiviral immune response that restricts viral replication in infected and in neighbouring cells (de wit et al., ) . however, studies have showed that family of covs can significantly suppressed human immune responses against viral infection by evading immune detection machinery (kikkert, ) . for instance, papain-like protease (plpro) domain of nsp of sars-cov interrelated with ifn regulatory factor (irf ) and inhibited its activation (devaraj et al., ; frieman et al., ) . besides, plpro was reported to cause deubiquitination (or inhibit ubiquitination) of tankbinding kinase (tbk ), rig-i, and irf (clementz et al., ; devaraj et al., ; frieman et al., ; sun et al., ) . the several functions and mechanisms adopted to counteract ifn induction, and strategies to develop resistance against ifn by previously pandemic hcovs are summarized earlier (kindler et al., ) . remarkably, sars-cov and mers-cov were reported to induced production of double-membrane vesicles that lack prrs, replicated in these vesicles, and thereby escaped host detection system for viral dsrna (de wilde et al., ; knoops et al., ) . moreover, covs induced very little ifn production in most of cell types (kindler et al., ) . thus, high levels of dsrna, which are generated during viral replication cycle (weber et al., ; zielecki et al., ) , do not caused an adequate induction of ifn system. moreover, antigen presentation subsequently stimulated body's humoral and cellular immunity on viral invasion, which are mediated by virus-specific b and t cells. t lymphocytes, including cluster of differentiation (cd + ) and cluster of differentiation (cd + ) t cells, play a central role against viral infection, stimulated b cells to produce virus-specific antibodies while cd + t cells directly kills virus-infected cells. also, humoral immunity, including complements such as c a, c a and antibodies, are critical in fighting viral infection (fig. ) (mathern and heeger, ; traggiai et al., ) . recent flow cytometric analysis of peripheral blood from sars-cov- -infected patients showed substantially reduced cd + and cd + t cells number while their status was excessively activated as evident from high proportions of human leukocyte antigen -dr isotype (hla-dr) (cd . %) and cd (cd . %) double positive fractions . similarly, acute phase response in patients with sars-cov was associated with severe decrease of cd + t and cd + t cells. even if there is no antigen, cd + and cd + memory t cells are known to persist for four years as observed in sars-cov recovered individuals and were able to perform t cell proliferation, delayed-type hypersensitivity (dth) j o u r n a l p r e -p r o o f response and production of ifn-γ (fan et al., ) . also, six years after sars-cov infection, specific t-cell memory response to sars-cov s peptide library was identified in of recovered sars patients (tang et al., ) . the specific cd + t cells were documented to exhibit a similar effect on mers-cov clearance in mice (zhao et al., ) . these discoveries could be helpful to deduce a valuable information for the rational design of vaccines against sars-cov- . for example, antibodies collected from a recovered patient were reported to neutralized mers-cov infection (niu et al., ) . moreover, t helper cells also produced proinflammatory cytokines to assist the defending cells. however, cov (sars-cov and mers-cov) were established to halt t cell function and induced their apoptosis mathern and heeger, ; yeung et al., ) . besides, sars-cov- assumed to attach with ace as in sars-cov infection, target and infect the same set of host cells zhou et al., b; zou et al., ) . additionally, ace -associated lung injury was documented in sars-cov infection kuba et al., ) ; s protein of sars-cov downregulates ace (glowacka et al., ; wang et al., b) and induce detachment of catalytically active ace ectodomain (haga et al., ; jia et al., ) . this results in nonfunctional pulmonary ace receptor which has been advised to be linked with acute lung injury (imai et al., ; kuba et al., ) ; decrease activity of ace further triggered reninangiotensin system (ras) dysfunction and caused enhance inflammation and vascular permeability (gheblawi et al., ) . in animal studies with murine acute respiratory distress (ard) model showed association of reduced ace function with an increased lung edema, neutrophil accumulation, enhanced vascular permeability, and diminished lung function . also, in human airway epithelia, constitutive shedding of ace receptor by activity of a metalloprotease (adam ), also called as tumour necrosis factor alpha (tnf-α) converting enzyme (tace), and disintegrin secrete functionally active soluble ace (sace ) (lambert et al., ) . hcovs infection and inflammatory cytokines like interleukin beta (il- β) and tnf-α were related with enhance ace shedding (haga et al., ; jia et al., ) . notably, in vitro studies presented close association of sars-cov s protein-induced ace shedding with tnf-α production (haga et al., ) . although, biological function of sace is yet unknown, however, recent studies have suggested direct involvement of sace in inflammatory responses against sars-cov, and possibly also connected with sars-cov- (fu et al., ) . additionally, apoptosis of type alveolar cells caused release of specific j o u r n a l p r e -p r o o f inflammatory mediators which further instigate macrophages to secrete three essential immune substances; interleukin- (il- ), interleukin- (il- ), and tnf-α; also called as cytokines. these immune substances in the bloodstream produced infection symptoms linked to hcovs . recent in vitro cell experiments showed that delay release of cytokines and chemokines occurred in respiratory epithelial cells, dendritic cells (dcs), and macrophages at the early stage of sars-cov infection (choi and joo, ) . like sars, mers-cov also infected human airway epithelial cells, thp- cells (a monocyte cell line), human peripheral blood monocyte-derived macrophages and dcs, and induced late but elevated levels of proinflammatory cytokines and chemokines (tynell et al., ; zhou et al., ) . notably, sars-cov- infection is suspected to cause pyroptosis in lymphocytes and macrophages. it was observed that lymphocytopenia is often seen in severe sars-cov- patients and cytokine release syndrome (crs) induced by sars-cov- was also considered to be facilitate by leukocytes other than t cells . a vast majority of patients ( . %) infected with sars-cov- have been logged for peripheral blood lymphopenia (guan et al., ) , supported the pulmonary infiltration of lymphocytes and/or cell damage via pyroptosis or apoptosis . previous pandemics triggered by mers-cov and sars-cov were also reported with massive production of chemokines and cytokines; sars-cov exhibited ccl , ccl , ccl , cxcl , cxcl , cxcl , etc.; and il- , il- , il- , il- beta, il- , ifn-alpha, ifn-gamma, tnf-α and transforming growth factor (tgf)-beta. likewise, mers-cov was reported for elevated expression of cytokines ifn-α, il- , and chemokine (cxcl- , ccl- , and cxcl- ) . hence, acute respiratory distress syndrome (ards) is caused by cytokine storm that triggers a destruction in host cells via immune system and subsequently results into multiple organs failure or death as stated in case of sars-cov- outbreak; similar observations were noted in case of sars-cov infection (kumar et al., ) . albeit, there is no direct data is available to corelate the participation of pro-inflammatory cytokines and chemokines in lung pathology through sars-cov and mers-cov, correlative observations and recorded from patients with severe disease suggested a role of hyper-inflammatory responses in hcov pathogenesis (fig. ) (channappanavar and perlman, ) . for instance, in mers-cov infection, plasmacytoid dendritic cells, but not mononuclear macrophages and dcs (scheuplein et al., ) , were induced to produce a large amount of ifns (choi and joo, ) . (yi et al., ) . despite of similar virus titers in respiratory tract, sars-cov-infected old nonhuman primates are more likely to develop immune dysregulation than infected young primates, leading to more severe disease manifestations (smits et al., ) . it seems that excessive inflammatory response rather than virus titer is more relevant to the death of the old nonhuman primates (smits et al., ) . similarly, in bagg albino/c (balb/c) mice infected with sars-cov, disease severity in old mice was related to early and disproportionately strong upregulation of ards-related inflammatory gene signals (rockx et al., ) . the rapid replication of sars-cov in balb/c mice induces delayed release of ifn-α/β, which was accompanied by influx of many pathogenic inflammatory mononuclear macrophages (channappanavar et al., ) . depleting inflammatory monocyte-macrophages or neutralizing inflammatory cytokine tnf protected the mice from fatal sars-cov infection. thus, inflammatory mediators contributes an vital role in pathogenesis of ards, which was estimated as an leading cause of death in patients infected with sars-cov or mers-cov lew et al., ) . it is now known that several proinflammatory cytokines consequences of cytokine storm contribute to the occurrence of ards (channappanavar and perlman, ; reghunathan et al., ) . these mechanisms also lead to activation of coagulation pathways. massive inflammation can impaired all the three control mechanisms like antithrombin iii, tissue factor pathway inhibitor, and protein c system (jose et al., ) ; with reduced anticoagulant concentrations due to reduced production and increasing consumption. this defective procoagulant-anticoagulant balance predisposes in the development of microthrombosis, disseminated intravascular coagulation, and multiorgan failure; as evident from severe sars-cov- pneumonia with raised d-dimer concentrations being a poor prognostic feature and disseminated intravascular coagulation common in nonsurvivors zhou et al., a) . in this over all proposed mechanism, proteinase-activated receptor- (par- ) acts as main thrombin receptor and mediates thrombininduced platelet aggregation, and interplay between coagulation, inflammatory, and fibrotic responses; all of these factors are an important aspects of pathophysiology of fibroproliferative lung disease (jose et al., ) , such as seen in sars-cov- . on the other hand, the proposed events of cytokine storms in case of sars-cov- was suggested to increased inflammationrelated biomarkers, including c-reactive protein (crp), ferroprotein, erythrocyte sedimentation j o u r n a l p r e -p r o o f rate (esr) and il- huang et al., ) . in conclusion, based on previous hcovs infection, severity and pathogenesis of sarscov- was suggested to divided into three stages; stage- , an asymptomatic incubation time with or without detectable virus; stage- , nonsevere symptomatic period and detection of viral particles; stage- , severe respiratory symptomatic stage and detection of high viral load . furthermore, based on previous studies of sars-cov, the inflammatory responses in sars-cov- infection can be classified into primary and secondary responses . initially, primary inflammatory responses produced subsequently viral infection, prior to arrival of neutralizing antibodies (nab). the activation of these factors is primarily driven by viralmediated ace downregulation and shedding, vigorous viral replication, and host antiviral defense system. secondary inflammatory responses are generated by the adaptive immunity and nab. moreover, virus-nab complex was also suggested to triggered fc receptor (fcr)-mediated inflammatory responses and acute lung injury that results in persistent viral replication and inflammatory responses from host macrophages (fig. ) (fu et al., ) . it was observed that patients could survive in primary inflammatory responses but secondary inflammatory responses could be fatal. secondary inflammatory responses in which virus-nab complex formed was considered as targeted to develop potential therapeutic strategy along with anti-inflammatory drugs (fu et al., ) . accumulating data on hcovs exhibits the importance of understanding the zoonotic viral transmission and pathogenesis in humans. recent studies on virus have established the viral proteins as prime target in the drug designing and vaccine development; however, this review have highlighted the utmost importance of intermediate host for the viral transmission to human. future approaches, therefore, should considered the strains from intermediate hosts in the therapeutic development pipelines to better understand the severity of virulence via genome recombination process in covs. we also concluded major damaged caused by the failure of host j o u r n a l p r e -p r o o f immune system against hcov infection and further caused by insurgence of cytokines which lead to severe mutilation of the host body. synergistic and/or multi-target strategies that check viral growth and malfunctioned immune system of the host cells simultaneously might also be successful in battle against hcovs. nevertheless, synergistic approaches must take into account crossponding to the complementary target pathways. when developing novel therapeutic strategies to check the immunoregulatory cytokines such as tnfβ and il , investigation should be considered on the viral strain and targeted organ specificity; for example, sars-cov- has more affinity to ace which are scattering on different organs like lung and kidney while mers-like cov can even infect t-cells. in addition, we should be cognizant of the feedback responses that produce with any treatment and consider the possibility to leveraged in a combinatorial fashion, taking into consideration the outcomes of preceding standard care and/or target immunoregulatory molecules will affect the efficacy and incidence of virulence. another utmost point to be consider is how to generalize the therapeutic decision under the different immunological responses to the viral infection; for instance, susceptibility of some persons and with asymptomatic symptoms or sever immune response to the infection. given the relatively high emergence of hcovs and potential threat to humans, future therapeutic strategies should involve deep immune profiling of the infected individuals and personalization of therapeutics when feasible to accelerate progress towards more effective treatment approaches. this goal is ever closer to becoming a reality as multiplexed imaging, immunophenotyping and mutational analysis tools are increasing the high-throughput process. although, many trials have failed before, but given the progress in our understanding on the interaction between host immune responses and viral escape plans, and the emerging sophisticated strategies we have reasons to be hopeful for the future successful treatment against hcovs. authors declares no conflict of interest. insights into the recent novel coronavirus (sars-cov- ) in light of past human coronavirus outbreaks cryo-electron tomography of mouse hepatitis virus: insights into the structure of the coronavirion activation of the sars coronavirus spike protein via sequential proteolytic cleavage at two distinct sites mechanisms of coronavirus cell entry mediated by the viral spike protein modulation of murine dendritic cell function by adenine nucleotides and adenosine: involvement of the a( b) receptor environmental contamination and viral shedding in mers patients during mers-cov outbreak in south korea emergence of novel coronavirus and covid- : whether to stay or die out? the coronavirus spike protein is a class i virus fusion protein: structural and functional characterization of the fusion core complex bats: important reservoir hosts of emerging viruses why snakes probably aren't spreading the new china virus modular organization of sars coronavirus nucleocapsid protein dysregulated type i interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in sars-cov-infected mice ifn-i response timing relative to virus replication determines mers coronavirus infection outcomes pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology a murine virus (jhm) causing disseminated encephalomyelitis with extensive destruction of myelin epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study preparedness and proactive infection control measures against the emerging novel coronavirus in china the pathogenesis and alternative treatment of sars-cov transmission characteristics of mers and sars in the healthcare setting: a comparative study middle east respiratory syndrome coronavirus efficiently infects human primary t lymphocytes and activates the extrinsic and intrinsic apoptosis pathways productive replication of middle east respiratory syndrome coronavirus in monocyte-derived dendritic cells modulates innate immune response deubiquitinating and interferon antagonism activities of coronavirus papain-like proteases new coronavirus threat galvanizes scientists preliminary epidemiological assessment of mers-cov outbreak in south korea origin and evolution of pathogenic coronaviruses this scientist hopes to test coronavirus drugs on animals in locked-down wuhan middle east respiratory syndrome coronavirus (mers-cov): announcement of the coronavirus study group coronavirus particle assembly: primary structure requirements of the membrane protein mers-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin a or interferon-alpha treatment sars and mers: recent insights into emerging coronaviruses regulation of irf- -dependent innate immunity by the papain-like protease domain of the severe acute respiratory syndrome coronavirus ecology, evolution and classification of bat coronaviruses in the aftermath of sars clinical features and virological analysis of a case of middle east respiratory syndrome coronavirus infection characterization of sars-cov-specific memory t cells from recovered individuals years after infection the nsp macrodomain promotes virulence in mice with coronavirus-induced encephalitis coronaviruses: an overview of their replication and pathogenesis furin cleavage of the sars coronavirus spike glycoprotein enhances cell-cell fusion but does not affect virion entry severe acute respiratory syndrome coronavirus papain-like protease ubiquitin-like domain and catalytic domain regulate antagonism of irf and nf-kappa b signaling understanding sars-cov- -mediated inflammatory responses: from mechanisms to potential therapeutic tools bat coronaviruses. bats and viruses angiotensin-converting enzyme : sars-cov- receptor and regulator of the renin-angiotensin system: celebrating the th anniversary of the discovery of ace differential downregulation of ace by the spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus nl the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- severe acute respiratory syndrome coronavirus phylogeny: toward consensus pathology and pathogenesis of severe acute respiratory syndrome isolation and characterization of viruses related to the sars coronavirus from animals in southern china pathogenetic mechanisms of severe acute respiratory syndrome modulation of tnf-alpha-converting enzyme by the spike protein of sars-cov and ace induces tnf-alpha production and facilitates viral entry a new virus isolated from the human respiratory tract identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity species-specific recognition of single-stranded rna via toll-like receptor and mers coronavirus in dromedary camel herd, saudi arabia tmprss and adam cleave ace differentially and only proteolysis by tmprss augments entry driven by the severe acute respiratory syndrome coronavirus spike protein from sars to mers: crystallographic studies on coronaviral proteases enable antiviral drug design identification of in vivo-interacting domains of the murine coronavirus nucleocapsid protein the discovery of angiotensin-converting enzyme and its role in acute lung injury in mice angiotensin-converting enzyme protects from severe acute lung failure human coronavirus oc infection induces chronic encephalitis leading to disabilities in balb/c mice cd l (l-sign) is a receptor for severe acute respiratory syndrome coronavirus cross-species transmission of the newly identified coronavirus -ncov ectodomain shedding of angiotensin converting enzyme in human airway epithelia zoonosis emergence linked to agricultural intensification and environmental change proteinase-activated receptors in fibroproliferative lung disease human coronavirus-hku infection among adults in cleveland innate immune evasion by human respiratory rna viruses interaction of sars and mers coronaviruses with the antiviral interferon response identification of a coronavirus hemagglutinin-esterase with a substrate specificity different from those of influenza c virus and bovine coronavirus sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum trilogy of ace : a peptidase in the reninangiotensin system, a sars receptor, and a partner for amino acid transporters angiotensin-converting enzyme in lung diseases a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury the role of superspreading in middle east respiratory syndrome coronavirus (mers-cov) transmission. euro surveillance : bulletin europeen sur les maladies transmissibles host immune response and immunobiology of human sars-cov- infection tumor necrosis factor-alpha convertase (adam ) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (sars-cov) receptor, angiotensin-converting enzyme- (ace ) severe acute respiratory syndrome coronavirus-like virus in chinese horseshoe bats a major outbreak of severe acute respiratory syndrome in hong kong fruit bats as reservoirs of ebola virus acute respiratory distress syndrome in critically ill patients with severe acute respiratory syndrome angiotensin-converting enzyme is a functional receptor for the sars coronavirus bats are natural reservoirs of sars-like coronaviruses human coronaviruses: a review of virus-host interactions accessory proteins of sars-cov and other coronaviruses epithelial cells lining salivary gland ducts are early target cells of severe acute respiratory syndrome coronavirus infection in the upper respiratory tracts of rhesus macaques drug treatment options for the -new coronavirus ( -ncov) genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding a comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? emerging novel coronavirus ( -ncov)-current scenario, evolutionary perspective based on genome analysis and recent developments the molecular biology of coronaviruses molecules great and small: the complement system recovery in tracheal organ cultures of novel viruses from patients with respiratory disease middle east respiratory syndrome coronavirus in bats, saudi arabia trypsin treatment unlocks barrier for zoonotic bat coronavirus infection host cell entry of middle east respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein immunology, infection, . genotype and phenotype of covid- : their roles in pathogenesis mers coronavirus neutralizing antibodies in camels differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins s, m and e genetic predisposition to acquire a polybasic cleavage site for highly pathogenic avian influenza virus hemagglutinin supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy ultrapotent human neutralizing antibody repertoires against middle east respiratory syndrome coronavirus from a recovered patient the history of toll-like receptors -redefining innate immunity are bats really 'special' as viral reservoirs? what we know and need to know. bats and viruses middle east respiratory syndrome coronavirus (mers-cov): animal to human interaction clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study coronavirus e-related pneumonia in immunocompromised patients isolation of mers coronavirus from a dromedary camel dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc innate recognition of intracellular pathogens: detection and activation of the first line of defense middle east respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study early upregulation of acute respiratory distress syndrome-associated cytokines promotes lethal disease in an aged-mouse model of severe acute respiratory syndrome coronavirus infection the coronavirus e protein: assembly and beyond co-circulation of three camel coronavirus species and recombination of mers-covs in saudi arabia animal coronaviruses: what can they teach us about the severe acute respiratory syndrome? revue scientifique et technique-office international des épizooties high secretion of interferons by human plasmacytoid dendritic cells upon recognition of middle east respiratory syndrome coronavirus toll-like receptor expression and function in human dendritic cell subsets: implications for dendritic cell-based anti-cancer immunotherapy homology-based identification of a mutation in the coronavirus rna-dependent rna polymerase that confers resistance to multiple mutagens covid- infection: the perspectives on immune responses additional changes to taxonomy ratified in a special vote by the international committee on taxonomy of viruses proteolytic activation of the sarscoronavirus spike protein: cutting enzymes at the cutting edge of antiviral research the m, e, and n structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles exacerbated innate host response to sars-cov in aged non-human primates human coronavirus nl infections in infants hospitalised with acute respiratory tract infections in south africa unique and conserved features of genome and proteome of sars-coronavirus, an early split-off from the coronavirus group lineage crosshost evolution of severe acute respiratory syndrome coronavirus in palm civet and human from sars to mers, thrusting coronaviruses into the spotlight coronavirus papain-like proteases negatively regulate antiviral innate immune response through disruption of sting-mediated signaling lack of peripheral memory b cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia an efficient method to make human monoclonal antibodies from memory b cells: potent neutralization of sars coronavirus middle east respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocyte-derived macrophages and dendritic cells genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mbio . van der hoek development of one-step, real-time, quantitative reverse transcriptase pcr assays for absolute quantitation of human coronaviruses oc and e clinical impact of human coronaviruses e and oc infection in diverse adult populations clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china. jama sars coronavirus entry into host cells through a novel clathrin-and caveolae-independent endocytic pathway review of bats and sars endocytosis of the receptorbinding domain of sars-cov spike protein together with virus receptor ace double-stranded rna is produced by positive-strand rna viruses and dna viruses but not in detectable amounts by negativestrand rna viruses differential expression of the middle east respiratory syndrome coronavirus receptor in the upper respiratory tracts of humans and dromedary camels characterization and complete genome sequence of a novel coronavirus, coronavirus hku , from patients with pneumonia discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus analysis of therapeutic targets for sars-cov- and discovery of potential drugs by computational methods a new coronavirus associated with human respiratory disease in china c. a new coronavirus associated with human respiratory disease in china dampened sting-dependent interferon activation in bats pathological findings of covid- associated with acute respiratory distress syndrome the structure and functions of coronavirus genomic ' and ' ends drug design targeting the main protease, the achilles' heel of coronaviruses design of wide-spectrum inhibitors targeting coronavirus main proteases mers coronavirus induces apoptosis in kidney and lung by upregulating smad and fgf covid- : what has been learned and to be learned about the novel coronavirus disease protein kinase r and the inflammasome regulation of antiviral innate immune signaling by stressinduced rna granules the proteins of severe acute respiratory syndrome coronavirus- (sars cov- or n-cov ), the cause of covid- crystal structure of sars-cov- main protease provides a basis for design of improved alphaketoamide inhibitors the life cycle of sars coronavirus in vero e cells rapid generation of a mouse model for middle east respiratory syndrome single-cell rna expression profiling of ace , the putative receptor of wuhan -ncov. biorxiv elevated exhaustion levels and reduced functional diversity of t cells in peripheral blood may predict severe progression in covid- patients clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study active replication of middle east respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis a novel coronavirus from patients with pneumonia in china coronavirus replication and reverse genetics human cell tropism and innate immune system interactions of human respiratory coronavirus emc compared to those of severe acute respiratory syndrome coronavirus single-cell rna-seq data analysis on the receptor ace expression reveals the potential risk of different human organs vulnerable to -ncov infection coronaviruses -drug discovery and therapeutic options middle east respiratory syndrome key: cord- -cja i hw authors: habibzadeh, parham; stoneman, emily k title: the novel coronavirus: a bird's eye view date: - - journal: int j occup environ med doi: . /ijoem. . sha: doc_id: cord_uid: cja i hw the novel coronavirus ( -ncov) outbreak, which initially began in china, has spread to many countries around the globe, with the number of confirmed cases increasing every day. with a death toll exceeding that of the sars-cov outbreak back in and in china, -ncov has led to a public health emergency of international concern, putting all health organizations on high alert. herein, we present on an overview of the currently available information on the pathogenesis, epidemiology, clinical presentation, diagnosis, and treatment of this virus. c oronaviruses typically result in respiratory and enteric infections affecting both animals and humans, and were considered relatively benign to humans before the severe acute respiratory syndrome (sars-cov) outbreak in and in china. [ ] [ ] [ ] [ ] a decade later, middle east respiratory syndrome coronavirus (mers-cov), another pathogenic coronavirus with a clinical picture reminiscent of sars, was isolated in patients presenting with pneumonia in the middle eastern countries. just recently, in december , a novel coronavirus ( -ncov) has emerged in wuhan, china and has turned into a global health concern. coronaviruses are enveloped positivestranded rna viruses that belong to the family coronaviridae and the order nidovirales. people around the globe the novel coronavirus ( -ncov) outbreak, which initially began in china, has spread to many countries around the globe, with the number of confirmed cases increasing every day. with a death toll exceeding that of the sars-cov outbreak back in and in china, -ncov has led to a public health emergency of international concern, putting all health organizations on high alert. herein, we present on an overview of the currently available information on the pathogenesis, epidemiology, clinical presentation, diagnosis, and treatment of this virus. are frequently infected with four human coronaviruses ( e, nl , oc , and hku with the first two classified as antigenic group and the latter two belonging to group ) typically leading to an upper respiratory tract infection manifested by common cold symptoms. however, coronaviruses, which are zoonotic in origin, can evolve into a strain that can infect human beings leading to fatal illness. examples are sars-cov, mers-cov, and the recently identified -ncov. the expansion of genetic diversity among coronaviruses and their consequent ability to cause disease in human beings is mainly achieved through infecting peridomestic animals, which serve as intermediate hosts, nurturing recombination and mutation events. the spike glycoprotein (s glycoprotein), which attaches the virion to the host cell membrane, is postulated to play a dominant role in host range restriction. while sars-cov infects type pneumocytes and ciliated bronchial epithelial cells utilizing angiotensin converting enzyme as a receptor, mers-cov exploits dipeptidyl peptidase (dpp ), a transmembrane glycoprotein, to infect type pneumocytes and unciliated bronchial epithelial cells. [ ] [ ] [ ] [ ] in general, coronaviruses first replicate in epithelial cells of the respiratory and enteric cells, which leads to cytopathic changes. thorough studies have not yet been conducted to elucidate the molecular basis of the pathogenicity of -ncov. however, preliminary data obtained through whole-genome sequencing of the viral rna extracted from host cell-depleted nasopharyngeal and sputum samples and subsequent bioinformatics analyses have shown that the novel virus is phylogenetically related to sars-related coronaviruses first isolated in chinese horseshoe bats during the period of to . , it has also been hypothesized that the novel virus might use angiotensin converting enzyme as a receptor similar to sars-cov. unlike sars-cov or mers-cov, primary human airway epithelial cells provide better growth conditions for -ncov than standard tissue culture cells. a series of patients with pneumonia of unknown etiology were initially reported by the health commission of hubei province, china, on december , ( fig ) . although patients were initially announced to be afflicted with this mysterious disease, the number rose to with seven critically ill patients; one death was noted in the subsequent report on january , . the chinese authorities reporting to who stated that some of the patients were operating dealers or vendors in the huanan seafood market, which was subsequently reported to be selling live and freshly slaughtered hunted animals. , several reports of clusters of cases among families and infection of health care workers pointed to human-to-human transmission of the virus. , , despite recognition of the outbreak within a few weeks by the chinese using their efficient surveillance network and laboratory infrastructure, efforts to prevent the spread of this virus were not sufficient; as of february , , at least cases with a death toll of in more than countries have been reported (fig ) . with a crowded population eclipsing that of new york city by more than . million and its role as one of china's major transportation hubs, the city of wuhan was the ideal breeding ground for an outbreak. peak travel season due to the chinese new year was probably an important factor that led to the global spread of the infection. in a study of cases infected up to january , the basic reproductive number, or r , of the virus was estimated to be approximately . . this means that each patient can, on average, spread the infection to more than two healthy persons. this number was around for the sars-cov outbreak, which was eventually contained as a result of efficient infec- , presence of cases with mild clinical presentation and lack of infrastructure to provide isolation for infected individuals and their close contacts, particularly in resource-limited countries, are nonetheless all hurdles to control this infection. furthermore, based on experience, proper precautionary measures to prevent nosocomial transmission of the virus is mandatory; the majority of patients with sars-cov and mers-cov had become infected in health care settings. considering the plethora of comorbid conditions present in hospital populations, dire complications could arise in the setting of an outbreak. overall, infection caused by the -ncov shares many clinical similarities with infection caused by sars-cov. a typical human coronavirus has an incubation period of - days; it is estimated to be - days for the -ncov, and - days for sars-cov. , , , infection with -ncov, similar to sars-cov, presents with non-specific symptoms such as malaise, fever, and dry cough at the prodromal phase. , , in a study of patients with confirmed -ncov infection, the mean duration from illness onset to the first medical visit was . ( % ci . to . ) days for cases with disease onset before january , , and . ( % ci . to . ) days for patients with illness onset between january and . a report by huang, et al, on confirmed cases of -ncov infection who were admitted to wuhan hospital indicated that fever ( %), cough ( %), dyspnea ( %), and myalgia or fatigue ( %) were the most common presenting signs and symptoms. in another report from china, these findings were corroborated. in contrast to re v i e w patients with typical human coronavirus infections, few of those affected with the novel coronavirus had upper respiratory tract signs and symptoms (eg, sore throat, rhinorrhea). unlike sars-cov, intestinal presentations (eg, diarrhea) seem to be infrequent in patients with -ncov. [ ] [ ] [ ] given the similarities between sars-cov and -ncov, it is tempting to speculate about viremia and affected tissues beyond the respiratory tract. however, we are not aware of any data on this yet. chest x-ray and computed tomography (ct) findings showed bilateral lung involvement in ( %) of confirmed patients studied in two reports, , again similar to infection with sars-cov. among these cases, ( %) had lymphopenia; ( %) had an elevation of either aspartate aminotransferase (ast) or alanine aminotransferase (alt) above the upper limit of the reference range , (also seen in sars-cov). among infection-related biomarkers, procalcitonin levels have been normal among most of the reported individuals; elevated levels were observed in those with secondary infections. , however, elevated serum ferritin and c-reactive protein levels were, respectively, reported in % and % of the patients reported by chen, et al. similar to the findings in sars-cov infection, an increase in plasma pro-inflammatory cytokines levels has also been reported, correlating with the severity of the illness. , however, increased levels of interleukin , which is an anti-inflammatory cytokine, suggest a pattern different from that of sars-cov infection. , further investigations to characterize the cytokine profile of patients could shed light on -ncov pathogenesis. in the wake of the peak of influenza and other respiratory viral infections in the northern hemisphere and nonspecific clinical findings resembling other cases of viral pneumonia, early detection of those infect-ed with -ncov is an onerous task for health care professionals around the globe. eliciting the exposure history of suspicious cases could have been an effective strategy in the earlier stages of the outbreak in china. however, the global spread of the virus and human-to-human transmission seen in recent weeks have made the situation more complicated. in general, infected patients had a median age ranging from to years; male individuals are more frequently infected. , , lack of serious disease in children is also a feature of sars-cov infection, and a feature of some (but not all) coronavirus infections in other species. immune-related genes on the x chromosome and sex hormones, which influence both innate and adaptive immune responses, might explain the higher susceptibility to the infection in males. , higher likelihood of exposure to the virus due to occupational risk could be another contributory factor. the full genomic sequence of the -ncov was released shortly after the start of the outbreak to public databases. this, in turn, paved the way for the development of pcr assays to detect the virus. rapid collection and nucleic acid amplification testing of appropriate respiratory samples (ie, nasopharyngeal and oropharyngeal swab in outpatient cases and sputum and/or endotracheal aspirate or bronchoalveolar lavage in patients with more critical conditions) for suspicious cases are currently recommended by who. there are no vaccines or specific antivirals for -ncov. nonetheless, there are ongoing efforts for vaccine development. remdesivir, an antiviral drug developed for the treatment of ebola virus disease, was used for the treatment of the first us case of -ncov. an ongoing randomized controlled trial evaluating the the novel coronavirus efficacy and safety of lopinavir-ritonavir and interferon-α b in patients infected with the novel coronavirus was launched on january , . however, isolation and supportive care including oxygen therapy, fluid management, and administration of antimicrobials for treatment of secondary bacterial infections to alleviate the symptoms and prevent end-organ dysfunction is currently recommended by who for suspected and confirmed cases requiring hospital admission. the novel coronavirus, which comes from a viral family that was thought to be rather benign before the turn of the century, has led to a public health emergency of international concern according to who. outbreaks like this highlight the importance of effective public health strategies to counteract the never-ending threats imposed by emerging pathogens. origin and evolution of pathogenic coronaviruses identification of a novel coronavirus in patients with severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome epidemiology and cause of severe acute respiratory syndrome (sars) in guangdong, people's republic of china isolation of a novel coronavirus from a man with pneumonia in saudi arabia a novel coronavirus from patients with pneumonia in china clinical virology epidemiology, genetic recombination, and pathogenesis of coronaviruses coronavirus infections---more than just the common cold host factors in coronavirus replication angiotensin-converting enzyme is a functional receptor for the sars coronavirus innate immune response of human alveolar type ii cells infected with severe acute respiratory syndrome-coronavirus molecular basis of binding between novel human coronavirus mers-cov and its receptor cd dipeptidyl peptidase is a functional receptor for the emerging human coronavirus-emc a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster genomic characterization and infectivity of a novel sars-like coronavirus in chinese bats and epidemiology of novel coronavirus: implications for virus origins and receptor binding chp closely monitors cluster of pneumonia cases on mainland chp provides further information on cluster of pneumonia cases in wuhan a novel coronavirus outbreak of global health concern importation and human-to-human transmission of a novel coronavirus in vietnam the chinese city of wuhan was a breeding ground for an outbreak, experts say. the coronavirus has infected more than people early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia dynamically modeling sars and other newly emerging respiratory illnesses: past, present, and future transmission characteristics of mers and sars in the healthcare setting: a comparative study epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with novel coronavirus in wuhan epidemiological, demographic, and clinical characteristics of cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome functions and regulation of t cell-derived interleukin- transmission of -ncov infection from an asymptomatic contact in germany sexual dimorphism in innate immunity the x chromosome in immune functions: when a chromosome makes the difference chinese researchers reveal draft genome of virus implicated in wuhan pneumonia outbreak available from www.who.int/publications-detail/laboratorytesting-for- -novel-coronavirus-in-suspectedhuman-cases- available from www.niaid.nih.gov/diseases-conditions/mers-sars-therapeutics-vaccines first case of novel coronavirus in the united states a randomized, open-label, blank-controlled trial for the efficacy and safety of lopinavir-ritonavir and interferon-alpha b in hospitalization patients with novel coronavirus infection. available from www. chictr.org.cn/showprojen.aspx?proj= (accessed available from www.who.int/ publications-detail/clinical-management-of-severeacute-respiratory-infection-when-novel-coronavirus-(ncov)-infection-is-suspected available from www.who.int/ news-room/detail/ - - -statement-on-thesecond-meeting-of-the-international-health-regulations-( )-emergency-committee-regarding-theoutbreak we would like to thank dr. mohammad sajadi from the institute of human virology, university of maryland for his invaluable comments. financial support: none. key: cord- -qp h un authors: stein, richard albert title: the coronavirus: learning curves, lessons, and the weakest link date: - - journal: int j clin pract doi: . /ijcp. sha: doc_id: cord_uid: qp h un in the space of just six weeks, a new coronavirus, from a family that historically was not viewed as a global health concern, has become daily headline news around the globe. the st century marked its arrival with the emergence of three previously unknown coronaviruses. sars-cov (severe acute respiratory syndrome coronavirus) was recognized in november [ , ], mers-cov (middle east respiratory syndrome coronavirus) in june [ , ], and -ncov in december [ ]. previously, human coronaviruses, known since the s, were viewed as being only marginally relevant to the clinic, except for infants, the elderly, and immunocompromised individuals [ , , ]. in the space of just six weeks, a new coronavirus, from a family that his torically was not viewed as a global health concern, has become daily headline news around the globe. the st century marked its arrival with the emergence of three previously unknown coronaviruses. sars-cov (severe acute respiratory syndrome coronavirus) was recognized in november , , mers-cov (middle east respiratory syndrome coronavirus) in june , , and -ncov in december . previously, human coronaviruses, known since the s, were viewed as being only marginally relevant to the clinic, except for infants, the elderly, and immunocompromised individuals. , , what these, and several other recent outbreaks have in common, is how fast they circled the world. outbreaks that centuries ago needed weeks or months to spread globally can today reach any continent within days. the first, spring wave of the spanish flu, at a time when travel by ship was the fastest way of transportation around the world, spread through the united states, europe, and possibly asia over six months. , the pandemic affected over a quarter of the world's population, caused - million deaths, more than the two world wars combined, and caused life expectancy at birth in the united states to drop by . years between and . , , in comparison, in - the sars-cov spread to countries within hours, and in the h n influenza virus spread to countries within weeks. in the most recent of the three coronavirus outbreaks, several clusters of patients with pneumonia started to be reported on december , from wuhan, china, and most of them were epidemiologically linked to the huanan seafood wholesale market. , [ ] [ ] [ ] the market was closed on january , . by february , , the virus, -ncov, was reported from > countries and special administrative regions, affected > people, and caused deaths. the ability of the virus to spread by human-to-human transmission was confirmed. a preliminary epidemiological analysis indicates that the incubation period of -ncov is similar to that of sars, but with a wider confidence interval, and longer than the one for the h n influenza strain. on february , , the disease caused by -ncov was named covid- , for coronavirus disease in . [ ] [ ] [ ] real-time information about the outbreak is available via an the prompt availability of the viral genome was critical for allowing comparisons with coronaviruses from previous outbreaks and helped make initial predictions. after the -ncov was isolated on january , , its sequence was published on january , . , the virus shares > % genetic similarity with the - sars-cov strain, is most closely related to coronaviruses of bat origin, its spike glycoprotein gene appears to have emerged by recombination between a bat coronavirus and a coronavirus of unknown origins, and relative synonymous codon usage bias analyses indicate that snakes may be a potential reservoir. the sars-cov spike protein receptor binds the angiotensin-converting enzyme (ace ) on host cells, an interaction that shapes cross-species and human-to-human transmission. , ace is a metallopeptidase expressed in numerous tissues, including alveolar epithelial cells and enterocytes. [ ] [ ] [ ] [ ] sequencing indicates that the -ncov might also use ace as a receptor. the -ncov spike receptor-binding domain is %- % similar at the genomic level to the one from the sars-cov from human, civet, or bat viruses. with, but not ideal for binding human ace , suggests that the virus has acquired the ability for human-to-human transmission, but this appears to be more limited than that of the - sars-cov strain. the mutation of this asparagine to threonine in -ncov was predicted to significantly increase the ability of the virus to bind the human ace receptor and should be closely monitored for. one of the earliest interventions during the -ncov outbreak involved quarantining an estimated - million people in multiple chinese cities, in what appears to be the largest mass quarantine in history. , it is still too early to visualize the impact of this initiative on the global dynamics of the outbreak, and retrospective analyses will be critical. quarantines, even though they are controversial, come at a high cost, and have been viewed with suspicion, were historically found to delay and slow the spread of various outbreaks. [ ] [ ] [ ] [ ] [ ] quarantines are one of the non-pharmaceutical interventions, which also include personal hygiene measures, cancellation of mass gatherings and public events, school and workplace closure, and travel restrictions. [ ] [ ] [ ] what all these interventions share is that at least during the initial stages of a new outbreak, particularly when a novel pathogen is involved and therapies are not yet available, they are one of the few options available. a lesson that flu taught us is that non-pharmaceutical interventions are at least as important as drugs or vaccines in controlling a pandemic. taiwan. , in italy, even though entry screening was conducted at two international airports, none of the individuals, including four probable sars cases, that were admitted for clinical evaluation, were referred to the hospitals by airport authorities. some of the limitations of screening measures, in the wake of an outbreak, include denying contact with ill individuals, taking antipyretic medication to conceal fever, and its reliance on the length of the incubation period of the infectious disease. about new infectious diseases were identified since , and new pathogens emerge at faster rates. , - every outbreak brings something new, provides opportunities to reap the benefits gained from past epidemics and pandemics, and provides novel lessons that will shape the framework to manage emerging infectious diseases. one aspect that all outbreaks share is their potential for rapid global dissemination through air travel. as we attempt to predict and quantitate the impact of international travel on an infectious disease outbreak and visualize the host, environmental, and microbial factors that make some outbreaks spread faster and others have higher mortality, it is worth noting that in , for the first time, the annual number of passengers exceeded three billion. an estimated one million people travel internationally every day, one million people travel between developing and developed countries every week, and the volume of airline passengers increases annually. in , for the first time, the daily number of flights exceeded an annual average of . it has become increasingly easy to reach any continent within hours, a period that is shorter than the incubation time of most contagious diseases. defined as contagious hosts that create more secondary contacts that most others in the population, will be a critical component of retrospective analyses, and there is an indication that super-spreading might already have occurred in the current outbreak. an important consideration, for this and future outbreaks, is understanding the types of different non-pharmaceutical interventions, their combined benefit, and the best timing for their implementation. this is both a learning curve and a new lesson in the wake of every epidemic, most likely riddled with differences even between two nearby cities impacted by the same outbreak. however, this is also the weakest link and the one that will indisputably assume a critical role in the management of zoonotic infectious diseases, a world where, as we know by now, history keeps repeating itself. as of february , , > , covid- infections and , deaths were reported. the first major outbreak in europe, and the largest one outside of asia, was reported in italy, with cases and deaths as of february , . in italy, the difficulty to trace the chain of the outbreak to the first infection in the country represents a huge setback in terms of the public health interventions that could help contain the spread of the virus. the a decade after sars: strategies for controlling emerging coronaviruses sars and mers: recent insights into emerging coronaviruses infection with middle east respiratory syndrome coronavirus replication and shedding of mers-cov in upper respiratory tract of inoculated dromedary camels the continuing -ncov epidemic threat of novel coronaviruses to global health -the latest novel coronavirus outbreak in wuhan, china effects of coronavirus infections in children human coronavirus and severe acute respiratory infection in southern brazil reviewing the history of pandemic influenza: understanding patterns of emergence and transmission influenza: the mother of all pandemics consequences of delays and imperfect implementation of isolation in epidemic control infectious disease threats in the twenty-first century: strengthening the global response the influenza epidemic's effects on sex differentials in mortality in the united states overview of the sars epidemic institute of medicine (us). iii, global challenges a new coronavirus associated with human respiratory disease in china epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding tracking the wuhan coronavirus a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster epidemiological characteristics of novel coronavirus: an interim review coronavirus updates: the illness now has a name: covid- . the new york times new coronavirus disease officially named covid- by the world health organization. national public radio coronavirus latest: who officially names disease covid- . nature world health organization. emergencies preparedness, response. pneumonia of unknown origin -china wuhan seafood market pneumonia virus isolate wuhan-hu- , complete genome cross-species transmission of the newly identified coronavirus -ncov reconstitution of the receptor-binding motif of the sars coronavirus receptor recognition and cross-species infections of sars coronavirus ace gene expression is up-regulated in the human failing heart a novel angiotensin-converting enzyme-related carboxypeptidase (ace ) converts angiotensin i to angiotensin - the novel angiotensin-converting enzyme (ace) homolog, ace , is selectively expressed by adult leydig cells of the testis tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis receptor recognition by novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars sars vaccine development animal origins of the severe acute respiratory syndrome coronavirus: insight from ace -s-protein interactions laboratory diagnosis of four recent sporadic cases of community-acquired sars china is about to find out whether its mass quarantine worked. bloomberg china's unprecedented quarantine of million people in wuhan is weeks old. here's what it's like in the isolated city nonpharmaceutical measures for pandemic influenza in nonhealthcare settings-international travel-related measures the influenza pandemic of - in two remote island nations: iceland and new zealand modeling the impact of air, sea, and land travel restrictions supplemented by other interventions on the emergence of a new influenza pandemic virus quarantine for pandemic influenza control at the borders of small island nations lessons from the history of quarantine, from plague to influenza a design of non-pharmaceutical intervention strategies for pandemic influenza outbreaks predicting support for non-pharmaceutical interventions during infectious outbreaks: a four region analysis effectiveness of workplace social distancing measures in reducing influenza transmission: a systematic review social measures may control pandemic flu better than drugs and vaccines public health interventions and epidemic intensity during the influenza pandemic fears are rising over the spread of china's deadly wuhan virus, which has now reached the us. here's how airports around the world are trying to stop it entry and exit screening of airline travellers during the a(h n ) pandemic: a retrospective evaluation border screening for sars in australia: what has been learnt? border screening for sars exit and entry screening practices for infectious diseases among travelers at points of entry: looking for evidence on public health impact public health interventions and sars spread use of quarantine to prevent transmission of severe acute respiratory syndrome-taiwan border screening for sars effectiveness of traveller screening for emerging pathogens is shaped by epidemiology and natural history of infection prediction and prevention of the next pandemic zoonosis infectious diseases are spreading more rapidly than ever before, who warns emerging virus diseases: can we ever expect the unexpected? global change and human vulnerability to vector-borne diseases the use and reporting of airline passenger data for infectious disease modelling: a systematic review infectious risks of air travel preparing for the next pandemic global surveillance, national surveillance, and sars how to cite this article: stein ra. the coronavirus: learning curves, lessons, and the weakest link key: cord- -tek u authors: sinderewicz, emilia; czelejewska, wioleta; jezierska-wozniak, katarzyna; staszkiewicz-chodor, joanna; maksymowicz, wojciech title: immune response to covid- : can we benefit from the sars-cov and mers-cov pandemic experience? date: - - journal: pathogens doi: . /pathogens sha: doc_id: cord_uid: tek u the global range and high fatality rate of the newest human coronavirus (hcov) pandemic has made sars-cov- the focus of the scientific world. next-generation sequencing of the viral genome and a phylogenetic analysis have shown the high homology of sars-cov- to other hcovs that have led to local epidemics in the past. the experience acquired in sars and mers epidemics may prove useful in understanding the sars-cov- pathomechanism and lead to effective treatment and potential vaccine development. this study summarizes the immune response to sars-cov, mers-cov, and sars-cov- and focuses on t cell response, humoral immunity, and complement system activation in different stages of hcovs infections. the study also presents the quantity and frequency of t cell responses, particularly cd (+) and cd (+); the profile of cytokine production and secretion; and its relation to t cell type, disease severity, and utility in prognostics of the course of sars, mers, and covid- outbreaks. the role of interferons in the therapy of these infections is also discussed. moreover, the kinetics of specific antibody production, the correlation between humoral and cellular immune response and the immunogenicity of the structural hcovs proteins and their utility in the development of a vaccine against sars, mers, and covid- has been updated. coronaviruses (covs) were discovered in the s as zoonotic spherical pathogens causing mostly respiratory or enteric diseases [ , ] . coronaviruses vary in size and are enveloped with club-shaped spikes on their surface [ ] [ ] [ ] . a helically symmetrical nucleocapsid comprising positive-sense single-stranded rna is one of the largest virus genomes, ranging from to kilobases in length [ ] . although covs are distributed mainly among mammals and birds, over the last years some cov infections have resulted in lethal epidemics in humans. since , when the first human coronavirus (hcov) was identified, seven hcovs species have been described [ ] . four of them, hcov- e, hcov-oc , hcov-nl and hcov-hku , lead to mild diseases such as the common cold, while the sars-cov, mers-cov, and sars-cov- caused severe disorders, manifesting acute respiratory system failures and fatalities [ ] . the first identified hcov, sars-cov, originated from southern china in and induced an epidemic of severe acute respiratory syndrome (sars) with a mortality rate of - % [ ] [ ] [ ] . the first case of mers-cov, it was also found that the total number of t lymphocytes, cd + , cd + , and naive cd + t cells was still lower one year post-sars-cov infection compared to the control value [ ] . only cd + t cells returned to normal level in the recovery period, probably as the effect of recirculation between blood and organs [ ] . the ability of the mers-cov to infect t cells and the activation of extrinsic and intrinsic apoptosis pathways in t cells was also proven [ ] . similar to sars-cov infection, effective transmission of mers-cov resulted in downregulation of th and high frequencies of reactive cd + t cells in the first phase of the disease, but not in the convalescent phase [ , ] . furthermore, a correlation between th and th downregulation and the fatality rate of mers-cov and sars-cov infection was found [ , [ ] [ ] [ ] . the newest reports have also documented an assessment of the t cell numbers in covid- patients. similar to sars and mers, the number of total t cells, cd + , and cd + t cells was significantly diminished in covid- patients in comparison to healthy controls and positively correlated with the severity of the disease [ , ] . moreover, an age-dependent reduction in t cell numbers was observed in covid- , with the lowest t cells numbers detected in individuals older than years old, indicating an enhanced susceptibility to sars-cov- infection in elderly patients. furthermore, besides the decreasing number of t cells, the limited function of these cells has been described as a result of enhanced expression of immune-inhibitory factors, such as programmed death receptor (pd ) or hepatitis a virus cellular receptor (tim- ) [ ] . a flow cytometry analysis illustrated significantly greater expression of the pd and tim- on t cell surfaces isolated from covid- patients in comparison to healthy controls [ ] . growing pd and tim- levels were found as patients progressed from prodromal to overtly symptomatic stages, suggesting that the surviving t cells lost their functionality, particularly in patients requiring intensive care unit care. moreover, stimulation of peripheral blood mononuclear cells (pbmcs) from group of severe covid- patients with peptides covering all viral proteins activated both cd + and cd + sars-cov- -specific t cells [ ] . furthermore, a greater cd + :cd + ratio in covid- patients was observed in comparison with control individuals [ ] . similar to sars-cov, sars-cov- -specific cd + t cells were identified as central memory t cells, based on cd ra and ccr expression. a mixed phenotype of cd + t cells in covid- patients was also documented [ ] . a low content of cd + t cells in peripheral blood of covid- patients and a negative relationship between viral and cd + titers were also reported [ ] . moreover, sars-cov- -specific cd + and cd + t cells were detected in~ % and % of covid- convalescents, respectively [ ] . the response of cd + t cell to sars-cov- s protein was also correlated with the specific igg and iga titers in patients who recovered from covid- [ ] . li et al. [ ] established detailed maps of t cell immune responses to sars-cov using pbmcs from sars convalescents. the new t cell epitopes were identified which induced a response to eight of fourteen sars proteins: replicase, orf , orf , orf , spike (s), envelope (e), membrane (m), and nucleocapsid (n). almost % of the responses were focused on structural proteins (s, e, m, and n), principally on s protein ( %), whereas the most abundant in sars-cov proteome replicase was much less immunogenic [ , ] . immune-informatic tools were used to identify significant cytotoxic t lymphocyte (ctl) and b cell epitopes in the sars-cov- surface glycoprotein [ ] . ahmed et al. [ ] documented s and n sars-cov- protein-derived epitopes, which were comparable to the sars-cov map b cell and t cell epitopes. the surface glycoprotein of sars-cov- was found to have . % identity and . % similarity to sars-cov [ ] . moreover, five ctl epitopes, three sequential b cell epitopes, and five discontinuous b cell epitopes in the viral surface glycoprotein were detected and described [ ] . despite their high similarity to sars-cov, of identified sequential ctl and b cell epitopes were at least partially unique to sars-cov- compared with bt-cov, sars-cov, and mers-cov. a molecular dynamics stimulation showed that all ctl epitopes bind strongly to the peptide-binding groove of corresponding mhc class i molecules [ ] . these features of ctl epitopes suggested their potential in induction of immune responses and, thereby, utility in a vaccine against sars-cov- . the t cell responses against the s and n proteins were documented as the most long-term reaction in sars-cov-infection [ ] . similar results, showing strong specific t cell response against structural proteins, including s, n, m, and e proteins, were noted in mers-cov infections [ ] [ ] [ ] [ ] . specific sars-cov- s and n proteins were also documented as the most immunogenic and greatly expressed during covid- [ , , ] . although cd + t cell activation was reported against s, m, and n proteins, as well as against nsp , nsp , orf a, and orf , only s protein induced a robust response [ ] . activation of cd + t cells was detected against sars-cov- s and m proteins and at least eight orfs [ ] . similar results were presented by le bert et al. [ ] , who proved the reactivity of both cd + and cd + t cells to the n protein and non-structural (nsp and nsp of orf ) proteins of sars-cov- in covid- convalescents. it was also shown that sars convalescents responded to the n protein of sars-cov- [ ] . uninfected individuals also revealed sars-cov- -specific cd + , indicating possibility of cross-reactive t cell stimulation with the other hcovs [ , ] . interestingly, sars-cov- -specific t cells in controls expressed a different pattern of immunodominance in comparison to sars and covid- convalescents [ ] . patients who recovered from sars or covid- responded mainly to n protein, whereas the control group revealed dominant reactivity to both n protein and orf -encoded proteins [ ] . cytokines, produced mainly by immune cells like macrophages, b and t lymphocytes, and mast cells, modulate the balance between humoral and cell-based immune responses [ ] . their concentration in biological fluids may be an important marker of immune system activity and disease progress. cytokines include several protein groups which vary in function, cell secretion, and target action. the current study reviewed the role of interleukins (ils) with tumor necrosis factors (tnfs), chemokines and interferons (ifns) in the immune response to hcovs. a comparison of the content of proinflammatory th and th cytokines in the serum of sars patients with healthy controls documented a significantly greater concentration of tnf-α, il- , il- , il- , and il- in the early stage of the sars-cov infection [ , ] . decreasing levels of these cytokines were correlated with the course of recovery from sars-induced pneumonia. furthermore, significantly greater contents of il- , il- , and il- were reported in fatal sars cases [ ] . the enhanced secretion of il- α, il- β, il- , il- il- , and ifn-γ as an antiviral and inflammatory response to mers-cov was also documented [ , , , ] . moreover, il- and il- were produced in a greater amount in response to mers-cov than sars-cov [ ] . interestingly, in vitro studies showed that enhanced il- and il- levels in sars and mers patients were observed exclusively in the presence of s protein [ , ] . among the cytokines involved in the immune response against hcovs, several have been proposed as potential predictors of disease cause and progression. it has been documented that increased il- concentration in plasma of sars patients was significantly increased in severe cases, but not in convalescent or control subjects, suggesting a positive correlation between serum il- level and disease severity [ ] . inversely, il- and tgf-β concentrations were significantly reduced in sars patients with a severe course of the disease [ ] . tnf-α was considered a predictor of disease progression due to its greatest level in the early stage of recovery [ ] . moreover, a decreased content of il- and increased level of il- were only found in convalescent patients [ ] . it was also proven that the il- profile in patient's serum indicated the cause of pneumonia-a significantly lower il- concentration was detected in sars patients compared to others. a detailed analysis showed that in a group of sars patients with severe symptoms, cytokine secretion was varied among different t cell subpopulations. it was shown that ifn-γ and tnf-α were produced both by cd + and cd + t cells, whereas the production of il- was typical exclusively for cd + [ ] . moreover, in this group of patients the number of polyfunctional memory cd + t cells producing more than one cytokine was significantly higher compared to sars patients with a mild or moderate course of disease [ ] . a similar effect was not observed for cd + t cell responses, although intensified degranulation was observed in severe course of sars via cd a activation on cd + t cells surface [ ] . stimulation of pbmcs from recovered sars patients with peptides overlapping the entire e protein, a membrane component of sars-cov, resulted in cytokine production by both cd + and cd + t cells [ ] . similar observations have been reported in studies concerning covid- . the lack of expression of the receptor for sars-cov- on t cells, ace , suggested that the limited t cell number in covid- patients was likely caused by the influence of cytokine signaling and not by the direct infection of t cells [ , ] . the stimulation of pbmcs from covid- patients with s protein peptides resulted in production of effector or th cytokines (ifn-γ, tnf-α, and il- ) and, to a lesser extent, th (il- , il- , il- , and il- ) and th (il- a, il- f, and il- ) cytokines [ ] . however, among the numerous serum cytokines, only tnf-α, il- , il- , and il- levels were significantly increased in sars-cov- infected patients [ , , ] . these changes were characteristic of severe progression of the disease, supporting the hypothesis that covid- is driven by proinflammatory cytokines, which are responsible for histological changes and clinically full-blown cases of the disease. among detected cytokines, il- appears to be the most significantly involved in covid- progress. chen et al. [ ] detected an enhanced level of il- r in severe cases of covid- , although no significant differences among examined and control groups were detected in il- [ ] . the presence of il- , greatly expressed in fatal sars cases, was also not detected in the plasma of covid- patients [ ] . moreover, the concentration of tnf-α, il- , and il- was negatively correlated with amounts of total t cells, cd + t cells, and cd + t cells, respectively. furthermore, serum concentrations of il- , il- , and tnf-α were significantly lower in patients in the disease resolution in comparison to the disease period, whereas the total number of t cells, cd + t cells, and cd + t cells was restored during the decline period of covid- . these results suggested that in sars-cov- infections, a high serum concentration of tnf-α, il- , and il- negatively regulated t cell survival and/or proliferation [ ] . interestingly, the production of cytokines by cd + (mainly il- and ifn-γ and trace amounts of il- , il- , il- , or il- α) was also reported in covid- convalescents [ ] . thus, the functional response of cd + against sars-cov- was suggested in recovered patients. chemokines are essential in determining immune cell localization [ ] , and some of them act as factors involved in response to hcovs. enhanced contents of ip- /cxcl- , mcp- /ccl- , mip- α/ccl- , and rantes/ccl- were identified in the lungs and peripheral blood of sars and mers patients [ , , , ] . moreover, both the production and secretion of these molecules were greater in response to mers-cov in comparison to sars-cov [ ] . the upregulation of cxcl- at both transcriptional and translational levels was proven in murine epithelial cells, lung fibroblast cells, monocyte-derived macrophages, and dendritic cells as a result of the overexpression of mers-cov n protein [ ] . high secretion and a persistent increase of cxcl- in mers-cov patients were associated with disease severity [ ] . mers-cov infection also resulted in cxcl- chemokine production by th cells [ , ] . the presence of chemokines and their action has not been reported in covid- , although the number of studies concerning sars-cov- infection is still limited. among crucial elements of the immediate antiviral response, interferons (ifns) are pivotal for limiting viral replication and spread. therefore, ifns were extensively studied as potential therapeutic tools of sars-cov and mers-cov infections. the presence of an enhanced level of ifn-γ was documented in sera of sars-cov-and mers-cov-infected patients [ , ] . similar to the other cytokines, the ifn-γ profile was correlated with the cause of pneumonia. ifn-γ production was significantly greater in sars patients compared to others [ ] . on the other hand, further studies documented relatively low ifn-γ production in response to sars-cov infection. zhou et al. [ ] found greater levels of ifn-γ in sera of mers patients compared to sars-cov-infected patients. moreover, scagnolari et al. [ ] showed that ifn-γ production in response to sars-cov was significantly lower compared to well-established ifn-inducing viruses, such as vesicular stomatitis (vsv) and newcastle viruses (ndv), suggesting a limited role of ifns in early host defense against sars-cov infection. the lack of the antiviral ifn response to sars-cov with simultaneous enhanced secretion of several proinflammatory cyto-and chemokines suggested that the virus suppresses the induction of ifn production [ ] . the natural host defense based on ifn action may be restricted because of the documented inhibition of ifns type i and cytokines production in toll-like receptor (tlr) , tlr , and retinoic acid-inducible gene (rif-i) pathways in response to sars-cov infection. this limitation occurs via suppressing the activation of transcription factors, such as interferon regulatory factor (irf ), nuclear factor (nf)-κb, and adaptor related protein complex (ap ) and downregulation of tnf receptor associated factor (traf) and traf [ ] . it was also documented that mers-cov n and m proteins inhibited the gene expression of ifns type i and iii, resulting in the host antiviral response impairment [ , ] . similar results were documented for sars-cov- infection. chen et al. [ ] showed the production of ifn-γ by cd + t cells in response to sars-cov- tended to be lower in severe ( . %) than in moderate ( . %) cases of covid- . however, among the very few reports concerning the role of ifns in covid- disease was a study documenting a lack of ifn-γ in the serum of patients infected with sars-cov- [ ] . on the other hand, further studies documented the utility of ifns in the treatment of sars-cov infection. chen et al. [ ] confirmed virus susceptibility to exogenous type i ifn. it was also shown that early administration of ifns-i decreased immunopathological changes via downregulation of the expression of factors inducing apoptosis; upregulation of hypoxia/hyperoxia-related genes and the regulation of tlr, cytokine, and chemokine signaling; and expression of mhc-, lysosome-, and fibrosis-related genes [ , ] . however, high-level virus replication resulted in retardation of ifns-i signaling, which promoted the cumulation of pathogenic inflammatory monocyte macrophages and resulted in increased cytokine and chemokine levels in lungs, vascular leakage, and reduced virus-specific t cell responses, and thereby strong lung pathology. animal models showed that genetic ablation of ifn-α/β receptor (ifnar) depletion protected from lethal infection, without affecting viral load [ ] , suggesting that ifns therapy may be effective mainly in the early stage of infection. it was also shown that ifns-i and tlr agonists were the most effective in sars and mers therapy, which activates interferons [ ] . the best results were observed for ifn-β a, which reduced mortality by % in comparison to patients, who received ifn-α a. the efficacy of ifns was lower in older patients [ ] . the ability to induce ifns mrna accumulation by sars-cov in pbmcs from healthy donors was also investigated by castilletti et al. [ ] , who proved that combination of ifn-α and ifn-γ strongly inhibited virus replication, while single cytokines were much less effective. an analysis of molecular mechanisms of the immune response to hcovs showed that effective cytokine production correlated to the availability of functional hcovs receptors. the effective increase in il- level was similar to concentration observed for s protein binding to sars-cov functional receptor, ace , or to neutralizing monoclonal antibody. it was documented that il- production also depended on nf-κb activation and translocation and was suppressed by an nf-κb inhibitor [ ] . moreover, the latest studies suggested that protein s could activate pbmcs via the tlr ligand. it was demonstrated that a lack of functional tlr , tlr , and tlr adaptor molecule (tram) enhanced the possibility of sars-cov infection, reduced lung function and increased lung pathology and mortality. the suppression of tlr adaptor molecule (trif) in mice infected with sars-cov resulted in changes in inflammation and positively correlated with acute respiratory distress syndrome [ ] . on the other hand, infection of macrophages with mers-cov resulted in a reduced capacity to produce tnf-α and il- and enhanced the il- secretion [ ] . the role of mers-cov s protein in upregulation of the irak-m expression, which is a negative regulator of tlr signaling, as well as expression of the transcriptional repressor ppar-γ was documented. moreover, it was documented that the immunosuppressive effect was mediated by dipeptidyl peptidase (dpp ), which competitively inhibits mers-cov via binding to common for mers-cov and dpp functional receptor, dpp r [ , ] . in human dendritic cells (dc), the induction of c-c motif chemokine receptor (ccr) , ccr , and ccr in the presence of sars-cov was detected [ ] . the sars-cov infection induced also significant upregulation of tnf-related apoptosis-inducing ligand (trail) gene expression in dcs [ ] . it was demonstrated that, in mers-cov infection, c-type leptin receptor (clr) was also upregulated and a retinoic acid-inducible-i-like receptor (rlr) pathway was activated [ ] . the main aspects of t cell response in hcovs infections are shown in figure . the animal model of sars-cov infection documented activation of the complement cascade in the lungs and showed that absence of complement significantly reduced the pathological changes in the respiratory tract, even though the viral load is the same. in the lungs of the transgenic mice deficient in c (c −/− ), which is the central component of the complement system, significantly lower neutrophils and inflammatory monocytes were presented than in infected controls [ ] . moreover, diminished cytokine and chemokine contents in both the lungs and serum of c −/− mice were humoral immune response restrains the infection via neutralizing antibodies production and prevents reinfection in the future [ ] . in sars, the presence of igg, igm, and iga antibody responses was detected during both the infection and convalescent phases, although with variable dynamics [ ] [ ] [ ] [ ] . the presence of specific igg and igm antibodies was also documented in the first two weeks of the sars-cov infection ( . % and %, respectively) [ , , , ] . the levels of igg and igm increased during the next two weeks to % and %, respectively. the serum samples examined days after the onset of disease were positive only for sars-specific igg [ , ] . a study analyzing the kinetics of specific antibody contents in plasma of sars patients presented by mo et al. [ ] also showed a further significant increase in igg antibody levels. the highest concentration of igg was documented on day , remaining at the same level until day . then, the igg content gradually decreases until day . the igm antibody level peaked shortly after its detection and, in contrast to previous studies, declined until day when igm was undetectable [ ] . similar results were found by chen et al. [ ] , who suggested that sars-cov-specific igg antibody, persisting for a longer time than specific igm and iga antibodies, was the primary humoral immune response against sars. however, a significantly lower level of igg was detected in severe than in mild or recovering sars patients, which may be a result of some kind of immune system dysfunction in long-suffering acute patients. however, li et al. [ ] reported that strong t cell responses correlated significantly with a higher level of neutralizing antibody activity. in contrast to memory t cell responses, ensuring long-term protection, the antibody response was transient in convalescent sars patients [ ] . cao et al. [ ] documented the presence of specific antibodies within three years from the onset of sars symptoms in . % of examined samples. however, six years post-infection, sars-cov-specific igg and ag-specific memory b cells were undetectable in sars convalescents, whereas memory t cell responses to a pool of sars-cov s peptides were revealed in % of convalescents. the most recent study reported presence of long-lasting memory t cells responding to sars-cov n protein in sars convalescents years after the sars pandemic [ ] . moreover, memory t cell response was stronger in former patients, who revealed severe clinical manifestations during sars [ ] . similar to sars-cov infection, igm and igg levels increased during the first week after sars-cov- infection. the greatest concentration of igm was detected in the second week, after which its content was reduced to initial level in most patients, whereas the igg level remained at a high level for a long period [ ] . interestingly, the igm and igg antibody levels were not significantly different among mild, severe, and critical disease groups [ ] . however, the levels of igg, iga, and ige were greater in covid- fatalities in comparison to survivors [ ] . igm and igg against n and s proteins of sars-cov- were also detected in covid- convalescents [ ] . the igg titer remained high for at least days post-discharge, whereas igm was detected only in newly recovered patients [ ] . moreover, negative correlation between viral and igg titers [ ] and a significant positive correlation between the content of neutralizing igg and the number of n protein-specific t cells was observed, suggesting interdependence between humoral and cellular immunity in sars-cov- infection [ , ] . the kinetics of specific igg and igm antibodies were also analyzed in the serum of mers patients. robust serological responses were detected in most patients during the second or third week after symptom onset [ ] [ ] [ ] . specific igm antibodies were detectable at the same time or slightly later than igg [ ] . interestingly, the whole group of survivors, and only half of all fatalities, produced igg and neutralizing antibodies [ ] . although the mers-cov antibody response in the early phase of infection correlated with reduction of the disease severity [ ] , the presence of antibodies did not allow to the virus removal from the lower respiratory tract [ ] . mers-cov-specific igg was also detectable one year post-infection in all severe disease survivors [ ] . on the other hand, alhetheel et al. [ ] found a very low rate of mers-cov-igg positive patients and a lack of correlation between nucleic acid and serological analysis [ ] . the presence of specific iga in serum and respiratory tract secretions of mers patients was also confirmed. moreover, the correlation between iga and igg concentration in serum of mers-cov-infected individuals was proven [ , ] . however, as the majority of studies concerning humoral response in mers used a limited number of patients, using serological analysis is not recommended as a tool to determine disease severity or prognosis. animal models showed that the main antibody responses were induced by the most exposed s protein of sars-cov [ ] [ ] [ ] . mice immunization with a vector encoding a transmembrane domain of s protein resulted in neutralizing antibody production and action. in consequence, viral replication in the lungs of mice was significantly reduced and immune defense was provided by a humoral but not a t cell-dependent immune mechanism [ ] . however, deming et al. [ ] showed that the efficacy of the humoral response to sars-cov s protein depended on the homology of the virus strain. vaccines including a virus replicon expressing sars-cov s protein ensured complete shortand long-term protection against homologous strain challenge in young and senescent mice. on the contrary, the implementation of a construct encoding a synthetic s protein gene of the most genetically different human strain resulted in complete short-term protection in vaccinated young mice and limited protection in senescent animals [ ] . high tolerance for the vaccine encoding the sars-cov s protein and its high immunogenicity has also been documented in humans, with specific antibodies being detected in % of subjects [ , ] . moreover, sars-cov-specific cd + t cell responses were observed in all vaccinated patients and cd + t cell responses in % of individuals [ ] . neutralizing b cell antibody responses to the sars-cov s protein were also major in sars convalescents, suggesting that a spike-based vaccine can be sufficient for a preventive vaccine, as it was previously demonstrated in animal models [ ] . as was mentioned above, the strongest response against sars-cov s protein was shown by the cd + t cells. the possible cooperation of cd + t cell and b cells in neutralizing ab producing was described previously by mitchison et al. [ ] , and the possibility of the enhanced reaction of plasma b cells, stimulated by cd + t cells, specific to the same protein, has also been suggested [ ] . several studies have documented the presence of antibodies generated against the n protein of sars-cov [ , ] and the high affinity of epitopic sites located in the n protein for forming peptide-antibody complexes in the serum of sars patients, particularly to days after the onset of infection. interestingly, vaccines containing sars-cov n protein failed to protect from homologous and heterologous challenges. in consequence, in the lungs of sars-cov-infected mice, the eosinophilic infiltrates were promoted and increased immunopathology was observed [ ] . the strongest humoral responses against s and n proteins were also detected in mers. although it was proven that mers-n-specific antibodies occurred later than s-specific antibodies [ ] , the vaccines containing mers-specific antibodies are still unknown. the main features of the humoral response in hcovs infections are presented in figure . despite the high range of sars-cov- infection, the severe course of the disease has mainly affected elderly patients, with children excluded from the risk group [ ] . moreover, despite the high rates of seropositivity of anti-receptor-binding domain (rbd) igg and igm ( % and %, respectively) and slightly lower rates of anti-n protein igg and igm measured after days of symptom onset, the disease was still active and clinical symptoms severe [ ] . to explain this phenomenon, antibody-dependent enhancement (ade) after previous exposure to other hcovs with a wide range of affinities has been proposed. in ade, infection is promoted through a virus binding to non-neutralizing antibodies from previous exposures to similar antigens. the virus-antibody immune complex binds to fc receptor (fcr) or complement receptors on the host cell surface, facilitating entry of the virus and sometimes enhancing its replication [ , ] . the results of ade are enhanced inflammatory process, overexpression and release of cytokines (cytokine storm) and multi-organ failure as a consequence of these processes. immune-mediated covs infections have been widely described. the vaccine against feline cov aggravated future disease via induction of infection-enhancing antibodies [ , ] . although the full-length sars-cov s protein stimulated protective immune response action in rodents, in human b cell lines it induced infection [ ] . in vitro studies have demonstrated, that anti-spike immune serum enhanced the infection of immune cells by sars-cov spike-pseudotyped lentiviral particles, as well as replication-competent sars-cov, via fcγ receptor ii (fcγrii), but not ace [ , ] . similarly, yip et al. [ ] documented that human macrophages may be infected by sars-cov via fcγrii. however, binding of an immune complex to fcγrii was not sufficient for ade induction, indicating that activation of the other signaling pathways downstream binding to fcγrii receptors is required [ ] . in a sars-cov infection of the promonocytic cell line expressing both fcγrii and ace , a high concentration of antibodies neutralized the virus, whereas a low content of antibodies induced ade [ ] . immunization of rhesus monkeys with a full length sars-cov s protein resulted in enhanced disease severity, with a dominant proinflammatory m -like macrophage profile in the lung tissue, increasing lung injury [ ] . moreover, macrophages produced a significantly greater amount of cytokines in the presence of deceased patients' serum and sars-cov in comparison with the virus alone [ ] . enhanced cytokine production was reduced after fcr blockade. on the contrary, in sars-cov the greatest neutralizing antibody titer was observed earlier in deceased patients in comparison with convalescents [ ] . however, a recent study showed a new mechanism for ade by engaging neutralizing antibodies. monoclonal neutralizing antibody (mab) binding to the mers-cov s protein induced changes in the s protein structure and mediated viral entry to the host cell via igg fcr [ , ] . moreover, ade of mers-cov admission depended on the mab dosage as well as the fcr expression on the cell surface [ ] . in humans, besides the immune cells (including monocytes) infiltrating lungs during pneumonia, epithelial cells of the lower respiratory tract also significantly expressed fcγr [ ] . in a severe course of sars and covid- substantial lung opacity was observed, indicating infiltration by monocytes [ , ] . the infection of human monocytes and macrophages by sars-cov- was also proven [ ] . furthermore, an early humoral response to sars-cov- and greater antibody titer were positively correlated with a delay in the viral clearance and, in consequence, with the severity of the disease [ ] . as mentioned above, great sequence identity and the presence of cross-reactive epitopes of sars-cov- and other hcovs were also documented [ , , ] . monocyte migration to the lungs and the presence of cross-reactive memory antibodies potentially promote the receptivity of elderly individuals to sars-cov- . the lack of immune memory of closely related hcovs (and the consequent inability of ade activation) might be responsible for the absence of clinical symptoms, as well as for the great frequency of undocumented sars-cov- infection, particularly in children [ ] . however, upregulation of ace which is significant component of the renin-angiotensin system (ras) has also been suggested as a cause of severe courses of hcovs infections. animal models demonstrated that angiotensin ii receptor type i (at r ) antagonists or ace inhibitors upregulated ace expression [ , ] . thus, the medicaments widely used in cardiac and hypertensive patients potentially promote the virus binding to the host cells. according to the above, an unequivocal assessment of ade presence in sars-cov- infection seems to be crucial in the vaccine development and antibody-based drug therapy. besides the application of specific anti-sars-cov- , the use of anti-ace with anti-fcγrii monoclonal antibodies to block ade activation and plasmapheresis for restraining cytokine storm elements in plasma has also been proposed as potentially the most effective method of covid- treatment [ ] . the animal model of sars-cov infection documented activation of the complement cascade in the lungs and showed that absence of complement significantly reduced the pathological changes in the respiratory tract, even though the viral load is the same. in the lungs of the transgenic mice deficient in c (c −/− ), which is the central component of the complement system, significantly lower neutrophils and inflammatory monocytes were presented than in infected controls [ ] . moreover, diminished cytokine and chemokine contents in both the lungs and serum of c −/− mice were detected, suggesting that inhibition of complement signaling might be an efficient therapeutic tool in the treatment of sars-cov infection. similarly, the complement system was inordinately activated in mers-cov-infected transgenic mice with human cd /dipeptidyl peptidase (hdpp ), which is a functional receptor for mers-cov. in response to mers-cov infection, enhanced contents of c a and c b- complement activation products in serum and lung tissues of hdpp -tg mice, respectively, were observed [ ] . inhibiting c a production by blocking its receptor (c ar) reduced lung damage and inflammatory responses [ ] . interestingly, the covid- non-survivors presented lower levels of c and c proteins at admission in comparison to patients who recovered [ ] . level of c protein was suggested as a predictor of mortality of covid- patients. recent research showed that mechanisms of responses against hcovs may also be enhanced by other elements of innate immunity. activation of human β-defensin (hbd ) resulted in the conjugation of this protein with the rbd of the mers-cov s protein (s rbd) [ , ] . in consequence, expression of chemokines able to recruit leukocytes (comprising monocytes, macrophages, natural killer cells, granulocytes, t cells, and dendritic cells) was promoted. moreover, enhanced expression of primary immune-inducing molecules (nod , tnf-α, il- β, and il- ) and antiviral factors (such as ifn-β, ifn-γ, mxa, pkr, and rnasel) were also detected, compared to treatment with s rbd alone. immunization of mice with hbd -conjugated s rbd enhanced the immunogenicity of s rbd and induced a stronger s rbd-specific neutralizing antibody response [ ] . the s rbd-hbd treatment also increased phosphorylation and activation of receptor-interacting serine/threonine-protein kinase and ifn regulatory factor . moreover, hbd promoted ccr -mediated nod signaling, inducing the production of type i ifns and an inflammatory response [ ] . although recognition of the relationship between sars-cov- infection and complement system activation is extremely important in defining the best path of treatment, the effect of sars-cov- on complement cascades is still unknown. li et al. [ ] analyzed the association between the cytokine pattern in acute infection and death in sars and suggested that the quality of immune response, rather than magnitude, may be critical in the progress of the disease. the investigation of innate, humoral, and t cell responses during the critical first - weeks may indicate whether they require immunosuppressing therapy or not. sars-cov- has induced the most widespread pandemic in recent decades. the presence of sars-cov- has resulted in almost . million covid- patients in countries and territories, including , fatalities (reported: june by john hopkins university). the differing severity of the covid- outbreak has affected different parts of the world for reasons which are still unclear. the epidemiological studies of a previous pandemic, sars, suggested that human-to-human transmission may enhance the immunogenicity of the virus and its virulence [ ] . as sars-cov- is the first hcov being transmitted directly among humans, it is highly probable that the wide range of the pandemic is a result of the way of transmission. although the phylogenetic similarity of sars-cov- concerned only sars-cov and mers-cov, but not common hcovs inducing mild infections of the respiratory system, the potential cross-reactivity of t cells and antibodies between these viruses and its potential impact on total immune responses and clinical outcomes cannot be excluded. moreover, the presence of mutations in the viral genome is also possible. the next danger is relatively late symptoms occurring in infected people and, in some cases, an asymptomatic course of infection, resulting in a lack of isolation in the early stage of the infection. on the other hand, the genetic similarity of sars-cov- , sars-cov, and to a lesser extent to mers-cov, the similarities between the structure of the epitopes and receptors, the course of the disease and the effects of the infection, allow undertaking a strategy against covid- based on experience gained during the previous pandemics until the mechanisms of covid- are better understood. the first studies related to covid- suggested a protective role of both cell-dependent and humoral immune responses in humans. similar to sars-cov and mers-cov, the sars-cov- infection primarily affected t lymphocytes, particularly cd + and cd + t cells, resulting in a reduction in their numbers and changes in cytokines secretion, including enhanced ifn-γ production by cd + t cells. several studies have also shown the diagnostic utility of serology in sars, mers, and covid- investigation. moreover, the correlation between the severity of the disease and potential immunological markers was documented, which may be a useful prognostic tool of the disease progression, and thereby, in the further course of the pandemic. based on previous experience, immune-informatic tools were used to define the structure of cytotoxic t lymphocyte and b cell epitopes. however, since sars-cov- antibody persistence and re-exposure occurrence are still unknown, further studies and a better understanding of the molecular mechanisms of immune responses to sars-cov- are essential in the new therapeutics development and evaluation of the efficiency of potential vaccines against sars-cov- . the viruses and their replication history and recent advances in coronavirus discovery the molecular biology of coronaviruses supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy cryo-electron tomography of mouse hepatitis virus: insights into the structure of the coronavirion coronavirus: how a large rna viral genome is replicated and transcribed properties of coronavirus and sars-cov- an overview of their replication and pathogenesis world-health-organization update -sars case fatality ratio, incubation period functional assessment of cell entry and receptor usage for sars-cov- and other lineage b betacoronaviruses isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan genomic characterization and epidemiology of novel coronavirus: implications for virus origins and receptor binding a new coronavirus associated with human respiratory disease in china the species severe acute eespiratory syndrome related coronavirus: classifying -ncov and naming it sars-cov- coronaviruses post-sars: update on replication and pathogenesis early transmission dynamics in wuhan, china, of novel coronavirusinfected pneumonia active monitoring of persons exposed to patients with confirmed covid- -united states community transmission of severe acute respiratory syndrome coronavirus the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application presymptomatic transmission of sars-cov- -singapore quasipecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation origin and evolution of pathogenic coronaviruses cross-species transmission of the newly identified coronavirus -ncov coronavirus host divergence and novel coronavirus (sars-cov- ) outbreak efficacy of various disinfectants against sars coronavirus sars coronavirus spike protein-induced innate immune response occurs via activation of the nf-kappab pathway in human monocyte macrophages in vitro overexpression of the nucleocapsid protein of middle east respiratory syndrome coronavirus up-regulates cxcl angiotensin-converting enzyme is a functional receptor for the sars coronavirus cryo-em structure of the sars coronavirus spike glycoprotein in complex with its host cell receptor ace the novel coronavirus ( -ncov) uses the sars-coronavirus receptor ace and the cellular protease tmprss for entry into target cells significant changes of peripheral t lymphocyte subsets in patients with severe acute respiratory syndrome rapid loss of both cd + and cd + t lymphocyte subsets during the acute phase of severe acute respiratory syndrome cell responses to whole sars coronavirus in humans dynamic changes of t lymphocyte subsets in the long-term follow-up of severe acute respiratory syndrome patients middle east respiratory syndrome coronavirus efficiently infects human primary t lymphocytes and activates the extrinsic and intrinsic apoptosis pathways immune responses to middle east respiratory syndrome coronavirus during the acute and convalescent phases of human infection mers-cov infection is associated with downregulation of genes encoding th and th cytokines/chemokines and elevated inflammatory innate immune response in the lower respiratory tract clinical and immunological features of severe and moderate coronavirus disease reduction and functional exhaustion of t cells in patients with coronavirus disease (covid- ). front phenotype and kinetics of sars-cov- -specific t cells in covid- patients with acute respiratory distress syndrome targets of t cell responses to sars-cov- coronavirus in humans with covid- disease and unexposed individuals immunoinformatics-aided identification of t cell and b cell epitopes in the surface glycoprotein of -ncov preliminary identification of potential vaccine targets for the covid- coronavirus (sars-cov- ) based on sars-cov immunological studies virus-specific memory cd t cells provide substantial protection from lethal severe acute respiratory syndrome coronavirus infection characteristics of traveler with middle east respiratory syndrome cells responding to the middle east respiratory syndrome coronavirus nucleocapsid protein delivered by vaccinia virus mva in mice middle east respiratory syndrome coronavirus m protein suppresses type i interferon expression through the inhibition of tbk -dependent phosphorylation of irf middle east respiratory syndrome coronavirus nucleocapsid protein suppresses type i and type iii interferon induction by targeting rig-i signaling sars-cov- -specific t cell immunity in cases of covid- and sars, and uninfected controls cytokines, inflammation and pain active replication of middle east respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis clinical progression and cytokine profiles of middle east respiratory syndrome coronavirus infection a pneumonia outbreak associated with a new coronavirus of probable bat origin clinical features of patients infected with novel coronavirus in chemokines: a new classification system and their role in immunity the immunobiology of sars sensitivity of sars/mers cov to interferons and other drugs based on achievable serum concentrations in humans severe acute respiratory syndrome coronavirus elicits a weak interferon response compared to traditional interferon-inducing viruses sars coronavirus papain-like protease inhibits the tlr signaling pathway through removing lys -linked polyubiquitination of traf and traf sars-cov regulates immune function-related gene expression in human monocytic cells dysregulated type i interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in sars-cov-infected mice coordinate induction of ifn-alpha and -gamma by sars-cov also in the absence of virus replication toll-like receptor signaling via trif contributes to a protective innate immune response to severe acute respiratory syndrome coronavirus infection middle east respiratory syndrome corona virus spike glycoprotein suppresses macrophage responses via dpp -mediated induction of irak-m and pparγ reduction of soluble dipeptidyl peptidase levels in plasma of patients infected with middle east respiratory syndrome coronavirus toll-like receptors, chemokine receptors and death receptor ligands responses in sars coronavirus infected human monocyte derived dendritic cells activation of c-type lectin receptor and (rig)-i-like receptors contributes to proinflammatory response in middle east respiratory syndrome coronavirus-infected macrophages antibodies to coronaviruses are higher in older compared with younger adults and binding antibodies are more sensitive than neutralizing antibodies in identifying coronavirus-associated illnesses profile of specific antibodies to the sars-associated coronavirus antibody response and viraemia during the course of severe acute respiratory syndrome (sars)-associated coronavirus infection kinetics of severe acute respiratory syndrome (sars) coronavirus-specific antibodies in laboratory-confirmed cases of sars chronological evolution of igm, iga, igg and neutralisation antibodies after infection with sars-associated coronavirus a novel coronavirus associated with severe acute respiratory syndrome clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study evaluation by indirect immunofluorescent assay and enzyme linked immunosorbent assay of the dynamic changes of serum antibody responses against severe acute respiratory syndrome coronavirus lack of peripheral memory b cell responses in recovered patients with severe acute respiratory syndrome: a six-year follow-up study potent and persistent antibody responses against the receptor-binding domain of sars-cov spike protein in recovered patients detection of igm and igg antibodies in patients with coronavirus disease abnormal immunity of non-survivors with covid- : predictors of mortality detection of sars-cov- -specific humoral and cellular immunity in covid- convalescent individuals kinetics of serologic responses to mers coronavirus infection in humans viral shedding and antibody response in patients with middle east respiratory syndrome coronavirus infection comparative serological study for the prevalence of anti-mers coronavirus antibodies in high-and low-risk groups in qatar characterization of anti-mers-cov antibodies against various recombinant structural antigens of mers-cov in an imported case in china mers-cov antibody responses year after symptom onset assessing the detection of middle east respiratory syndrome coronavirus igg in suspected and proven cases of middle east respiratory syndrome coronavirus infection infectious middle east respiratory syndrome coronavirus excretion and serotype variability based on live virus isolates from patients in saudi arabia suggested new breakpoints of anti-mers-cov antibody elisa titers: performance analysis of serologic tests a dna vaccine induces sars coronavirus neutralization and protective immunity in mice vaccine efficacy in senescent mice challenged with recombinant sars-cov bearing epidemic and zoonotic spike variants induction of specific immune responses by severe acute respiratory syndrome coronavirus spike dna vaccine with or without interleukin- immunization using different vaccination routes in mice a sars dna vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a phase i clinical trial t-cell-b-cell cooperation assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus profile of antibodies to the nucleocapsid protein of the severe acute respiratory syndrome (sars)-associated coronavirus in probable sars patients susceptibility of the elderly to sars-cov- infection: ace- overexpression, shedding, and antibody-dependent enhancement (ade) temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study antibody-dependent enhancement of virus infection and disease antibody-dependent enhancement of viral infection: molecular mechanisms and in vivo implications early death after feline infectious peritonitis virus challenge due to recombinant vaccinia virus immunization antibody-dependent enhancement of feline infectious peritonitis virus infection in feline alveolar macrophages and human monocyte cell line u by serum of cats experimentally or naturally infected with feline coronavirus antibodies against trimeric s glycoprotein protect hamsters against sars-cov challenge despite their capacity to mediate fcgammarii-dependent entry into b cells in vitro anti-severe acute respiratory syndrome coronavirus spike antibodies trigger infection of human immune cells via a ph-and cysteine protease-independent fcγr pathway antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus immunodominant sars coronavirus epitopes in humans elicited both enhancing and neutralizing effects on infection in non-human primates anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection antibody responses against sars coronavirus are correlated with disease outcome of infected individuals a conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in middle east respiratory syndrome coronavirus spike protein molecular mechanism for antibody-dependent enhancement of coronavirus entry the protein cell atlas webpage clinical characteristics of coronavirus disease in china sars: radiological features host-viral infection maps reveal signatures of severe covid- patients viral kinetics and antibody responses in patients with covid- antibody dependent enhancement due to original antigenic sin and the development of sars. front. immunol. , , effect of angiotensin-converting enzyme inhibition and angiotensin ii receptor blockers on cardiac angiotensin-converting enzyme upregulation of angiotensin-converting enzyme (ace) in hepatic fibrosis by ace inhibitors anti-ace and anti-fcγrii monoclonal antibodies: a possible treatment for severe cases of covid- . drug des. dev blockade of the c a-c ar axis alleviates lung damage in hdpp -transgenic mice infected with mers-cov human β-defensin plays a regulatory role in innate antiviral immunity and is capable of potentiating the induction of antigen-specific immunity human β-defensin is involved in ccr -mediated nod signal transduction, leading to activation of the innate immune response in macrophages funding: this research received no external funding. the authors declare no conflict of interest. key: cord- -s nd hz authors: gaffney, adam w.; himmelstein, david; bor, david; mccormick, danny; woolhandler, steffie title: home sick with coronavirus symptoms: a national study, april–may date: - - journal: j gen intern med doi: . /s - - - sha: doc_id: cord_uid: s nd hz nan reports from hospitals and locales have highlighted racial/ethnic disparities in covid- outcomes. however, few national studies in the usa have examined disparities among persons with symptoms suggestive of covid- . we analyzed a unique, nationally representative survey to assess demographic characteristics and social vulnerabilities among those with symptoms attributed to the coronavirus. we analyzed data on adults age - in weeks (april -may ) and (may - ) of the census bureau's household pulse survey (hps), which collects data on pandemic-related health and financial problems. individuals reporting not working the preceding week were asked why; one of response options was "… because i am/ was sick with coronavirus symptoms." (previous research demonstrated that . % of americans correctly identify fever, cough, and dyspnea as the three leading covid- symptoms). we compared the demographic characteristics, health insurance status, food insecurity, and prevalence of covid- in their state of residence (divided into quartiles), of those selecting this response to two other groups: ( ) those working and ( ) persons out-ofwork because of a non-coronavirus-related illness/ disability. we performed univariate logistic regressions to evaluate the association of each factor with being out-sick due to coronavirus symptoms relative to each comparator group. we generated nationally representative estimates (and standard errors) using hps' sample weights (and replicate weights) and stata/ se . . our sample included , adults working the past week, out-sick with coronavirus symptoms, and out-ofwork because of a non-coronavirus illness/disability. during may - , . million workers nationally were out-sick because of coronavirus symptoms. table presents characteristics of that group and the comparator groups. relative to both other groups, those out-sick with coronavirus symptoms were younger and more likely to be people of color: . % were black (vs. . % of those working and . % of those not-working due to a non-coronavirus illness/disability), . % were asian (vs. . % and . %), and . % were hispanic (vs. . % and . %). those out-sick with coronavirus symptoms were lesseducated and had lower incomes than those working; their education levels and incomes were more similar to those not working due to a non-coronavirus illness/disability. they had larger household size: . % lived in a household with + members, vs. less than a quarter in each comparison group. . % of those out-sick with coronavirus symptoms were uninsured, vs. % in each comparison group; . % were food insecure, vs. . % among those working and . % among those out-sick for non-coronavirus symptoms/disability. finally, we observed an association between states' prevalence of coronavirus and being out-sick with coronavirus symptoms: . % of americans out-sick with coronavirus symptoms resided in a state in the top quartile of coronavirus prevalence, while only . % lived in a bottom-quartile state. in contrast, individuals in the two comparison groups were divided roughly equally among the four state quartiles. minority race/ethnicity, low income, and residence in a state with high covid prevalence were associated with work absence because of coronavirus symptoms in april-may . this national-level evidence of the disparate impact of covid- bolsters reports based on diagnoses from regions and hospital systems, as well as our previous findings of an increase in illness-related work absence in april that disproportionately affected minorities. we also identified social vulnerabilities-uninsurance and food insecurity-among many out-sick with coronavirus symptoms, which likely intensifies their risk of health and financial harms. our study has strengths and limitations. the census bureau recruited respondents via email and text messages to generate almost-real-time data; the trade-off was poorer response rates, which, despite weighting designed to account for nonresponse, may compromise generalizability. additionally, the survey did not involve performance of diagnostic testing; some of those with "coronavirus symptoms" no doubt had other illnesses. however, the correlation between the statelevel covid- infection rate and the proportion out-sick with coronavirus symptoms is reassuring, as is the consistency of findings across the two comparison groups. the high rate of uninsurance among those with "coronavirus symptoms" that we observed could, of course, obstruct medical evaluation and other care even among those with other illnesses. during the covid- pandemic, poor and minority americans have been doubly disadvantaged: they are more often infected, but have fewer household resources and inferior health protection. protecting the health and welfare of these patients must be a policy priority. *univariate logistic regressions. the dependent variable is employment status (out-sick with coronavirus symptoms versus working, or out-sick with coronavirus symptoms versus not working due to noncoronavirus illness/disability) and the independent variable is the indicated characteristic (e.g., age category, sex) †white, black, asian, and other are non-hispanic whites, non-hispanic blacks, non-hispanic asians, and non-hispanic others. hispanic individuals may be of any race ‡ , individuals had missing data on income ( . % of n = , sample) §insurance status is defined similar to the approach used by the american community survey. we considered individuals insured if they report private insurance (through an employer), private insurance (individually obtained), tricare, medicare, medicaid, or veterans health administration coverage; those who report not having each of these insurance types (including those who only report indian health service or "other" insurance) are considered uninsured. others (n = in our sample) were treated as missing ( . % of n = , sample) || we top-coded the categorical household size variable at ¶this is based on a four-category variable that we re-categorized as a binary variable: not insecure (either enough food or enough but not the types wanted) vs. insecure (sometimes not enough food or often not enough food). n = with missing data on current food security ( . % of n = , sample) **data on state-level per , population coronavirus infections was downloaded from the cdc on june , ; data is current as of june , . the total survey population was divided into quartiles based on the coronavirus infection rate in their state (using sample weights) disparities in outcomes among covid- patients in a large health care system in california source of the data and accuracy of the estimates for the household pulse survey disparities in coronavirus reported incidence, knowledge, and behavior among us adults united states covid- cases and deaths by state. cdc covid data tracker illness-related work absence in mid-april was highest on record measuring household experiences during the coronavirus (covid- ) pandemic key: cord- -kci uw u authors: majid, sabhiya; farooq, rabia; khan, mosin s.; rashid, samia; bhat, showkat a.; wani, hilal a.; qureshi, waseem title: managing the covid- pandemic: research strategies based on the evolutionary and molecular characteristics of coronaviruses date: - - journal: sn compr clin med doi: . /s - - -z sha: doc_id: cord_uid: kci uw u coronavirus disease (covid- ), an ongoing global health emergency, is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome coronavirus (sars-cov- ). emerging in wuhan, china, in december , it spread widely across the world causing panic—worst ever economic depression is visibly predictable. coronaviruses (covs) have emerged as a major public health concern having caused three zoonotic outbreaks; severe acute respiratory syndrome-cov (sars-cov) in – , middle east respiratory syndrome-cov (mers-cov) in , and currently this devastating covid- . research strategies focused on understanding the evolutionary origin, transmission, and molecular basis of sars-cov- and its pathogenesis need to be urgently formulated to manage the current and possible future coronaviral outbreaks. current response to the covid- outbreak has been largely limited to monitoring/containment. although frantic global efforts for developing safe and effective prophylactic and therapeutic agents are on, no licensed antiviral treatment or vaccine exists till date. in this review, research strategies for coping with covid- based on evolutionary and molecular aspects of coronaviruses have been proposed. coronaviruses (covs) are spherical rna viruses, deriving name from latin word "corona" or crown as they appear like a royal crown under the electron microscope due to characteristic spike projections on their spherical surface. covs belong to family coronaviridae within order nidovirales, which further has two subfamilies: orthocoronavirinae and torovirinae. subfamily orthocoronavirinae encompasses four genera: alpha coronavirus, beta coronavirus, gamma coronavirus, and delta coronavirus [ ] . beta coronaviruses are a subgroup of the coronavirus family, large enveloped positive-sense singlestranded rna (+ssrna) viruses able to infect a wide variety of mammals and avian species, causing mainly respiratory or enteric diseases [ ] . discovered long back in s, hcov- e and hcov-oc were known to cause common cold in humans. to date, seven beta coronaviruses are known to cause human disease-the prevalent strains, hcov e, hku , nl , and oc , typically cause mild infections of the upper respiratory tract in humans [ ] [ ] [ ] . however, scenario has altered in the past two decades with covs becoming a major public health concern as three strains, sars-cov [ , ] , mers-cov [ , ] , and the newly identified sars-cov- , are associated with serious respiratory diseases and have led to severe zoonotic outbreaks [ ] [ ] [ ] . the sars-cov pandemic initiated in guangdong province, china, in . the rabia farooq and mosin s. khan have contributed equally as second authors infected patients exhibited pneumonia symptoms with a diffused alveolar injury which lead to acute respiratory distress syndrome (ards); the disease quickly spread worldwide causing serious illnesses and nearly deaths in - [ , ] . mers-cov epidemic took place in [ , ] . in both cases, the infected patients manifested severe acute pneumonia, but while sars-cov infected mainly the lower respiratory tract, mers-cov caused more pronounced gastrointestinal symptoms, often associated with kidney failure [ , ] . the world health organization (who) has reported a total number of mers-cov cases with associated deaths from to january [ ] . sars-cov- and the covid- pandemic currently, the novel coronavirus, sars-cov- alternatively termed ncov, has caused panic with who declaring it as a global health emergency on january [ ] . it was initially identified in the city of wuhan, china, in december ; patients presented with severe viral pneumonia and respiratory illness. the number of cases has been mounting since then to whopping figure of around six and half million globally [ ] [ ] [ ] [ ] . the disease caused by sars-cov- has been named covid- , a highly transmittable and pathogenic respiratory infection, which has become a public health emergency of international concern as no clinically approved antiviral drug or vaccine is available-though few broad spectrum antiviral drugs and drug combinations in clinical trials have resulted in clinical recovery [ ] [ ] [ ] [ ] [ ] . convalescent plasma (cp) therapy has recently been shown to be well tolerated, and severe covid- cases could potentially improve the clinical outcomes by neutralizing viremia [ ] . transmission is via respiratory droplets or aerosols on exposure to coughing, sneezing, and close contact with an infected person [ ] . social distancing, face masks, and frequent hand sanitization are recommended preventive measures. personal protective gear as recommended is to be used by healthcare workers for their safety. containing the outbreak before it can spread is the best way to prevent pandemics. border closures, screening at airports, and checkpoints-classical measures implemented in pandemics-can reduce spread of the virus but will not be a fool-proof strategy [ , ] . millions of people travel every day from one country to another; a disease originating in one country can rapidly spread to other countries regardless of distances between them. this is particularly visible in the rapid spread of covid- , which affected almost every country in the world within months of the first reported case. information technology is playing its own role with numerous apps coming up, purportedly helping cope with awareness, management, and controlling spread of this disease-like "aarogya setu app" in india. this disease can remain asymptomatic during around days incubation period of sars-cov- . the sars and mers covs evade immune responses during longer incubation periods. the spectrum of covid- disease is broad-most commonly reported symptoms of are fever, myalgia or fatigue, dry cough, and dyspnea. around % of infections are mild, resolving within a week without any specific treatment or hospitalization. amongst hospitalized cases, pneumonia, sepsis, respiratory failure, and ards are frequently encountered complications, and in severe cases, progressive respiratory failure can be fatal [ ] [ ] [ ] . overproduction of early response pro-inflammatory cytokines can result in cytokine storm leading to vascular hyperpermeability, reduced anticoagulant concentration, impaired anticoagulant-procoagulant balance predisposing to development of microthrombosis, disseminated vascular coagulation, and multi-organ failure [ ] . this is evidenced in severe covid- pneumonia where raised d-dimer is a poor prognostic feature and disseminated intravascular coagulation is common in non-survivors [ ] . as clinical manifestations of covid- range from mild to moderate, more systematic symptoms and severe radiological abnormalities are seen in older patients [ ] . children and younger adults can remain as asymptomatic carriers [ ] [ ] [ ] . the possibility for gastrointestinal involvement in sars-cov- infection and feco-oral transmission has been suggested [ ] . who has estimated overall mortality rate of . % in spite of the significant infectivity rate, majority deaths typically occurring amongst elderly patients, patients having multiple comorbidities, and immune compromised population [ ] . the covid- epidemic has reached worldwide resonance; global efforts are being undertaken to characterize the molecular features and evolutionary origins of this virus. covs are typically harboured in mammals and birds-being common in camels, cattle, cats, bats, and other animals [ ] [ ] [ ] . alpha and beta coronaviruses circulate in mammals, including bats. gamma coronaviruses mostly infect avian species and a few mammalian species, whereas delta coronaviruses infect birds and mammals [ , ] . animal covs are known to cause important diseases in animals and are responsible for economic losses in domestic animals or bird. although rare, zoonotic events do occur wherein animal covs acquire the ability to infect humans and further spread through human-to-human transmission [ , ] . studies have shown that bats harbour covs that are ancestral to sars-cov which have been circulating in bats for a long time before genetically changing and jumping to humans [ ] . rhinolophus bats were found to have anti-sars-cov antibodies suggesting bats as a source of viral replication [ ] . further, studies have revealed that palm civets and raccoon dogs, of chinese local food markets, harbour sars-related covs (sarsr-covs) suggesting that they could be key reservoir of infection and may be secondary hosts. this detection of sarsr-covs in bats and small animals in retail markets may indicate an interspecies transmission from bats to small animals and finally to humans [ ] . in , samples from the healthy persons of hong kong on molecular assessment showed . % frequency rate of antibodies against sars-cov, indicating that sars-cov might have been circulating in humans before causing the outbreak in [ ] . mers-cov reportedly has camels as a zoonotic source or primary host [ ] . in a recent study, mers-cov was also detected in pipistrellus and perimyotisbats, favouring bats as key host and transmitting medium of this virus [ ] . metagenomics analysis of phylogenetic relationships between sars-cov- , sars-cov, bat sars r-covs, and bat cov revealed that sars-cov- genome (~ . kb) shares . % sequence identity with sars-cov. again, close phylogenetic relationship between sars-cov- and a bat cov, % identical at whole genome level, points to bat origin of sars-cov- and bats as probable "key reservoirs" [ ] . overall, these studies highlight bats as carriers of viruses with zoonotic and devastating potential. however, intermediate source of origin and transfer to humans is not known; further studies are needed to determine whether the virus was transmitted to humans by an intermediate host. nevertheless, rapid human-to-human transfer has been widely confirmed, already reported from more than countries in the world [ , ] . coronaviruses will continue to infect multiple species and cell types, including humans due to their ability to recombine and mutate. the source and spread of these covs necessitate to be evidently firmed; urgency finance for investigation on systematic basis of their spread and their pools is required to frame preventive plans to hold and regulate such outbreaks. in the phylogenetic connection between extremely pathogenic covs, their transitional zoonotic source requires to be vigorously studied. role of variations in human doings, biomes, and environment in leading to such pandemics requires to be studied as the changes in pathogen types, disease burden, and distribution have arisen largely due to human activity. in the last century, there was a reduced burden of infectious diseases due to improved nutrition, better hygiene, and use of vaccines and antimicrobials. however, in recent decades, there is an upsurge of disease emergence and propensity to pandemics much due to swelling global travel and trade, increasing human and livestock populations. viruses have broad range of hosts and are emerging pathogens [ ] . in , the united nations environment programme (unep) warned that zoonotic diseases are related to the health of ecosystems. zoonoses are opportunistic and increase with changes in animal or human hosts, environment, or pathogen itself. pathogens have passed between animals and humans in the last century due to reduction in ecosystems by human intervention and population growth. humans have encroached into animal habitats and disturbed natural buffer zones between animals and humans leading to emergence of zoonosis. livestock serves as a bridge between wildlife and human infections and forms a part of wildlife-livestock-human interface. consumer demand for livestock has increased due to economic growth leading to rigorous livestock farming near and around cities, thereby, expanding chances of zoonotic diseases. in addition, natural source of disease resistance is genetic diversity but "intensive livestock rearing" often produces genetic similarities within herds and flocks, making them susceptible to pathogen spillover from wild animals. consumption of wild animals in wet markets can also facilitate animal to human transmission. frequent climate change tells upon the survival of microbes in the environment, suggesting the more frequency of pandemics due to rapid change in climate [ ] . thus, if we need to stop such pandemics in the future, we need to focus on the influence of human activities on ecosystems. experiments on monitoring of human and wildlife health will improve understanding and preparedness for potential pandemics. it invites for collaborative, trans-disciplinary, and international efforts as summarized by the "one health approach"-a concept of combining human, animal, and environmental components to address global health challenges having ecological interdependence. "one health approach" wherever adopted is seen to have significant impacts on control of infectious diseases [ ] . ultimately, "if we have a robust plan for protecting nature, nature will protect humanity". last but not the least, strategies to curb the transmission of virus should be put in place in a more stringent way. the correct use of personal protective equipment (ppe) and regular and thorough hand hygiene are key measures in the prevention and control against infection through contact transmission, droplet transmission, and airborne virus particles. in addition, maintaining a constant and regular supply of drugs is indispensable during the pandemic. healthcare professionals are at three times higher risk than common individuals so their body temperature, nucleic acid, and specific antibodies for covid- should be monitored regularly. during pandemic, psychological illness is rampant so individuals especially healthcare workers should be evaluated for psychological illness, if any. our understanding of the virus deepens, and with the constant improvement of diagnosis, treatment, and strategies for prevention and control, healthcare professionals should continue to actively collect and improve their services based on the latest information [ ] . a crucial need to counteract the covid- pandemic has arisen; no specific drug or vaccine is available as yet. for effective therapeutics and vaccine development elucidation of genetic features and molecular constituents of covs including sars-cov- , unravelling the mechanisms of infection, molecular basis of virus-host interaction, its regulation, and host responses is needed. global efforts are being undertaken-biotechnological, molecular, and bioinformatic advances have been helpful in making available details related to the genomics and proteomics of these covs, especially sars-cov- in a very short time [ ] . the covs are~ - nm in diameter, containing singlestranded rna ranging from to kbs in length as nucleic material, being enveloped in lipid bilayer derived from the host cell membrane. the structural together with few nonstructural proteins (nsps) are coded within the ′ end of the viral genome, whereas the ′ two-thirds of the genome codes for nsps that are important in viral replication, including the rna-dependent rna polymerase (rdrp) [ , ] . rna of covs codes for four major structural proteins involved in its replication as well, termed as spike (s), membrane (m), envelope (e), and nucleocapsid (n) proteins. some beta coronaviruses also code for protein hemagglutinin esterase (he). the s, m, and e proteins lie in the viral envelope. the s protein is heavily glycosylated forming homotrimeric spikes on the surface of the viral particle required for binding and entry into host cells. amongst the four, m protein is the most abundant and important protein giving the virion primarily its shape; besides, it interacts with other structural proteins to perform various functions. interaction of s proteins with m proteins is needed for its incorporation into new virions [ ] [ ] [ ] . in the same way, m protein along with the smallest one e protein which is found in small quantities is involved in virus assembly, forming of mature viral envelopes, and release of viral particles from host cells. e protein is mostly expressed in the infected cell; it is important for production and maturation of the virus, and its interaction with psd /dlg/zo- (pdz) proteins involved in host cell processes is important for viral infection. the n protein is located in the core of the viral particle forming the nucleocapsid of viral rna and is involved in replication [ , ] . generally, the transcription and replication of covs take place in the host cell cytoplasm following viral entry. spike proteins of the virus bind with the host receptor, structural changes occur followed by endocytosis, which is ph dependent [ ] , and the virus releases its rna inside the host cell cytoplasm. translation of the ′ end of viral rna produces the rdrp, which uses viral rna as a template to generate series of virus-specific mrnas or sub-genomic mrnas from sub-genomic negative strand intermediates. translation of sub-genomic mrnas leads to production of structural and nonstructural viral proteins; they share the same ′ ends and the same leader sequence of - nucleotides at their ′ ends [ ] . once sufficient, structural proteins and genomic viral rna are synthesized; viral assembly and budding occur in smooth-walled vesicles in the endoplasmic reticulum-golgi intermediate compartment (ergic) [ ] . rna of coronavirus is polycistronic containing approximately seven genes: ′ region mainly contains large replicase gene for replication and transcription process, and the ′ region contains nonessential accessory proteins expressed from sub-genomic mrnas [ ] . the large replicase gene at ′ end encodes replication-transcription complexes (rtcs) amongst covs which comprise of two overlapping open reading frames (orfs), orf a and orf b. translation of these orfs results in two very large polyproteins, polyprotein a (pp a) and polyprotein ab (pp ab), further leading to formation of nonstructural proteins by co-and post-translational modifications by various proteinases. orf b encodes enzymes which are needed in rna replication and its transcription. all covs contain specific genes in orf downstream regions that encode proteins for viral replication, nucleocapsid, and spike formation [ , ] . covs contain doublemembrane vesicles (dmvs) which are attached with rtcs; these dmvs are derived from network of modified er membranes, also referred to as convoluted membranes (cms) [ ] . the replication of covs is inhibited by addition of drugs in the early-secretory phase or by addition of rnai [ ] . genome of this lethal virus has been isolated; a total of whole genome sequences of sars-cov- could be downloaded from the gisaid database as depicted in fig. (https://www.gisaid.org/cov /). sequences that likely had spurious mutations resulting from sequencing errors were indicated in the comment field of the gisaid data. its genome is a +ssrna virus having , bp length with ′ poly a tail and ′ cap. genbank: mn . ; locus mn (https://www. ncbi.nlm.nih.gov/nuccore/mn ), having aa protein sequence; locus qhi (https://www.ncbi. nlm.nih.gov/protein/qhi . ). the genome of the sars-cov- reportedly is over % identical to the previous sars-like bat cov, and according to the evolutionary tree, sars-cov- lies close to sars-cov. the orf ab is the largest gene in sars-cov- which encodes the pp ab protein and nsps. the orf a gene encodes for pp a protein which also contains nsps. further, the pp a and pp ab encoded by the orf a/b give rise to viral proteases, papain-like protease (plpro), and c cleavage-like protease ( clpro/mpro), for creating non-structural proteins (rdrp, helicases) [ ] . mpro is a crucial enzyme facilitating viral replication and transcription. recent studies have indicated notable variations in sars-cov and sars-cov- such as the absence of a protein and fluctuation in the number of amino acids in b and c protein in sars-cov- [ , ] . spike glycoprotein of the sars-cov- has reportedly modified via homologous recombination; it is a mixture of bat sars-cov and a not known beta-cov [ ] . attachment and entry of covs into host cells is mediated by "s" protein on outer surface of covs. s protein has two domains: s and s [ ] . within s domain, receptor-binding domain (rbd), located at the c-terminus in sars-cov and mers-cov, mediates binding to the associated host cell receptor, while the s domain brings about the merger between viral and host cell membranes through endosomal pathway, leading to the entry of the viral genome into the cytoplasm of host cell. the virus may infect multiple hosts as the receptorbinding domain (rbd) is loosely attached to it [ , ] . covs mostly identify carbohydrates or amino peptidases as a key receptor for entry to human cells [ ] . the mechanism of entry of cov in host cell is governed by cellular proteases including human airway trypsin-like protease (hat), cathepsins, and transmembrane protease serine (tmprss ) which cleave spike protein and start further infiltration [ ] . varied covs bind to diverse receptors on host cells. mers-cov binds to dipeptidyl-peptidase (dpp , also known as cd ) receptor. human angiotensin-converting enzyme (hace ), a zinc-dependent carboxypeptidase, responsible for regulating blood pressure, also acts as a receptor of entry for sars-cov, hcov-nl , and sars-cov- [ ] [ ] [ ] . the critical lysine residue on the hace receptor recognizes glutamine residues in the rbd region of sars-cov- [ ] . comprehensive pathogenic mechanism of sars-cov- is depicted in fig. [ ] . current studies have indicated % homology between amino acid sequence of rbd of sars-cov- and sars-cov [ ] and notable variations between sars-cov and sars-cov- such as the absence of a protein and variation in the number of amino acids in b and c protein in sars-cov- [ ] . as per a recent study, s protein of sars-cov- has higher affinity to ace receptor as compared with s protein of sars-cov which might be attributed to the n t mutation in spike protein of sars-cov- . the spike protein of sars-cov- binds to hace which is highly expressed in the lungs and heart. studies suggest that there is an elevation in angiotensin ii in covid- patients which advocates that binding of covid- to ace leads to enhanced conversion of angiotensin ii from angiotensin i through the renin-angiotensin-aldosterone system (raas) thereby increasing cardio-myocyte hypertrophy and high blood pressure leading to myocardial injury, myocarditis, and cardiac arrhythmias [ ] . in case of diabetics, there is an altered production of cytokine, impaired t cell-mediated immune response, inhibition of neutrophil chemotaxis, ineffective microbial clearance, and phagocytic cell dysfunction which together with the entry of coronavirus into host pneumocytes mediated by ace receptor adds to the severity of covid- in patients with diabetes mellitus. so, ace may play a key role in the severity of covid- infection in diabetic patients [ ] . the coronavirus-human interactome x-ray crystallography has determined the crystal structures of cov-human interactomes to fully understand the initial step of infection at molecular level. for the first time, crystalline structure for hcov-nl s -ctd complexed with human ace was discovered followed by sars-cov s -ctd complexed with ace , displaying common receptors [ , ] which was followed by mers-cov s -ctd complexed with human dpp [ ] . overall binding mode of ace with sars-cov- -rbd is nearly identical to that of the sars-cov-rbd as per the recent elucidation of their crystal structure. there are amino acid residues in rbd of sars-co-v, majority of which are highly conserved, or share alike side chain properties with rbd of sars-cov. crystal structure of sars-cov- -rbd complexed with ace is available at protein data bank (pdb) [ ] . presently, no registered antiviral drug for use in patients with covid- is there. on top of it, there is no efficient vaccine available for covid- in humans. the standard of care is "supportive" and includes drugs like protease inhibitors (lopinavir/ritonavir; darunavir + ritonavir; darunavir/ cobicistat); chloroquine or hydroxychloroquine; tocilizumab, monoclonal antibody against chimeric antigen receptor t cells; nucleotide inhibitor like remdesivir (a broad-spectrum antiviral); methylprednisolone mg × /day; and antibiotic therapy using third-generation cephalosporin, clarithromycin, or azithromycin or alternatively fluoroquinolones in case of secondary bacterial infections [ ] . a crucial need for a clinical research and therapeutic strategy to counteract this epidemiological outbreak remains. we have no empirical enveloped cure or vaccine for this potentially fatal disease; coordinated international efforts for developing therapeutics and vaccines for sars-cov- are needed. although several clinical trials are currently underway to test possible therapies, current response to the covid- outbreak has been largely limited to monitoring/containment. various biotechnological, molecular tools, and advances in bioinformatics have been instrumental in making available details related to the genomics and proteomics of this virus. some light has been shed on genetic features, molecular constituents, and mechanisms of infection. armed with this information research is progressing at a rapid pace to develop therapeutic strategies, neutralizing antibodies and vaccines to address this disease covid- which has spread as a pandemic of mammoth proportions. a wide variety of therapeutic options are being evaluated in an earnest attempt to find a cure. a drug, from time of its inception to qualifying all three phases of clinical trials, can take years to reach market; nevertheless, coordinated international efforts and adequate funding can make drugs against covid- available within a record time. bioinformatics and in silico drug modelling, a boon for speedy drug development, are being exploited. recent in silico master regulator analysis has shed light on sars-cov- /human interactome detailing the host receptor recognition. features of the human interactome most affected by the infection including apoptotic and mitochondrial mechanisms and downregulation of the ace protein receptor have been propounded [ ] . there is an upregulation of ace in diabetes and hypertension as they are being treated by ace inhibitors and angiotensin ii type-i receptor blockers (arbs). ace is also increased by drugs such as thiazolidinediones and ibuprofen. consequently, the increased expression of ace would facilitate infection with covid- and increase the risk of developing severe fatal covid- viral infection. a further aspect that should be investigated is the genetic predisposition for an increased risk of sars-cov- infection, which might be due to ace polymorphisms that have been linked to diabetes mellitus, cerebral stroke, and hypertension, specifically in asian populations. summarizing this information, the sensitivity of an individual might result from a combination of both therapy and ace polymorphism [ ] . expectedly, development of neutralizing antibodies may take less time due to their speedy trials and high specificity, as a prompt option repurposing of broad spectrum antiviral agents and their combinations is being frantically evaluated. since its emergence, sars-cov- has drawn well-deserved attention. it led to a pandemic that has shocked and devastated the human world, shattering its economy-massive economic recession is predicted. it is likely that these coronaviruses will continue to emerge and evolve, causing both human and veterinary outbreaks due to their ability to recombine, mutate, and infect multiple species and cell types, including humans. the future of human cov outbreaks will depend not only on how the viruses will evolve but also on the development of efficient prevention, treatment strategies, and our preparedness to deal with them. priority funding for research on mechanistic basis of transmission of coronaviruses from one species to other, their reservoirs, zoonotic diseases, possible role of environmental changes, and pollution in leading to such epidemics is needed to face the imminent challenge of such repeated outbreaks. very rapid and efficient human-to-human transmission is confirmed which is of immense concern necessitating speedy development of therapeutic modalities. neutralizing antibodies and vaccines could play significant roles in controlling covid- . studies on humancoronavirus interactome developing suitable therapeutic agents and vaccines are needed. research at accelerated pace is needed to translate into therapies and vaccines. hopefully, lessons from handling this outbreak will allow us to be better prepared in the future-the viruses can keep coming. coronaviruses of man discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus occurrence and frequency of coronavirus infections in humans as determined by enzyme-linked immunosorbent assay human coronaviruses: what do they cause? antivir ther viral infection of the lower respiratory tract identification of a novel coronavirus in patients with severe acute respiratory syndrome severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia clinical features and viral diagnosis of two cases of infection with middle east respiratory syndrome coronavirus: a report of nosocomial transmission a new coronavirus associated with human respiratory disease in china a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus outbreak of global health concern management and prevention of sars in china . van den brand jma, smits sl, haagmans bl. pathogenesis of middle east respiratory syndrome coronavirus who. middle east respiratory syndrome coronavirus world-health-organization statement on the second meeting of the international health regulations centers-of-disease-control-and-prevention confirmed -ncov cases globally european centre for disease prevention and control data china's cdc detects a large number of new coronaviruses in the south china seafood market in wuhan novel coronavirus: where we are and what we know return of the coronavirus clinical features of patients infected with novel coronavirus in wuhan the continuing -ncov epidemic threat of novel coronaviruses to global health -the latest novel coronavirus outbreak in wuhan, china clinical features of patients infected with novel coronavirus in wuhan effectiveness of convalescent plasma therapy in severe covid- patients epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study pneumonia of unknown origin -china from sars-cov to wuhan ncov outbreak: similarity of early epidemic and prediction of future trends a familial cluster of pneumonia associated with the novel coronavirus indicating personto-person transmission: a study of a family cluster clinical course and outcomes of critically ill patients with middle east respiratory syndrome coronavirus infection a novel coronavirus from patients with pneumonia in china covid- : consider cytokine storm syndromes and immunosuppression d-dimer levels on admission to predict in-hospital mortality in patients with covid- . j thrombosis hemostasis ct imaging features of novel coronavirus ( -ncov) clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china clinical course and risk factors for mortality of adult in patients with covid- in wuhan, china: a retrospective cohort study clinical characteristics of patients infected by sars-cov- in wuhan analysis of factors associated with disease outcomes in hospitalised patients with novel coronavirus disease an epidemiological study on covid- : a rapidly spreading disease coronaviruses in avian speciesreview with focus on epidemiology and diagnosis in wild birds middle east respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study severe acute respiratory syndrome coronavirus-like virus in sn compr chinese horseshoe bats molecular evolution of human coronavirus genomes epidemiology, genetic recombination, and pathogenesis of coronaviruses epidemiology and cause of severe acute respiratory syndrome (sars) in people's republic of china zoonotic origins of human coronaviruses the proximal origin of sars-cov- possible bat origin of severe acute respiratory syndrome coronavirus . emerg infect dis wet markets-a continuing source of severe acute respiratory syndrome and influenza? covid- infection: origin, transmission, and characteristics of human coronaviruses bat origin of human coronaviruses the origin, transmission and clinical therapies on coronavirus disease (covid- ) outbreak -an update on the status molecular epidemiology, evolution and phylogeny of sars coronavirus world-health-organization coronavirus disease (covid- ) outbreak human coronaviruses: a review of virus-host interactions zoonosis emergence linked to agricultural intensification and environmental change zoonoses and one health: a review of the literature wuchang fangcang shelter hospital: practices, experiences, and lessons learned in controlling covid- . sn compr clin med cryo-electron tomography of mouse hepatitis virus: insights into the structure of the coronavirion the molecular biology of coronaviruses coronavirus: organization, replication and expression of genome mechanisms and enzymes involved in sars coronavirus genome expression pre-fusion structure of a human coronavirus spike protein the m, e, and n structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles the role of flexibility and conformational selection in the binding promiscuity of pdz domains genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding role of endocytosis and low ph in murine hepatitis virus strain a cell entry subgenomic negative-strand rna function during mouse hepatitis virus infection a contemporary view of coronavirus transcription current insights into the genomics of novel coronavirus: sars-cov- an overview of their replication and pathogenesis intracellular processing of the n-terminal orf a proteins of the coronavirus mhv-a requires multiple proteolytic events sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum e glycoprotein and broadly neutralizing antibodies that target them coronaviruses: drug discovery and therapeutic options structure-based design of antiviral drug candidates targeting the sars-cov- main protease emerging coronaviruses: genome structure, replication, and pathogenesis discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing. msphere multibasic cleavage site in the spike protein of sars-cov- is essential for infection of human lung cells structure of sars coronavirus spike receptor binding domain complexed with the receptor structure of mers-cov spike receptor-binding domain complexed with human receptor dpp the bittersweet promise of glycobiology the novel coronavirus ( -ncov) uses the sars-coronavirus receptor ace and the cellular protease tmprss for entry into target cells angiotensin-converting enzyme is a functional receptor for the sars coronavirus human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry ace of the heart: from angiotensin i to angiotensin ( - ) identification of a coronavirus hemagglutinin-esterase with a substrate specificity different from those of influenza c virus and bovine coronavirus covid- infection: origin, transmission, and characteristics of human coronaviruses genome composition and divergence of the novel coronavirus ( -ncov) originating in china the association of cardiovascular diseases and diabetes mellitus with covid- (sars-cov- ) and their possible mechanisms crystal structure of nl respiratory coronavirus receptor-binding complexed with its human receptor structural basis of receptor recognition by sars-cov- molecular basis of binding between novel human coronavirus mers-cov and its receptor cd crystal structure of sars-cov- spike receptor-binding domain bound with ace clinical management of adult coronavirus infection disease (covid- ) positive in the setting of low and medium intensity of care: a short practical review master regulator analysis of the sars-cov- /human interactome covid- outbreak: an update on therapeutic options publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations acknowledgements we acknowledge all the patients who have been key: cord- - ybfiz f authors: decaro, nicola; lorusso, alessio title: novel human coronavirus (sars-cov- ): a lesson from animal coronaviruses date: - - journal: vet microbiol doi: . /j.vetmic. . sha: doc_id: cord_uid: ybfiz f the recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus (sars-cov- ), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. the novel coronavirus (cov) recognises, with high probability, a zoonotic origin but the role of animals in the sars-cov- epidemiology is still largely unknown. however, covs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face cov infections in animals, which could represent a model for sars-cov- infection in humans. in the present paper, we provide an up-to-date review of the literature currently available on animal covs, focusing on the molecular mechanisms that are responsible for the emergence of novel cov strains with different antigenic, biologic and/or pathogenetic features. a full comprehension of the mechanisms driving the evolution of animal covs will help better understand the emergence, spreading, and evolution of sars-cov- . eighteen years after the emergence of severe acute respiratory syndrome (sars) in china and years after the emergence of middle east respiratory syndrome (mers) in saudi arabia, a novel coronavirus (cov) epidemic, recently classified as pandemic by the who, is threatening the human population worldwide (zhou et al., ) . the disease, now referred to as coronavirus disease , is caused by a novel human cov, which was initially denominated novel coronavirus ( -ncov) and later renamed as sars coronavirus (sars-cov- ) the by coronavirus study group of the international committee on taxonomy of viruses (gorbalenya et al., ) . covid- emerged in december in wuhan city, hubei province, china, in humans exposed to wildlife at the huanan seafood wholesale market, which is the largest seafood market in central china, and where different species of farm and wild animals are commonly sold (lorusso et al., ) . the epidemic has then expanded not only to neighbouring asian countries, but also to other continents (https://www.who.int/ docs/default-source/coronaviruse/situation-reports/ -sitrep- -covid- .pdf?sfvrsn=c ea _ ). . a list of human covs is showed in table . historically, only two human covs (hcovs) had been known before the sars emergence, namely hcov- e, an alphacoronavirus originated in bats and transmitted to humans through alpacas, and hcov-oc , a betacoronavirus which had passed from rodents to humans through cattle (corman et al., (corman et al., , . after - sars epidemic, the renovated interest in hcovs allowed the discovery of two additional viruses, the alphacoronavirus hcov-nl and the betacoronavirus hcov-hku , derived from bats and rodents, respectively (tao et al., ) . all these four viruses are usually responsible for mild respiratory symptoms in immunocompetent patients. sars-cov and mers-cov are two unrelated betacoronaviruses originated in bats and transmitted to humans by wild carnivores and dromedary camels, respectively. in contrast to other hcovs, these two viruses displayed an increased virulence, causing severe pneumonia and even the death of affected people, with mortality rates of about % and %, respectively (guarner, ) . the occurrence of three highly pathogenic covs with a zoonotic origin in less than two decades, highlights the role of animals in generating covs with increased virulence that can adapt to humans, causing epidemics (and eventually pandemics) with high impact on human health. indeed, cov infections of veterinary interest have been known since almost a century (cavanagh, ; pedersen, ; decaro et al., ) , so that animal covs are paradigmatic of how this large family of viruses evolves, generating strains with different biological properties. in addition, the efforts done in veterinary medicine https://doi.org/ . /j.vetmic. . received march ; received in revised form april ; accepted april evolve rapidly, changing their antigenic profile, tissue tropism or host range by means of two distinct mechanisms. the viral replicase (an rna dependent-rna polymerase) does not possess a good proof reading activity, therefore the incorporation of wrong nucleotides at each replication cycle and the consequent accumulation of mutations in the viral genome lead to a progressive differentiation of the viral progeny from the parental strain. this mechanism, which is well known for influenza viruses being responsible for the so called antigenic drift, may cause the progressive adaptation of the viral surface proteins to the cell receptors of new animal species, increasing the viral fitness. in addition, the particular replicating machinery of covs facilitates recombination events due to the presence of consensus sequences upstream each gene. therefore, in the case of coinfection by more than one cov strain, the rna polymerase can jump from the rna of a strain to that of the other one, synthetizing a hybrid rna containing sequences from both viruses. recombination can occur not only with genomic sequences of other covs (homologous recombination), but also with rnas of different viruses and other organisms (heterologous recombination) (luytjes et al., ; banner and lai, ; lai, ; zeng et al., ; huang et al., ) . recombination is an alternative mechanism that let covs acquire novel biological properties in terms of virulence, host range and tissue tropism, so that cov strains, which are non-pathogenic or lowpathogenic in the original host, may increase their pathogenicity in the same species or adapt to different species spreading in the new host with exceptional rapidity (banner and lai, ) . the occurrence of three human cov epidemics in less than years, along with the emergence of less pathogenic human covs, arises some questions on how these viruses that have their reservoirs in bats and rodents may overcome the species barriers jumping to humans. the animal-to-human transmission of viruses has been already occurred in the past, but it seems that its frequency has been increased in the last decades, involving in a short time span not only covs, but also a plethora of genetically and biologically different viruses with zoonotic potential, such as ebola virus, influenza viruses, flaviviruses, hendra and nipah viruses (mcmahon et al., ) . climate changes that are intensifying in this first quarter of the st century are favouring the spread of vector-borne diseases through increasing the proliferation of vectors and predisposing to their occupation of new ecological niches. the emergence in temperate climate areas such as europe of vectorborne diseases caused by viruses considered exotic until few years ago (west nile virus, usutu virus, chikungunya virus) accounts for a progressive geographic expansion of tropical diseases thanks to the ongoing phenomenon of tropicalisation (mcmahon et al., ) . deforestation and urbanization are other major factors that facilitate the spill-over of zoonotic agents to humans by reducing the habitat of wildlife and increasing the chances of contacts between wild animals (like bats, rodents and birds) and human beings (beena and saikumar, ; lorusso et al., ) . this could be the case of ebola virus, hendra and nipah viruses, hantavirus and coronavirus infections. in addition, the close contact between human beings and different animal species sold at the wet markets of east asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like covs. it is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic h n avian influenza and sars) have emerged in the same chinese province of guangdong where the contact between humans and animals is closer (lorusso et al., ) . table reports the most important avian cov species recognised so far and their associated diseases. the number of avian species in which covs have been detected in the last years is humongous. since the emergence of sars-cov in , there has been increased interest in table main coronaviruses in domestic and domesticated avian species. schalk and hawn ( ); beach and schalm ( ) ; beaudette and hudson ( ) turkey ( respiratory and kidney disease spackman et al. ( ) n. decaro and a. lorusso veterinary microbiology ( ) covs in other species, including birds. prior to that time, our knowledge of covs in avian species was limited largely to three birds of the order galliformes, i.e., domestic fowl (gallus gallus), turkeys (genus meleagris) and pheasants (phasianidae), with their infectious bronchitis virus (ibv), turkey coronavirus (tcov), and pheasant coronavirus (phcov), respectively. these three viruses were considered for a long-time different species for several reasons such as the diverse pathotype (enterotropic or respirotropic), host range and genetic relatedness of the s protein (cavanagh, ) . this scenario radically changed after the discovery of several novel covs with high genetic diversity from different avian species and the novel rules for species designation of the coronavirus study group (csg https://talk.ictvonline.org/ictv-reports/ ictv_ th_report/positive-sense-rna-viruses- /w/posrna_viruses/ /coronaviridae). all these viruses as well as analogous ibv-like covs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (cavanagh et al., ; circella et al., ; domanska-blicharz et al., ; torres et al., ; hughes et al., ; liu et al., ; wille et al., ; jordan et al., ; bande et al., ; suryaman et al., ) have been assigned to the same viral species known as avian coronavirus (acov) within the subgenus igacovirus of genus gammacoronavirus. ibv and ibv-like strains are commonly detected in both gallinaceous and non-gallinaceous birds, also asymptomatically (cavanagh, ) . this might suggest that these species would act as wild reservoirs, spreading ibv strains over the world (de wit et al., ) . as for the huge economic impact of the disease it causes, ibv is one of the most studied covs over the last decades. ibv causes the infectious bronchitis (ib), a term adopted in for describing the main clinical characteristics of a transmissible respiratory disease of poultry detected for the first time in north dakota (usa). ib has been now diagnosed worldwide and is one of the most important viral diseases of poultry characterised by respiratory signs, but it can also affect the kidneys and reproductive tract following viremia with a severity that differs depending on the involved viral strain (cavanagh and gelb, ) . the disease also affects wild and ornamental birds chen et al., ) . ib control has been hampered by the intricate ibv evolution, which has been entailed, over the years, by the emergence of many different antigenic or genotypic types, commonly referred to as variants, with divergent molecular, biological, and antigenic properties. being a cov, ibv has, indeed, a considerable ability to change both by mutation and by homologous recombination events, which may cause, along with replicase stuttering or slippage, also insertions and deletions in the genome (cavanagh and gelb, ) . if these mechanisms involve the hypervariable region s , they frequently result in the emergence of new ibv variants. although many new variants are not successful, a few may emerge, spread, causing devastating disease either worldwide or in limited geographic areas. currently lineages have been recognized, categorized into six genotypes (gi to gvi) (valastro et al., ) . through their s protein, ibv and ibv-like viruses recognise as cellular host receptor the α , -linked sialic acid glycan, widely distributed in the respiratory tract and in several other host tissues, factor which may explain the tropism also for several organs of the infected host (winter et al., (winter et al., , shahwan et al., ; ambepitiya wickramasinghe et al., ) . extensive use of vaccines has greatly contributed to the high variability of ibv strains thorough recombination between vaccine and field viruses and viral selection pressure resulting from vaccination and presence of partially immune birds (gandon and day, ; gandon et al., ; bande et al., ) . important ibv-like strains are tcov, responsible for enteritis in turkey (also known as bluecomb disease), guinea fowl coronavirus (gfcov) and quail coronavirus (qcov) responsible for fulminating enteric disease in guinea fowl and quail, respectively cavanagh, ; liais et al., ) . tcov, gfcov and qcov are evolutionarily distant from acov based on the s protein. while ibv is a primarily respiratory pathogen, tcov causes gastrointestinal disease (liais et al., ; guy, ) . enterotropism has also been observed for some ibv serotypes; however, all ibv strains infect primarily the respiratory tract, resulting in mild to severe inflammation of the nasal and tracheal epithelia (cavanagh, (cavanagh, , . the s domain of the s protein is highly variable, with the amino acid sequences of ibv and tcov from the usa sharing < % sequence identity. phylogenetic analysis of the s gene shows, indeed, grouping of ibv and ibv-like viruses on the one hand and tcov-us, gfcov and qcov on the other hand (ambepitiya wickramasinghe et al., a) . accordingly, the emergence of covs in turkeys in the usa was proposed to have resulted from recombination events involving ibvs and an as-yet-unidentified cov donating a novel s gene. this switch contributed largely to determine the in vivo tissue tropism of tcov and related viruses. intriguingly, the s protein of these covs requires nonsialylated type poly-lacnac structures on n-glycan cores for binding. this is in marked contrast to the α , -linked sialic acid glycan binding of ibv and ibv-like viruses (ambepitiya wickramasinghe et al., b) . the s subdomain of a tcov isolate from france in (tcov-fr) had only % sequence identity to that of the tcov-us strain (maurel et al., ) . this diversity was biologically evident by the prominent tropism for the epithelium of the bursa of fabricius and only mild tropism for the small intestine of turkey. tcov-fr s protein did not show, indeed, affinity for nonsialylated type poly-lacnac (ambepitiya wickramasinghe et al., a) . this genetic diversity between tcovs is in accordance with several recombination events involving ibvs on different continents with several unknown covs. on the one hand, the s genes of gfcov/fr/ (isolated in france in ) and tcov-us share significant genetic relationships, and thus these viruses must have acquired their s gene from a common ancestor. on the other hand, gfcov/fr/ and fr tcov have a very similar genetic background in other genes. two recombination events may be responsible for the genesis of tcov-us and fr tcov. a first event occurred between an ibv eu recipient strain and an unknown acov donor, resulting in a virus with a new s gene, whose evolution would have resulted in fr tcov and gfcov/fr/ . a second recombination event involving a us ibv recipient and gfcov/fr/ would have generated us tcov viruses, which share a stronger s gene similarity with gfcov/fr/ than with fr tcov . additional covs distinct from acovs and mainly circulating in ducks (duck coronavirus, dcov), pigeons (pigeon coronavirus, pcov), or geese (goose coronavirus, gcov) have been identified (cheng et al., ; jonassen et al., ; muradrasoli et al., ; kim and oem, ; zhuang et al., ; papineau et al., ) . although their genome seems to fulfill the official ictv criteria required to distinguish a new species within the gammacoronavirus genus, ictv approval is still pending. historically, covs of birds were all included in the gammacoronavirus genus and, in turn, all covs belonging to this genus were identified only in birds. however, this suggestion was rebutted by the evidence of a cov belonging to the gammacoronavirus genus in a beluga whale first discovered in (viral species beluga whale coronavirus sw species, subgenus cegacovirus, genus gammacoronavirus) (mihindukulasuriya et al., ) , and of three novel covs, bucov hku , thcov hku , and mucov hku in birds of the order passeriformes, namely bulbuls (pycnonotus jocosus), thrushes (turdidae) and munias (lonchura punctulate), respectively, which did not cluster phylogenetically with extant covs identified in birds. these latter three viruses were distinct from known covs forming a unique cluster in the phylogenetic tree, which was the basis for generation of the deltacoronavirus genus (woo et al., ) . importantly, additional novel viruses belonging to this novel genus were detected in wild birds chu et al., ; durães-carvalho et al., ; torres et al., ) . these viruses cluster with previously unclassified covs detected in various asian carnivores, i.e., the asian leopard cat (prionailurus bengalensis) and chines ferret badger (nyctereutes procyonoides) (dong n. decaro and a. lorusso veterinary microbiology ( ) et al., ) . covs belonging to the betacoronavirus genus, which are strictly related to mouse hepatitis virus (mhv), were also described in wild birds, including parrots, in brazil (durães-carvalho et al., ) . interestingly, this was not the first detection of viruses belonging to the betacoronavirus genus in birds. often overlooked is the discovery over years ago of a cov from the manx shearwater (puffinus puffinus), a bird that visits the shores of britain in summer (nuttall and harrap, ; cavanagh et al., ) . this virus was also related to mhv. however, at that time, considering the unusual finding and that the virus was isolated by passage of shearwater material in the brains of mice, it was speculated that the detected virus was an mhv strain already present in the mice before inoculation (cavanagh, ) . bats are an ancient and heterogeneous group of ecologically important mammals, representing nearly a quarter of all mammalian diversity on earth. they belong to the order chiroptera and further classified in two suborders yinpterochiroptera and yangochiroptera. the first includes the non-echolocating pteropodidae family (megabats) and five echolocating rhinolophoidea microbat superfamilies. yangochiroptera contain thirteen echolocating microbat families (tsagkogeorga et al., ) . bats are thought to host a large plethora of viruses. these include, amongst the others, lyssaviruses, filoviruses, henipaviruses, and reoviruses (calisher et al., ) . before sars-cov epidemic, bats were not known to host covs. indeed, the first evidence of a bat cov was published in . after the sars epidemic, there was a boost in interest regarding searching for novel covs in various animals, including bats. to date, over novel covs have been identified in bats and approximately % of the bat virome sequenced to date is composed of covs (chen et al., ) . this data has been made available following the massive surveillance, coupled with the advent of next-generation sequencing (ngs) technology, which has been performed in wild animals banerjee et al., ) . just a small portion of these covs have been officially recognised by the ictv; many others are still pending for official designation. cov species detected in bats and officially recognised by the ictv are listed in table and the following chapter reasonably discusses only officially recognized bat cov species. bats can carry and transmit covs into local bat populations via migration even though little is known about the migratory patterns of these animals. closely related covs can be detected in the same bat species living at locations separated by thousands of miles (drexler et al., ) and different cov species or genera can be found in different bat species living at the same roosting sites. however, some covs have been shown to be species-specific. accordingly, regional patterns of bat cov outbreaks at species level can be deduced from the population distribution of their respective bat hosts. although bats seem to develop clinical diseases induced by several viruses and bacteria (mühldorfer et al., ) , generally covs do not cause apparently overt disease in these mammals, also experimentally. this phenomenon seems to be related with peculiar characteristics of their immune system (ahn et al., ; brook et al., ) . based upon genomic data available so far, it is widely accepted that while birds represent the reservoir for covs belonging to genera gammacoronavirus and deltacoronavirus, bats are the natural reservoir for alpha-and betacoronaviruses. however, only betacoronaviruses of subgenera sarbecovirus, merbecovirus, nobecovirus and hibecovirus have been detected in bats so far. given that several betacoronaviruses from the subgenus embecovirus have been discovered in rodents, it was speculated that rodent covs may be the ancestors of currently circulating viruses belonging to this subgenus . covs have been detected at high frequency in bats in all continents, with alphacoronaviruses being more widespread than betacoronaviruses . subgenus colacovirus (genus alphacoronavirus) officially comprises the viral species bat coronavirus cdphe , so far composed by two bat covs strains named cdphe /usa/ and myotis lucifugus cov (myl-cov), which share a . % nucleotide identity across the whole genome. both strains have been detected in myotis lucifugus bats (vespertilionidae) also known as the northern american little brown bats. the former was detected in in colorado (genbank acc. no. kf ), while the latter was reported in in canada. this virus was identified in the intestines and lungs and associated with minimal pathology or inflammation (subudhi et al., ) . subgenus decacovirus (genus alphacoronavirus) comprises the species rhinolophus ferrumequinum alphacoronavirus hub- composed so far by btms-al-phacov/gs and btrf-alphacov/hub strains discovered in china in myotis spp. and rhinolophus ferrumequinum bats, respectively. these two viruses share very high sequence identities (higher than %), which dramatically decrease in the s genes (only % nucleotide identity) (wu et al., ) . woo et al., ) shares an % sequence identity with severe acute diarrhoea syndrome-coronavirus (sads-cov) of pigs . these two viruses are now included in the same viral species rhinolophus bat coronavirus hku (subgenus rhinacovirus, genus alphacoronavirus). viral strains btkynl - a, btkynl - b, btkynl - and btkynl - a, identified in in triaenops afer bats from kenya, form the viral species nl -related bat coronavirus strain btkynl - b that is part of the subgenus setracovirus (genus alphacoronavirus) along with human coronavirus nl (tao et al., ) . in this regard, a bat origin has been strongly suggested for two of the less-pathogenic hcovs causing mild respiratory symptoms in immunocompetent people, namely hcov- e and hcov-nl , both belonging to the alphacoronavirus genus. whereas hcov- e (subgenus duvinacovirus) recognises as direct ancestor an alphacoronavirus from alpacas, which in turn derives from e-related covs identified in hipposiderid bats (corman et al., ) , hcov-nl is likely a recombinant virus originating from the distantly related e-related covs associated with hipposiderid bats and covs associated with triaenops afer bats (tao et al., ) (table ). the s protein of hcov-nl is more closely related to that of e-related covs, whereas the rest of the genome with covs included in the nl -related bat coronavirus strain btkynl - b species (tao et al., ) . different from the bovine coronavirus (bcov)-like viruses that cause enteric disease, in a novel alpaca cov was associated to respiratory disease in california, usa. full-length genome analysis showed that this respiratory alpaca cov was closely related to the alphacoronavirus hcov- e (subgenus duvinacovirus) (crossley et al., ) . more recently, close relatives of hcov- e were detected in african hipposiderid bats. interestingly, both bat and alpaca viruses displayed an intact accessory gene orf located at the genomic ' end, while hcov- e retained only a conserved trs preceding remnants of this orf, suggesting its loss after acquisition of a e-related cov by humans. therefore, hcov- is likely a descendant of the alpaca alphacoronavirus (corman et al., ) . strains forming the viral species bat hp-betacoronavirus zhejiang (subgenus hibecovirus, genus betacoronavirus) were discovered in hipposideros pratti bats from china in (wu et al., ) . strain ro-batcov gccdc was identified from stools of rousettus leschenaultii, a species of fruit bats (pteropodidae) of southern asia, which were collected in yunnan province, china, in (huang et al., ) . ro-batcov gccdc shows a small intact orf of nucleotides embedded between the n and ns a genes. this orf has no homology to any known coronavirus, and the encoded protein exhibited . % amino acid identity with the p protein encoded by the first orf of segment s of bat fusogenic orthoreoviruses (genus orthoreovirus, species nelson bay orthoreovirus, also known as pteropine orthoreovirus). these viruses are double-stranded segmented rna viruses, belonging to the family reoviridae, and are able to cause severe pneumonia in humans (chua et al., ; lorusso et al., ) . ro-batcov gccdc is included in the viral species rousettus bat coronavirus gccdc within the subgenus nobecovirus, genus betacoronavirus. rousettus bat coronavirus hku , belonging to subgenus nobecovirus, was also identified in rousettus leschenaultii and in other bat species (mendenhall et al., ) . this virus was first detected in in guangdong province in china (woo et al., ) . subsequent studies suggested that the virus was widely distributed and is circulating in different bat species (ge et al., ) . covs from the bthku -like cluster were also detected in hipposidereos commersoni and rousettus aegyptiacus bats in kenya (tong et al., ) . being a fruit bat, rousettus leschenaultii has a wider flying range than most of the insectivorous bats in china, thus it may carry viruses over long distances. a comparison of the reported hku -cov sequences showed a high genetic diversity within this viral species (luo et al., a, b; lau et al., ; ge et al., ) . when mers-cov was first isolated in the middle east in and its genome sequenced, it was found that it was most closely related to ty-batcov hku discovered in tylonycteris pachypus and pi-batcov hku discovered in pipistrellus abramus, which were the only known members of subgenus merbecovirus at that time. these two viruses are now the prototype strains of tylonycteris bat coronavirus hku and pipistrellus bat coronavirus hku viral species, respectively, within subgenus merbecovirus, genus betacoronavirus. although mers related covs (mers-rcovs) were lately discovered, mers-cov was much closer in the s region to hku -cov than to mers-rcov or hku -cov. indeed, dipeptidyl peptidase (dpp ), the receptor for mers-cov, is also the receptor for hku , but neither for hku nor for early discovered mers-rcovs. however, hku prefers bat dpp over human dpp , whereas mers-cov shows the opposite trend . so far, hku -covs are only carried by tylonycteris spp. bats (t. pachypus and t. robustula) and are relatively conserved; hku -covs are found in different pipistrellus spp. bats, including p. abramus, p. pipistrellus and p. minus . due to the current sars-cov- pandemic, attention should be given to the viral species severe acute respiratory syndrome-related coronavirus (sars-rcov,subgenus sarbecovirus, genus betacoronavirus) and middle east respiratory syndrome-related coronavirus (mers-rcov, subgenus merbecovirus, genus betacoronavirus), which enclose sars-cov and mers-cov, the first two highly pathogenic covs that were discovered in humans. in , at the beginning of the sars epidemic, almost all early human index patients had animal exposure in a market place, in guangdong province, before developing disease. after sars-cov was identified, its rna and/or specific antibodies were found in masked palm civets (paguma larvata) and animal handlers in a market place. however, later investigations of farmed and wild-caught civets revealed that sars-cov strains found in market civets were transmitted to them by other wild animals (tu et al., ; kan et al., ) . subsequently, novel covs related to human sars-cov (sars-rcovs) were discovered in horseshoe bats (genus rhinolophus) in china and hong kong lau et al., ) . these sars-rcovs showed genome sequence identity of - % among themselves and - % identity to human or civet sars-cov isolates. sars-rcovs were detected in rhinolophus spp. bats of other regions of china (tang et al., ; woo et al., ; yuan et al., ; ge et al., ) . sars-rcovs with higher genetic diversity with respect to chinese strains were also detected in rhinolophid bats from slovenia, bulgaria and italy in europe (drexler et al., ; rihtaric et al., ; balboni et al., ) . covs related to sars-rcov were also detected in hipposideros spp. and chaerophon spp. bats from ghana, kenya and nigeria (hu et al., ) . these evidences suggested that bats may be the natural hosts for sars-cov and that wild carnivores were only intermediate hosts. although these sars-rcovs showed high sequence identity to sars-cov, they were demonstrated to be unable to bind to the human cell angiotensin converting enzyme ii (ace ) receptor, the receptor of sars-cov, as a consequence of deletions in their s protein (ren et al., ) . besides, the theory of bat origin of sars-cov lacked a powerful support due to the failure of direct isolation of this virus from bats. thus, considering that no direct progenitor of sars-cov was found in bats and that rna recombination is the fuel for cov evolution, it has been proposed that sars-cov emerged through recombination of bat sars-rcovs. this hypothesis was made after the evidence of a single bat cave in yunnan, china, with very high covs diversity and considering that, within the identified covs, all genetic elements needed to form sars-cov have been identified in that single cave (ge et al., ) . recombination analysis also strongly supported the hypothesis that the civet sars-cov strain sz originated following a recombination event of two existing bat strains, wiv and rf (hu et al., ) . moreover, wiv , the closest relative to sars-cov that has been found in bats so far (more than % nucleotide identity, higher than that of any other bat sars-rcovs ( - %)), likely arose through recombination of two other prevalent bat sars-rcov strains. the most frequent recombination breakpoints were within the s gene and upstream of orf , which encodes an accessory protein. these genes were also involved in the crucial adaptation pathways of sars-cov from bats to wild carnivores, from wild carnivores to humans, and from human to human (cui et al., ) . wiv has been shown to have the capacity to bind to the human, civet and bat cell ace receptor (ge et al., ) . the isolation in cellculture of a highly related sars-cov strain, coupled with the evidence of a functional s protein capable of using the same ace receptor, provided robust and conclusive evidence for the bat origin of sars-cov. an additional sars-rcov strain has been shown, by reverse genetics studies, to have the capacity to bind to the human ace receptor (menachery et al., ) . quite the opposite, a direct bat cov highly related to mers-cov of humans was never detected. indeed, the genome sequences of mers-cov in human and dromedaries possess only around - % nucleotide identities to those of the other members of subgenus merbecovirus from different bats. human mers-covs were instead almost identical to mers-covs identified in dromedary camels (camelus dromedaries). lately, genomic sequence analyses indicated that covs now belonging to the mers-rcov species were found in several bat species from two bat families, vespertilionidae and nycteridae (lelli et al., ; de benedictis et al., ; corman et al., a, b; anthony et al., ; moreno et al., ; wong et al., ) . however, none of these mers-rcovs is a direct progenitor of mers-cov, as their s proteins differ substantially from that of the human virus. the closest relative to mers-cov of humans and dromedary camels is mers-rcov strain neoromicia/ isolated from neoromicia capensis bats in south africa (geldenhuys et al., , table ). a short sequence (around nucleotides) of viral rna identical to that of mers-cov was also detected in a taphozous perforates bat in saudi arabia (memish et al., ) . overall, although it is widely accepted that mers-cov ancestor is in bats, further studies are warranted in order to discover the precise mechanisms of its emergence in dromedary camels and humans. it was suggested that mers-cov ancestors had been circulating in bats for very long time. mers-cov has evolved to adapt to use human receptor and the dpp -recognising bat coronaviruses like hku may follow up, thereby posing a serious risk to human health. recent mers-rcovs were shown to have the capacity to bind to the dpp as entry cell receptor as they acquired the s through recombination with hku -like viruses (luo et al., a, b) . as for the recent and threatening covid- outbreak in humans, we certainly know that sars-cov- belongs to the species sars-rcov together with sars-cov from humans and sars-rcovs from wild carnivores and horseshoe bats (genus rhinolophus) (gorbalenya et al., ; zhou et al., ; wu et al., ) . epidemiological investigations revealed that many initial patients were exposed to wildlife at the huanan seafood wholesale market (south china seafood market), which is the largest seafood market in central china (lorusso et al., ) . sars-cov- has been assigned to an existing species of hundreds of known viruses largely isolated from bats. these viruses have names derived from sars-cov, but only the viral isolates originating from the - outbreak have been confirmed to cause sars in humans (gorbalenya et al., ) . importantly, it has also been confirmed that sars-cov- uses the ace receptor through the receptor binding domain (rbd) of the s protein (hoffmann et al., ; zhou et al., ) . likely, also sars-cov- has a bat origin. according to genome sequences available so far, the most closely related virus ( . % of nucleotide sequence identity) to sars-cov- is strain batcovratg identified from a bat, rhinolophus affinis, from yunnan province, china, followed by sars-rcovs identified from pangolins (tang et al., ) . the receptor-binding spike protein of sars-cov- is highly divergent from other covs with less than % nucleotide sequence identity to all previously described sars-rcovs, except for a . % nucleotide identity to batcovratg (zhou et al., ) . although sars-cov- uses the ace receptor, five out six critical amino acid residues in rbd were different between sars-cov- and sars-cov; the same residues were instead identical to those of pangolin sars-rcovs and, in turn, only one of these residues was identical to those of batcovratg (tang et al., ) , although this latter shows the highest nucleotide sequence identity with sars-cov- along the whole genome. thus, it was tempting to speculate that sars-cov- rbd region might have originated from recent recombination event in pangolins or that sars-cov- and sars-rcovs of pangolins represent the result of coincidental evolution (lam et al., ; tang et al., ) . overall, it remains to be solved whether also sars-cov- needed an intermediate (and amplification) host before being able to infect humans as it was the case for sars-cov and other hcovs. since a mammal reservoir has not yet been identified, a prudent use of specific antigens is strongly recommended for serological diagnosis of sars-cov- in animals as cross-reactions with viruses of the alphacoronavirus genus, widespread in animals, might occur (sun and meng, ) . analogously to bats, but with a lesser extent, also rodents have been recently demonstrated to play a significant role in the evolution of cov, in particular of those belonging to subgenus embecovirus of genus betacoronavirus. rodentia (rodents) is the largest order of mammals with more than species worldwide, representing a major source of zoonotic infectious diseases (han et al., ) . for decades, only one species of coronavirus, murine coronavirus (subgenus embecovirus, genus betacoronavirus), has been associated with rodents. the prototype virus, which was named mouse hepatitis virus (mhv), was first isolated in mice in (cheever et al., ) . a mhv variant was lately identified in rats in (parker et al., ) . rat coronavirus (rcov) causes epidemics of respiratory disease in laboratory rat colonies. the two prototype strains of rcov are sialodacryoadenitis virus (sdav) and parker's rcov (rcov-p) (bhatt et al., ; parker et al., ) . both strains infect the respiratory tract, and sdav can also infect the eye, salivary and lacrimal glands. young rats are especially susceptible to rcov with the infection occurring in the lower respiratory tract and developing into interstitial pneumonia (parker et al., ) . together with feline infectious peritonitis virus (fipv) and ibv, mhv has been one of the most strictly animal cov studied ever. mhv is a natural pathogen of mice, normally infecting the liver, gastrointestinal tract, and central nervous system, causing a wide range of disease, including hepatitis, gastroenteritis, and acute and chronic encephalomyelitis. importantly, it served as model for cov replication and pathogenesis, with emphasis for neuro-invasion and neurovirulence (weiss and navas-martin, ) . as for the additional structural protein he, some strains (such as jhm) of mhv contain the he protein, while others (such as a ) do not yokomori et al., ) . the role of rodents in the evolution of covs belonging to embecoviruses has been recently highlighted by means of the discovery of a novel betacoronavirus in norway rats (rattus norvegicus) in china. this virus forms a separate species named china rattus coronavirus hku (chrcov hku ) within the embecovirus subgenus. although designated as a novel species, this virus possessed genome characteristics that resemble to those of both betacoronavirus- and murine coronavirus, suggesting that chrcov hku represents the murine origin of betacoronavirus- , with interspecies transmission from rodents to other mammals having occurred centuries ago (lau et al., ) . genus betacoronavirus consists of five subgenera, with bat covs being including in all but one of subgenus embecovirus, where rodent, human and bovine covs are included (https://talk.ictvonline.org/ taxonomy/). this supports the hypothesis that rodent covs were the ancestors of embecoviruses of other animals, while bats are the natural reservoirs for all other betacoronaviruses. importantly, rodent covs are not restricted to genus betacoronavirus. a deep virological screening was performed in rodents sampled in zhejiang province, china, during - , with nearly % of rodents testing positive for cov . in particular, covs were detected in striped field mice (apodemus agrarius), norway rats, lesser ricefield rats (rattus losea), asian house rat (rattus tanezumi) and chinese white-bellied rat (niviventer confucianus). amplicons of the replicase gene sequences were recovered from ( %) of the cov rna positive rodent samples described above and whole genome or nearly whole genome sequences (> %) were recovered from and cov positive samples, respectively. by means of whole genome sequence analysis, authors were able to identify a divergent alphacoronavirus, which was lately officially designated as species lucheng rn rat coronavirus (lrnv) within the subgenus luchacovirus, and two novel betacoronaviruses termed longquan aa mouse coronavirus (lamv) and longquan rl rat coronavirus (lrlv) and assigned to the two established species betacoronavirus- and murine coronavirus, respectively . moreover, lrnv seems to be a recombinant virus as its n protein gene is more closely related to those of the genus betacoronavirus. overall, the discovery of rodent-associated covs belonging to subgenera that are distinct from those including bat covs warrants further investigations upon the role played by rodents in the evolution and emergence of these viruses. sars-cov replication has been studied in mice, syrian golden and chinese hamsters. the most severe symptoms of sars were observed in aged animals. indeed, aged mouse model of sars-cov has been generated (gretebeck and subbarao, ) . transgenic mice expressing human ace were also developed to closely mimic sars-cov infection in humans. some animal models have been tested and analysed on the genomic and proteomic level to study the pathogenesis of sars-cov. therefore, we have reason to believe that such models would work also for sars-cov- . quite the opposite, studies have demonstrated that mice, guinea pigs and hamsters are not susceptible to experimental mers-cov infection, mainly because their homologous dpp molecules table coronaviruses in domestic swine and associated diseases. do not function as receptors for mers-cov entry (cockrell et al., ) . the first mouse model of mers infection reported in involved transducing animals with recombinant adenovirus encoding human dpp (hdpp ) molecules intranasally, and this resulted in replication of mers-cov in the lungs. this mouse model also showed clinical symptoms of interstitial pneumonia, including inflammatory cell infiltration, and thickened alveolar and mild oedema (song et al., ) . currently, six covs are circulating in swine (table ). these include four alphacoronaviruses, transmissible gastroenteritis virus of swine (tgev) and its derivative porcine respiratory coronavirus (prcov) (subgenus tegacovirus), porcine epidemic diarrhoea virus (pedv) (subgenus pedacovirus) and sads-cov (subgenus rhinacovirus), one betacoronavirus, porcine haemagglutinating encephalomyelitis virus (phev) (subgenus embecovirus), and one deltacoronavirus, porcine deltacoronavirus (pdcov) (subgenus buldecovirus). tgev, pedv, sads-cov and pdcov are responsible for acute gastroenteritis in swine, with fatal infections in piglets born to seronegative sows, prcov causes a mild respiratory disease and phev is the causative agent of neurological and/or digestive disease in pigs (mora-díaz et al., ; wang et al., ). tgev was first described in uk in s, representing the oldest known swine cov. tgev and prcov are closely related to canine coronavirus (ccov) and feline coronavirus (fcov) forming with these carnivore covs a unique species, referred to as alphacoronavirus- . based on the analysis of the accessory protein gene orf , it has been postulated that tgev has originated from ccov type ii (ccov-ii), since while ccov type i (ccov-i) exhibits an intact gene, both ccov-ii and tgev, which are strictly related in the s gene, have only remnants of orf (lorusso et al., ) . prcov, in turn, has derived from tgev through the deletion of ≈ nucleotides at the ' end of the s gene (corresponding to ≈ amino acids at the n-terminus of the spike protein) and consequent change of the major tissue tropism from the enteric to the respiratory epithelium. this large deletion caused the loss of sialic acid binding activity that allows the attachment to mucins and mucin-type glycoproteins, so that tgev but not prcov is able overcome the intestinal mucus barrier, having access to the gut mucosa . prcov shares some epitopes for neutralising antibodies with tgev, so that its extensive circulation in swine herds has resulted in a drastic reduction of tge outbreaks worldwide. pedv was introduced in the pig population in the s, likely as a consequence of a spillover event from bats. the virus was first described in europe and had been primarily maintained as an endemic pathogen in european and asian swine populations until its introduction into north america in . pedv is more strictly related to a scotophilus bat coronavirus than to other known alphacoronaviruses, including tgev and human alphacoronaviruses hcov- e and hcov-nl . therefore, pedv and btcov/ / likely have a common evolutionary precursor and a cov cross-species transmission may have occurred between bats and pigs (banerjee et al., ) . accordingly, pedv contains signature motifs at the ′-untranslated region that are shared by bat covs, thus providing further support of the evolutionary origin of pedv from bats and potential cross-species transmission (huang et al., ) . currently, different pedv genotypes are described based on the s gene: i) g a pedv, including classical european and asian strains with moderate virulence; ii) g pedv, also called "original us pedv", comprising highly virulent strains that originated in asia and are now widespread in the usa; iii) g b pedv, which is represented by the so-called s-indel strains, i.e., strains presenting insertions and deletions in the s gene that are associated with mild clinical outbreaks. these strains are natural recombinant pedvs with a g -like genomic backbone carrying an s region of g a strains; iv) s n-terminal domain-deletion (ntd-del) strains that are g -like strains containing a to -aa deletion within the n-terminal domain of the s subunit, also associated to mild clinical forms (hou and wang, ) . recombinant strains between pedv and tgev have been also reported in europe (akimkin et al., ; belsham et al., ; boniotti et al., ) . sadv-cov, now referred to as swine enteric alphacoronavirus (seacov), is another virulent swine enteric alphacoronavirus that originated from bats, sharing an % sequence identity with a bat alphacoronavirus hku -cov. since viruses displaying a - % sequence identity to sads-cov were detected in rhinolophus spp. bats, sads-cov and hku -cov likely descend from a common ancestor . accordingly, both viruses now belong to the unique species rhinolophus bat coronavirus hku . in contrast, phev, which was first described in in nursery pigs with encephalomyelitis in ontario, canada, has not derived from bat covs, but its evolutionary history is tightly intermingled with other two closely related betacoronavirus, hcov-oc and the oldest known bcov, with which phev may have common ancestors (vijgen et al., ) and is included in the same viral species, betacoronavirus- (corman et al., ) . most probably, hcov-oc and phev descend from a rodent betacoronavirus through preliminary adaptation to bcov, from which they may have emerged in the context of a pandemic recorded historically at the end of the th century (corman et al., ) . pdcov was recently detected in in hong kong during cov molecular surveillance in avian and mammalian species. this swine deltacoronavirus seems to recognise another different ancestor, likely emerging from a host-switching event between avian and mammal covs. the most closely related pdcov relative has been identified in quail deltacoronavrus uae-hku and the virus has been proposed to be a recombinant between other two avian deltacoronaviruses, sparrow cov hku and bulbul cov hku . all these deltacoronavirus are now members of the same species coronavirus hku (lau et al., ) . pigs were found to be susceptible to experimental infection with the betacoronavirus mers-cov (vergara-alert et al., ), while sars-cov rna was detected in pigs and wild boars wang et al., ) . in contrast, a recent experimental infection demonstrated that pigs are not susceptible to sars-cov- . few studies have been carried out to assess the circulation of covs in farmed or free-ranging wild boars (sus scrofa). antibodies against tgev/prcov were detected in some animals in slovenia (vengust et al., ) and croatia (roic et al., ) and pedv rna was demonstrated in south korea (lee et al., ) . a wild boar sold at a live animal market of guangzhou, china, was positive for sars-cov rna . the main covs infecting ruminants are reported in table . the oldest known ruminant cov is bcov, which is also the prototype of the species betacoronavirus- (subgenus embecovirus, genus betacoronavirus). this virus is able to cause a variety of clinical forms, including enteric disease with high mortality rates in neonate calves, winter disease (a severe enteric form) in lactating cows (decaro et al., b) , and a respiratory disease, also known as shipping fever, in cattle of all ages, with a higher prevalence in - month-old calves (decaro et al., a) . it was postulated that the presence of genetic signatures differentiates enteric and respiratory bcovs (hasoksuz et al., ) , but it was ultimately evident that the same virus strain could be responsible for simultaneous appearance of enteric and respiratory disease in the same animals (chouljenko et al., ) . it has been postulated that bcov originated from a rodent cov (corman et al., ) . very recently, a novel cov, representing a new viral species, referred to as china rattus coronavirus hku (chrcov-hku ), was detected in norway rats in china. this virus was phylogenetically distinct from mhv and hcov-hku and displayed genome features that were intermediate between bcov and mhv. therefore, chrcov hku may represent the murine origin of bcov and rodents are likely an important reservoir for ancestors of subgenus embecovirus (lau et al., ) . bcov is paradigmatic of how covs are able to cross the interspecies barriers, establishing its derivatives as separate viral lineages affecting the respiratory and/or enteric tract of humans (hcov-oc ), swine (phev), horses (equine coronavirus, ecov), and dogs (canine respiratory coronavirus, crcov). a number of bcov-related viruses, all currently included in the unique species betacoronavirus- , have been detected in the enteric and/or respiratory tract of domestic and wild ruminants. these bcov-like covs include viruses of domestic and domesticated ruminants that were reported in sheep and goats (reinhardt et al., ; yang et al., ) , water buffalo (bubalus bubalis) (decaro et al., c) , llamas (lama lama) and alpacas (vicugna pacos) (cebra et al., ; jin et al., ) . in the wild, bcov-like covs were demonstrated in six species of the cervidae family, which are caribou/ reindeer (rangifer tarandus caribou), elk/wapiti (cervus elephus), samber deer (cervus unicolor), white-tailed deer (odocoileus virginianus), sika deer (cervus nippon yesoensis) and water deer (hydropotes inermis) (amer, ) . similar viruses were also found to circulate in the giraffe (giraffa camelopardalis) (hasoksuz et al., ) , several species of antelopes (alekseev et al., ; chung et al., ) , wisent (bison bonasus), himalayan tahr (hemitragus jemlahicus) (chung et al., ) , and dromedary camels (camelus dromedarius) (woo et al., ) . the last strain, detected in the united arab emirates and consequently named dromedary camel coronavirus uae-hku- (dccov uae-hku ), was slightly divergent from other bcov-like viruses (woo et al., ) . dromedary camels are susceptible to mers-cov infection, developing asymptomatic infections or mild upper respiratory disease, so that they are considered the natural host of mers-cov, with adult animals in many countries in the middle east as well as in north and east africa showing > % seroprevalence to the virus (hemida et al., b) . although human-to-human transmission has occurred outside middle east due to travel-associated patients with mers and has caused large clusters of human cases within healthcare facilities in saudi arabia, jordan and united arab emirates, it remains inefficient and sustained community transmission has not being documented so far, thus suggesting multiple virus introduction into the human population by infected dromedaries (hemida et al., b) . more recently, a phylogenetic study of mers-cov full-genome sequences revealed recombination signatures that defined five major phylogenetically stable lineages, all of which contained human and camel mers-cov sequences (sabir et al., ) . in the same study, an alphacoronavirus strictly related to hcov- e was found in the respiratory tract of dromedary camels of saudi arabia (sabir et al., ) . although some studies ruled out the susceptibility of other domestic ruminants to mers-cov (reusken et al., ; adney et al., ) , a recent study detected specific antibodies and rna in sera and nasal secretions, respectively, of domestic ruminants raised in africa, including sheep, goats and cattle (kandeil et al., ) . llamas were found to be susceptible to experimental infections with mers-cov (vergara-alert et al., ). the only cov that has been so far known in horses is ecov, which is a bcov-descendant betacoronavirus (subgenus embecovirus). ecov was first isolated from the faeces of a diarrhoeic foal in (ecov-nc ) in north carolina, usa (guy et al., ) , and was initially believed to only affect foals. since , the virus has been recognised in japan, europe and the usa as a new, clinically important, enteric virus of adult horses (pusterla et al., ) . despite mers-cov was successfully adapted to the in-vitro growth in equine cell lines (meyer et al., ) , serological and molecular table coronaviruses in domestic and domesticated ruminants and associated diseases. sabir et al. ( ) n. decaro and a. lorusso veterinary microbiology ( ) investigations have demonstrated that horses are not naturally infected by mers-cov (meyer et al., ; hemida et al., a) , nor they are susceptible to experimental infection (adney et al., ; vergara-alert et al., ) . however, surprisingly, mers-cov rna was detected in respiratory specimens of three donkeys of from egypt (kandeil et al., ) , a finding that requires further confirmation. a molecular survey aimed to assess cov circulation in horses in saudi arabia and oman has detected two dccov uae-hku strains in enteric samples of horses (hemida et al., a) . scarce data are available about cov circulation in donkeys. these equids are susceptible to ecov infection since positive rt-pcr results were obtained from a donkey in ireland (nemoto et al., ) . in addition, three donkeys ( . %) of from egypt tested positive for mers-cov rna in their nasal secretions (kandeil et al., ) . covs of carnivores are listed in table . three covs are known in dogs, i.e., two alphacoronaviruses of the subgenus tegacovirus, namely ccov-i and ccov-ii, and one betacoronavirus of the subgenus embecovirus, namely crcov. ccovs (species alphacoronav-irus- ) are commonly responsible for mild, self-limiting enteritis in pups . although they are neglected viruses and vaccination is not recommended due to the absence of an effective challenge model, two independent studies have demonstrated their significant involvement in the onset of acute canine enteritis (duijvestijn et al., ; dowgier et al., ) . the evolutionary history of ccovs is tightly intermingled with that of tgev and fcovs. ccov-i possesses a divergent spike protein and the intact form of an additional gene, orf , whose remnants are present in ccov-ii and, at a lesser extent, in tgev. therefore, ccov-ii has likely emerged as a consequence of recombination between the original ccov-i and an unknown cov in the s gene and of progressive loss of orf (lorusso et al., ) . a further recombination occurred in the very ' end of the s gene between ccov-ii and tgev, giving rise to back recombinant ccov-ii strains, also known as tgevlike ccovs, having a spike protein n-terminus of tgev in a ccov-ii backbone (decaro et al., , . consequently, the ccov taxonomy was revised, with classical and tgev-like strains being referred to as ccov-iia and ccov-iib, respectively. while ccovs are usually involved in mild forms of diarrhoea, there are some hypervirulent strains that are associated to severe, haemorrhagic, sometimes fatal gastroenteritis. in addition, ccov-iia strains, designated pantropic ccov, that are able to spread systemically and cause severe disease and the death of infected dogs have been reported in italy (buonavoglia et al., ; alfano et al., ) , other european countries (decaro et al., ) and south america (pinto et al., ) . genomic sequences from pantropic ccovs were analysed, but no obvious genetic signatures that may have caused the switch in pathogenicity were found (decaro and buonavoglia, ; decaro et al., ) . different from ccov-i and ccov-ii, the betacoronavirus crcov is associated with mild respiratory signs and has been proposed as an etiological agent of canine infectious respiratory disease (cird) together with other viral and bacterial agents . the virus was first detected firstly in uk in (erles et al., ) and subsequently in other european and extra-european countries (decaro et al., (decaro et al., , mitchell et al., ; maboni et al., ; piewbang et al., ; more et al., ) . being a bcov derivative, crcov possesses the same genomic organisation, with some differences in accessory orfs located between the s and e protein genes. in particular, while some crcovs possess a unique . kda protein gene directly downstream of the s protein gene, other canine bcov-like covs display the canonical set of bcov accessory genes but with truncated forms of the . kda protein gene . in cats, two alphacornavirus- genotypes are known, namely fcov type i (fcov-i) and fcov type ii (fcov-ii), the latter being generated as table coronaviruses in domestic and domesticated carnivores and associated diseases. jakob, jacob ( , pedersen et al. ( ) cat ( erles et al. ( ) n. decaro and a. lorusso veterinary microbiology ( ) a consequence of recombination events between ccov-ii and fcov-i that generated viruses with a ccov-ii genomic region, encompassing orf b, orf (s gene), orf abc, orf (e gene), and partial orf (m gene), in the context of an fcov-i backbone (pedersen, ) . both genotypes are involved in the development of feline infectious peritonitis (fip), a perivascular pyogranulomatosis of cats that may occur in two clinical forms, effusive and non-effusive fip, which are characterised by prevalence of effusions in the body cavities and of pyogranulomatous lesion in organs, respectively. fip occurs as a consequence of a change in tissue tropism of an enteric fcov strain (feline enteric coronavirus, fecv), infecting enterocytes of the intestinal villi, that acquires the ability to infect monocytes/macrophages switching to the more virulent fipv, which is responsible for systemic infections and dysregulation of the proinflammatory cytokines (addie et al., ) . the changes responsible for the pathogenetic shift have been investigated for many decades, being suggested to be variably represented by point mutations located in the s gene (rottier et al., ) , deletion/insertion in the group-specific genes c (vennema et al., ; chang et al., ) , b (vennema et al., ) or a (kennedy et al., a) . however, none of these differences appeared to consistently correlate with disease phenotype. more recent studies have identified specific genetic signatures in the s gene of fcov-i that are implicated in monocyte/macrophage tropism. two amino acid substitutions, m l and/or s a, corresponding to nucleotide mutations a t/c and t g, respectively, in the viral genome, together distinguished fcovs found in the tissues of fip cats from those found in the faeces of healthy cats without fip in > % of cases (chang et al., ) . however, subsequent studies concluded that these mutations are likely to be markers of systemic fcov infection rather than fip per se (porter et al., ; barker et al., ) . two alphacoronaviruses, both belonging to subgenus minacovirus, are currently known in mustelids, namely mink coronavirus (mcov- ) and ferret coronavirus (frcov). mcov- has been recently identified as the etiological agent of mink epizootic catarrhal gastroenteritis (ecg), an infectious disease of farmed american (neovison vison) and european (mustela lutreola) mink first described in (larsen and gorham, ) and later affecting several million mink in different countries (vlasova et al., ) . the disease is observed at greater frequency in mink of ≥ months and is characterised by seasonality, high morbidity (approaching %) and low mortality (< %). recent full-genome analysis demonstrated that mcov- is phylogenetically distant from ccovs and fcovs, being closely related to frcov (vlasova et al., ) . presently, the two viruses are considered separate species within subgenus minacovirus (https://talk.ictvonline.org/taxonomy/). frcov has been recognised as the causative agent of epizootic catarrhal enteritis (ece), first described in in domestic ferrets (mustela putorius furo) in the eastern part of the usa (williams et al., ) and subsequently reported in domestic and laboratory ferrets throughout the world (murray et al., ) . analogous to fcov, frcov exists in two different pathotypes: i) ferret enteric coronavirus (frecv) is associated to ece, a highly contagious diarrhoeal disease also known as green slime disease, which affects mainly young ferrets with morbidity and mortality rates similar to those of ecg; ii) ferret systemic coronavirus (frscv) is responsible for a systemic diseases of ferrets, which is characterised by pyogranulomatous perivasculitis and peritonitis resembling to those of fip (murray et al., ) . similar to fip, wise et al. ( ) have shown that frecv and frscv differ significantly in spike protein and that deletions in frcov c may also correlate with the severe pathotype of frscv. recombination in the s, c and e genes between different frcov has been also reported (lamers et al., ) . different covs were found to circulate in wild carnivores. ccovs were detected in wolves (canis lupus), red foxes (vulpes vulpes), eurasian otters (lutra lutra), common genets (genetta genetta) (alfano et al., ; rosa et al., ) . ccov-like viruses were also found in african wild carnivores, including spotted hyenas (crocuta crocuta) and silver-backed jackals (canis mesomelas) (goller et al., ) . fcovs have a wide circulation in non-domestic felids (kennedy et al., (kennedy et al., , , with fip cases being reported in servals (felis serval) (juan-salles et al., ) , cheetah (acinonyx jubatus) (kennedy et al., b) , mountain lion (puma concolor) (stephenson et al., ) , and european wildcat (felis silvestris) (watt et al., ) . divergent alphacoronavirus- viruses were detected in chinese ferret badger (nyctereutes procyonoides) and raccoon dog (melogale moschata) (dong et al., ) . the same study reported the identification in asian leopard cat (prionailurus bengalensis) and chinese ferret badger of an unclassified cov, which was closely related to gammacoronaviruses in most parts of the genome, whereas the s gene displayed the highest sequence identity to alphacoronaviruses (dong et al., ) . with the discovery of deltacoronaviruses, these viruses were later included in this novel genus along with avian and porcine strains (woo et al., ; wang et al., ) . some domestic and wild carnivores are also susceptible to sars-cov infection. while the potential natural reservoirs are horseshoe bats, sars-like cov strains were found to be widespread in masked palm civets (paguma larvata) and raccoon dogs, which were suspected to be intermediate hosts (guan et al., ) . full-genomic comparative analysis has shown that sars-like covs isolated from palm civets are under strong selective pressure and are genetically most closely related to sars-cov strains infecting humans early in the outbreaks (song et al., ) . sequence analysis of the sars-cov-like virus in masked palm civets indicated that they were highly homologous to human sars-cov with nucleotide identity over . %, indicating the virus has not been circulating in the population of masked palm civets for a very long time (shi and hu, ) . a chinese ferret-badger (melogale moschata) was found to have neutralising antibodies against sars-cov (guan et al., ) , whereas sars-cov rna was detected in naturally infected cats and red foxes (vulpes vulpes), but not in domestic dogs . there was, however, a single dog testing positive for sars-cov (https://apps.who.int/iris/bitstream/handle/ / /who_cds_csr_gar_ . _eng.pdf). among carnivores, sars-cov- is able to infect cats, ferrets and, at a lesser extent, dogs . in , a highly divergent cov, tentatively named sw , was discovered a deceased beluga wale (delphinapterus leucas) with pneumonia and hepatic necrosis (mihindukulasuriya et al., ) . the virus was only distantly related to ibv, so that it now represents the prototype of the single mammalian cov species belonging to the genus gammacoronavirus, namely beluga wale coronavirus sw (bwcov-sw ) (subgenus cegacovirus). few years later, related gammacoronaviruses were retrieved from faecal samples of three indo-pacific bottlenose dolphins (tursiops aduncus), which were named bottlenose dolphin cov (bdcov) hku . comparative genome analysis showed that bdcov-hku and bwcov-sw have similar genome characteristics and structures, displaying a % nucleotide sequence identity each to other (woo et al., ) . a novel betacoronavirus distantly related to mers-cov was detected in the faeces of european hedgehogs (erinaceus europaeus), an insectivorous mammal belonging to a related order of chiroptera, from germany. the virus was tentatively referred to as erinaceus cov (ericov) (corman et al., b) and covs found in hedgehogs in france, england and italy had an identity from % to % with the ericov (monchatre- leroy et al., ; saldanha et al., ; delogu et al., ) . these hedgehog covs are are now included in a unique species, hedgehog coronavirus (subgenus merbecovirus). the virus was not associated to any form of disease, so that western european hedgehog is a reservoir host of ericov in the absence of apparent disease, suggesting that hedgehogs in addition to bats may contribute to the evolution of merbecovirus (saldanha et al., ) . a slightly divergent merbecovirus was later found in amur hedgehogs (erinaceus amurensis) in china and was poposed as a prototype of a separate species, namely erinaceus amurensis hedgehog coronavirus hku (ea-hedcov hku ) . a novel coronavirus, named wénchéng shrew coronavirus (wesv) was detected in shrews (suncus murinus) in china . wesv is highly divergent from other alphacoronaviruses, exhibiting less than . % amino acid similarity to any known members of the genus alphacoronavirus in the coronavirus-wide conserved domains of the replicase polyprotein pp ab and less than . % amino acid similarity to the other three coronavirus genera. however, taking into account the current ictv criteria, wesv is sufficiently divergent to be considered a distinct member of the genus alphacoronavirus, but not a new genus of the subfamily orthocornavirinae . covs have been known in veterinary medicine since many decades; some of these viruses, such as ibv, swine enteric covs, bcov and mustelid covs, can cause diseases that have a great impact on the farm industry. other covs, namely fipv, frscv and mhv, cause severe disease in companion (cats, ferrets) or laboratory (mice) animals. animal covs are paradigmatic on how covs evolve through accumulation of point mutations and homologous (and heterologous) recombination, generating different genotypes and pathotypes. these virus variants may have different antigenic properties, escaping the host immunity induced by vaccines, as is the case of ibv. alternatively, they may have a different tissue tropism in the same host that can increase or decrease the virus pathogenicity, as observed for the virus pairs fecv/fipv or frecv/frscv and tgev/prcov, respectively. in other circumstances, the cov evolution may result in the switch of the host range from one animal species to another one or from animals to humans. the former event is well documented in veterinary medicine, with a plethora of viruses being originated from ibv and bcov that adapted to different animal species. however, the most interesting scenario is the jumping and further adaptation of an animal cov to humans. there is increasing evidence that all hcovs currently known recognise an animal origin, with bat or rodent covs being the most probable ancestors. in most instances, it was suggested that other mammals served as intermediate hosts prior to final adaptation to humans, i.e., alpacas and cattle for the low-pathogenic hcov- e and hcov-oc , respectively, and wild carnivores and dromedary camels for the high-pathogenic sars-cov and mers-cov, respectively. other two hcovs, namely hcov-nl and hcov-hku , were likely derived from bats and rodents, respectively, but whether this transmission required an intermediate mammalian host is presently unknown. the origin of sars-cov- should be zoonotic, since highly related sequences were detected in bats, but a definitive intermediate host has been not identified so far. what should we expect from the current pandemic? when hcov-oc crossed the species barrier to infect humans from domestic livestock around , an epidemic of respiratory infection was recorded. even though, several years later, influenza was suspected to be the cause of it, in that pandemic involvement of central nervous system was more pronounced than in other influenza outbreaks. this evidence is further supported by molecular studies claiming that the most recent common ancestor of bcov and hcov-oc emerged around (vijgen et al., ) and by the fact that hcov-oc can be neuroinvasive (arbour et al., ) . likely, hcov-oc crossed species to infect dogs becoming established in this species as crcov . a similar scenario could be observed with sars-cov- with dogs and, at a greater extent, cats. apparently, cats represent, within the domestic animals which have been experimentally infected, the host, together with ferrets, which is able to sustain more efficiently sars-cov- replication . furthermore, based on structural studies and biochemical experiments, sars-cov- seems to have an rbd that binds with high affinity to ace also from ferrets and cats (andersen et al., ) . reasonably, a full comprehension of the animal cov molecular evolution, host range and pathobiology is beneficial to better understand the mechanism driving the emergence and adaptation to humans of zoonotic covs. the present review has highlighted that in the last years, also thanks to the availability of novel sequencing technologies, we have witnessed a large number of novel covs being discovered in a large number of animals. truth to be told, it was difficult for us to summarise, in this single review, all covs detected in animals and the tight interaction existing between them and human covs. among animals, it is evident that bats are the group of mammals that harbor the largest number of covs and that many other animal covs recognise their ancestors in bat covs. in an excellent review (cui et al., ) written by the group coordinated by dr. zheng-li shi of the wuhan institute of virology, hubei, (china), city infamously known for being the epicenter and origin of the covid- outbreak, authors stated that "...given the prevalence and great genetic diversity of bat sars-rcovs, their close coexistence and the frequent recombination of covs, it is expected that novel variants will emerge in the future". this forecasting statement was not surprising to coronavirologists and it was not, importantly, surprising to those scientists that daily deal with the plethora of viruses existing at the human/animal health interface. although scientists were well aware of this hazard, no substantial actions were taken forward the limitations of strict and repeated contacts between humans and wildlife. indeed, whereas biological mechanisms underlying viral evolution are not under human control, social and cultural habits can be modified accordingly through a deep and pounding informative campaigns. if to the human habits we sum the impact of modern agricultural practices and urbanization and the decrease of vital space for wildlife, it is quite easy to understand that, if countermeasures are not taken, we will face novel serious health emergencies of animal origin in the following years with tremendous social and economic impact on our lives. as clearly demonstrated by the sars-cov- emergence, covs are the main characters of this intricate puzzle characterised by the interactions of viral biological mechanisms and human habits. our review was reasonably prepared also to highlight (once more!) how covs originate, evolve, jump, mutate and infect their host. could have the current covid- outbreak been avoided? answering this question is not relevant now, but actions to avoid the next viral spillover from animals to humans is certainly a priority. this task needs to be coupled with massive genomic surveillance in wild animals not limited to covs. massive sequencing of sars-cov- strains detected in humans and covs of wildlife will help further assess the origin of this novel human pandemic and plan future measures able to reduce the risk of emergence of new cov spillover events. however, additional tasks should be provisionally addressed in order to reduce the risk of future cov pandemic like the current one. these include: i) prevention of animal-to-human infections through a ban of the wet markets and a more friendly management of the environment; ii) studies on cov-host interactions to be performed both in vitro (cell cultures, ex-vivo explants of the respiratory tract) and in vivo (animals susceptible to sars-cov- infection); iii) development of new anticoronaviral drugs and evaluation of their efficacy in cell cultures and animal models. feline infectious peritonitis. abcd guidelines on prevention and management inoculation of goats, sheep, and horses with mers-cov does not result in productive viral shedding dampened nlrp -mediated inflammation in bats and implications for a special viral reservoir host new chimeric porcine coronavirus in swine feces bovine-like coronaviruses isolated from four species of captive wild ruminants are homologous to bovine coronaviruses, based on complete genomic sequences dentification of pantropic canine coronavirus in a wolf (canis lupus italicus) in italy circulation of pantropic canine coronavirus in autochthonous and imported dogs binding of avian coronavirus spike proteins to host factors reflects virus tropism and pathogenicity novel receptor specificity of avian gammacoronaviruses that cause enteritis host tissue and glycan binding specificities of avian viral attachment proteins using novel avian tissue microarrays bovine-like coronaviruses in domestic and wild ruminants the proximal origin of sars-cov- further evidence for bats as the evolutionary source of middle east respiratory syndrome coronavirus neuroinvasion by human respiratory coronaviruses detection of a virus related to betacoronaviruses in italian greater horseshoe bats isolation and metagenomic identification of avian leukosis virus associated with mortality in broiler chicken global distributions and strain diversity of avian infectious bronchitis virus: a review random nature of coronavirus rna recombination in the absence of selection pressure bats and coronaviruses limitations of using feline coronavirus spike protein gene mutations to diagnose feline infectious peritonitis cultivation of the virus of infectious bronchitis emerging horizon for bat borne viral zoonoses. virus dis characterization of a novel chimeric swine enteric coronavirus from diseased pigs in central eastern europe in characterization of the virus of sialodacryoadenitis of rats: a member of the coronavirus group recovery and characterization of a coronavirus from military dogs with diarrhea porcine epidemic diarrhea virus and discovery of a recombinant swine enteric coronavirus coronavirus genome structure and replication accelerated viral dynamics in bat cell lines, with implications for zoonotic emergence first complete genome sequence of european turkey coronavirus suggests complex recombination history related with us turkey and guinea fowl coronaviruses canine coronavirus highly pathogenic for dogs bats: important reservoir hosts of emerging viruses coronaviruses in poultry and other birds coronavirus avian infectious bronchitis virus infectious bronchitis coronaviruses from pheasants (phasianus colchicus) are genetically closely related to coronaviruses of domestic fowl (infectious bronchitis virus) and turkeys potential pathogens in feces from unweaned llamas and alpacas with diarrhea feline infectious peritonitis: insights into feline coronavirus pathobiogenesis and epidemiology based on genetic analysis of the viral c gene spike protein fusion peptide and feline coronavirus virulence a murine virus jhm causing disseminated encephalomyelitis with extensive destruction of myelin. isolation and biological properties of the virus sars-associated coronavirus transmitted from human to pig identification and survey of a novel avian coronavirus in ducks dbatvir: the database of bat-associated viruses detection of specific antibodies to the nucleocapsid protein fragments of severe acute respiratory syndrome-coronavirus and scotophilus bat coronavirus- in three insectivorous bat species comparison of genomic and predicted amino acid sequences of respiratory and enteric bovine coronaviruses isolated from the same animal with fatal shipping pneumonia coronaviruses in bent-winged bats (miniopterus spp genomic characterizations of bat coronaviruses ( a, b and hku ) and evidence for co-infections in miniopterus bats avian coronavirus in wild aquatic birds a previously unknown reovirus of bat origin is associated with an acute respiratory disease in humans detection and characterization of bovine-like coronaviruses from four species of zoo ruminants coronavirus associated with an enteric syndrome on a quail farm mouse dipeptidyl peptidase is not a functional receptor for middle east respiratory syndrome coronavirus infection rooting the phylogenetic tree of middle east respiratory syndrome coronavirus by characterization of a conspecific virus from an african bat characterization of a novel betacoronavirus related to middle east respiratory syndrome coronavirus in european hedgehogs evidence for an ancestral association of human coronavirus e with bats hosts and sources of endemic human coronaviruses identification and characterization of a novel alpaca respiratory coronavirus most closely related to the human coronavirus e origin and evolution of pathogenic coronaviruses infectious bronchitis virus variants: a review of the history, current situation and control measures alpha and lineage c betacov infections in italian bats canine coronavirus: not only an enteric pathogen serological and molecular evidence that canine respiratory coronavirus is circulating in italy respiratory disease associated with bovine coronavirus infection in cattle herds in southern italy severe outbreak of bovine coronavirus infection in dairy cattle during the warmer season biological and genetic analysis of a bovine-like coronavirus isolated from water buffalo (bubalus bubalis) calves recombinant canine coronaviruses related to transmissible gastroenteritis virus of swine are circulating in dogs an update on canine coronaviruses: viral evolution and pathobiology recombinant canine coronaviruses in dogs european surveillance for pantropic canine coronavirus molecular surveillance of traditional and emerging pathogens associated with canine infectious respiratory disease eco-virological preliminary study of potentially emerging pathogens in hedgehogs (erinaceus europaeus) recovered at a wildlife treatment and a transmissible gastroenteritis in pigs covid- from veterinary medicine and one health perspectives: what animal coronaviruses have taught us detection and molecular characterization of infectious bronchitis-like viruses in wild bird populations detection of a novel and highly divergent coronavirus from asian leopard cats and chinese ferret badgers in southern a molecular survey for selected viral enteropathogens revealed a limited role of canine circovirus in the development of canine acute gastroenteritis genomic characterization of severe acute respiratory syndrome-related coronavirus in european bats and classification of coronaviruses based on partial rna-dependent rna polymerase gene sequences enteropathogen infections in canine puppies: (co-)occurrence, clinical relevance and risk factors coronaviruses detected in brazilian wild birds reveal close evolutionary relationships with beta-and deltacoronaviruses isolated from mammals detection of a group coronavirus in dogs with canine infectious respiratory disease bat coronaviruses in china a previously undescribed coronavirus associated with respiratory disease in humans evidences of parasite evolution after vaccination imperfect vaccines and the evolution of pathogen virulence a hemagglutinating virus producing encephalomyelitis in baby pigs metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in china isolation and characterization of a bat sars-like coronavirus that uses the ace receptor a metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in neoromicia bats within south africa coronavirus genotype diversity and prevalence of infection in wild carnivores in the serengeti national park the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- . coronaviridae study group of the international committee on taxonomy of viruses animal models for sars and mers coronaviruses isolation and characterization of viruses related to the sars coronavirus from animals in southern china three emerging coronaviruses in two decades turkey coronavirus enteritis characterization of a coronavirus isolated from a diarrheic foal a new virus isolated from the human respiratory tract middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation rodent reservoirs of future zoonotic diseases isolation of bovine respiratory coronaviruses from feedlot cattle and comparison of their biological and antigenic properties with bovine enteric coronaviruses biologic, antigenic, and full-length genomic characterization of a bovine-like coronavirus isolated from a giraffe coronavirus infections in horses in saudi arabia and oman dromedary camels and the transmission of middle east respiratory syndrome coronavirus (mers-cov) sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor emerging highly virulent porcine epidemic diarrhea virus: molecular mechanisms of attenuation and rational design of live attenuated vaccines bat origin of human coronaviruses discovery of a rich gene pool of bat sars-related coronaviruses provides new insights into the origin of sars coronavirus origin, evolution, and genotyping of emergent porcine epidemic diarrhea virus strains in the united states a bat-derived putative cross-family recombinant coronavirus with a reovirus gene genetically diverse coronaviruses in wild bird populations of northern england studies on broiler's ibv and ib-like virus from guinea fowl therapeutische, kasuistische und statistische mitteilungen aus der klinik für kleine haustiere an der reichstierarzneischule in utrecht (holland) analysis of the genome sequence of an alpaca coronavirus molecular identification and characterization of novel coronaviruses infecting graylag geese anser anser feral pigeons columbia livia and mallards anas platyrhynchos identification of avian coronavirus in wild aquatic birds of the central and eastern usa an outbreak of feline infectious peritonitis in captive servals (felis serval): clinical, pathological, and immunohistochemical findings calf diarrhea coronavirus. the lancet molecular evolution analysis and geographic investigation of severe acute respiratory syndrome coronavirus-like virus in palm civets at an animal market and on farms middle east respiratory syndrome coronavirus infection in non-camelid domestic mammals deletions in the a orf of feline coronavirus associated with an epidemic of feline infectious peritonitis detection of feline coronavirus infection in captive cheetahs (acinonyx jubatus) by polymerase chain reaction detection of feline coronavirus in captive felidae in the usa detection of feline coronavirus infection in southern african nondomestic felids surveillance of avian coronaviruses in wild bird populations of korea a novel coronavirus associated with severe acute respiratory syndrome identifying sars-cov- related coronaviruses in malayan pangolins naturally occurring recombination in ferret coronaviruses revealed by complete genome characterization a new mink enteritis: an initial report severe acute respiratory syndrome coronavirus-like virus in chinese horseshoe bats coexistence of different genotypes in the same bat and serological characterization of rousettus bat coronavirus hku belonging to a novel betacoronavirus subgroup recent transmission of a novel alphacoronavirus, bat coronavirus hku , from leschenault's rousettes to pomona leaf-nosed bats: first evidence of interspecies transmission of coronavirus between bats of different suborders discovery of a novel coronavirus, china rattus coronavirus hku , from norway rats supports the murine origin of betacoronavirus and has implications for the ancestor of betacoronavirus lineage a discovery and sequence analysis of four deltacoronaviruses from birds in the middle east reveal interspecies jumping with recombination as a potential mechanism for avian-to-avian and avian-to-mammalian transmission identification of a novel betacoronavirus (merbecovirus) in amur hedgehogs from china. viruses wild boars harbouring porcine epidemic diarrhea virus (pedv) may play an important role as a pedv reservoir detection of coronaviruses in bats of various species in italy novel avian coronavirus and fulminating disease in guinea fowl isolation of avian infectious bronchitis coronavirus from domestic peafowl pavo cristatus and teal anas gain, preservation, and loss of a group a coronavirus accessory glycoprotein molecular characterization of a canine respiratory coronavirus strain detected in italy a new member of the pteropine orthoreovirus species isolated from fruit bats imported to italy novel coronavirus (sars-cov- ) epidemic: a veterinary perspective longitudinal surveillance of betacoronaviruses in fruit bats in yunnan province discovery of novel bat coronaviruses in south china that use the same receptor as middle east respiratory syndrome coronavirus sequence of mouse hepatitis virus a mrna : indications for rna recombination between coronaviruses and influenza c virus canine infectious respiratory disease: new insights into the etiology and epidemiology of associated pathogens first full-length sequences of the s gene of european isolates reveal further diversity among turkey coronaviruses recovery in tracheal organ cultures of novel viruses from patients with respiratory disease ecosystem change and zoonoses in the anthropocene middle east respiratory syndrome coronavirus in bats, saudi arabia a sars-like cluster of circulating bat coronaviruses shows potential for human emergence identification of a lineage d betacoronavirus in cave nectar bats (eonycteris spelaea) in singapore and an overview of lineage d reservoir ecology in se asian bats serologic assessment of possibility for mers-cov infection in equids identification of a novel coronavirus from a beluga whale by using a panviral microarray european surveillance of emerging pathogens associated with canine infectious respiratory disease identification of alpha and beta coronavirus in wildlife species in france: bats, rodents, rabbits, and hedgehogs porcine hemagglutinating encephalomyelitis virus: a review a serological survey of canine respiratory coronavirus in new zealand detection and full genome characterization of two beta cov viruses related to middle east respiratory syndrome from bats in italy diseases and causes of death in european bats: dynamics in disease susceptibility and infection rates role of enteric pathogens in the aetiology of neonatal diarrhoea in lambs and goat kids in spain prevalence and phylogeny of coronaviruses in wild birds from the bering strait area (beringia) ferret coronavirus-associated diseases the first detection of equine coronavirus in adult horses and foals in ireland isolation of a coronavirus during studies on puffinosis, a disease of the manx shearwater (puffinus puffinus) isolation and characterization of viruses associated with transmissible enteritis (bluecomb) of turkeys genome organization of canada goose coronavirus, a novel species identified in a mass die-off of canada geese rat coronavirus (rcv): a prevalent, naturally occurring pneumotropic virus of rats isolamento di un coron-avirus simile da quaglie giapponesi (coturnixcoturnix japonica) con sindrome respiratoria:prima descrizione della malattia ed isolamentodel virus an update on feline infectious peritonitis: virology and immunopathogenesis cross-sectional investigation and risk factor analysis of community-acquired and hospital-associated canine viral infectious respiratory disease complex characterization of pantropic canine coronavirus from brazil pathogenic differences between various feline coronavirus isolates isolation of a porcine respiratory, nonenteric coronavirus related to transmissible gastroenteritis identification of a novel coronavirus in bats amino acid changes in the spike protein of feline coronavirus correlate with systemic spread of virus from the intestine and not with feline infectious peritonitis enteric coronavirus infection in adult horses two genotypes of canine coronavirus simultaneously detected in the fecal samples of dogs with diarrhea the behaviour of recent isolates of human respiratory coronavirus in vitro and in volunteers: evidence of heterogeneity among e-related strains diagnosis of coronavirus in sheep in valdivia province difference in receptor usage between severe acute respiratory syndrome (sars) coronavirus and sars-like coronavirus of bat origin middle east respiratory syndrome coronavirus (mers-cov) serology in major livestock species in an affected region in jordan identification of sars-like coronaviruses in horseshoe bats (rhinolophus hipposideros) in slovenia electron microscopy of coronavirus-like particles characteristic of turkey bluecomb disease prevalence of antibodies to selected viral pathogens in wild boars (sus scrofa) in croatia in - and - unveiling patterns of viral pathogen infection in free-ranging carnivores of northern portugal using a complementary methodological approach acquisition of macrophage tropism during the pathogenesis of feline infectious peritonitis is determined by mutations in the feline coronavirus spike protein co-circulation of three camel coronavirus species and recombination of mers-covs in saudi arabia extension of the known distribution of a novel clade c betacoronavirus in a wildlife host an apparently new respiratory disease of baby chicks transmissible gastroenteritis virus infection: a vanishing specter sialic acid binding properties of soluble coronavirus spike (s ) proteins: differences between infectious bronchitis virus and transmissible gastroenteritis virus a review of studies on animal reservoirs of the sars coronavirus susceptibility of ferrets, cats, dogs, and different domestic animals to sars-coronavirus- identification of a new transcriptional initiation site and the corresponding functional gene b in the murine coronavirus rna genome cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human from sars to mers, thrusting coronaviruses into the spotlight isolation of infectiousbronchitis virus from pheasants feline infectious peritonitis in a mountain lion a persistently infecting coronavirus in hibernating myotis lucifugus, the north american little brown bat antigenic cross-reactivity between the nucleocapsid protein of severe acute respiratory syndrome (sars) coronavirus and polyclonal antisera of antigenic group i animal coronaviruses: implication for sars diagnosis isolation and characterization of avian coronavirus from healthy eclectus parrots (eclectus roratus) from indonesia prevalence and genetic diversity of coronaviruses in bats from on the origin and continuing evolution of sars-cov- surveillance of bat coronaviruses in kenya identifies relatives of human coronaviruses nl and e and their recombination history detection of novel sars-like and other coronaviruses in bats from kenya an avian coronavirus in quail with respiratory and reproductive signs gammacoronavirus and deltacoronavirus in quail phylogenomic analyses elucidate the evolutionary relationships of bats enteric coronavirus-like coronavirus particles in sheep s gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification a serological survey of selected pathogens in wild boar in slovenia feline infectious peritonitis viruses arise by mutation from endemic feline enteric coronaviruses livestock susceptibility to infection with middle east respiratory syndrome coronavirus complete genomic sequence of human coronavirus oc : molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event evolutionary history of the closely related group coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus oc molecular characterization of a new species in the genus alphacoronavirus associated with mink epizootic catarrhal gastroenteritis surveillance on severe acute respiratory syndrome associated coronavirus in animals at a live animal market of guangzhou in detection and genetic characterization of deltacoronavirus in pigs discovery, diversity and evolution of novel coronaviruses sampled from rodents in china discovery of a highly divergent coronavirus in the asian house shrew from china illuminates the origin of the alphacoronaviruses emerging and re-emerging coronaviruses in pigs an extended outbreak of infectious peritonitis in a closed colony of european wildcats (felis silvestris) coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus. microbiol high prevalence and putative lineage maintenance of avian coronaviruses in scandinavian waterfowl coronavirus-associated epizootic catarrhal enteritis in ferrets sialic acid is a receptor determinant for infection of cells by avian infectious bronchitis virus infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent comparative sequence analysis of the distal one-third of the genomes of a systemic and an enteric ferret coronavirus an apparently new syndrome of porcine epidemic diarrhoea global epidemiology of bat coronaviruses characterization and complete genome sequence of a novel coronavirus, coronavirus hku , from patients with pneumonia molecular diversity of coronaviruses in bats comparative analysis of twelve genomes of three novel group c and group d coronaviruses reveals unique group and subgroup features comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group c coronavirus coronavirus genomics and bioinformatics analysis discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in gammacoronavirus deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases a new coronavirus associated with human respiratory disease in china serosurveillance of viral diseases in korean native goats (capra hircus) receptor usage and cell entry of bat coronavirus hku provide insight into bat-to-human transmission of mers coronavirus biosynthesis, structure, and biological activities of envelope protein gp of murine coronavirus intraspecies diversity of sars-like coronaviruses in rhinolophus sinicus and its implications for the origin of sars coronaviruses in humans structure of coronavirus hemagglutinin-esterase offers insight in corona and influenza virus evolution isolation of a novel coronavirus from a man with pneumonia in saudi arabia genomic analysis and surveillance of the coronavirus dominant in ducks in china funding were provided by the italian ministry of health, izs am / rc , ricerca corrente "ngs e diagnostica molecolare in sanità animale: fast d ", recipient alessio lorusso. supplementary material related to this article can be found, in the online version, at doi:https://doi.org/ . /j.vetmic. . . key: cord- -q inrxcm authors: lai, michael m. c. title: sars virus: the beginning of the unraveling of a new coronavirus date: - - journal: j biomed sci doi: . /bf sha: doc_id: cord_uid: q inrxcm severe acute respiratory syndrome (sars) virus caused a severe outbreak in several regions of the world in . the virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern china. its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. however, distinct patterns of several open reading frames in the sars virus genome may contribute to its severe virulence. the potential mutability of the coronavirus genome may pose problems in the control of future sars outbreaks. the mechanism of sars pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. the life cycle of the sars virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. vaccines offer an important preventive measure for possible future recurrences of sars, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in sars virus pathogenesis. the comparative studies of other coronaviruses offer insights into the understanding of sars virus. severe acute respiratory syndrome (sars) virus caused a severe outbreak in several regions of the world in . the virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern china. its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. however, distinct patterns of several open reading frames in the sars virus genome may contribute to its severe virulence. the potential mutability of the coronavirus genome may pose problems in the control of future sars outbreaks. the mechanism of sars pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. the life cycle of the sars virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. vaccines offer an important preventive measure for possible future recurrences of sars, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in sars virus pathogenesis. the comparative studies of other coronaviruses offer insights into the understanding of sars virus. the identification of a novel coronavirus as the etiological agent of severe acute respiratory syndrome (sars) has given an impulse to research on the coronavirus family, which has long been relegated to the status of a scientifically interesting but medically unimportant virus family. it is not that coronavirus has never been important; in fact, coronavirus infections of farm animals, such as pigs or chickens, are so common and devastating that vaccinations against these viruses are routinely performed. in humans, coronavirus infections are responsible for almost / of common colds in wintertime [ , ] , and the virus has been repeatedly implicated, but never confirmed as one of the causative agents of multiple sclerosis [ , ] . nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public's interest in this virus family until the sudden emergence of the sars coronavirus [ , , ] , which caused the first new infectious disease of this millennium. the numerous past studies of the coronavirus family then quickly provided a blueprint for understanding the sars virus. however, the contagiousness and high mortality rate of the sars virus are unparalleled to the other known human and animal coronaviruses; thus, sars coronavirus is unique in multiple ways. the understanding of this virus, including its origin, molecular properties and pathogenesis, will be crucial for the future management of this infectious disease. since the studies on the sars virus are very limited so far, this review aimed at investigating the possible properties of the virus based primarily on comparative studies of other coronaviruses. coronaviruses are divided into three antigenically distinct groups, which are also consistent with the genetic relatedness of these viruses [ ] . group i consists of human coronavirus e (hcov- e), porcine transmissible gastroentefitis virus (tgev), porcine respiratory coronavirus (prcv), feline infectious peritonitis virus (fipv) and enteritis virus (fecov), canine coronavirus (ccov) and others. group ii consists of human coronavirus oc (hcov-oc ), mouse hepatitis virus (mhv), bovine coronavirus (bcov) and others. group iii consists of avian species, including chicken infectious bronchitis virus (ib¥) and turkey coronavirus (tcov). the newly discovered sars virus cross-reacts with antibodies of group i coronaviruses [ ] . however, its genetic sequence indicates that it belongs to none of these three groups. it is of about equal distance from both groups ii and iii in the coronavirus family phylogenetic tree in nucleic acid or protein sequence [ , , ] . a similar conclusion is reached irrespective of which viral rna region is used for comparison. thus, sars virus represents a new group of coronavirus. although this virus most likely originated from a wild animal (see next section), the sars virus has been well adapted in humans, as evidenced by the high person-to-person transmissibitity of the virus. thus, it is most appropriately named human coronavirus sars strain. however, its official taxonomic status remains to be decided. since the first reported occurrence of sars in southern china, speculation on the origin of sars virus has largely focused on the animal species in that region. because the genetic sequence of sars virus is distinct and distant from that of any known coronaviruses in domestic animals, the sars virus most likely originated from a wild animal. the search for coronaviruses in wild animals eventually turned up a coronavirus in civet cats in a market in guangdong province. the civet cat coronavirus is very closely related to the sars virus, with more than % sequence homology [ , a, ] . recent reports indicate that sars virus is distinct from the civet cat virus by limited deletions and mutations. the extent of the coronavirus infection among wild animals is not yet clear [ a] . the animal handlers appear to be at risk for the infection as a higher proportion of them have antibodies against sars virus [ a]. however, none of these data have so far been confirmed. although plausible, the civet cat virus as the origin of sars virus remains to be established. it is possible that civet cats were infected with the virus from another animal species. in either case, the critical questions are whether there is extensive horizontal transmission between animals, and whether the jump of the virus from animals to human was a rare and accidental event or portends frequent occurrences in the future. the answers to these questions will determine whether these animals are viable reservoirs for future sars outbreaks. thus, epidemiological studies of coronavirus infections in wild animals are critical tbr control of future sars outbreaks. although coronaviruses, in general, infect only the animal species of their natural origin, they are known to jump to other species relatively easily. the human coronavirus oc is very closely related in genetic sequence to bcov [ , ] ; thus, there is no doubt that the virus jumped from one species to the other. bcov has also been reported to infect humans occasionally, causing diarrhea [ , ] . when mhv was passaged in tissue culture cells, the virus eventually adapted to growing in human cells [ , ] . although the mechanism of such an adaptation is not known, it is likely that it was the result of mutations in certain viral genes. thus, there is considerable latitude in species specificity of coronaviruses. so far, sars virus has been shown to infect humans and macaque monkeys [ ] . whether it can infect other animal species in natural infections and experimental inoculations may determine the extent of natural reservoirs for sars virus and the feasibility of establishing animal models for it. complete sars virus genome sequences have been determined from more than twenty different isolates so far. these sequences showed extremely high conservation, indicating that they were all derived from a common source and did not diverge significantly during the first [ , ] . sequence comparison with those of orfs of the other known coronaviruses reveals a similar pattern of gene organization, namely, gene la-lb (replicase and protease genes), spike (s), envelope (e), membrane (m) and nucleocapsid (n) in the order of ' to ' ends [ ] . notably, the sars virus genome does not encode a hemagglutinin-esterase (he) protein, which is present in most of the group ii coronaviruses. interspersed between these well-characterized genes are a series of orfs of unknown functions. at a quick glance, the sars virus rna has rfs between the s and e genes and an additional - rfs between the m and n genes. this gene organization most closely resembles that of group iii coronaviruses. in the sars virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral rna, is very similar to that of the murine coronavirus mhv, except that it contains only one papain-like protease (plpro- ) ( fig. ) . thus, the plpro- of sars virus is likely responsible tbr the cleavage of all the nterminal proteins of gene l a, which is normally carried out by plpro- in murine comnavirus [ ] . it is noted that group iii coronaviruses have only one plpro. however, the sars virus genome has remnants of the plpro-i sequence; furthermore, the sars virus has the equivalent of the leader peptide (p ), which is missing in the group iii viruses. the remaining sequences of gene la-lb are highly conserved among all of the coronaviruses [ , ] . therefore, orfs la and lb are likely translated into a polyprotein by a ribosomal frameshifting mechanism [ ] . all of the potential gene products in gene la-lb are relatively conserved between sars and other coronaviruses. the c-like protease ( clpro) is likely responsible for the cleavage of all the remaining proteins in gene a- b [ ] . based on the predicted cleavage site specificity, the sars virus gene la-lb is likely processed into thirteen final protein products. the functions of these gene products are mostly unknown; nevertheless, they are likely involved in viral rna replication. in mhv, all the rnanegative temperature-sensitive mutants are mapped in the genetic regions covering almost the entire gene [ ] . [ ]. it should be noted that some of the protein-processing intermediates, in addition to the final products, may also function in viral replication. overall, from the perspective of gene organization, the "-half of the sars virus genome appears to be more closely related to group ii viruses, whereas the "-half more closely resembles group iii virnses. therefore, sars virus may have been derived from recombination between a group ii and a group iii virus. however, the published sequence analysis indicated that the entire sars virus rna resembled that of group ii viruses; no evidence of recombination was noted [ , ] . since the genetic sequence of sars virus is approximately equidistant between group ii and iii viruses, the possible presence of recombination might not have been evident from sequence analysis alone. regardless, recombination is probably not the triggering event for the jumping of the virus from animals to humans, since the recombination most likely occurred between the ancestral coronaviruses. coronavirus genes (except for gene ) are typically expressed from subgenomic mrnas, which share a common leader sequence at the '-end, but initiate at different places from the consensus intergenic sequences or transcription regulatory sequences (trs) in the genome and extend toward the '-end of the genome [ ]. the transcription initiation sequences are typically rich in u, c, and a residues and highly conserved in front of each gene. each mrna (except for the smallest) is physically polycistronic, but can be used to translate only the '-most orf. in rare situations, several orfs are translated from a single mrna, e.g. mrna of ibv and mrna of mhv, by internal initiation or other mechanisms, such as an internal ribosomal entry site, which are not completely understood. these unconventional translation mechanisms are not efficient; as a result, these gene products are usually not very abundant. these orfs typically encode viral nonstructural proteins, except for the e protein in some coronaviruses. significantly, the orfs between the structural protein genes are extremely heterogeneous among different coronaviruses in terms of the number of potential gene products and the method of their expression. they are not essential for viral replication in cell culture; however, recent studies suggest that deletions of these 'nonessential' orfs could result in the reduction of viral virulence [ , ] . conceivably, some of these orfs in sars virus could be responsible for the high virulence of this virus. a report shows that five subgenomic mrnas were detected in vero cells infected with the sars virus [ ] . thus, some of the orfs are expected to be expressed by internal initiation if they are translated at all. however, it is possible that additional subgenomic mrnas are transcribed; the amounts of the various subgenomic mrnas vary tremendously among different coronaviruses, depending on the strength of the transcription-start signals [ ] . the less abundant subgenomic mrnas frequently were missed in northern blot analysis. indeed, the analysis of the sars virus genome detected many more consensus intergenic sequences (ucuaaac and related sequences), which can potentially be used for transcription initiation [ , ] . a recent study detected eight subgenomic mrna species in sars virus-infected cells [ ] . in general, coronaviruses have four envelope proteins: s, m, e and he. the spike protein forms the characteristic spikes that are the namesake of the virus. the s protein is often cleaved into s and $ domains by intra-and extracellular proteases; the cleavage often enhances the viral infectivity [ ] . however, the s protein of some viruses, such as feline, is not cleaved, and yet the virus is fully infectious [ ] . sequence analysis of the s protein of sars virus suggests that it will not be cleaved. the spikes bind to the receptor on the target cells; the receptor-bind-ing domain is typically localized in the n-terminus of the s domain [ , ] . the spike consists of oligomeric structures, which are formed by the heptad repeats in the $ domain ( fig. ) . typically, there are two heptad repeats in the coronavirus $ proteins. $ also contains a fusion peptide sequence, which is responsible for the fusion activity associated with coronaviruses. significantly, the optimum ph for the spike-induced fusion differs from virus to virus; while most mhv strains cause fusion at the neutral ph [ ] , some variant viruses induce fusion at ph . [ ] . since the ph requirement of membrane fusion dictates the mechanism of virus entry (either by fusion at the plasma membrane or by endocytosis), different coronaviruses may use different entry mechanisms. sars virus also causes syncytia formation in vivo, but not in the cultured vero cells [ ] . as the s protein of sars virus possesses most of the features of the s proteins of other coronaviruses, it will be interesting to know the conditions, such as protease sensitivity and ph dependence of membrane fusion, that enhance the sars virus infectivity. it should be noted that both s and $ contain the neutralization epitopes of mhv [ ] and that there is a hypervariable region in s , which is frequently mutated or deleted in the coronaviruses. such mutations very often change the biological or pathogenic properties of the virus. the m and e proteins are the minimum protein units for virus assembly [ , ] . both are integral membrane proteins. m protein resides not only on the viral envelope, but in the viral internal core as well [ ] . in the cells, m protein is anchored in the golgi complex, thus dictating the site of virus assembly to the er-golgi complex [ ] . the expression of m and e proteins together is sufficient to trigger the formation of virus-like particles (vlp). when s protein is coexpressed with m and e proteins, the s protein is incorporated into vlp with presumably authentic conformation. such a vlp can infect cells [ ] . thus, these vi_ps will be an excellent candidate as a potential vaccine. intriguingly, it has recently been shown that e protein may not be absolutely required for viral infectivity [ ] . sars virus has comparable structural proteins. he protein is seen only in some group ii coronaviruses; it is not required for viral infectivity even in those viruses (e.g. mhv, hcov-oc ) that contain the he protein. however, he protein may be involved in the infection of bcov, as a monoclonal antibody against he protein can inhibit bcov infection [ ] . the he protein binds to certain sialic acid residues and possesses an acetyl-esterase activity. it is conceivable that he protein provides the initial binding contact between the virus and the target cells; however, subsequent tight and specific binding may be mediated by the s protein. he protein bears sequence homology with the hemagglutinin protein of influenza c virus, thus prompting suggestions that recombination has taken place between an ancestral coronavirus and an influenza virus [ ] . sars virus does not encode the he protein. the final structural protein is n protein, which likely interacts with viral rna and makes up the viral core and nucleocapsid. it is interesting to note that the coronavirus particles appear to include both an icosahedral core and an internal helical nucteocapsid [ ] . n protein is present in both structures. sars virus has typical n protein structural motifs, including several rna-binding domains. coronaviruses have an envelope that reflects the lipid composition of the cellular membranes. however, remarkably, coronavirus is one of the very few enveloped viruses that are able to cause enteric infections. thus, the viral envelope certainly can resist the harsh environment of the gastrointestinal tract, namely, the acidic environment of the stomach and the bile and lytic enzymes of the small intestines. the structural and chemical basis for such unusual resistance is not yet clear. correspondingly, sars patients very often show gi symptoms, and the virus is usually detected in the stool [ ] . therefore, the envelope of sars virus likely consists of unusual structures. indeed, it has been shown that sars virus can survive in diarrheal stool for as long as days and on a dry surface for h (world health organization bulletin). these unusual envelope properties have implications for the control of the sars outbreaks. as an rna virus, sars virus can be expected to undergo mutation at a very high frequency. with an estimated error frequency of x . for rna-dependent rna polymerases in general, the sars virus genome can be expected to accumulate an average of three mutations per round of rna replication. thus, sars virus, like all other rna viruses, probably consists of a collection of rna quasispecies [ ] . such a high frequency of mutation implies that the tkna viral genome is inherently limited in size. coronaviruses are obvious aberrations. yet, despite having an extraordinarily long rna genome, sars virus and other coronaviruses appear to be relatively genetically stable. to date, the predominant rna species from different sars patients appear to be quite homogeneous. the various sars virus isolates from different geographical regions differ by no more than ten amino acids in the entire genome. it is not clear whether these differences confer any differences in the biological properties of the virus. nevertheless, they allow epidemiological tracing of the virus transmission routes. it appears that two different lineages of the sars virus can be independently traced [ ] . whether the virus will undergo a higher frequency of mutation in the future once seasonal changes occur or after specific drug treatments are introduced is an issue of concern. however, there has been no investigation of the nature of rna quasispecies of sars virus derived from different patients so far. such rna quasispecies may represent potential sources of viral divergence. coronaviruses have another powerful genetic means for evolution: rna recombination, which occurs at a very high frequency [ ] . in theory, recombination may not only introduce genome alterations but, paradoxically, balance the deleterious effects of mutations by removing the undesirable defects [ ] . this ability may explain why coronavirus can maintain such a long rna genome. the ability of coronaviruses to recombine may stem from the nonprocessive nature of coronavirus rna polymerase, which mediates discontinuous rna synthesis during mrna transcription [ ] . in natural infections, both mutation and recombination have been demonstrated to contribute to the evolution of the coronaviruses. avian coronavirus ibv continues to undergo antigenic changes in the field through both mutation and recombination involving the s gene. recombination could occur between the field isolates and the vaccine strains of ibv [ , ] . this evolution causes problems in vaccination strategies, as multiple vaccines directed against different viral serotypes must be used simultaneously. another example is the emergence of porcine respiratory coronavirus (prcov) from the enteric tgev in europe as well as in the us in the s [ ] . again, this shift in viral tissue tropism and virulence was due to deletions and mutations in the s gene. this evolution turned out to be beneficial to the livestock industry because the resultant prcov is considerably less virulent than the parental tgev and, in fact, was used as an attenuated virus vaccine for tgev. a feline comnavirus has also been demonstrated to have undergone recombination with a canine coronavirus, resulting in changes in the biological properties of the virus [ ] . the ability of the coronavirus to recombine has been utilized as a genetic tool for manipulating the coronavirus genome. until recently it had been impossible to apply reverse genetic methods for studying coronaviruses because of the large size of its genome. taking advantage of the ability of coronavirus to recombine with not only other coronaviruses but also viral rna fragments, masters and his colleagues have developed techniques to introduce mutations into mhv defective interfering rna and allow it to recombine with a temperature-sensitive mutant (the mutation being in the n protein-coding region) of mhv [ ] . by selecting wild-type viruses capable of growing at the high temperature and using other selection markers, it is now possible to engineer mutations into certain viral rna regions or exchange certain viral genes between different coronaviruses [ ] . this technique has been applied only to mhv so far. however, a flood of reports in the last years has shown that full-length infectious cdna clones can be obtained for several coronaviruses, including tgev, mhv, hcov- e, pedv and ibv [ , , , ] . these cdna clones have added to the arsenal of coronavirus genetic tools. it is anticipated that the full-length sars virus cdna will be available soon. both this cdna and the targeted recombination approach may provide the reverse genetic tools for studying sars virus. the temptation to manipulate the sars virus genome will be great. however, i must add a word of caution before such attempts are made. the scientific community must be vigilant in guarding against the misuse of these genetic tools to alter the sars virus genome or create chimeric coronaviruses involving sars virus genes. i propose a moratorium on these types of experiments until the various concerned international communities agree upon specific guidelines. the potential for unleashing a more virulent new sars virus is simply too onerous to be ignored. coronaviruses, in general, cause disease by both cytocidal and immune-mediated mechanisms. most coronavirus infections in cell culture result in lysis or apoptosis of the infected cells [ ] . furthermore, the virus causes cell fusion, resulting in the formation of cell syncytia. these cytopathic effects (cpe) are usually the results of viral replication. for example, the coronavirus mobilizes cellular vesicles to form the viral replication complex [ ] , which may disrupt the golgi complex [ ] . sars virus also causes cpe in vero cells; furthermore, it causes syncytia formation in the lung tissue, suggesting that it causes cytocidal effects. another eerie similarity between sars virus and other coronaviruses is their ability to induce fibrosis; e.g. certain strains of mhv cause fibrosis in the liver [ ] , and sars virus causes fibrosis in the lung [ ] . the n protein of mhv has been shown to stimulate the promoter activity of the prothrombinase gene [ ] , which correlates with the fibrin deposit in the liver associated with mhv infection. a similar mechanism may be involved in the fibrosis of the lung induced by sars virus. immune responses also contribute to the pathogenesis of several coronaviruses. most notably, cytotoxic t cells and cytokines play a very significant role in the neuropathology caused by mhv [ ] . on the other hand, humoral antibodies are important for the disease associated with fipv, in which certain antibodies against the viral s protein induce severe peritonitis symptoms [ , ] . in the case of sars, there is an occurrence of cytokine storms and accumulation of inflammatory cells, particularly macrophages in the lung, during the peak of the disease [ ] , suggesting that both innate and adaptive immune responses are important for the disease. thus, the clinical management of sars should consider not only antiviral but anti-inflammatory strategies as well. several viral genes are likely involved in viral pathogenesis. most importantly, the spike protein gene affects viral pathogenesis not only by determining the host target cell specificity but by other mechanisms as well. as exemplified above, the emergence of the weakly virulent prcv from the virulent enteric tgev was the result of mutations in the s gene [ ] . also, it has been shown that a single mutation in the s gene of mhv can significantly alter the tissue tropism and virulence of the virus [ ] . the so-called 'non-essential orfs' may also play a role in viral pathogenesis. these genes are not necessary for viral replication in tissue culture cells, as experimental or natural deletions of any one of these genes did not affect the ability of the virus to replicate. however, some of these deletion mutants show much lower virulence than the wild-type virus in infections in animals [ ] . tt is significant that sars virus shows significant divergence of these orfs from other coronaviruses. a preliminary report shows that the civet cat coronavirus has a nucleotide deletion, which caused two non-essential orfs to fuse into one, creating a new orf in the sars virus [ a]. it will be very interesting to find out if this new orf contributes to the virulence of the sars virus. other viral gene products may also alter cellular responses to the viral infection. for example, m protein of tgev can induce interferon [ ] , and e protein of mhv can induce apoptosis [ ] . they may modulate the course of viral infection. another important issue in the pathogenesis of sars virus is whether the virus can cause chronic persistent infection. this issue concerns the possible presence of chronic carriers, who may serve as the source of continuing sars outbreaks. although human coronaviruses typically cause short, self-limiting illnesses, most of the animal coronaviruses are known to cause persistent infection. the best studied coronavirus in this regard is feline coronavirus fecov; infected animals can continue to shed virus tbr as long as months after infection, even though these animals do not show symptoms [ ] . tgev also shows a similar tendency, in which the virus can be detected in the respiratory tract of the infected animals several months after infection [ , ] . mhv can persist in the central nervous system many months after intracraniat inoculation [ ] . thus, the ability to persist is a common feature of most coronaviruses under some conditions. sars virus may also have this property. so far, viral rna reportedly has been detected in patients' stool more than days after infection (world health organization bulletin). coronavirus primarily infects the epithelial cells of the gi and respiratory tracts, but the virus can replicate in many cell types, particularly macrophages. sars virus also infects a wide spectrum of cell types; it has been detected in the blood, lung, liver and kidney, and in various bodily secretions, including stool and urine [ ] . thus, sars virus may induce systemic infection. the primary determinant of target cell specificity of the virus is the nature of its cellular receptors. type i coronaviruses use aminopeptidase n (cd ) of various animal species as receptors in a species-specific manner [ , ] , while a type ii coronavirus (mhv) uses the carcinoembryonic antigen as recenor [ ] . the receptors for type iii viruses and sars virus are not yet known. it should be noted that the virus easily adapts to cell lines of different animal species, probably by using other related molecules as a receptor [ ] . thus, the specificity of the spike-receptor interaction may not be very rigid. interruption of the binding between the spike protein and the receptor will be a potential means of inhibiting viral infection. the next step of virus infection is virus entry. the mode of virus entry for coronavirus may vary between different viruses. although most viruses appear to enter cells by fusion at the plasma membranes, some viruses may enter cells by acidic ph-dependent endocytosis. regardless, the fusion activity is likely important for virus entry. several functional domains, including the heptad repeat, which is important for oligomerization of the spike protein, the putative fusion peptide, and the receptor-binding domain of the s protein, will be good targets for antivirals. macromolecular synthesis, including transcription, translation and protein processing, offers many potential molecular targets as well. most notably, proteases, rnadependent rna polymerases (rdrp) and helicases are good targets. unfortunately, in vitro rdrp assays are still neither efficient nor specific, precluding their use as a molecular tool for drug screening. in vitro protease assays for both clpro and plpro, in contrast, are well established [ , ] . the protease activity is essential for viral protein processing and rna replication; inhibition of the protease function shuts off viral rna synthesis instantaneously [ ] . thus, the proteases are potentially powerful targets for antivirals. furthermore, the x-ray crystallographic structure for the clpro is available [ ] , as is a computation model for the sars virus clpro [ ] . these in addition, the processes of virus assembly, which likely occurs in the er-golgi intermediate compartment [ ] , and virus exit, which occurs through the cellular secretory pathway, are also potential antiviral targets. it has been known that the e and m proteins are the minimum components for virus assembly, forming vlp in the absence of other viral proteins [ , ] . the cellular machinery involved in the formation of virus particles is still not clear; it is a potential antiviral target as well. the prospect for sars vaccines is uncertain. several potential approaches are feasible. the killed whole virus vaccine is attractive because of the availability of a robust cell culture system that yields a large quantity of virus particles. attenuated virus vaccines are still unattainable because the parameters for virus attenuation are not yet well defined. ultimately, the attenuation of viral virulence needs to be verified preclinically in animal models. recombinant subunit vaccines consisting of the spike protein alone or in combination with other viral proteins can be prepared by using the recombinant proteins themselves or delivered by virus vectors or as dna plasmids. these approaches are technically feasible. however, the timetable for the development of any of these vaccines is lengthy, and the potential success of vaccine development may be hindered by the lack of accessibility to animal models and a suitable population base for clinical trials. at the present time, the macaque monkey is an acceptable animal model. however, with the sars epidemic virtually over worldwide, it will be difficult to test the efficacy of these vaccines. eventually, 'ring' vaccination (vaccination of the at-risk populations around the exposed people) may have to be attempted. nevertheless, vaccine development is clearly a top priority, as vaccines are the main weapons in the arsenal against future outbreaks, whether they are natural or man-made (i.e. bioterrorism) in origin. a survey of the currently available animal coronavirus vaccines offers a glimpse of the potential efficacy of sars vaccines. live attenuated vaccines have been used effectively against ibv. sometimes, a killed virus vaccine is used as a booster to the primary attenuated virus vaccine [ ] . the drawbacks of these vaccines are that ibv exists in multiple antigenic types and that the virus undergoes t?equent antigenic changes as a result of mutations and recombination. therefore, multiple viruses of different serotypes must be used in combination vaccines to protect against most ibv serotypes. for tgev, live attenuated virus vaccines have been used to vaccinate the adult pigs. the vulnerable piglets receive the protective antibodies through milk. improvement in lactogenic immunity is therefore the aim of tgev vaccine development. killed canine coronavirus has proven to be efficacious as a vaccine experimentally [ ] , although it is not routinely used because of the lack of necessity. on the other hand, feline coronavirus vaccines have been proven to be not only inefficacious; worse yet, the?, have been shown to lead to even more severe viral infections in the vaccinated cats [ ] . enhancement of viral infections by vaccines is probably due to the phenomenon of antibody-dependent enhancement (ade), in which antibodies against certain epitopes of the spike protein complex with the virus particles and enhance their infectivity [ . it is difficult to predict how the candidate sars virus vaccines will behave. if immune response plays an important role in the pathogenesis of sars, then an effective sars vaccine may turn out to be as elusive as the fipv vaccines. similar difficulties have plagued the developments of other viral vaccines, such as dengue virus, hiv, hepatitis c virus. sars is the first newly emerged infectious disease in this century. it is not likely to be the last one. even though the sars outbreak is now under control after a devastating run of more than months that affected and threatened many countries worldwide, the virus will continue to pose a threat in the near future. because of possible human and animal reservoirs for the virus, sars may return in the coming months or years. in the short term, the isolation and quarantine of patients and exposed individuals remain the only effective means of containing an outbreak. valuable experience in disease control was gained from this first outbreak; thus, the future outbreaks of sars and other emerging and re-emerging respiratory infectious diseases will likely be limited to sporadic occurrences. hopefully, intensive studies of the sars virus in the near future will provide sufficient understanding of its molecular biology and mechanism of pathogenesis to enable the development of antiviral drugs and vaccines. only then can we effectively control the disease. pet theory comes to the fore in fight against sars engineering the largest rna virus genome as an infectious bacteria artificial chromosome induction of apoptosis in murine coronavims-infected cultured cells and demonstration of e protein as an apoptosis inducer structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain coronavirus main proteinase ( clpro) structure: basis for design of anti-sars drugs identification of the catalytic sites of a papaln-like cystein proteinase of murine coronavirus two amino acid changes at the n-terminus of transmissible gastroenteritis coronavirus spike pro. tein result in the loss of enteric tropism establishing a genetic recombination map for murine coronavirus strain a comptementation groups persistent infection promotes crossspecies transmissibility of mouse hepatitis virus episodic evolution mediates interspecies transfer of a murine coronavirus the production of recombinant infectious di-particles of a murine coronavirus in the absence of helper virus an efficient ribosomal frame-shifting signal in the polymerase-encoding region of the coronavirus ibv two coronaviruses isolated from central nervous system tissue of two multiple sclerosis patients reverse genetics system for the avian coronavirus infectious bronchitis virus induction of alpha interferon by transmissible gastroenteritis coronavirus: role of transmembrane glycoprotein el nucleotide and predicted amino acid sequences of all genes encoded by the ' genomic protion ( kb) of respiratory bovine coronaviruses and comparisons among respiratory and enteric coronaviruses monoclonal antibody analysis of neutralization and antibody-dependent enhancement of feline infectious peritonitis virus stably expressed fipv peplomer protein induces cell fusion and elicits neutralizing antibodies in mice the group-specific murine coronavirus genes are not essential, but their deletion, by reverse genetics, is attenuating in the natural host aminopeptidase n is a major receptor for the entero-pathogenic coronavirus tgev monoclonal antibodies to bovine coronavirus: characteristics and topographical mapping of neutralizing epitopes on the e and e glycoproteins fulminant hepatic failure in murine he~patitis virus strain infection: tissue-specific expression of a novel fg prothrombinase quasi-species: the concept and the word molecular basis of virus evolution. cambridge identification of a novel coronavirus in patients with severe acute respiratory syndrome aetiology: koch's postulates fulfilled for sars virus alteration of the ph dependence of coronavirusinduced cell fusion: effect of mutations in the spike glycoprotein major receptor-binding and neutralization determinants are located within the same domain of the transmissible gastroenteritis virus (coronavirus) spike protein fusiondefective mutants of mouse hepatitis virus a contain a mutation in the spike protein cleavage signal coronavirus genome: prediction of putative functional domains in the nonstructural polyprotein by comparative amino acid sequence analysis isolation and characterization of viruses related to the sars coronavirus from animals in southern china characterization of a coronavirus isolated from a diarrheic foal switching species tropism: an effective way to manipulate the feline coronavirus genome a human rna viral cysteine proteinase that depends upon a unique zn +-binding finger connecting the two domains ofa papain-like fold persistence and evolution of feline coronavirus in a closed cat-breeding colony feline coronavirus type ii strains - and - originate from a double recombination between feline coronavirus type i and canine coronavirus sequence analysis of nucleocapsid gene and leader rna of human coronavirus oc identification of mouse hepatitis virus papain-iike proteinase activity sars virus: the beginning of the unraveling of a new seroepidemiologic survey of coronavirus (strain oc ) related infections in a children's population coronavirns m proteins accumulate in the golgi complex beyond the site of virion budding mouse hepatitis virus type (jhm strain)-induced fatal central nervous system disease. i. genetic control and the murine neuron as the susceptible site of disease anderson lj, sars working group. a novel coronavirus associated with severe acute respiratory syndrome localization of neutralizing epitopes and the receptor-binding site within the amino-terminal amino acids of the murine coronavirus spike protein the small envelope protein is not essential for routine coronavirus replication sequence evidence for rna recombination in field isolates of avian coronavirus infectious bronchitis virus protection of chickens after live and inactivated virus vaccination against challenge with nephropathologenic infectious bronchitis virus pa/wolgemuth/ genetic recombination ill rna viruses recombination and its evolutionary effects on viruses with rna genomes molecular basis of virus evolution. cambridge the molecular biology of coronaviruses coronaviridae and their replication porcine respiratory coronavirus: molecular features and virus-host interactions syncytia formation induced by coronavirus infection is associated with fragmentation and rearrangement of the golgi apparatus targeted recombination within the spike gene of murine coronavirus mouse hepatitis virus a :q is a determinant of hepatotropism induction of caspasedependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus scqnence of mouse hepatitis virus a mrna :indications for rnarecombination between coronavirus and influenza c virus mhv infection of the cns: mechanisms of immune-mediated control seroepidemiologic studies of coronavirus infection in adults and children lung pathology of fatal severe acute respiratory syndrome the nucleocapsid protein of murine hepatitis virus type induces transcription of the novel fgl prothrombinase gene sars in china: tracking the roots of a killer transmissible gastroenteritis coronavirus gene is not essential but influences in vivo virus replication and virulence coronavirus as a possible cause of severe acute respiratory" syndrome analysis of second-site revellants of a murine coronavirus nucleocapsid protein deletion mutant and construction of nucleocapsid protein mutants by targeted rna recombination efficacy of an inactivated canine coronavirus vaccine in pups the transmissible gastroenteritis coronavirus contains a spherical core shell consisting of m and n proteins characterization of a novel coronavirus associated with severe acute respiratory syndrome comparative full-length genome sequence analysis of sars coronavirus isolates and common mutations associated with putative origins of infection processing of the coronavirus mhv-jhm polymerase polyprotein: identification of precursors and proteolytic products spanning kilodaltons of orfla colocalization and membrane association of murine hepatitis virns gene products and de novo-synthesized viral rna in infected cells unique and conserved features of genome and proteome of sars-coronavirus, an early split-off from the coronavirus group lineage human coronavirus gene expression in the brains of multiple sclerosis patients viral replicase gene products suffice for coronavirus discontinuous transcription sorting of progeny coronavirus from condensed secretory proteins at the exit from the trans-golgi network of att cells recovery of transmissible gastroenteritis virus from chronically infected experimental pigs rottier pjm. nucleocapsid-independent assembly of coronavirus-like particles by co-expression of viral envelope protein genes evidence of natural recombination within the st gene of the infectious bronchitis virus monoclonal antibodies to the peplomer glycoprotein of coronavirus mouse hepatitis virus identify two subunits and detect a conformationai change in the subunit released under mild alkaline conditions antibody-mediated enhancement of disease in feline infectious peritonitis: comparisons with dengue hemorrhagic fever receptor for mouse hepatitis virus is a member of the carcinoembryonic antigen family of glycoproteins human aminopeptidase n is a receptor for human coronavirus e systematic assembly of a full-length infectious cdna of mouse hepatitis virus strain a biological and genetic characterization of a hemagglutinating coronavirus isolated from a diarrhoeic child processing ofthe human coronavirus e replicase polyproteins by the virus-encoded c-like proteinase: identification of proteolytic products and cleavage sites common to ppla and pplab the beginning of the unraveling of a new coronavirus key: cord- - gupfqnl authors: martinez-perez, clara; alvarez-peregrina, cristina; villa-collar, cesar; sánchez-tena, miguel Ángel title: citation network analysis of the novel coronavirus disease (covid- ) date: - - journal: int j environ res public health doi: . /ijerph sha: doc_id: cord_uid: gupfqnl background: the first outbreaks of the new coronavirus disease, named covid- , occurred at the end of december . this disease spread quickly around the world, with the united states, brazil and mexico being the countries the most severely affected. this study aims to analyze the relationship between different publications and their authors through citation networks, as well as to identify the research areas and determine which publication has been the most cited. methods: the search for publications was carried out through the web of science database using terms such as “covid- ” and “sars-cov- ” for the period between january and july . the citation network explorer software was used for publication analysis. results: a total of , publications were found with , citations generated in the network, with june being the month with the largest number of publications. the most cited publication was “clinical characteristics of coronavirus disease in china” by guan et al., published in april . nine groups comprising different research areas in this field, including clinical course, psychology, treatment and epidemiology, were found using the clustering functionality. conclusions: the citation network offers an objective and comprehensive analysis of the main papers on covid- and sars-cov- . coronaviruses (coronaviridae) are a family of viruses that cause infections in humans and animals. it is a zoonotic disease, i.e., it can be transmitted from animals to humans through direct contact with infected animals or their secretions [ , ] . in , sars-cov- caused almost cases in countries and had a % mortality rate. between that year and december , no further cases were detected in humans [ ] . then, a group of pneumonia cases with an unknown origin was reported in wuhan, in the chinese province of hubei, on december [ ] . on january , the chinese authorities identified a new outbreak of the coronaviridae family after analyzing several samples from the respiratory tract, which was subsequently named sars-cov- [ , ] . on february, the general director of the who (world health organization) announced "covid- " as the name of the disease caused by sars-cov- . a month later, the who declared the pandemic status following an increase in the number of cases, which had reached , infections and more than deaths in countries [ ] . in europe, the first case was detected in france on january, and the virus then spread to nine other countries in just one month (belgium, finland, france, germany, italy, russia, spain, sweden and the united kingdom). by march, the number of positive cases in europe had increased to , [ ] . meanwhile, between january and february, positive cases were reported in the americas in the search of publications was carried out using the web of science (wos) database with the following search terms: "covid- ", "sars-cov- ", "the coronavirus disease " and "corona virus disease ". these terms were selected bearing in mind the study objective; additionally, these are the most common terms in all research fields. since the results of the search comprised some articles shared by several fields, the boolean operator not was used in the second search ("sars-cov- " not "covid- "), the third search ("the coronavirus disease " not "sars-cov- " not "covid- ") and the fourth search ("corona virus disease " not "the coronavirus disease " not "sars-cov- " not "covid- "). additionally, the search was carried out by selecting "subject" as the search field, and it was limited by abstract, title and keywords. in this way, we covered all articles that included other terms, such as " novel coronavirus", " novel coronavirus diseases" or " -ncov". the period selected was from january to july . furthermore, web of science makes it possible for users to add references to their library when conducting bibliographic searches directly in external databases or library' catalogs. with regards to the citation indexes, social sciences citation index, science citation index expanded and emerging sources citation index were used. on the other hand, given that the way in which authors and institutions cite works may vary, the citespace software was used to standardize the data. the date on which the publications were searched and downloaded was july . the publications were analyzed using the citation network explorer software, which allows the researcher to analyze and visualize citation networks of scientific publications. furthermore, it is possible to download citation networks directly from web of science and manage citation networks that include millions of publications and related citations. therefore, a citation network composed of several millions of publications can be the starting point from where a deeper analysis can be conducted to obtain a small subnetwork with publications on the same subject. a quantitative analysis of the most mentioned publications in a period was carried out using the attribute citation score. therefore, not only the internal connections within the web of science database but also any external connections were quantified, meaning that other databases were considered [ ] . citnetexplorer provides several techniques for the analysis of publication citation networks. the clustering functionality is achieved using the formula developed by van eck in (equation ( )) [ ] . then, to assign a group to each publication, the clustering functionality was applied. as a result, the most related publications are usually found in the same group based on citation networks [ ] . finally, the core publications were analyzed using the identifying core publications functionality, which consists of identifying the publications that are considered the core of a citation network; that is, they have a minimum number of connections with other core publications, so those that are irrelevant may be eliminated. the number of connections is established by the researchers, so the higher the value of this parameter, the lower the number of core publications [ ] . in this study, the publications that have four or more citations in the citation network were considered. additionally, the drilling down functionality, which allows for a deeper analysis of each of the groups at different levels, was also used. the vosviewer software (centre for science and technology studies (cwts), leiden, the netherlands) was used to create and visualize bibliometric networks (journals, researchers, individual publications, bibliographic relationships, etc.) through graphs. the first articles on covid- were published at the beginning of , so the period of time selected was from january to july . a total of , publications and , citation networks were found in the search in wos. among all the publications, . % were articles, . % were editorial material, . % were letters, . % were reviews, . % were news items and . % were edits, book reviews, retractions or meeting abstracts. figure shows the publications with greater weights and the group to which they belong. the color of an article represents its group, and the lines that connect the elements represent links. the number of publications on covid- has increased since april (january-march : . % of the publications; april-december : . % of the publications). june was the month with the largest number of publications, with publications and citation networks ( figure ). table shows the most cited publications in this citation network. the most cited article is that of guan et al. [ ] , published in april , with a citation index of . in this publication, patients were included from december (when the disease first broke out) to january . the patients were from hospitals in different regions of mainland china, out of which were excluded because they had been admitted to the icu (intensive care unit), were on invasive mechanical ventilation or had died. the most common symptoms were fever ( . % when admitted to hospital and . % during hospital stay), cough ( . %) and diarrhea ( . %). in addition, ground-glass opacity of the lung was the most common radiological finding in thorax computed tomography (ct) scans ( . %), and . % of patients presented lymphocytopenia upon admission. the average hospitalization time was days. during the first two months of the outbreak, covid- spread quickly throughout china. the disease often presented with different degrees of severity, as patients frequently showed no signs of fever or unusual radiological findings. when analyzing the most cited articles, can be found on the symptoms, viral transmission and experimental treatment methods [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . there are two that address unusual clinical symptoms and findings [ , ] , and there is one that compares how covid- affects patients with cancer and those without cancer [ ] . the research on covid- is multidisciplinary. the fields of internal medicine ( . %) and public environmental occupational health ( . %) are worth mentioning ( figure ). medicine is the main area of publication in the field of health, as it is one of the oldest research fields [ ] . similarly, public environmental occupational health has been studied for centuries. however, this research field has significantly increased in the past few years [ ] . the quartile according to the scimago journal rank (sjr) is included in the table to show the importance and relevance of the main journals that have published the most articles, a dimension selected based on its quality and the fact that its use is widespread among the international scientific community. quartiles are based on the rank of each journal within its topic and are measured by assessing the distribution of the impact factor of a given journal for that topic category. scimago journal rank is a website of scientometric and informetric values, which allow researchers to monitor the behavior and impact of their contributions on an international scale; that is, it measures the scientific influence of the journals according to the number of citations. the citations are weighted depending on their field and prestige [ ] . table shows the journals with the largest number of publications. after comparing our results with the first bibliometric publications on covid- , we could observe that the journals with the largest number of publications were as follows: journal of medical virology, which has the most publications (n = ), followed by chinese journal of tuberculosis and respiratory diseases (n = ), journal of travel medicine (n = ), journal of clinical medicine (n = ), lancet (n = ), radiology (n = ) and jama (n = ) [ ] . as shown in table , the authors with the largest number of publications on covid- were wang y ( . %), mahase e ( . %) and li y ( . %). the united states ( . %), china ( . %) and italy ( . %) were the countries with the highest publication rates (figure ) . similarly, the study by fan et al. [ ] analyzed the countries with the highest rates of publication and found that the authors with a large number of publications on covid- in english-language journals were as follows: li y had the highest number of published papers ( , . %), followed by benvenuto d, eurosurveillance editorial team and leung gm ( , . %) and angeletti s, gao gf, ran j, wei y, wu jt and yang g ( , . %). as regards chinese journals, the authors with the largest numbers of publications were as follows: wang yg and yang fw published the highest number of papers ( , . %), followed by wang yj ( , . %). similarly, the study by belli et al. [ ] analyzed the first weeks after the outbreak and found that china represented . % of the publications, followed by the us with . %. the most frequently used keywords were "covid- " ( publications), "coronavirus" ( publications) and "sars-cov- " ( publications). figure shows the most used keywords from the most relevant publications. this is consistent with the study conducted by fan et al. [ ] , in which the most common keywords in english-language publications were "sars-cov- ", "covid- ", "china", "sars", "epidemic", "adult", "psychological", "nucleic acids", "plague" and "infection". moreover, the most common keywords used in chinese journals were "covid- ", "sars-cov- ", "prevention and control", "traditional chinese medicine", "computed tomography", "epidemic", "public health", "mers", "pneumonia" and "male". by using the clustering function, each publication in the citation network is assigned to a group, which means that publications that are close in the citation network must belong to the same group. consequently, each of these groups consists of publications that are strongly connected through their citations. in this way, it could be interpreted that every group represents a different topic in the scientific literature. in order to differentiate the groups, each of them has been assigned a specific color. additionally, the links between groups have been marked using colored lines. the clustering function identified groups, of which have a significant number of articles; however, the remaining groups only account for . % ( figure ). table shows the information of the citation networks for the nine main groups, listed from the largest to the smallest according to their size. in group , publications and citations were found throughout the network. the most cited publication is that of guan et al. [ ] , published in april in the new england journal of medicine, which is also at the top of the most cited publications. in this group, the different articles analyze the viral transmission of sars-cov- , the most frequent symptoms (fever, cough, diarrhea, etc.) and experimental treatment methods such as chloroquine phosphate (figure ). for group , publications and citations were found throughout the network. the most cited publication is that of liang et al. [ ] , published in march in lancet oncology. in this paper, the authors discuss how cancer patients are more vulnerable to covid- than people without cancer. this is due to their immunosuppressive status resulting from malignant neoplasm or cancer treatments such as chemotherapy. furthermore, these patients have a worse prognosis. therefore, three control strategies were established for cancer patients during the covid- crisis: • postpone surgery and chemotherapy treatment in patients diagnosed with cancer in a stable state. • improve staff protection. increase surveillance or provide more intensive treatment when cancer patients are infected with sars-cov- , especially in elderly patients or those with comorbidities. by analyzing the articles belonging to group , it can be noticed that they address how covid- can affect patients with cancer and how they should be treated. additionally, they discuss the different methods of transmission, namely, through droplets, aerosols or contact with elements such as metal. consequently, an analysis of protection methods against covid- is offered, both for health professionals and other members of staff, with the final recommendation being to opt for telemedicine. additionally, the procedure for performing tracheotomies in the icu and in the operating room is also explained (figure ). in group , publications and citations were found throughout the network. the most cited publication is that of chen et al. [ ] , published in april in lancet psychiatry. this article analyzed the physical and psychological pressures to which health professionals were exposed. to this end, a psychological response plan was developed, covering three main areas: • development of a medical/psychological intervention team, which provided online courses in order to guide medical staff to deal with common psychological issues. • a psychological hotline team, which provided guidance and supervision on solving psychological issues. psychological interventions, providing group activities aimed at relieving stress. moreover, health professionals presented diverse concerns, namely, infecting their relatives, poor knowledge of the disease, lack of protective equipment, inability to treat patients and poor rest. therefore, hospitals were forced to improve their resting areas, food supply and safety measures. they concluded in this study that preserving the mental health of employees is essential to improving the management of infectious diseases; however, it is still uncertain which approach would be the best. therefore, the articles belonging to group address the psychological problems of health professionals, medical students and patients (anxiety, stress or depression). furthermore, they show methods of treatment aimed at reducing mental health issues, such as support supervisors or online mental health services (questionnaires, books, communication programs, psychological guidance or cognitive therapy) (figure ). in group , publications and citations were found throughout the network. the most cited publication is that of shi et al. [ ] , published in april in lancet infectious diseases. the authors described findings from thorax computed tomography (ct) scans over the course of the disease. patients were grouped depending on the onset of the symptoms and the results of their first ct scan. as a result, the authors found that covid- pneumonia causes abnormalities that can be found in ct images of the thorax, even in asymptomatic patients, as well as the quick development of ground-glass focal opacities, which evolve from unilateral to bilateral diffuse lesions and advance or coexist with pulmonary consolidations over - weeks. therefore, they concluded that combining ct assessment and clinical and laboratory findings could help in providing an early diagnosis of covid- pneumonia. articles from this group focus on clinical findings in computerized tomography images from the lungs due to covid- pneumonia ( figure ) . in group , publications and citations were found throughout the network. the most cited publication is that of mao et al. [ ] , published in april in jama neurology. in this article, the authors analyze neurological disturbances in patients infected with covid- . they examined hospitalized patients, and the neurological disturbances were categorized as follows: • central nervous system manifestations: dizziness, headache, altered states of consciousness, acute cerebrovascular disease, ataxia and seizures. • peripheral nervous system manifestations: taste, sight, smell and nervous alterations. manifestations of muscular-skeletal lesions. the study showed that . % of the patients presented neurological alterations. they advised that, upon detecting any neurological disturbance, doctors should consider covid- as a differential diagnosis in order to avoid late or erroneous diagnosis. when analyzing the total number of articles in this group, it is clear that their main aim is to analyze neurological alterations related to covid- ( figure ). in group , publications and citations were found throughout the network. the most cited publication is that of emanuel et al. [ ] , published in may in the new england journal of medicine. this article analyzes the lack of healthcare resources in us hospitals during the covid- crisis, namely, icu beds, respiratory ventilators, qualified healthcare personnel for critical care units, personal protective equipment and medication. in this sense, they presented recommendations to maximize the benefits (saving the largest number of lives or saving the largest number of years of life by giving priority to patients who will survive longer after treatment), to treat all patients in an equal manner, to encourage and reward instrumental value (the instrumental value could be fostered by giving priority to those who can save others, or rewarding those who have saved others in the past) and to give priority to the most disadvantaged (those who are sick or the youngest people). articles in this group analyzed how to take advantage of and distribute limited critical care resources during a pandemic. furthermore, in order to avoid further outbreaks, these authors determined that social distancing could be necessary until and that continuous surveillance of covid- should be conducted, given that a resurgence of contagion could be possible until (figure ). in group , publications and citations were found throughout the network. the most cited publication is that of dong et al. [ ] , published in march in jama: journal of the american medical association. this article analyzed whether sars-cov- could be transmitted in the uterus from the infected mother to her baby before birth. to this end, both the mother and baby underwent a thorax ct scan; furthermore, rt-pcr (reverse transcription-polymerase chain reaction) was conducted for sars-cov- nucleic acid through a nasopharyngeal swab, and igm (immunoglobulin m) and igg (immunoglobulin g) antibodies, cytokines and other biochemical markers in the blood were analyzed. additionally, vaginal secretions of the mother during labor were tested with rt-pcr. the results of the analysis showed that newborns born from a mother with covid- had high antibody levels and unusual cytosine test results two hours after birth. high igm antibody levels suggest that the newborn was infected in the uterus since these antibodies are not transferred to the fetus from the mother. although the possibility of infection at birth cannot be dismissed, igm antibodies do not usually appear until - days after the infection. conversely, igg antibodies may be transmitted to the fetus through the placenta and may appear at a later time than igm antibodies, so high igg levels could be a symptom of maternal or infant infection. the articles in this group address coronavirus infection in children and babies ( figure ). in group , publications and citations were found throughout the network. the most cited publication is that of luo et al. [ ] , published in february in the chinese journal of integrative medicine. this study consisted of an analysis of chinese medicine and its potential use for preventing covid- . to this end, provinces in china were treated with "chinese medicine" to strengthen qi and protect it from external pathogens by dispersing wind, dissipating heat and reducing humidity. they found that the chinese herbal formula could be an alternative treatment approach to prevent covid- in a population at high risk. nevertheless, further studies are necessary to confirm this theory. in this group, the articles analyze the use of traditional medicine to protect patients from covid- . in addition, they also establish that environmental pollution can be a trigger for enhanced transmission of covid- ( figure ) . in group , publications and citations were found throughout the network. the most cited publication is that of fang et al. [ ] , published in april in lancet respiratory medicine. this article shows the importance of half-face masks for preventing the spread of respiratory infections. evidence shows that covid- can be transmitted even before the carrier shows any symptoms, and, thus, the transmission rate could be reduced if everyone, including those who are already infected but asymptomatic and yet contagious, wore masks. these articles emphasize that authorities should optimize the distribution of masks, prioritizing frontline health workers and the needs of the most vulnerable population, as the latter is more susceptible to infection and mortality, including older adults and people with other underlying medical conditions. this group analyzes the different methods for individual protection, such as half masks, safety spectacles, gloves, facial shields, respirators, air purifiers and robes ( figure ). after analyzing the relationships among the nine main groups using the drilling down functionality, a connection between groups and ( figure ) was found. furthermore, it was found that publications by the authors an p, baud d and chen cj appear in both groups. thirteen sub-clusters were found (figure ) , five of which have a significant number of publications ( table ). the rest of the groups are relatively small, with fewer than publications and citation networks. sixteen sub-clusters were found (figure ), only four of which have a significant number of publications ( table ). the rest of the groups are relatively small, with fewer than publications and citation networks. alterations in the digestive system as a result of covid- blood clotting alterations in covid- patients. clinical findings can help not only to identify the cause of death but also to provide new ideas on the pneumonia's pathogenesis related to sars-cov- . this may help doctors to give an appropriate response or to provide a therapeutic strategy for critical patients and thus reduce the mortality rate. sars-cov- uses sars-cov's ace receptor for the input and the tmprss serine protease for the priming of protein s. treatment using cytokines and/or tocilizumab is likely to become one of the effective approaches for critically ill covid- patients. it has been shown that digestive symptoms are common in covid- patients. furthermore, these patients showed longer blood clotting time and increased hepatic enzyme levels. however, more sample studies are needed to confirm these findings. covid- patients show signs of venous thromboembolism. it has been proven that an anticoagulant therapy, mainly low molecular weight heparin, seems effective. however, more studies are necessary to establish the type of medication, the dose and the optimal duration of the prophylaxis. evaluate the incubation period of covid- and its effects on public health. evaluate the efficiency of the contention methods for reducing covid- outbreaks. the presence of sars-cov- on different surfaces is very similar to that of sars-cov- . the epidemiological differences between these viruses may be due to the high viral loads in the respiratory tract and the possibility that sars-cov- -infected people could transmit the virus while being asymptomatic. the mean period of incubation is of days, and in most of the people, the symptoms appear within days. however, these numbers vary between mild cases and severe cases. containment methods, such as social distancing or the use of masks, have proven to be effective in limiting virus transmission. therefore, the general public must be aware of the recommendations regarding covid- contention. public health authorities must keep tracking the situation to obtain new information about the virus and its outbreaks in order to estimate the risk of further outbreaks with greater precision. the main databases, such as web of science or scopus, make it possible to create citation networks. however, their usefulness is limited when conducting a systematic review of all of the existing literature on a subject, as they do not offer a general overview of the connections among the citations of a group of publications. for this reason, the citnetexplorer software was selected, as it allows the researcher to visualize, analyze and explore citation networks of scientific publications. hence, citnetexplorer offers a more detailed analysis through the creation of citation networks when compared to other databases, such as web of science or scopus [ ] . the main goal of this study was to analyze the existing literature on covid- . it should be taken into consideration that the search was carried out before the existence of an effective vaccine against sars-cov- in humans. in order to identify relevant publications, the web of science database was used, which is one of the most comprehensive databases, as its searching range goes back to the year . nevertheless, it must be taken into consideration that web of science only accepts international journals once they have undergone a rigorous selection process. thus, once the existing bibliography had been downloaded from wos, the citnetexplorer software allowed us to collect and analyze every available piece of literature on covid- to date. furthermore, the connections between fields of study and the different research groups were obtained through the analysis of citation networks. the function called "clustering" was used to collect the results, and the publications were then grouped according to the relationships among the citations. the drilling down function was used to examine the existing bibliography for each group, and the core publication function was used to show the main publications, that is, to show the publications with a minimum number of citations. therefore, these functions make it possible to conduct a complete study and analysis of the research on the field of study. the first publication on covid- was published by bogoch et al. [ ] on january in the travel medicine journal. when this article was published, there was news about a pneumonia outbreak in wuhan, china. consequently, the authors analyzed the potential for the international dissemination of this disease through air travel. subsequently, numerous research pieces followed the same idea, including studies on epidemic processes, as well as measures and strategies for prevention and control. in doing so, they analyzed the source of infection, mode of transmission, the population's susceptibility and other influencing factors. when comparing these articles to previous studies on other viruses, such as sars-cov or mers cov, they found that the most frequent transmission routes, like respiratory droplets and direct contact, were the same as those for covid- [ , ] . furthermore, it was found that, even though covid- does not seem as severe as sars-cov and mers-cov, the sudden increase in the number of cases and growing evidence of human transmission suggest that this virus is more infectious [ , ] . the countries with the largest number of publications are china, the us and italy. at the beginning of the pandemic, as expected, most of the research works published in international journals were written by chinese researchers. however, this has been a cause of major concern among frontline health workers and politicians due to the language barrier. currently, publications mainly cover the symptomatology and focus on finding an effective vaccine against covid- . this explains why research is being carried out in this field in countries with higher income and thus better infrastructures, which leads to an increasing number of publications. we suppose that countries with lower income focus on other research fields, such as transmission or epidemiology, although with fewer publications [ , ] . similarly, the upward trend in numbers of publications in countries such as the us or the uk has been linked to a combination of factors, such as the fact that they are english-speaking countries or the possible connections between different research groups within the scientific community [ , ] . other bibliometric studies on covid- and sars-cov- , such as those conducted by lou et al. [ ] and tran et al. [ ] , have found a significant increase in the number of publications over the last few months. comparing our bibliographical research to theirs, we found that june was the month in which the number of publications was significantly larger when compared to other months. as more publications become available in the upcoming months, we foresee that these numbers will grow significantly. the reason for this might be that our research scope was wider and comprised more types of documents and a longer period. furthermore, of the studies in june, the research by mcgonagle et al. [ ] should be highlighted, as they found that patients with severe pneumonia related to covid- might show signs of systemic hyperinflammation (macrophage activation syndrome) or cytokine storm (secondary hemophagocytic lymphohistiocytosis). in this sense, the clinical features of covid- are diverse, from the asymptomatic state to acute respiratory distress syndrome and multiple organ dysfunction. the study conducted by chen et al. [ ] showed that the progression of the disease was linked to increased inflammatory cytokines, namely, il , il , il , gcsf, ip , mcp , mip a and tnfα. additionally, the study conducted by casey et al. [ ] found that, in some patients, covid- was related to a hypercoagulable state and to an increased risk of venous thromboembolism. in addition, they found that, unlike patients with pulmonary embolism, positive covid- cases rarely showed hemoptysis. on the other hand, the study conducted by yang et al. [ ] suggested that the gastrointestinal tract and the liver could also be infected by the sars-cov- . this is due to the gastrointestinal epithelial cells and hepatic cells expressing ace enzymes (main receptor of sars-cov- ). these findings prove that, even when sars-cov- has been eliminated from the respiratory tract in some patients, the virus continues replicating through the gastrointestinal tract and could be excreted in the feces. the study by xu et al. [ ] analyzed the characteristics of pediatric patients with covid- and found that % of them recurrently tested positive in rectal swabs, even after the nasopharyngeal tests had come back negative. in turn, the study by ellul et al. [ ] showed a broad range of neurological manifestations in covid- patients. sixteen out of the patients in chinese hospitals and out of the patients in french hospitals showed signs of encephalopathy. moreover, guillain-barré syndrome was found in of the patients. on the other hand, anosmia and ageusia were frequent and could occur in the absence of other clinical features, while - % of hospitalized patients showed apoplexy. regarding the treatment, various antiviral medications have been tested, such as ribavirin and lopinavir/ritonavir, which are commonly used in the treatment and prevention of aids. thus, the study showed that a patient treated with lopinavir/ritonavir together with ribavirin had better results when compared to those to whom only ribavirin was administered [ ] . chloroquine has also been used as a form of treatment and has shown antiviral effects on the cells of primates infected by sars-cov. similarly, in the research by vincent et al. [ ] , a favorable inhibition of the virus spread was observed when the cells were treated with chloroquine before or after sars-cov infection. it should be noted that the use of remdesivir was authorized on july as the first conditionally marketable treatment. this facilitates early access to medication in emergency public health situations. this antiviral is a treatment against covid- for adults and teenagers aged or over who suffer from pneumonia and who require supplementary oxygen [ ] . on the other hand, there are currently possible vaccines from different laboratories, of which are in a preclinical phase and are in the clinical phase [ ] . research conducted by gao et al. [ ] was published recently, and it reports a pilot-scale production of picovacc, a possible vaccine that would inactivate the sars-cov- virus. this vaccine has created antibodies in mice, rats and non-human primates. they also neutralized strains representative of sars-cov- , which might suggest a greater possible neutralizing capacity against other strains. this leads us to believe that there is a strong probability of developing an effective vaccine for humans shortly. additionally, upon development/availability and approval of a vaccine or a new effective treatment against sars-cov- , we believe it necessary to carry out a new search and citation analysis. the future of covid- is still uncertain. this is due to the lack of knowledge of the clinical progression of this illness. in particular, many patients experience a recurrence of symptoms after periods of showing no signs, or they show symptoms such as febricula, asthenia or headaches for a longer period. moreover, some patients test positive again in the pcr test after testing negative. this might be due to the sensitivity of this test, especially when the viral charge is lower and/or when the viral rna is on the threshold of the detection rate of the test [ ] . on the other hand, whether covid- can also have after-effects is still to be determined. the research by zhang et al. [ ] found that . % of survivors showed signs of pulmonary fibrosis. we recognize that there is still further research to be conducted in order to confirm whether covid- can have after-effects or whether it varies depending on the severity of the condition. consequently, the number of studies on covid- is constantly on the increase since more research is needed in order to fight this illness. citation network studies are becoming more numerous, as this is the only analysis method that provides a global overview of the different research fields within a specific topic. furthermore, citnetexplorer software facilitates the analysis of all existing research on a specific topic through detailed studies. this could change how studies in different research areas are conducted. in conclusion, this research offers a specific and objective analysis of the main articles on covid- and sars-cov- . in addition, it was possible to visualize, analyze and explore the most cited articles and citation networks existing to date using the web of science database and the citation network explorer database. by doing so, we have obtained information regarding the epidemiology, clinical features, diagnosis and treatment of covid- . the importance of neurological and gastrointestinal alterations in a high percentage of positive cases of covid- is also worth mentioning. in addition to the great progress made towards effective treatment, the research conducted by gao et al. must be highlighted, as it shows the first results regarding the creation of the first vaccine for humans. therefore, covid- disease is a relevant field for researchers, with the number of publications continuously on the increase. consequently, the clinical progression of the disease will be understood in the upcoming months, and a new vaccine and an effective treatment will be discovered soon. in this way, this paper contributes to a better understanding of the information structure by identifying, in chronological order, the pieces of knowledge on different aspects of covid- that are interconnected. furthermore, this paper explores researchers' capacity to generate scientific knowledge on international health crises in order to advance our understanding of this pandemic and control its effects. novel coronavirus ( -ncov) situation reports animal coronavirus: lessons for sars enfermedad por coronavirus, covid- severe acute respiratory syndrome coronavirus isolate wuhan-hu- , complete genome clinical features of patients infected with novel coronavirus in world health organization. world health organization director-general's opening remarks at the media briefing on covid- - covid- ): epidemiology, pathogenesis, diagnosis, and therapeutics actualización epidemiológica: nuevo coronavirus (covid- ) coronavirus disease (covid- ) situation report- report of the who-china joint mission on coronavirus disease (covid- ). available online the sars epidemic in hong kong: what lessons have we learned? consistent detection of novel coronavirus in saliva stability of sars-cov and other coronaviruses in the environment and on common touch surfaces and the influence of climatic conditions: a review stability of sars-cov- in different environmental conditions chloroquine or hydroxychloroquine for prophylaxis of covid- hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro maternal and neonatal outcomes of pregnant women with covid- pneumonia: a case-control study practical guidance for the prevention of thrombosis and management of coagulopathy and disseminated intravascular coagulation of patients infected with covid- análisis de citación y de redes sociales para el estudio del uso de revistas en centros de investigación: an approach to the development of collections citnetexplorer: a new software tool for analyzing and visualizing citation networks clinical characteristics of coronavirus disease in china clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor pathological findings of covid- associated with acute respiratory distress syndrome clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study aerosol and surface stability of sars-cov- as compared with sars-cov- covid- : consider cytokine storm syndromes and immunosuppression cancer patients in sars-cov- infection: a nationwide analysis in china breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies a trial of lopinavir-ritonavir in adults hospitalized with severe covid- severe acute respiratory syndrome coronavirus (sars-cov- ) and coronavirus disease- (covid- ): the epidemic and the challenges presumed asymptomatic carrier transmission of covid- radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study detection of sars-cov- in different types of clinical specimens the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- are patients with hypertension and diabetes mellitus at increased risk for covid- infection? time course of lung changes at chest ct during recovery from coronavirus disease (covid- ) covid- and italy: what next? case-fatality rate and characteristics of patients dying in relation to covid- in italy the obvious in a nutshell: science, medicine, knowledge, and history. ber. wiss. public, environmental, and occupational health research activity in arab countries: bibliometric, citation, and collaboration analysis mapping the situation of research on coronavirus disease- (covid- ): a preliminary bibliometric analysis during the early stage of the outbreak bibliometric analysis on covid- : a comparison of research between english and chinese studies. front. public health coronavirus mapping in scientific publications: when science advances rapidly and collectively, is access to this knowledge open to society? mental health care for medical staff in china during the covid- outbreak neurologic manifestations of hospitalized patients with coronavirus disease fair allocation of scarce medical resources in the time of covid- possible vertical transmission of sars-cov- from an infected mother to her newborn can chinese medicine be used for prevention of corona virus disease (covid- )? a review of historical classics, research evidence and current prevention programs evidence for gastrointestinal infection of sars-cov- anticoagulant treatment is associated with decreased mortality in severe coronavirus disease patients with coagulopathy the incubation period of coronavirus disease (covid- ) from publicly reported confirmed cases: estimation and application pneumonia of unknown etiology in wuhan, china: potential for international spread via commercial air travel routes of transmission of influenza a h n , sars cov, and norovirus in air cabin: comparative analyses transmission of sars and mers coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination preliminary estimation of the basic reproduction number of novel coronavirus ( -ncov) in china, from to : a data-driven analysis in the early phase of the outbreak estimating the unreported number of novel coronavirus ( -ncov) cases in china in the first half of january : a data-driven modelling analysis of the early outbreak timely research papers about covid- in china countries are hoarding medical supplies-here's why it damages the global response to covid- research trends in science education from to : a content analysis of publications in selected journals a bibliometric analysis of the health field regarding social networks and young people coronavirus disease : a bibliometric analysis and review studies of novel coronavirus disease (covid- ) pandemic: a global analysis of literature the role of cytokines including interleukin- in covid- induced pneumonia and macrophage activation syndrome-like disease epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study covid- pneumonia with hemoptysis: acute segmental pulmonary emboli associated with novel coronavirus infection implications of gastrointestinal manifestations of covid- characteristics of pediatric sars-cov- infection and potential evidence for persistent fecal viral shedding neurological associations of covid- chloroquine is a potent inhibitor of sars coronavirus infection and spread european commission secures eu access to remdesivir for treatment of covid- rapid development of an inactivated vaccine candidate for sars-cov- epidemiologic features and clinical course of patients infected with sars-cov- in singapore long-term bone and lung consequences associated with hospital-acquired severe acute respiratory syndrome: a -year follow-up from a prospective cohort study key: cord- -wvx q authors: nan title: note from the editors: novel coronavirus ( -ncov) date: - - journal: euro surveill doi: . / - .es. . . . sha: doc_id: cord_uid: wvx q nan the situation has continued to evolve rapidly since then and just a few weeks later, as at january, laboratory-confirmed cases and deaths have been reported [ ] including some cases detected outside mainland china [ ] . meanwhile, on january , the novel coronavirus, currently named -ncov, was officially announced as the causative agent by chinese authorities [ ] . in order to support public health action, viral genome sequences were released by chinese researchers on january [ ] and days later, four further sequences were also made available on the global initiative on sharing all influenza data (gisaid) (https://www.gisaid.org/). while more cases are being reported on a daily basis and there is evidence for some human-to-human transmission in china, a number of important questions remain unanswered. for example, there is no certainty about the source of the outbreak, the transmissibility of the virus as well as the clinical picture and severity of the disease. in this issue of eurosurveillance, we are publishing two articles on different aspects of the newly emerged -ncov. one is a research article by corman et al. on the development of a diagnostic methodology based on rt-pcr of the e and rdrp genes, without the need for virus material; the assays were validated in five international laboratories [ ] . before this publication, a description of the assays had already been made publically available on a dedicated who webpage [ ] to support rapid development of laboratory testing capacities. the other is a rapid communication where researchers based in hong kong report on their attempt to estimate the severity among hospitalised cases of -ncov infection through modelling based on publically available information, mainly from wuhan health authorities [ ] . it also points out the need for more detailed information to make an informed evaluation of the situation as basis for public health decision-making. today, the who director-general tedros adhanom ghebreyesus, taking into consideration the deliberations of the members of the international health regulations (ihr) emergency committee on -ncov in their second meeting, decided not to declare a public health emergency of international concern. international health organisations such as the european centre for disease prevention and control (ecdc) and the who are monitoring the situation and provide regular updates. ecdc has set up a dedicated webpage on which updates and risk assessments with focus on europe are available: https://www.ecdc.europa.eu/en/ novel-coronavirus-china. undiagnosed pneumonia -china (hu): request for information european centre for disease prevention and control (ecdc) risk assessment: outbreak of acute respiratory syndrome associated with a novel coronavirus novel coronavirus genome. virological detection of novel coronavirus ( -ncov) by real-time rt-pcr laboratory testing for novel coronavirus ( -ncov) in suspected human cases. interim guidance real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in wuhan, china, as at this is an open-access article distributed under the terms of the creative commons attribution (cc by . ) licence. you may share and adapt the material, but must give appropriate credit to the source, provide a link to the licence and indicate if changes were made.any supplementary material referenced in the article can be found in the online version. key: cord- -e gok ot authors: huang, fangfang; li, ying; leung, elaine lai-han; liu, xiaohua; liu, kaifeng; wang, qu; lan, yongqi; li, xiaoling; yu, haibing; cu, liao; luo, hui; luo, lianxiang title: a review of therapeutic agents and chinese herbal medicines against sars-cov- (covid- ) date: - - journal: pharmacol res doi: . /j.phrs. . sha: doc_id: cord_uid: e gok ot the epidemic of pneumonia (covid- ) caused by novel coronavirus (sars-cov- ) infection has been listed as a public health emergency of international concern by the world health organization (who), and its harm degree is defined as a global “pandemic”. at present, the efforts of various countries focus on the rapid diagnosis and isolation of patients, as well as to find a treatment that can combat the most serious impact of the disease. the number of reported covid- virus infections is still increasing. unfortunately, no drugs or vaccines have been approved for the treatment of human coronaviruses, but there is an urgent need for in-depth research on emerging human infectious coronaviruses. clarification transmission routes and pathogenic mechanisms, and identification of potential drug treatment targets will promote the development of effective prevention and treatment measures. in the absence of confirmed effective treatments, due to public health emergencies, it is essential to study the possible effects of existing approved antivirals drugs or chinese herbal medicines for sars-cov- . this review summarizes the epidemiological characteristics, pathogenesis, virus structure and targeting strategies of covid- . meanwhile, this review also focus on the re-purposing of clinically approved drugs and chinese herbal medicines that may be used to treat covid- and provide new ideas for the discovery of small molecular compounds with potential therapeutic effects on novel covid- . broad-spectrum antiviral drug in the prevention and treatment of malaria [ ] . cq/hcq block viral from entering into cells by inhibiting glycosylation of host receptors, proteolytic processing, and endosomal acidification, as well as regulate immunity through attenuation of cytokine production, inhibition of autophagy and lysosomal activity in host cells [ , ] . cq can inhibit sars-cov- infection at a low-micro molar concentration and hcq is more potent than cq [ , ] . a multicenter clinical trial involving more than a dozen hospitals in china showed that cq can improve radiologic findings, enhance viral clearance and reduce disease progression in the treatment of patients with covid- , so china has included cq in the recommendations regarding the prevention and treatment of covid- [ , , ] . at the same time, another clinical trial showed that hcq can significantly shorten the clinical recovery time and promote the absorption of pneumonia among patients with covid- [ ] . notably, azithromycin reinforced the effect of cq/hcq in covid- patients, but the publishing journal's society subsequently declared that the trial did "not meet the society's expected standard" [ , ] . conversely, the higher cq dosage should not be recommended for critically ill patients with covid- because of its potential safety hazards, especially when taken concurrently with azithromycin and oseltamivir [ , ] . in summary, although cq/hcq have shown anti-sars-cov- efficacy both in vivo and in vitro trials as well as relatively well tolerated, some clinical trial designs and outcome data have not been submitted or published to peer review [ ] . it is not recommended in the use of cq/hcq for covid- outside of the hospital or a clinical trial due to lack of reliable efficacy data and potential toxic effects [ , ] . remdesivir (gs- ), a prodrug of gs- developed by the american pharmaceutical company gilead sciences, showed promise at the peak of the ebola virus outbreak due to its low ec and host polymerase selectivity against the ebola virus [ , ] . subsequently, research about it also showed significant anti-sars-cov and mers-cov activity [ , ] . as a nucleoside analog with exonuclease resistance, remdesivir is metabolized to active nucleoside triphosphates that effectively prevents the elongation of the rna chain by inhibiting rna polymerase, but will not be digested with a viral exonuclease (nsp ) with proofreading activity [ ] . compared with ribavirin, penciclovir, nitazoxanide, nafamostat, chloroquine and favipiravir (t- ), remdesivir j o u r n a l p r e -p r o o f has the best efficacy and the lowest toxic side effects on anti-sars-cov- in vero e cells [ ] . the united states first reported the clinical case of remdesivir in the treatment of sars-cov- associated pneumonia [ ] . currently, a number of clinical trials are ongoing, aiming to verify the safety and antiviral activity of remdesivir in the treatment of covid- . clinical findings of the team of professor cao bin of the china-japan friendship hospital suggested that the remdesivir is adequately tolerated but do not provide significant clinical or antiviral effects in severe patients with covid- [ ] . however, the results of the global clinical trial are believed that remdesivir can relieve symptoms and reduce mortality, especially for patients in intensive care who require mechanical ventilation [ ] . meanwhile, the clinical trials in chicago have suggested that early covid- patients benefit more due to the reduction of lung damage [ ] . in conclusion, remdesivir is still in the consideration of one of the most promising drugs for treatment covid- currently [ ] . lopinavir/ritonavir (lpv/r), also known as kaletra, is an oral combination agent for treating hiv approved by the fda, which has shown anti-coronavirus efficacy in studies of sars and mers [ ] [ ] [ ] [ ] . as a new protease inhibitor, lpv/r interrupts viral nucleic acid replication via inhibition of clpro [ ] . xushun guo's team at sun yat-sen university school of medicine derived a homology modeling to confirm that lpv/r significantly inhibited the function of cep_c to prevent the sars-cov- reproduction cycle [ ] . in addition, two groups in china and korea have reported lpv/r can improve the clinical symptoms of patients with covid- [ , ] . besides, lpv/r can achieve better antiviral effects when used with interferon or ninavir than alone [ ] . however, the latest evidence suggests that it may cause liver damage and prolong hospital stay in the covid- infected patients [ ] . furthermore, no benefit was observed with lpv/r treatment beyond standard care in hospitalized adult patients with severe covid- [ ] . therefore, whether lpv/r can become an important adjuvant drug in anti-sars-cov- therapy and improve the clinical outcome of patients remains to be determined. j o u r n a l p r e -p r o o f previously, we summarized small molecules currently used/planned to treat covid- , which may be an important short-term strategy for the treatment of covid- , but their efficacy and safety in covid- need to be further confirmed by clinical trials. drug development against covid- appears to be crucial in the context of a rapidly evolving epidemic, however, the conventional development of new drugs is time-consuming with safety concern. therefore, it seems unrealistic to synthesize new drugs and perform safety and toxicity tests over a short period of time. antiviral therapy with chinese herbal medicines have been recorded for a long time in chinese history, and previous studies have shown that chinese herbal medicines have great potential for preventing sars transmission [ ] . given the low toxicity and availability of chinese herbal medicines, screening active compounds targeting viral or host targets from chinese herbal medicines may be a potential strategy for treating covid- . in this review, we summarized potential chinese herbal medicines ( table ) that may treat covid- by targeting proteins such as spike protein, ace , clpro, plpro and rdrp. we also predicted the binding affinities between these compounds and covid- related targets by molecular docking, with a focus on six compounds: quercetin, andrographolide, glycyrrhizic acid, baicalin, patchouli alcohol, and luteolin. and the binding patterns of these six compounds to the key targets of sars-cov- are shown in figure . quercetin, a flavonoid compound, is widespread in fruit and vegetables. as a dietary source compound, quercetin exerts diverse biological activities including anti-inflammatory, anti-oxidant, anti-viral, anti-allergic, anti-cancer, mood-improving as well as vasoprotective [ ] [ ] [ ] . studies have found that quercetin exhibits antiviral properties against a variety of viruses, including influenza a virus (iav) [ ] , hepatitis c virus (hcv) [ ] , enterovirus (ev ) [ ] , and sars-cov, etc [ , ] . it has been confirmed that quercetin showed a good inhibitory effect on sars-cov clpro expressed in pichia pastoris, with an inhibition rate of % [ ] . in addition, enzyme inhibition assays in vitro also showed that quercetin had inhibitory activity against sars-cov clpro [ ] . since the clpro sequence of sars-cov- is highly similar to that of sars-cov [ , ] , we speculated that quercetin may also exhibit antiviral effects on sars-cov- . however, it has not been documented whether quercetin inhibits sars-cov- , so we docked quercetin to clpro as well as other key targets, and the docking results showed that quercetin bound well to each target, with a binding energy of - . kcal/mol to clpro. surprisingly, we found that quercetin bounds better to spike protein, ace , rdrp and plpro indicating good potential against sars-cov- . in addition, it has a wide range of sources with relatively low cost, so it is worth testing its efficacy against sars-cov- infection. andrographolide, the main active component isolated from the extract of the herb andrographis paniculata, has a wide range of biological activities including immunity regulation, anti-virus, anti-bacteria, anti-parasite, anti-tumor, and anti-hyperglycemia [ , ] . previous studies have shown that andrographolide has a broad spectrum of antiviral properties, which inhibits various virus infections including influenza a virus (iav) [ ] , human immunodeficiency virus (hiv) [ ] , chikungunya virus (chikv) [ ] , dengue virus (denv) [ , ] , and enterovirus d (ev-d ) [ ] . atchara paemanee et al. suggested that andrographolide may exert j o u r n a l p r e -p r o o f broad-spectrum antiviral activity by interfering a variety of cellular pathways (including autophagy, unfolded protein response (upr) pathway and oxidative stress, etc.). they further found the anti-dengue virus activity by acting on grp , a key regulator of unfolded protein response [ ] . in addition, andrographolide exerts antiviral activity against h n by inhibiting the activation of rlrs signaling pathways and thereby improving h n virus-induced cell death [ ] . to test the anti-viral activity against sars-cov- , we docked andrographolide with key targets, and the results also showed that andrographolide bound well to the key targets including spike protein, ace , clpro, rdrp and plpro, which indicated that andrographolide has potential efficacy against sars-cov- . moreover, enmozhi, s. k. et al. proved andrographolide as a potential inhibitor of sars-cov- clpro through in silico studies [ ] . overall, as a plant-derived compound, andrographolide is widely distributed with low cytotoxicity, but its potent antiviral activity against a variety of viruses calls for further investigation. glycyrrhizic acid is a plant product isolated from the traditional chinese medicine licorice rdrp and spike is - . kcal/mol, - . kcal/mol, - . kcal/mol, - . kcal/mol, respectively. it can be seen that glycyrrhizic acid also has strong binding affinity to other targets. given the antiviral effect of glycyrrhizic acid on sars-cov, and its potential interaction with ace , we speculated that glycyrrhizic acid may have potential to treat sars-cov- . moreover, glycyrrhizic acid plays an important role in inhibiting immune hyperactivation and cytokine storm factor development [ ] , therefore, we believe it is worth testing its efficacy against sars-cov- infection. baicalin and specific binding to proteases by itc map, native electrospray ionization mass spectrometry (esi-ms) and its chemical structure [ ] . at the same time, we used molecular docking to study the docking of baicalin to other key targets of sars-cov- , in which the binding energy of baicalin to the target plpro was - . kcal/mol. the results of docking showed that baicalin bounds strongly to other targets of sars-cov- (table ) . therefore, it can be reasonably speculated that baicalin is one of the potential drugs for covid- treatment. in view of the low toxic effect of baicalin, its effect against sars-cov- warrants further study. patchouli alcohol (pa), a tricyclic sesquiterpene compound extracted from the traditional chinese medicine patchouli, has a wide range of pharmacological and biological effects including antiviral, immunomodulatory, anti-inflammatory, antioxidative, and antitumor [ ] . pa has been found to have anti-influenza a (iav) effect in vitro, while h n virus is the most sensitive to pa [ ] . in addition, yunjia yu et al. found that intracellular pi k/akt and erk/mapk signaling pathways may be involved in the anti-iav effect of pa and pa significantly inhibits the in vitro proliferation of different iav, suggesting that pa may block iav infection by directly killing viral particles and interfering with some early stages after viral adsorption [ ] . another study showed that pa also has an effect against influenza virus (ifv) in vivo and enhances protection against ifv infection in mice by enhancing host immune responses and attenuating systemic and pulmonary inflammatory responses [ ] . to investigate the anti-sars-cov- activity of pa, we investigated the possibility of pa binding to sars-cov- related targets using molecular docking ( table ). the docking results showed that the binding effect of pa and rdrp was satisfactory, which provided some support for the antiviral effect of pa. the above study results showed that patchouli alcohol had antiviral effect and also modulated the levels of inflammatory cytokines, suggesting that pa may be a novel and effective antiviral and anti-inflammatory drug for covid- . luteolin, a natural flavonoid extracted from chinese herbal medicine, displays multiple biological activities, including anti-inflammatory, anti-cancer, antioxidant, antiviral, and heart protective [ ] . it was reported that luteolin can interfere with the virus in early virus life cycle, to a certain extent, block the absorption and internalization of influenza virus, thereby inhibited the replication of iav [ ] . the above experiments suggested that luteolin is a potential antiviral drug that inhibits viral replication by regulating host proteins. in addition, minhua peng et al. confirmed luteolin inhibited the dengue virus ns b/ns protease activity by analyzing the nucleotide sequence of the luteolin-resistant escape mutant [ ] . it also has been documented luteolin has an anti-epstein-barr virus (ebv) effect, and in immunoblot analysis, μg/ml of luteolin showed a significant inhibitory effect on ebv lytic cycle [ ] . another study showed that luteolin extracted from torreya nucifera is an effective sars-cov clpro inhibitor [ ] . to interrogate the anti-sars-cov- effect of luteolin, we performed molecular docking of luteolin to j o u r n a l p r e -p r o o f key targets of sars-cov- . the docking results showed that luteolin bound well to the key target of sars-cov- . among them, the binding energy of luteolin to ace was - . kcal/mol ( table ). taken together, luteolin has a good antiviral effect, which suggests that luteolin may be a potential drug for the treatment of covid- . the results of molecular docking are shown in table . from the target point of view, the binding effect of ace and plpro with these natural compounds was more prominent; while from the natural compounds, the lowest binding energy was - . kcal/mol for cryptotanshinone and plpro, while the highest was - . kcal/mol for lignan and clpro, that is to say, the range of binding energy was from - . kcal/mol to - . kcal/mol, which indicated that the natural compounds had a good binding effect with the target. our aim of docking was to select natural compounds with high potential efficacy against sars-cov- , but it should be pointed out that these compounds cannot be considered to treat covid- only by such a screen which is aimed to provide priority to focus. furthermore, the d structure of the targets we used were based on the reported gene sequences. if the virus mutates during transmission, new screening is recommended. in conclusion, our review summarizes more than a dozen of natural compounds classified as antiviral/pneumonic protectors, which may directly inhibit sars-cov- . however, their actual effect in the treatment of covid- needs to be verified by further studies. covid- poses a great threat to global health and safety. it is an urgent task for us to control the spread of the epidemic and reduce the mortality rate as soon as possible. but so far, the specific mechanism of the virus is still unclear, and no specific drug has been developed for the virus. at treatment. this review also has limitations. the large and rapidly published literature on covid- 's treatment means that the findings and recommendations are constantly evolving as new evidence arises. it is not uncommon that drugs that proved effective at an early stage based on small-scale clinical trials later turned out to be ineffective. we look forward to the cooperation of all scientists around the world to develop effective drugs to treat current and future potential sars-cov- infections to control the further spread of the epidemic. all authors have read and approved the final submission. there is no conflict of interest associated with this article. outbreak of pneumonia of unknown etiology in wuhan, china: the mystery and the miracle a novel coronavirus from patients with pneumonia in china a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster who, who director-general's remarks at the media briefing on -ncov on who, statement on the second meeting of the international health regulations ( ) emergency committee regarding the outbreak of novel coronavirus initial public health response and interim clinical guidance for the viral architecture of sars-cov- with post-fusion spike revealed by cryo-em a pneumonia outbreak associated with a new coronavirus of probable bat origin genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor structure, function, and antigenicity of the sars-cov- spike glycoprotein structural and functional basis of sars-cov- entry by using human sars-cov- invades host cells via a novel route: cd -spike protein sars-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum coronaviruses: an overview of their replication and pathogenesis sars-cov- infects t lymphocytes through its spike protein-mediated membrane fusion cytokine release syndrome breadth of concomitant immune responses prior to patient recovery: a case report of non-severe covid- neutrophil extracellular traps (nets) as markers of disease severity in covid- covid- : immunopathology and its implications for therapy covid- : risk for cytokine targeting in chronic inflammatory diseases? coronaviruses -drug discovery and therapeutic options learning from the past: possible urgent prevention and treatment options for severe acute respiratory infections caused by -ncov structural basis of influenza virus fusion inhibition by the antiviral drug arbidol the androgen-regulated protease tmprss activates a proteolytic cascade involving components of the tumor microenvironment and promotes prostate cancer metastasis discovery of baicalin and baicalein as novel, natural product inhibitors of sars-cov- cl protease in vitro thiopurine analogue inhibitors of severe acute respiratory syndrome-coronavirus papain-like protease, a deubiquitinating and deisgylating enzyme thiopurine analogs and mycophenolic acid synergistically inhibit the papain-like protease of middle east respiratory syndrome coronavirus the palm subdomain-based active site is internally permuted in viral rna-dependent rna polymerases of an ancient lineage remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro pharmacologic treatments for coronavirus disease (covid- ): a review effects of chloroquine on viral infections: an old drug against today's diseases, the lancet infectious diseases targeting endosomal acidification by chloroquine analogs as a promising strategy for the treatment of emerging viral diseases covid- : a recommendation to examine the effect of hydroxychloroquine in preventing infection and progression breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) national health commission of the people's republic of china the multicenter collaboration group of department of science and technology of guangdong province and health commission of guangdong province for chloroquine in the treatment of novel coronavirus pneumonia., expert consensus on chloroquine phosphate for the treatment of novel coronavirus pneumonia efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical trial hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus (sars-cov- ) infection: a randomized clinical trial the qt interval in patients with covid- treated with hydroxychloroquine and azithromycin chloroquine and hydroxychloroquine as available weapons to fight covid- fda cautions against use of hydroxychloroquine or chloroquine for covid- outside of the hospital setting or a clinical trial due to risk of heart rhythm problems caution needed on the use of chloroquine and hydroxychloroquine for coronavirus disease controlled trial of ebola virus disease therapeutics coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov host factors in coronavirus replication first case of novel coronavirus in the united states remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial compassionate use of remdesivir for patients with severe covid- clinical benefit of remdesivir in rhesus macaques infected with sars-cov- remdesivir as a possible therapeutic option for the covid- screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture efficacy and biological safety of lopinavir/ritonavir based anti-retroviral therapy in hiv- -infected patients: a meta-analysis of randomized controlled trials role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings treatment of middle east respiratory syndrome with a combination of lopinavir-ritonavir and interferon-beta b (miracle trial): study protocol for a randomized controlled trial lopinavir-ritonavir: a new protease inhibitor molecular modeling evaluation of the binding effect of ritonavir, lopinavir and darunavir to severe acute respiratory syndrome coronavirus proteases patients of covid- may benefit from sustained lopinavir-combined regimen and the increase of eosinophil may predict the outcome of covid- progression case of the index patient who caused tertiary transmission of covid- infection in korea: the application of lopinavir/ritonavir for the treatment of covid- infected pneumonia monitored by quantitative rt-pcr arbidol combined with lpv/r versus lpv/r alone against corona virus disease : a retrospective cohort study clinical features of covid- -related liver damage a trial of lopinavir-ritonavir in adults hospitalized with severe covid- patients with novel coronavirus pneumonia a randomised, open, controlled trial for darunavir/cobicistat or lopinavir/ritonavir combined with thymosin a in the treatment of novel coronavirus pneumonia (covid- ) favipiravir (t- ), a broad spectrum inhibitor of viral rna polymerase favipiravir versus arbidol for covid- : a randomized clinical trial an orally bioavailable broad-spectrum antiviral inhibits sars-cov- in human airway epithelial cell cultures and multiple coronaviruses in mice baricitinib as potential treatment for -ncov acute respiratory disease successful recovery of covid- pneumonia in a renal transplant recipient with long-term immunosuppression effectiveness of glucocorticoid therapy in patients with severe novel coronavirus pneumonia anticoagulant treatment is associated with decreased mortality in severe coronavirus disease patients with coagulopathy the coronavirus (sars-cov- ) surface protein (spike) s receptor binding domain undergoes conformational change upon heparin binding zn( +) inhibits coronavirus and arterivirus rna polymerase activity in vitro and zinc ionophores block the j o u r n a l p r e -p r o o f replication of these viruses in cell culture clinical characteristics of coronavirus disease in china drug treatment options for the -new coronavirus ( -ncov) clinical study of arbidol hydrochloride tablets in the treatment of novel coronavirus pneumonia doravirine: a new non-nucleoside reverse transcriptase inhibitor for the treatment of hiv infection antivirals targeting the neuraminidase hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china a real-world study for lopinavir/ritonavir (lpv/r) and emtritabine (ftc) / tenofovir alafenamide fumarate tablets (taf) regimen in the treatment of novel coronavirus pneumonia (covid- ) tenofovir disoproxil fumarate: a nucleotide reverse transcriptase inhibitor for the treatment of hiv infection open-label, controlled trial for evaluating of the efficacy and safety of baloxavir marboxil, favipiravir, and lopinavir-ritonavir in the treatment of novel coronavirus pneumonia (covid- ) patients baloxavir marboxil for uncomplicated influenza in adults and adolescents an open, controlled clinical trial for evaluation of ganovo combined with ritonavir and integrated traditional chinese and western medicine in the treatment of novel coronavirus infection (covid- ) analysis of hepatitis c virus decline during treatment with the protease inhibitor danoprevir using a multiscale model multicenter study for the treatment of dipyridamole with novel coronavirus pneumonia therapeutic effects of dipyridamole on covid- patients with coagulation dysfunction covid- losartan for patients with covid- not requiring hospitalization angiotensin receptor blockers as tentative sars-cov- therapeutics safety of hydroxychloroquine, alone and in combination with azithromycin, in light of rapid wide-spread use for covid- : a multinational, network cohort and self-controlled case series study comparative effectiveness and safety of ribavirin plus interferon-alpha, lopinavir/ritonavir plus interferon-alpha and ribavirin plus lopinavir/ritonavir plus interferon-alphain in patients with mild to moderate novel coronavirus pneumonia ribavirin and interferon therapy for critically ill patients with middle east respiratory syndrome: a multicenter observational study the efficacy and safety of triazavirin for novel coronary pneumonia (covid- ): a multicenter, randomized, double blinded clinical study of novel nlrp inflammasome inhibitor (tranilast) in the treatment of novel coronavirus pneumonia clinical study on the treatment of patients with novel coronavirus pneumonia (covid- ) by ebastine the use of an herbal formula by hospital care workers during the severe acute respiratory syndrome epidemic in hong kong to prevent severe acute respiratory syndrome transmission, relieve influenza-related symptoms, and improve quality of life: a prospective cohort study quercetin: a flavonol with multifaceted therapeutic applications? fitoterapia quercetin as an antiviral agent inhibits influenza a virus (iav) entry, viruses effect of quercetin on hepatitis c virus life cycle: from viral to host targets inhibition of enterovirus replication and viral c protease by quercetin flavonoid-mediated inhibition of sars coronavirus c-like protease expressed in pichia pastoris biflavonoids from torreya nucifera displaying sars-cov cl(pro) inhibition multi-targeting andrographolide and its natural analogs as potential therapeutic agents broad-spectrum antiviral properties of andrographolide andrographolide inhibits influenza a virus-induced inflammation in a murine model through nf-kappab and jak-stat signaling pathway, microbes infect anti-hiv activity of semisynthetic derivatives of andrographolide and computational study of hiv- gp protein binding activity of andrographolide against a proteomic analysis of the anti-dengue virus activity of andrographolide replication by inhibiting the acidification of virus-containing endocytic vesicles, front microbiol andrographolide as an anti-h n drug and the mechanism related to retinoic acid-inducible gene-i-like receptors signaling pathway andrographolide as a potential inhibitor of sars-cov- main protease: an in silico approach volatiles profiling in medicinal licorice roots using steam distillation and solid-phase microextraction (spme) coupled to chemometrics liquorice may tackle sars glycyrrhizin, an active component of liquorice roots, and replication of sars-associated coronavirus antiviral activity of glycyrrhizic acid derivatives against sars-coronavirus glycyrrhizin, an active component of licorice roots, reduces morbidity and mortality of mice infected with lethal doses of influenza virus potential natural compounds for preventing sars-cov- ( -ncov) analysis on the application of traditional chinese medicine in the treatment of covid- by suppressing cytokine storm one-compound-multi-target: combination prospect of natural compounds with thrombolytic therapy in acute ischemic stroke baicalin ameliorates oxidative apoptosis by restoring mitochondrial dynamics in the spleen of chickens via the opposite modulation of nf-kappab and nrf /ho- signaling pathway during mycoplasma gallisepticum infection in vitro susceptibility of clinical isolates of sars coronavirus to selected antiviral compounds inhibitory activities of baicalin against renin and angiotensin-converting enzyme availability, pharmaceutics, security, pharmacokinetics, and pharmacological activities of patchouli alcohol, evid based complement alternat med antiviral potential of erk/mapk and pi k/akt/mtor signaling modulation for middle east respiratory syndrome coronavirus infection as identified by temporal kinome analysis inhibition effects of patchouli alcohol against influenza a virus through targeting cellular pi k/akt and erk/mapk signaling pathways oral administration of patchouli alcohol isolated from pogostemonis herba augments protection against influenza viral infection in mice novel extraction techniques and pharmaceutical activities of luteolin and its derivatives luteolin decreases the yield of influenza a virus in vitro by interfering with the coat protein i complex expression luteolin escape mutants of dengue virus map to prm and ns b and reveal viral plasticity during maturation bioactive constituents of lindernia crustacea and its anti-ebv effect via rta expression inhibition in the viral lytic cycle flavonoid baicalin hiv- infection at the level of viral entry anti-sars coronavirus c-like protease effects of isatis indigotica root and plant-derived phenolic compounds discovery of potential multi-target-directed ligands by targeting host-specific sars-cov- structurally conserved main protease($) emodin blocks the sars coronavirus spike protein and angiotensin-converting enzyme interaction emodin inhibits current through sars-associated coronavirus a protein effective inhibition of mers-cov infection by resveratrol kaempferol derivatives as antiviral drugs against the a channel protein of coronavirus specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus tanshinones as selective and slow-binding inhibitors for sars-cov cysteine proteases structure-based drug design, virtual screening and high-throughput screening rapidly identify antiviral leads targeting covid- clinical efficacy of matrine and sodium chloride injection in treatment of cases of covid- decoction in the treatment of novel coronavirus pneumonia lianhuaqingwen exerts anti-viral and anti-inflammatory activity against novel coronavirus (sars-cov- ) traditional chinese medicine for treatment of coronavirus disease : a review covid- : an update on the epidemiological, clinical, preventive and therapeutic evidence and guidelines of integrative chinese-western medicine for the management of novel coronavirus disease multidrug treatment with nelfinavir and cepharanthine against covid- key: cord- -ujq mxk authors: chen, bin; tian, er-kang; he, bin; tian, lejin; han, ruiying; wang, shuangwen; xiang, qianrong; zhang, shu; el arnaout, toufic; cheng, wei title: overview of lethal human coronaviruses date: - - journal: signal transduct target ther doi: . /s - - - sha: doc_id: cord_uid: ujq mxk coronavirus infections of multiple origins have spread to date worldwide, causing severe respiratory diseases. seven coronaviruses that infect humans have been identified: hcov- e, hcov-oc , hcov-nl , hcov-hku , sars-cov, mers-cov, and sars-cov- . among them, sars-cov and mers-cov caused outbreaks in and , respectively. sars-cov- (covid- ) is the most recently discovered. it has created a severe worldwide outbreak beginning in late , leading to date to over million cases globally. viruses are genetically simple, yet highly diverse. however, the recent outbreaks of sars-cov and mers-cov, and the ongoing outbreak of sars-cov- , indicate that there remains a long way to go to identify and develop specific therapeutic treatments. only after gaining a better understanding of their pathogenic mechanisms can we minimize viral pandemics. this paper mainly focuses on sars-cov, mers-cov, and sars-cov- . here, recent studies are summarized and reviewed, with a focus on virus–host interactions, vaccine-based and drug-targeted therapies, and the development of new approaches for clinical diagnosis and treatment. coronaviruses are crown-like particles with spikes protruding from their surface. they are enveloped viruses with single-stranded, positive-sense rna (+ssrna) genomes of approximately - kb, which is currently the largest known genome size for an rna virus. rna viruses are divided into five branches. , certain groups in a particular branch might be related to and/or share features with viruses classified in another branch. in branch are the leviviruses and eukaryotic relatives (e.g., mitoviruses, narnaviruses, ourmiaviruses); branch represents several +rna virus families (of eukaryotes) (e.g., orders picornavirales and nidovirales, and the families caliciviridae, potyviridae, astroviridae, and solemoviridae) and several dsrna viruses (e.g., partitiviruses and picobirnaviruses); in branch are certain +rna viruses such as the supergroups of alphaviruses and offlaviviruses, the nodaviruses, tombusviruses, and many small and novel groups; in branch are dsrna viruses such as the cystoviruses, reoviruses, and totiviruses; branch consists of −rna viruses. coronaviruses were classified as most likely related to branch , and belong to the order nidovirales, and the family coronaviridae. in , the international committee on taxonomy of viruses divided the coronaviridae into the orthocoronavirinae and letovirinae subfamilies. according to their host targets, coronaviruses can also be divided into animal and human coronaviruses. many diseases in domestic animals are related to animal coronaviruses, such as canine respiratory coronavirus, which causes respiratory disease in dogs. the highly pathogenic human coronaviruses belong to the subfamily coronavirinae from the family coronaviridae. the viruses in this subfamily group into four genera: alphacoronavirus, betacoronavirus, gammacoronavirus, and deltacoronavirus. the classic subgroup clusters are labeled a- b for the alphacoronaviruses and a- d for the betacoronaviruses. to date, including the recently discovered sars-cov- , there are seven coronaviruses that infect humans. human coronavirus (hcov)- e, hcov-nl , hcov-oc , or hcov-hku cause only the common cold, whereas the severe acute respiratory syndrome coronavirus (sars-cov) or the middle east respiratory syndrome coronavirus (mers-cov) cause relatively high mortality and emerged in and , respectively. notably, sars-cov- is currently causing a worldwide epidemic. sars-cov and mers-cov belong to subgroups b and c of the betacoronaviruses, respectively, , whereas sars-cov- is a new member of the betacoronaviruses distinct from sars-cov and mers-cov. figure shows the phylogenetic tree of rna viruses. the estimated mutation rates of coronaviruses (covs) are moderate to high compared to those of other ssrna viruses. there are two gene loci that are sites of variation in sars-cov. one of these sites is located in the spike (s) protein gene. the second major site of variation is the accessory gene open reading frame orf . in mers-cov, the major sites of variation are located in the s, orf b, and orf genes. the major differences in the sequence of the s gene of sars-cov- are three short insertions in the n-terminal domain and changes in four out of five of the key residues in the receptor-binding motif. the organizations of the genome and gene expression are similar for all coronaviruses. orf a/b, located at the ′ end, encodes nonstructural proteins (nsps) (named nsp -nsp ); other orfs at the ′ end encode structural proteins, including the s, envelope (e), membrane (m), and nucleocapsid (n) proteins. the mutations in sars-cov- have become a hot research topic. the surface proteins of sars-cov and batcov-ratg , the nearest potential bat precursors of sars-cov- , have and % sequence identity, respectively, to that of sars-cov- . compared to that of sars-cov, the antigenic surface of sars-cov- is highly divergent compared to other covs. since its outbreak began at the end of , sars-cov- has acquired mutations throughout its genome, and there are already hundreds of virus strains distributed worldwide. according to gisaid.org, as of may , there were , full genome sequences available, and the s clade of the full genome tree contains the largest group of viruses, indicating that mutations in orf -l s are most frequent. the temporal resolution assumes an average nucleotide substitution rate of × − substitutions per site per year. based on these mutations, researchers found that sars-cov- can be divided into two subtypes. they reported that the snps at locations and , show strong linkage; the "ct" haplotype was defined as the "l" type because t , encodes leucine, while the "tc" haplotype was defined as the "s" type because c , encodes serine, which is in accordance with another study that divided sars-cov- into two types. the "l" type seems to be more prevalent and aggressive, but the "s" type may be ancestral, as sites and , were identical to the orthologous sites in the most closely related viruses. patients may be infected by either or both types. from the gisaid update, compared with ratg , there are differences in the receptor-binding interface, which may have favored host switching. data related to the sequence and mutations of sars-cov- are also available and continuously updated online through the china national center for bioinformation (cncb) (https://bigd.big.ac.cn/ncov). the history of sars-cov, mers-cov, and sars-cov- the first case of sars was discovered in foshan, china, in november . infections occurred through either direct or indirect contact with patients. by july , sars-cov had spread to over countries, causing reported cases and deaths. after that, no additional infections were detected, and the sars pandemic was declared over. sars-cov was first isolated from himalayan palm civets (hpcs) from a live-animal market in guangdong, china. , other animals, such as raccoon dogs (nyctereutes procyonoides), along with human workers from the same market, also showed evidence of viral infection. multiple studies have demonstrated that the reservoirs of several coronaviruses, including sars-cov-like and mers-cov-like viruses, were bats. , although palm civets might have been intermediary hosts of sars-cov, researchers often concluded there was no evidence that these animals were the ultimate sources of sars-cov, and the viruses cannot circulate directly in palm civets in the wild. in , guan and zheng's team investigated a live-animal retail market in guangdong, focusing on recently captured wild animals and human consumption. the animals sampled included seven wild and one domestic animal species. they collected nasal fig. phylogenetic tree of coronaviruses based on full-length genome sequences. all complete genome sequences of coronavirus were downloaded from the ncbi reference sequence database, refseq. the tree was constructed using maximum likelihood estimation (mle) by mega x, with clustal omega as the multiple sequence alignment method, and bootstrap replicates. only bootstraps ≥ % values are shown. the seven known human-infecting coronaviruses are indicated with a red star and fecal samples with swabs and then used reverse transcriptionpolymerase chain reaction (rt-pcr) to test for viral nucleic acid from the n gene of the human sars-cov. the rt-pcr assay results showed that samples from four of six hpcs were positive; the other seven species (beaver, chinese ferret-badger, chinese hare, chinese muntjac, domestic cat, hog-badger, and raccoon dog) sampled were negative. mers-cov was first found in in a lung sample from a year-old patient who died of respiratory failure in jeddah, saudi arabia. on september , a similar type of virus named human coronavirus was isolated from a patient with severe respiratory infection. cases have also been reported in other countries. mers has a % mortality rate, and since it emerged in the human population in june , it has caused substantial morbidity and mortality. , from until january , , the total number of laboratory-confirmed mers-cov infection cases reported globally to the world health organization (who) was , with associated deaths, covering countries (www. who.int/csr/don/ -january- -mers-united-arab-emirates/en). cases of mers from other countries were linked to travel to the middle east. , mers-cov was identified from the saliva of a patient with acute pneumonia and renal failure in jeddah (ksa). mers-cov can be detected in respiratory tract secretions, as well as in feces, serum, and urine. [ ] [ ] [ ] in addition, it has been isolated from environmental objects such as bedsheets, bedrails, intravenous fluid hangers, and x-ray devices. in the case of known camel infection, mers-cov was transmitted from a camel to a human, which was confirmed by rna sequencing. at the end of december , the first clusters of patients with pneumonia caused by sars-cov- were reported in wuhan, china. the basic reproduction number of sars-cov- is approximately . , indicating that each patient would on average spread the infection to . people. human-to-human transmission of sars-cov- occurred rapidly, and the atypical symptoms during the early stage may be a further disadvantage. moreover, human infection might have begun months prior to the official announcement of the outbreak. to prevent further spread, stricter screening and surveillance are needed at travel hubs. early detection, diagnosis, and treatment are also effective measures to contain the epidemic. nonetheless, the fatality rate of sars-cov- is lower than that of sars, with an estimated mortality risk of %. sars-cov- was first isolated from clinical specimens using human airway epithelial cells and the vero e and huh- cell lines. approaches to assess virions include isolation from lower respiratory tract specimens and artificially infected specific pathogen-free human airway epithelial cells. fluorescence quantitative pcr with primers designed according to specific sequences and serological testing aimed at igg and igm can be used to detect the virus. sars-cov, mers-cov, and sars-cov- pose major challenges to global health, causing infections in large parts of the world. sars-cov was found in countries and mers-cov in countries, while sars-cov- was found in countries by th may, . details on the pandemics caused by sars-cov- are shown in box , highlighting the status of the coronavirus-caused diseases worldwide. epidemiological analysis and symptoms of sars, mers, and coronavirus disease (covid- ) the clinical manifestations of sars include hypoxia, cyanosis, high fever (above °c), accelerated breathing or respiratory distress syndrome, and shortness of breath. x-rays show changes to the lungs to varying degrees. the who case definition ( ) includes the following: ( ) fever higher than °c or history of such in the past days, ( ) radiological evidence of new infiltrates consistent with pneumonia, ( ) chills, cough, malaise, myalgia, or known history of exposure, and ( ) positive test for sars-cov by one or more assays. similar to sars-cov infection, mers-cov infection manifests as a severe lower respiratory tract infection with extrapulmonary involvement and high fatality rates. symptomatic patients may present fever, chills, stiffness, myalgia, discomfort, cough, shortness of breath, and gastrointestinal symptoms of diarrhea, vomiting, and abdominal pain. pneumonia is common, and severe infection with acute respiratory failure, renal failure, and shock is particularly frequent among older patients. previous studies have estimated that approximately . - % of mers-cov infections may be asymptomatic. , it must be noted that immunocompromised people are at high risk of mers-cov infection. for covid- , fever, cough, myalgia, and fatigue are most commonly observed at illness onset; less commonly observed are sputum production, hemoptysis, and headache, among others. , similar to sars and mers, some patients develop acute respiratory distress syndrome (ards). around % of infected patients only develop mild symptoms, with mild pneumonia or no pneumonia. and % are severe and critical status, respectively. patients requiring icu care tend to be much older and are more likely to have underlying comorbidities, such as hypertension and diabetes. additionally, symptoms such as pharyngeal pain and anorexia are reported at higher rates among those admitted to the icu than among non-icu patients. histopathologically, symptoms such as diffuse alveolar damage (dad), loss of cilia, squamous metaplasia, denudation of bronchial epithelia, and giant-cell infiltrate often occur in the lungs of patients with sars. the number of macrophages increases prominently in the alveoli and the interstitium. according to the morphological changes, observed, most authors have subclassified lung lesions in sars into two or three consecutive phases: an acute exudative inflammatory phase, a fibrous proliferative phase, and a final fibrotic stage, although there is considerable overlap in histological findings among these phases. the main features of the first phase include extensive hyaline membrane formation, edema, alveolar hemorrhage, and fibrin exudation in alveolar spaces. the second phase includes widening of septae, pneumocyte hyperplasia, and organizing fibromyxoid and cellular exudates. , the third phase includes septal and alveolar fibrosis. several autopsies of sars patients have demonstrated secondary bronchopneumonia, and the pathogens identified mainly consist of staphylococcus aureus, mucor sp., aspergillus sp., pseudomonas aeruginosa, and cytomegalovirus. sars-cov also greatly affects the immune system. for example, hemorrhagic necrosis is usually obvious in the lymph nodes and spleen. as described above, sars-cov attacks immune cells, especially t cells and macrophages, with approximately % of lymphocytes and % of monocytes in the circulation becoming infected. , under the influence of the virus, the patient's germinal centers disappear, and both t and b lymphocytes are depleted. in the spleen, the white pulp shrinks, hemorrhage and necrosis occur in the red pulp, and the periarterial lymphatic sheaths decrease. , , with regard to the immune system, sars-cov can infect the lymphoid component of the intestine. for this reason, the patient's submucosal lymphoid tissue atrophies. sars-cov can also infect epithelial cells in the mucosa of the small and large intestines, and the digestive tract may undergo mild diffuse inflammation and atrophy of the submucosal lymphoid tissues. according to previous reports, symptoms in the liver include extensive hepatocyte mitosis, balloon degeneration of hepatocytes, mild to moderate lymphocytic infiltrates, fatty degeneration, and central lobular necrosis. additionally, apoptosis of liver cells has been confirmed in some cases. on autopsy, the kidneys of some sars patients showed focal bleeding and acute tubular necrosis of different degrees. one of the major complications of ards is acute kidney injury. , , in many other cases, the features are nonspecific, including benign hypertensive nephrosclerosis and autolysis. moreover, researchers have detected viral particles and genome sequences in the cytoplasm of neurons of the hypothalamus and cortex in the brain, which suggests that the virus can cross the blood-brain barrier and cause degeneration and necrosis of neurons, edema, extensive glial cell hyperplasia, and cellular infiltration. pneumocytes and epithelial syncytial cells are important targets of mers-cov. the lung tissue presents dad. severe peripheral vascular diseases, patchy cardiac fibrosis, and hepatic steatosis have also been found in other organs. another symptom is bronchial submucosal gland necrosis. renal biopsy may show acute tubulointerstitial nephritis and acute tubulosclerosis with protein casts. in covid- patients, a bilateral (sometimes unilateral) distribution of patchy shadows and ground glass opacity in the lungs is typical, based on ct scans. plasma concentrations of interleukins (ils) , , and , granulocyte-colony stimulating factor, interferon (ifn)-γ-inducible protein , monocyte chemoattractant protein , macrophage inflammatory protein α, and tumor necrosis factor α are increased in most dying patients. , in addition, neutrophilia related to cytokine storms induced by virus invasion, coagulation activation related to a sustained inflammatory response, and acute kidney injury related to the effects of the virus, hypoxia, and shock, may be involved in mortality. those who survive intensive care may experience long-term lung damage and fibrosis due to aberrant and excessive immune responses. moreover, researchers found that as sars-cov- spread and changed across generations, clinical symptoms started to differentiate those infected previously from those infected more recently. the initial symptoms are becoming more insidious, which indicates that the virus may gradually evolve into an influenza-like virus and lie dormant for longer in asymptomatic patients. in conclusion, in terms of outbreak times, sars-cov was the earliest, followed by mers-cov, then sars-cov- . to date, mers-cov has the longest duration of infection, and sars-cov- appears to be the most infectious. sars-cov, mers-cov, and sars-cov- infections have similar symptoms, including fever, cough, myalgia, and shortness of breath, among others. the common transmission methods and symptoms of the three coronavirus infection are shown in fig. . structural studies of sars-cov, mers-cov, and sars-cov- sars-cov is a coronavirus with a diameter of approximately nm. coronaviruses are the largest +ssrna viruses and contain at least orfs, protein combines with viral rna to form a nucleocapsid, which is involved in the replication of sars-cov and is the most abundant protein in virus-infected cells. , the m protein is a membrane glycoprotein that is involved in budding and envelope formation. the s protein of sars-cov is a type i transmembrane (tm) glycoprotein that is responsible for viral binding, fusion and entry into cells, as well as antibody induction. , the s protein contains a signal peptide (sp: amino acids - ) and three domains called the extracellular domain (amino acids - ), the tm domain (amino acids - ) and the intracellular region (amino acids - ). the extracellular domain consists of two subunits: s and s . the fragment located in the middle region of the s subunit (amino acids - ) is the angiotensin-converting enzyme (ace ) receptor-binding region. the s subunit comprises a fusion peptide (fp) and two x -valent element repeats (hr and hr ) that are responsible for fusion between the virus and the target cell membrane. thus, the s protein may be key to develop a vaccine to generate antibodies and block virus binding and fusion in the coronaviruses (fig. ) . the ′ end of the sars virus genome encodes structural proteins and helper proteins, of which orf a, orf , orf a, and orf b have been proven to be viral structural proteins involved in the formation of viral particles. the ′ end of the genome encodes nonstructural proteins (nsps), which are important for virus assembly, and may enable the design of small molecule drugs and/or vaccines. mers-cov belongs to lineage c of the genus betacoronavirus (βcov) in the family coronaviridae, order nidovirales, and it is the first lineage c cov and the sixth cov known to cause human infection. mers-cov is an enveloped +ssrna virus similar to other covs, but the amino acid sequence homology between mers-cov and other known covs is less than %. orf a and orf b located in the first two-thirds of the mers-cov genome are involved in virulence and encode nsps (nsp - ). the remaining third of the genome encodes four structural proteins, the s, e, m, and n proteins, as well as five accessory proteins (orf , orf a, orf b, orf , and orf b). [ ] [ ] [ ] the flanking regions of the genome contain the ′ and ′ untranslated regions (utrs). most mers-cov proteins are found in the cytoplasm. to date, the ns b protein and the orf a-encoded protein are the only known coronavirus proteins to be detected in the nucleus. nsp suppresses host gene expression in infected cells, and its rna cleavage-inducing function promotes virus assembly/budding. nsp is a viral ′-o-methyltransferase ( ′-o-mtase) that encodes critical functions in immune modulation and infection, suggesting that nsp is a conserved universal candidate for rapid design of a live attenuated vaccine. orf a's protein can mask viral dsrna to play a role in immune evasion, including type ifn and protein kinase r-mediated antiviral stress responses. mers-cov nsp is a full-length coronavirus helicase that contains multiple domains, including an n-terminal cys/his rich domain with three zinc atoms, a beta-barrel domain and a c-terminal superfamily (sf) helicase (sf ) core with two reca-like subdomains. this protein might interfere with the nonsensemediated mrna decay pathway to avoid degradation of viral rna. the mers-cov s protein can recognize dipeptidyl peptidase (dpp ) on the cell surface, promoting the fusion of the viral envelope and the cell membrane. the mers-cov s protein, a -amino acid type i tm glycoprotein located on the viral envelope surface, is composed of s and s subunits. the structure of the s protein consists of four parts: an sp located at the n terminus (amino acids - ), an extracellular domain (amino acids - ), a tm domain (amino acids - ), and an intracellular domain (amino acids - ). the s subunit contains two independent domains, an n-terminal domain (ntd, amino acids - ) and a c-terminal domain (amino acids - ), both of which may function as receptor-binding domains (rbds); these domains serve as critical targets for the development of vaccines and therapeutics , and facilitate the involvement of the s subunit in cell receptor (dpp ) binding. the core structure of the mers-cov s protein rbd is a five-stranded antiparallel sheet with several short helices, in which three disulfide bonds stabilize the core by connecting c to c , c to c , and c to c . , the accessory subdomain of the c-domain is a hypervariable region for receptor recognition fig. clustering of the spike protein of each coronavirus. fifty-four spike protein sequences filtered from each coronavirus coding sequences were clustered using the clans (cluster analysis of sequences) program on the website of mpi bioinformatics toolkit. each colored dot represents the spike protein sequence of each coronavirus. dots in the same color mean they are of the same genus, and each line shows the similarity of two sequences, with darker lines indicating higher similarity (lower e values). the coronaviridae family includes the following genera: alphacoronavirus (colored in green); betacoronavirus (red); gammacoronavirus (orange), and deltacoronavirus (blue). the indicated sars-cov, mers-cov, and sars-cov- belong to the genus of betacoronavirus and is called the receptor-binding motif (rbm). the accessory subdomains in sars-cov and mers-cov differ, resulting from divergent evolution and leading to the use of different receptors. dpp consists of an n-terminal hydrolase and a cterminal β-propeller domain composed of eight lancets and the rbd. the s subunit of mers-cov contains an fp (residues - ), an hr domain (residues - ), an hr domain (residues - ), a tm domain (residues - ), and an intracellular domain (residues - ). the s subunit is responsible for fusion between the virus and the target cell membrane. after the s subunit binds to dpp , the s subunit inserts its fp into the target cell membrane to change its conformation. its hr helix then forms a homotrimer with an exposed surface that has three highly conserved hydrophobic grooves, and binds with hr to form a six-helix bundle ( -hb) core structure, which facilitates fusion by bringing the viral and cell membranes into close proximity. the genetic material of mers-cov then enters the host cell via the fusion pore. sars-cov- , which causes covid- , is a spherical betacoronavirus with a diameter of - nm and unique spikes ranging from to nm. its rna has the typical betacoronavirus organization, containing a ′ utr, a gene encoding the replicase complex (orf a/b), the s gene, e gene, m gene, and n gene, a ′ utr, and several unidentified nonstructural orfs. , the length of the sequences is nt for the ′ terminal region, nt for the ′ terminal region, nt for the s gene, nt for the e gene, nt for the m gene, and nt for the n gene. the , nt-long orf a/b gene contains predicted nsps. similar to sars-cov, there is a predicted orf gene that is nt in length and located between the m and n orf genes. nucleotides , , and may be the recombination breakpoints because based on the fragments from nt to nt and nt to the end, sars-cov- seems to be related to bat-sl-covzc and bat-sl-covzxc ; however, when considering the region from nt to nt , sars-cov- is mostly likely to be grouped with sars-cov and bat sars-like covs. more research is required to analyze the recombination of the genome as a whole. with over % of its conserved replicase complex being different from those of other betacoronaviruses, sars-cov- solely occupies a newly created subclade within the sarbecovirus subgenus. , bats may be its natural host, but owing to several arguments including the complicated environment in the wet markets in wuhan, this remains unclear, and further research is needed. , [ ] [ ] [ ] the free energy of the spike protein of sars-cov- is much lower than that of sars-cov, indicating that sars-cov- is more stable than sars-cov. the high similarity of the rbd sequences and of the spike protein structures between sars-cov- and sars-cov, , , also the simulation of the spike protein of sars-cov- binding to ace , the receptor of sars-cov, and results shown that ace plays a vital role in sars-cov- entry into hela cells, indicating that sars-cov- also uses ace for cell entry. structural modeling of the ace -b at complex (b at is used to obtain stable ace ) suggests that the complex can bind two s proteins simultaneously, providing important clues to the molecular basis of coronavirus recognition and infection. the rbd-ace binding free energy for sars-cov- is significantly lower than that for sars-cov, in accordance with the fact that sars-cov- is more infectious than sars-cov. a recent study found that cd , a kind of tm glycoprotein, facilitates cell entry of sars-cov- functionally, and its affinity constant with the s protein is . × − m. table shows a comparison of the structures of sars-cov, mers-cov, and sars-cov- . the specific function of the sars-cov- proteins, including s, e, m, and n proteins, need further study. in conclusion, sars-cov, mers-cov, and sars-cov- are similar in structure. their major proteins are structural proteins, including the s, e, m, and n proteins, accessory protein, and nsps (nsp - ). all these viruses rely on the s protein to identify cell targets and fuse with membranes. their s proteins are composed of s and s subunits. the s subunit contains an ntd and a c-domain, in which there is an rbd. the accessory subdomain of the c-domain is a hypervariable region for receptor recognition and is called the rbm. the difference is that sars-cov recognizes ace , sars-cov- recognizes ace and cd , but mers recognizes dpp , which results from the difference between the accessory subdomains of sars-cov, sars-cov- , and mers-cov. the function of the accessory and nonstructural proteins of these three viruses is related to viral replication and assembly, hence linked to virulence. pathogenesis of sars-cov, mers-cov, and sars-cov- sars-cov and sars-cov- are nearly identical in terms of invasion and self-replication, whereas mers-cov has different targets. the cellular receptor of sars-cov and sars-cov- is ace , plus cd for sars-cov- , while that of mers-cov is dpp . the human ace protein is a typical zinc metallopeptidase that comprises amino acids and contains a single catalytic domain. it is a type i integral membrane glycoprotein that is oriented with an extracellular n terminus and a catalytic site that functions in metabolizing circulating peptides. it is believed that there is a virus-binding hot spot on ace that is not pre-existent or preorganized but is induced to form upon virus binding. the hot spot consists of a salt bridge surrounded by hydrophobic tunnel walls. the general structural features of the hot spot favor virus binding: it is located in a region on ace that is furthest from the membrane, relatively flat, and free of glycosylation and is thereby easily accessible to viruses. the hot spot is mainly an intrinsic property of ace , but it is also a dynamic structure and receives structural contributions from both ace and the viruses, with the contributions of ace being more pronounced. dpp is a type ii transmembrane glycoprotein that consists of approximately amino acids. dpp contains an n-terminal hydrolase and a cterminal β-propeller domain composed of eight lancets. the s protein rbd binds to the side surface of the dpp propeller and the amino acid residues in lancets and , including k , q , t , r , r , q , a , l , and i . the pathogenic mechanism of sars-cov is believed to include two parts: the virus injures target cells directly, and subsequent immune system dysfunction leads to indirect injury. sars-cov spreads via droplet and contact transmission and via the fecal-oral route. through droplet inhalation, the virus enters the respiratory tract and invades epithelial cells. infection and replication of the virus and local inflammatory changes contribute to lung tissue damage. subsequently, sars-cov infects circulating and resident immune cells. the key cells in this step consist mainly of t cells and macrophages. the viruses are then carried to other organs, including secondary lymphoid organs, by these circulating immune cells. sars-cov resembles hiv because both viruses attack immune cells and cause immunodeficiency. sars-cov causes lung injury mainly by inhibiting the function of ace . the virus binds to ace via the spike protein, downregulating its function and contributing to lung injury. ace is an important component of the renin-angiotensin system (ras). in this system, angiotensinogen is first converted to angiotensini (angi) by renin, and then angiis converted to ang ii under the influence of ace . ace downregulates the levels of angi and ang ii, which can bind to the ang ii type i (at ) receptor and cause certain types of lung injury, mainly pulmonary hypertension, pulmonary fibrosis, and acute lung injury. ang ii can directly induce pulmonary artery smooth muscle cells to grow or proliferate rapidly through at , thus causing pulmonary hypertension. ang ii contributes to pulmonary fibrosis by promoting the expression of the profibrotic cytokine transforming growth factor-b , causing fibroblasts to convert to myofibroblasts and accumulate collagen. several strategies can be used by the virus to escape the innate immune response. normally, viral pathogen-associated molecular patterns (pamps) are detected by host pattern recognition receptors (prrs). pamps include viral dsrna and mrna, and prrs include retinoic acid-inducible gene i protein (rig-i) and melanoma differentiation-associated protein (mda ). production of type i ifn is induced via the nuclear factor-κb (nf-κb) pathway. when ifn binds to the ifnα/β receptor, signal transducer and activator of transcription (stat) proteins are activated, which increases the production of other antiviral proteins and thus blocks sars-cov replication for further infection. additionally, sars-cov could encode several proteins that hinder the signaling cascades downstream of prrs. the cell receptor of mers-cov is dpp , which is widely expressed on epithelial cells in the prostate, alveoli, kidneys, liver, and small intestine and on activated leukocytes; thus, the range of mers-cov tissue tropism is broader than that of any other similar coronavirus. mers-cov infection of dendritic cells and macrophages can lead to the continuous production of proinflammatory cytokines and chemokines (such as tnf-α, il- , cxcl- , ccl- , ccl- , ccl- , and il- ). compared to sars-cov infection, mers-cov infection can cause higher expression levels of il- , ifn-γ, ip- /cxcl- , mcp- /ccl- , mip- α/ccl- , rantes/ccl- , and il- . induction of immune cell-recruiting cytokines/chemokines might lead to the infiltration of a large number of immune cells into the lower respiratory tract, causing severe inflammation and tissue damage. mers-cov can also infect t cells and lead to apoptosis, avoiding the host immune response and facilitating faster spread. mers-cov has also evolved a mechanism to escape the host cell immune system. when host sensors initiate signaling pathways, transcription of type i ifn genes begins, and the type i ifn response, which is an essential component of antiviral innate immunity, is initiated. [ ] [ ] [ ] ifn activates the transcription of numerous ifn-stimulated genes (isgs) and synthesizes ′, ′oligoadenylate ( - a), which causes rnase l activation. [ ] [ ] [ ] activated rnase l can cleave both viral and host ssrna, leading to translation stagnation and apoptosis and limiting virus replication and transmission in vitro and in vivo. , however, the mers-cov protein ns b has phosphodiesterase activity and antagonizes rnase l via enzymatic degradation, leading to inference with ifn signaling. although ns b is mainly expressed in the nucleus, the expression level of the ns b protein in the cytoplasm is sufficient to prevent activation of rnase l. in addition, the mers-cov m, orf a, orf b, and orf proteins are reported to be strong ifn antagonists, among which the orf a, orf b, and orf proteins inhibit both type i ifn induction , , and nf-κb signaling pathways, which are similar to the type i ifn signaling pathway, providing a possible mechanism for mers-cov evasion of innate immunity. , for sars-cov- , the first cluster of patients was believed to be associated with a seafood market. however, due to the identification of patients without direct exposure to the market, transmission between humans was proven. hospital-related transmission has also been detected via infected medical workers and hospitalized patients. main routes of transmission include respiratory droplets, close contact, and extended exposure to aerosol environments loaded with high concentrations of virions. in addition to transmission through the respiratory tract, exposure of unprotected eyes to sars-cov- might cause acute respiratory infection. notably, the virus can be transmitted during the incubation period. the tm protease serine type (tmprss ) primes the s protein of sars-cov- for cell entry. based on analysis of the ace rna expression profile in normal human lungs, sars-cov- mainly infects type ii alveolar (at ) cells (only . % of human lung cells can express ace , % of which are at cells), and they express many other genes that facilitate sars-cov- infection; moreover, cd was also reported that it probably functionally facilitates cell entry of sars-cov- . high expression of ace has also been detected in cells of the digestive system, such as upper esophageal cells; accordingly, this system is a potential route of infection. in addition to the lungs and intestines, other organs, such as the heart, esophagus, kidney, bladder, testis, ileum, and adipose tissue, also express ace , and the expression level is higher than that in the lungs. , certain tumor tissues have higher expression of ace , making cancer patients more vulnerable than other people. in conclusion, sars-cov and sars-cov- bind cells expressing ace . they affect the ras system due to the affinity for ace (much stronger with sars-cov- than with sars-cov), leading to the onset of symptoms. mers-cov causes symptoms by producing inflammatory cytokines and invading t cells. the specific pathogenic mechanisms of these three viruses are illustrated in fig. . diagnostic methods in addition to clinical manifestations, definitive diagnosis and confirmation of a coronavirus infection requires specific testing. the criteria for the diagnosis of sars from the who include ( ) fever higher than °c or history of such in the past days, ( ) radiological evidence of new infiltrates consistent with pneumonia, ( ) chills, cough, malaise, myalgia, or known history of exposure, and ( ) positive tests for by at least one assay. as for mers, the criteria for the diagnosis according to the who include ( ) fever, cough, and hospitalization with suspicion of lower respiratory tract lesion, ( ) history of contact with probable or confirmed cases, ( ) history of travel or residence within the arabian peninsula, and ( ) positive tests by a pcr-based detection method using respiratory samples, such as nasopharyngeal swabs, nasopharyngeal or tracheal aspirates, bronchoalveolar lavage (bal) and induced sputum, or by serological tests such as the rapid immunochromatographic assay using highly selective monoclonal antibodies at room temperature. the initial criteria for the diagnosis of sars included ( ) a history of travel or residence in wuhan within weeks before the onset of illness, ( ) exposure to patients from wuhan with fever and respiratory symptoms within weeks before the onset of illness or the existence of clusters of diseases, ( ) fever accompanied by radiographic features of pneumonia, a normal or decreased total number of white blood cells, or a decreased lymphocyte count, and ( ) fluorescence pcr testing positive for nucleic acids of sars-cov- . , , [ ] [ ] [ ] early diagnosis of mers is difficult, but several highly specific and sensitive molecular and serologic assays exist for diagnosis in both animals and humans. among them, a rapid immunochromatographic assay can detect mers-cov antigens based on the detection of the mers-cov nucleocapsid protein in a short time frame; the relative sensitivity and specificity of this test are . and %, respectively. nucleic acid tests, such as real-time pcr tests, were mostly used to detect virus in the early stage of the outbreak of sars-cov- , although this approach requires a relatively long time and is not conducive to accelerating diagnosis or large-scale application. therefore, alternative, rapid diagnostic kits for sars-cov- may be used. for example, the colloidal gold detection kit uses serum, plasma, or whole blood samples to detect igm/igg antibodies for diagnosis on the th day of infection or the rd day after onset and requires only min. the nucleic acid detection kit for six respiratory viruses, including sars-cov- and influenza a virus, uses thermostatic amplifier chips for diagnosis. by detecting different infections, it may help distinguish people with influenza from those with other viral infections. a newly developed fig. pathogenesis of sars-cov, mers-cov, and sars-cov- . sars-cov and sars-cov- play a pathogenic role by inhibiting ace . under the influence of renin and ace, angiotensinogen is converted into ang ii. through the at receptor, ang ii acts as a lung injury-promoting factor, and in some cases, may cause vascular constriction, an inflammatory response, cell proliferation, fibrosis, and apoptosis of alveolar epithelial cells, resulting in diseases such as pulmonary hypertension, pulmonary fibrosis, and acute lung injury. ace converts ang ii into ang ( - ), and through the mas receptor, ang ( - ) play roles in vasodilation, antiproliferative activity, and antioxidant activity. sars-cov downregulates the activity of ace and causes an increase in the amount of ang ii and lung injury. mers-cov infection of dendritic cells and macrophages can lead to the continuous production of pro-inflammatory cytokines and chemokines, leading to a large number of immune cells infiltrating a patient's lower respiratory tract, causing severe inflammation and tissue damage. mers-cov can infect t-cells from human lymphoid organs and causes the peripheral blood inducing apoptosis by intrinsic and extrinsic pathways, thus avoiding host immune response detection method, nanopore targeted sequencing, also has the potential for efficiently detecting viruses in a reasonable time. moreover, it could identify other respiratory viruses and monitor changes in virulence and transmissibility caused by viral mutations. therapeutic agents all patients should be treated in isolation. based on previous studies, drugs may be developed to inhibit cell entry. several strategies have been investigated to identify specific antivirals targeting the s protein, including mers-rbd-targeted nabs that block viral attachment, peptide inhibitors targeting s to prevent the formation of the fusion core, and small molecules without defined mechanisms. sdpp has been found to bind mers-cov rbd with high affinity, suggesting that sdpp could serve as a blocker for mers-cov attachment to and entry into cells. , one study reported a monoclonal antibody, d , that binds to the ntd to inhibit cellular entry of mers-cov. experiments have shown that d not only inhibits the binding of mers-cov to cells but also has effects after viral-cell attachment. d inhibits virus invasion by blocking the binding of the s subunit to the receptor and interfering with the conformational transformation of the s subunit when the virus fuses with the cell membrane. a peptide fragment spanning residues - of the s protein exerts neutralization activity by inhibiting membrane fusion and the entry of mers-cov, suggesting that it is possible to develop vaccines targeting this neutralizing epitope. griffithsin, a lectin derived from red algae, binds to oligosaccharides on the surface of sars-cov s protein and may also prove effective against sars-cov- . , researchers found that antibodies raised against sars-cov, such as css- , - , - , and - , could cross-neutralize sars-cov- by reducing s-driven cell entry, although the efficiency was lower than that observed for sars-cov. meplazumab, an anti-cd humanized antibody, binds with the cd in competition with the s protein, thus significantly inhibiting virus from invading cells and reducing the time of negative conversion. , chloroquine could effectively inhibit sars-cov- in vitro, and hydroxychloroquine was even more potent than chloroquine. , hydroxychloroquine could significantly help reduce the virus load, and azithromycin could reinforce its effect. arbidol could also contribute to condition improvement. note that these studies were generally limited and further trials and development are necessary. protease inhibitors also have the potential for coronavirus therapeutics. protease inhibitors, including disulfiram, lopinavir, and ritonavir, have been reported to be effective against sars and mers, and disulfiram, a drug for alcohol dependence, was reported to inhibit the papain-like protease (plpro) of mers-cov and sars-cov in cell cultures. , in vitro, sars-cov can be inhibited by both -mercaptopurine and -thioguanine targeting plpro. when used together with ribavirin, the protease inhibitors lopinavir and ritonavir have improved the outcomes of patients with sars compared with those achieved with the use of ribavirin alone. such inhibitors are also being tested in patients infected with sars-cov- , but whether these inhibitors effectively suppress clpro and plpro of sars-cov- remains controversial. drugs such as colistin, valrubicin, icatibant, bepotastine, epirubicin, epoprostenol, vapreotide, aprepitant, caspofungin, perphenazine, prulifloxacin, bictegravir, nelfinavir, and tegobuvir bind to the main protease of sars-cov- , and thus, are potential candidates. lianhua-qingwen formula, a kind of traditional chinese medicine, has been also recently described theoretically as a potential treatment candidate against the main virus protease. the serine protease inhibitor camostat mesylate could partly block sars-cov- infection of lung cells by inhibiting tmprss . viral rna synthesis blockers also have potential. remdesivir has broad-spectrum activity against mers-cov and sars-cov in cell cultures and animal models and is currently in clinical development for the treatment of ebola virus disease. , it was also reported positively based on a patient with sars-cov- infection in the us, and another study showed that it was able to inhibit the virus. ribavirin is often used to treat sars and mers, but it is uncertain whether it is potent enough against covid- . , regardless, when used alone, ribavirin has minimal activity against sars-cov and may cause strong side effects. it is often used together with corticosteroids. , a preclinical study of galidesivir (bcx ), an adenosine analog, revealed antiviral activity against sars-cov and mers-covcov. a study of favipiravir (t- ), a guanine analog, proved its activity against sars-cov- , and randomized trials of favipiravir plus interferon-α (chictr ), and favipiravir plus baloxavir marboxil (chictr ) are in progress. corticosteroids may be used to treat sars patients to suppress lung inflammation; although this therapy is not associated with mortality in patients with mers, it is associated with delayed clearance of mers-cov rna. , moreover, clinical evidence does not support the use of corticosteroids for covid- treatment. regarding antibodies, plasma therapy using convalescent plasma from fully recovered patients is effective against these coronaviruses, including sars-cov- . , tocilizumab (antihuman il- receptor) may curb immunopathology and trials are ongoing now. a study of novel monoclonal antibodies against the mers-cov spike protein suggests that mabs can be utilized for the identification of specific mutations of mers-cov. wang et al. provided an all-hydrocarbon-stapled peptide that likely mimics the native conformation of the c-terminal short α-helical region of the mers-cov s protein, which can block the formation of the hexameric coiled-coil fusion complex to inhibit viral-cell membrane fusion. , current treatments for sars mainly include ribavirin, ifn α, plasma therapy, host-directed therapies, and systemic corticosteroids. , due to the lack of clinical trial data, adequate supportive care supplemented with different combinations of drugs remains the main treatment for patients. , for mers, despite many studies in humans, there is no consensus on the best treatment; thus, randomized clinical trials are needed to assess potential treatment options. several therapeutics are in development, including convalescent plasma, lopinavir/ritonavir, ribavirin, ifn and novel therapies, including polyclonal antibodies and broad-spectrum antivirals. antimicrobial peptides (amps) may be used as alternative therapeutic agents, and many have been effective even against bacterial proteases agents. antiviral drugs with effective activity in vitro include neutralizing monoclonal antibodies, antiviral peptides, mycophenolic acid, lopinavir, ifn, ribavirin, nitazoxamide, mycophenolate mofetil (mmf), alisporivir, silvestro, and corticosteroids. , , although there is no agreement on the most ideal treatment option to cure covid- , much research activities and pursued routes are underway. potential host-targeted agents the host-directed strategy is another approach for limiting viral replication. host proteases such as cathepsin b and cathepsin l can cleave the spike protein of sars-cov. drugs such as camostat inhibit host serine proteases and then interfere with the entry of sars-cov, but they may cause many significant side effects. , pegylated ifn α- a and - b may be used to stimulate innate antiviral responses in patients, and chloroquine, an approved immune modulator, was reported to have inhibitory effects against sars-cov- under certain conditions. researchers have also proposed that some commercially available drugs with suitable safety profiles, such as metformin, glitazones, fibrates, sartans, and atorvastin, as well as nutrient supplements and biologics, might reduce immunopathology, boost immune responses, and prevent or curb ards. in addition, ongoing cellular therapies using mesenchymal stromal cells from allogeneic donors have been shown to reduce nonproductive inflammation and affect tissue regeneration and are being evaluated in phase / trials in patients with ards; these therapies may be assayed in sars-cov- -infected patients. , , expansion of antiviral t cells as cellular drugs could aid in preparing t cell products for adjunct treatment of patients with severe infection. overall, there are similarities and differences among the treatments for these three coronaviruses. notably, we summarize the potential drugs and vaccines in table . vaccination could be used to prevent infection or to reduce disease severity. different kinds of vaccines, such as dna vaccines, recombinant proteins, subunit vaccines, and inactivated viruses, were described. however, the highly sophisticated immune evasion mechanisms of viral pathogens and their high mutation rates make human vaccine development a major challenge. the four nsps ( clpro, plpro, helicase, and rdrp), which are key enzymes in the viral life cycle, and the s protein, which is responsible for receptor binding during cell entry, are attractive targets for developing vaccines against coronaviruses. among them, the s protein is most commonly targeted. based on previous studies, it is believed that the s protein receptor-binding domain (s-rbd) located in the s subunit is an important target for the development of a sars vaccine, especially the key neutralizing region, cnd. indeed, cnd can induce a strong neutralizing antibody response and crossprotection against sars-cov mutants. one study showed that a recombinant fusion protein (designated rbd-fc) containing the -amino acid rbd and a human igg fc fragment can induce highly potent antibody responses in immunized rabbits. the antibodies inhibited sars-cov infection (serum dilution of : , ), and they are believed to be safer than other types of vaccines. additionally, with chloroplast transgenic technology, it is possible to combine the fusion gene s-rbd and the carrier molecule cholera toxin b subunit into the tobacco chloroplast genome to obtain a chloroplast transgenic tobacco plant that stably expresses the oral sars-cov subunit vaccine. for mers, vaccines based on the viral s protein include full-length s or strimer protein-based vaccines such as a full-length s-based simian adenovirus vector vaccine (chadox ) and dna vaccine (gls- ), s -based vaccines such as an ad vector encoding mers-cov s extracellular domain (ad .mers-s ) and an rabv vector encoding an s -elicited antibody, , rbd-based vaccines, and vaccines based on other regions. it has been confirmed that the s proteins of sars-cov and sars-cov- are quite similar, but researchers recently found that the three monoclonal antibodies developed to bind to the s protein of sars-cov, s , m , and r do not cross-react with the s protein rbd of sars-cov- , simian adenovirus vector vaccine (chadox );an ad vector encoding mers-cov s extracellular domain (ad .mers-s ); an rabv vector encoding s elicit antibody; rbd-based vaccines , , , overview of lethal human coronaviruses chen et al. suggesting that tailored vaccines and antibodies against sars-cov- must be designed. dna vaccines are also quite promising. specific igg antibodies against sars-cov can be promoted by the s gene dna vaccine. as mentioned above, the s protein of sars-cov plays an important role during the pathogenic process, and synthetic peptides induced by dna vaccine in escherichia coli elicit specific antibodies against the sars-cov s protein which might provide another approach for further developing sars-cov vaccines. , to evaluate the safety and immunogenicity of a plasmid dna vaccine (gls- ) that expresses the s protein of mers-cov, a phase i clinical trial on healthy volunteers was conducted in , but the results were not reported. another phase i trial utilizing the viral vector, chimpanzee adenovirus, oxford university # (chadox ), containing the mers-cov s protein expression gene was started by oxford university in january . in addition, camel vaccines against mers-cov are a consideration. at present, at least two promising candidate camel vaccines are undergoing development, and field trial evaluation is in progress. , one study found that the rbd fragment covering spike residues - is a key neutralizing receptor-binding fragment and an ideal candidate for mers vaccines. another potential neutralizing epitope is a peptide fragment covering - residues of the s protein which blocks the membrane fusion and cellular entry of mers-cov (fig. ) . other approaches recombinant viruses may be employed to generate an immune response against the viruses. there are two kinds of recombinant viruses which are promising for designing a protective vaccine. the first is a defective or nonpathogenic vector capable of expressing viral proteins, and the second is a vector that can be assembled in a test tube to stimulate the assembly of virus-like particles. adenosine deaminase (ada), a kind of human enzyme, could interact with dpp , therefore, ada could compete with mers-cov as a natural antagonist when the virus attempts to bind to cells. in addition, anti-dpp can play a similar role, however, it is not practical to use this method in vivo because dpp has important functions in the regulation of several different signaling pathways. questions concerning the coronavirus-host interactions this topic has intrigued the community. understanding certain mechanisms about virus interactions will support drug research activities. for instance, it was found that sars-cov- has a stronger, more rapid spreading ability than many known viruses. is it possible that it invades host cells via additional novel routes, not limited to ace ? for example, cd is probably involved in virus invasion. is there an s-like protein involved in invasion? the affinity of the human ace protein for the rbd of the new coronavirus is - times higher than it is for that of the sars virus, which likely explains why sars-cov- spreads more swiftly. there is a distinct insert present in the peptide fragment spanning of s /s loop of the sars-cov- s protein, which is not shared the similarity with sars-cov or any sars-related viruses. does this peptide loop impact on the entry pathway type of sars-cov- , compared to other known betacoronavirus lineage b? furthermore, the s protein is likely cleaved during virus assembly and delivery to the cell surface by golgi-resident proprotein convertases such as furin, which is different from the behavior of its close relatives. furin is found in a variety of human tissues, including the lungs, liver, and small intestine. therefore, which are exactly the cell types that sars-cov- may attack? yet, in relation to the last two questions, it should be noted that studies are also necessary to investigate any possibility of receptor-independent virus entry. the sars-cov- genome encodes nonstructural proteins, structural proteins, and accessory proteins. clpro, plpro, helicase, and rdrp, which belong to the first type, and the s protein, which belongs to the second, have been recognized as promising targets for developing antiviral agents against sars-cov and mers-cov, which therefore may be applied to sars-cov- . nonetheless, the rapid identification of effective interventions against sars-cov- is a major challenge. however, the subject of using currently known antiviral drugs has been frequently brought up by the community as a potential short-term strategy to combat sars-cov- . drugs affecting such targets and their status for sars-cov- are listed below. the main candidates as inhibitors of clpro include other agents for sars-cov- fig. the targets of the different drug candidates against the three coronaviruses. common targets against the three coronaviruses are mainly the s protein and the s /s subunits, pl protein, rdrp, cl protein, and helicase. the figure shows drug candidates (in black) and vaccines (in red). among them, remdesivir has been trending in the news recently. it inhibits the rdrp, is in phase iii for sars-cov- , and may have an effect on the three viruses. ribavirin in combination with a pegylated interferon may also have an effect against the three viruses. ritonavir and lopinavir, which inhibit the clpro and are in phase iii for sars-cov- , have an effect on both sars-cov- and mers-cov. dna vaccines and vaccines based on the s protein or subunits of the s protein are in development lopinavir, ritonavir, darunavir, cobicistat, and asc f (phase iii, in combination with oseltamivir, for sars-cov- ). candidates as inhibitors of plpro include thiopurine analogs, compound (preclinical), and remdesivir (phase iii for mars-cov). , favipiravir, ribavirin (randomized trial for sars-cov- ), and remdesivir are among the candidate inhibitors of rdrp. previously, compounds that may interfere with atpase and helicase activities were reported (before covid- ), such as bananins, -hydroxychromone derivatives, and triazole derivatives (preclinical). , candidates that may suppress viral entry by targeting the s protein include peptide p and α-helical lipopeptides (preclinical), and those targeting the s subunit of the s protein mainly include hr p, hr m, hr l, hr l, hr p, and hr l (preclinical). due to the strong affinity between ace receptor and the rbd of sars-cov- , another opportunity might be through the development of antibodies to block ace . the second method is to use a large amount of soluble ace to directly block the spike protein. the third method is to find a drug that directly inhibits the spike membrane fusion process, such as the aids drug enfuvirtide. the fourth approach is to identify an agent that inhibits the activity of disintegrin and metalloproteinase (adam ), which may also prevent viral release and proliferation in cells and protect ace and the lungs. mrna vaccine technology sars-cov- vaccines are already under development. the mrna and dna vaccines are promising approaches to prevent cellular invasion by similar coronaviruses in the future. in january , the coalition for epidemic preparedness innovations (cepi) announced three partnerships to develop a new coronavirus vaccine. among them, moderna and inovio presented mrna and dna vaccine technologies, respectively. the goal of the three teams is to have at least one candidate vaccine capable of preventing coronavirus infection in weeks, to be tested in a phase i clinical trial. moderna's vaccine model is designed to use mrnas to safely pre-expose the immune system to a small amount of encoded proteins usually generated by the pathogen, so that the immune system becomes prepared to fight future pathogens and prevent infection. the candidate genes developed by moderna contain mrnas, and combining multiple mrnas into a single vaccine might be useful to rapidly induce responses, which is an approach that may be applied for future, emerging pandemic threats too. at the same time, because the mrna in the cell will be degraded over time, the mrna vaccine will not continue to produce antigen components for a long time, which can avoid the risk of continued stimulation of the immune system. generally, mrna vaccines are also described as simple to prepare and to yield remarkable results. additional advantages, as well as disadvantages, of nucleic acid-based vaccines were described in detail. furthermore, the basis of traditional vaccines, proteins or polysaccharides, cannot be straight forward applied at present against many pathogens. therefore, mrna vaccines would be suitable for achieving rapid, mass production of emergency vaccines in the event of a major epidemic. however, because rna is easily degraded, inducing cells to absorb mrna quickly is a challenge. in recent years, the method for delivery of mrna into cells has been greatly improved, and stemirna and moderna have adopted nanolipid (lpp or lnp (lipid nanoparticle)) drug-loading technology. however, this is still to be developed for mrnas. furthermore, ensuring safety and effectiveness is another challenge for viral mrna vaccines, and clinical validation will have to be carried out carefully. moderna is a worldwide leader in mrna therapy, with currently nine mrna-type vaccine candidates (e.g., mrna- against sars-cov- ). the national institutes of allergy and infectious diseases (niaid) of the national institutes of health (nih) and the mrna vaccine giant moderna have teamed up to bring the new coronavirus vaccine possibly to phase ii within a few months, and phase iii late this year. simultaneously, in january , the translational medicine platform of dongfang hospital affiliated with tongji university cooperated with stemirna (shanghai) biotechnology co., ltd. to rapidly promote the development of a new coronavirus mrna vaccine. in february , the chinese scientific research team announced that animal testing of the newly developed coronavirus vaccine has begun. if animal testing goes well, this new vaccine will enter human clinical trials within a few months. also in february , zhuhai livanda biotechnology co., ltd. announced that the first batch of new coronavirus mrna vaccine standard samples completed during the spring festival had been delivered to relevant national authorities on for animal testing and efficacy verification. the researchers detected the production of target antibodies in mouse serum at day following immunization. the company claimed that this was also the first time worldwide that new coronavirus vaccines developed based on mrna technology have resulted in antibodies in animals. livanda is currently pushing ahead with the project through extensive cooperation with the academy of military medical sciences, the guangdong provincial institute of supervision, and the macau university of science and technology. the antigen used in its development is the same as that used by moderna. dna vaccine technology dna vaccine technology may have many advantages (e.g., safe, fast, less technical barriers), along with potential limitations too. a phase i human clinical trial of the mers-cov vaccine has proven its safety and effectiveness. the dna vaccine based on the sars-cov s protein developed by the team of barney graham and gary nabel of the us-nih vaccine research center (vrc) has achieved positive results in animal experiments and a clinical phase i trial. , inovio pharmaceuticals has accumulated extensive safety and immunogenicity data for mers-cov vaccine studies. because of the high degree of similarity between mers-cov and sars-cov- , lessons from such a vaccine development process may be beneficial for the development of a dna vaccine against sars-cov- . since january , inovio has been collaborating with several experts and companies (some in china), and has currently already begun phase i clinical trials of the dna vaccine ino- . china's cansino biologics might be the leader as it was announced it has moved to phase ii testing of a vaccine called ad -ncov. the latter is currently often being reported as a dna vaccine, but to be precise, it uses viral vectors (adenovirus) to deliver dna related to sars-cov- . part of the project is carried out currently with the chinese military medical research institute. the vaccine candidate is constructed using genetic engineering methods and defective human type adenovirus as a vector that can express the sars-cov- s antigen, to stimulate the body to produce strong humoral or cellular immunity. sars-cov and mers-cov belong to subgroups b and c of the betacoronaviruses, respectively, and sars-cov- is a new member of betacoronaviruses, distinct from sars-cov and mers-cov. sars-cov and sars-cov- are similar in terms of invasion and self-replication, whereas mers-cov has different targets. the cellular receptor of sars-cov and sars-cov- is ace , plus cd for sars-cov- , while that of mers-cov is dpp (cd ). all of them evolved a mechanism to escape the host cell immune system. sars-cov and sars-cov- affect the ras system by suppressing ace , leading to the onset of symptoms. mers-cov causes symptoms by producing inflammatory cytokines and invading t cells. sars-cov, mers-cov, and sars-cov- infections have similar symptoms, including fever, cough, myalgia, and shortness of breath, among others. current treatments for sars mainly include ifn-α, antiviral treatments (e.g., ribavirin), plasma therapy, host-directed therapies, and systemic corticosteroids. for mers, several therapeutics are in development, including convalescent plasma, lopinavir/ritonavir, ribavirin, ifn, and novel therapies, including polyclonal antibodies, broad-spectrum antivirals, and amps. for covid- , candidates mainly include drugs targeting the s protein, nonstructural proteins ( clpro, plpro, helicase, and rdrp), and viral rna synthesis blockers such as remdesivir and ribavirin. vaccines such as dna vaccine, mrna vaccine, and recombinant vaccines are being rapidly developed. so far this century, human beings have experienced several epidemic outbreaks, and each outbreak had a negative impact at different levels, including health, economy, and even psychology and human behavior. in the future, more precautious measures should be available to guide individuals and groups to take effective emergency measures and to support social stability, and physical and mental health. furthermore, additional studies of coronaviruses and disease epidemics should continue, to support the preparation for future responses, medical therapies, vaccines, and methods of relieving personal anxiety. this review has highlighted several approaches, and the names and progress related to several compounds and biologics currently under research and development, as well as the companies and researchers involved in these efforts. for future directions, it has also described the differences and similarities, as well as the potential routes and possibilities for targeting each of the main three viruses investigated here. epidemiology, genetic recombination, and pathogenesis of coronaviruses origins and evolution of the global rna virome classify viruses-the gain is worth the pain detection of a group coronavirus in dogs with canine infectious respiratory disease human coronaviruses: what do they cause? epidemiology and cause of severe acute respiratory syndrome (sars) in guangdong, people's republic of china isolation of a novel coronavirus from a man with pneumonia in saudi arabia ecology, evolution and classification of bat coronaviruses in the aftermath of sars a pneumonia outbreak associated with a new coronavirus of probable bat origin characterization of spike glycoprotein of sars-cov- on virus entry and its immune cross-reactivity with sars-cov on the origin and continuing evolution of sars-cov- isolation and characterization of viruses related to the sars coronavirus from animals in southern china mutations, recombination and insertion in the evolution of -ncov sars and mers: recent insights into emerging coronaviruses global epidemiology of bat coronaviruses from sars to mers, thrusting coronaviruses into the spotlight challenges presented by mers corona virus, and sars corona virus to global health middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease mers-cov as an emerging respiratory illness: a review of prevention methods the middle east respiratory syndrome (mers) viral shedding and antibody response in patients with middle east respiratory syndrome coronavirus infection a case report of a middle east respiratory syndrome survivor with kidney biopsy results kinetics and pattern of viral excretion in biological specimens of two mers-cov cases environmental contamination and viral shedding in mers patients during mers-cov outbreak in south korea human intestinal tract serves as an alternative infection route for middle east respiratory syndrome coronavirus a novel coronavirus from patients with pneumonia in china early transmission dynamics in wuhan, china, of novel coronavirusinfected pneumonia clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan, china evolution and variation of -novel coronavirus pattern of early human-to-human transmission of wuhan transmission dynamics of novel coronavirus ( -ncov) modelling the epidemic trend of the novel coronavirus outbreak in china therapeutic options for the novel coronavirus ( -ncov) clinical features of patients infected with novel coronavirus in wuhan genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding severe acute respiratory syndrome: clinical and laboratory manifestations mers-cov outbreak in jeddah-a link to health care facilities reducing mortality from -ncov: host-directed therapies should be an option characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention severe acute respiratory syndrome: historical, epidemiologic, and clinical features pathogenetic mechanisms of severe acute respiratory syndrome studies of severe acute respiratory syndrome coronavirus pathology in human cases and animal models the clinical pathology of severe acute respiratory syndrome (sars): a report from spatiotemporal interplay of severe acute respiratory syndrome coronavirus and respiratory mucosal cells drives viral dissemination in rhesus macaques organ distribution of severe acute respiratory syndrome (sars) associated coronavirus (sars-cov) in sars patients: implications for pathogenesis and virus transmission pathways severe acute respiratory syndrome associated coronavirus is detected in intestinal tissues of fatal cases sars-associated viral hepatitis caused by a novel coronavirus: report of three cases impact of acute kidney injury on outcome in patients with severe acute respiratory failure receiving extracorporeal membrane oxygenation acute renal impairment in coronavirus-associated severe acute respiratory syndrome multiple organ infection and the pathogenesis of sars clinicopathologic, immunohistochemical, and ultrastructural findings of a fatal case of middle east respiratory syndrome coronavirus infection in the united arab emirates epidemiological and clinical characteristics of cases of novel coronavirus pneumonia in wuhan, china: a descriptive study caution: clinical characteristics of covid- patients are changing at admission yeast expression and characterization of sars-cov n protein the sars coronavirus nucleocapsid protein-forms and functions nucleocapsid protein recruitment to replication-transcription complexes plays a crucial role in coronaviral life cycle sars-associated coronavirus focus on middle east respiratory syndrome coronavirus (mers-cov) molecular characteristics, functions, and related pathogenicity of mers-cov prospects for a mers-cov spike vaccine mers-cov: understanding the latest human coronavirus threat the structural and accessory proteins m, orf a, orf b, and orf of middle east respiratory syndrome coronavirus (mers-cov) are potent interferon antagonists middle east respiratory syndrome coronavirus ns b protein inhibits host rnase l activation the endonucleolytic rna cleavage function of nsp of middle east respiratory syndrome coronavirus promotes the production of infectious virus particles in specific human cell lines middle east respiratory syndrome coronavirus nonstructural protein is necessary for interferon resistance and viral pathogenesis structural insights into the middle east respiratory syndrome coronavirus a protein and its dsrna binding mechanism crystal structure of middle east respiratory syndrome coronavirus helicase middle east respiratory syndrome coronavirus (mers-cov) entry inhibitors targeting spike protein interaction of n-acetyl-seryl-aspartyl-lysyl-proline with the angiotensin-converting enzyme -angiotensin-( - )-mas axis attenuates pulmonary fibrosis in silicotic rats crystal structure of the receptor-binding domain from newly emerged middle east respiratory syndrome coronavirus potent neutralization of mers-cov by human neutralizing monoclonal antibodies to the viral spike glycoprotein molecular basis of binding between novel human coronavirus mers-cov and its receptor cd association of host tropism of middle east syndrome coronavirus with the amino acid structure of host cell receptor dipeptidyl peptidase complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in wuhan a pneumonia outbreak associated with a new coronavirus of probable bat origin host and infectivity prediction of wuhan novel coronavirus using deep learning algorithm molecular mechanism of evolution and human infection a new coronavirus associated with human respiratory disease in china evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission structure of dimeric full-length human ace in complex with b at sars-cov- invades host cells via a novel route: cd -spike protein the emerging role of ace in physiology and disease a virus-binding hot spot on human angiotensin-converting enzyme is critical for binding of two different coronaviruses angiotensin-converting enzyme in lung diseases a potential therapeutic role for angiotensin-converting enzyme in human pulmonary arterial hypertension tmprss and adam cleave ace differentially and only proteolysis by tmprss augments entry driven by the severe acute respiratory syndrome coronavirus spike protein middle east respiratory syndrome coronavirus efficiently infects human primary t lymphocytes and activates the extrinsic and intrinsic apoptosis pathways activation of the chicken type i interferon response by infectious bronchitis coronavirus murine coronavirus mouse hepatitis virus is recognized by mda and induces type i interferon in brain macrophages/microglia ribonuclease l and metal-ion-independent endoribonuclease cleavage sites in host and viral rnas viral encounters with ', '-oligoadenylate synthetase and rnase l during the interferon antiviral response dimeric structure of pseudokinase rnase l bound to - a reveals a basis for interferon-induced antiviral activity homologous ', '-phosphodiesterases from disparate rna viruses antagonize antiviral innate immunity middle east respiratory syndrome coronavirus accessory protein a is a type i interferon antagonist the orf b-encoded accessory proteins of middle east respiratory syndrome coronavirus and two related bat coronaviruses localize to the nucleus and inhibit innate immune signalling a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster -ncov transmission through the ocular surface must not be ignored transmission of -ncov infection from an asymptomatic contact in germany sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor single-cell rna expression profiling of ace , the putative receptor of wuhan -ncov the digestive system is a potential route of -ncov infection: a bioinformatics analysis based on single-cell transcriptomes the single-cell rna-seq data analysis on the receptor ace expression reveals the potential risk of different human organs vulnerable to wuhan -ncov infection. front two things about covid- might need attention development and validation of a rapid immunochromatographic assay for detection of middle east respiratory syndrome coronavirus antigen in dromedary camels the sars, mers and novel coronavirus (covid- ) epidemics, the newest and biggest global health threats: what lessons have we learned? middle east respiratory syndrome coronavirus (mers-cov) infection: epidemiology, pathogenesis and clinical characteristics mers: progress on the global response, remaining challenges and the way forward nanopore target sequencing for accurate and comprehensive detection of sars-cov- and other respiratory viruses mers-cov spike protein: targets for vaccines and therapeutics identification of a receptor-binding domain in the s protein of the novel human coronavirus middle east respiratory syndrome coronavirus as an essential target for vaccine development repurposing of clinically developed drugs for treatment of middle east respiratory syndrome coronavirus infection structural definition of a neutralization epitope on the n-terminal domain of mers-cov spike glycoprotein the amino acids - of the mers-cov spike protein induce neutralizing antibodies: implications for the development of vaccines and antiviral agents coronaviruses-drug discovery and therapeutic options meplazumab treats covid- pneumonia: an open-labelled, concurrent controlled add-on clinical trial remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus (sars-cov- ) hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial arbidol combined with lpv/r versus lpv/r alone against corona virus disease : a retrospective cohort study thiopurine analogs and mycophenolic acid synergistically inhibit the papain-like protease of middle east respiratory syndrome coronavirus interferon alfacon- plus corticosteroids in severe acute respiratory syndrome: a preliminary study potential inhibitors against -ncov coronavirus m protease from clinically approved medicines theoretical study of the anti-ncp molecular mechanism of traditional chinese medicine lianhua-qingwen formula (lqf) broad-spectrum antiviral gs- inhibits both epidemic and zoonotic coronaviruses first case of novel coronavirus in the united states development of a standard treatment protocol for severe acute respiratory syndrome corticosteroid therapy for critically ill patients with middle east respiratory syndrome clinical evidence does not support corticosteroid treatment for -ncov lung injury retrospective comparison of convalescent plasma with continuing high-dose methylprednisolone treatment in sars patients aberrant pathogenic gm-csf+ t cells and inflammatory cd +cd + monocytes in severe pulmonary syndrome patients of a new coronavirus characterization of novel monoclonal antibodies against merscoronavirus spike protein discovery of hydrocarbon-stapled short α-helical peptides as promising middle east respiratory syndrome coronavirus (mers-cov) fusion inhibitors a systematic review of therapeutic agents for the treatment of the middle east respiratory syndrome coronavirus (mers-cov) identification of a broad-spectrum antiviral small molecule against severe acute respiratory syndrome coronavirus and ebola, hendra, and nipah viruses by using a novel high-throughput screening assay current treatment options and the role of peptides as potential therapeutic components for middle east respiratory syndrome (mers): a review cell therapy in acute respiratory distress syndrome challenges and responses in human vaccine development receptor-binding domain of sars-cov spike protein induces highly potent neutralizing antibodies: implication for developing subunit vaccine expression of b subunit of e. coli heat-labile enterotoxin in the progenies of transgenic tobacco bred by crossing nuclear-and chloroplast-transgenic lines immunogenicity of an adenoviral-based middle east respiratory syndrome coronavirus vaccine in balb/c mice one-health: a safe, efficient, dual-use vaccine for humans and animals against middle east respiratory syndrome coronavirus and rabies virus cryo-em structure of the -ncov spike in the prefusion conformation dna vaccine of sars-cov s gene induces antibody response in mice chadox and mva based vaccine candidates against mers-cov elicit neutralising antibodies and cellular immune responses in mice an orthopoxvirus-based vaccine reduces virus excretion after mers-cov infection in dromedary camels searching for an ideal vaccine candidate among different mers coronavirus receptor-binding fragments-the importance of immunofocusing in subunit vaccine design adenosine deaminase acts as a natural antagonist for dipeptidyl peptidase -mediated entry of the middle east respiratory syndrome coronavirus inhibition of middle east respiratory syndrome coronavirus infection by anti-cd monoclonal antibody an emerging role of dipeptidyl peptidase (dpp ) beyond glucose control: potential implications in cardiovascular disease structural modeling of -novel coronavirus (ncov) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to sars-cov and related sars-like coronaviruses comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov disulfiram can inhibit mers and sars coronaviruspapain-like proteases via different modes de novo design of α-helical lipopeptides targeting viral fusion proteins: a promising strategy for relatively broad-spectrum antiviral drug discovery structure-based discovery of middle east respiratory syndrome coronavirus fusion inhibitor new vaccine technologies to combat outbreak situations safety and immunogenicity of an anti-middle east respiratory syndrome coronavirus dna vaccine: a phase , open-label, single-arm, dose-escalation trial a dna vaccine induces sars coronavirus neutralization and protective immunity in mice a sars dna vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a phase i clinical trial potent binding of novelcoronavirus spike protein by a sars coronavirus-specific human monoclonalantibody potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s protein that blocks receptor association potent cross-reactive neutralization of sars coronavirus isolates by human monoclonal antibodies exceptionally potent neutralizationof middle east respiratory syndrome coronavirus by human monoclonalantibodies interaction between heptad repeat and regions inspike protein of sars-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors fusion mechanism of -ncov andfusion inhibitors targeting hr domain in spike protein the authors gratefully acknowledge the financial support from the national natural science foundation of china (grant no. ), and the . . project for disciplines excellence, west china hospital, sichuan university (zyyc to w.c.). competing interests: the authors declare no competing interests.open access this article is licensed under a creative commons attribution . international license, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the creative commons license, and indicate if changes were made. the images or other third party material in this article are included in the article's creative commons license, unless indicated otherwise in a credit line to the material. if material is not included in the article's creative commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. to view a copy of this license, visit http://creativecommons. org/licenses/by/ . /. key: cord- -gqem bxj authors: allam, zaheer title: oil, health equipment, and trade: revisiting political economy and international relations during the covid- pandemic date: - - journal: surveying the covid- pandemic and its implications doi: . /b - - - - . - sha: doc_id: cord_uid: gqem bxj the covid- pandemic saw disruptions at an unprecedented global scale with deep societal impacts in cities, countries, and regions. moreover, in a time of global urgent need for personal protective equipment, ventilators, and other health appliances and gear, both air and sea transport were halted, disconnecting manufacturing nations with consumer nations. with steep rise in demand, and impacted supply chains, nations, which were previously hailing collaborative calls to fight the pandemic, were seen to enter into a trade war of health equipment. with borders closed, nationalist policies were on the rise coupled with fears of tech-powered surveillance states. on the commodities market, the price of oil crashed leading to uncertainties as to the future for oil producing nations as the end point of the pandemic was still unclear. altogether, the pandemic put on test not only economic structures but also geopolitical ones, where it is seen as the biggest challenge since world war ii. this chapter surveys the impacts of the pandemic on the global political landscape and outlines concerns and questions for sustaining a peaceful shared future. the covid- pandemic took the world by surprise, as it started slowly in wuhan, china, with the first known cases being only , by the time it became identified. however, in a space of months, it had transformed from being just another type of coronavirus, to a "public emergency of global concern", to a global pandemic. in the course of writing this chapter, the coronavirus responsible for the covid- had spread from wuhan, the initial epicenter, to the whole of china, to its neighbors, and finally, to countries and territories (worldometer, ) . the number of confirmed cases also increased from the first known cases to over million confirmed cases and over , casualties (spotlight, ) . during the same period, the epicenter for this virus had moved from china, to europe and to the united states, and in each of those regions; large-scale devastation, deaths, and economic disruptions have been observed. however, on the impacts, no single country has been spared since even those with few confirmed cases have experienced one or more forms of disruptions, especially due to the widespread suspension of international and local transportation, thereby interrupting supply chains of different products and services, disruption of tourism industry, manufacturing sector, schooling systems, and others. those disruptions also affected small-scale businesses, which in most countries have been offering lifelines to the majority of the population. as the pandemic spread, the whole world was seen to be collaborating in fighting the virus. for instance, when the epicenter was in china, it received personal protective equipment (ppe) and medical supplies from the united states, its immediate trade and power competitor (u.s. embassy in georgia, ). also, when the situation started to worsen in the united states, russia, its longtime foe, sent a plane full of medical supplies to help them respond to the virus as reported by seligman ( ) . besides sharing of health equipment, there have been numerous monetary aid flows between nations, organisations, and even individual contributions targeting regions and countries that were vulnerable and those that were overwhelmed by the disease. for instance, cuba showed incredible generosity by sending medical personnel to different places such as italy, south africa, and other nations that are understaffed in their hospitals (petkova, ) . despite the widespread togetherness and empathy toward those that were highly hit, when the pandemic started to become serious in almost every part of the world -with the number of confirmed cases and deaths starting to grow exponentially, countries started to close their borders and institute stringent measures. others banned entry of foreigners, and permanent residents and citizens returning from countries affected by the virus were forced to quarantine for a minimum of days. other countries imposed nationwide lockdowns and curfews, only exempting essential service providers. in other instances, countries such as russia (afp, ), germany (hodgson, ) , india (suneja, ) , and also those in the european regions (euroean commission, ) imposed strict requirements and regulations that were to guide the exportation of ppes (glöckle, ) . such actions were taken in each individual country, and region, as it became apparent that the world was experiencing a shortage of the ppes and other medical supplies, despite the increasing number of people getting infected. the shortage of those ppes was confirmed by the world health organization which was calling on countries with manufacturing capabilities to assist those struggling with to acquire those, so as to reduce exposure of health workers and other frontline personnel fighting against covid- . in some cases, for instance, in bangladesh (mahmud, ) , italy (aljazeera, ) , and the united kingdom (express & star, ) , health workers had been reported to have paid the ultimate price of life after being infected while in hospital with lack of sufficient ppes, being taunted as one of the reasons for medical personnel infection. the shortages and strains globally were prompted by the widespread lockdown that countries had imposed, thus resulting to reduce the global supply of raw materials and from the shutting down of factories that produce those products. the shortages also came due to the restriction on international travels, both air and sea, where the little available resources could not reach different parts of the globe in time or would not reach at all. these disruptions in the production/manufacturing sectors and in the supply chain also prompted countries to retreat to formulate nationalist policies that put their interests first. for instance, in most economies, especially in developed countries, there is a notable rush to provide economic stimulus and family reliefs to caution businesses, thus allowing them to continue maintaining the service of employees even during those periods when operations were almost completely grounded. the family reliefs were advanced to caution citizens and permanent residents from the harsh economic realities that covid- had exposed the global population. on this, the united states offered a $ trillion stimulus package (carney, ) , whereas germany, though it is the green light from its parliament, offered a billion euros ($ billion) to mitigate the disruptions brought by the pandemic (reuters, a) . in the united kingdom, morales et al. ( ) report that the government had announced over . billion pounds ($ . billion) to support the selfemployed. similar measures have been advanced in different other countries, which adds to the protectionism shown through border restrictions and banning of flights and exportation of medical supplies. in the united states, president donald trump went further to ban immigration to the united states (zere, ) to protect americans against competition for the few jobs available where almost million had filed unemployment claims by april , (jones, ) . those forms of protectionism, though justified, show how this pandemic has exposed economies, including developed ones. in the less developed economies, the situation was tougher and as reported by united nations world food programme, by the end of this year, the number of the hungry would double to million people (anthem, ) , and such would be brought by the numerous impacts of covid- in those economies. therefore, even as nations look inwardly, there is need for such with capacity to assist to consider doing so as the pandemic shook every social structures as well as the economic foundations of vulnerable economies. since globalization, the world's engines had been running smoothly and had never been halted, even in times of turmoil in some parts of the globe. but the unexpected has happened for the first time, where covid- pandemic was seen to have prompted the grinding halt of not a few but all of the world's engines. the unavoidable lockdowns and stringent border restrictions and travel suspensions just being a few of the underlying factors that made the running of the world engines untenable. the other factors are the morbidity levels across the globe that the disease caused and the unimaginable fear on the humanity and governments, including the most powerful ones, like in the west and in the north. the challenges that the world faced started in china, where the coronavirus started slowly, but within days, it spread widely and in unprecedented levels warranting the closure of all economic activities, including manufacturing sectors and industries. the disruptions in china immediately had ripple effects on all other parts of the world, especially noting that china has, for a long time, been the world's manufacturing capital. the disruptions came just when the consumer demand for different products in other countries from different parts of the world was on a high and rising as depicted in a "united nations conference on trade and development (unctad)" report showing that exports in grew by . % in , with china being the world's leading merchandise trader of the year (unctad, ). on this, developed economies alone exported goods worth us$ billion, whereas least developed economies also exported us$ billion worth of goods (wto, ). during the same period, it is noted that due to favorable trade, the total gross domestic product (gdp) for the entire globe rose to us$ . trillion (wto, ). this figure represents a % growth increase in the gdp from to , where there has been no disruption. surprisingly, export of pharmaceuticals has been the second best performing (a . % yearly rise since ) after the professional and management consultancy sectors. the united states was the largest exporter globally, spending over us$ . trillion in (wto, ). when the coronavirus broke in china, other countries tried to step up and fill the market gap that it left, but this was also short lived, especially to the speed at which the coronavirus spread from china to the rest of the world, especially to europe, which is exporter of manufactured goods, especially pharmaceuticals, as shown by workman ( ) . the spread of the virus prompted lockdowns, border restrictions, and travel bans, meaning that even available products would become hard to export to different parts of the world. on the same, demand for different products reduced significantly, with that of medical supplies and ppes shooting to an alltime high, as scarcity, hoarding, and export restrictions all playing a part. even after china overcame the virus, and resumed its production, it was becoming difficult to ship manufactured goods, first, because of the travel restrictions, and second, because of the deteriorating economic landscapes in different economies, with a substantial number of people losing their jobs globally. according to a report by the china's national bureau of statistics, the recovery of the country's production (purchasing manager's index of . points) has been far much better compared with the recovery in demand for the products (cnbs, ). this could be explained by the fact that apart from china, most of major exporters like the united states were still experiencing unprecedented challenges of covid- and were yet to lift lockdown restrictions, leaving alone opening their borders or suspending travel bans. the disruption in the supply chain also placed tremendous pressures on existing products on the market, with some facing an exponentially demand that could not be met, while the demand for others experienced an unimaginable plunge. those that experienced an increase demand include pharmaceuticals, ppes, ventilators, and other products required in the health sectors, especially with the ranging impacts of coronavirus. according to a who modeling, every month, there is need for million medical masks, million examination gloves, and at least . million goggles (who, ) . in most economies, there were report of exceeding shortages, prompting the who to urge those with manufacturing capacity to help in producing these items in large quantities (who, ) . in other countries such as the united states, it was reported that the government was prompted to force, through an executive order, major companies such as general motors (gm) to produce ventilators to help bridge the gap that the increasing confirmed cases for coronavirus created (haynes, ) . the motor company was later joined by other companies such as ford and tesla in helping the government by mass producing the urgently needed ventilators and other medical supplies. in europe, the carmakers joined to help build ventilators whose demand was skyrocketing, but with very little supply available (kinch et al., ) . globally, parker ( ) estimated that over , extra ventilators were required to satisfy the global hospital demand, with , of those required in the united states; hence, the interventions by those companies could not have come at a better time. in other places, such as in the oil-producing countries, including the united states, the impacts of covid- on different economic sectors such as transport and manufacturing saw the demand for oil and oil products plummeting in rates not experienced in recent history. this prompted a slump in the oil prices, as far as % in the organization of the petroleum exporting countries (opec) (turak, ) , with the prices in the united states for the first time in history going below us$ (suleymanova, ) . the fall in prices even prompted the opec to contemplate reducing their production capacity to void the losses and overproduction. this move was, however, not welcome by all partners, especially by russia, which rejected such calls (faucon and said, ) . in the succeeding section, more on the impacts of the trade disruption will be discussed, especially the consequences that ensued. while countries rushed to institute nationwide lockdowns and impose restriction on the transport sectors, leaving only a few essential service providers to operate, their actions led to an immediate effect on the energy sector. in many economies, including china, the united states, and a large number of european economies, the demand for energy plummeted rapidly, causing a subsequent crash in the oil markets as introduced earlier. with this, for the first time in history, the pressure in the oil market demanded a reduction in production to check on the losses prompted by the reduced oil prices and also by the reduced demand. according to theinternational energy agency (iea), in the month of april alone, the demand for oil across the globe fell by an average of million barrels per down, compared with demand for the same last year (iea, ). this reduction was the lowest that has been witnessed since . the price of crude oil in april was also reduced to a historical low of negative usd- , meaning that the producers were forced to pay buyers for them to take the oil away as nobody wanted to hold onto oil (ambrose, ) . following these unprecedented times, the opec and its allies reached an agreement after lengthy parlays to recommend a reduction in production of approximately . million barrels per day (mb/d) beginning as of may (stevens, ) , which is also the largest cut in production in history. in the agreement, the deal was that each member would reduce their normal daily production, such that, when accumulated, the total reduction would amount to . million barrels per day. for instance, mexico agreed to lower its daily production by , bpd, to be maintained for months (may ejune ) (stillman et al., ) . thereafter, each of the countries that were part of the meeting would taper their production, to ensure that the daily production would not be over . mb/d, as compared with a similar period last year. this would last from july to december . as from january to april , the production is expected to maintain a reduction rate of . mb/ d when another meeting will be held to review the situation market situation (opec, ). in the non-opec countries, their accumulated total of oil production reduction is expected to drop by . million b/d between may and june. also, between july and december, due to some increase in demand as some states, countries, and even region will have gradually started opening up their economies and hence, increase the demand for oil to certain levels, the reduction in these non-opec countries will improve to reach . million b/d (eia, ). but such projection will depend on whether the situation of covid- pandemic will have improved, especially in the united states, which is currently the most affected country globally. these reductions in production were necessary, especially noting that in the united states, the prices of crude oil had plunged from a high of $ per barrel to a low of -$ in just hours after there was an oversupply prompted by lack of storage facilities (ngai et al., ) . in canada, this was seen to have fell by approximately . % in a span of only month from us$ . per barrel (sönnichsen, a) to us$ . per barrel (sönnichsen, b) between march and april . since the discovery of oil, and the subsequent demand for it in different economic sectors across the globe, oil has always been a highly valued commodity, with oil-producing countries enjoying very healthy economic growth over the years. in particular, most of the countries in the gulf region can attribute their high economic growth to their oil endowment. but, the unexpected covid- outbreak and the subsequent rapid spread of the coronavirus threw into disarray those economies, as their economic lifeline was threatened by the low demand for oil. the most challenging part on this is the uncertainty as to how long the covid- crisis was to last and how far down will this have plunged the oil market. as has been discussed earlier, oil-producing nations braced themselves for further drops in demand and prepared to continue lowering their production till (eia, ). this projection could be somehow pegged on the fact that health experts and agencies have warned that the earliest a vaccine for the virus could be made available is late (cullen, ) . and with such, it means that it would be long before countries resume to their previous normal or at least adopt to "a new normal," which cannot be predicted how it will treat the oil market. for now, oil posed as one of the sectors that had supported the economy is on its knee in many economies, forcing governments to consider bailout plans for it. for instance, lefebvre ( ) reported that in the united states, president trump was planning as to how to bail the industry, before it completely collapses. according to experts, the recovery of this market is dependent on how long the industries that rely on it will be grounded and how they will also recover post-covid- (rechtsteiner, ) . and, by the look at how the opec and its allies crafted their recommendations, it may take a substantial amount of time before the industry regains its previous economic metrics. the situation would even worsen if the recession that has been projected to succeed the covid- crisis will actualize. on this, from a historical perspective, recessions have always had bad impact on the oil and energy market (mahalik and mallick, ) , and the coming one would be no different. furthermore if different nations, regions, and economies were to decide to transition out of oildependent economies by embracing renewable energy, this would mark a positive outlook toward a new global political economic landscape. but it would be a setback to the oil-producing countries, which will also be recovering from both the impacts of covid- , which have substantially affected them, and also from the recession. as the spread of covid- reached (by the time of writing) to over countries and territories, and the number of those infected continues to increase from the current figure of . million, and the deaths reaching almost , globally, the scarcity of medical supplies continues to remain one of the stumbling blocks (who, ) . at the beginning, this shortage was attributable to the reduction in the manufacturing activities, more so in china after it instituted a statewide lockdown and restricted any forms of activities except for the supply of essential supplies (bradsher and alderman, ) . later on, as from the end of march , the country's manufacturing sector gradually returned, reaching an operation capacity of almost % by mid-april (cnbs, ). but, even as they started to produce the much needed medical supplies, they faced the unprecedented challenge in the supply chain as travel across and within most countries had been suspended or banned. though the country has a robust and excellent link to almost all parts of the globe due to air and shipping routes, moving the manufactured good became a sudden challenge. as those challenges were being experienced, on local scenes, there was mounting pressure on existing stocks of health equipment, especially as the number of those needing hospitalization continues to swell. in some countries, to supplement the diminishing stocks they had, the local manufacturing sectors were put to maximum operational capacities, but still their efforts seemed not to suffice to satisfy increasing demand. for instance, in the united states, m and the prestige ameritech companies (martineau, ) , the largest producers of n masks, together with other local small competitors, initiated their full operation capacities to meet the demand for over million n masks that the health sector had estimated would be required in march, but their effort only allowed them to produce a maximum of million masks (leary and hufford, ) . this was computed even after president trump had invoked the defense production act (dpa) to force the m company to increase their production capacity and to stop exporting any mask outside of america (heilweil, ) . in europe, the same scenario of shortage was live and hurting (tsang, ) , and the potential companies such as innovatec gmbh & co.kg based in germany and bavaria-based sandler ag and others that could fill the gap were only managed to do this after june or august (burger, ) . however, even after their input, the global requirement for respirators was not expected to be met. for instance, it is estimated that europe needs at least million n masks every day, which translates to more than . billion masks a year, and this could change if the number of infections were to increase (burger, ) . local companies were not anticipating a pandemic, or such a surge in demand was insufficiently prepared to meet this demand. amid those supply shortages, governments, besides that of the united states, have set to force companies prioritize production of medical supplies and, in other cases, have seized the control of shipment and supply of those products to ensure that they remain within the boundaries of the country. for instance, in the united states, the control of production, supply, and shipment of these vital supplies was now under the federal emergency management agency (fema) (kanno-youngs and nicas, ) . it was accused of using korean war-era production tactics where the government would force companies to prioritize government orders over any other clients (kanno-youngs and nicas, ) . in the united kingdom, though in soft tone, prime minister boris johnson urged car makers in the country to prioritize manufacturing of ventilators and other supplies that could ease the pressure in the medical sphere (faulconbridge et al., ) . in czech republic, the government adopted the same approach taken by the russian, indian, and german governments by banning the exportation of medical supplies (stickings, ) . furthermore, the czech government was also gearing to control and regulate the sale of those supplies locally, to ensure that it could supply health workers and medical fraternities whenever and wherever required ( zurovec, ) . in other cases, governments have even been accused of applying underhand tactics to ensure they have supplies in their country. for instance, the us government was accused by the local government of berlin of "piracy" for redirecting over , masks en route to germany to be used locally (bbc, a). these had been exported by the m company, but the government "confiscated" the shipment and returned it to the united states. germany also lost over million masks in a kenyan airport in march in unclear circumstances (simsek, ) . in south korea, anyone implicated of hoarding masks or any other medical items in high demand in hospital was assured of a years jail term or fines/penalties reaching up to $ , (choi, ) . in indonesia, the security officers were forced to conduct a wide search after it became clear that people had purchased and stockpiled masks, with an aim of hoarding them until prices were favorable. in one warehouse, they were able to seize a consignment of , masks and arrested the owners who are facing jail terms of hefty penalties for their actions (williams, ) . these and many other actions and strategies that governments across the globe have undertaken to ensure that they secure every available medical supplies in their countries only exemplify that medical supplies have now been branded as high-value commodities and are guarded with every ounce of energy and force. such moves, coupled with border restrictions and banning of foreign citizens, and the counteraccusations on responsibility of governments on stopping or escalating the spread of coronavirus could pose serious security threats. such scenarios are uncommon and could only be traced back to situations witnessed during the world war ii (ww ) and will be expounded further in the next section. with the increased pressure on trade, which has prompted governments to take unprecedented and drastic actions such as those discussed earlier, all aimed at safeguarding local health, social, and economic stabilities, there have been little relative global governmentled action of meaningful significance. in particular, it has been noted that each government has formulated and implemented their own unique policies and measures without regard of what their neighbors, trade partners, or competitors are doing or which policies they have in place. the surprising aspect from the approaches that each government has taken is that all are meant to address a common enemy, which, as argued by guy ( ) , could be defeated in a much easier way if there was global coordination and unity. to the contrary, the solitary approach by governments has been seen to arouse local, regional, and international disagreements and disharmonies that are a threat to global security. for instance, before the emergence of coronavirus in wuhan, china, the united states and china were engaged in trade wars, which led to us banning products from china and imposing heavy taxes on others (ap, ; bbc, ) . but the rivalry between these global economic giants was awakened by the emergence of coronavirus, with the united states accusing china of hiding information, thus affecting us preparedness (sevastopulo and manson, ) . the disharmony escalated with the united states halting its funding to the world health organization (who) and accusing of the latter of collaborating with china in misinforming the world about the emergence of the virus (smith, ) . with no endpoint as to when the covid- crisis may end, plus the numerous challenges such as the shortages in the health sector, the widespread job loss, the social tension as people get tired of staying at home, and other issues, there are fears that more drastic actions may be inevitable. on this, it would not be surprising to see people, groups, or even governments use excessive force in a bid to demand some compliance on a number of pressing concerns. in fact, even such has started in china, where locals have been reported in a number of occasions to have violently attacked minority groups (mostly africans) by ejecting them from their apartments and preventing them from accessing restaurants, food store, and other basic facilities (davidson, ) . in the heilongjiang province, china, there also looms heightened discord between local government and the russian government due to suspension of the suifenhe land port over the coronavirus cases reported to be from chinese nationals returning from russia (wu, ) . suspending the port meant curtailing movement of trade within the border towns between the two countries; for this reason, the russian side threatened to deport the chinese citizens (qi and sheng, ) . while these examples exemplify the delicate situations that were live in different parts of the world, an urgent global solution and guideline were required on different issues. one of the bodies that is taking leadership on this front, especially on global collaboration on the health sector, is the who, but its soar relationship with the united states, which is also its major financier, is proving a difficult situation. on the same, its reputation was questioned when its director-general publicly accused taiwan of racism and personal attacks on him (hioe, ) , where taiwan launched a scathing counterattack accusing the who chief's accusation as "imaginary and irresponsible" (bbc, b). others who would be expected to have provided leadership included the united states, being a superpower and the largest economy, but their solitary approach to fighting the coronavirus, including suspending flights, banning noncitizens, and banning exportation of medical supplies from its land showed the contrary (fuchs, ; reuters, b; zere, ) . the european union fell short when it launched strict export regulation on health supplies, amid scarcity in other areas, especially to vulnerable nations (euroean commission, ). therefore, it is incumbent upon a global unbiased organization, to take charge and ensure that the geopolitical tensions being witnessed do not escalate to events or situations that would jeopardize global peace. and on this, the un body was rightly constituted for such a noble cause, especially noting that it was formed to ensure that world peace is maintained (un). while it is true that the un secretary general has invariably called for global unity to find a lasting solution, the powerful arm of this body, the un security council, has conspicuously been missing on the front line, especially to ensure that peace will not be threatened (gladstone, ) . with the current reluctant approach to this global crisis by the un security council, there are fears that the deepening crisis escalating to conflicts may arise. to put this into perspective, as noted earlier, the united states had already withdrawn its funding to the who, and previously, it had also halted its financial support to unesco, another un body. if the covid- crisis continues, hence causing more economic, social, and even political strains, there are possibilities that other key financiers of these international bodies may also follow the lead by the united states and withdraw their financial support, and instead, redirect the funding internally to support different sectors locally. with such a scenario, that would leave the un with limited resources; thus, it would not be in a position to undertake its responsibility or even safeguard the strides it has already made in different spheres globally. unfortunately, the actions of halting financial support for such bodies in times of the covid- pandemic impact not only on the health sector but also on other related sectors. this will also act as a dangerous international precedence in world diplomacy and international relations. on this, it is worth noting that, besides the coronavirus, the world is still under serious threats from other sever threats such as climate change and hunger. and, already, the world food programme have indicated that by the end of the year, following the emergence of coronavirus, those facing acute hunger globally would double to reaching over million people (anthem, ) . similarly, in respect to climate change, if history was to repeat itself, it would be disastrous as the gains already achieved, especially in regard to paris agreement, and others would be watered down as nations try to restore their economies. russia bans export of masks, hazmat suits to fight coronavirus one hundered italian doctors have died of coronavirus oil prices dip below zero as producers forced to pay to dispose of excess risk of hunger pandemic as covid- set to almost double acute hunger by end of trump's % tariffs on $ billion in chinese goods take effect available at trump escalates trade war with more china tariffs coronavirus: us accused of 'piracy' over mask 'confiscation coronavirus: who chief and taiwan in row over 'racist' comments the world needs masks. china makes them, but has been hoarding them europe's scramble for face masks prompts longer term rethink senate unanimously passes $ t coronavirus stimulus package face mask and hand sanitizer hoarders face $ , fine and up to years in prison under new south korean law amid coronavirus spread decline of major economic indicators significantly narrowed down in march coronavirus vaccine won't be ready until end of under "most optimistic chineseofficial: claims of racial targeting are 'reasonable concerns short-term energy outlook commission publishes guidance on export requirements for personal protective equipment the nhs workers who have died during the coronavirus pandemic russia blocks opec response to coronavirus make us ventilators to fight coronavirus, uk asks ford and rolls royce the us-china coronavirus blame game is undermining diplomacy security council 'missing in action' in coronavirus fight export restrictions under scrutiny e the legal dimensions of export restrictions on personal protective equipment coronavirus shows we are not at all prepared for the security threat of climate change trump invokes defense production act to force gm to make ventilators trump ordered more n masks. m says his tactics could make the shortage worse who director-general accuses taiwan of campaign against him involving available at: ft.com/content/ c a fc-a - -a -fe a dcc faa jobless claims climb to million in six weeks as covid- layoffs continue to rise swept up by fema': complicated medical supply system sows confusion carmakers in europe, us switch to ventilator production trump administration orders million face masks from m for coronavirus pandemic energy consumption, economic growth and financial development: exploring the empirical linkages for india hundreds of doctors in bangladesh infected with coronavirus the 'surreal' frenzy inside the us' biggest mask maker virus aid package beats financial crisis stimulus oil plunges below zero for first time in unprecedented wipeout the th (extraordinary) opec and non-opec ministerial meeting concludes more ventilators needed to cope with coronavirus outbreak cuba has a history of sending medical teams to nations in crisis ) china, russia appear to be in discord over whether to re-open land poart amid pandemic oil prices could remain depressed for at least a year. here's why factbox: germany's anti-coronavirus stimulus package portugal to treat migrants as residents during coronavirus crisis russia sends plane with medical supplies to us for coronavirus response donald trump threatens to freeze funding for who german shipment of million masks lost in kenya trump halts world health organisation funding over coronavirus 'failure western canadian select (wcs) crude oil monthly price western canadian select (wcs) crude oil weekly prices global death toll from coronavirus tops opec and allies finalize record oil production cut after days of discussion countries around the world hoard medical supplies to tackle coronavirus: germany and russia ban exports, south korea stockpiles masks and india limits paracetamol sales mexico reaches deal with u.s. to cut oil production allowing for opecþ output cuts crash! us crude futures turn negative for first time in history government bans exports of certain masks, ventilators, raw material for masks oil prices may now be at a bottom after historic opec deal coronavirus aid from u.s. groups arrives in china maintain international peace and security shortage of personal protective equipment endangering health workers worldwide police seize , face masks from indonesian warehouse after country's first coronavirus case sparks panic buying and soaring prices drugs and medicine exports by country report coronavirus cases world trade statistical review remote chinese city hit by coronavirus after weeks of feeling safe trump's travel ban: thousands of lives in limbo respirator prices will be regulated due to coronavirus key: cord- - ccrkfsa authors: putter, jeffrey s.; seghatchian, jerard title: an update on covid- infection control measures, plasma-based therapeutics, corticosteroid pharmacotherapy and vaccine research date: - - journal: transfus apher sci doi: . /j.transci. . sha: doc_id: cord_uid: ccrkfsa this communication provides a compilation on aspects of covid- infection control measures, describes the potential role of therapeutic plasma exchange to reduce fatality rates, addresses precautions concerning dexamethasone pharmacotherapy and updates the current status on the availability of vaccines. as part of passive immunotherapy, it focuses on various blood derivatives. these include coronavirus neutralising antibodies extracted from different sources to be administered as a pure hyper concentrate intramuscularly or for upgrading and standardising the specific potency of high affinity antibodies. these processes are intended to compose standardised pooled bioproducts of corona convalescent plasma/cryosupernatant that are pathogen inactivated for additional safety by well-established uv technologies. for the best practice of optimising plasma exchange, hyper concentrate nab should be added to the cryosupernatant, which contains some of the active principles of corona convalescent plasma. the cryosupernatant apart from the high molecular weight viscous part of cold insoluble proteins that are removed, is equivalent to ccp, but makes it safer for general application. such a bioproduct is often used routinely for substitution therapy of thrombotic thrombocytopenic purpura. alternative resources of large-scale specific coronavirus antibodies warrant further exploration such as cadaveric donations. the early uses of therapeutic plasma exchange and low molecular weight heparin, for any clinical trial in development is warranted, in order to interdict the intense inflammatory/kinin driven cascade. because coronavirus positive patients are highly prone to thrombosis, thromboprophylaxis is necessary, even some time after recovery guided by the laboratory data. exchange, hyper concentrate nab should be added to the cryosupernatant, which contains some of the active principles of corona convalescent plasma. the cryosupernatant apart from the high molecular weight viscous part of cold insoluble proteins that are removed, is equivalent to ccp, but makes it safer for general application. such a bioproduct is often used routinely for substitution therapy of thrombotic thrombocytopenic purpura. alternative we are well cognizant of a nefarious strain of the coronavirus sars cov that has been eclipsing the globe causing unprecedented health and economic chaos to the current generation. in a spirit of oneness to combat this marauding infection, we are challenged to develop and harness an arsenal of well-validated tools for the purposes of precision diagnoses, monitoring and treatment. vigilance in these key areas is critical to protect our national health and economies against a formidable adversary. currently, a collaboration of all international scientific and medical entities is summoned in an effort to develop effective preventative strategies to slow down the spread of this virus. equally important are optimising therapeutics to reduce the morbidity and mortality associated with this infection run amok. certain wellknown interests have sought to downplay the seriousness of the coronavirus problem in order to advance their own political agendas. one notable unsubstantiated allegation is that up to % of patient cases are harmless when in reality, the serious illness rate has fluctuated up to %. multiplicities of dangerous complications attendant to the virus, which cannot be ignored, include sepsis, refractory acute respiratory distress syndrome and multi-organ dysfunction and the severe vascular insults of thromboembolism and stroke. the propagation of the disease is of particular concern to a vulnerable patient population over the age of years and among the icu patients, wherein mortality rates may exceed % for the elderly. contemporaneously, there are some significant gaps in leadership, often sending misinformation to the public that threatens the capacity to safely reopen. one poignant example is non-compliance in wearing face masks. there is very fine line between encouraging liberty for all juxtaposed to being responsible members of the society; working in concert to follow the medical guidelines and conscientiously foster public health safety. given that the coronavirus has dangerous capacity to cause consequential morbidity and mortality in spite of contemporary therapeutic modalities, we need to aggressively pursue new treatment strategies within our armamentarium, one being therapeutic plasma exchange. as the virus can cause excess inflammatory mediators such as cytokines and chemokines to circulate, in theory it would be advantageous to exchange patients with fresh frozen plasma or convalescent plasma containing a fixed dose of coronavirus neutralising antibody, nab, if available from a donor. the perpetuation of the coronavirus onslaught interestingly appears to be non-seasonal in nature and quite pernicious, an apparent continuous wave of infection worldwide. of special concern to public health officials is the potential devastating impact of other viruses such as influenza in the fall superimposed on the coronavirus plague. this is especially an issue for those that are susceptible, not having received an influenza vaccination. the incidence of coronavirus disease activity in the population appears to fluctuate from partially controlled at lock down to exponential growth of virus dissemination upon opening. the latter problem is thought to be consequent to a lapse in executing effective infection control practices by some noncompliers, with consistency, in the public. historically, "passive immunotherapy" has a positive track record as in the treatment of the ebola virus; these are smaller observational studies but they encourage therapeutic use for coronavirus too [ , ] . in consideration of the very low risk of complications of plasma exchange therapy, it is a very attractive first treatment option for coronavirus. this is practicable if the usage is standardised, such as the use of ( .) "a minipool of pathogen reduced ccp with an elevated dose of neutralising antibodies from at least two ccp donations" or as a second viable preparation alternative, ( .) namely a homogenous standardised cryosupernatant with a fixed potency of neutralising antibody, as previously proposed by one of us [ ] . in order to apply the use of passive immunotherapy consistently, coronaplasma bioproducts for transfusion exchange should be standardised with respect to the level, potency and avidity of antibodies such as would be advantageous in the processing of minipool convalescent plasma [ ] . moreover, the antibody levels of ccp can be boosted by hyperimmune covid antibodies obtainable by using a promising on line affinity column separation methodology or otherwise, as described earlier [ ] ; and such a pure hyperimmune coronavirus antibody can be delivered by intramuscular injections with fixed potency and could be prioritised to healthcare workers initially. alternatively, the above purer hyperimmune products can be used for upgrading the antibody content of the potential pool of ccp or its cryosupernatant, that will be essential as the carrier of such bioproduct in therapeutic plasma exchange (tpe). incorporating these hyperimmune products in plasma exchange is believed to have potential therapeutic value. to this end, it is currently indeterminate precisely which components of exchange plasmas might be integral to modulate the hyperinflammatory and hypercoagulable states triggered by the virus. exploring further, some large-scale alternative practicable sources of coronavirus neutralising antibodies are warranted for implementation. one possibility is consented cadaveric donations, either from the serum or a pulmonary lavage solution, but clearly in advance of decomposition. such an approach, if proven to be viable, could alleviate the time and cost-pressure and the need for higher throughput that make developing therapeutic neutralising antibodies at the right dose a real challenge to overcome, given the limited availability of corona convalescent plasma. regarding the importance of continual quality and safety improvement strategies related to harvesting corona nab, all bioproducts for reinfusion need to have pathogen reduction whether used as hyperimmune immunoglobulins or using targeted affinity column processing methods. in fact, this is a current requirement for all human derived bioproducts for which safety practices are already in place. affinity column processing is a favoured option, to mainly enrich the useful circulatory corona autoantibodies. in concert with the manufacturers, sterilized bioproducts in ampule format could be produced immediately to satisfy demand. it is important to highlight that circulating coronavirus antigen has been identified by rna assays in some adults who recovered from the infection. as a result of the possibility of a transmissible virus, the implementation of pathogen reduction methodology therefore must become an integral part of all reinfusion programs as highlighted before [ , ] . we propose early targeted therapeutic plasma exchange in combination with inflammatory t-cells, monocytes, neutrophils and macrophages. there is thought to be a predisposition to cytokine and/or chemokine release in selected patients triggering a dangerous hyperimmune reaction and associated severe cytopathic effects such as a rapidly progressive pulmonary edema and acute hypercoagulability [ ] . one observation is that patients having the poorest medical outcomes after contracting the infection have a tendency to a higher viral load, an rnaemia as assessed by pcr but not always a consistent finding. paradoxically, those that develop the highest titers of high affinity antibodies against the virion appear to have the poorest outcomes compared to patients with less severe disease. there is ongoing research into this inter-individual variability in response to coronavirus infection; to determine why these factors appear to be associated with an increased risk of developing a hyperimmune response and heightened allo/autoimmunity in some patients [ , ] and impairing special t-cell and macrophage function essential for host defenses and recovery from the virus and/or nosocomial infection [ ] . by comparison, it is instructive to reflect historically about the role of corticosteroids and the influensa a h n v outbreak. when studied in that pandemic, very early treatment by corticosteroids of ards occurred in a selected cohort of patients, the french registry that specifically excluded confounding comorbidities other than obesity. statistical analyses showed no medical benefit and yielded poorer outcomes, excess deaths in association with the steroids [ ] . this leads us to view extremely cautiously the current recommendation for dexamethasone to treat oxygen dependent covid- patients. moreover, an endorsement of the use of dexamethasone absent precise guidelines to initiate treatment is of concern. ostensibly, patient's that would recover absent steroids may receive it anyway and now the ones we propose to protect are exposed to indeterminate risk. nevertheless, the fact is that vaccines take time to be fully implemented on a large scale globally. even if any of the trials indicate that such a vaccine is potentially working, a key question is whether there is a durable protective response to promote herd immunity and for how long. it is for this reason that it is more than likely a requirement to implement several different types of effective candidate vaccines and our newer proposal of passive immunity through safer pooled ccp with an upgraded nab protocol in parallel. the covid- pandemic has created unique challenges all over the world for infection control. in retrospect, given the easy respiratory transmission of the virus, we should have: ( .) marshalled earlier efforts by the manufacturers to ramp-up production of n masks to effectively filter out the virus; and ( .) promoted national educational campaigns on how to properly wear masks. as the virus shall likely linger with us for some years to come, it would clearly be productive to institute these two simple control measures going forward; current vaccine trials appear promising in the hope to abort the covid- pandemic but are not a panacea. the vaccine is likely to be ineffective for some and non-administered by many for various personal reasons. as a result, we need to encompass a range of therapeutic tools such as tpe, plasma derivatives and well-selected pharmacotherapies to supplant vaccines in order to treat the worst complications of this respiratory viral disease. a continuous wave of infection is already in place in some parts of europe and the usa. in the absence of a reliable vaccine, preparation of hyperimmune coronavirus nab must be pursued consistently and with standardisation from all sources. treatment for emerging viruses: convalescent plasma and covid- convalescent plasma, an apheresis research project by targeting and motivating the fully recovered covid- patients: a rousing message of clinical benefits to both donors/ recipients alike use of convalescent whole blood or plasma collected from patients recovered from ebola virus disease for transfusion as an empirical treatment during outbreaks ebola virus convalescent blood products: where we are now and where we may need to go covid- , induced activation of haemostais, and immune reactions: can an auto-immune reaction contribute to the delayed severe complications observed in some patients low-cost dexamethasone reduces death by up to one third in hospitalised patients with severe respiratory complications of covid- . recovery trial #:~:text=the% recovery% trial% involves% many% thousands% of% doctors% c dexamethasone for covid- ? not so fast early corticosteroids in severe influenza a/h n pneumonia and acute respiratory distress syndrome safety and immunogenicity of the chad)x ncov- vaccine against sars-cov- : a preliminary report of a phase / , single-blind, randomized controlled trial. www.thelancet estimating the extent of asymptomatic covid- and its potential for community transmission: systematic review and meta-analysis pathophysiology, transmission, diagnosis, and treatment of coronavirus disease (covid- ) key: cord- - yi tz authors: poon, l. . c.; yang, h.; dumont, s.; lee, j. c. s.; copel, j. a.; danneels, l.; wright, a.; costa, f. da silva; leung, t. y.; zhang, y.; chen, d.; prefumo, f. title: isuog interim guidance on coronavirus disease (covid‐ ) during pregnancy and puerperium: information for healthcare professionals – an update date: - - journal: ultrasound obstet gynecol doi: . /uog. sha: doc_id: cord_uid: yi tz nan in response to the world health organization (who) statements and international concerns regarding the coronavirus disease (covid- ) outbreak, the international society of ultrasound in obstetrics and gynecology (isuog) is issuing the following guidance for management during pregnancy and puerperium. given the uncertainty regarding many aspects of the clinical course of covid- in pregnancy, frequently updated information may help obstetricians and ultrasound practitioners in counseling pregnant women and further improve our understanding of the pathophysiology of covid- in pregnancy. this statement, which is an update on our previous interim guidance (appendix s ), is not intended to replace other previously published interim guidance on evaluation and management of covid- -exposed pregnant women and should be considered in conjunction with relevant advice from organizations such as: american college of obstetricians and gynecologists (acog): https://www.acog.org/clinical-information/phys ician-faqs/covid- -faqs-for-ob-gyns-obstetrics centers for disease control , caused by severe acute respiratory syndrome coronavirus (sars-cov- ), is a global public health emergency. since the first case of covid- pneumonia was reported in wuhan, hubei province, china, in december , the infection has spread rapidly to the rest of china and beyond , . coronaviruses are enveloped, non-segmented, positivesense ribonucleic acid (rna) viruses belonging to the family coronaviridae, order nidovirales . the epidemics of the two β-coronaviruses, severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov), have caused more than cumulative cases in the past two decades, with mortality rates of % for sars-cov and % for mers-cov [ ] [ ] [ ] [ ] . sars-cov- belongs to the same β-coronavirus subgroup and it has genome similarity of about % and % with sars-cov and mers-cov, respectively . sars-cov- is spread by respiratory droplets and direct contact (when body fluids of an infected person touch another person's eyes, nose or mouth, or an open cut, wound or abrasion). it should be noted that sars-cov- has been found in a laboratory environment to be viable on plastic and stainless-steel surfaces for up to h, whereas on copper and cardboard it is viable for up to h . sars-cov- also remains viable and infectious in aerosols for hours, raising the possibility of airborne transmission. the report of the world health organization (who)-china joint mission on coronavirus disease (covid- ) estimated a high r (reproduction number) of - . . the latest report from who , on april th , estimated the global mortality rate of covid- to be . %. however, other reports, which utilized appropriate adjustment for the case ascertainment rate and the time lag between onset of symptoms and death, suggested the mortality rate to be lower, at . % . huang et al. first reported on a cohort of patients with laboratory-confirmed covid- pneumonia. they described the epidemiological, clinical, laboratory and radiological characteristics, as well as treatment and clinical outcome of the patients. subsequent studies with larger sample sizes have shown similar findings , . the most common symptoms reported are fever ( . %) and cough ( . %) . myalgia or fatigue ( . %), expectoration ( . %) and dyspnea ( . %) are also reported . diarrhea ( . %) and nausea and vomiting ( . %) are less common . breslin et al. observed similar covid- severity in pregnant patients ( . % mild disease, . % severe disease and . % critical disease) to that reported in non-pregnant patients . on admission, ground-glass opacity is the most common radiologic finding on computed tomography (ct) of the chest ( . %) . no radiographic or ct abnormality was found in of ( . %) patients with non-severe disease and in five of ( . %) patients with severe disease. lymphocytopenia was reported to be present in . % of patients on admission . elevated c-reactive protein and lactic dehydrogenase were observed in . % and . % of patients, respectively. breslin et al. screened asymptomatic pregnant patients admitted to the labor ward, and found that . % of them tested positive; however, . % of these patients developed symptoms during admission or early postpartum . universal testing for covid- remains a topic of debate and its need is determined mainly by local protocol and prevalence of the disease. a recent study from new york, usa, reported that a relatively large proportion ( . %) of patients without any symptoms admitted for delivery tested positive for sars-cov- . of these patients, % developed fever before discharge from the hospital. this indicates the potential problem with triaging patients based merely on symptoms in areas with widespread community infection. pregnancy is a physiological state that predisposes women to respiratory complications of viral infection. due to the physiological changes in their immune and cardiopulmonary systems, pregnant women are more likely to develop severe illness after infection with respiratory viruses . in , pregnant women accounted for % of patients infected with influenza a subtype h n virus, but they accounted for % of h n -related deaths . in addition, sars-cov and mers-cov are both known to be responsible for severe complications during pregnancy, including the need for endotracheal intubation, admission to an intensive care unit (icu), renal failure and death , . the case fatality rate of sars-cov infection among pregnant women is up to % . currently, however, there is no evidence that pregnant women are more susceptible to sars-cov- or that those with covid- are more prone to developing severe pneumonia , - . over and above the impact of covid- on a pregnant woman, there are concerns relating to the potential effect on fetal and neonatal outcome; therefore, pregnant women require special attention in relation to prevention, diagnosis and management. based on the limited information available as yet and our knowledge of other similar viral pulmonary infections, the following expert opinions are offered to guide clinical management. case definitions are those included in the who's interim guidance, 'global surveillance for covid- caused by human infection with covid- virus' . • a patient with acute respiratory illness (fever and at least one sign/symptom of respiratory disease (e.g. cough, shortness of breath)) and a history of travel to or residence in a location reporting community transmission of covid- during the days prior to symptom onset; or • a patient with any acute respiratory illness and who has been in contact (see definition of contact below) with a confirmed or probable covid- case in the last days prior to symptom onset; or • a patient with severe acute respiratory illness (fever and at least one sign/symptom of respiratory disease (e.g. cough, shortness of breath)) and who requires hospitalization and in the absence of an alternative diagnosis that fully explains the clinical presentation. a contact is defined as a person who experienced any one of the following exposures during the days before and the days after the onset of symptoms of a probable or confirmed covid- case: note: for confirmed asymptomatic cases, the period of contact is measured from days before to days after the date on which the sample that led to confirmation was taken. • a suspected case for which laboratory testing for covid- is inconclusive; or • a suspected case for which testing could not be performed, for any reason. a person with laboratory confirmation of covid- , irrespective of clinical signs and symptoms. evidence suggests that a proportion of transmissions occur from cases with no or mild symptoms that do not provoke healthcare-seeking behavior . under these circumstances, in areas in which local transmission occurs, an increasing number of cases without a defined chain of transmission is observed and a lower threshold for suspicion in patients with severe acute respiratory infection may be recommended by health authorities . any suspected case should be tested for sars-cov- using available molecular tests, such as quantitative reverse transcription polymerase chain reaction (qrt-pcr). lower-respiratory-tract specimens likely have a higher diagnostic value compared with upperrespiratory-tract specimens for detecting sars-cov- . the who recommends that, if possible, lowerrespiratory-tract specimens, such as sputum, endotracheal aspirate or bronchoalveolar lavage, be collected for sars-cov- testing . if patients do not have signs or symptoms of lower-respiratory-tract disease or specimen collection for lower-respiratory-tract disease is clinically indicated but collection is not possible, upper-respiratory-tract specimens of combined nasopharyngeal and oropharyngeal swabs should be collected. if initial testing is negative in a patient who is strongly suspected of having covid- , the patient should be resampled, with a sampling time interval of at least day, and specimens collected from multiple respiratory-tract sites (nose, sputum, endotracheal aspirate). additional specimens, such as blood, urine and stool, may be collected to monitor the presence of virus and the shedding of virus from different body compartments. when qrt-pcr analysis is negative for two consecutive tests, covid- can be ruled out. the who has provided guidance on the rational use of ppe for covid- . when conducting aerosol-generating procedures (e.g. tracheal intubation, non-invasive ventilation, cardiopulmonary resuscitation, manual ventilation before intubation), healthcare workers are advised to use respirators (e.g. fit-tested n , ffp or equivalent standard) with their ppe , . the centers for disease control and prevention (cdc) additionally considers procedures that are likely to induce coughing (e.g. sputum induction, collection of nasopharyngeal swabs and suctioning) as aerosol-generating procedures and cdc guidance includes the option of using a powered air-purifying respirator , . chest imaging, especially ct scan, is essential for evaluation of the clinical condition of a pregnant woman with covid- [ ] [ ] [ ] . fetal growth restriction (fgr), microcephaly and intellectual disability are the most common adverse effects from high-dose (> mgy) radiation exposure , . according to the american college of radiology and american college of obstetricians and gynecologists, when a pregnant woman undergoes a single chest x-ray examination, the radiation dose to the fetus is . - . mgy, which is negligible, while the radiation dose to the fetus is . - . mgy from a single chest ct scan or ct pulmonary angiogram [ ] [ ] [ ] . chest ct scanning has high sensitivity ( %) for diagnosis of covid- . in a pregnant woman with suspected covid- , a chest ct scan may be considered as a primary tool for the detection of covid- in epidemic areas . informed consent should be acquired (shared decision-making) and a radiation shield applied over the gravid uterus. because of the logistics involved in performing a ct scan on critically ill patients, and the need for thorough cleaning of the ct unit after imaging a covid- patient, a portable chest x-ray is an acceptable alternative to a ct scan. a ct pulmonary angiogram is generally used in preference to a ventilation/perfusion scan on clinical suspicion of pulmonary embolus and should not be withheld during pregnancy. during the covid- pandemic, it has been proposed that ultrasound examination of the lungs of a pregnant woman with suspected covid- could be carried out at the same time as the obstetric scan, in order to minimize the risk of radiation as well as streamline the clinical assessment of these patients. this mode of lung imaging could also be considered when chest x-ray and ct scan are not available. however, management should be determined by the clinical features and severity of the disease, and not be based merely on diagnostic imaging. a practical guide on how to perform lung ultrasound examination in pregnant women with suspected covid- was published recently . in brief, the lung ultrasound scan can be performed using any type of machine and any type of transducer (including linear, convex and microconvex). detailed guidance regarding cleaning of ultrasound equipment and transducers in the context of covid- has been provided in the article 'isuog safety committee position statement on safe performance of obstetric and gynecological scans and equipment cleaning in context of covid- ' . on ultrasound, horizontal 'a-lines' are the hallmark of the normal lung. when the lung loses normal aeration, but is not completely consolidated, it generates different shapes and lengths of vertical artifacts, usually called 'b-lines'. when the density of the peripheral lung parenchyma is increased, ultrasound examination shows a white area (the so-called 'ultrasonographic white lung'), in which neither a-lines nor separated b-lines are visible. consolidation appears as an irregular hypoechoic area, and pleural effusion appears anechoic. a videoclip and images demonstrating these findings can be found in the original article . following the obstetric abdominal ultrasound examination, with the patient in a supine position, the examiner can simply move the probe from the abdomen to the chest, scanning the anterior and lateral areas of the thorax. the examination should cover the whole pulmonary area, from basal to upper areas of the thorax. four vertical lines (right mid-axillary line, right parasternal line, left parasternal line and left mid-axillary line) can be followed in order to perform a systematic examination. with the patient in a sitting or lateral position, the posterior paravertebral surface of the thorax should then be scanned, from basal to upper areas or along posterior-axillary lines according to the patient's position. refer to appendix . triage of pregnant patients who potentially have covid- is of great importance in order to reduce the risk of exposure for patients and healthcare workers alike . setting up a triage station outside the obstetric ward and outpatient clinic is essential, allowing for systematic and thorough screening (appendix ) for symptoms (e.g. fever, cough, sore throat) and risk factors (based on travel history, occupation, contact and cluster (tocc)). temperature should be checked. when concern is raised about a potential covid- patient, i.e. due to symptoms and/or tocc risk factors, a surgical facemask should be put on the patient and she should be separated from other patients, preferably in an isolated covid- unit. healthcare workers should don appropriate ppe for the management of pregnant women with suspected/probable/confirmed covid- , , . refer to appendix . suspected, probable and confirmed cases of covid- should ideally be managed by designated tertiary hospitals with effective isolation facilities and protection equipment . suspected/probable cases should be treated in isolation and confirmed cases should be managed in a negative-pressure isolation room, when available; otherwise, designated covid- units can help reduce spread by cohorting affected patients with dedicated staffing. designated hospitals should set up a dedicated operating room and a neonatal isolation ward. ideally, the operating room and neonatal isolation ward should have negative-pressure ventilation. when it is not possible to set up negative-pressure ventilation for operating rooms, it is advisable to discuss with the hospital engineer whether it is appropriate to switch off their positive-pressure ventilation. all attending medical staff should don ppe (fit-tested n , ffp or equivalent-standard respirator, eye protection (goggles and/or face shield), disposable fluid-resistant and impermeable protective gown and double gloves) when providing care for confirmed cases of covid- , , . however, in areas with widespread local transmission of the disease, health services may be unable to provide such levels of care to all suspected, probable or confirmed covid- cases. pregnant women with a mild clinical presentation may not initially require hospital admission, and home confinement can be considered, provided that this is possible logistically and that monitoring of the woman's condition can be ensured . if negative-pressure isolation rooms are not available, patients should be isolated in single rooms, or grouped together once covid- has been confirmed. for transfer of confirmed cases, the attending medical team should don ppe and keep themselves and their patient a minimum distance of m, or feet, from any individuals without ppe. when an inpatient has confirmed covid- , vigilant maternal monitoring (including oxygen saturation monitoring) is of paramount importance, allowing for rapid initiation of supportive care . although not yet validated in covid- pregnant patients, a modified early obstetric warning score (meows) can be used to enable early recognition of critical illness , . an adapted meows chart is provided in appendix . when the maternal condition requires additional care, this should not be withheld due to pregnancy. respiratory indications for transfer to an isolated negative-pressure room in the icu include pulmonary edema, need for airway protection and necessity of mechanical ventilation . patients with hypoxemic respiratory failure should be admitted to the icu as soon as possible. multidisciplinary care (obstetricians, maternal-fetal-medicine subspecialists, intensivists, obstetric anesthetists, internal-medicine or respiratory physicians, midwives, virologists, microbiologists, neonatologists, infectious-disease specialists) is essential, particularly because some pregnancy-related diseases can cause findings similar to those of severe covid- (e.g. pulmonary embolism) and because the physiologic changes of pregnancy may affect management (e.g. optimal maternal positioning, changes in respiratory physiology affecting appropriate ventilator settings). particular attention should be paid to fluid and electrolyte balance. symptoms should be treated, for example with antipyretic medicines. maternal vital signs (preferably using meows) and oxygen saturation level should be monitored vigilantly to minimize maternal hypoxia. arterial blood-gas analysis should be conducted. repeat chest imaging (when indicated) should be performed. complete blood count should be evaluated regularly, with renal-and liver-function testing and coagulation testing. ( ) the approach to symptomatic treatment and surveillance is the same as for suspected/probable cases. conservative fluid administration is advised , . fluid balance should be evaluated regularly to minimize the risk of fluid overload . isotonic crystalloid fluid is the first choice of fluid to be administered. ( ) currently, there is no proven antiviral treatment for covid- patients, although a number of drugs are being trialed therapeutically in patients with severe symptoms. decisions regarding antiviral, antimalarial and antibiotic treatment should be undertaken in conjunction with local infectious-disease experts, and with the obstetrician providing advice on potential maternal or fetal effects of any treatment regimen. a summary of potential treatments, including hydroxychloroquine, lopinavir/ritonavir, interferon β- b, tocilizumab, azithromycin and remdesivir, is provided in appendix s . ( ) in non-pregnant covid- patients, comorbidities such as hypertension or diabetes seem to increase the risk for progression to severe disease, with poorer clinical outcome . therefore, it is advisable to monitor closely pregnant patients with these comorbidities and to be aware of this increased risk. ( ) the degree of severity of covid- pneumonia is defined by the infectious diseases society of america/american thoracic society guidelines for community-acquired pneumonia (appendix s ) , . ( ) severe pneumonia is associated with a high maternal and perinatal mortality rate; there is, therefore, a requirement for aggressive treatment, including supporting measures with hydration, oxygen therapy and chest physiotherapy. the case should be managed in a negative-pressure isolation room in the icu, with the woman in a semi-recumbent or prone position, if feasible. support should be provided by a multidisciplinary team . ( ) antibacterial treatment: appropriate antibiotic treatment in combination with antiviral treatment should be used promptly when there is suspected or confirmed secondary bacterial infection, following discussion with microbiologists. ( ) blood-pressure monitoring and fluid-balance management: in patients without septic shock, conservative fluid-management measures should be undertaken . excessive fluid can worsen hypoxemia in severe disease without shock , . in patients with septic shock, fluid resuscitation and inotropes are required to maintain an average arterial pressure ≥ mmhg and a lactate level < mmol/l , . the hour- surviving sepsis campaign bundle of care is a concise and practical approach to initial care for (suspected) sepsis . this bundle of care is provided in appendix s . the who advises administration of - ml crystalloid intravenous fluid in the first - min, as a bolus . ( ) oxygen therapy: supplemental oxygen should be used to maintain oxygen saturation > % , ; oxygen should be given promptly to patients with hypoxemia and/or shock, and the method of ventilation should be according to the patient's condition and following guidance from the intensivists and obstetric anesthetists . accelerated hypoxemia in pregnancy is possible, due to increased oxygen consumption and reduced functional residual capacity . the intensivist should be aware of a higher likelihood of difficult intubation and greater risk of aspiration during pregnancy. ( ) medically indicated preterm delivery should be considered by the multidisciplinary team on a case-by-case basis. early delivery may aid ventilation, allowing for prone ventilation if required. ( ) even in confirmed covid- patients, other causes for maternal collapse should be examined . it has been reported that viral pneumonia in pregnant women is associated with an increased risk of preterm birth, fgr and perinatal mortality . based on nationwide population-based data from taiwan, it was demonstrated that pregnant women with viral pneumonia (n = ) had an increased risk of preterm birth, fgr and having a newborn with low birth weight and apgar score < at min, compared with those without pneumonia (n = ) . a case series of pregnant women with sars-cov in hong kong, china, reported three maternal deaths, that four of seven patients who presented in the first trimester had spontaneous miscarriage, four of five patients who presented after weeks had preterm birth and two mothers recovered without delivery but their ongoing pregnancies were complicated by fgr . currently, there are limited data regarding the impact on the fetus of maternal sars-cov- infection. there is an apparent increase of iatrogenic preterm birth but not of spontaneous preterm birth; therefore, cervical-length screening is not recommended. fever is common in covid- patients. previous data have demonstrated that maternal fever in early pregnancy can cause congenital structural abnormalities involving the neural tube, heart, kidney and other organs [ ] [ ] [ ] . however, a study of pregnant women reported that the rate of fever in early pregnancy was %, while the incidence of fetal malformation in this group was . % . among the viable pregnancies with data collected at - weeks of gestation, in the pregnant women with a reported temperature > • c lasting - days in early pregnancy, compared to those without a fever in early pregnancy, the overall risk of fetal malformation was not increased (odds ratio = . ( % ci, . - . )) . previous studies have reported no evidence of congenital infection with sars-cov, and currently there are no data on the risk of congenital malformation when sars-cov- infection is acquired during the first or early second trimester of pregnancy . if appropriate, giving advice via telephone or videoconferencing to patients with suspected/probable/confirmed covid- can be considered . when the patient has to be seen in hospital, early triage and isolation measures should be applied; all healthcare workers attending these patients should wear appropriate ppe , . management in a negative-pressure room is advised for confirmed cases. however, if this is not available, a dedicated single consultation room, from which any unnecessary equipment has been removed, is advised. thorough disinfection between patients, according to local protocols, is essential, especially of high-touch surfaces , . hospital admission might be required for pregnant patients with suspected/probable/confirmed covid- , either because of the disease itself or for obstetric reasons. a separate (part of the) obstetric ward should be reserved for these patients, preferably with negative-pressure rooms for confirmed cases. this ward should use dedicated equipment, such as cardiotocography (ctg) or ultrasound machines . this equipment should not be removed from the room/ward without appropriate disinfection. prompt review by senior team members and, if necessary, multidisciplinary review, is advised for these patients . even if a patient is managed in an isolation ward, woman-centered and skilled care with psychosocial support remains important . additionally, thromboprophylaxis must be considered for all pregnant women who are managed as inpatients, especially in those with severe disease, unless delivery is imminent (within h) , , . the royal college of obstetricians and gynaecologists advises prophylactic low-molecular-weight heparin for all pregnant women admitted with covid- , and this should also be considered in outpatient self-isolating patients on a case-by-case basis, according to risk factors . however, if the patient decompensates rapidly, a thorough risk-benefit analysis should be made regarding the administration of thromboprophylaxis, due to safety concerns regarding its use in conjunction with neuraxial analgesia. following maternal assessment, ctg for fetal heart-rate (fhr) monitoring, at an appropriate gestational age according to local practice, should be undertaken, as well as ultrasound assessment of fetal growth and amniotic fluid volume, with umbilical artery doppler if necessary. in severe covid- cases, the fetal scan can be performed once the patient is stabilized. all sonographers/sonologists should don appropriate ppe when undertaking the ultrasound scan . adequate cleaning of ultrasound equipment and transducers should be performed before further use . pregnant women with confirmed sars-cov- infection who are asymptomatic, or recovering from mild illness, should be monitored with -weekly ultrasound assessments of fetal growth and amniotic fluid volume, with umbilical artery doppler if necessary , . when the infection is acquired in the first or early second trimester of pregnancy, a detailed morphology scan at - weeks of gestation is indicated, and these pregnancies should be monitored carefully after recovery. the pregnancy should be managed according to the clinical findings, regardless of the timing of infection during pregnancy. all clinical visits for obstetric emergencies should be carried out in agreement with current local guidelines. all routine follow-up appointments should be postponed by days or until positive test results (or two consecutive negative test results) are obtained. recommendations on how to prioritize obstetric ultrasound services are provided in separate documents , . refer to appendix . covid- itself is not an indication for delivery, unless there is a need to improve maternal oxygenation. for suspected, probable and confirmed cases of covid- , delivery should be conducted in a negative-pressure isolation room whenever possible. the timing and mode of delivery should be individualized, dependent mainly on the clinical status of the patient, gestational age and fetal condition . in the event that an infected woman has spontaneous onset of labor with optimal progress, she can be allowed to deliver vaginally . continuous fetal and frequent maternal monitoring is essential in these patients. therefore, for optimum care as well as for the protection of the medical team, given evidence of presence of the virus in feces and the inability of healthcare workers to use adequate ppe during the delivery, water birth should be avoided , . shortening the second stage by operative vaginal delivery can be considered, as active pushing while wearing a surgical mask may be difficult for the woman to achieve . with respect to a pregnant woman without a diagnosis of covid- , but who might be a silent carrier of the virus, we urge caution regarding the practice of active pushing while wearing a surgical mask, as it is unclear if there is an increased risk of exposure to any healthcare professional attending the delivery without ppe, because forceful exhalation may significantly reduce the effectiveness of a mask in preventing the spread of the virus by respiratory droplets . during labor, excessive intravenous fluid should be avoided, especially when administering oxytocin, since this could worsen fluid overload due to its antidiuretic effect . oxytocin should be administered in an isotonic crystalloid such as . % nacl solution. induction of labor can be considered when the cervix is favorable, but there should be a low threshold to expedite the delivery when there is fetal distress, poor progress in labor and/or deterioration in maternal condition. septic shock, acute organ failure or fetal distress should prompt emergency cesarean delivery (or termination, if legal, before fetal viability) . donning ppe is time-consuming, and this may prolong the decision-to-delivery interval, but it is imperative. women and their families should be informed about this possible delay, which may be of particular importance in category- cesarean delivery. both regional anesthesia and general anesthesia can be considered, depending on the clinical condition of the patient and after consultation with the obstetric anesthetist. as general anesthesia is considered an aerosol-generating procedure, regional anesthesia is preferred. when appropriate, an early epidural should be considered for a laboring woman with confirmed covid- . concerning the presence of a birth-partner during childbirth, we advise adherence to local protocols. it is advisable to give the asymptomatic birth-partner a surgical facemask and they must follow strict hand hygiene . however, when the partner is symptomatic, they must remain in isolation and therefore cannot attend the delivery. for preterm cases requiring delivery between and + weeks of gestation, we urge caution regarding the use of antenatal steroids (dexamethasone or betamethasone) for fetal lung maturation in a critically ill patient, because this can potentially worsen her clinical condition and the administration of antenatal steroids might delay the delivery that is necessary for management of the patient, especially when there is a need to improve maternal oxygenation . the use of antenatal steroids should be considered according to risk-benefit analysis and in discussion with infectious-disease specialists, maternal-fetal-medicine subspecialists and neonatologists , . we advise against the use of steroids in women at risk for late preterm delivery (between and weeks of gestation). such risk-benefit analysis and discussion should likewise be applied to the use of tocolysis in women presenting with spontaneous preterm labor. miscarried embryos/fetuses and placentae of covid- pregnant women should be treated as infectious tissues and should be disposed of appropriately. at present, it is uncertain whether there is a risk of vertical mother-to-baby transmission of sars-cov- . in two studies, with a combined total of pregnant women with covid- in the third trimester, amniotic fluid, cord blood and neonatal throat swab samples tested negative for sars-cov- , suggesting there was no evidence of vertical transmission in women who developed covid- pneumonia in late pregnancy , . furthermore, in the study by qiu et al., vaginal secretion samples tested negative for sars-cov- rna . notably, a neonate born to a pregnant woman with covid- tested positive for sars-cov- rna in the pharyngeal swab sample h after birth, but it was subsequently confirmed that qrt-pcr testing of the placenta and cord blood was negative for sars-cov- , suggesting that intrauterine vertical transmission might not have occurred , . two studies recently explored the possibility of vertical transmission of sars-cov- in a combined total of seven affected pregnancies by testing for sars-cov- -specific antibodies (immunoglobulins g and m (igg and igm)) in neonatal serum samples , . their conclusion, that sars-cov- could be transmitted in utero, was based on the presence of igm antibodies, detected by recently developed automated chemiluminescence immunoassays, in blood drawn from three neonates following birth. however, for all three cases, the neonatal respiratory samples tested negative for sars-cov- rna. in the study of dong et al., the observed rapid decline (within days) of anti-sars-cov- igg levels in the infant, along with a decline in igm antibodies, strongly suggests that neonatal anti-sars-cov- igg antibodies were derived transplacentally from the mother, and not actively induced by the presumed neonatal infection . in order to further investigate the possibility of vertical transmission of sars-cov- , appropriately matched biological samples, including cord blood, placental tissue, amniotic fluid and amnion-chorion-interface swab, should be collected immediately after delivery, using aseptic technique, from women with covid- . a neonatal pharyngeal swab can also be collected. if possible, testing for sars-cov- of the miscarried fetus/placenta of covid- pregnant women should be undertaken. in addition to testing for sars-cov- rna by qrt-pcr, serological testing could be an important supplement in order to clarify the issue of vertical transmission of the virus. longitudinal follow-up for - months of infants born to covid- women should be undertaken . regarding neonatal management of suspected, probable and confirmed cases of maternal covid- , the umbilical cord should be clamped promptly and the neonate should be transferred to the resuscitation area for assessment by the attending pediatric team. there should be different healthcare workers taking care of the mother and the baby in order to minimize the risk of cross-contamination. there is insufficient evidence regarding whether delayed cord clamping increases the risk of infection to the newborn via direct contact . in units in which delayed cord clamping is recommended, clinicians should consider carefully whether this practice should be continued. there is also currently insufficient evidence regarding the safety of breastfeeding and the need for mother-baby separation , . if the mother is severely or critically ill, separation appears to be the best option, with attempts to express breastmilk in order to maintain milk production. for this, there should be a dedicated breast pump and the machine should be washed thoroughly, according to the manufacturer's recommendations, after each use . if the patient is asymptomatic or mildly affected, breastfeeding and colocation (also called rooming-in) can be considered by the mother in coordination with healthcare providers, or may be necessary if facility limitations prevent mother-baby separation. since the main concern is that the virus may be transmitted by respiratory droplets rather than breastmilk, breastfeeding mothers should wash their hands and wear a three-ply surgical mask before touching the baby. in case of rooming-in, the baby's cot should be kept at least m from the mother's bed, and a physical barrier, such as a curtain or glass, may be used , . the need to separate mothers with covid- from their newborns, with the consequence that they are unable to breastfeed directly, may impede early bonding as well as establishment of lactation . these factors will inevitably cause additional stress for mothers in the postpartum period. as well as caring for their physical wellbeing, medical teams should consider the mental wellbeing of these mothers, showing appropriate concern and providing support when needed , . at the time of writing, there are no effective drugs or vaccines to prevent covid- . therefore, personal protection should be considered in order to minimize the risk of contracting the virus. a. good personal hygiene should be maintained: during the covid- pandemic period, close contact with others should be consciously avoided, participation in any gathering in which a distance of at least m between individuals cannot be maintained should be avoided, attention should be paid to hand washing and hand sanitizer (with % alcohol concentration) used frequently , . b. a three-ply surgical mask should be worn when visiting a hospital or other high-risk area. c. medical assistance should be sought promptly for timely diagnosis and treatment when symptoms such as fever and cough are experienced. common symptoms at onset of illness include fever, dry cough, myalgia, fatigue, dyspnea and anorexia. ideally, medical staff assigned to care for suspected, probable or confirmed cases of covid- should minimize contact with other patients and colleagues, with the aim of reducing the risk of exposure and potential transmission. i. medical staff who have been exposed unexpectedly, while without ppe, to a covid- pregnant patient, should be quarantined or self-isolate for days. j. pregnant healthcare professionals should follow risk-assessment and infection-control guidelines following exposure to patients with suspected, probable or confirmed covid- . . pregnant women with confirmed covid- should ideally be managed by designated tertiary hospitals, and they should be informed of the risk of adverse pregnancy outcome. . negative-pressure isolation rooms should be set up for safe labor, delivery (including cesarean section) and postpartum (including neonatal) care. . during the covid- pandemic period, a detailed history regarding tocc and clinical manifestations should be acquired routinely from all pregnant women attending for routine care. . chest imaging, especially ct scan, should be included in the work-up of pregnant women with suspected, probable or confirmed covid- . . suspected/probable cases should be treated in isolation and confirmed cases should be managed in a negative-pressure isolation room. a woman with confirmed infection who is critically ill should be admitted to a negative-pressure isolation room in the icu. . antenatal examination and delivery of pregnant women with covid- should be carried out in a negative-pressure isolation room on the labor ward. human traffic around this room should be limited when it is occupied by an infected patient. . all medical staff involved in management of infected women should don appropriate ppe (fit-tested n , ffp or equivalent-standard respirator, eye protection (goggles and/or face shield), disposable fluid-resistant and impermeable protective gown and double gloves). . management of covid- pregnant women should be undertaken by a multidisciplinary team (obstetricians, maternal-fetal-medicine subspecialists, intensivists, obstetric anesthetists, midwives, internal-medicine or respiratory physicians, virologists, microbiologists, neonatologists, infectious-disease specialists). . vigilant maternal monitoring (including oxygensaturation monitoring) of all covid- patients is paramount, allowing for rapid commencement of supportive care. the use of a meows chart is recommended. . timing and mode of delivery should be individualized, dependent mainly on the clinical status of the patient, gestational age and fetal condition. . both regional anesthesia and general anesthesia can be considered, depending on the clinical condition of the patient and after consultation with the obstetric anesthetist. if possible, regional anesthesia is preferable due to a lower risk of transmission in comparison with general anesthesia. . at present, limited data suggest that there is no evidence of vertical mother-to-baby transmission in women who develop covid- in late pregnancy, although case reports of potential vertical transmission have emerged. . there is currently insufficient evidence regarding the safety of breastfeeding and the need for mother-baby separation. if the mother is severely or critically ill, separation appears to be the best option, with attempts to express breastmilk in order to maintain milk production. if the patient is asymptomatic or mildly affected, breastfeeding and colocation (rooming-in) can be considered by the mother in coordination with healthcare providers. . healthcare professionals engaged in obstetric care and those who perform obstetric ultrasound examinations should be trained and fitted appropriately for ppe. . we strongly recommend submitting cases to local, regional or international registries for sars-cov- -infected pregnant women, with the aim of answering the many clinical and scientific questions in relation to the impact of covid- during pregnancy. isuog interim guidance on novel coronavirus infection during pregnancy and puerperium: information for healthcare professionals safety and efficacy of different anesthetic regimens for parturients with covid- undergoing cesarean delivery: a case series of patients world health organization. novel coronavirus -china epidemiology, genetic recombination, and pathogenesis of coronaviruses a novel coronavirus associated with severe acute respiratory syndrome isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome coronavirus (mers-cov) pregnancy and perinatal outcomes of women with severe acute respiratory syndrome genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding aerosol and surface stability of sars-cov- as compared with sars-cov- report of the who-china joint mission on coronavirus disease world health organization. coronavirus disease (covid- ) likelihood of survival of coronavirus disease clinical features of patients infected with novel coronavirus in wuhan, china clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan clinical characteristics of coronavirus disease in china novel coronavirus patients' clinical characteristics, discharge rate and fatality rate of meta-analysis covid- infection among asymptomatic and symptomatic pregnant women: two weeks of confirmed presentations to an affiliated pair of new york city hospitals universal screening for sars-cov- in women admitted for delivery pregnancy and infection influenza a(h n ) virus illness among pregnant women in the united states middle east respiratory syndrome coronavirus (mers-cov) infection during pregnancy: report of two cases & review of the literature clinical management of severe acute respiratory infection when covid- is suspected an analysis of pregnant women with covid- , their newborn infants, and maternal-fetal transmission of sars-cov- : maternal coronavirus infections and pregnancy outcomes clinical manifestations and outcome of sars-cov- infection during pregnancy clinical characteristics and intrauterine vertical transmission potential of covid- infection in nine pregnant women: a retrospective review of medical records clinical features and obstetric and neonatal outcomes of pregnant patients with covid- in wuhan, china: a retrospective, single-centre, descriptive study clinical analysis of pregnant women with novel coronavirus pneumonia world health organization. global surveillance for covid- caused by human infection with covid- virus: interim guidance substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov ) european centre for disease prevention and control. risk assessment on covid- world health organization. laboratory testing for novel coronavirus ( -ncov) in suspected human cases rational use of personal protective equipment for coronavirus disease (covid- ) and considerations during severe shortages centers for disease control and prevention. interim infection prevention and control recommendations for patients with suspected or confirmed coronavirus disease (covid- ) in healthcare settings. isuog safety committee position statement on use of personal protective equipment and hazard mitigation in relation to sars-cov- for practitioners undertaking obstetric and gynecological ultrasound coronavirus disease (covid- ): role of chest ct in diagnosis and management relation between chest ct findings and clinical conditions of coronavirus disease (covid- ) pneumonia: a multicenter study correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases imaging the pregnant patient for nonobstetric conditions: algorithms and radiation dose considerations discussion: severe mental retardation and cancer among atomic bomb survivors exposed in utero american college of obstetricians and gynecologists. committee opinion no. quality initiatives: guidelines for use of medical imaging during pregnancy and lactation how to perform lung ultrasound in pregnant women with suspected covid- isuog safety committee position statement on safe performance of obstetric and gynecological scans and equipment cleaning in context of covid- care of the pregnant woman with covid- in labor and delivery: anesthesia, emergency cesarean delivery, differential diagnosis in the acutely ill parturient, care of the newborn, and protection of the healthcare personnel executive management summary and short report of outcome -management guidelines for obstetric patients and neonates born to mothers with suspected or probable severe acute respiratory syndrome (sars) interim clinical guidance for management of patients with confirmed coronavirus disease (covid- ) bacterial sepsis in pregnancy maternal collapse in pregnancy and the puerperium handbook of covid- prevention and treatment. the first affiliated hospital royal college of obstetricians & gynaecologists. coronavirus (covid- ) infection in pregnancy comorbidity and its impact on patients with covid- in china: a nationwide analysis diagnosis and treatment of adults with community-acquired pneumonia. an official clinical practice guideline of the infectious diseases society of america/american thoracic society consensus guidelines on the management of community-acquired pneumonia in adults coronavirus disease (covid- ) and pregnancy: what obstetricians need to know current challenges in the management of sepsis in icus in resource-poor settings and suggestions for the future the surviving sepsis campaign bundle: update acute respiratory failure and mechanical ventilation in pregnant patient: a narrative review of literature pneumonia during pregnancy: has modern technology improved maternal and fetal outcome? pneumonia and pregnancy outcomes: a nationwide population-based study maternal illness, including fever, and medication use as risk factors for neural tube defects associations between maternal fever and influenza and congenital heart defects maternal febrile illnesses, medication use, and the risk of congenital renal anomalies fever in pregnancy and the risk of congenital malformations: a cohort study infants born to mothers with severe acute respiratory syndrome isuog consensus statement on organization of routine and specialist obstetric ultrasound services in context of covid- guidelines for pregnant women with suspected sars-cov- infection isuog consensus statement on rationalization of early-pregnancy care and provision of ultrasonography in context of sars-cov- prolonged presence of sars-cov- viral rna in faecal samples novel coronavirus infection and pregnancy water intoxication-a dangerous condition in labor and delivery rooms corticosteroids as adjunctive therapy in the treatment of influenza coronavirus in pregnancy and delivery: rapid review clinical characteristics of covid- in pregnancy: analysis of nine cases sars-cov- is not detectable in the vaginal fluid of women with severe covid- infection a case report of neonatal coronavirus disease in china antibodies in infants born to mothers with covid- pneumonia possible vertical transmission of sars-cov- from an infected mother to her newborn intrauterine vertical transmission of sars-cov- : what we know so far clinical analysis of neonates born to mothers with -ncov pneumonia american college of obstetricians and gynecologists centers for disease control and prevention. considerations for inpatient obstetric healthcare settings. from the frontlines of covid- -how prepared are we as obstetricians: a commentary infection prevention and control during health care when novel coronavirus (ncov) infection is suspected guideline for isolation precautions: preventing transmission of infectious agents in health care settings irish maternity early warning system (imews) v : national clinical guideline hydroxychloroquine in systemic lupus erythematosus and rheumatoid arthritis and its safety in pregnancy hydroxychloroquine in lupus pregnancy antirheumatic medications in pregnancy and breastfeeding safety and efficacy of lopinavir/ritonavir during pregnancy: a systematic review lopinavir and atazanavir in pregnancy: comparable infant outcomes, virological efficacies and preterm delivery rates triple antiretroviral compared with zidovudine and single-dose nevirapine prophylaxis during pregnancy and breastfeeding for prevention of mother-to-child transmission of hiv- (kesho bora study): a randomised controlled trial fda drug safety communication: serious health problems seen in premature babies given kaletra (lopinavir/ritonavir) oral solution drugs and lactation database (lactmed) interferon-beta exposure during first trimester is safe in women with multiple sclerosis-a prospective cohort study from the german multiple sclerosis and pregnancy registry pregnancy outcomes from the global pharmacovigilance database on interferon beta- b exposure the association between exposure to interferon-beta during pregnancy and birth measurements in offspring of women with multiple sclerosis drugs and lactation database (lactmed) the eular points to consider for use of antirheumatic drugs before pregnancy, and during pregnancy and lactation critical review of the current recommendations for the treatment of systemic inflammatory rheumatic diseases during pregnancy and lactation associations between macrolide antibiotics prescribing during pregnancy and adverse child outcomes in the uk: population based cohort study associations between use of macrolide antibiotics during pregnancy and adverse child outcomes: a systematic review and meta-analysis the safety of macrolides during lactation use of macrolides in mother and child and risk of infantile hypertrophic pyloric stenosis: nationwide cohort study use of antibiotics during pregnancy and risk of spontaneous abortion association between antibiotic prescribing in pregnancy and cerebral palsy or epilepsy in children born at term: a cohort study using the health improvement network perinatal pharmacokinetics of azithromycin for cesarean prophylaxis pharmacokinetics of transfer of azithromycin into the breast milk of african mothers prophylactic and therapeutic remdesivir (gs- ) treatment in the rhesus macaque model of mers-cov infection a randomized, controlled trial of ebola virus disease therapeutics first newborn baby to receive experimental therapies survives ebola virus disease appendix flowchart for assessment of coronavirus disease (covid- ) risk in obstetric-unit attendees. ct, computed tomography; ppe, personal protective equipment; qrt-pcr, quantitative reverse transcription polymerase chain reaction; sars-cov- , severe acute respiratory syndrome coronavirus ; tocc, travel, occupation, contact and cluster. the following supporting information may be found in the online version of this article:appendix s summary of changes from previous interim guidance appendix s potential drugs for treatment of covid- in pregnant women appendix s infectious diseases society of america/american thoracic society criteria for defining severe community-acquired pneumonia , appendix s hour- surviving sepsis campaign bundle of care key: cord- -c v kbw authors: han, yan-jie; ren, zhi-guang; li, xin-xin; yan, ji-liang; ma, chun-yan; wu, dong-dong; ji, xin-ying title: advances and challenges in the prevention and treatment of covid- date: - - journal: int j med sci doi: . /ijms. sha: doc_id: cord_uid: c v kbw since the end of , a new type of coronavirus pneumonia (covid- ) caused by the severe acute respiratory syndrome coronavirus- (sars-cov- ) has been spreading rapidly throughout the world. previously, there were two outbreaks of severe coronavirus caused by different coronaviruses worldwide, namely severe acute respiratory syndrome coronavirus (sars-cov) and the middle east respiratory syndrome coronavirus (mers-cov). this article introduced the origin, virological characteristics and epidemiological overview of sars-cov- , reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of covid- . the spread of covid- , which first appeared in december , is still increasing rapidly. , at present, cases of covid- caused by sars-cov- have been found in many countries around the world. , according to the latest data of beijing time, may , , there were , , confirmed cases and , deaths worldwide. on january , , the covid- epidemic requires a coordinated international response, indicating that it may pose risks to multiple countries. sars-cov- was isolated from the airway epithelial cells of patients with viral pneumonia in wuhan. compared with known coronaviruses that can infect humans, the sars-cov- structure has certain differences, so it is defined as the seventh coronavirus. sars-cov- belongs to the order nidovirales, coronaviridae. it has an envelope and contains a very large rna virus genome. the d structure of the coronavirus, obtained by cryo-electron tomography, reveals that it is spherical and has an envelope. coronavirus is characterized by spikes sticking out from the surface, which in part have the same characteristics as sars-cov, and other four human coronaviruses hcov-nl (human coronavirus nl ), hcov- e (human coronavirus e), hcov-oc (human coronavirus oc ), and hcov-hku (human coronavirus hku ), which only cause mild respiratory diseases. virus-cell receptor binding and the production of structurally complete virus particles. , importantly, homology modeling shows that the sars-cov- binding domain to the ace receptor is structurally similar to sars-cov. , despite the presence of amino acid mutations in its receptor binding domain, multiple key amino acids are changed. , however, the amino acid perfectly maintains the stability of the mutual structural conformation of the virus s-protein and the ace receptor in a holistic manner. preliminary revealed virus uses ace receptor to enter the cell. , so far, there are no specific drugs specifically used to prevent and treat coronavirus. if there are no vaccine and/or specific antiviral drugs during a virus outbreak, non-specific therapeutic interventions are often used to prevent acute complications and reduce severe morbidity and mortality, such as providing supportive care, including adequate rest, rehydration and analgesics. at the same time, traditional chinese medicine, hormonal drugs, broad-spectrum antibiotics, antivirals, antifungals and interferon-α b can be utilized to minimize the risk of co-infection. in addition, there is no direct clinical evidence which has shown specific anti-sars-cov- efficacy, and further substantial research is needed to pay attention to related adverse reactions. ribavirin (ribavirin) is a synthetic nucleoside antiviral agent with broad-spectrum antiviral activity and inhibits both dna and rna viruses. it is usually used in aerosolized form for adults and children in treatment of respiratory syncytial virus pneumonia. early in vitro studies have shown that administration of ribavirin can enhance the in vitro activity of interferon. ribavirin has anti-mers-cov activity in vitro when used alone or in combination with interferon alpha. clinical studies have shown that ribavirin and regulated interferon alpha- a treatment can significantly improve the -day survival rate and slightly improve the -day survival rate in patients with mers-cov infection. the timing of initiation of antiviral therapy is critical to the treatment of most patients with viral infections. adults: mg/time, intravenous infusion, to times a day, the course of treatment does not exceed days. however, the side effects of ribavirin limit its use to some extent. the use of high-dose ribavirin may be related to hemolytic anemia, neutropenia, teratogenicity, and cardiopulmonary distress. in view of the curative effect of ribavirin in the treatment of diseases caused by sars-cov and mers-cov, it is expected to become one of the effective drugs to treat coronavirus. redesivir (rdv, gs- ), a nucleoside analogue, is a drug under investigation, it has not been approved for marketing in any country yet. it can exert therapeutic effects by inhibiting the synthesis of viral nucleic acids and has antiviral activity. gilead sciences, inc. believes that antiviral nucleic acid analogs, such as ribavirin, will be cut out by the coronavirus exonuclease exon when integrated into viral rna during the treatment of coronavirus infection, but rdv is resistant to exon. the resistance results in rdv treatment of coronavirus are more effective than other nucleic acid drugs. previously, rdv was mainly used as a test drug against ebola virus, and it has a strong anti-filovirus efficacy in vitro. in vitro tests, rdv can effectively inhibit the activity of sars-cov and mers-cov. for both mers-cov and sars-cov, its half effective concentration (ec ) is . μmol/l. in contrast, lopinavir-ritonavir ec values are respectively μmol/l and μmol/l. however, as an effective potential drug for sars-cov- , rdv takes an emergency approach after weighing the risks and benefits. on february , , beijing china-japan friendship hospital led two independent random, double-blind, controlled clinical trials, one for patients with new-type coronavirus mild-to-moderate pneumonia in hospitalized adults ( cases), and one for patients with severe coronavirus-infected adults ( cases), to verify the efficacy and safety of ribavirin. the experiments are currently undergoing. lopinavir and ritonavir (kaletra/aluvia) is the first-line drug for the clinical treatment of aids. , developed by abbott, marketed in , mainly combined with viral protease to inhibit protease function. lopinavir-ritonavir is a compound tablet consisting of lopinavir and ritonavir. lopinavir is a sensitive substrate for cytochromes cyp a and p-glycoprotein. it can block the division of gag-pol polyprotein and has a high protein binding rate in plasma. ritonavir is a substrate of cyp a , p-glycoprotein and cyp d , which inhibit hiv protease: enzymes cannot break down the precursor of gag-pol polyprotein. ritonavir can inhibit cyp a-mediated lopinavir metabolism, resulting in higher lopinavir concentrations. in vitro studies showed that lopinavir and ribavirin can inhibit the replication of mers-cov and sars-cov. adults: mg/ mg each time, orally, bid, and the course of treatment does not exceed days. darunavir (prezista) is a second-generation hiv- protease inhibitor. it was first marketed in the united states in july . it was developed by tibotec, a subsidiary of johnson & johnson. darunavir, ritonavir, ritonavir and the combination of other retroviral drugs can be used to treat hiv infection. it can selectively inhibit the cleavage of hiv-encoded gag-pol polyprotein in virally infected cells, thereby inhibiting viral replication. darunavir in particular patient population (including pregnant women, pediatrics, patients with hiv- infection and co-infection with viral hepatitis) is also safe and effective. transmembrane protease serine (tmprss ) inhibitors may be used to block sars-cov- infection and then used to treat covid- . ace is a metal peptidase, expressed on major viral target cells such as lung cells and intestinal epithelial cells, and its catalytic domain binds to the s protein of sars-cov with high affinity. for viral infectivity, host cell proteases affect the s protein cleavage is crucial. tmprss can activate the spike protein of sars by lysing the spike protein on the cell surface, which in turn binds to ace and enters the host cell. tmprss is expressed in ace -positive cells in the human lung. it is shown that tmprss may play an important role in the transmission of sars-cov in the human respiratory tract. so far, multiple studies showed that sars-cov- is likely to bind to human ace receptors and thus invades the human body. , , many sars-cov- prevention and treatment drugs are screened with the ace receptor as a target. in view of the important role of tmprss in influenza virus and coronavirus infections, tmprss inhibitors might be useful for clinical treatment. favipiravir (avigan) is a broad-spectrum antiviral drug that selectively inhibits the rna polymerase of influenza viruses. it was approved for marketing in japan in march and it is used for antiviral treatment of influenza a and b. it is converted into an active phosphoribosylated form in the cell and recognized as a substrate by viral rna polymerase. favipiravir is active against a variety of influenza viruses including a (h n ) pdm , a (h n ), and a (h n ) avian influenza viruses, and has a synergistic effect with oseltamivir. in addition to its anti-influenza activity, favipiravir blocks the replication of many other rna viruses, including alphaviruses, flaviviruses (yellow fever and west nile virus), enteroviruses (poliomyelitis virus and rhinovirus), influenza a virus, respiratory syncytial virus and norovirus. , a number of marketed drugs with antiviral activity, such as favipiravir, were discovered, and follow-up studies need further verification by animal experiments and clinical trials. (umifenovir) is a synthetic broad-spectrum antiviral compound developed by the ussr research center for medicinal chemistry, used to prevent and treat human influenza a and b influenza infections and post-influenza complications. abidol was used as an anti-influenza virus drug for decades. abidol is active against many dna/rna and enveloped/non-enveloped viruses and inhibits membrane fusion between virus particles and plasma membrane and between virus particles and endosome membrane by embedding in membrane lipids. at present, darunavir and abidol are used in patients with pneumonia infected by a novel coronavirus in zhejiang province. the follow-up treatment effect needs further verification. resveratrol is a natural compound found in grape seeds, peels and red wine. , resveratrol has antiviral activity against respiratory viruses and certain anti-inflammatory effects, so it can be used as an adjuvant treatment for respiratory infections. resveratrol has a wide range of antiviral effects by down-regulating inflammatory signal transduction, which is mainly associated with the inhibition of viral replication, viral protein synthesis, gene expression, and nucleic acid synthesis. [ ] [ ] [ ] in vitro model evaluations show that resveratrol significantly inhibits mers-cov virus infection in a dose-dependent manner and prolongs the survival time of infected cells, which may be related to resveratrol's reduction of nucleocapsid (n) protein expression. nucleocapsid (n) protein is a multifunctional protein essential for cov replication. in addition, resveratrol down-regulates mers-cov-induced apoptosis in vitro. in the case of continuous administration, resveratrol can inhibit mers-cov at lower doses. another study shows that resveratrol also has a significant inhibitory effect on the emerging positive sense rna chikungunya virus, indicating that resveratrol may become a candidate drug for the treatment of new rna viruses. after a cell is infected by a virus, it can synthesize and secrete a substance that can interfere virus replication and enhance antiviral ability of nearby cells. this substance is called interferon. human interferon is subdivided into type i and type ii. the host's inherent interferon response is critical to control viral replication after infection. interferon response can be enhanced by recombinant interferon or interferon inducer. recombinant interferon α and interferon β can inhibit the replication of sars-cov and mers coronavirus in vitro and in animal models. among all subtypes, interferon β b has the best antiviral effect on mers-cov. , various combinations of interferon alpha or interferon beta with other antivirals, such as ribavirin, lopinavir, and ritonavir were used to treat patients with sars and mers. in vivo and in vitro studies showed that the combination of ribavirin with ifnα may have a synergistic effect. the "pneumonitis diagnosis and treatment scheme for new coronavirus infection (trial version )" states that aerosolized interferon alpha can be used as a trial treatment against sars-cov- virus to improve the virus clearance effect of respiratory mucosa in patients. adults: million iu or equivalent dose of interferon alpha each time, add ml of sterile water for injection or normal saline, inhale by atomization, bid. polyinosinic acid-polycytidylic acid is a synthetic analog of dsrna, which can strongly induce type i interferon. however, a recent study showed that the a protein of double-stranded rna-binding domain interacts with polyinosinic acid-polycytidylic acid, thereby inhibiting polyinosinic acid-polycytidylic acid or sendai virus-induced interferon production, but experiments show that polycytidylic acid can still significantly reduce mers-cov load in balb/c mice. nitroxanide (ntz) is another effective type i interferon inducer. it is currently used clinically to treat parasitic infections. it was originally marketed in mexico under the trade name daxon/colufas in , then listed in the united states under the trade name alinia in . it is a synthetic thiazolyl-salicylic acid derivative. in cell culture assays, nitrazine can inhibit the replication of a variety of rna and dna viruses, including respiratory syncytial virus, parainfluenza virus, and coronavirus. nitroxanide has a broad-spectrum antiviral activity: rotavirus, norovirus, hbv, hcv, dengue virus, yellow fever, japanese encephalitis virus. it has been evaluated in phase ii and phase iii clinical trials for the treatment of hcv infection and the treatment of influenza. , cyclophilins (cyclophilins, cyps) belong to the peptidyl-prolyl isomerases (ppiase) family, which are involved in the replication of rna viruses, including human immunodeficiency virus , hepatitis c virus and influenza virus. cyclophilin a is the main cellular target of the immunosuppressive drug cyclosporin a (csa). csa is a classic immunosuppressive drug. it binds to the cell cyclophilin to inhibit calcineurin, thereby preventing the translocation of the nuclear factor of activated t cells from to the nucleus, interleukin and the transcription of genes. csa can inhibit the replication of almost all species of coronavirus in a dose-dependent manner in vitro. cell culture experiments indicated that csa strongly inhibited the replication of sars-cov, mers-cov, human coronavirus e, feline coronavirus, avian infectious bronchitis virus, and mouse hepatitis virus, but they showed a significant blocking effect only in the early stages of replication. compared to other rna viruses ( . - µm), a higher csa concentration ( µm) is required to block coronavirus replication, which indicates that the coronavirus is less sensitive to csa treatment. as an effective and broad-spectrum coronavirus inhibitor, csa and its analogs have good research and development prospects. chloroquine phosphate is a widely used antimalarial and autoimmune disease drug and has recently been reported as a potential broad-spectrum antiviral drug. , chloroquine phosphate can block virus infection by up-regulating the ph of endosomes, required low for virus-cell fusion, and inhibiting glycosylation of cellular receptors. it specifically interacts with sugar-modifying enzymes or glycosyltransferases in human cells. it has been demonstrated that chloroquine phosphate may have an inhibitory effect on quinone reductase , which is structurally adjacent to udp-n-acetylglucosamine -epi-isomerase, thus affecting the biosynthesis of sialic acid. the presence of a sialic acid moiety in the coronavirus receptor ace may explain the inhibitory effect of chloroquine phosphate on sars-cov replication and other functions. , recent cellular experiments showed that chloroquine phosphate is very effective in controlling sars-cov- infection in vitro, and it plays a role in the entry phase and post-entry phase of sars-cov- infection in vero e cells. in addition to its antiviral activity, chloroquine phosphate has immunomodulatory activity and can synergistically enhance its antiviral effect in vivo. given the above characteristics of chloroquine phosphate, it is likely to be clinically applicable to sars-cov- . chlorpromazine is an antipsychotic used to treat schizophrenia. in , chlorpromazine was marketed in france under the trade name largactil; in , it was approved by the fda to be marketed under the trade name thorazine. after most viruses attach to host surface receptors, they enter cells using endocytosis mechanisms (catenin-dependent and independent pathways). sars uses clathrin-dependent mechanisms to enter host cells. it has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit hcv, alpha virus, and various coronaviruses including human coronavirus e, sars-cov and mers-cov in vitro. imatinib (gleevec) is a small molecule inhibitor. nobartis was first marketed in the united states in . it is clinically used to treat chronic myeloid leukemia and malignant gastrointestinal stromal tumors. imatinib is specifically designed to target abelson tyrosine-protein kinase . abl kinase is a non-receptor tyrosine kinase that exists in the nucleus and mitochondria, and mediates a wide range from embryonic morphogenesis to viral infection cellular processes. abl kinase is required for sars-cov and mers-cov to replicate in vitro. as an in vitro inhibitor of sars-cov and mers-cov, imatinib can significantly reduce the titers and inhibit their development process. imatinib's anti-coronavirus activity was mainly manifested in the early stages of infection and worked by inhibiting the fusion of viral particles on the endosomal membrane. monoclonal antibodies (mab) were successfully used to treat various diseases. passive immunotherapy using neutralizing monoclonal antibodies (mab) is an effective preventive and therapeutic agent for emerging viruses. sars-cov and mers-cov have always been a global public health threat. to date, no vaccines or specific therapies have been approved for diseases caused by these two viruses. neutralizing antibodies are a major component of protective immunity against human viral infections. in vivo antibody responses mobilize a mixture of dynamic mabs that work in concert to target various antigens on viral envelope glycoproteins. neutralizing mabs can be achieved by a variety of techniques, such as hybridoma technology, humanized mice, phage or yeast, and single b cell isolation. more and more mabs were developed, with high efficacy against emerging viruses in vitro and in infected animal models. spike glycoproteins play a key role in mediating virus entry and have the capacity to induce protective antibody responses in infected individuals. consistently with it, spike proteins are the main targets of neutralizing antibodies. regeneron et al. used velocimmune mice to generate fully human non-competitive monoclonal antibodies that bind to mers-cov spike protein, and the characterization of two lead monoclonal antibody candidates (regn and regn ) were performed in vitro and in vivo. both mabs effectively neutralize mers-cov in vitro. moreover, in vivo studies in infected mouse models showed that treatment of infected mice can decrease lung virus titers. currently, multiple mabs for sars-cov and mers-cov are undergoing the phase Ⅰ clinical trial, which has promising prospects for the treatment of new viral diseases. based on the above studies, neutralizing antibodies to spike proteins on the surface of sars-cov- may be the first therapy considered by researchers. recently, genbank has released the sars-cov- genomic sequence (mn . ). spike protein can be used as an immunogen to screen mice or rabbits for neutralizing antibodies. however, the development of this traditional method is slow. many time-saving methods have been developed, such as the rapid identification of viral neutralization lead candidate phages or yeast display libraries by expressing fragments of antibodies, and their application to the screening of neutralizing antibodies. on march , , a new virus fusion research team (cevi fusion research team) led by the korea chemical research institute found antibodies that can fight against sars-cov- . the structure of the spike protein of the sars-cov- is very similar to that of middle respiratory syndrome (mers) and sars, and it was confirmed that the latter can be combined with its neutralizing antibody. blood-derived immunotherapy based on recovered patients can be used to treat infections including measles virus, lhasa virus, sars coronavirus and influenza a h n virus. this method is also applicable to the treatment of sars-cov- . rehabilitated patients with new coronavirus pneumonia will produce high-titer polyclonal antibody immune responses to different antigens of sars-cov- . some of these polyclonal antibodies may neutralize the virus and prevent a new round of infection. this can be achieved by donating plasma and whole blood into infected patients. as of today there are more patients with new coronavirus pneumonia in rehabilitation, and plasma can be provided for the treatment of infections if necessary. on january , , the state administration of traditional chinese medicine conducted clinical observations of the "qingfei paidu decoction" in shanxi, hebei, heilongjiang, and shaanxi provinces. by february , confirmed cases have been treated. the total effective rate has reached more than %. on february , it began to be promoted and used in china. the main drug composition of the prescription is "ephedra g, roasted licorice g, almond g, raw gypsum ~ g (first fried), guizhi g, alisma g, polyporus g, atractylodes g, poria g, bupleurum g, scutellaria baicalensis g, ginger pinellia g, ginger g, aster g, winter flower g, shegan g, asarum g, yam g, citrus aurantium g, tangerine peel g, patchouli g". the prescription can be used to treat scov-infected pneumonia patients with light, normal, and severe types, and can also be used according to actual conditions in the treatment of critically ill patients. with the spread of the covid- epidemic, scientists around the world are actively exploring potentially effective drugs to fight against new coronaviruses, especially rdv for injection. after evaluating the risks and benefits, on february , , active treatment was taken in the wuhan epidemic area, and a phase iii clinical trial was conducted, which brought dawn to the clinical treatment of covid- . however, there are many difficulties in the development of coronavirus drugs, which restrict the development and application of drugs. firstly, coronaviruses are rna viruses with variability, and this is the reason why new types of coronaviruses with novel structures easily appear. the drugs used in the past may not be effective for this new type of coronavirus or have only weak effects. secondly, many drugs have high ec /cmax ratios in the clinic and are prone to severe side effects. for example, the use of high-dose ribavirin may be related to hemolytic anemia, neutropenia, and cardiopulmonary distress. in addition, virus research is highly risky, and general experimental conditions are difficult to meet biosafety requirements, so screening techniques, animal models, and suitable animal experimental platforms are limited. moreover, the severe epidemic caused by coronavirus has the characteristics of timeliness. there are also some difficulties in clinical trial resources and recruitment of patients with related diseases into clinical trials. although research of these coronaviruses are based on the results of genome sequencing and bioinformatics, some screening models such as sars and mers virus-infected cells, some small mechanisms based on different mechanisms of action such as nucleic acid synthesis inhibitors, protease inhibitors, and polymerase inhibitors have been established. since low specificity of research and exploration, there is no clinical evidence to show the efficacy of broad-spectrum antiviral drugs against coronavirus. further substantial research is needed and attention should be given to certain toxic side effects. the most effective way to fight against the virus remains the vaccine. compared with the long cycle required for drug development, the vaccine takes a relatively short time and has a strong protective effect. monoclonal antibodies have better effects, stronger specificity, and higher safety, but they also require more time and cost to develop. compared to sars and mers, humans have made great progress in understanding the new coronavirus, the mechanism of drug action, research and development strategies, both in terms of knowledge and technology. in the waiting period for the development of new coronaviruses, china is now using multiple drugs to treat new coronaviruses. although there are many risks, it is undeniably the most effective approach at present. according to chinese anti-sars-cov- diagnosis and treatment program and treatment experience, a combination of multiple drugs is adopted, but it is not recommended to use or more antiviral drugs (table ) . this will alleviate the symptoms of the patient and enhance the patient's immunity, thereby achieving the purpose of treating the disease. covid- ) outbreak a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster emerging understandings of -ncov nowcasting and forecasting the potential domestic and international spread of the -ncov outbreak originating in wuhan, china_ a modelling study advances in covid- : the virus, the pathogenesis, and evidence-based control and therapeutic strategies clinical course and outcomes of critically ill patients with sars-cov- pneumonia in wuhan, china: a single-centered, retrospective, observational study a novel coronavirus from patients with pneumonia in china overlapping and discrete aspects of the pathology and pathogenesis of the emerging human pathogenic coronaviruses sars-cov, mers-cov, and -ncov stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis sars and mers: recent insights into emerging coronaviruses coronavirus envelope protein: current knowledge receptor recognition mechanisms of coronaviruses: a decade of structural studies genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding a pneumonia outbreak associated with a new coronavirus of probable bat origin therapeutic options for middle east respiratory syndrome coronavirus (mers-cov) -possible lessons from a systematic review of sars-cov therapy ribavirin and interferon alfa- a for severe middle east respiratory syndrome coronavirus infection: a retrospective cohort study in vitro antiviral activity of ribavirin against severe fever with thrombocytopenia syndrome virus common adverse events associated with the use of ribavirin for severe acute respiratory syndrome in canada diagnostic accuracy of the recognition of stroke in the emergency room (rosier) score and ct brain in an hiv population notice on the new coronavirus pneumonia diagnosis and treatment program observation on the curative effect of ribavirin and vidarabine monophosphate in the treatment on hand foot and mouth disease intravenous palivizumab and ribavirin combination for respiratory syncytial virus disease in high-risk pediatric patients coronavirus susceptibility to the antiviral remdesivir (gs- ) is mediated by the viral polymerase and the proofreading exoribonuclease late ebola virus relapse causing meningoencephalitis: a case report screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture pharmacokinetics and drug-drug interactions of lopinavir-ritonavir administered with first-and second-line antituberculosis drugs in hiv-infected children treated for multidrug-resistant tuberculosis week efficacy of lopinavir/ritonavir monotherapy in virologically suppressed patients with hiv: a randomized non-inferiority trial (anrs dream) role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings darunavir stands up as preferred hiv protease inhibitor kinetics analysis of consecutive hiv proteolytic cleavage of the gag-pol polyprotein sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor tissue distribution of ace protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis tmprss and adam cleave ace differentially and only proteolysis by tmprss augments entry driven by the severe acute respiratory syndrome coronavirus spike protein efficient multiplication of human metapneumovirus in vero cells expressing the transmembrane serine protease tmprss tmprss : a potential target for treatment of influenza virus and coronavirus infections a new antiviral drug-favipiravir favipiravir as a potential countermeasure against neglected and emerging rna viruses favipiravir (t- ), a novel viral rna polymerase inhibitor favipiravir (t- ), a broad spectrum inhibitor of viral rna polymerase identification of broad-spectrum antiviral compounds and assessment of the druggability of their target for efficacy against respiratory syncytial virus (rsv) the synthetic antiviral drug arbidol inhibits globally prevalent pathogenic viruses an antioxidant resveratrol significantly enhanced replication of hepatitis c virus in vitro antiviral activity of resveratrol against respiratory viruses antiviral activity of resveratrol effective inhibition of mers-cov infection by resveratrol the coronavirus nucleocapsid is a multifunctional protein fluvastatin interferes with hepatitis c virus replication via microtubule bundling and a doublecortin-like kinase-mediated mechanism antiviral actions of interferons pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses coronaviruses -drug discovery and therapeutic options ribavirin and interferon-β synergistically inhibit sars-associated coronavirus replication in animal and human cell lines severe acute respiratory syndrome coronavirus as an agent of emerging and reemerging infection middle east respiratory syndrome coronavirus a protein is a double-stranded rna-binding protein that suppresses pact-induced activation of rig-i and mda in the innate antiviral response nitazoxanide: a first-in-class broad-spectrum antiviral agent effect of nitazoxanide in adults and adolescents with acute uncomplicated influenza: a double-blind, randomised, placebo-controlled, phase b/ trial cyclophilins and cyclophilin inhibitors in nidovirus replication suppression of coronavirus replication by cyclophilin inhibitors the sars-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors cyclosporin a inhibits the replication of diverse coronaviruses new insights into the antiviral effects of chloroquine in vitro inhibition of severe acute respiratory syndrome coronavirus by chloroquine remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro clathrin-dependent entry of severe acute respiratory syndrome coronavirus into target cells expressing ace with the cytoplasmic tail deleted coronavirus s protein-induced fusion is blocked prior to hemifusion by abl kinase inhibitors abelson kinase inhibitors are potent inhibitors of severe acute respiratory syndrome coronavirus and middle east respiratory syndrome coronavirus fusion human monoclonal antibodies as candidate therapeutics against emerging viruses neutralizing monoclonal antibodies as promising therapeutics against middle east respiratory syndrome coronavirus infection assessment of immunoreactive synthetic peptides from the structural proteins of severe acute respiratory syndrome coronavirus pre-and postexposure efficacy of fully human antibodies against spike protein in a novel humanized mouse model of mers-cov infection the ebola epidemic crystallizes the potential of passive antibody therapy for infectious diseases selection of vaccinia virus-neutralizing antibody from a phage-display human-antibody library screening of fda-approved drugs using a mers-cov clinical isolate from south korea identifies potential therapeutic options for passive immunotherapy: assessment of convalescent serum against ebola virus makona infection in nonhuman primates enhancement of infectivity of a non-syncytium inducing hiv- by scd and by human antibodies that neutralize syncytium inducing hiv- convalescent plasma: new evidence for an old therapeutic tool? progress in screening research on effective chinese medicine prescriptions adverse events associated with high-dose ribavirin: evidence from the toronto outbreak of severe acute respiratory syndrome this work was supported by the national natural science foundation of china (nos. , ) and the henan provincial science foundation program (no. ). the study was conceived by x. the authors have declared that no competing interest exists. key: cord- -mwj qby authors: mackay, ian m.; arden, katherine e. title: mers coronavirus: diagnostics, epidemiology and transmission date: - - journal: virol j doi: . /s - - - sha: doc_id: cord_uid: mwj qby the first known cases of middle east respiratory syndrome (mers), associated with infection by a novel coronavirus (cov), occurred in in jordan but were reported retrospectively. the case first to be publicly reported was from jeddah, in the kingdom of saudi arabia (ksa). since then, mers-cov sequences have been found in a bat and in many dromedary camels (dc). mers-cov is enzootic in dc across the arabian peninsula and in parts of africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. precisely how virus transmits to humans remains unknown but close and lengthy exposure appears to be a requirement. the ksa is the focal point of mers, with the majority of human cases. in humans, mers is mostly known as a lower respiratory tract (lrt) disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in % to % of those infected. however, mers-cov has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. older males most obviously suffer severe disease and mers patients often have comorbidities. compared to severe acute respiratory syndrome (sars), another sometimes- fatal zoonotic coronavirus disease that has since disappeared, mers progresses more rapidly to respiratory failure and acute kidney injury (it also has an affinity for growth in kidney cells under laboratory conditions), is more frequently reported in patients with underlying disease and is more often fatal. most human cases of mers have been linked to lapses in infection prevention and control (ipc) in healthcare settings, with approximately % of all virus detections reported among healthcare workers (hcws) and higher exposures in those with occupations that bring them into close contact with camels. sero-surveys have found widespread evidence of past infection in adult camels and limited past exposure among humans. sensitive, validated reverse transcriptase real-time polymerase chain reaction (rt-rtpcr)-based diagnostics have been available almost from the start of the emergence of mers. while the basic virology of mers-cov has advanced over the past three years, understanding of the interplay between camel, environment, and human remains limited. electronic supplementary material: the online version of this article (doi: . /s - - - ) contains supplementary material, which is available to authorized users. an email from dr ali mohamed zaki, an egyptian virologist working at the dr soliman fakeeh hospital in jeddah in the kingdom of saudi arabia (ksa) announced the first culture of a new coronavirus to the world. the email was published on the website of the professional emerging diseases (promed) network on th september [ ] (fig. ) and described the first reported case, a year old man from bisha in the ksa. this information led to the rapid discovery of a second case of the virus, this time in an ill patient in the united kingdom, who had been transferred from qatar for care [ ] . the new virus was initially called novel coronavirus (ncov) and subsequentlty entitled the middle east respiratoy syndrome coronavirus (mers-cov). as of nd of september , there have been , detections of viral rna or virus-specific antibodies across countries (additional file : figure s ) confirmed by the world health organization (who), with over a third of the positive people dying (at least , %) [ ] . since that first report, a slow discovery process over the following two to three years revealed a virus that had infected over % of adult dromedary camels (dc; camelus dromedarius) in the ksa [ ] , also dcs across the arabian peninsula and parts of africa that are a source of dc imports for the ksa [ ] . to date, mers-cov has not been detected in dcs tested in zoos or herds from other parts of the world [ ] [ ] [ ] [ ] . occasionally, virus is transmitted from infected dcs to exposed humans. subsequent transmission to other humans requires relatively close and prolonged exposure [ ] . the first viral isolate was patented and concerns were raised that this would restrict access to both the virus and to viral diagnostics [ , ] . however, sensitive, validated reverse transcriptase real-time polymerase chain reaction (rt-rtpcr)-based diagnostics were quickly described and virus was made freely available subject to routine biosafety considerations [ ] . subsequent epidemiology and research has identified the cell receptor as exopeptidase dipeptidyl peptidase (dpp ; also called cd ); that mers-cov has a broad tropism, replicating better in some cells lines and eliciting a more proinflammatory response than sars-cov; is widespread in dcs; has the potential to infect other animals and that mers kills its human host more often than sars did ( - % versus % for sars [ ] ) [ ] [ ] [ ] [ ] [ ] . in humans, overt disease was given the name middle east respiratory syndrome, with the acronym mers. from intermittent animal-to-human spill-over events, the mers-cov spreads sporadically among people, causing more severe disease among older adults, especially males, with pre-existing diseases. the spread of mers-cov among humans has often been associated with outbreaks in hospitals, with around % of all cases to date involving healthcare workers (hcws). although dcs appear to suffer the equivalent of a 'common cold' from mers-cov infection, in humans, the virus can be a more serious and opportunistic pathogen associated with the death of up to % of reported cases. it has yet to be established whether infections thought to have been acquired from an animal source produce a more severe outcome than those spread between humans [ ] . studies have established that the mean incubation period for mers is five to six days, ranging from two to days, with to days between when illness begins in one person and subsequently spreads to another [ ] [ ] [ ] [ ] . among those with progressive illness, the median time to death is to days, ranging from five to days [ , ] . fever and gastrointestinal symptoms may form a prodrome, after which symptoms decline, only to be followed by a more severe systemic and respiratory syndrome [ , ] . the first who case definition [ ] defined probable cases of mers based on the presence of febrile illness, cough and requirement for hospitalization with suspicion of lower respiratory tract (lrt) involvement. it also included roles for contact with a probable or confirmed case or for travel or residence within the arabian peninsula. if strictly adhered to, only the severe syndrome would be subject to laboratory testing, which was the paradigm early on [ ] . from july , the revised who case definition included the importance of seeking out and understanding the role of asymptomatic cases and from june , the who definition more clearly stated that a confirmed case included any person whose sample was rt-pcr positive for mers-cov, or who produced a seroconversion, irrespective of clinical signs and symptoms. [ ] [ ] [ ] apart from the who and the ksa ministry of health reports, asymptomatic or subclinical cases of mers-cov infection were documented in the scientific literature although not always as often as occurred early on [ , ] . the ksa definition of a case became more strict on th may , relying on the presence of both clinical features and laboratory confirmation [ ] . testing of asymptomatic people was recommended against from december [ ] , reinforced by a case definition released by the ksa ministry of health in june [ ] . the ksa has been the source of % of human cases. severe mers is notable for its impact among older men with comorbid diseases including diabetes mellitus, cirrhosis and various lung, renal and cardiac conditions [ ] [ ] [ ] . interestingly in june , an outbreak in south korea followed a similar distribution [ , ] . among laboratory confirmed cases, fever, cough and upper respiratory tract (urt) signs and symptoms usually occur first, followed within a week by progressive lrt distress and lymphopaenia [ ] . patients often present to a hospital with pneumonia, or worse, and secondary bacterial infections have been reported [ , ] . disease can progress to acute respiratory distress syndrome and multiorgan system failure [ ] . mers has reportedly killed approximately % of all reported cases, % of cases in the ksa, yet only % of cases in south korea, where mortality ranged from % among younger age groups to % among those aged years and above [ ] ; all may be inflated values with asymptomatic or mild infections sometimes not sought or not reported [ ] . general supportive care is key to managing severe cases [ ] . children under the age of years are rarely reported to be positive for mers-cov, comprising only . % (n = ) of total reported cases. between st september and nd december , a study described the then tally of paediatric cases in the ksa, which stood at (two to years of age; median years); nine were asymptomatic ( %) and one infant died [ ] . in amman, jordan, , samples from hospitalized children under the age of two years with fever and/or respiratory signs and symptoms were tested but none were positive for mers-cov rna, despite being collected at a similar time to the first known outbreak of mers-cov in the neighbouring town of al-zarqa [ ] . a second trimester stillbirth occurred in a pregnant woman during an acute respiratory illness and while not rt-rtpcr positive, the mother did subsequently develop antibodies to mers-cov, suggestive of recent infection [ ] . her exposure history to a mers-cov rt-rtpcr positive relative and an antibody-reactive husband, her incubation period and her symptom history met the who criteria for being a probable mers-cov case [ ] . diagnostic methods were published within days of the promed email announcing the first mers case [ ] , including several now gold standard in-house rt-rtpcr assays (fig. ) as well as virus culture in vero and llc-mk cells [ , , ] . a colorectal adenocarcinoma (caco- ) epithelial cell line has since been recommended for isolation of infections mers-cov [ ] . we previously [ ] .). open reading frames are indicated as yellow rectangles bracketed by terminal untranslated regions (utr; grey rectangles). fs-frame-shift. predicted regions encompassing recombination break-points are indicated by orange pills. created using geneious v . [ ] and annotated using adobe illustrator. beneath this is a schematic depicting the location of rt-pcr primers (blue arrows indicate direction) and oligoprobes (green rectangles) used in the earliest rt-rtpcr screening assays and conventional, semi-nested (three primers) rt-pcr confirmatory sequencing assays [ , ] . publication order is noted by first [ th september ; red] and second [ th december ; orange] coloured rectangles; both from corman et al. [ , ] those assays recommended by the who are highlighted underneath by yellow dots [ ] . the nseq reverse primer has consistently contained one sequence mismatch with some mers-cov variants. an altered version of that from mackay im, arden ke. middle east respiratory syndrome: an emerging coronavirus infection tracked by the crowd. virus res vol : - with permission from elsevier [ ] reviewed the broad tropism of mers-cov [ ] . however, as is well described, cell culture is a slow, specialised and insensitive method [ ] while pcr-based techniques are the preferred method for mers-cov detection. the first open reading frames (orf a and b; fig. ) have become a key diagnostic and taxonomic target for cov species identification. with less than % identity between the amino acid sequence of mers orf ab and betacoronavirus relatives, tylonycteris bat hku and pipistrellus bat hku , it can be concluded that it is a novel and distinct virus. mers-cov is predicted to encode ten open reading frames with ' and ' untranslated regions [ ] . the structural proteins include the spike (s), envelope (e), membrane (m) and nucleocapsid (n) [ ] . the products of orf a and orf b are predicted to encode nonstructural proteins. the majority of specimen testing to date has employed validated rt-rtpcr assays shown to be sensitive and specific [ , , ] . the realstar® kit uses these whorecommended assays [ ] . the target sequences of these screening assays have not changed among genomes examined until at least mid- (imm observation). other rt-rtpcr assays have been developed and validated for use as laboratory-based diagnostic tools [ ] [ ] [ ] . additionally, loop-mediated [ , ] or recombinase polymerase [ ] isothermal assays have been designed for field deployment. the detection of mers-cov antigen has not been common to date but the combination of short turnaround time from test to result, high throughput and identification of viral proteins makes this an attractive option. detection of viral proteins rather than viral rna indicates the likely presence of infectious virus. the first rapid immunochromatographic tool described could detect recombinant mers-cov nucleocapsid protein from dc nasal swabs with % sensitivity and % specificity compared to rt-rtpcr [ ] . a different approach used a monoclonal antibody-based capture elisa targeting the mers-cov nucleocapsid protein with a sensitivity of tcid and % specificity [ ] . demonstration of a seroconversion to a mers-cov infection meets the current who definition of a case so optimized and thoroughly validated sero-assays employed alongside good clinical histories are useful to both identify prior mers-cov infection and help support transmission studies. because serology testing is, by its nature, retrospective, it is usual to detect a viral footprint, in the form of antibodies, in the absence of any signs or symptoms of disease and often in the absence of any viral rna [ ] . strategic, widespread sero-surveys of humans using samples collected after are infrequent. much of the arabian peninsula and all of the horn of africa lack baseline data describing the proportion of the community who may have been infected by a mers-cov. however, sero-surveys have had widespread use in elucidating the role of dcs as a transmission source for mers-cov. because of the identity shared between dc and human mers-cov (see molecular epidemiology: using genomes to understand outbreaks), serological assays for dc sero-surveys should be transferrable to human screening with minimal re-configuration. also, no diagnostically relevant variation in neutralization activity have been found from among a range of circulating tested mers-cov isolates and sera, so whole virus or specific protein-based sero-assays should perform equivalently in detecting serological responses to the single mers-cov serotype [ ] . the development of robust serological assays requires reliable panels of wellcharacterized animal or human sera, including those positive for antibodies specific to mers-cov, as well as to likely sources of cross-reaction [ ] . obtaining these materials was problematic and slowed the development and commercialization of antibody detection assays for human testing [ ] . a number of commercial elisa kits, immunofluorescent assays (ifa) kits, recombinant proteins and monoclonal antibodies have been released [ , [ ] [ ] [ ] [ ] . initially, conventional ifas were used for human sero-surveys. these relied on mers-cov-infected cell culture as an antigen source, detecting the presence of human anti-mers-cov igg, igm or neutralizing antibodies in human samples [ , , ] . no sign of mers-cov antibodies was found among , sera from patients visiting hospital in jeddah, from through , prior to the description of mers-cov [ ] . nor did ifa methods detect any sign of prior mers-cov infection among a small sample of healthy blood donors from another hospital in jeddah (collected between jan and dec ) [ ] . of slaughterhouse workers, only eight ( . %) were positive by ifa, and those sera could not be confirmed by virus neutralization (nt) test. the study indicated that hcov-hku was a likely source of crossreactive antigen in the whole virus ifa [ ] . whole virus mers-cov ifa also suffered from some cross-reactivity with convalescent sars patient sera and this could not be resolved by an nt test which was also cross-reactive [ ] . ifa using recombinant proteins instead of whole-virus ifa, has been shown to be a more specific tool [ ] . since asymptomatic zoonoses have been posited [ ] , an absence of antibodies to mers-cov among some humans who have regular and close contact with camels may reflect the rarity of actively infected animals at butcheries, a limited transmission risk associated with slaughtering dcs [ ] , a pre-existing cross-protective immune status or some other factor(s) resulting in a low risk of disease and concurrent seroconversion developing after exposure in this group. ifa using recombinant proteins instead. some sero-assays have bypassed the risks of working with infectious virus by creating transfected cells expressing recombinant portions of the mers-cov nucleocapsid and spike proteins [ , ] , or using a recombinant lentivirus expressing mers-cov spike protein and luciferase [ , ] . a pseudo particle neutralization (ppnt) assay has seen widespread used in animal studies and was at least as sensitive as the traditional microneutralization (mnt) test. [ , , [ ] [ ] [ ] ] studies using small sample numbers and ppnt found no evidence of mers-cov neutralizing antibody in sera from children with lrt infections between may and may , sera from to year old male blood donors and selfidentified animal workers from the jazan region of the ksa during [ , ] . similarly, a study of four herdsmen in contact with an infected dc herd in al-ahsa, eight people who had intermittent contact with the herd, veterinary surgeons and support staff who were not exposed to the herd, three unprotected abattoir workers in al-ahsa and controls who were not exposed to dcs in any professional role, found none with serological evidence of past mers-cov infection using the ppnt assay [ ] . a delay in the neutralizing antibody response to mers-cov infection was associated with increased disease severity in south korea cases with most responses detectable by week three of illness while others, even though disease was severe, did not respond for four or more weeks [ ] . the implications for our ability to detect any response in mild or asymptomatic cases was not explored but may be a signifcant factor in understanding exposure in the wider community. a jordanian outbreak of acute lrt disease in a hospital in was retrospectively found to be associated with mers-cov infection, initially using rt-rtpcr, but subsequently, and on a larger scale, through positivity by elisa and ifa or mnt test. [ , , ] this outbreak predated the first case of mers in the ksa. the elisa used a recombinant nucleocapsid protein from the group betacoronavirus bat-cov hku to identify antibodies against the equivalent crossreactive mers-cov protein [ ] . it was validated using sera collected from people with prior hcov-oc , hcov- e, sars-cov, hcov-nl , hrv, hmpv or influenza a(h n ) infections but was reportedly less specific than the recombinant ifa discussed above. it was still considered an applicable tool for screening large sample numbers [ ] . a protein microarray expressing the s protein subunit has also been validated and widely used for dc testing [ , ] . detection of mers-cov infection using elisa or s subunit protein microarray [ ] is usually followed by confirmatory ifa and/ or a plaque-reduction neutralization (prnt) [ , , ] or mnt test. [ , , ] this confirmatory process aims toensure the antibodies detected are able to specifically neutralize the intended virus and are not more broadly reactive to other coronaviruses found in dcs (bovine cov, bcov) or humans (hcov-oc , hcov- e, hcov-nl , hcov-hku , sars-cov). in the largest study of human sera, a tiered diagnostic process assigned both recombinant ifa and recombinant elisa positive sera to 'stage ' seropositivity. a stage seropositive result additionally required a suitably titred prnt result [ ] . the study found sera collected in to from , ( . %) people in ksa provinces contained mers-cov antibodies, but significantly higher proportions in occurred in camel shepherds (two of ; . %) and slaughterhouse workers (five of ; . %) [ ] . contemporary surveys are needed. mers-cov does not appear to be easily transmitted from dcs to humans, or perhaps it is [ ] , but generally does not trigger a detectable immune response if only mild disease or asymptomatic infection results. serology assays are in need of further validation in this area so care is required when moving newly developed diagnostic serology algorithms from a research setting to one that informs public health decisions. this was reinforced when a false positive us case, purported to have been infected after a handshake and two face-to-face meetings, did not withstand further confirmatory analysis using a more specific, nt assay and was subsequently retracted [ , ] . the who recommends sampling from the lrt for mers-cov rt-rtpcr testing, especially when sample collection is delayed by a week or more after onset of symptoms. [ ] lrt samples are also best for attempting isolation of infectious virus, although the success of culture is reduced when disease persists [ ] . recommended sample types include bronchoalveolar lavage (bal), tracheal/tracheobronchial aspirate, pleural fluid and sputum [ , ] . fresh samples yield better diagnostic results than refrigerated material [ ] and if delays in testing of ≥ h are likely, samples (except for blood) should be frozen at − °c [ ] . if available, lung biopsy or autopsy tissues can also be tested [ ] . the urt is a less invasive and more convenient sampling site however, and an oropharyngeal and throat swab or a nasopharyngeal aspirate/wash are recommended when urt sampling is to be conducted [ ] . paired sera, collected two to three weeks apart are preferable for serological testing while a single sample is suggested to be sufficient if collected two weeks after onset of disease or a single serum collected during the first - days if conducting rt-rtpcr [ , ] . human urine and stool have been found to contain mers-cov rna to days after symptom onset [ , , ] and are listed as samples that should be considered [ , ] . in two cases that arrived in the netherlands, urine was rt-rtpcr negative but faeces was weakly positive and sera were rt-rtpcr positive for five days or more [ ] . the finding of mers-cov viral rna in serum provides an avenue for retrospective pcr-based studies if respiratory samples are unavailable [ ] . rnaaemia may also correlate with disease severity; signs of virus were cleared from the serum of a recovered patient, yet lingered until the death of another [ ] . clinically suspected mers cases may return negative results by rt-rtpcr. data have shown one or more negative urt samples may be contradicted by further urt sampling or the use of lrt samples, which is preferred [ , , ] . higher viral loads occur in the lrt compared to the urt. [ , , , ] this fits with the observation that the majority of disease symptoms are reported to manifest as systemic and lrt disease [ ] . however, on occasion, even lrt specimens from mers cases may initially be negative, only to later become positive by rt-pcr [ ] . this may be due to poor sampling when a cough is absent or non-productive or because the viral load is low [ ] . despite this both the largest human mers-cov studies [ , [ ] [ ] [ ] and smaller ones [ , , ] , use samples from the urt. it is then noteworthy that one study reported an association between higher loads in the urt and worse clinical outcome including intensive care and death [ ] . at writing, no human data exist to define whether the virus replicates solely or preferentially in the lrt or urt, or replicates in other human tissues in vivo although mers-cov rna has been detected from both the urt and lrt in a macaque monkey model [ ] .the distribution of dpp in the human upper airways is also not well described. individual human case studies report long periods of viral shedding, sometimes intermittently and not necessarily linked to the presence of disease symptoms. [ , , , ] in one instance, a hcw shed viral rna for days in the absence of disease [ ] . it is an area of high priority to better understand whether such cases are able to infect others. over three quarters of mers cases shed viral rna in their lrt specimens (tracheal aspirates and sputum) for at least days, while only % of contacts were still shedding rna in their urt specimens [ , ] . in the only study to examine the effect of sample type on molecular analysis, nasopharyngeal aspirates (npa; an urt sample), tracheal aspirates, sputa and three bal were examined. the tracheal aspirates and bal returned the highest viral load values followed by npa and sputum. unsurprisingly, higher viral loads generally paralleled whole genome sequencing and culture success and, in npa testing, were significantly correlated with severe disease and death [ , , ] . this study demonstrated the importance of lrt sampling for whole genome sequencing. when tested, samples positive for mers-cov are often negative for other pathogens [ , , , ] . however, many studies make no mention of additional testing for endemic human respiratory viruses [ , , , ] . when viruses are sought, they have included human herpesvirus (hhv), rhinoviruses (hrv), enteroviruses (ev), respiratory syncytial virus (rsv), parainfluenzavirus types , and (pivs),influenzaviruses (ifvs), endemic hcovs, adenoviruses (advs) metapneumovirus (mpv) and influenza a\h n virus; co-detections with mers-cov have been found on occasion [ , , , , ] . bacterial testing is sometimes included (for example, for legionella and pneumococcus) but the impact of bacterial co-presence is also unclear [ , [ ] [ ] [ ] . further testing of the lrt sample from the first mers case used ifa to screen for some viruses (negative for ifv, pivs, rsv and advs) and rt-pcr for others (negative for adv, evs, mpv and hhvs) [ ] . rt-pcr also detected mers-cov. the who strongly recommends testing for other respiratory pathogens [ ] but with this recommendation often discounted, there are limited data to address the occurrence and impact of co-infections or alternative viral diagnoses among both mers cases and their contacts. little is known of other causes of mers-like pneumonia in the ksa or of the general burden of disease due to the known classical respiratory viruses. testing of adult pilgrims performing the hajj in to has not detected any mers-cov. in , nasal swabs from pilgrims collected prior to leaving for or departing from the ksa were tested [ ] . in , testing was significantly scaled up with , nasopharyngeal swabs from , incoming pilgrims and , swabs from outgoing pilgrims tested [ ] . it should be noted that most pilgrims arrived from mers-free countries. a further swabs were taken from pilgrims with influenza-like illness [ , ] . in earlier hajj gatherings, it was found that influenza viruses circulated widely, whilst other viruses, often rhinoviruses, circulated more selectively, interpreted as indicating their importation along with foreign pilgrims. [ ] [ ] [ ] over time, increased influenza vaccination has been credited for a fall in the prevalence of influenza like illnesses among hajj pilgrims. [ ] a lrt sample is often not collected for these studies [ , , ] , so false negative findings are a possibility although little is known about the initial site of mers-cov infection and replication; it may have been assumed it was the lrt because disease was first noticed there but the urt may be the site of the earliest replication. in jeddah between march and july (hereafter called the jeddah- outbreak; fig. ), there was a rapid increase in mers cases, accompanied by intense screening; approximately , samples from in and around the region were tested in a month yielding around mers-cov detections (~ % prevalence) [ ] . among , individuals sampled and tested across the ksa between october and september , ( . %) detections were made in a hospital-centric population which included hospitalized cases (n = , ; . %), their families (n = ; . %) and associated hcws (n = , ; . %) [ ] . among the detections, ( . %) were hcws and ( . %) were family contacts [ ] . the - % prevalence of active mers-cov infections is not dissimilar to the hospital-based prevalence of other human covs. [ ] however, the proportion of deaths among those infected with mers-cov is much higher than that known for the hcovs nl , hku , e or oc in other countries, and even above that for sars-cov; it is not a virus that could reasonably be described as a "storm in a teacup". it is the low transmission rate that has prevented worldwide spread, despite many "opportunities". very early in the mers outbreak, some animals were highly regarded as either the reservoir or intermediate host(s) of mers-cov with three of the first five cases having contact with dcs [ , , ] . today, animal mers-cov infections must be reported to the world organization for animal health as an emerging disease [ ] . a summary of the first mers cases reported by the who defined animal contact with humans as being direct and within days prior to symptom onset [ ] . this definition made no specific allowance for acquisition from dcs through a droplet-based route, which is very likely route for acquisition of a virus that initially and predominantly causes respiratory disease [ ] . camels are known to produce high levels of mers-cov rna in their urt and lungs [ ] . providing support for a droplet transmission route and perhaps indicating the presence of rna in smaller, drier droplet nuclei, mers-cov rna was identified in a high volume air sample collected from a barn housing an infected dc [ ] . the precise source from which humans acquire mers-cov remains poorly studied but it seems likely that animal and human behavioural factors may play roles (fig. ) [ ] . these factors may prove important for human cases who do not describe any dc contact [ ] nor any contact with a confirmed case. whether the who definition of animal contact is sufficient to identify exposure to this respiratory virus remains unclear. wording focuses on consumption of dc products but does not specifically ascribe risk to a droplet route for acquisition of mers-cov from dc [ ] . some mers patients are listed in who disease notices as being in proximity to dcs or farms, but the individuals have not described coming into contact with the animals. no alternative path for acquiring infection is reported in many of these instances. what constitutes a definition of "contact" during these interviews has been defined for one study [ ] . despite this lack of clarity, the who consider that evidence linking mers-cov transmission between dcs to humans is irrefutable (fig. ) [ ] . the possibility that bats were an animal host of mers-cov was initially widely discussed because of the existing diversity of coronaviruses known to reside among them [ ] [ ] [ ] [ ] . conclusive evidence supporting bats as a source for human infections by mers-cov has yet to be found, but bats do appear to host ancestral representatives [ , ] . however, these are not variants of the same virus nor always within the same phylogenetic lineage as mers-cov; they are each a genetically distinct virus. bat-to-human infection by mers-cov is a purely speculative event. the only piece of mers-cov-specific evidence pointing to bats originates from amplification of a nt fragment of the rnadependent rna polymerase gene of the mers-cov genome, identified in a faecal pellet from an insectivorous emballonuridae bat, taphozous perforatus found in bisha, the ksa [ ] . while very short, the sequence of the fragment defined it as a diagnostic discovery. subsequently a link to dcs was reported [ ] and that link has matured into a verified association [ , ] (fig. ) . (see figure on previous page.) fig. monthly detections of mers-cov (blue bars) and of cases who died (red bars) with some dates of interest marked for to th september . an approximation of when dc calving season [ ] and when recently born dcs are weaned is indicated. spring (green) and summer (orange) in the arabian peninsula are also shaded. note the left-hand y-axis scale for and which is greater than for / . sources of these public data include the who, ministries of health and flutrackers [ ] [ ] [ ] . earlier and subsequent versions of this chart are maintained on a personal blog [ ] . modified and reprinted from mackay im, arden ke. middle east respiratory syndrome: an emerging coronavirus infection tracked by the crowd. virus res vol : - with permission from elsevier [ ] dcs, which make up % of all camels, have a central presence in the arabian peninsula where human-dc contact ranges from little to close [ ] . contact may be commonplace and could occur in variety of ways (fig. a) . there are several large well-attended festivals, races, sales and parades which feature dcs and dcs are also kept and bred close to populated areas in the ksa [ , ] . dc milk and meat are widely consumed and the older dc is an animal of ritual significance after the hajj pilgrimage [ ] . however, mers-cov infection frequency is reportedly much lower than is the widespread and frequent habit of eating, drinking and preparing dc products. daily ingestion of fresh unpasteurized dc milk is common among the desert bedouin and many others in the ksa. dc urine is also consumed or used for supposed health benefits. despite camel butchery being a local occupation, neither butchers nor other at-risk groups are identifiable among mers cases; this may simply be a reporting issue rather than an unexplainable absence of mers. a small case-control study published in identified direct dc contact, and not ingestion of products, to be associated with onset of mers [ ] . the first sero-survey of livestock living in the middle east region was conducted during - [ ] . dcs were sampled from a mostly canary island-born herd and from omani dcs (originally imported from the horn of africa) [ ] . a neutralising antibody assay found only % of strongly seropositive canary island [ ] . b camel-to-human infections appear to be infrequent, while human-to-human spread of infection is regularly facilitated by poor ipc in healthcare settings where transmission is amplified, accounting for the bulk of cases. there are human mers cases that do not fall into either category of source and it is unclear if these acquired infection through some entirely separate route, or from cases that escaped diagnosis. c hypothetical ways in which subclinical (when infection may not meet a previously defined clinical threshold of signs and/or symptoms) or asymptomatic (no obvious signs or measured, noticed or recalled symptoms of illness) mers-cov infection may be implicated in transmission dc sera could neutralise mers-cov while all omani dc sera had high levels of specific mers-cov neutralizing antibody [ ] . this indicated that dcs had in the past been infected by mers-cov, or a very similar virus. since this study, a host of peer-reviewed reports have looked at both dcs and other animals, and the possibility that they may host mers-cov infection. seropositive dcs have been found throughout the arabian peninsula including oman, the ksa, qatar, jordan, the united arab emirates (uae), kuwait as well as sudan, somalia, egypt, tunisia, nigeria, kenya and ethiopia in africa and the canary islands [ , [ ] [ ] [ ] [ ] [ ] . other animals tested include sheep, cows, pigs, horses, donkeys, mules, birds, water buffalo, goats, bactrian camels, llamas and guanaco (south american camelids) but none had detectable neutralising antibody against mers-cov [ , , , , , , ] . no virology or serology studies of human samples from areas in africa where there are camels with a history of mers-cov have been reported to date. however,an absence of unexplained pneumonia that may be attributable to mers-cov infection may not signal the absence of virus among humans in each country but simply reflect a lack of expensive epidemiology studies conducted by resource-poor countries. it is thus unclear whether mers-cov, or an antigenically related cov, is an unrecognized pathogen in these regions, perhaps circulating for even longer than it has been known in the arabian peninsula [ ] . mers-cov rna has also been detected in dc samples, and recovery of infectious virus has also been achieved from dc samples [ , , , , [ ] [ ] [ ] [ ] [ ] . from some of these, full or majority length genomes of mers-cov have been sequenced [ , , ] . dc versions of mers-cov were found to be as similar to each other, as were variants detected from different humans over time and across distance. antibody screening assays have also detected crossreactive antibodies in sera. these were identified as such by screening sera against similar viruses, for example bcov or hcov-oc (as an antigenic facsimile for bcov). it is possible that other mers-cov-like viruses also reside within dcs, but this does not detract from the definitive finding of mers-cov genetic sequences in both dcs and humans [ , , ] . screening studies have shown that juvenile dcs are more often positive for virus or viral rna while older dcs are more likely to be seropositive and rna or virus negative [ , , ] . in adult dcs, mers-cov rna has been detected among animals with pre-existing antibody, suggesting re-infection is possible [ , ] . viral loads among positive dcs can be very high [ , , , , ] and dcs have been found positive both when ill with urt respiratory signs [ , , , ] or when apparently healthy [ ] . these findings indicate dcs host natural mers-cov infections. furthermore, stored dc sera have revealed signs of mers-cov in dcs which date back over three decades (the earliest collected in ) [ , , ] . older sera have not been tested and so precisely how long dcs have been afflicted by mers-cov, whether the virus is enzootic among them, introduced to them decades or centuries ago from bats in africa or the arabian peninsula, or they are the subject of regular but short-lived viral incursions from an as yet unknown host, cannot be answered. researchers sought to determine a direction for infection; were dcs transmitting virus to humans or were humans infecting dcs? at a qatari site, a farm owner and his employee became ill in mid-october and tested positive for mers-cov rna in a sputum and throat swab sample, respectively. rt-rtpcrs found mers-cov rna in of positive dc nasal swabs at the farm; six ( %) positive by two or more assays [ ] . the results indicated a recent outbreak had occurred in this herd; the first indication of mers-cov rna found within dcs with a temporal association to human infections. three positive dc samples were confirmed by sequencing a nt portion of the spike gene; these sequences were identical to each other, again with close homology to other human and dc mers-cov sequences [ ] . the dcs and human contacts yielded orf a and orf b sequences differing by only a single nucleotide each, clustering closely with the hafr-al-batin_ _ variant [ ] . subsequent case studies found evidence of a concurrent human and dc infection and the direction of that infection was inferred to be from the ill dcs and to their human owners [ , , ] . partial genome sequences indicated that a human and a mers-cov rt-rtpcr positive dc had been infected by a variant of the same virus, harbouring the same distinct pattern of nucleotide polymorphisms. [ ] all nine dc in the owner's herd, serially sampled, reacted in a recombinant s antigen elisa, with the two animals that had been rt-rtpcr positive showing a small, verifiable rise in antibody titre [ ] . a rise in titre theoretically begins to days after dc infection [ ] . the authors suggested that the rise in titre in dc sera which occurred alongside a declining rna load, while the patient was actively ill and hospitalized, indicated that the dcs were infected first followed by the owner [ , ] . bcov antibodies were also present, and rising in one of the two rt-rtpcr positive animals but no animal's antibodies could neutralise bcov infection [ ] . camel calving season occurs in the winter months (between late october and late february; fig. ) and this may be a time when there is increased risk to humans of spill-over due to new infections among naïve dc populations [ ] . what role maternal camel antibody might play in delaying infection of calves remains unknown [ , ] . juvenile dcs appear to host active infection more often than adult dcs and thus the sacrificial slaughter of dcs, which must be five years of age or older (termed a thane), may not be accompanied by significant risk of exposure to infection. in contrast to earlier results, slaughterhouse workers who kill both younger and older dcs, may be an occupational group with significantly higher incidence of seropositivity to mers-cov when animals have active mers-cov infections [ , , [ ] [ ] [ ] . expanded virological investigations of african dcs may lead to more seropositive animals and geographic areas in which humans may be at risk. it is possible that there are areas where humans already harbour mers-cov infections that have not been identified because of an absence of laboratory surveillance. virological investigations of bats may lead to findings of ancestral viruses and viral 'missing links' and identifying any other animal sources of zoonotic spread is important to inform options for reducing human exposures [ , ] . infectious mers-cov added to dc, goat or cow milk and stored at °c could be recovered at least h later and, if stored at °c, recovery was possible for up to h [ ] . mers-cov titre decreased somewhat when recovered from milk at °c but pasteurization completely ablated mers-cov infectivity [ ] . in a subsequent study, mers-cov rna was identified in the milk, nasal secretion and faeces of dcs from qatar [ ] . a single study has examined the ability of mers-cov to survive in the environment [ ] . plastic or steel surfaces were inoculated with tcid of mers-cov at different temperature and relative humidity (rh) and virus recovery was attempted in cell culture. at high ambient temperature ( °c) and low rh ( %) mers-cov remained viable for h [ ] . by comparison, a well known and efficently transmitted respiratory virus, influenza a virus, could not be recovered in culture beyond four hours under any conditions [ ] . aerosol experiments found mers-cov viability only decreased % at low rh at °c. in comparison, influenza a virus decreased by % [ ] . mers-cov survival is inferior to that previously demonstrated for sars-cov [ ] . for context, pathogenic bacteria can remain viable and airborne for min in a coughed aerosol and can spread m. mers-cov's ability to remain viable over long time periods gives it the capacity to thoroughly contaminate a room's surfaces when occupied by an infected and symptomatic patient [ ] . whether mers-cov can remain adrift and infectious for extended periods (truly airborne) remains unknown. such findings expand our understanding of the possibilities for droplets to transmit respiratory viruses in many settings, including hospital waiting rooms, emergency departments, treatment rooms, open intensive care facilities and private patient rooms. the nature and quality of air exchange, circulation and filtration are important variables in risk measurement and reduction as is the use of negative pressure rooms to contain known cases. droplet spread between humans is considered the mechanism of human-to-human transmission and the need for droplet precautions was emphasized after the al-ahsa hospital, the ksa and the south korean outbreaks [ , , , ] . by extrapolation, aerosol-generating events involving dcs (urination, defecation, and preparation and consumption of dc products) should be factored into risk measurement and reduction efforts and messaged using appropriate context. the provision of evidence supporting the best formulation of personal protective equipment to be worn by hcws who receive, manage or conduct procedures on infectious cases remains a priority. mers-cov was found and characterized because of its apparent association with severe, and therefore more obvious, illness in humans; we were the canaries in the coal mine. sero-assays and prospective cohort studies have yet to determine the extent to which milder or asymptomatic cases contribute to mers-cov transmission chains. however, transmission of mers-cov is defined as sporadic (not sustained), intra-familial, often healthcare associated, inefficient and requiring close and prolonged contact [ , , , , , , ] in a household study, of ( %) contacts of mers-cov positive index patients were rna or antibody positive; the rate of general transmission, even in outbreaks is around % [ ] . it seems that the majority of human cases of mers-cov, even when numbers appear to increase suddenly, do not readily transmit to more than one other human so to date, the localized epidemic of mers-cov has not been self-sustaining [ ] [ ] [ ] [ ] [ ] . that is to say, the basic reproduction number (r ) -the average number of infections caused by one infected individual in a fully susceptible populationhas been close to one throughout various clusters and outbreaks. if r was greater than , a sustained increase in case numbers would be expected. some r o calculations may be affected by incomplete case contact tracing, limited community testing and how a case is defined. that mers has had a constant presence in the arabian peninsula since is due to ongoing, sporadic spill-over events from dcs amplified by poorly controlled hospital outbreaks. the first known mers human-to-human transmission event was one characterized by acute lrt disease in a healthcare setting in jordan. in stark contrast, a sero-survey of hcw who were sometimes in close and prolonged contact with the first, fatal mers-cov case in [ ] , found none of the hcw had seroconverted four months later, despite an absence of eye protection and variable compliance with required ppe standards [ ] . early on in the mers story, samples for testing were mostly collected from patients with severe illness and not those with milder acute respiratory tract infections. contacts of confirmed mers cases were often observed for clinical illness, but not tested. these omissions may have confounded our understanding of mers-cov transmission and biased early data towards higher numbers of seriously ill and hospitalized patients, inflating the apparent proportion of fatal cases. case-control studies were not a focus. as testing paradigms changed and contacts were increasingly tested, more asymptomatic and mild infections were recognized [ ] . a rise in the cases termed asymptomatic (which enlarge the denominator for calculations of the proportion of fatal cases, defined in [ ] ) resulted in a drop in the proportion of fatal cases during the jeddah- outbreak. historically, such rises are consistent with changing definitions and laboratory responses and clinical management of a newly discovered virus infection that was first noted only among the severely ill. upon follow-up, over three-quarters of such mers-cov rna positive people did recall having one or more symptoms at the time, despite being reported as asymptomatic [ ] raising some question over the reliability of other reported data. the proportion of fatal mers cases within the ksa compared to outside the ksa, as well as the age, and sex distribution change in different ways when comparing mers outbreaks. approximately % of mers cases ( of ) in the ksa were fatal betwen and december while % ( of ) died among those occurring outside of the ksa. the total number of male cases always outnumber females and the proportion of male deaths is always greater than the proportion of females who die. however the proportion of male deaths from total males with mers is a similar figure to that for females. in the ksa, there is a greater proportion of younger males among cases and deaths than were observed from the south korean or the jeddah- outbreaks (additional file : figure s ). why these aspects have differed may be due to differences in the time to presentation and diagnosis, the nature and quality of supportive care, the way a person became infected (habits, exposure to a human or zoonotic source, viral load, route of infection) or the extent to which different populations are burdened by underlying diseases [ ] . as a group, hcws comprised % of mers cases in the ksa and south korea. it is apparent that the weekly proportion of infected hcws increases alongside each steep rise in overall detections (fig. ) . in may , the who published guidelines for ipc during care of probable or confirmed cases of mers-cov infection in a healthcare setting [ ] . this is explainable because to date, each case rise has been intimately associated with healthcare-facility related outbreaks [ ] . these rises in mers-cov detections can decrease the average age during each event because hcws are usually younger than inpatients with mers. healthcare facilities have been a regular target for suggested improvements aimed at improving infection prevention and control (ipc) procedures [ , ] . most of the analysis of mers-cov genetics has been performed using high throughput or "deep" sequencing methods for complete genome deduction [ ] [ ] [ ] . mers-cov was the first subject of such widespread use of deep sequencing to study an emerging viral outbreak with global reach. the technique can produce genomic [ ] [ ] [ ] . earlier and subsequent versions of this chart are maintained on a personal blog [ ] length coverage in a single experiment with highly repetitious measurement of each nucleotide position [ , ] . despite assays having been published early on, subgenomic sequencing, once the mainstay of viral outbreak studies, has less often been published during mers-cov characterization [ ] . as more genomes from both humans and dcs have been characterized, two clades have become apparent; a and b (fig. ) . clade a contains only human-derived mers-cov genomes from jordan, while clade b comprises the majority of human and camel genomes deduced thus far [ ] . two studies during , one looking at jeddah- mers-cov variants and another looking at a variant exported from south korea to china, have now identified signs of genetic recombination among mers-cov variants. while human and camel whole genome sequences have retained > % identity with each other, members of genetically distinct lineages can and do swap genetic material when suitable conditions and coinfections co-occur [ ] [ ] [ ] . shared identity implies that the major source for human acquisition is the dc, rather than another animal, although more testing of other animal species is needed to confirm that conclusion. over a month, a dc virus sequenced on different occasions did not change at all indicating a degree of genomic stability in its host, supporting that dcs are the natural, rather than intermediate, host for the mers-cov we know today [ ] . to date, recombination has been localised to breakpoints near the boundary between orf a and orf b regions, within the spike gene [ ] and in the orf b region (fig. ) [ ] . it is not unexpected that recombination should occur since it is well known among other covs [ ] and because the majority of mers-cov whole genomes collected from samples spanning three years ( - ) and from humans, camels and different countries have shown close genetic identity to each other, with just enough subtle variation to support outbreak investigations so long as whole genome sequencing is applied [ , , , , , [ ] [ ] [ ] . changes in genome sequence may herald alterations to virus transmissibility, replication, persistence, lethality or response to future drugs. if we have prior knowledge of the impact of genetic changes because of thorough characterization studies, we can closely fig. the genetic relationship between mers-cov nucleotide sequences (downloaded from genbank using the listed accession numbers and from virological.org [ ] ). this neighbour joining tree was created in mega v using an alignment of human and dcderived mers-cov sequences (geneious v . [ ] ). clades are indicated next to dark (clade a) or pale (clade b) blue vertical bars. camel icons denote genomes from dcs. healthcare or community outbreaks are boxed and labelled using previously described schemes [ , ] monitor the genomic regions and better understand any changes in transmission or disease patterns as they occur. genetic mutations noted during the largest of human outbreaks, jeddah- , did not impart any major replicative or immunomodulatory changes when compared to earlier viral variants in vitro [ , ] . however, we understand very little of the phenotypic outcomes that result from subtle genetic change in mers-cov genomes. to date no clinical relevance or obvious in vivo changes to viral replication, shedding or transmission has been reported or attributed to mutations or to new recombinant viruses [ ] . but vigilance and larger, more contemporary and in vivo studies are needed. genome sequence located to a distinct clade were identified from an egyptian dc that was probably imported from sudan. this does not fit into either of the current clades [ , , ] . a virus sequenced from a neoromicia capensis bat was more closely related to mers-cov than other large bat-derived sequences had been to that point, but the genome of a variant of a mers-cov has yet to be discovered and deduced from any bat [ ] . analyses of mers-cov genomes have shown that most single nucleotide differences among variants were located in the last third of the genome (fig. ) , which encodes the spike protein and accessory proteins [ ] . at least nine mers-cov genomes contained amino acid substitutions in the receptor binding domain (rbd) of the spike protein and codons (n-terminal region), (rbd), (in heptad repeat ), and bear investigation as markers of adaptive change [ , ] . the spike protein had not changed in the recombinant mers-cov genome identified in china in but was reported to have varied at a higher rate than that for complete mers-cov genomes, among south korean variants [ , ] . this highlights that subgenomic regions may not always contain enough genetic diversity to prove useful for differentiating viral variants. despite this, one assay amplifying a nucleotide fragment of the spike s domain gene for sanger sequencing agreed with the results generated by the sequencing of a some full genomes and was useful to define additional sequence groupings [ ] . genomic sequence can also be used to define the geographic boundaries of a cluster or outbreak and monitor its progress, based on the similarity of the variants found among infected humans and animals when occurring together, or between different sites and times (fig. ) [ ] . this approach was employed when defining the geographically constrained mers hospital outbreak in al-ahsa, which occurred between st april and rd may , as well as clusters in buraidah and a community outbreak in hafr al-batin, the ksa. genomic sequencing identified that approximately mers-cov detections from a community outbreak in hafr al-batin between june and august may have been triggered by an index case becoming infected through dc contact [ ] . sequencing mers-cov genomes from the al-ahsa hospital outbreak indicated that multiple viral variants contributed to the cases but that most were similar enough to each other to be consistent with human-tohuman transmission. molecular epidemiology has revealed otherwise hidden links in transmission chains encompassing a period of up to five months [ ] . however, most outbreaks have not continued for longer than two to three months and so opportunities for the virus to adapt further to humans through co-infection and sustained serial passage have been rare [ ] . in riyadh- , genetic evidence supported the likelihood of multiple external introductions of virus, implicating a range of healthcare facilities in an event that otherwise looked contiguous [ , , ] . riyadh is a nexus for camel and human travel and has had more mers cases than any other region of the ksa to date but also harbours a wide range of mers-cov variants [ , , ] . however the south korean outbreak originated from a single infected person, resulting in three to four generations of cases [ , ] . studies of this apparently recombinant viral variant did not find an increased evolutionary rate and no sign of virus adaptation thus the outbreak seems to have been driven by circumstance rather than circumstance together with mutation [ ] . for many mers cases detected outside the arabian peninsula, extensive contact tracing has been performed and the results described in detail. contact tracing is essential to contain the emergence and transmission of a new virus and today it is supported by molecular epidemiology. although it is an expensive and time consuming process, contact tracing can identify potential new infections and through active or passive monitoring, react more rapidly if disease does develop. results of contact tracing to date have found that onward transmission among humans is an infrequent event. for example, there were contacts, both symptomatic and asymptomatic, of a case treated in germany who travelled from the uae but no sign of virus or antibody were found in any of them [ ] . the very first mers case had made contact with hcws and others, but none developed any indication of infection [ ] . in a study of contacts of a case treated in france, only seven matched the definition for a possible case and were tested; one who had shared a m hospital room while in a bed . m away from the index case for a prolonged period was positive [ ] . none of the contacts of the first two mers cases imported into the usa in contained any mers-cov footprint [ ] and none of the contacts of two travellers returning to the netherlands developed mers-cov antibodies or tested rna positive [ , ] . analyses of public data reveal many likely instances of nosocomial acquisition of infection in the arabian peninsula and these data may be accompanied by some details noting contact with a known case or facility. one example identified the likely role of a patient with a subclinical infection, present in a hospital during their admission for other reasons, as the likeliest index case triggering a family cluster [ ] . contact tracing was a significant factor in the termination of a outbreak involving multiple south korean hospitals [ ] . such studies demonstrate the necessity of finding and understanding a role for mild and asymptomatic cases, together with restricting close contact or prolonged exposure of infected people to others, especially older family members and friends with underlying disease (fig. c) . the hospital-associated outbreak in jeddah in was the largest and most rapid accumulation of mers-cov detections to date. the greatest number of mers-cov detections of any month on record occurred in jeddah in april. the outbreak was mostly (> % of cases) associated with human-to-human spread within hospital environments and resulted from a lack of, or breakdown in, infection prevention and control [ , , ] . a rise in fatalities followed the rapid increase in case numbers. in two large outbreaks occurred. south korea was the site of the first large scale outbreak outside the arabian peninsula and produced the first cases in both south korea and china, occurring between may and july . this was closely followed by a distinct outbreak in ar riyad province in the ksa which appeared to come under control in early november. after staying in bahrain for two weeks, a year old male ( m) travelled home to south korea via qatar, arriving free of symptoms on the th may [ ] . he developed fever, myalgia and a cough nearly a week later ( th ). he visited a clinic as an outpatient between the th and th of may and was admitted to hospital a on the th [ ] . he was discharged from hospital a on the th then visited and was admitted to the emergency department of hospital b on the th . during this second stay, a sputum sample was taken and tested positive for mers-cov on the th [ , ] , triggering transfer to the designated isolation treatment facility. over a period of days, the index case was seen at three different hospitals, demonstrating a key feature of "hospital shopping" that shaped the south korean outbreak. approximately people were infected during this time [ ] . in total cases were generated in this outbreak, all linked through a single transmission chain to m; cases died [ ] . in south korea, the national health insurance system provides for relatively low cost medical care, defraying some costs by making family members responsible for a portion of the ministration of the sick, resulting in them sometimes staying for long periods in the rooms that often have more than four beds in them [ ] . other factors thought to have enabled this outbreak included unfamiliarity of local clinicians with mers, ease with which the public can visit and be treated by tertiary hospitals, the custom of visiting sick friends and relatives in hospitals, the hierarchical nature of korean society, crowded emergency rooms, poor ipc measures, a lack of negative pressure isolation rooms and poor inter-hospital communication of patient disease histories [ , [ ] [ ] [ ] . all of the reported transmission occurred across three or four generations and apart from one unknown source, were all hospital-acquired [ , , , [ ] [ ] [ ] . few clinical details about these cases have been reported to date and detail on transmission and contact tracing is minimal. the hospitals involved were initially not identified, governmental guidance and actions produced confusing messages and there was very limited communication at all early on which resulted in unnecessary concern, distrust and a distinct economic impact [ , [ ] [ ] [ ] . early in the outbreak, a infected traveller, the son of an identified case in south korea, passed through hong kong on his way to china where he was located, isolated and cared for in china [ , , ] . no contacts became ill. the outbreak was brought under control in late july/ early august [ ] after improved ipc measures were employed, strong contact tracing monitoring and quarantine, expanded laboratory testing, hospitals were better secured, specialized personnel were dispatched to manage cases and international cooperation increased [ , ] . a review of public data showed that, as for mers in the ksa, older age and the presence of underlying disease were significantly associated with a fatal outcome in south korea. [ ] even though r is < , super-spreading events facilitated by circumstances created in healthcare settings and characterized by cluster sizes over , such as this one, are not unexpected from mers-cov infection [ ] . the dynamic of an outbreak depends on the r and an individual's viral shedding patterns, contact type and frequency, hospital procedures and population structure and density [ ] . in the region of ar riyad, including the capital city of riyadh, a hospital based cluster began, within a single hospital, from late june [ ] . by mid-september there had been approximately cases reported but the outbreak appeared to been brought under control in november. it became apparent early on that mers-cov spread relatively ineffectively from human-to-human. despite ongoing and possibly seasonal introduction of virus to the human population via infected dcs and perhaps other animals yet to be identified, the vast majority of mers-cov transmission has occurred from infected to uninfected humans in close and prolonged contact through circumstances created by poor infection control in health care settings. this opportunistic virus has had its greatest impact on those with underlying diseases and such vulnerable people, sometimes suffering multiple comorbidities, have been most often associated with hospitals, creating a perfect storm of exposure, transmission and mortality. it remains unclear if this group are uniquely affected by mers-cov or if other respiratory virus infections, including those from hcovs, produce a similarly serious impact. in south korea, a single imported case created an outbreak of cases and deaths that had a disproportionate impact on economic performance, community behaviour and trust in government and the health care system. household human-to human transmission occurs but is also limited. educational programs will be essential tools for combatting the spread of mers-cov both within urban and regional communities and for the health care setting. vigilance remains important for containment since mers-cov is a virus with a genetic makeup that has been observed for only three years and is not stable. among all humans reported to be infected, nearly % have died. continued laboratory testing, sequencing, analysis, timely data sharing and clear communication are essential for such vigilance to be effective. global alignment of case definitions would further aid accurate calculation of a case fatality ratio by including subclinical case numbers. whole genome sequencing has been used extensively to study mers-cov travel and variation and although it remains a tool for experts, it appears to be the best tool for the job. mers and sars have some clinical similarities but they also diverge significantly [ ] . defining characteristics include the higher pfc among mers cases (above % in and currently at - %; well above the % of sars) and the higher association between fatal mers and older males with underlying comorbidities. for the viruses, mers-cov has a broader tropism, grows more rapidly in vitro, more rapidly induces cytopathogenic change, triggers distinct transcriptional responses, makes use of a different receptor, induces a more proinflammatory state and has a delayed innate antiviral response compared to sars-cov. there appears to be a - % prevalence of mers-cov in the ksa with a % chance of secondary transmission within the household. there is an increased risk of infection through certain occupations at certain times and a much greater chance for spread to other humans during circumstances created by humans, which drives more effective transmission than any r would predict on face value. nonetheless, despite multiple mass gatherings that have afforded the virus many millions of opportunities to spread, there have remarkably been no reported outbreaks of mers or mers-cov during or immediately after these events. there is no evidence that mers-cov is a virus of pandemic concern. nonetheless, hospital settings continue to describe mers cases and outbreaks in the arabian peninsula. as long as we facilitate the spread of mers-cov among our most vulnerable populations, the world must remain on alert for cases which may be exported more frequently when a host country with infected camel reservoirs is experiencing human clusters or outbreaks. the mers-cov appears to be an enzootic virus infecting the dc urt with evidence of recent genetic recombination. it may once have had its origins among bats, but evidence is lacking and the relevance of that to today's ongoing epidemic is academic. thanks to quick action, the sensitive and rapid molecular diagnostic tools required to achieve rapid and sensitive detection goal have been in place and made widely available since the virus was reported in . rt-pcr testing of lrt samples remains the gold standard for mers-cov confirmation. serological tools continue to emerge but they are in need of further validation using samples from mild and asymptomatic infections and a densely sampled cohort study to follow contacts of new cases may address this need. similarly, the important question of whether those who do shed mers-cov rna for extended periods are infectious while appearing well, continues to go unanswered. it is even unclear just how many 'asymptomatic' infections have been described and reported correctly which in turn raises questions about the reliability of other clinical data collection to date. while the basic virology of mers-cov has advanced over the course of the past three years, understanding what is happening in, and the interplay between, camel, environment and human is still in its infancy. additional file : figure s . the severe respiratory illness caused by a novel coronavirus middle east respiratory syndrome coronavirus (mers-cov) -saudi arabia middle east respiratory syndrome coronavirus infection in dromedary camels in saudi arabia middle east respiratory syndrome: an emerging coronavirus infection tracked by the crowd absence of mers-coronavirus in bactrian camels, southern mongolia seroepidemiology of middle east respiratory syndrome (mers) coronavirus in saudi arabia ( ) and australia ( ) and characterisation of assay specificity middle east respiratory syndrome coronavirus infection not found in camels in japan absence of mers-cov antibodies in feral camels in australia: implications for the pathogen's origin and spread lack of middle east respiratory syndrome coronavirus transmission from infected camels tensions linger over discovery of coronavirus as outbreak continues middle east respiratory syndrome coronavirus (mers-cov): evidence and speculations cumulative number of reported probable cases of sars in-vitro renal epithelial cell infection reveals a viral kidney tropism as a potential mechanism for acute renal failure during middle east respiratory syndrome (mers) coronavirus infection replicative capacity of mers coronavirus in livestock cell lines human coronavirus emc does not require the sars-coronavirus receptor and maintains broad replicative capability in mammalian cell lines isolation of a novel coronavirus from a man with pneumonia in saudi arabia human cell tropism and innate immune system interactions of human respiratory coronavirus emc compared to those of severe acute respiratory syndrome coronavirus state of knowledge and data gaps of middle east respiratory syndrome coronavirus (mers-cov) in humans epidemiological, demographic, and clinical characteristics of cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study family cluster of middle east respiratory syndrome coronavirus infections hospital outbreak of middle east respiratory syndrome coronavirus mers outbreak in korea: hospital-to-hospital transmission middle east respiratory syndrome coronavirus (mers-cov) infections in two returning travellers in the netherlands first cases of middle east respiratory syndrome coronavirus (mers-cov) infections in france, investigations and implications for the prevention of human-tohuman transmission case definition for case finding severe respiratory disease associated with novel coronavirus middle east respiratory syndrome coronavirus case definition for reporting to who. interim case definition as of middle east respiratory syndrome coronavirus | case definition for reporting to who revised interim case definition for reporting to who -middle east respiratory syndrome coronavirus (mers-cov): interim case definition as of transmission of mers-coronavirus in household contacts screening for middle east respiratory syndrome coronavirus infection in hospital patients and their healthcare worker and family contacts: a prospective descriptive study case definition and surveillance guidance for mers-cov testing in saudi arabia infection prevention/control and management guidelines for patients with middle east respitaory syndrome coronavius (mers-cov) infection infection prevention and control guidelines for middle east respiratory syndrome coronavirus (mers-cov) infection middle east respiratory syndrome coronavirus in children characteristics and outcomes of middle east respiratory syndrome coronavirus patients admitted to an intensive care unit in jeddah, saudi arabia risk factors for primary middle east respiratory syndrome coronavirus illness in humans, saudi arabia preliminary epidemiological assessment of mers-cov outbreak in south korea mortality risk factors for middle east respiratory syndrome outbreak, south korea clinical course and outcomes of critically ill patients with middle east respiratory syndrome coronavirus infection estimating the risk of middle east respiratory syndrome (mers) death during the course of the outbreak in the republic of korea invited editorial: mers-cov an emerging viral zoonotic disease: three years after and counting middle east respiratory syndrome coronavirus disease in children middle east respiratory syndrome coronavirus not detected in children hospitalized with acute respiratory illness in stillbirth during infection with middle east respiratory syndrome coronavirus detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction assays for laboratory confirmation of novel human coronavirus (hcov-emc) infections infectious middle east respiratory syndrome coronavirus excretion and serotype variability based on live virus isolates from patients in saudi arabia development and evaluation of a 'real-time' rt-pcr for the detection of enterovirus and parechovirus rna in csf and throat swab samples mers: emergence of a novel human coronavirus genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans laboratory testing for middle east respiratory syndrome coronavirus | interim guidance performance and clinical validation of the realstar mers-cov kit for detection of middle east respiratory syndrome coronavirus rna real-time reverse transcription-pcr assay panel for middle east respiratory syndrome coronavirus laboratory testing for middle east respiratory syndrome coronavirus development and evaluation of novel real-time reverse transcription-pcr assays with locked nucleic acid probes targeting leader sequences of human-pathogenic coronaviruses realtime sequence-validated loop-mediated isothermal amplification assays for detection of middle east respiratory syndrome coronavirus (mers-cov) a sweet spot for molecular diagnostics: coupling isothermal amplification and strand exchange circuits to reverse transcription recombinase polymerase amplification assay for the detection of middle east respiratory syndrome coronavirus development and validation of a rapid immunochromatographic assay for detection of middle east respiratory syndrome coronavirus antigen in dromedary camels a sensitive and specific antigen detection assay for middle east respiratory syndrome coronavirus investigation of an imported case of middle east respiratory syndrome coronavirus (mers-cov) infection in serological assays for emerging coronaviruses: challenges and pitfalls middle east respiratory syndrome coronavirus immunoassays test characteristics: anti-mers-cov elisa camel (igg) recombivirus anti-middle east respiratory syndrome coronavirus (mers-cov) elisa kits ncov / novel coronavirus) nucleocapsid antibody, mouse mab is mers another sars? investigation of anti-middle east respiratory syndrome antibodies in blood donors and slaughterhouse workers in jeddah and makkah, saudi arabia, fall cross-reactive antibodies in convalescent sars patients' sera against the emerging novel human coronavirus emc ( ) by both immunofluorescent and neutralizing antibody tests asymptomatic mers-cov infection in humans possibly linked to infected camels imported from oman to united arab emirates contact investigation for imported case of middle east respiratory syndrome seroepidemiology for mers coronavirus using microneutralisation and pseudoparticle virus neutralisation assays reveal a high prevalence of antibody in dromedary camels in egypt a safe and convenient pseudovirus-based inhibition assay to detect neutralizing antibodies and screen for viral entry inhibitors against the novel human coronavirus mers-cov middle east respiratory syndrome (mers) coronavirus seroprevalence in domestic livestock in saudi arabia mers coronavirus in dromedary camel herd, saudi arabia middle east respiratory syndrome coronavirus (mers-cov) serology in major livestock species in an affected region in jordan lack of mers coronavirus neutralizing antibodies in humans, eastern province, saudi arabia sparse evidence of mers-cov infection among animal workers living in southern saudi arabia during . influenza other respir viruses kinetics of serologic responses to mers coronavirus infection in humans hospital-associated outbreak of middle east respiratory syndrome coronavirus: a serologic, epidemiologic, and clinical description epidemiological findings from a retrospective investigation specific serology for emerging human coronaviruses by protein microarray middle east respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study antibodies against mers coronavirus in dromedary camels presence of middle east respiratory syndrome coronavirus antibodies in saudi arabia: a nationwide, cross-sectional, serological study cdc concludes indiana mers patient did not spread virus to illinois business associate middle east respiratory syndrome: what clinicians need to know interim guidelines for collecting, handling, and testing clinical specimens from patients under investigation (puis) for middle east respiratory syndrome coronavirus (mers-cov characteristics of traveler with middle east respiratory syndrome distinct immune response in two mers-cov-infected patients: can we go from bench to bedside? a family cluster of middle east respiratory syndrome coronavirus infections related to a likely unrecognized asymptomatic or mild case association of higher mers-cov virus load with severe disease and death, saudi arabia an appropriate lower respiratory tract specimen is essential for diagnosis of middle east respiratory syndrome (mers) lack of nasal carriage of novel corona virus (hcov-emc) in french hajj pilgrims returning from the hajj , despite a high rate of respiratory symptoms health protection agency ukncit. evidence of person-to-person transmission within a family cluster of novel coronavirus infections prevalence of mers-cov nasal carriage and compliance with the saudi health recommendations among pilgrims attending the hajj a case of long-term excretion and subclinical infection with middle east respiratory syndrome coronavirus in a healthcare worker middle east respiratory syndrome coronavirus (mers-cov) causes transient lower respiratory tract infection in rhesus macaques virological and serological analysis of a recent middle east respiratory syndrome coronavirus infection case on a triple combination antiviral regimen middle east respiratory syndrome coronavirus (mers-cov) viral shedding in the respiratory tract: an observational analysis with infection control implications respiratory tract samples, viral load and genome fraction yield in patients with middle east respiratory syndrome ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: an observational study laboratory-confirmed case of middle east respiratory syndrome coronavirus (mers-cov) infection in malaysia: preparedness and response a case of imported middle east respiratory syndrome coronavirus infection and public health response viral respiratory infections among hajj pilgrims in influenza a and b viruses but not mers-cov in hajj pilgrims acute respiratory infections in travelers returning from mers-cov-affected areas changes in the prevalence of influenza-like illness and influenza vaccine uptake among hajj pilgrims: a -year retrospective analysis of data soaring mers cases cause pandemic jitters, but causes are unclear co-circulation of four human coronaviruses (hcovs) in queensland children with acute respiratory tract illnesses in recovery from severe novel coronavirus infection human isolate . who statement on the fifth meeting of the ihr emergency committee concerning mers-cov | who statement mers-cov in upper respiratory tract and lungs of dromedary camels, saudi arabia evidence for camel-to-human transmission of mers coronavirus taking stock of the first mers coronavirus cases globally-is the epidemic changing? human-dromedary camel interactions and the risk of acquiring zoonotic middle east respiratory syndrome coronavirus infection. zoonoses public health summary of current situation, literature update and risk assessment middle east respiratory syndrome coronavirus in bats, saudi arabia emerging infectious diseases associated with bat viruses bats and their virome: an important source of emerging viruses capable of infecting humans coronavirus diversity, phylogeny and interspecies jumping rooting the phylogenetic tree of middle east respiratory syndrome coronavirus by characterization of a conspecific virus from an african bat middle east respiratory syndrome coronavirus: another zoonotic betacoronavirus causing sars-like disease link between mers virus and camels worries breeders dromedary camels and the transmission of middle east respiratory syndrome coronavirus (mers-cov) fiqh us-sunnah antibodies against mers coronavirus in dromedary camels geographic distribution of mers coronavirus among dromedary camels acute middle east respiratory syndrome coronavirus infection in livestock dromedaries mers coronavirus neutralizing antibodies in camels serological evidence of mers-cov antibodies in dromedary camels (camelus dromedaries) in laikipia county middle east respiratory syndrome coronavirus antibody reactors among camels in dubai serologic assessment of possibility for mers-cov infection in equids mers coronaviruses in dromedary camels middle east respiratory syndrome coronavirus in dromedary camels: an outbreak investigation middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels isolation of mers coronavirus from a dromedary camel prevalence of middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels in abu dhabi emirate human infection with mers coronavirus after exposure to infected camels, saudi arabia detection of the middle east respiratory syndrome coronavirus genome in an air sample originating from a camel barn owned by an infected patient high proportion of mers-cov shedding dromedaries at slaughterhouse with a potential epidemiological link to human cases replication and shedding of mers-cov in upper respiratory tract of inoculated dromedary camels evidence for camel-to-human transmission of mers coronavirus the holy qur'an sacrificing an animal at mina occupational exposure to dromedaries and risk for mers-cov infection stability of middle east respiratory syndrome coronavirus (mers-cov) under different environmental conditions middle east respiratory syndrome coronavirus (mers-cov) rna and neutralising antibodies in milk collected according to local customs from dromedary camels the effects of temperature and relative humidity on the viability of the sars coronavirus viability of pseudomonas aeruginosa in cough aerosols generated by persons with cystic fibrosis middle east respiratory syndrome coronavirus: transmission and phylogenetic evolution middle east respiratory syndrome coronavirus: epidemic potential or a storm in a teacup? an observational, laboratory-based study of outbreaks of mers-coronavirus in jeddah and riyadh, kingdom of saudi arabia assessment of the mers-cov epidemic situation in the middle east region assessing the pandemic potential of mers-cov interhuman transmissibility of middle east respiratory syndrome coronavirus: estimation of pandemic risk middle east respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility transmission dynamics and control of ebola virus disease (evd): a review health care worker contact with mers patient, saudi arabia middle east respiratory syndrome coronavirus: epidemiology and disease control measures age-specific and sex-specific morbidity and mortality from avian influenza a(h n ) mers-cov outbreak in jeddah-a link to health care facilities infection prevention and control during health care for probable or confirmed cases of novel coronavirus (ncov) infection full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus transmission and evolution of the middle east respiratory syndrome coronavirus in saudi arabia: a descriptive genomic study spread, circulation, and evolution of the middle east respiratory syndrome coronavirus mers-cov recombination: implications about the reservoir and potential for adaptation middle east respiratory syndrome coronavirus recombination and the evolution of science and public health in china origin and possible genetic recombination of the middle east respiratory syndrome coronavirus from the first imported case in china laboratory investigation and phylogenetic analysis of an imported middle east respiratory syndrome coronavirus case in greece middle east respiratory syndrome coronavirus quasispecies that include homologues of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in saudi arabia community case clusters of middle east respiratory syndrome coronavirus in hafr al-batin, kingdom of saudi arabia: a descriptive genomic study middle east respiratory syndrome coronavirus (mers-cov) summary and literature update-as of reliable typing of mers-cov variants with a small genome fragment variations in spike glycoprotein gene of mers-cov molecular epidemiology of hospital outbreak of middle east. respiratory syndrome middle east respiratory syndrome coronavirus (mers-cov) in the republic of korea microevolution of outbreak-associated middle east respiratory syndrome coronavirus, south korea first confirmed cases of middle east respiratory syndrome coronavirus (mers-cov) infection in the united states, updated information on the epidemiology of mers-cov infection, and guidance for the public, clinicians, and public health authorities followup of contacts of middle east respiratory syndrome coronavirus-infected returning travelers, the netherlands press release -who, korea-who joint mission on mers cov call for infection control to stem mers infection control and mers-cov in health workers an outbreak of middle east respiratory syndrome coronavirus infection in south korea middle east respiratory syndrome coronavirus (mers-cov) -republic of korea samsung hospital to invest w b in post-mers improvements why the panic? south korea's mers response questioned intensified public health measures help control mers-cov outbreak in the republic of korea south korean mers outbreak spotlights lack of research complete genome sequence of middle east respiratory syndrome coronavirus isolated in south korea complete genome sequence of middle east respiratory syndrome coronavirus (mers-cov) from the first imported mers-cov case in china urgent call for research on middle east respiratory syndrome (mers) in korea middle east respiratory syndrome (mers) in asia: lessons gleaned from the south korean outbreak no respite for korean economy even as mers patients recover middle east respiratory syndrome coronavirus (mers-cov) -china mers in south korea and china: a potential outbreak threat? objective determination of end of mers outbreak, south korea updates on mers outbreak (as of : on surveillance operation for the st confirmed case of middle east respiratory syndrome coronavirus in response to the patient's prior travel to jeju island the role of superspreading in middle east respiratory syndrome coronavirus (mers-cov) transmission moh holds the first press conference to update community and media on mers severe acute respiratory syndrome vs. the middle east respiratory syndrome middle east respiratory syndrome coronavirus (mers-cov) - case list of moh/who novel coronavirus mers ncov announced cases geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data recent evolution patterns of the middle east respiratory syndrome coronavirus (mers-cov) preliminary analysis of middle east respiratory syndrome coronavirus (mers-cov) sequences from korea and china any unreferenced opinions expressed herein are those of the authors and do not necessarily represent the views of any employer or institution. our thanks go to andrew rambaut, maia majumder, marion koopmans and hale abdali for helpful discussions on social media and cmam and riam for patience. the authors declare that they have no competing interests.author's contributions imm and kea contributed equally to this work and read an approved the final manuscript. key: cord- -aqh zxgh authors: el homsi, maria; chung, michael; bernheim, adam; jacobi, adam; king, michael j.; lewis, sara; taouli, bachir title: review of chest ct manifestations of covid- infection date: - - journal: eur j radiol open doi: . /j.ejro. . sha: doc_id: cord_uid: aqh zxgh coronavirus disease- (covid- ) is a viral pandemic that started in china and has rapidly expanded worldwide. typical clinical manifestations include fever, cough and dyspnea after an incubation period of - days. the diagnosis is based on rt-pcr test through a nasopharyngeal swab. because of the pulmonary tropism of the virus, pneumonia is often encountered in symptomatic patients. here, we review the pertinent clinical findings and the current published data describing chest ct findings in covid- pneumonia, the diagnostic performance of ct for diagnosis, including differential diagnosis, as well the evolving role of imaging in this disease. serum immunoglobulins (igm and igg) can be used to diagnose recent infection to covid- [ ] . for example, a study demonstrated that the positive detection rate is increased ( . %) when combining igm assay with rt-pcr compared to rt-pcr alone ( . %) [ ] . a total of original papers published in english totaling over patients were reviewed [ , . reviews and case reports were excluded. most reviewed papers originate from china [ , - , - , - , - ] and the remainder from japan [ , ] , korea [ ] and italy [ , ] . three papers were in collaboration between chinese and us institutions [ , , ] . chest radiography (cxr) findings in patients with covid- have been described in small case series [ , ] . cxr is negative in %- . % of cases despite positive findings on chest ct ( fig. ) [ , ] . the most common radiographic finding is opacification, often with a peripheral and lower lung distribution [ , ] (fig. ) . thus, cxr is not recommended for routine diagnosis of covid- , but may be helpful for follow-up. a low dose, chest ct without intravenous contrast is generally used for evaluation [ ] . typically, covid- pneumonia presents with bilateral peripheral patchy ground-glass opacities (ggo) with or without consolidation [ , , ] (fig. , ) . ggos may have a rounded morphology [ , , , , ] in up to % of the cases (fig. ) . superimposed interlobular septal thickening can also be present, resulting in a crazy-paving pattern (fig. ) . vascular enlargement, air bronchograms, and a halo sign have also been described (fig. ) . the ggos and consolidative lesions are larger than cm in % of cases [ ] . the lower lobes and posterior portions are more frequently involved [ ] . mediastinal and hilar lymphadenopathy, pleural effusions or thickening, discrete pulmonary nodules, and pulmonary cavitation have been rarely described in the chinese series [ , , ]. an italian study described lymphadenopathy in up to % of cases [ ] . table shows the prevalence of various imaging findings on chest ct at initial presentation. a japanese study described that asymptomatic patients tend to have more ggo ( %) and less consolidation ( %) compared with symptomatic patients ( % and %) [ ] . cxr and chest ct can be negative in up to . % of patients, especially in early and/or non severe disease [ ] . in mild cases, ct findings consist more frequently of ggo alone ( %), followed by ggo with consolidation ( %) [ ] . severe cases with a clinical acute respiratory distress syndrome (ards) picture present with widespread dense consolidative opacification on ct (see below). several studies categorized covid- ct findings into several stages based on time since the onset of symptoms [ , , , , ] . these were classified into main successive stages: early, intermediate and late [ ] and a fourth resorptive stage [ ] .  early stage (≤ days): more than half of the patients have negative chest ct ( %). the remaining patients have predominantly ggo ( %) and consolidation ( %). imaging findings when present were often unilateral [ ] . similar findings were described in another study [ ] , which demonstrated that in early disease . % of cases present with a solitary lesion seen in % of cases in the right lower lobe.  intermediate stage ( - days): as the disease progresses, more ggo ( %) and consolidation ( %) are noted bilaterally ( %) and with a peripheral lung distribution ( %). only % of patients have negative chest ct [ ] . % and % of patients have ggo and consolidation, respectively. the imaging findings are bilateral in % and peripheral-predominant in % of cases [ ] .  absorption stage/fourth stage (> days): % and % of patients have ggo and consolidation, respectively. the imaging findings are bilateral in % and peripheralpredominant in % of cases [ ] . when patients improve, the lung disease evolves and organizes, and fibrous bands may appear [ , , , ] . a "reverse-halo sign" is occasionally observed and can be an indication of organizing pneumonia [ , ] . in severe cases, the consolidation and ggo increase and involve all five lung lobes, resulting in a dense consolidative appearance and characterized by diffuse alveolar damage, usually with a poor prognosis [ ] (fig. . ) it has been suggested that imaging can help predict severity of covid- disease. for example, a study showed that a severity score based on cxr at initial presentation in nonelderly patients ( - y) predicts outcome (hospital admission and intubation) [ ] . another study suggested that severe/fatal cases were more likely to have more extensive and diffuse disease with more frequent architectural distortion and bronchiectasis compared to mild/common cases [ ] . however, more data is needed particularly in comparison with blood tests, such as cytokine levels. oncology patients: a retrospective study in oncologic patients showed similar findings of ggo ( %) and patchy consolidation ( . %). the presence of the latter at admission was associated with worse outcome [ ] . pediatric and pregnant patients: few studies have described chest ct findings in children [ ] [ ] [ ] [ ] who tend to have milder findings. the largest study included patients [ ] , % of whom had normal chest ct, % had ggo, and % had consolidation with a surrounding halo (which was considered a typical finding in this population). bilateral disease was observed in % of cases. co-infection with another pathogen was identified in %- % of the cases [ , ] . another study [ ] found that pregnant women have more consolidation (up to %) as compared with the non-pregnant population ( %). pregnant woman also manifested with bilateral and peripheral-predominant ggo. pleural effusions were more commonly encountered in pregnant than in non-pregnant women, up to % versus %. elderly population: older patients (> y) have similar (classic) chest ct findings [ ] . however, they tend to have more areas of lung involvement with more lobes affected and more pleural thickening [ ] . similar findings were obtained in another study [ ] , where patients older than years had more extensive disease with more consolidation as compared with patients younger than . they tended to have more architectural distortion, bronchiectasis, mediastinal and hilar lymphadenopathy and pleural effusions and worse outcomes than younger patients [ ] . covid- and pulmonary embolism: an increased incidence of acute pulmonary embolism in hospitalized covid- patients has been reported [ ] . out of patients, % had an acute pulmonary embolism and it was associated with elevated d-dimer (up to . ug/ml). covid- can be associated with pulmonary embolism especially when d-dimer is elevated (fig. ) , and preventive anticoagulation has been recommended in hospitalized patients [ ] . [ , ] . a study performed by bai et al found that of radiologists had high specificity ( - %) and moderate sensitivity ( - %) in distinguishing covid- pneumonia from other viral pneumonias, although there was variability in radiologist performance [ ] . compared to viral pneumonia, covid- tends to have a more peripheral distribution, greater ggo, increased vascular enlargement and a "reverse-halo sign". zhao et al also demonstrated that covid- had more frequent bilateral ggos compared to non-covid- viral infections [ ] . key findings less frequent in covid- pneumonia compared to non-covid pneumonia included air bronchograms, centrilobular nodules, tree-in-bud opacities, bronchial wall thickening and a reticular pattern [ , ] . other coronavirus organisms with genetic resemblance to covid- can produce similarly devastating pulmonary syndromes, including sars ( . % mortality rate) and mers ( . % mortality rate) [ , ] . while there have been no documented cases of sars since , mers cases are still reported sporadically. all three of these infections cause peripheral multifocal airspace opacities (ggo and/or consolidation), without pneumothorax, cavitation or lymphadenopathy. differences in the imaging appearances have been reported, as sars tends to be unilateral and focal in distribution ( %) and mers patients can develop pleural effusion ( %) [ , ] . both sars and mers are associated with constriction of the pulmonary vasculature, whereas enlargement of the vasculature has been reported in covid- [ ] . pulmonary fibrosis was reported as a late manifestation in mers, but not in sars. the longterm sequelae of covid- remain to be determined; however, early publications indicate a fibrotic phase characterized by reticulation, interlobular septal thickening and traction bronchiectasis [ , ] . finally, a variety of other noninfectious pulmonary diseases can produce imaging findings on ct that may overlap with covid- pneumonia, including pulmonary edema, ards, organizing pneumonia, prior treatment (i.e. drug toxicity or radiation pneumonitis/fibrosis), pulmonary infarction, alveolar hemorrhage, and interstitial lung diseases [ ] . both ards and bacterial superinfection can complicate covid- pneumonia. while there is an abundance of literature being published at a rapid rate, results of these studies must be scrutinized and interpreted with caution as a variety of sources of bias may produce artificially high performance characteristics of ct and certain imaging findings for covid- pneumonia [ ] . ultimately, given the variable and non-specific nature of the imaging findings in covid- , integration of clinical history, laboratory tests, in addition to quantitative approaches including machine learning or artificial intelligence (ai, see below), are needed for accurate assessment. several studies compared the accuracy of chest ct against rt-pcr [ , , , , ] . abnormal chest ct findings can be present despite a negative rt-pct with a sensitivity ranging between %- % [ , , , ] . however, according to raptis et al this high sensitivity can be explained by a selection bias of the studied population and low threshold for positive disease on chest ct [ ] . using rt-pcr as a reference, specificity of chest ct ranges between %- % and accuracy between %- % [ , ] . the positive predictive value and accuracy of chest ct were higher in patients older than years. % of cases had improvement of imaging findings before negative conversion of rt-pcr [ ] . the positive rate of rt-pcr was %- % [ , , ] . this can be explained by the fact that rt-pcr was obtained through throat swabs which have low positive rates [ , ] as viral pneumonia does not usually produce purulent sputum [ ] . with the rapid evolution of this outbreak, the global community of radiologists has convened to construct guidelines and position statements regarding the appropriate use of imaging during this pandemic. early in the outbreak, hospitals in china were using chest ct in many suspected patients, as well as to follow-up the progression of lung disease. in the us, the centers for disease control and prevention (cdc), the american college of radiology (acr), the society of thoracic radiology (str), and the american society of emergency radiology (aser) issued their position statements recommending against the use of ct for widespread screening and diagnosis of covid- , instead reserving ct for those cases with clinical suspicion for complications like abscess or empyema [ ] [ ] [ ] . this was largely spurred by the early research on chinese patients which showed that imaging, specifically ct, has a wide range in sensitivity for detecting covid- pneumonia [ , ] . in addition, the ct imaging features of covid- j o u r n a l p r e -p r o o f page of are sometimes nonspecific and can overlap with other infections as discussed above. the positive predictive value of ct is low in locations where covid- prevalence is low [ ] . the multinational consensus statement of the fleischner society [ ] recommended chest ct for patients with moderate to severe symptoms or with mild disease with associated comorbidities or with worsening respiratory symptoms. the european society of radiology (esr) and the european society of thoracic imaging (esti) outlined their recommendations in a consensus document, stating that chest ct should not be performed as a screening tool in patients with "mild or no symptoms" [ ] . however, they add on that chest ct may play a useful role in patients with milder symptoms who have co-morbidities (e.g. diabetes, obesity, chronic respiratory disease, etc.). in their statement, they also note that with further research, information gained from a baseline ct in covid- patients may play an important role in predicting who will have poor outcomes or need ventilation. with the spread of covid- globally and the increasing number of cts performed in patients under investigation (puis), there have been frequent questions in the radiology community regarding the optimal way to report ct findings potentially attributable to covid- pneumonia. a national expert panel of thoracic radiologists gathered to produce a consensus statement on this topic, subsequently endorsed by the radiological society of north america (rsna), the str, and the acr [ ] . chest ct findings were classified for covid- pneumonia into four groups: typical appearance, indeterminate appearance, atypical appearance, and negative for pneumonia. standardized language templates are provided in [ ] with the goal of decreasing reporting variability and increasing clarity by using consistent language. the question of whether to include terminology such as "coronavirus" or "covid- " in reports remains an area of debate. the authors acknowledge that for patients with unexpected findings that could be attributable to covid- , the matter is complex and consultation with local clinical colleagues is needed to establish an approach. the term "viral pneumonia" is considered a reasonable alternative. given the variable sensitivity in rt-pcr for the diagnosis of early covid- and the overlap in the imaging appearances with other pulmonary diseases, ai approaches have been applied in an effort to improve the diagnostic accuracy of ct. in a recent retrospective multicenter study of , chest cts from , patients, a deep learning model detection neural network (covnet) in an independent test set demonstrated excellent per-exam auc, sensitivity and specificity of . , % and %, respectively for detecting covid- compared to cap and other nonpneumonias [ ] . other studies using deep learning approaches have found similar results with reported aucs up to . [ , ] and accuracy up to . % [ ] for the classification of covid- from non-covid- pulmonary infection. a recently published algorithm integrating chest ct and clinical history in patients presenting early in the course of the disease reached an auc of . and had higher sensitivity ( . %) when compared to a senior thoracic radiologist ( . %) and a thoracic radiology fellow ( %). the algorithm was able to identify % of cases presenting with positive rt-pcr but normal chest ct. this method may have a role for a quick diagnosis of covid- pneumonia with ct [ ] . more work in terms of performance and clinical implementation/acceptance is needed. page of covid- is a new rapidly spreading pandemic. it has typical ct findings with ggos and consolidation often with a peripheral and lower lung distribution. in early disease, imaging findings can be absent; therefore, ct chest cannot be used as a screening method, and rt-pcr remains the reference diagnostic test. ai may play a role in the rapid diagnosis of covid- , but more data is needed to assess its added value. there is no conflict of interest associated with this publication and there has been no financial support for this work posterior chest x-ray shows ill-defined opacities in the lateral aspect of the right lung (arrows). (b) axial noncontrast chest ct image shows ground-glass opacities with a peripheral distribution in both upper lobes (arrows). there is superimposed interlobular septal thickening with visible intralobular lines in the ground-glass opacity (crazy paving pattern). (c) reconstructed coronal chest ct image shows corresponding multifocal bilateral ground-glass opacities with a peripheral distribution (arrows). genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding structure of the rna-dependent rna polymerase from covid- virus presenting characteristics, comorbidities, and outcomes among patients hospitalized with covid- in the characteristics of and important lessons from the coronavirus disease (covid- ) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention clinical features of patients infected with novel coronavirus in clinical characteristics of covid- patients with digestive symptoms in hubei, china: a descriptive a comparative study on the clinical features of covid- pneumonia to other pneumonias digestive symptoms in covid- patients with mild disease severity: clinical presentation, stool viral rna testing, and outcomes gastrointestinal symptoms and covid- : case-control study from the united states acute-onset smell and taste disorders in the context of covid- : a pilot multicenter pcr-based case-control study isolated sudden onset anosmia in covid- infection. a novel syndrome? anticoagulant treatment is associated with decreased mortality in severe coronavirus disease patients with coagulopathy hematological findings and complications of covid- clinical course and risk factors for mortality of adult inpatients with covid- in wuhan, china: a retrospective cohort study a pneumonia outbreak associated with a new coronavirus of probable bat origin detection of novel coronavirus ( -ncov) by real-time rt-pcr improved molecular diagnosis of covid- by the novel, highly sensitive and specific covid-specimens detection of sars-cov- in different types of clinical specimens sensitivity of chest ct for covid- : comparison to rt-pcr a serological assay to detect sars-cov- seroconversion in humans profiling early humoral response to diagnose novel coronavirus disease (covid- ) radiological findings from patients with covid- pneumonia in wuhan, china: a descriptive study relationship to duration of infection clinical features and chest ct manifestations of coronavirus disease (covid- ) in a single-center study in ct imaging features of novel coronavirus ( -ncov) imaging features of coronavirus disease (covid- ): evaluation on thin-section ct covid- ): role of chest ct in diagnosis and management emerging novel coronavirus ( -ncov) pneumonia imaging manifestations and diagnostic value of chest ct of coronavirus disease (covid- ) in the xiaogan area chest ct findings in patients with corona virus disease and its relationship with clinical features clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by sars-cov- the role of imaging in novel coronavirus pneumonia (covid- ) relation between chest ct findings and clinical conditions of coronavirus disease (covid- ) pneumonia: a multicenter study coronavirus disease : initial chest ct findings ct features of coronavirus disease pneumonia in patients in wuhan, china early clinical and ct manifestations of coronavirus disease (covid- ) pneumonia chest radiographic and ct findings of the novel coronavirus disease (covid- ): analysis of nine patients treated in korea chest ct features of covid- in chest ct findings in cases from the cruise ship "diamond princess correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases performance of radiologists in differentiating covid- from viral pneumonia on chest ct imaging profile of the covid- infection: radiologic findings and literature review initial ct findings and temporal changes in patients with the novel coronavirus pneumonia ( -ncov): a study of patients in chest ct for typical -ncov pneumonia: relationship to negative rt-pcr testing diagnostic performance of chest ct to differentiate covid- pneumonia in non-high-epidemic area in japan time course of lung changes on chest ct during recovery from novel coronavirus (covid- ) pneumonia imaging and clinical features of patients with novel coronavirus sars-cov- clinical characteristics and imaging manifestations of the novel coronavirus disease (covid- ):a multi-center study in wenzhou city initial clinical features of suspected coronavirus disease in two emergency departments outside of hubei, china covid- pneumonia manifestations at the admission on chest ultrasound, radiographs, and ct: single-center study and comprehensive radiologic literature review recommendation of low-dose ct in the detection and management of covid- a scoping review evolution of computed tomography manifestations in five patients who recovered from coronavirus disease (covid- ) pneumonia chest imaging appearance of covid- infection clinical and chest radiography features determine patient outcomes in young and middle age adults with covid- clinical characteristics of covid- -infected cancer patients: a retrospective case study in three hospitals within wuhan chest computed tomography in children with covid- respiratory infection high-resolution computed tomography manifestations of pediatric patients with novel coronavirus clinical and ct imaging features of the covid- pneumonia: focus on pregnant women and children clinical and ct features in pediatric patients with covid- infection: different points from adults deep convolutional neural network-aided detection of portal hypertension in patients with cirrhosis findings of acute pulmonary embolism in covid- patients, the lancet infectious diseases covid- and thrombotic or thromboembolic disease: implications for prevention, antithrombotic therapy, and follow-up coronavirus disease (covid- ): a perspective from china outbreak of novel coronavirus (covid- ): what is the role of radiologists? a novel coronavirus emerging in china -key questions for impact assessment middle east respiratory syndrome coronavirus: what does a radiologist need to know? radiology perspective of coronavirus disease (covid- ): lessons from severe acute respiratory syndrome and middle east respiratory syndrome -novel coronavirus severe adult respiratory distress syndrome in two cases in italy: an uncommon radiological presentation covid- ): a critical review of the literature to date covid- ): a critical review of the literature to date acr recommendations for the use of chest radiography and computed tomography (ct) for suspected covid- infection economics/acr-position-statements/recommendations-for-chest-radiography-and-ct-for-suspected-covid -infection aser covid- task force: faqs. aser website str covid- position statement. str website s. six, a role for ct in covid- ? what data really tell us so far the role of chest imaging in patient management during the covid- pandemic: a multinational consensus statement from the fleischner society european society of, i. the european society of thoracic, covid- patients and the radiology department -advice from the european society of radiology (esr) and the european society of thoracic imaging (esti) radiological society of north america expert consensus statement on reporting chest ct findings related to covid- . endorsed by the society of thoracic radiology, the american college of radiology, and rsna rapid ai development cycle for the coronavirus (covid- ) pandemic: initial results for automated detection & patient monitoring using deep learning ct image analysis deep learning enables accurate diagnosis of novel coronavirus (covid- ) with ct images deep learning system to screen coronavirus disease artificial intelligence-enabled rapid diagnosis of patients with covid- more than lobes affected uncommon findings centrilobular nodules tree-in-bud nodularity key: cord- -wl z l authors: putrino, alessandra; raso, mario; magazzino, cosimo; galluccio, gabriella title: coronavirus (covid- ) in italy: knowledge, management of patients and clinical experience of italian dentists during the spread of contagion date: - - journal: bmc oral health doi: . /s - - - sha: doc_id: cord_uid: wl z l background: the coronavirus infection that emerged in china in the last few months of has now spread globally. italy registered its first case in the second half of february, and in a short time period, it became the top country in europe in terms of the number of infected people and the first in the world in terms of deaths. the medical and scientific community has been called upon to manage the emergency and to take measures. dentists also need to take new precautions during their clinical activity to protect themselves, coworkers and patients from the risks of contagion and to avoid further spread of infection. methods: following the data published in the international literature as well as the guidelines and directives constantly updated by the who and by the national health authorities, a questionnaire to be completed anonymously was submitted online to italian dentists using social tools and online professional platforms. the collected data were processed statistically, providing descriptive data and analysis of correlations of the most significant parameters using the pearson’s χ , the likelihood-ratio χ , cramér’s v, fisher’s exact test, goodman and kruskal’s γ, and kendall’s τb (p < . ). results: a total of dentists from italy participated in the survey. a good level of scientific knowledge about coronavirus and the extra precautionary measures needed to limit the spread was related to the age of respondents and their sex. coming from areas with higher concentrations of cases affected knowledge, level of attention and perception of risk related to dental activity. conclusions: at the moment, there are no therapies or vaccines to contain the infection with the new coronavirus that is causing many infections, many of which are fatal, worldwide. dentists are one of the categories at highest risk of encountering diseases and infections because they work in close proximity with patients, and in their procedures, there is always contact with aerosols with high bacterial and viral potential. therefore, during this covid- emergency, it is important that dentists are properly informed and take the appropriate precautionary measures. human coronaviruses are a group of rna viruses able to cause respiratory, gastrointestinal and central nervous system diseases. the first human coronavirus (hcov) was detected in the mid- s [ ] . in december , the seventh coronavirus known to infect humans was found in china (wuhan city, hubei province) [ ] . on january , the world health organization (who) announced the temporarily named ncov- , now called sars-cov- , as the novel coronavirus pathogen responsible for the increasing number of new pneumonia cases [ , ] . since that day, the number of cases in china and progressively in many other parts of the world has increased (fig. ) , and with it, the number of people who died because of this infection as the primary or contributory cause of preexisting illness [ ] . on march , the who stated that the novel coronavirus outbreak was a pandemic (fig. ) . the scientific community is still making numerous efforts to clarify the etiology, pathogenicity, and characteristics of the virus to establish the mechanisms underlying human-to-human transmission and possible treatments [ ] [ ] [ ] [ ] [ ] . although there are many cases of recovery, the number of deceased subjects has increased with the spread, particularly affecting older subjects with previous severe pathologies [ , ] . the first detection of the virus in italy was in a case of two chinese tourists from wuhan who were later treated at the spallanzani hospital of rome. the entire tourist group of the chinese couple was then quarantined for two weeks in the same hospital and then released after negative results of the clinical and serologic controls [ ] . on february, the first locally transmitted case, a -year-old man who never travelled in china, emerged in northern italy, lombardy region, codogno town, and since then, the number of cases has increased (fig. ) in the whole area and progressively increased in many other northern regions until the virus has spread to affect the entire italian territory. as the number of swab tests for suspected cases has continued to increase, the italian authorities have started to adopt preventive measures to try to isolate the affected areas and block the spread of the infections and a nationwide lockdown went into effect on march. the death toll, at the (table ) . italian government, the ministry of health, civil protection and other competent bodies at the local level are constantly engaging in this emergency, providing instructions to citizens and health workers and updating the population on the evolution of the situation [ ] [ ] [ ] [ ] . even dentists have been involved in the management of this emergency through indications on prevention and safety measures to be observed in their clinical activity due to the high level of exposure for operators and dental patients. in the last weeks the number of health workers infected has risen: many nurses and doctors on the coronavirus front lines are working without adequate personal protective equipment (ppe), exposing themselves to great risk and some of them have been infected while on duty. already, doctors have died, and of them were dentists [ ] . a direct correlation between their death and coronavirus infection was not, however, ascertained but many of them were engaged in the management of infections. the novel coronavirus was recently identified in the saliva of infected patients. dental clinical procedures generate droplets and aerosols that can lead to viral transmission [ ] . contamination on surfaces and diffusion by contact, conceivable due to the characteristics of dental activity, require a great deal of attention from dentists, who should adopt simple but effective practical strategies to stop the possible spread of the virus. the suggested procedures include preappointment patient risk evaluation through a specific questionnaire; frequent hand hygiene; appropriate individual protective equipment; insulation of the oral cavity with a rubber dam after mouth rinses, which are suggested with peroxide %; the use of antiretraction handpieces; disinfection after every dental treatment; and appropriate waste management [ ] . in italy there are more than , dentists (about per inhabitants), differently distributed at the regional level ( table ). the management of dental activity can play an important role in limiting the infections. due to the increasing involvement of a large part of the population in the global epidemic situation in italy, the present study aimed to assess the knowledge about the new coronavirus, the perception of risk and the clinical management of the risk related to infection during the first month of the italian epidemic in an online survey of italian dentists. moreover, due to the rapid change in the number of infected individuals, a further analysis aimed to evaluate the progressive perception of the risks. this study used a questionnaire-based survey. the original version of the survey was piloted among a group of dentists to ensure suitability, validity, practicability and interpretation of answers. on the basis of the comments and suggestions obtained, the questionnaire was revised. the questionnaire was developed and forwarded to italian dentists in italian and translated into english for the presentation of this research (supplementary file ). scientific bases for the development of questions about the new coronavirus came from consultation of the scientific literature available on this subject, more specifically addressed to virologists, specialists, biologists, and general practitioners and epidemiological content that traced the data on coronavirus infection since its first appearance in china [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] . additionally, as a source of scientific information and as an aid for the processing of a part of the questionnaire presented to italian dentists, circulars issued by the ministry of health containing protocols and guidelines aimed at health professionals during the outbreak and informative material disclosed by dental associations were also considered. the questionnaire was uploaded online to the free survey platform survio.com (© survio, hlinky , brno, czech republic) through a specially created user profile. the generated link was shared on professional group and contact networks on the main social channels (lin-kedin, facebook, and whatsapp), inviting italian dentists to share the link with other colleagues in further professional groups to widen the spread of the survey as much as possible. the assurance that those who would respond to the survey were regular dentists was given by the fact that all online professional groups and networks, of which none of the authors are an administrator, referred to (also for the dissemination of the questionnaire) by regulation are closed and approve registrations only when the registration number of the national professional register is originally provided. the responses were validated only for fully completed questionnaires, in fact the system automatically rejected incomplete questionnaires. the data collected were absolutely anonymous, and tracing the identity of the subjects was not possible. a total of open-and close-ended questions were developed (table ) . seven questions helped to obtain a profile of the practitioner (age group; sex; type of clinical activity-private, hospital or both; qualification-specialist or not; territorial provenance-specifying region; the number of citizens of their city; and the number of patients treated daily). six questions were intended to evaluate the direct influence of the coronavirus epidemic on the dentist's clinical activity (presence or absence of infected cases in their region; questions of patients about coronavirus; patients appearing to be worried or not about possible infections with coronavirus during dental procedures; effective decrease or not in patient appointment number since the coronavirus outbreak onset; adoption of special measures taken during professional activity since the coronavirus emergency started in italy; and which prevention methods are possibly used). the remaining eleven questions aimed to assess the level of scientific knowledge on coronavirus from a qualitative point of view and the dentist's perception of the problem related to this emergency in dental clinical practice. each respondent to the questionnaire corresponded to a form with all answers provided. the subjects were anonymous and were marked only with a number that reflected the chronological order of compilation. the form showed the day and time when the questionnaire was completed. the project did not need formal ethical approval since it collected general opinions that do not contain clinical data and neither personal data. according to the current regulation of the ethics committee of the higher institute of health (istituto superiore di sanità), the ethical aspects that need evaluation, approval and monitoring of trial protocols relate to epidemiological, evaluation and medical-social projects that require the collection of personal data. according to the national data protection authority (garante per la protezione dei dati personali), "personal data" are first and last name, images, tax code, ip address and license plate number. the compilation of the survey was anonymously carried out on a voluntary basis without the possibility to trace the identity of the subjects, as the system does not store even the ip addresses of the users accessing the link. before the start of the survey, informed consent was presented on the main page; the participant had to agree (by checking a box) that their anonymously provided answers could be used in this research for scientific purposes. for statistical examination of the data, the online platform automatically generated descriptive statistical analysis on the main page; the analysis could therefore be downloaded as an excel or spss spreadsheet for further statistical analysis. in this study, descriptive statistical analysis was carried out. several measures of association was performed including, the common pearson's χ , the likelihood-ratio χ , cramér's v, fisher's exact test, goodman and kruskal's γ, and kendall's τb. the level of statistical significance was set at . . the software used is stata . (statacorp llc, tx, usa). the pearson's and likelihood-ratio χ test for the independence of the rows and columns. the null hypothesis (h ) is that there is no relationship. to reject this we need a p < . (at % confidence). cramér's v is a measure of association between two nominal variables. it goes from to , where indicates strong association. γ and τb are measures of association between two ordinal variables (both have to be in the same direction, i.e. negative to positive, low to high). both go from − to . negative shows inverse relationship, closer to a strong relationship. γ is recommended when there are lots of ties in the data. τb is recommended for square tables. fisher's exact test is used when there are very few cases in the cells (usually less than , with an overall frequency of less than %). it tests the relationship between two variables. the null is that variables are independent [ ] [ ] [ ] [ ] [ ] . the survey was online for weeks from february to march . the link received visits, but only dentists responded to the survey by completing it. the results of the descriptive statistics were collected in table . most dentists carried out their professional activity in a private practice ( . %).the age group of up to years old (yo) and the group between and yo were the most represented (respectively, between . and . %). the distribution between the two sexes was equivalent ( . % males and . % females). over . % of dentists were general dentists, % are dentists without a recognized dental specialty (italian universities provide years of postgraduate programs in orthodontics, oral surgery and pediatric dentistry. they are the only recognized dental specialties) and . % are dental specialists ( . % were orthodontists, approximately % were oral surgeons, and just over % were specialists in pediatric dentistry). the answers related to the geographical location of the workplace mapped across the whole country, representing italy from north to south and including the larger islands (sicily and sardinia) (fig. ) . most of the respondents ( . %) were from moderately or highly populated cities. fourty % of the dentists who participated in the survey treat more than patients per day. almost % of dentists completed the questionnaire when there were positive cases in their region of sars-cov- infection. fifty percent of respondents did not notice a decrease in visits since the outbreak spread. more than % of patients asked questions about coronavirus to their dentist. according to the clinicians who participated in the study, the majority of patients (more than %) would not be worried about getting coronavirus infection during dental treatment. almost % of dentists said they were fairly informed about coronavirus. despite of the self-estimated knowledge about the infection, answers to the following questions assessing knowledge on the subject revealed a different reality. most respondents obtained scientific information about coronavirus through italian institutions ( . %); television, newspapers and social media ( . %); professional associations ( %); scientific literature (l . %); and other colleagues ( . %). only a very small percentage ( . %) specified other channels of information or that they were not fully informed ( . %). almost % correctly answered the questions about the definition of coronavirus, the . % correctly answered about ncov and . % about sars-cov- . most respondents, on the other hand, incorrectly answered the question on the definition of covid- (almost %). almost % of the subjects were very clear about the types of possible symptoms that accompany the infection, and in . % of cases, they correctly indicated how the new coronavirus is transmitted from person to person. however, the . % of dentists knew that the national federation of surgeons and dentists (federazione nazionale dei medici chirurghi ed. odontoiatri-fnomceo) has provided healthcare professionals with a free online course to disseminate useful information about the virus. sixty nine percent of dentists who completed the questionnaire had taken safety and prevention measures against workplace infection since coronavirus spread. almost % of them had taken all the recommended safety measures (telephone history collection, increased frequency of washing hands and environmental surfaces, and personal protective equipment such as gloves, disposable gowns and facemasks with adequate filters). fifty point % of respondents were concerned 'enough' about the spread of infection in italy. overall, almost % of dentists who took part in the survey considered the dental profession neither safe nor free from the risk of contagion for both patients and healthcare professionals. the measures of association results were collected in tables , and . in regards to the sex (table ) , both χ test statistics show a significance level < . for quality of information (question number ), level of information related to questions and and for risk perception related to question ; so we can safely assume that some differences exist between groups. therefore, we conclude that there is evidence of a statistically significant difference between male and female on these variables. we can confidently reject the null hypothesis that these two variables are statistically independent in that population. in other words, we can conclude that there is some relationship between sex and each of these four variables. in fact, for these variables the cramér's v values are > . , which indicates a non-negligible association. moreover, the goodman and kruskal's lambda for the relationship between sex and level of information related to question number , and sex and risk perception related to question is > . , in line with previous results. all these findings are confirmed by fisher's exact test results, since in these four cases the hypothesis of variables' independence is rejected, and we conclude that there is some kind of relationship between variables. concerning the age (table ) , the pearson and likelihood-ratio χ tests present a p-value < . only for the relationship with the variable quality of information (question number ). we reject the null hypothesis of no association at conventional level of statistical significance, because it emerges a dependence of the rows and columns. thus, in this case we can conclude that some differences emerge between groups. moreover, in this case cramér's v is > . : there is a small but statistically significant association between these variables. if we consider the region (table ) , the pearson and lr χ tests show a p-value < . for level of information related to questions number and , and correct risk management related to question number ; therefore, we conclude that some relationship exists between region and each of these three variables. here, the cramér's v are > . , which indicate a statistically significant association. since sars-cov- can be transmitted from person to person by droplets, contact and through saliva, dental patients and dentists and their coworkers can be easily exposed to novel coronavirus infections [ , , ] . in the period of contagion outbreak from the new coronavirus, information about the virus has become increasingly the subject of attention of the media, such as television, the internet, and social channels. however, it was only when the first cases began to register in italy that professional associations and dental professionals began to take a deeper interest in the problem. dental professionals had to refer only to the official communication of the ministry, whose law decrees lacked specific references to the dental profession. male dentists believed to be very well informed about coronavirus unlike female colleagues who had a more cautious opinion on their knowledge of the subject (pearson χ test . -p . ; lr χ test . -p . ). dentists between the ages of - believe they were well informed compared to younger colleagues who judged sufficient their knowledge (pearson χ test . -p . ; lr χ test, . -p . ). male dentists showed to have a significantly clearer idea of the taxonomic characteristics of the virus (pearson χ test . -p . ; lr χ test . -p . ). most were aware of the main features of coronaviruses but confused the term covid- with the virus itself ( . %). the definition of covid- was provided more correctly by the dentists of lazio, lombardy, emilia-romagna and sicily but the same regions, with the exception of sicily, reported the greatest number of incorrect answers (which overall exceeded the correct ones) the most informed dentists on the possibility to access a free online course on the new coronavirus promoted by the fnomceo (national federation of surgeons and dentists) were those from lazio, followed by those from lombardy, sicily and tuscany (lr χ test . p . ). quite important for the population and for the spread of epidemics is the preventive approach of dentists. for the possibilities of transmission from person to person, most are properly informed ( . %). female dentists were better informed on this aspect (pearson χ test . -p . ; lr χ test . -p . ). compared to age, younger dentists were significantly better informed about the transmission routes of the virus than other age groups (pearson χ test, . -p . ; lr χ test . -p . ). more than % of respondents to the survey were aware of the wide variety of symptoms with which the infection can occur, which is encouraging because it means that a diagnostic suspicion and a report to the authorities regulating the execution of swab tests of potentially infected individuals can also be appropriately carried out by a dentist. it is important to consider that transmission may occur through asymptomatic patients and that symptoms when covid- is present can also be mild and confused with a simple cold or flu [ ] . its manifestation does not always culminate with severe symptomatology accompanied by respiratory failure up to interstitial pneumonia. the asymptomatic incubation period takes approximately - days, and in these days, persons without symptoms can spread the virus. for this reason, it is important to add to the information required of the patient in the medical history, the report of a possible contact with infected or potentially infected people or of trips to the areas where the infection has spread. many dentists ( %) who responded to the survey chose to ask this question of their patients, judging it to be important. at the time of the virus's main spread, it was recommended to perform a telephone triage even before seeing the patient to assess whether to visit or to postpone the appointment. at the time of the survey, performed between february rd and march th, just over % of dentists did not notice a reduction in the number of visits despite the spread of the virus. it must be specified that after two weeks from the start of this research many work activities were suspended by the government by extraordinary decree, but the clinical dental activity was allowed only for the management of emergencies provided by dentists equipped with adequate personal protective equipment (ppe). the definition of "adequate ppe" for dentists is a matter of debate because above all the surgical masks used routinely by dentists would not have sufficient filters to protect from infection. the use of facemasks with ffp or ffp filters, highly protective than the surgical ones, does not seem to be considered necessary for routine dental activity, even if this has not been clearly said nor denied. the absence of a sample calculation and the methodology used in the dissemination of the survey represent limitations in this research. anyway the distribution of the respondents in the national territory was quite homogenous (proportionate to the extension of the individual regional territories) and the greatest proportion came from medium-large cities. although . % of dentists said that patients have asked questions about coronavirus, they agree that patients feeling worried about contracting the infection through dental care has not emerged ( . %). most of the dentists ( %) adopted additional preventive practical measures, a sign of a growing and widespread awareness ( . %) of the risk of contributing to the spread of contagion through dental activity. there were regions where the number of dentists who claimed to have taken additional contagion prevention measures during their clinical activity was significantly higher than others. this was especially true for regions such as lazio, lombardy, emilia romagna and campania. it is interesting to note that regions such as veneto which since the beginning of the spread of the virus in italy has been one of the first regions and among the most affected had not the same attitude (pearson χ test, . -p . ; lr χ test . -p . ). the female gender appeared significantly more concerned than the male gender about the spread of coronavirus infection (pearson χ test . -p . ; lr χ test . , p . ). dentists belonging to the younger age groups were found to be much more convinced than their older colleagues that this epidemic has future repercussions on the dental profession as it is not without risk (pearson χ test, . -p . ). dental treatment procedures always involve close contact with the patient, and this setup does not allow the maintenance of an adequate safe distance. it is extremely important that dentists equip themselves with appropriate individual safety devices (masks, gloves, protective goggles, hair caps and shirts). a recent article in the new york times, referring to the database "o'net" used by the department of labor to describe the various physical aspects of different professions, highlighted that the occupational categories in which you come into physical contact with others are those where the risk of covid- is highest. dentists are at the top of the ranking for work-related risk [ ] . in this survey, dentists affirmed the constant use of these safety devices as prescribed by the italian medical guidelines of safety in workplaces [ ] . when aerosol procedures are carried out, the presence of saliva and blood increases the spread of germs, bacteria and viruses. ensuring a change of air in the workplace and in the waiting room is a simple but important measure chosen by . % of dentists in this survey. this measure should always be adopted by dentists and not only in this situation. equally essential is to wash hands more frequently and disinfect them with alcohol-based solutions. this provision should also be encouraged for patients before entering the operating dental unit. these recommendations, together with those of not shaking hands with anyone, were accepted by . and . % of respondents, respectively. the data that emerged on the cleansing measures also include the cleaning of the clinical contact surfaces, such as buttons, handles and work surfaces. thorough cleaning has proven to be a mandatory and indispensable choice for prevention, as it is proven that the coronavirus family, including sars-cov- , can survive on plastic, metal and glass surfaces for up to days and can be efficiently deactivated through disinfection procedures with - % ethanol, . % hydrogen peroxide or . % sodium hypochlorite within min. the use of . - . % benzalkonium chloride or . % chlorhexidine digluconate does not have the same effectiveness [ ] . it must be said that the majority of dentists paid great attention to the measures to be taken; indeed, . % of them said they had adopted all the preventive measures listed so far. this is the most severe epidemic that has hit italy in the past years, and it will probably be one of the most severe viral pandemics of modern times. as no specific therapies are available at the moment for the new coronavirus, prevention and early containment of further spread can be crucial to control the pandemic. for this reason, dentists, similar to other medical practitioners, aware of the risk associated with carrying out their professional activity, at this moment limited to the management of dental emergencies only, have the responsibility in this situation to know the characteristics of the virus through precise and accurate information and to assume a careful and proactive attitude for the protection of their patients and of their entire community, working in the containment of this social emergency even if not directly involved in the treatment of affected patients. dentists at this time, however, should only work if they have the individual protective equipment recommended to high-risk healthcare workers [ , ] . after the pandemic emergency when people's professional activities and lives can slowly return to normal, the experience and the not-quite-finished risk of a recurrence of new cases of infection will require that dentists also follow new health safety protocols whose definition will be necessary. supplementary information accompanies this paper at https://doi.org/ . /s - - - . additional file . "questionnaire" contains the english version of the questionnaire realized for the survey in this research. abbreviations who: world health organization; ppe: personal protection equipment connected to the survey. informed consent was presented on the main page of the online platform used to complete the survey. before the start of the survey the participant had to accept and agree that filling out the questions meant that his anonymously provided answers were used for the research presented in the introduction. not applicable. a new virus isolated from the human respiratory tract clinical features of patients infected with novel coronavirus in wuhan world health organization (who) novel coronavirus ( -ncov) severe respiratory disease associated with a novel infectious agent-letters to doctors genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan a familial cluster of pneumonia associated with the novel coronavirus indicating personto-person transmission: a study of a family cluster a pneumonia outbreak associated with a new coronavirus of probable bat origin genome composition and divergence of the novel coronavirus (covid- ) originating in china genomic diversity of sars-cov- in coronavirus disease patients differential diagnosis in patients under investigation for the novel coronavirus (sars-cov- ) coronavirus disease (covid- ) -novel coronavirus severe adult respiratory distress syndrome in two cases in italy: an uncommon radiological presentation protezione civile italiana. emergenze coronavirus. elenco dei medici caduti nel corso dell'epidemia di covid- coronavirus covid- impacts to dentistry and potential salivary diagnosis transmission routes of -ncov and controls in dental practice mathematical methods of statistics the logic of inductive inference measures of association for cross classifications the treatment of ties in rank problems on the criterion that a given system of deviations from the probable in the case of a correlated system of variables is such that it can be reasonably supposed to have arisen from random sampling -ncov transmission through the ocular surface must not be ignored consistent detection of novel coronavirus in saliva. clin infect diseases transmission of -ncov infection from an asymptomatic contact in germany the workers who face the greatest coronavirus risk. the new york times, th testo coordinato con il d.lgs. agosto , n. in gazzetta ufficiale n. del aprile persistence of coronaviruses on inanimate surfaces and their inactivation with biological agents shortage of personal protective equipment endangering health workers worldwide world health organization. rational use of personal protective equipment for coronavirus disease publisher's note springer nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations not applicable.authors' contributions ap designed the study and was the major contributor to writing the manuscript. mr coordinated the development of the online questionnaire, data management and extrapolation. cm was responsible for statistical analysis of the results. gg researched the bibliography sources and reviewed the final manuscript. all authors read and approved the final manuscript. no funding needed. the datasets used and/or analysed during the current study available from the corresponding author on reasonable request. this research does not contain data require ethics approval. the current regulation of the ethics committee of the higher institute of health (istituto superiore di sanità, rome th may ) stipulates that projects with epidemiological, medico-social and evaluative contents need evaluation, approval and monitoring of trial protocols only if they contain personal data according to the legislative decrees on clinical trials and function of the ethics committees (decreto legislativo giugno , n. ; decreto ministeriale febbraio ). the official definition of "personal data" is given by the national data protection authority (garante per la protezione dei dati personali, https://www.garanteprivacy.it/home/diritti/cosa-intendiamo-per-dati-personali -regolamento (ue) / art. ). the term "personal data" includes information about first and last name, images, tax code, ip address and license plate number. the platform on which the anonymous questionnaire was completed does not allow to trace the ip address of the person who the authors declare that they have no competing interests. key: cord- -tsjwnvkk authors: khamassi khbou, médiha; daaloul jedidi, monia; bouaicha zaafouri, faten; benzarti, m’hammed title: coronaviruses in farm animals: epidemiology and public health implications date: - - journal: vet med sci doi: . /vms . sha: doc_id: cord_uid: tsjwnvkk coronaviruses (covs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. the geographic distribution of animal covs is worldwide and prevalences were reported in several countries across the five continents. the viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. in certain cases, cov infections are responsible of huge economic losses associated or not to highly public health impact. despite being enveloped, covs are relatively resistant pathogens in the environment. coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross‐species transmission easy. in fact, increasing contact between different animal species fosters cross‐species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human‐animal interface. if contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making covs a persistent threat to both humans and animals. a global network should be established for the surveillance and monitoring of animal covs. covs isolated from carnivores, herbivores and omnivores fosters the interspecies transmission and virus adaptation to new hosts (song et al., ) . in fact, cross-species transmission and host jumping are the most important driver for virus emergence (holmes, ) and covs specifically are dotted with a high rate of mutation and recombination, making them a continuous threat for humanity. mutations result from errors during viral genome replication by the rna-dependent rna polymerase, which reaches . × - nucleotide substitutions per site per day for the sars-cov and the accumulated mutations at some sites could have important implication on virus properties (vega et al., ) . recombination appears to be more important in cov genome than mutation; it consists of gaining genome fragment from another cov, which implies the adaptation to new hosts (worobey & holmes, ) . as consequences of such genomic mutation and recombination the transmissible gastroenteritis virus (tgev) of swine and the bovine cov (bcov) likely originated from the closely related canine coronavirus (ccov) (pratelli, ) . a deletion that occurred in the s protein of the tgev resulted in the rising of the porcine respiratory cov with a marked changing tropism from the gastrointestinal to the respiratory tract (peiris, ) . there is evidence that the feline infectious peritonitis virus (fipv) is originated from the feline enteric cov (fecov) by mutation in the region of the s /s of the spike protein (licitra et al., ) . the best opportunity that would allow viruses to jump new species occurs at the moment of feeding, when a predator consumes prey and all the viruses infecting it (french & holmes, ) . beside feeding, physical contact between different host species increase host range expansion probability (wang, vlasova, kenney, & saif, ) as it was the case for the swine influenza viruses (subtypes h n and h n ) and the nipah virus that were transmitted from pigs to humans (chua et al., ; gray et al., ) . new porcine cov emerged in china (guangdong province) in , namely the swine acute diarrhoea syndrome cov (sads-cov) with high sequence identity to bat-cov hku (gong et al., ) . the high density of pig farms and slaughterhouses in guangdong province associated to the wide distribution of bat species explained the cross-species transmission. indeed, as pork meat is considered as the most commonly consumed meat in non-muslim countries, pigs may be an effective intermediate host for the emergence of novel covs of highly public health concerns (wang, su, bi, wong, & gao, ). coronaviruses of farm animals including large and small ruminants, dromedaries, horses, pigs and chickens were reviewed; cetacean covs were also considered, as marine mammals are a food source in many countries around the world. the aim of this review is to summarize the epidemiological knowledge about covs of farm animals, to discuss the public health implications and to address the gap of knowledge useful for future research direction. & stokstad, ). furthermore, high animal density seems to be the main bcov risk factors (boileau & kapil, ) . the bcov is one of the main causative agents of neonatal calf diarrhoea during the first month of life (ammar et al., ; brandão et al., ) and the most common deathly disease in calves (gomez & weese, ) . other studies showed that bcov may be involved in to % of neonatal diarrhoea cases (alfieri et al., ) . in adult cattle, the wd occurs as epidemics during winter and is characterized by a contagious watery diarrhoea, fever, depression and reduced milk yield (toftaker et al., ) . singasa, songserm, lertwatcharasarakul, and arunvipas ( ) reported that milk production might decrease up to % for weeks during the bcov infection. vaccines are available for the prevention of bcov infections in neonatal calves and in adult. an inactivated virus vaccine was developed for pregnant cows to enhance passive maternal immunization of calves via colostrum and prevent neonatal diarrhoea (decaro et al., ) . another inactivated hemagglutinating antigens-enriched vaccine showed their efficacy to protect cattle against wd (takamura, matsumoto, & shimizu, ) . the bcov was also associated, alone or with other pathogens, to respiratory infections such as enzootic pneumonia in calves and shipping fever in young cattle (saif, ) . the prevention from respiratory cov in cattle is based on multivalent killed or attenuated-live intra-nasally administrated vaccines (hay et al., ; richeson et al., ) . a bovine-like cov in water buffalo (bubalus bubalis) was first described in in bulgaria, using serological methods (muniiappa, mitov, & kharalambiev, ) . the sequencing of the isolated buffalo cov from italy, showed sequence homology with the bcov, with some differences justifying its classification as a new variant of bcov and was named as bubaline cov (bucov) (decaro, martella, et al., ) . in italy, gastroenteritis disease among water buffalo calves is caused by both bucov and bcov (decaro et al., ) . closely related strains to the bcov (displaying % sequence homology) were also detected among faecal samples of domestic buffaloes in bangladesh (lau et al., ) . infection of water buffalo calves was also reported from three districts in egypt, with an overall molecular prevalence of . % ( / ) in faecal samples (el- sadek et al., ) ( table ) . although the bcov is initially a cattle virus, it is occurring also in small ruminants, in which it was neglected for a long time due to its low prevalence and insignificant clinical manifestation (amer et al., ) . in australia, sheep were reported in to excrete cov-like particles that were visualized by electron microscopy examination during a diarrhoea episode (tzipori, smith, makin, & mccaughan, ) . the infection of small ruminants by the bcov is rather to occur through close contact with cattle in mixed flocks than as a natural infection (tråvén, carlsson, lundén, & larsson, ) . the most recent study in ghana reported anti-bcov antibodies in f i g u r e phylogenetic tree of different representative covs based on the spike (s) protein gene (the strain responsible for the pandemic sars-cov- in humans is shown with the bolded character among the betacoronavirus genus). the shown animals are hosts from where the corresponding covs were isolated. the sequences of all animal covs were downloaded from the national center for biotechnology information (ncbi) genbank database (https://www.ncbi.nlm.nih.gov/genba nk/). the tree was constructed using the neighbour-joining method (bootstrap resampling = , replicates and bootstrap values are indicated as % at branch points) (saitou & nei, ) . the evolutionary distances were computed using the maximum composite likelihood method (tamura et al., ) and are in the units of the number of base substitutions per site. all positions containing either gaps or missing data were eliminated. there were a total of positions in the final dataset. evolutionary analyses were made with mega (kumar et al., ) box (burimuah et al., ) (table ) . nowadays, it is well established that dromedaries are the natural host of the mers-cov and a source for human and other domestic animals infections (kandeil et al., ) . since the first case of human infected by the mers-cov was identified in september in saudi arabia (world health organization, ), interest to dromedaries as sources of the virus increased and the isolated strains were shown to be genetically very similar to those isolated from humans (omrani, al-tawfiq, & memish, ) . the close contacts between infected dromedaries and humans enhance the continuing zoonotic transmission and may explain why the mers-cov continues to occur in humans (de wit et al., ) . moreover, the mers-cov was also detected in sheep, goats and donkeys reared close to camels (kandeil et al., ) . transmission from dromedaries to humans occurs by direct contact with mucous and nasal discharge or by consumption of meat or raw milk (gossner et al., ; mirkena et al., ) . indeed, mers-cov rna was detected using qrt-pcr in whole and skimmed milk collected from milking animals that were kept with camels that have frequent contact with multiple origin camels participating at racing events . the mers-cov detection in dromedaries is difficult as the infection is asymptomatic. however, experimental mers-cov infection of dromedaries caused mild to moderate rhinitis with nasal discharge, tracheitis and bronchitis in addition to the shedding of a large amount of virus from the respiratory tract (haverkamp et al., ) . several studies showed that the wild strains of the mers-cov circulate in dromedaries in more than countries across africa and the middle east ( figure ) , with high seroprevalences rates recorded from egypt ( %) (ali et al., ) , nigeria ( %) (reusken, messadi, et al., ) dromedaries increases with age, reaching %- % in adults (harrath & abu duhier, ) . in experimentally challenged dromedaries, a modified orthopox-based vaccine expressing the mers-cov spike protein conferred mucosal immunity. this vaccine induced a significant reduction of virus shedding, and the conferred protection was associated with neutralizing antibodies production (haagmans et al., ) . as a strategy to prevent human contaminations, mass vaccination of camels is discussed (dighe et al., ) . following a severe diarrhoea outbreak that induced high morbidity and the equine coronavirus (ecov) was isolated for the first time from a foal in north carolina (usa) (guy, breslin, breuhaus, vivrette, & smith, ) , since then, multiple outbreaks were documented in different countries but epidemiological information on ecov still scanty (pusterla, vin, leutenegger, mittel, & divers, ) . the ecov was reported from japan, saudi arabia, france, the united kingdom and the united states (table ). phylogenetic analyses showed that ecov isolated from japan and the united states, were genetically close (nemoto et al., ) . the morbidity rates of ecov infection ranged from % to % and the lethality rate is classified from rare to % (fielding et al., ; oue et al., ; oue, morita, kondo, & nemoto, ; pusterla et al., ) . up to % of infected horses remain asymptomatic, while their faeces contain the ecov (pusterla et al., ) . the transmission route of the ecov occurs through a faecal-oral route (pusterla et al., ) and the disease occurs mainly in winter (nemoto et al., ) . the ecov could be detected from diarrheic horses to weeks after the beginning of the infection (pusterla et al., ) but also from healthy horses (hemida, elmoslemany, et al., ) . the peak of faecal shedding occurs to days after the onset of the disease (bryan et al., ) and nasal secretions could be positive to the ecov at this moment, but the epidemiological role of these secretions in transmitting the virus is not known (nemoto et al., ) . according to the observations of pusterla, vin, leutenegger, mittel, and divers ( ), draft horses showed higher infection rate than other breeds, this could be explained by the stress induced by working conditions. some attempts of vaccination using the bcov gave promising results but need further investigations (nemoto et al., ) . six coronaviruses were isolated from pigs belonging to three genera: (table ) , beside a re-emerging highly virulent strains of the pedv that were described since (sun et al., ) . the tge is the sole mammalian disease caused by a cov in the world (piñeyro et al., ) . domestic animals such as cats and dogs may play a role as host for the tgev (sestak & saif, ) . as for most of mammalian covs, the tge occurs during winter after an incubation period varying between hr and days (pensaert, ) . the course of the disease is characterized by vomiting and profuse diarrhoea and is marked by high morbidity and mortality rates mainly among piglets (animal health australia, ). although pigs of all ages are susceptible to the tgev infection, animals older than weeks display milder clinical symptoms than piglets (piñeyro et al., ) . as the tgev shares common epitopes for neutralizing antibodies with prcv, a significant decrease of the tge incidence occurred as a consequence of the cross protection conferred by the prcv (wesley & woods, ) . the emergence of the phe was traced back to in canada, with the occurrence of high several episodes of vomiting, wasting and anorexia followed by neurological signs in pig nurseries (roe & alexander, ) . in , the virus was isolated from baby pigs suffering from encephalomyelitis (greig et al., ) , then several outbreaks with similar clinical signs were reported in canada and europe and the disease was named vomiting and wasting disease (vwd) (cartwright et al., ) . in , the phev was classified as a cov (greig et al., ) and subsequently the disease was reported the colostral immunity transferred to newborn piglets, which is considered as the best way to prevent from the infection (rho et al., ) . the porcine epidemic diarrhoea (ped) was reported for the first time in england in , but the viral aetiology was only proved in (pensaert & de bouck, ) . the pedv spread to other european countries (belgium, france, hungary and czech republic…) (pensaert & martelli, ) and to asia where it became enzootic particularly in most prosper pork industry countries like china, south korea and philippines (song & park, ) . the economic losses induced by the occurrence of the ped are dramatic since, high mortality rate is associated to the infection, mainly among < days old piglets (antas & woźniakowski, ) . mortality reached % in newborn and suckling piglets in japan during and (sueyoshi et al., ) and in thailand during and (puranaveja et al., ). in the united states, the pedv emerged in , where almost % of the pig population died in less than year after several outbreaks stevenson et al., ) and spread to mexico and canada in (kochhar, ) . sow's sera and piglets sera after suckling (paudel et al., ) . in japan, live attenuated virus is used since (usami, yamaguchi, & kumanomido, ) and oral vaccination started in south korea and philippines, since and respectively (garcia et al., ; park et al., ) . as new virulent strains are circulating, trials for more effective vaccine are undergoing using swine-poxvirus-based vaccines designed to express the a epitope of the spike protein (yuan, lin, li, he, & fan, ) . the porcine respiratory coronavirus (prcv) is a mutant of the tgev, due to a deletion in spike gene (laude et al., ) . it was identified first in belgium in (pensaert, callebaut, & vergote, ) and spread to almost all european countries including france (madec et al., ) , denmark (have, ) and the united kingdom (brown & cartwright, ) . the prcv was soon reported from the united states (halbur et al., ) and japan (usami et al., ) . most of the prcv infections are subclinical or inducing mild symptoms (caswell & williams, ) , this could be due to the low proinflammatory cytokines synthesis activation (van reeth, labarque, nauwynck, & pensaert, ) . the prcv is still detected upto the st day in the lungs of experimentally infected pigs and high titres reached . median tissue culture infectious doses (tcdi ) per gram of lung tissue (jung et al., ) . faecal shedding of prcv was also reported from % ( / ) of sentinel pigs introduced in prcv-infected herds (costantini et al., ) . because of the insignificant clinical course of the prcv infection, neither treatment nor vaccination, is applied. however, countries exporting live pigs need negative status to prcv, which could be obtained only if piglets are pre-weaned early at the th day, together with strict all-in, all-out managed barns, rigorous disinfection and cleaning of pig barns and regular seronegative tests in sows (burlatschenko & arsenault, ) . the porcine deltacoronavirus ( moreover, in orally pdcov-inoculated calves, a persisting faecal viral rna shedding associated to pdcov-specific serum igg antibody responses were observed (jung et al., ) . there is no commercial available vaccine for the prevention from the pdcov infection (zhang, liu, et al., ) . active surveillance programme effectively led to the decrease of the pdcov herd-level prevalence below . % in two years in canada (ajayi et al., ) . the swine acute diarrhoea syndrome virus (sads-cov) has emerged in pigs in china since august (zhou, sun, et al., ) . this virus, also qualified as porcine entreric alphacoronavirus (peav) or swine enteric coronavirus (secov) (pan et al., ) was associated with the occurrence of severe diarrhoea of suckling piglets in guangdong province in (gong et al., ; pan et al., ) and (zhou, li, et al., ) , and in fujian province in . the economic loss induced by the sads-cov was dramatically high, as , piglets in four farms, died from the infection in guangdong province, where the first human sars epidemic started in . this virus is antigenically distinct from the pedv, the tgev and the pdcov (yang, yu, & huang, ) . nevertheless, the complete genome sequencing of the n and the s genes showed a high nucleotides homology ( %- %) with those of four bat-cov hku (gong et al., ) . during the first outbreak in china, the sads-cov infection was controlled by immunizing pregnant sows using inactivated filtrated virus obtained from infected piglets intestines (zhou, sun, et al., b) . as there is an urgent need to develop efficient vaccines to control the sads-cov in pigs, trials on attenuation of a virulent strain via cell culture passage are now on-going . decaa new chimeric virus containing the s protein of the pedv on a tgev backbone was discovered in italy in and might circulate there from mid- to according to boniotti et al. ( ) . this recombinant virus was also detected in germany, central eastern europe and slovakia precluding for an old circulation in europe (akimkin et al., ; belsham et al., ; mandelik et al., ) . in , a novel beta-cov was isolated from domestic rabbit and characterized as rabbit coronavirus hku (rbcov hku ), causing no clinical manifestation. the virus was detected in . % ( / ) rabbit faecal samples using rt-pcr and phylogenetic analysis showed that the novel rbcov hku is most closely related to betacoronavirus species (bcov, ecov, ccov, hcov-oc ) . the authors hypothesized that the virus may have emerged as a result of interspecies transmission between different animal species in chinese markets. three species of sea mammals were shown to be susceptible to covs: harbor seals, white beluga whale and bottlenose dolphins. in , three captive seals (phoca vitulina) at the miami seaquarium expressed acute enteritis associated with dehydration and leucocytosis. the pathological examination showed bronchoalveolar oedema and haemorrhage. fluorescent antibody staining yielded positive results to tgev, fipv and ccov antisera, which precluded to an alpha-cov, but the virus was not yet assigned to the genus (bossart & schwartz, ). ten years later, a captive beluga whale (delphinapterus leucas), in the united states suffering from a generalized pulmonary disease, died from acute liver failure caused by a cov (mihindukulasuriya, wu, st. leger, nordhausen, & wang, ) . phylogenetic analyses revealed that the causative agent was closely related to the infectious bronchitis virus (ibv) of chickens, and the pathogen, named bwcov sw was assigned to the gamma-cov genus (de groot et al., ) . in bottlenose dolphins (tursiops aduncus), the first report of a avian covs are the main representative of the gamma-cov genus, including the ibv in chickens as the most studied cov, and unique among all other animal covs. similar covs to the ibv were detected and isolated from domestic galliformes: turkey (tcov), guinea fowl (gfcov) and pheasants (phcov) (cavanagh, ) , but also from non-galliformes namely: columbiformes, psittaciformes and anseriformes (domanska-blicharz et al., ; jonassen et al., ) . seven other avian covs are included in the delta-cov genus . only the ibv will be treated in this section. the first isolation of the ibv was made in s in the united states (massachusetts) and it was thought that only one serotype exists, until exists, until , when jungherr et al. ( in , valastro et al. ( ) suggested a method to harmonize the nomenclature of the ibv using a phylogeny-based classification and complete genome sequencing of the s gene. today, the ibv is divided to seven genotypes including distinct viral lineages based on the complete s gene sequencing xu et al., ) . the geographic distribution of the ibv is worldwide (figure ) and some genotypes are present more in certain regions than in others. indeed, two different lineages gi- and gii- were considered as specific to europe (fan et al., ) , while gi- , gi- and giv- were considered specific to north america (lin & chen, ) and the gi- is an exclusively south american lineage, very prevalent in brazil and uruguay (marandino et al., ) . the ibv is a highly contagious virus of the upper respiratory tract of chickens, leading to % morbidity and a mortality rate ranging from % to % depending upon several factors such as the age of the birds, their immune status, and the involvement of secondary pathogens (ramakrishnan & kappala, ) . the ibv infects chickens of all ages, although young are most susceptible, and may die directly from the ibv infection or from mixed infections mainly caused by escherichia coli, leading to heavy losses to the breeding industry (jackwood, ) . in brazil, which is considered as the biggest broiler meat exporter (nääs, mollo neto, canuto, waker, oliveira, & vendrametto, ) , the total loss (in us$) induced by the ibv infection were estimated per , birds to , . and to . , in breeders and broiler respectively (colvero et al., ) . except the sars-cov, the mers-cov and the most recent sars-cov- , the other documented human covs are specific to human beings (corman et al., ) . it is well established that domestic or wild animals were involved in the three epidemics either as reservoir or as intermediate hosts. the & xu, ) . several wild animals, including palm civets (paguma larvata), raccoon dogs (nyctereutes procyonoides) and horseshoe bats (rhinolophus hipposideros) were involved in the sars-cov epidemic during and were tested positive using virological and or serological tests (guan et al., ) . while phylogenetic analyses showed that bats are reservoir for the sars-cov and allowing genetic recombination, civets seem to be an intermediate host, as they were tested negative in their wild free lands (su et al., ) . the showed that the mers-cov evolve exclusively in camels while humans act as terminal host (dudas et al., ) . the epidemiology of mers remains to date not well understood, as heavily exposed persons to infected camels lead only to seropositivity and any of persons confirmed with the mers-cov reported previous exposure to infected animals (hemida, elmoslemany, et al., ) . the main factor that could play a role in the transmission of mers-cov from infected dromedaries to humans, is the consumption of raw camel milk . neither the consumption of meat and organs nor the consumption of urine for medicinal use might cause the infection of humans (adney et al., ) and further investigations on experimentally inoculated animals are needed to confirm such definite conclusions. for the current covid- epidemic, the bat involvement as advanced by is not excluded, as the sars-cov- displayed % identity to the whole genome of bat-cov. moreover the sars-cov- was closely related to five wild animal covs, including civets and pangolin . experimental studies showed that ferrets and cats are highly susceptible to the sars-cov- . after an intra-nasal inoculation of plaque-forming units (pfu) to multiple animal species including dogs, cats and ferrets, the infectious virus was detected in nasal turbinate, soft palate and tonsils of all inoculated ferrets. the sars-cov- rna was also detected in rectal swabs and efficacious droplet transmission was confirmed among exposed cats . the phylogenetic studies associated to amino acid sequence comparison of the ace receptor has predicted cow, buffalo, goat, sheep and swine, as well as other wild species as the potential intermediate hosts for the sars-cov- (qiu et al., ) . these findings highlighted the threat from the interspecies transmission of the sars-cov- between multiple animal species, and from animals to human and vice versa. multiple factors are playing an important role in increasing the exposure of humans to covs of infected animals. intensification of livestock production implies increasing animal density in farms and increasing movement of human and vehicles on and off farms, which promotes pathogen transmission and spreading (cutler, fooks, & van der poel, ) . the intensively development of swine industry the last decade is considered of high risk for the trigger of severe pandemic viruses for humans (borkenhagen, salman, ma, & gray, ) . this was shown particularly with swine influenza viruses, and nipah virus. indeed, swine exposed workers displayed significantly higher titers (in hemagglutination inhibition assay) against swine influenza subtypes h n and h n than nonexposed workers (odds ratio = . and % confidence interval: [ . - . ] (gray et al., ) . in late and , several fatal encephalitis cases (n = ) caused by a paramyxovirus were recorded in malaysia (chua, ) and quickly spread to singapore (paton et al., ) . respiratory disease and encephalitis were recorded few weeks ago in pigs in the same district and the isolated virus, named nipah virus, was shown to be transmitted from bats to pigs, then to humans (chua et al., ) . the consequences of anthropogenic activities leading to deforestation, habitat fragmentation and replacement of natural vegetation by crops definitely modify wildlife biology. these anthropogenic activities foster wildlife migration and create new environments that increase host, vector and pathogen contacts (jones et al., ) . indeed, the deforestation was incriminated in the occurrence of the nipah virus outbreak by pushing fruitbats (the natural reservoir of the nipah virus) to pig farms high-density areas and fostered the contact between both species (chua et al., ) . it is well established that animals and animal product trade foster pathogens spreading (travis, watson, & tauer, ) . a study on livestock trade network assessment in europe, showed that pigs (for fattening and slaughter) and cattle (for fattening) were ranked second as the most heavily moved animal species within europe in , which foster the risk for exotic diseases introduction (hardstaff, häsler, & rushton, ) . thousands of wild animals are traded in asian markets every day, such as raccoon dogs, pangolin, masked palm civets, ferret badgers and hedgehogs (www.anima lasia.org). as several domestic and wild animals were shown to harbour covs, handling, touching or eating these animals, could increase the risk for humans to be in contact with covs. rodents have a worldwide distribution and were shown to harbour more than known pathogens infecting both animals and humans (meerburg, singleton, & kijlstra, ) , including covs . bats also are considered to be the most abundant and diverse vertebrate after rodents (rodhain, ) , with more than , known species and worldwide geographic distribution (teeling, jones, & rossiter, ) . bats are considered as an important reservoir of highly lethal zoonotic viruses and were shown to harbour more covs than any other animal species (hu et al., ) . indeed, beside the sars-cov, the sars-cov- and the mers-cov, two porcine covs, have a bat-cov origin: the sads-cov and the pedv (banerjee, kulcsar, misra, frieman, & mossman, ) . the geographical range of some bat species was estimated to expand by near to % in the last four decades as a response to climate change (ancillotto, santini, ranc, maiorano, & russo, ) . one could imagine, that this expansion would be favourable to a higher contact likelihood with wild and domestic animals. mixing different animal species would increase covs host jumping probability. the bcov contaminates sheep and goats, when they share the same barns or graze with infected cattle (tråvén et al., ) . the mers-cov was also detected from sheep, goats and donkeys kept in close contact with infected dromedaries (reusken et al., ) . the ability of covs to mutate and to adapt to a new environment makes them a continuous threat to human lives and to domestic animals, mainly of farm industries. pig covs are well described and documented in part because pork meat is the most widely consumed in several countries around the world. nevertheless, data on several animal covs are scarce from multiple countries, mainly from africa. there is an urgent need to characterize the extent of covs infections among domesticated animals in the world using serological investigations for screening, virological studies as confirmatory and phylogenetic studies as comprehensive of the mutation and recombination phenomena. continuous surveillance programme for covs genetic evolution should be implemented and would serve for at risk areas prediction. to date, only one mammal animal cov is registered in the oie list, namely the tgev and one avian, the ibv. more attention should be given to the other animal covs and a specific surveillance system must be implemented in all the oie member countries to monitor the introduction and the emergence of novel cov strains in new areas. strict regulation is to be implemented for farm animal trade. thus, it is urgent to assess if meat, milk, semen and other animal by-products are at risk for humans, either through manipulation, process or consumption. the accumulated knowledge needs to be compiled, broaden and extensive to predict and prevent further fatal pandemic like the covid- . no ethical approval was required as this is a review article with no original research data. the authors acknowledge the valuable contribution of professor mohamed hussni omar from cornell university for the english revision of the manuscript. the authors declare that they have no conflict of interest. replication and shedding of mers-cov in upper respiratory tract of inoculated dromedary camels herd-level prevalence and incidence of porcine epidemic diarrhoea virus (pedv) and porcine deltacoronavirus (pdcov) in swine herds in ontario new chimeric porcine coronavirus in swine feces prevalence of endemic enteropathogens of calves in new zealand dairy farms middle east respiratory syndrome coronavirus infection in dromedary camels in saudi arabia dairy calf rearing unit and infectious diseases: diarrhea outbreak by bovine coronavirus as a model for the dispersion of pathogenic microorganisms systematic, active surveillance for middle east respiratory syndrome coronavirus in camels in egypt bovine-like coronaviruses in domestic and wild ruminants prevalence of rotavirus (garv) and coronavirus (bcov) associated with neonatal diarrhea in calves in western algeria extraordinary range expansion in a common bat: the potential roles of climate change and urbanisation. the science of nature disease strategy: transmissible gastroenteritis (version . ). canberra (australia) current status of porcine epidemic diarrhoea (ped) in european pigs bats and coronaviruses characterization of a novel chimeric swine enteric coronavirus from diseased pigs in central eastern europe in bovine coronavirus associated syndromes. veterinary clinics of north america: food animal practice molecular and antigenic characterization of bovine coronavirus circulating in argentinean cattle during - porcine epidemic diarrhea virus and discovery of a recombinant swine enteric coronavirus animal influenza virus infections in humans: a commentary acute necrotizing enteritis associated with suspected coronavirus infection in harbor seals (phoca vitulina) investigating the introduction of porcine epidemic diarrhea virus into an ohio swine operation molecular analysis of brazilian strains of bovine coronavirus (bcov) reveals a deletion within the hypervariable region of the s subunit of the spike glycoprotein also found in human coronavirus oc new porcine coronavirus? veterinary record detection of equine coronavirus in horses in the united kingdom sero-prevalence, cross-species infection and serological determinants of prevalence of bovine coronavirus in cattle, sheep and goats in ghana weaning and segregation vomiting and wasting disease of piglets respiratory system coronaviruses in poultry and other birds potential pathogens in feces from unweaned llamas and alpacas with diarrhea seroprevalence of porcine respiratory coronavirus in selected korean pigs decline of transmissible gastroenteritis virus and its complex evolutionary relationship with porcine respiratory coronavirus in the united states development of an immunochromatographic strip for serological diagnosis of porcine hemagglutinating encephalomyelitis virus isolation and characterization of porcine epidemic diarrhea viruses associated with the disease outbreak among swine in the united states nipah virus: a recently emergent deadly paramyxovirus anthropogenic deforestation, el niño and the emergence of nipah virus in malaysia assessing the economic burden of avian infectious bronchitis on poultry farms in brazil hosts and sources of endemic human coronaviruses advances in virus research respiratory and fecal shedding of porcine respiratory coronavirus (prcv) in sentinel weaned pigs and sequence of the partial s-gene of the prcv isolates identification of a novel coronavirus possibly associated with acute respiratory syndrome in alpacas (vicugna pacos) in california public health threat of new, reemerging, and neglected zoonoses in the industrialized world coronaviridae. in virus taxonomy: ninth report of the international committee on taxonomy of viruses sars and mers: recent insights into emerging coronaviruses spotlight on avian pathology: infectious bronchitis virus respiratory disease associated with bovine coronavirus infection in cattle herds in southern italy a candidate modified-live bovine coronavirus vaccine: safety and immunogenicity evaluation characterisation of bubaline coronavirus strains associated with gastroenteritis in water buffalo (bubalus bubalis) calves biological and genetic analysis of a bovine-like coronavirus isolated from water buffalo (bubalus bubalis) calves a systematic review of mers-cov seroprevalence and rna prevalence in dromedary camels: implications for animal vaccination development of a multiplex rt-pcr for the detection of major diarrhoeal viruses in pig herds in china detection and molecular characterization of infectious bronchitis-like viruses in wild bird populations development of multi-specific humanized llama antibodies blocking sars-cov- /ace interaction with high affinity and avidity. emerging microbes and infections porcine deltacoronavirus in mainland china a transmissible gastroenteritis in pigs mers-cov spillover at the camel-human interface investigation of rota and corona viruses as causative agents for diarrhea in egyptian calves genetic analysis of avian coronavirus infectious bronchitis virus in yellow chickens in southern china over the past decade: revealing the changes of genetic diversity, dominant genotypes, and selection pressure coronaviruses: an overview of their replication and pathogenesis disease associated with equine coronavirus infection and high case fatality rate an ecosystems perspective on virus evolution and emergence characterisation of porcine epidemic diarrhea virus isolates during the - outbreak in the philippines vaccines for porcine epidemic diarrhea virus and other swine coronaviruses viral enteritis in calves. the canadian veterinary journal = la revue veterinaire canadienne a new bat-hku -like coronavirus in swine novel findings from a beta coronavirus outbreak on an american miniature horse breeding farm in upstate new york. equine veterinary education human-dromedary camel interactions and the risk of acquiring zoonotic middle east respiratory syndrome coronavirus infection swine workers and swine influenza virus infections encephalomyelitis of swine caused by a haemagglutinating virus vi. morphology of the virus a hemagglutinating virus producing encephalomyelitis in baby pigs isolation and characterization of viruses related to the sars coronavirus from animals in southern china characterization of a coronavirus isolated from a diarrheic foal an orthopoxvirus-based vaccine reduces virus excretion after mers-cov infection in dromedary camels pathogenicity of three isolates of porcine respiratory coronavirus in the usa livestock trade networks for guiding animal health surveillance sero-prevalence of middle east respiratory syndrome coronavirus (mers-cov) specific antibodies in dromedary camels in tabuk, saudi arabia infection with a new porcine respiratory coronavirus in denmark: serologic differentiation from transmissible gastroenteritis virus using monoclonal antibodies experimental infection of dromedaries with middle east respiratory syndrome-coronavirus is accompanied by massive ciliary loss and depletion of the cell surface receptor dipeptidyl peptidase associations between exposure to viruses and bovine respiratory disease in australian feedlot cattle first detection of bovine coronavirus in yak (bos grunniens) and a bovine coronavirus genome with a recombinant he gene coronavirus infections in horses in saudi arabia and oman mers coronavirus in dromedary camel herd, saudi arabia dromedary camels and the transmission of middle east respiratory syndrome coronavirus (mers-cov) evolution of rna viruses detection, sequence analysis, and antibody prevalence of porcine deltacoronavirus in taiwan bat origin of human coronaviruses: emerging and re-emerging pathogens in humans and animals review of infectious bronchitis virus around the world porcine deltacoronavirus prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in south korea analysis of the genome sequence of an alpaca coronavirus molecular identification and characterization of novel coronaviruses infecting graylag geese (anser anser), feral pigeons (columbia livia) and mallards (anas platyrhynchos) zoonosis emergence linked to agricultural intensification and environmental change altered pathogenesis of porcine respiratory coronavirus in pigs due to immunosuppressive effects of dexamethasone: implications for corticosteroid use in treatment of severe acute respiratory syndrome coronavirus calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus immunologic differences in strains of infectious bronchitis virus middle east respiratory syndrome coronavirus infection in non-camelid domestic mammals. emerging microbes and infections excretion and persistence of bovine coronavirus in neonatal calves prevalence of a novel bovine coronavirus strain with a recombinant hemagglutinin/ esterase gene in dairy calves in china canada porcine epidemic diarrhea in canada: an emerging disease case study seroprevalence and risk factors for infection with equine coronavirus in healthy horses in the usa mega : molecular evolutionary genetics analysis version . for bigger datasets coronavirus: how a large rna viral genome is replicated and transcribed first genome sequences of buffalo coronavirus from water buffaloes in bangladesh isolation and characterization of a novel betacoronavirus subgroup a coronavirus, rabbit coronavirus hku , from domestic rabbits porcine respiratory coronavirus: molecular features and virus-host interactions detection and phylogenetic analysis of porcine deltacoronavirus in korean swine farms causative agents and epidemiology of diarrhea in korean native calves structure, function, and evolution of coronavirus spike proteins full-length genome sequence of porcine deltacoronavirus strain usa/ia/ / complete genome sequence of a novel swine acute diarrhea syndrome coronavirus susceptibility of chickens to porcine deltacoronavirus infection mutation in spike protein cleavage site and pathogenesis of feline coronavirus infectious bronchitis virus variants: molecular analysis and pathogenicity investigation bovine coronavirus in neonatal calf diarrhoea in iran role of transportation in spread of porcine epidemic diarrhea virus infection. united states novel genotype of infectious bronchitis virus isolated in china coronaviridae une étude épidémiologique à propos des manifestations d'allure grippale chez le porc en croissance the detection and phylogenetic analysis of porcine deltacoronavirus from guangdong province in southern china first outbreak with chimeric swine enteric coronavirus (secov) on pig farms in slovakia -lessons to learn genetic and antigenic heterogeneity of infectious bronchitis virus in south america: implications for control programmes porcine deltacoronavirus from the united states neonatal calf diarrhea: propagation, attenuation, and characteristics of a coronavirus-like agent rodent-borne diseases and their risks for public health rodent-borne diseases and their risks for public health vers une identification de nouveaux virus respiratoires bovins identification of a novel coronavirus from a beluga whale by using a panviral microarray camel production systems in ethiopia: a review of literature with notes on mers-cov risk factors first detection of equine coronavirus (ecov) in europe detecting and monitoring porcine hemagglutinating encephalomyelitis virus porcine hemagglutinating encephalomyelitis virus: a review first detection and characterisation of porcine hemagglutinating encephalomyelitis virus in the czech republic demonstration of coronavirus infection in buffaloes brazilian chicken meat production chain: a -year overview antibody response to equine coronavirus in horses inoculated with a bovine coronavirus vaccine experimental inoculation of equine coronavirus into japanese draft horses complete genome analysis of equine coronavirus isolated in japan genetic evidence of middle east respiratory syndrome coronavirus (mers-cov) and widespread seroprevalence among camels in kenya middle east respiratory syndrome coronavirus (mers-cov): animal to human interaction. pathogens and global health sars-cov- infection in farmed minks, the netherlands isolation of an equine coronavirus from adult horses with pyrogenic and enteric disease and its antigenic and genomic characterization in comparison with the nc strain epidemic of equine coronavirus at obihiro racecourse, hokkaido, japan in discovery of a novel swine enteric alphacoronavirus (seacov) in southern china prevalence of respiratory pathogens in diseased, non-vaccinated, routinely medicated veal calves porcine epidemic diarrhea vaccine evaluation using a newly isolated strain from korea dual enteric and respiratory tropisms of winter dysentery bovine coronavirus in calves outbreak of nipah-virus infection among abattoir workers in singapore evaluation of antibody response of killed and live vaccines against porcine epidemic diarrhea virus in a field study coronaviruses transmissible gastroenteritis in swine isolation of a porcine respiratory, non-enteric coronavirus related to transmissible gastroenteritis a new coronavirus-like particle associated with diarrhea in swine porcine epidemic diarrhea: a retrospect from europe and matters of debate experimental inoculation of neonatal piglets with feed naturally contaminated with porcine epidemic diarrhea virus first retrospective studies with etiological confirmation of porcine transmissible gastroenteritis virus infection in argentina the evolutionary processes of canine coronaviruses chinese-like strain of porcine epidemic diarrhea virus prevalence of equine coronavirus in nasal secretions from horses with fever and upper respiratory tract infection emerging outbreaks associated with equine coronavirus in adult horses equine coronavirus: an emerging enteric virus of adult horses. equine veterinary education enteric coronavirus infection in adult horses geographic information system emergence of porcine epidemic diarrhea viruses with the novel s genes in tibetan pigs in the qinghai-tibetan plateau in china predicting the angiotensin converting enzyme (ace ) utilizing capability as the receptor of sars-cov- hemagglutinating encephalomyelitis coronavirus infection in pigs isolation of mers coronavirus from dromedary camel avian infectious bronchitis virus. recent advances in animal virology middle east respiratory syndrome coronavirus (mers-cov) rna and neutralising antibodies in milk collected according to local customs from dromedary camels middle east respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels: a comparative serological study. the lancet infectious diseases geographic distribution of mers coronavirus among dromedary camels mers-cov infection of alpaca in a region where mers-cov is endemic emerging strains of porcine epidemic diarrhoea virus (pedv) in mexico detection and genetic analysis of porcine hemagglutinating encephalomyelitis virus in south korea vaccination management of beef cattle: delayed vaccination and endotoxin stacking. veterinary clinics of north america -food animal practice molecular epidemiology of coronavirus in faeces of brazilian calves and peruvian camelid herds chauves-souris et virus : des relations complexes a disease of nursing pigs previously unreported in ontario outbreak of diarrhea among preweaning alpacas (vicugna pacos) in the southern peruvian highland retrospective study, full-length genome characterization and evaluation of viral infectivity and pathogenicity of chimeric porcine deltacoronavirus detected in vietnam different lineage of porcine deltacoronavirus in thailand, vietnam and lao pdr in bovine respiratory coronavirus. veterinary clinics of north america: food animal practice winter dysentery in adult dairy cattle: detection of coronavirus in the faeces. the veterinary record diseases of swine the neighbor-joining method: a new method for reconstructing phylogenetic trees coronaviruses: a paradigm of new emerging zoonotic diseases. pathogens and disease detection of bovine coronavirus in calf diarrheic samples by indirect antigen capture elisa and rt-pcr evaluation of equine coronavirus fecal shedding among hospitalized horses coronavirus envelope protein: current knowledge trends in emerging viral infections of swine susceptibility of ferrets, cats, dogs, and different domestic animals to sars-coronavirus- . biorxiv genetic characterization of bovine coronavirus in vietnam molecular and phylogenetic characterization of bovine coronavirus virus isolated from dairy cattle in central region infectious agents associated with diarrhoea in neonatal foals in central kentucky: a comprehensive molecular study porcine epidemic diarrhoea virus: a comprehensive review of molecular epidemiology, diagnosis, and vaccines cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human emergence of porcine epidemic diarrhea virus in the united states: clinical signs, lesions, and viral genomic sequences isolation of respiratory bovine coronavirus, other cytocidal viruses, and pasteurella spp from cattle involved in two natural outbreaks of shipping fever epidemiology, genetic recombination, and pathogenesis of coronaviruses an immunohistochemical investigation of porcine epidemic diarrhoea outbreak of porcine epidemic diarrhea in suckling piglets genetic characterization and phylogenetic analysis of porcine deltacoronavirus (pdcov) in shandong province attenuation of a virulent swine acute diarrhea syndrome coronavirus strain via cell culture passage field study of bovine coronavirus vaccine enriched with hemagglutinating antigen for winter dysentery in dairy cows prospects for inferring very large phylogenies by using the neighbor-joining method epidemic and genetic characterization of porcine epidemic diarrhea virus strains circulating in the regions around hunan phylogeny, genes, and hearing: implications for the evolution of echolocation in bats evaluation of serological assays available in a biosafety level laboratory and their application for survey of middle east respiratory syndrome coronavirus among livestock in ethiopia a cohort study of the effect of winter dysentery on herd-level milk production bovine respiratory syncytial virus and bovine coronavirus antibodies in bulk tank milk -risk factors and spatial analysis serum antibodies to bovine coronavirus in swedish sheep the spread of pathogens through trade in wildlife. revue scientifique et technique de l'oie confirmed cases of sars-cov- in animals in the united states antibody response of pregnant sows to porcine epidemic diarrhea virus live vaccine and maternally-derived antibodies of the piglets s gene-based phylogeny of infectious bronchitis virus: an attempt to harmonize virus classification. infection high prevalence of middle east respiratory coronavirus in young dromedary camels in jordan. vector-borne and zoonotic diseases differential production of proinflammatory cytokines in the pig lung during different respiratory virus infections: correlations with pathogenicity mutational dynamics of the sars coronavirus in cell culture and human populations isolated in prevalence of enteric pathogens in diarrheic and non-diarrheic samples from pig farms with neonatal diarrhea in the north east of spain genetic variability of the s subunit of enteric and respiratory bovine coronavirus isolates detection and genetic characterization of deltacoronavirus in pigs porcine coronavirus hku detected in us states discovery, diversity and evolution of novel coronaviruses sampled from rodents in china detection and characterization of new coronavirus in bottlenose dolphin bat-origin coronaviruses expand their host range to pigs emerging and re-emerging coronaviruses in pigs. current opinion in virology coronavirus pathogenesis induction of protective immunity against transmissible gastroenteritis virus after exposure of neonatal pigs to porcine respiratory coronavirus prevalence of coronavirus antibodies in iowa swine discovery of seven novel mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavi discovery of a novel bottlenose dolphin coronavirus reveals a distinct species of marine mammal coronavirus in gammacoronavirus coronavirus disease , weekly situation report. who/covid middle east respiratory syndrome coronavirus (mers-cov) global summary and assessment risk world organisation of animal health ( ) evolutionary aspects of recombination in rna viruses isolation and characterization of a highly pathogenic strain of porcine enteric alphacoronavirus causing watery diarrhoea and high mortality in newborn piglets the structure and functions of coronavirus genomic ' and ' ends swine enteric alphacoronavirus (swine acute diarrhea syndrome coronavirus): an update three years after its discovery bovine coronavirus (bocv) infection in calves with diarrhoea and their dams efficacy and immunogenicity of recombinant swinepox virus expressing the truncated s protein of a novel isolate of porcine epidemic diarrhea virus prevalence of middle east respiratory syndrome coronavirus (mers-cov) in dromedary camels in abu dhabi emirate porcine deltacoronavirus: overview of infection dynamics, diagnostic methods, prevalence and genetic evolution genomic characterization and pathogenicity of porcine deltacoronavirus strain chn-hg- from china prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern china from the re-emerging of sads-cov infection in pig herds in southern china retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern china fatal swine acute diarrhoea syndrome caused by an hku -related coronavirus of bat origin a pneumonia outbreak associated with a new coronavirus of probable bat origin countrywide survey for mers-coronavirus antibodies in dromedaries and humans in pakistan key: cord- - mazd eu authors: beeraka, narasimha m.; sadhu, surya p.; madhunapantula, subbarao v.; rao pragada, rajeswara; svistunov, andrey a.; nikolenko, vladimir n.; mikhaleva, liudmila m.; aliev, gjumrakch title: strategies for targeting sars cov- : small molecule inhibitors—the current status date: - - journal: front immunol doi: . /fimmu. . sha: doc_id: cord_uid: mazd eu severe acute respiratory syndrome-corona virus- (sars-cov- ) induced coronavirus disease - (covid- ) cases have been increasing at an alarming rate ( . million positive cases as on june ), causing high mortality ( , , deaths as on june ) and economic loss (a . % shrink in global economy in ) across countries globally. the clinical manifestations of this disease are pneumonia, lung injury, inflammation, and severe acute respiratory syndrome (sars). currently, there is no vaccine or effective pharmacological agents available for the prevention/treatment of sars-cov infections. moreover, development of a suitable vaccine is a challenging task due to antibody-dependent enhancement (ade) and th- immunopathology, which aggravates infection with sars-cov- . furthermore, the emerging sars-cov- strain exhibits several distinct genomic and structural patterns compared to other coronavirus strains, making the development of a suitable vaccine even more difficult. therefore, the identification of novel small molecule inhibitors (nsmis) that can interfere with viral entry or viral propagation is of special interest and is vital in managing already infected cases. sars-cov- infection is mediated by the binding of viral spike proteins (s-protein) to human cells through a -step process, which involves angiotensin converting enzyme- (ace ) and transmembrane serine protease (tmprss)- . therefore, the development of novel inhibitors of ace /tmprss is likely to be beneficial in combating sars-cov- infections. however, the usage of ace- inhibitors to block the sars-cov- viral entry requires additional studies as there are conflicting findings and severe health complications reported for these inhibitors in patients. hence, the current interest is shifted toward the development of nsmis, which includes natural antiviral phytochemicals and nrf- activators to manage a sars-cov- infection. it is imperative to investigate the efficacy of existing antiviral phytochemicals and nrf- activators to mitigate the sars-cov- -mediated oxidative stress. therefore, in this review, we have reviewed structural features of sars-cov- with special emphasis on key molecular targets and their known modulators that can be considered for the development of nsmis. covid- is a devastating disease caused by a coronavirus related to the one that caused outbreaks of severe acute respiratory syndrome (sars) in the year ( , ) . middle east respiratory syndrome (mers)-related coronavirus is an infamous member of this cohort. covid- , which is caused by the sars-cov- infection, was detected in wuhan, china in december . the world health organization (who) declared this infection a pandemic on march due to its severity and rapid spread across the globe. as of june , sars-cov- had infected . million individuals, and caused , , deaths across countries worldwide ( table ) . coronaviruses (cov) belongs to a family of single-stranded rna viruses (+rna) that can infect a variety of mammals such as bats and humans ( ) . sars-cov- contains rna of , nucleotide length, which codes for , amino acids ( ) . the rna has a ' cap and ' poly-a tail and produces a poly-protein a/ ab (pp a/pp ab) in the host ( ) . sars-cov- belongs to beta cov category and appears in a crown shape with a size of ∼ - nm (figure ) . gene sequencing data revealed that sars-cov- has and % sequence similarity with bat sars-like-cov-zxc and human sars-cov, respectively ( , ) . the spike (s) proteincoding gene mutation in the nsp and nsp regions results in the replacement of glycine (g) with serine (s) at position (g s), and an isoleucine (i) replaced with proline (p) at amino acid position (i p). due to these mutations, the invading potential of sars-cov- has increased significantly toward host tissues. this virus can also be transmitted through the respiratory droplets from coughs and sneezes of infected individuals ( ) . this mode of aerosol transmission is possible, especially, when protracted exposure occurs in closed areas ( ) . the incubation time of the virus varies significantly from individual to individual. in general it takes about days from the day of infection to the first appearance of symptoms. however, in a few cases the symptoms may appear only after weeks ( ) . members of coronaviridae are known to induce respiratory complications in humans ( , ) . at first, sars-cov, mers-cov, and sars-cov- varieties were transmitted from animals to humans which triggered severe respiratory diseases ( ) ( ) ( ) . however, subsequent transmission occurred among humans primarily due to physical contact. hence, conventional preventive measures such as physical isolation were implemented to avoid propagation of early infection across the human population ( , ) . similar to the sars-cov, the pathological manifestations of sars-cov- could induce lung malfunction in humans as indicated by the severe acute respiratory syndrome and pneumonia ( ) . recent studies reported that sars-cov- infection can induce mild, moderate, and severe illness in infected patients ( ) . clinical manifestations of this infection include chronic pneumonia, sepsis, septic shock, fever, and dry cough ( ) . a progressive respiratory failure during this infection may lead to sudden death ( ) . mild illness resulting from a sars-cov- infection is characterized by the presence of malaise, headache, low fever and dyspnea. in the case of moderate illness from sars-cov- , the complication is manifested by the presence of cough and mild pneumonia. severe illness from sars-cov- is associated with chronic pneumonia, cough, sars, hypoxia, and tachypnea (in children) followed by respiratory, and cardiovascular system failure ( ). the autopsy and biopsy reports of sars-cov- patients revealed severe edema with pulmonary tissue exudates, focal reactive hyperplasia, damage to pneumocytes as well as alveolar macrophages, and patchy cellular infiltration ( ) . coronavirus-induced lung damage has been demonstrated experimentally by several investigators in animal models ( ) . for instance, the sialodacryoadenitis virus and parker's rcov were shown to induce damage to alveolar type-i cells through the expression of pro-inflammatory cytokines, and chemokines such as cinc- , cinc- , lix, mip- α, and fractalkines ( ) ( ) ( ) ( ) ( ) ( ) ( ) . for example, fractalkine promotes the infiltration of cytotoxic lymphocytes in the alveolar epithelium thereby inducing a severe inflammatory response ( , ) . similarly, mip- α confers the chemotaxis of immune cells via il- β and tnf-α inflammatory mediators ( , ( ) ( ) ( ) ( ) . therefore, these animal models could be used to develop effective pharmacological agents against sars-cov- infections. studies from several laboratories have demonstrated that the entry of sars-cov- into human cells is facilitated by ace- ( ) . ace- is a member of the renin-angiotensin system (ras), which plays a vital role in cardiovascular and renal homeostasis. ace- and tmprss facilitates the entry of the virus into host cells during sars-cov- infection ( ). in addition, there are other proteases such as aminopeptidase n (apn) which plays a prominent role for the entry of hcov-nl and hcov- e into host cells ( ) ( ) ( ) ( ) . apn is a membrane-bound glycoprotein that mediates the zincdependent protease activity during the entry and or replication of coronavirus strains into host cells ( , , ) . hence, the ace- receptor's down-modulation may prevent sars-cov- viral entry/replication ( ) . the s-protein of sars-cov and other coronavirus strains are different in their structural and functional domains ( ). s-protein can bind to the n-terminus of ace- receptors on the outer surface of host cells including respiratory epithelium of the lungs ( ) ( ) ( ) . identifying the key amino acid residues in s-protein of the sars-cov- strain may benefit virologists and medical scientists to develop better therapeutic agents. however, to date these details are not known, hence, there is an immediate requirement to identify the amino acids involved in binding s-proteins to ace- receptors on host cell surfaces. furthermore, investigations should also focus on establishing the structural similarities of s-protein motifs that are interacting with the ace- receptors of other coronavirus strains ( ) ( ) ( ) ( ) ( ) . these investigations might help in deciphering molecular strategies to target receptor binding sites of ace- proteins with sars-cov- using novel therapeutics and vaccines to avoid membrane fusion process and viral entry ( ) . the tmprss protease can foster the entry of the sars-cov- virus by activating the s-protein for virus-host cell membrane fusion, consequently enhancing viral replication in the host cells ( , ( ) ( ) ( ) ( ) ( ) . tmprss plays a vital role in generating inflammatory cytokines and chemokines in lung epithelial cells by cleaving s-protein during coronavirus infections including sars-cov- . hence, tmprss is another potential therapeutic target to consider for the novel drug development against sars-cov- ( ) ( ) ( ) . prevention and treatment of sars-cov- infections are achieved at different levels ( ) . the primary approach involves physical isolation to prevent the spread of virus from individual to individual; the second approach involves inhibiting the entry of virus into human cells and the third method includes treating the infected individuals to minimize inflammatory reactions and blocks cathepsin l required for sars-cov processing note: yet to be examined against sars-cov- infection blocks sars-cov interaction with ace- note: yet to be examined against sars-cov- infection [n-( , -dioxo- , -dihydroanthracen- yl)benzamide] blocks sars-cov fusion to host cell membrane note: yet to be examined against sars-cov- infection ( ) nct numbers were obtained from https://clinicaltrials.gov/. pulmonary damage. although physical isolation is the ideal way of limiting the spread, in reality this approach is difficult to execute, hence, many pharmacological companies are actively involved in developing small molecule inhibitors to prevent the entry of the virus into human hosts ( , ) . in this regard several nsmis have been investigated to treat sars-cov; but, significant breakthroughs are yet to come for treating sars-cov- ( ) ( table ) . adedeji et al. ( ) reported the discovery and characterization of novel inhibitors to block sars-cov replication via different mechanisms. one mechanism uses screening of small molecule inhibitors using "hiv- pseudotyped with sars-cov surface glycoprotein s (sars-s)" ( , ) . "ssaa e " is a novel small molecule inhibitor, which blocks the interaction of cov sars-s with ace- receptors, thus blocking the viral entry ( ) . another nsmi is "ssaa e " reported to be involved in blocking the cathepsin l, which is required for cov-sars-s processing to mediate viral entry into the host cell ( ) . ssaa e is another nsmi, which can block the fusion of viral membranes with host cell surfaces ( ) (figure ). since the pathological aspects and genomic similarity of sars-cov- virus with sars-cov, the above strategies of inhibition may figure | molecular pathogenesis of sars-cov- in human lung cells. binding of s-protein of sars-cov- to the ace- receptors triggers the processing of ace- through adam- /tnf-α-converting enzyme and induces the "ace- shedding" into the extracellular space and facilitates uptake of sars-cov- followed by the development of sars. alternatively, the entry of sars-cov- by membrane tmprss serine protease'/hat (human airway trypsin-like protease)-mediated cleavage of ace can facilitate sars-cov s-glycoprotein-mediated virus entry. even though, several nsmis targeting these processes were described and their mode of action against coronavirus were delineated, their efficacy against sars-cov- is yet to be tested. be considered for developing potent pharmacological agents to prevent sars-cov- infections ( ) . however, the prospective research should address the efficacy of these inhibitors against sars-cov- infections. cytokine storm was predominantly reported during sars-cov- infection. targeting cytokine-mediated inflammatory responses induced by sars-cov- is another viable approach for mitigating the complications of viral infection. in this regard, chang et al. ( ) , documented the inflammatory cascades mediated through intracellular signaling pathways conferred by the sars-cov in both lung epithelial cells and fibroblasts. authors of this study have reported that s-protein of sars-cov efficiently mediate the il- release in the infected lung cells by activating mapkinases, and activator protein- (ap- ) without intervention of nf-kb cascade ( ) . this study suggested a promising lead for novel rational drug design through the identification of a "specific sequence motif of sprotein functional domain, " which is responsible for inducing il- -mediated inflammatory response in lungs ( ) . baricitinib is a pharmacological agent, which was reported to block the sars-cov- viral entry and inflammation through the inhibition of ap -associated protein kinase (aak ), cyclin g-associated kinase, and janus kinase- and ( ) . chloroquine (cq) and hydroxychloroquine (hcq) were reported to be effective in mitigating the coronaviral load ( , ) . cq and hcq not only inhibit the entry of sars-cov- but also change the ph of acidic intracellular organelles such as endosomes and lysosomes thereby preventing membrane fusion reactions. however, many contradictions and queries prevail pertaining to the use of hcq for the treatment of covid- . at the time of the submission of this review, results of many clinical trials are yet to be announced, hence, the efficacy of hcq for inhibiting sars-cov- infection is still a possibility. prospective studies should focus on testing the fda approved inhibitors of "abl- kinases, " "pi k/akt/mtor" signaling, and "mapkinase" pathways against sars cov- . since these pathways are involved in cell survival, inflammatory cytokines production, and proliferation of cells, targeted downregulation of these pathways is likely to mitigate the exacerbations induced by coronavirus. in this direction, many of these inhibitors are currently being tested against sars-cov- ( table ) ( ) ( ) ( ) . for instance, sorafenib, which inhibits raf, is being experimented in preclinical models and early clinical trials ( ) . likewise, the efficacy of il- receptor antagonists and tnf-α receptor antagonists for blocking the rat coronavirus-mediated chemokine production was already proven effective in animal models ( , , ) . further studies testing the safety and efficacy are warranted before considering these inhibitory agents for treating individuals infected with sars-cov- ( ). however, the concept of "one drug to treat all" should be followed to combat several devastating viral infections ( , ) . for instance, the ebola, marburg, and sars-cov- are undoubtedly devastating viral pathogens, which can induce high mortality as they transmit rapidly via air and body fluids ( ) . outbreaks of these viruses occur sporadically and currently there are no clinically approved nsmis available to combat these viruses. a recent report by taylor et al. ( ) demonstrated the efficacy of a synthetic adenosine analog, bcx in blocking a broad spectrum of viral species viz., "coronaviruses, paramyxoviruses, and bunyaviruses" as these viruses could induce sars, measles, and mumps. bcx could efficiently block both ebola and marburg viral titers in non-human primate models by targeting viral rna polymerase ( , ) . hence, this molecule should be tested for further studies against sars-cov infections in humans. targeting the membrane protease involved in viral s-protein processing and the viral entry into host cells is another approach in mitigating sars-cov- . the host cellular proteases viz., "trypsin, ", "miniplasmin, " "human airway trypsin like protease, " "tryptase clara, " and "tmprss " could cleave the ha glycoprotein located in influenza a virus and thereby promote viral entry into lung cells ( ) . the usage of serine protease inhibitors such as camostat and aprotinin significantly blocked the replication of influenza virus in epithelial cells of lungs and bronchioles ( ) . in addition, these nsmis could block the release of inflammatory mediators such as cytokines, il- and tnf-α, during this infection ( ) . tmprss is a key protein involved in the pathogenesis of several seasonal viral infections including influenza, h n , h n , and h n ( ) ( ) ( ) ( ) . tmprss cleaves the s-protein of coronavirus to produce unlocked, fusion-catalyzing viral forms and binds to the host cell surface thereby enhancing rapid viral entry ( , , ( ) ( ) ( ) ( ) ( ) . both sars-cov and mers-cov could rapidly enter into the host cells as tmprss can facilitate viral binding to the cell surface ( , , , , , ) . tmprss also plays a vital role in the immuno-pathology of coronavirus infections including sars-cov- across lungs by inducing lung fibrosis ( ) . hence, the emerging research should promote the development of nsmis to target these proteases thereby hindering the entry of sars-cov- into host cells. a proof-of-concept study by iwata-yoshikawa et al. ( ) reported that sars-cov failed to replicate in the bronchioles and lungs of tmprss knockout mice. authors of this study reported elevated expression of tlr -mrna expression in the lungs of "sars-cov-inoculated tmprss -deficient mice" and showed enhanced tlr- mediated localization of dsrna into endosomes ( ) . in this study, tmprss knockout has resulted in downregulation of inflammatory cytokines and chemokine expression, which are involved in the bronchiolitis obliterans organizing pneumonia (boop), sars, and pulmonary fibrosis in sars-cov infection ( , , ) . the intricate sars-cov- pathogenesis is similar to that of sars-cov. studies have reported the efficacy of ifns to block sars-cov in cell line models but not against sars-cov- . among ifnα/ -β/ and -γ, the ifn-β was reported to be the most potent blocker of sars-cov growth ( , ( ) ( ) ( ) ( ) . furthermore, ifn-β and-γ have a synergistic effect in blocking sars-cov viral replication ( , ) . however, the effect of this combination against sars-cov- is not yet reported. therefore, future studies should focus on determining the efficacy of ifnα/ -β/ and -γ against sars-cov- infections. unlike small molecule inhibitors, sirnas are specific and can be designed to mitigate sars-cov associated structural proteins by targeting orf ( , ), orf ( , ), orf a ( , , ) , and orf a ( , ( ) ( ) ( ) . for example, sirnas sisc and sisc have shown success in cultured cells as well as in preclinical mouse models in inhibiting the sars infection without causing toxicity ( ) . several other reports have also recently demonstrated the efficacy of sirnas to inhibit the expression of sars-cov genes coding for cl protease in cell line models ( ) ( ) ( ) ( ) ( ) ( ) ( ) . the activity of sars-cov cl protease is essential for viral replication as this protein is involved in the processing of viral proteins ( ) . selective optimization and screening of hexa-chlorophene analogs can be "active cl protease inhibitors" during a sars-cov infection ( ) . hence, the pharmacological agents/sirnas targeting these pathways may likely produce effective clinical outcomes in sars-cov- infections. however, clinical studies should test the utility of these agents/sirna in reducing the burden of infections caused by sars-cov- ( ). the genome of coronaviruses is reported to be significantly involved in coding both structural proteins, and non-structural proteins (nsp's) for the effective viral replication ( ) . the nsp's (nsp c and nsp ) are required for novice cov viral particle formation through viral orf ab polyprotein processing ( ) . several nsmis were reported to target these non-structural proteins in coronavirus infections to treat sars ( ) . for instance, grl , a bendioxolane derivative, could target papain-like proteinases like nsp ( , , , ) , whereas choloropyridinyl indolecarboxylate targets nsp ( , ( ) ( ) ( ) and a "combination of zinc derivatives with pyrithione" targets nsp ( , ) ; ranitidine bismuth citrate targets nsp ( ) ( ) ( ) ( ) ( ) . monoclonal antibodies; cr ( ), mab- ( ), mdef- ( ) , ampligen ( ), polyiclc ( , ) , stinging nettle lectin ( ) , and tapi- (a tace-inhibitor) ( ) are anticoronaviral agents tested in vivo models of sars. for instance, a study showed that amiodarone (a known anti-arrhythmic agent) effectively targets coronaviral spreading in in vitro models ( ) . working in a similar fashion, / humanized antibodies can neutralize coronaviruses thereby reduce the complications caused by viral infections ( ) . however, the above nsmis should be tested against sars-cov- viral associated proteins and against the activity of nsp's to derive an effective therapeutic intervention. prospective research must focus on the development of novel "helicase inhibitors, viral attachment inhibitors, and activity of rhesus θ -defensin" that block sars-cov- infection using in vitro, in vivo, and clinical studies ( ) . hence, the development of nsmis to target the synthesis of nsp's in sars-cov- may deliver cellular antiviral responses by blocking their replication in host cells ( , , ) . repurposing existing drugs is another strategy widely under consideration to target key proteins involved in the sars-cov- infection. in this regard, the existing nsmis viz., antivirals (umefenovir, remdesivir, nitazoxanide, favipiravir, ritonavir, lopinavir, ifns), anticytokines, antimalaria drugs (chloroquine, hydroxychloroquine), and passive antibody therapies are currently being evaluated to improve clinical outcomes in sars-cov- infected patients ( , , , , ) . however, these agents require additional experimental and clinical validations before being tested in sars-cov- infections. for example, hydroxychloroquine (anti-malarial drug) and the tocilizumab (immunosuppressive drug) are preferred currently to mitigate viral entry and cytokine production in the sars-cov- infection. these drugs are being tested in ongoing trails in china and italy ( , ) . priming the spike (s)-protein of coronavirus by host cells using membrane proteases is a necessary process for viral entry and replication, which further determines zoonotic potential of coronaviruses ( ) . a recent report by markus hoffmann et al. ( ) investigated the protease dependence of sars-cov- for its entry into cells. for example, sars-cov- uses the tmprss protease for its priming ( ) . inhibition of tmprss using camostat mesylate retarded the viral entry into caco- cells ( ). camostat mesylate could be recommended as an nsmi for human clinical trials to combat the sars-cov- virus ( ). this report delineated the ability of neutralizing antibody responses against s-protein to block the sars-cov- entry into host cells ( ) . the serum antibody responses raised to combat the "sars-s protein/ace- interface" during the sars-cov- infection indicates that the vaccination strategy may be an effective therapeutic modality against the covid- infection ( ). ace- catalytic efficacy is significantly higher than ace for angiotensin-ii ( ) . several compounds, such as mln- , were screened according to structure-based/substrate-based studies through virtual screening for inhibiting ace- activity ( ) ( ) ( ) ( ) . ace- is predominantly expressed in lungs, brain, heart, blood vessels, and renal organs ( , ) . ace- is essential for cardiovascular homeostasis, and cns homeostasis as ace- confer redox homeostasis by mitigating ang-ii-induced oxidative stress ( ) . however, in covid- , ace- acts as receptor on human respiratory epithelial cells for sars-cov- binding ( ). a recent report by markus hoffmann et al. ( ) provided evidence that the sars-cov- strain use its spike (s)-protein to bind to ace- . authors of this paper have also demonstrated the efficiency of tmprss in sars-cov- viral strain priming in host cells ( ) . therefore, targeting ace- could be a viable strategy to prevent the entry of sars-cov- into the human system. however, a recent report by guan et al. ( ) cautioned that the administration of ace inhibitors significantly induced adverse clinical outcomes in covid- patients due to severe hypertension, coronary artery disease, and chronic renal failure; hence, further use of ace inhibitors to treat covid- infections was halted ( ) ( ) ( ) . in another report diaz ( ) hypothesized that covid- patients receiving i.v. infusions of aceis and arbs (at -receptor blockers) are at a higher risk of attaining severe disease pathogenesis. hence, they supported the development of nsmis such as "tmprss inhibitors to treat sars-cov- infections ( )". the failure of disease management and lack of selective therapies could be due to the intricate covid- pathogenesis induced by the sars-cov- infection. hence, the early recognition of disease is essential for effective management of covid- ( ) . although, several reports delineated the efficacy of certain nsmis viz., ribavirin, promazine, and imp dehydrogenase inhibitors to inhibit in vivo models of sars-cov replication, later, they were proven ineffective ( , ( ) ( ) ( ) . a report by reghunathan et al. ( ) showed that the immune response produced against sars-cov may be different from other viral infections as indicated by the lack of upregulation in mhc-i genes, cytokines, and ifns or complementmediated cytolysis in peripheral blood mononuclear cells (pbmcs). the failure in the development of a vaccine is due to antibody-dependent enhancement and th- immunopathology ( ) ( ) ( ) . pegylated ifn-α inhibits viral replication of sars-cov and offers protection against type i pneumocytes in lungs ( ) . a significant reason for the failure or lack of selective therapies against sars-cov- -induced sars is the intricate immune system mediated pathophysiology ( ) . other reports by law et al., also detailed similar mechanisms ( , ) . sars-cov can evade host ifn-mediated viral growth inhibition by activating ifn-regulatory factor ( ) . furthermore, sars-cov could induce apoptosis in lymphocytes in vitro using "orf a, orf a, and orf b, e protein, and n protein" ( ) ( ) ( ) ( ) . for instance, the sars-cov can evade immunity as indicated by the decline in cd and cd t cells ( ) . therefore, it is necessary to uncover the complement-based cytolysis in human patients in response to the sars-cov- strain as this virus executes unusual mechanisms to evade the human immune system consequently inducing pathogenesis and mortality. the prospective research should focus on this viral-mediated immune signaling with respect to sars-cov for developing effective nsmis. intravenous (iv) hyperimmune globulin therapy is one of the immunotherapies known to downmodulate pro-inflammatory cytokines and mitigate the severity of infection in covid- patients. iv infusion of immunoglobulins composed of a high dose of antibodies, which can bind to a number of inhibitory receptors viz., fc gamma receptor iib (fcγriib) ( , ) and fcγriic ( ) and confer anti-inflammatory responses against sars-cov- (completed clinical trials: hyperimmune plasma nct ). oxidative stress is significantly induced by several viral infections inside the lungs through the downregulation of redox regulator nuclear factor-erythroid related factor (nrf- ) ( ). nrf- is a leucine-zipper transcription factor ( ) expressed predominantly in nasal epithelium, epithelial cells of lungs, and alveolar macrophages ( , ) . disruption of nrf- and keap interaction triggers the activation of the anti-oxidant defense mechanism ( ) . for instance, nrf- activation offers protection against inflammation and lung injury induced by influenza viral infections and respiratory syncytial virus (rsv) through the anti-oxidant defense pathway ( ) . several viral proteins in the host cells can foster optimum levels of ros-mediated oxidative stress to facilitate viral metabolism and the viral replication cycle without killing host cells ( , ( ) ( ) ( ) ( ) . recent seminal studies described the active role of viruses in inhibiting the nrf- pathway ( ) ( ) ( ) . for instance, the positive regulation of nrf- in modulating the thiol redox system and oxidative stress for the survival of infected astrocytes was observed in moloney murine leukemia virus and hiv virus ( ) . the hcv virus could induce the downregulation of nrf- dependent nqo , gclc, and gpx and modulate oxidative stress ( , ) . an rsv infection mediates proteasomal degradation, deacetylation, and sumoylation of nrf- consequently causing the downregulation of nqo , cat, and sod gene expression ( ) . hence, nrf- activators are potential anti-viral agents, which can be tested against the sars-cov- infection ( ) . future research is highly imperative in unraveling the underlying activity of nrf- for emerging sars-cov- survival by analyzing nrf target genes nqo , gclc, and gpx. in addition, the sars-cov- mediated expression of serine and cysteine proteases in different cell lines should be investigated in relation to nrf- activation, which is a beneficial strategy to combating sars-cov- pathogenesis. however, in the case of certain viral infections, it is imperative to develop nrf- inhibitors to protect the host cells ( ) . for instance, the marburg virus (a causative agent for lethal hemorrhagic fever) can modulate oxidative stress by activating nrf- dependent signaling through the blockade of "vp- viral protein" binding to keap ( ) . therefore, vp- dependent nrf activation can mediate the upregulation of genes ho (heme oxygenase)- , nqo , and gclm ( ) . in the case of dengue virus, the viral particles could induce er stress and activate nrf- signaling, which then lead to tnf-α secretion ( ) . in this scenario, it is crucial to uncover any underlying mechanisms of emerging sars-cov- survival through the modulation of oxidative stress via nrf- signaling in different cells of different organs including lungs ( ) . the prospective lindera erythrocarpa makino ( ) celastrol (quinone methide triterpene) inhibits tat-induced hiv- infection tripterygium wilfordii ( ) bakuchiol (phenolic isoprenoid) psoralea corylifolia l. ( ) rupestonic acid (sesquiterpene) artemisia rupestris l. (continued) frontiers in immunology | www.frontiersin.org research studies should focus on the development of nrf- modulators against sars-cov- . natural products were proven to offer protection against virusinduced oxidative stress by modulating anti-oxidant defense pathways ( , ) . for instance, the administration of egcg has mitigated viral replication of "influenza a/bangkok/ / infection" by activating nrf- to attenuate virus-induced oxidative stress, inflammation, and apoptosis in lung cells ( ) . similarly, the cytoprotective and antioxidant efficacy of nrf- was reported against pr influenza-a viral infection in at-i and at-ii cells ( ) . prospective research should focus on testing the efficacy of several natural products to block sars-cov- viral replication by ascertaining nrf- mediated antioxidant responses. studies have also shown the activation of host cellular transmembrane proteases (for example, serine proteases, cysteine proteases), which can further foster a prompt viral entry and viral replication in host cells by reducing nrf- expression ( ). decline in proteolysis of the above proteases can actuate the propagation of several human viruses viz., influenza, hiv, nipah, ebola, and coronaviruses (sars-cov, mers-cov, sars-cov- ) ( , , ( ) ( ) ( ) . in this scenario, similar to influenza-a virus ( ) , it is highly important to unravel the influence of nrf- expression on tmprss , and human airway trypsin-like protease during sars-cov- -mediated inflammatory conditions and oxidative stress in lungs. the downregulation of the nrf- gene is correlated to serine protease activity and consequent influenza viral entry ( ) . recent studies have demonstrated the efficacy of natural nrf- activators viz., egcg and sulforaphane (sfn) for blocking viral entry/viral replication as well as promoting antiviral mediators rig-i, ifn-β, and mxa ( ) . in this context, it is essential to demonstrate the effects of nutritional interventions like sfn and egcg against sars-cov- induced oxidative stress by modulating nrf- signaling. evidence has demonstrated the use of naturally occurring nrf activators for mitigating viral infections/post-viral infection induced complications. for example, α-luminol is a natural nrf- activator, which confers the protection of astrocytes against the momul virus ( ) . egcg enhances nuclear nrf- levels during tat-induced hiv- infection and offers protection against virus induced oxidative stress ( ) . tanshinone ii a can induce upregulation of nrf- expression and mitigates ros production during tat-induced hiv- infection via modulating ampk/nampt/sirt signaling in host cells ( ) . sfn enhances the phagocytic function of "hiv-infected alveolar macrophages in lungs" by activating nrf- signaling, which further induces downstream antioxidant cascades ( ) . lucidone is effective for the nrf- mediated blockade of dengue virus by inducing heme oxygenase- ( ) ; rographolide could induce nrf- induced antioxidant defenses against influenza a in lung cells ( ) ; celastrol can mediate nrf- induced antioxidant defenses against hiv- tat-induced inflammation ( ) . broccoli sprouts containing sfn acts as a nrf- activator to reduce influenza-induced infection in lung cells ( ) . bakuchiol and rupestonic acid are phytoconstituents that confer nrf- activation thereby promoting nqo gene expression and ho- -mediated interferon activity to enhance antioxidant response against influenza virus in lung cells ( , ) . curcumin is another significant compound that can modulate nrf- signaling and enhance the generation of ifn-β to offer protection against the influenza virus ( ) . curcumin can mitigate this viral infection by modulating tlr / , p /jnk mapk, and nf-κb pathways ( ) . however, studies are required to decipher the activity of these phytochemicals against sars-cov- ( table ) . a recent report by drȃgoi ( ) hypothesized that the potent natural nrf- activators viz., resveratrol, sfn, curcumin, and asea redox should be evaluated in different combinations with conventional drugs against sars-cov- infection in both in vitro and in vivo models and to further deduce a correlation between nrf- activity and sars-cov- viral entry/replication. sars-cov- is progressively inducing a high mortality rate across the globe due to the lack of selective therapeutic interventions or vaccination. recent reports by lu et al. ( ) and xu et al. ( ) delineated that the s-protein of sars-cov- and sars co-v exhibit similar -d pharmacophore in the receptor binding domain (rbd) of ace- of human cells. covid- patients are characterized by the severe viral pathogenesis due to extensive cytokine storm viz., tnf-α, il- β, il- , ifnγ, and mcp- in infected lung tissues ( ) . a report by chen and du ( ) hypothesized that the phyto-constituents such as "baicalin, scutellarin, hesperetin, nicotianamine, and glycyrrhizin" may deliver anti-sars-cov- effects. hesperetin glycoside abundant in citrus fruits, which can inhibit the sars-cov clpro ( ) . the activity of this molecule must be examined against serine/cysteine proteases, which support sars-cov- viral entry/replication. traditional citrus flavonoids were frontiers in immunology | www.frontiersin.org reported to have a potential to act against sars-cov- as studied by molecular docking studies. molecular docking simulations, lc-ms studies described the efficacy of citrus flavonoids (ex. naringenin) in binding to ace- , and mitigating inflammationinduced lung injury by the sars-cov- virus ( ) . further studies should evaluate these compounds in preclinical models to determine the safety and efficacy against the sars-cov- infection. natural products such as di/tri-terpenoids, lignoids were proven to inhibit the viral replication of coronaviruses in vitro ( ) ; griffithsin could block coronaviral entry by binding to the sars-cov spike glycoprotein ( ) . tsl- can block coronaviral entry/replication; leaf extracts of toona sinesis roem effectively blocked sars-cov replication ( ) . betulinic acid, savinin can act as competitive inhibitors against sars-cov cl protease to block viral entry ( ) . the research gap must be filled to develop nutritional therapeutic interventions by investigating the efficacy of these phytochemicals against sars-cov- viral entry. seeds of psorelia corylifolia exhibit inhibitory effects against the sars-cov papain-like protease required for coronavirus entry/replication. the efficacy of these molecules should be examined against sars-cov- ( ) ( table ). the active site pockets of main proteases such as lu and gtb in sars-cov- are reported to be involved in conferring viral entry/fusion; hence, these sites should be considered as the potential drug targets against sars-cov- ( ) . a molecular docking study by khaerunnisa et al. ( ) reported the predicted efficacy of bioactive compounds against above sars-cov- main protease (mpro) sites viz., "nelfinavir, lopinavir, kaempferol, quercetin, luteolin- glucoside, demethoxycurcumin, naringenin, apigenin- -glucoside, oleuropein, curcumin, catechin, epicatechin-gallate, zingerol, gingerol, and allicin" ( table ) . the life-threatening consequences of the covid- pandemic remain high due to lack of selective targeted therapies and vaccination strategies. this is primarily due to extreme genomic variability of rna viruses as well as variations in the host-cell invading mechanisms. hence, this review benefits virologists, medical scientists, and cell biologists to ascertain and develop nsmis, nrf- modulators, and clinically viable vaccines to combat this devastating sars-cov- strain. however, many more preclinical and clinical studies are required to uncover the therapeutic efficacy of potential phytochemicals, natural nrf modulators, and several nsmis against the sars-cov- infection. furthermore, studies are also warranted to overcome ade responses, and th- immunopathology for the development of safe and efficacious vaccines against sars-cov- . in summary, this review provides an overview on the existing knowledge and shows directions to various areas that require immediate attention. nb, ss, and sm: idea development, data collection, manuscript preparation, writing, and proof reading. as, vn, and lm: cross referencing, data collection, and proof reading. sm, ga, and rr: editing, literature search, and proof reading. ss: execution of the literature search. all authors contributed to the article and approved the submitted version. isolation and characterization of viruses related to the sars coronavirus from animals in southern china pegylated interferon-α protects type pneumocytes against sars coronavirus infection in macaques coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus evaluation and treatment coronavirus (covid- ) genomic characterization of the novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia the novel coronavirus ( -ncov) uses the sarscoronavirus receptor ace and the cellular protease tmprss for entry into target cells coronaviruses as the cause of respiratory infections middle east respiratory syndrome: emergence of a pathogenic human coronavirus laboratory testing for coronavirus disease (covid- ) in suspected human cases: interim guidance. world health organization sars and mers: recent insights into emerging coronaviruses a novel coronavirus outbreak of global health concern pulmonary pathology of early phase novel coronavirus (covid- ) pneumonia in two patients with lung cancer attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking ′ -o-methyltransferase activity rat coronaviruses infect rat alveolar type i epithelial cells and induce expression of cxc chemokines. virol il- and neutrophil elastase levels in the respiratory tract of infants with rsv bronchiolitis pathogenicity of influenza viruses with genes from the pandemic virus: functional roles of alveolar macrophages and neutrophils in limiting virus replication and mortality in mice the role of neutrophils in the pathogenesis of rhinovirus infections neutrophils induce damage to respiratory epithelial cells infected with respiratory syncytial virus expression of respiratory syncytial virus-induced chemokine gene networks in lower airway epithelial cells revealed by cdna microarrays rhinovirus stimulation of interleukin- in vivo and in vitro: role of nf-κb cx c chemokines: cell sources and physiopathological implications cxc chemokines and their receptors are expressed in type ii cells and upregulated following lung injury cxcr is critical for dsrna-induced lung injury: relevance to viral lung infection modeling the early events of severe acute respiratory syndrome coronavirus infection in vitro covid- , ace and the cardiovascular consequences angiotensinconverting enzyme is a functional receptor for the sars coronavirus a crucial role of angiotensin converting enzyme (ace ) in sars coronavirus-induced lung injury human coronavirus nl employs the severe acute respiratory syndrome coronavirus receptor for cellular entry human aminopeptidase n is a receptor for human coronavirus e identification of a new human coronavirus identification of residues critical for the human coronavirus e receptor function of human aminopeptidase n the nef protein of human immunodeficiency virus establishes superinfection immunity by a dual strategy to downregulate cell-surface ccr and cd renin-angiotensin system in human coronavirus pathogenesis induction of il- release in lung cells via activator protein- by recombinant baculovirus displaying severe acute respiratory syndrome-coronavirus spike proteins: identification of two functional regions structural characterization of the sars-coronavirus spike s fusion protein core mosaic structure of human coronavirus nl , one thousand years of evolution the s proteins of human coronavirus nl and severe acute respiratory syndrome coronavirus bind overlapping regions of ace crystal structure of nl respiratory coronavirus receptor-binding domain complexed with its human receptor modulation of tnf-α-converting enzyme by the spike protein of sars-cov and ace induces tnf-α production and facilitates viral entry differential downregulation of ace by the spike proteins of severe acute respiratory syndrome coronavirus and human coronavirus nl efficient activation of the severe acute respiratory syndrome coronavirus spike protein by the transmembrane protease tmprss middle east respiratory syndrome coronavirus infection mediated by the transmembrane serine protease tmprss tmprss activates the human coronavirus e for cathepsin-independent host cell entry and is expressed in viral target cells in the respiratory epithelium the spike protein of the emerging betacoronavirus emc uses a novel coronavirus receptor for entry, can be activated by tmprss , and is targeted by neutralizing antibodies tmprss contributes to virus spread and immunopathology in the airways of murine models after coronavirus infection arguments in favor of remdesivir for treating sars-cov- infections clinical features of patients infected with novel coronavirus in wuhan novel inhibitors of severe acute respiratory syndrome coronavirus entry that act by three distinct mechanisms inhibition of sars-cov replication cycle by small interference rnas silencing specific sars proteins, a/ b, a/ b and s a noncovalent class of papain-like protease/deubiquitinase inhibitors blocks sars virus replication severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand x-ray structure and biological evaluation design, synthesis and antiviral efficacy of a series of potent chloropyridyl ester-derived sars-cov clpro inhibitors rapid discovery and optimization of therapeutic antibodies against emerging infectious diseases amiodarone alters late endosomes and inhibits sars coronavirus infection at a post-endosomal level antiviral activity of arbidol and its derivatives against the pathogen of severe acute respiratory syndrome in the cell cultures toona sinensis roem tender leaf extract inhibits sars coronavirus replication salvianolic acid y: a new protector of pc cells against hydrogen peroxide-induced injury from salvia officinalis tace antagonists blocking ace shedding caused by the spike protein of sars-cov are candidate antiviral compounds evaluation of immunomodulators, interferons and known in vitro sars-cov inhibitors for inhibition of sars-cov replication in balb/c mice induction of interferon-γ-inducible protein by sars-cov infection, interferon alfacon and interferon inducer in human bronchial epithelial calu- cells and balb/c mice increased sensitivity of sars-coronavirus to a combination of human type i and type ii interferons interferon-beta and interferongamma synergistically inhibit the replication of severe acute respiratory syndrome-associated coronavirus (sars-cov) remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro potential inhibitor of covid- main protease (mpro) from several medicinal plant compounds by molecular docking study nelfinavir was predicted to be a potential inhibitor of -ncov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation antiviral drugs specific for coronaviruses in preclinical development a -amino acid fragment of the sars coronavirus s protein efficiently binds angiotensin-converting enzyme baricitinib as potential treatment for -ncov acute respiratory disease inhibition of human coronavirus e infection in human epithelial lung cells (l ) by chloroquine: involvement of p mapk and erk chloroquine and hydroxychloroquine as available weapons to fight covid- antiviral potential of erk/mapk and pi k/akt/mtor signaling modulation for middle east respiratory syndrome coronavirus infection as identified by temporal kinome analysis repurposing of kinase inhibitors as broad-spectrum antiviral drugs repurposing of clinically developed drugs for treatment of middle east respiratory syndrome coronavirus infection biologic basis for interleukin- in disease differences between anti-tumor necrosis factor-alpha monoclonal antibodies and soluble tnf receptors in host defense impairment protection against filovirus diseases by a novel broad-spectrum nucleoside analogue bcx designing defenses against deadly viruses bcx -a broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of ebola virus disease host envelope glycoprotein processing proteases are indispensable for entry into human cells by seasonal and highly pathogenic avian influenza viruses the serine protease inhibitor camostat inhibits influenza virus replication and cytokine production in primary cultures of human tracheal epithelial cells tmprss is essential for influenza h n virus pathogenesis in mice tmprss is a host factor that is essential for pneumotropism and pathogenicity of h n influenza a virus in mice the host protease tmprss plays a major role in in vivo replication of emerging h n and seasonal influenza viruses a mutant h n influenza virus uses an alternative activation mechanism in tmprss knockout mice by loss of an oligosaccharide in the hemagglutinin stalk region influenza and sars-coronavirus activating proteases tmprss and hat are expressed at multiple sites in human respiratory and gastrointestinal tracts evidence that tmprss activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response tmprss and adam cleave ace differentially and only proteolysis by tmprss augments entry driven by the severe acute respiratory syndrome coronavirus spike protein wild-type human coronaviruses prefer cell-surface tmprss to endosomal cathepsins for cell entry a transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry cleavage and activation of the severe acute respiratory syndrome coronavirus spike protein by human airway trypsin-like protease proteolytic activation of the sars-coronavirus spike protein: cutting enzymes at the cutting edge of antiviral research vegf and bfgf are highly expressed in intraluminal fibromyxoid lesions in bronchiolitis obliterans organizing pneumonia in vitro susceptibility of clinical isolates of sars coronavirus to selected antiviral compounds treatment of sars with human interferons severe acute respiratory syndrome-related coronavirus is inhibited by interferon-α potent inhibition of sars-associated coronavirus (scov) infection and replication by type i interferons (ifn-α/β) but not by type ii interferon (ifn-γ) the molecular biology of sars coronavirus an overall picture of sars coronavirus (sars-cov) genome-encoded major proteins: structures, functions and drug development m and n proteins of sars coronavirus induce apoptosis in hpf cells the sars-coronavirus membrane protein induces apoptosis through modulating the akt survival pathway ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the n-terminal domain of n protein structure of the sars coronavirus nucleocapsid protein rna-binding dimerization domain suggests a mechanism for helical packaging of viral rna severe acute respiratory syndrome coronavirus a accessory protein is a viral structural protein sars coronavirus a protein blocks cell cycle progression at g /g phase via the cyclin d /prb pathway sars coronavirus protein a interacts with human ap a-hydrolase using sirna in prophylactic and therapeutic regimens against sars coronavirus in rhesus macaque sirna targeting the leader sequence of sars-cov inhibits virus replication inhibition of genes expression of sars coronavirus by synthetic small interfering rnas inhibition of severe acute respiratory syndrome virus replication by small interfering rnas in mammalian cells inhibition of sars-cov replication by sirna prophylactic and therapeutic effects of small interfering rna targeting sars coronavirus screening of drugs by fret analysis identifies inhibitors of sars-cov cl protease recent developments in anti-severe acute respiratory syndrome coronavirus chemotherapy deubiquitinating activity of the sars-cov papain-like protease selectivity in isg and ubiquitin recognition by the sars coronavirus papain-like protease drug design targeting the main protease, the achilles' heel of coronaviruses characterization and inhibition of sarscoronavirus main protease enzymatic activity of the sars coronavirus main proteinase dimer a second, non-canonical rna-dependent rna polymerase in sars coronavirus zn + inhibits coronavirus and arterivirus rna polymerase activity in vitro and zinc ionophores block the replication of these viruses in cell culture identification and characterization of severe acute respiratory syndrome coronavirus replicase proteins molecular cloning, expression, and purification of sars-cov nsp multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase inhibition of sars coronavirus helicase by bismuth complexes bismuth complexes inhibit the sars coronavirus human monoclonal antibody as prophylaxis for sars coronavirus infection in ferrets single-dose intranasal administration with mdef (adenovirus vectored mouse interferon-alpha) confers protection from mortality in a lethal sars-cov balb/c mouse model interferon alfacon inhibits sars-cov infection in human bronchial epithelial calu- cells a new mouse-adapted strain of sars-cov as a lethal model for evaluating antiviral agents in vitro and in vivo toll like receptor- ligand poly-iclc promotes the efficacy of peripheral vaccinations with tumor antigen-derived peptide epitopes in murine cns tumor models nonstructural proteins and of feline coronavirus form a : heterotrimer that exhibits primer-independent rna polymerase activity new nsp isoform suggests mechanism for tuning viral rna synthesis breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies a trial of lopinavirritonavir in adults hospitalized with severe covid- the proximal origin of sars-cov- trypsin treatment unlocks barrier for zoonotic bat coronavirus infection twoyear prospective study of the humoral immune response of patients with severe acute respiratory syndrome hydrolysis of biological peptides by human angiotensinconverting enzyme-related carboxypeptidase evaluation of angiotensin-converting enzyme (ace), its homologue ace and neprilysin in angiotensin peptide metabolism ace : from vasopeptidase to sars virus receptor structure-based pharmacophore design and virtual screening for novel angiotensin converting enzyme inhibitors role of the ace /angiotensin - axis of the renin-angiotensin system in heart failure angiotensin-converting enzyme (ace ), but not ace, is preferentially localized to the apical surface of polarized kidney cells ace -mediated reduction of oxidative stress in the central nervous system is associated with improvement of autonomic function clinical characteristics of coronavirus disease in china evolution of the novel coronavirus from the ongoing wuhan outbreak and modeling of its spike protein for risk of human transmission hypothesis: angiotensin-converting enzyme inhibitors and angiotensin receptor blockers may increase the risk of severe covid- evaluation of interferon inducers, ribavirin and mouse hyperimmune serum in a pathogenesis/lethal mouse model using a mouse-adapted sars-cov enhancement of the infectivity of sars-cov in balb/c mice by imp dehydrogenase inhibitors, including ribavirin is the anti-psychotic, -( -(dimethylamino) propyl) phenothiazine (promazine), a potential drug with which to treat sars infections?: lack of efficacy of promazine on sars-cov replication in a mouse model expression profile of immune response genes in patients with severe acute respiratory syndrome implications of antibody-dependent enhancement of infection for sars-cov- countermeasures pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology immunization with sars coronavirus vaccines leads to pulmonary immunopathology on challenge with the sars virus inhibition of beta interferon induction by severe acute respiratory syndrome coronavirus suggests a two-step model for activation of interferon regulatory factor chemokine upregulation in sars-coronavirus-infected, monocyte-derived human dendritic cells the sars coronavirus nucleocapsid protein induces actin reorganization and apoptosis in cos- cells in the absence of growth factors the a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in vero e cells overexpression of a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway g /g arrest and apoptosis induced by sars-cov b protein in transfected cells significant changes of peripheral t lymphocyte subsets in patients with severe acute respiratory syndrome selective blockade of the inhibitory fcγ receptor (fcγriib) in human dendritic cells and monocytes induces a type i interferon response program ligation of fc gamma receptor iib inhibits antibody-dependent enhancement of dengue virus infection immunomodulation by ivig and the role of fc-gamma receptors: classic mechanisms of action after all? front immunol therapeutic modulation of virus-induced oxidative stress via the nrf -dependent antioxidative pathway oxidative stress induced by hiv- reverse transcriptase modulates the enzyme's performance in gene immunization thiol chemistry and specificity in redox signaling antiviral activity of nrf in a murine model of respiratory syncytial virus disease influenza a virus induction of oxidative stress and mmp- is associated with severe lung pathology in a mouse model mitochondrial injury, oxidative stress, and antioxidant gene expression are induced by hepatitis c virus core protein cellular oxidative stress response controls the antiviral and apoptotic programs in dengue virus-infected dendritic cells the pathogenesis of influenza virus infections: the contributions of virus and host factors viral-mediated inhibition of antioxidant enzymes contributes to the pathogenesis of severe respiratory syncytial virus bronchiolitis respiratory syncytial virus induces nrf degradation through a promyelocytic leukemia protein-ring finger protein dependent pathway hiv- decreases nrf /are activity and phagocytic function in alveolar macrophages astrocytes survive chronic infection and cytopathic effects of the ts mutant of the retrovirus moloney murine leukemia virus by upregulation of antioxidant defenses hepatitis c virus impairs the induction of cytoprotective nrf target genes by delocalization of small maf proteins hepatitis c virus triggers mitochondrial permeability transition with production of reactive oxygen species, leading to dna damage and stat activation respiratory syncytial virus infection downregulates antioxidant enzyme expression by triggering deacetylationproteasomal degradation of nrf dimerization controls marburg virus vp -dependent modulation of host antioxidative stress responses marburgvirus hijacks nrf -dependent pathway by targeting nrf -negative regulator keap activation of nrf by the dengue virus causes an increase in clec a, which enhances tnf-α production by mononuclear phagocytes nrf expression modifies influenza a entry and replication in nasal epithelial cells nrf protects human alveolar epithelial cells against injury induced by influenza a virus endosomal proteolysis of the ebola virus glycoprotein is necessary for infection two-step conformational changes in a coronavirus envelope glycoprotein mediated by receptor binding and proteolysis characterization of severe acute respiratory syndrome-associated coronavirus (sars-cov) spike glycoprotein-mediated viral entry proteolytic activation of influenza viruses by serine proteases tmprss and hat from human airway epithelium retrovirusinduced oxidative stress with neuroimmunodegeneration is suppressed by antioxidant treatment with a refined monosodium α-luminol (galavit) egcg inhibits tat-induced ltr transactivation: role of nrf , akt, ampk signaling pathway tanshinone ii a inhibits tat-induced hiv- transactivation through redox-regulated ampk/nampt pathway activating the nrf -mediated antioxidant response element restores barrier function in the alveolar epithelium of hiv- transgenic rats lucidone suppresses dengue viral replication through the induction of heme oxygenase- activity of andrographolide and its derivatives against influenza virus in vivo and in vitro celastrol ameliorates hiv- tat-induced inflammatory responses via nf-kappab and ap- inhibition and heme oxygenase- induction in astrocytes effect of broccoli sprouts on nasal response to live attenuated influenza virus in smokers: a randomized, double-blind study bakuchiol is a phenolic isoprenoid with novel enantiomer-selective antiinfluenza a virus activity involving nrf activation chinese herbal medicine compound yi-zhi-hao pellet inhibits replication of influenza virus infection through activation of heme oxygenase- inhibition of curcumin on influenza a virus infection and influenzal pneumonia via oxidative stress, tlr / , p /jnk mapk and nf-κb pathways the spectral properties of (-)-epigallocatechin -o-gallate (egcg) fluorescence in different solvents: dependence on solvent polarity electrophilic tuning of the chemoprotective natural product sulforaphane pharmacokinetics and tissue distribution study of tanshinone iia after oral administration of bushen huoxue qubi granules to rats with blood stasis syndrome celastrol: a spectrum of treatment opportunities in chronic diseases the active compounds derived from psoralea corylifolia for photochemotherapy against psoriasis-like lesions: the relationship between structure and percutaneous absorption -triazolecontaining derivatives of rupestonic acid: click-chemical synthesis and antiviral activities against influenza viruses biological activities of curcuminoids, other biomolecules from turmeric and their derivatives-a review asea redox supplement" [ars]) should be clinically tested as adjuvants in all types of medium and severe cases of aggressive respiratory viral infections (including influenza a/b/c, sars, mers, covid- , measles, avian influenza etc.) based on their extrapolated cytoprotective antioxidant effects (especially on vital organs), including the cytoprotection offered by ars on the cardiac muscle of dmd patients which can be extrapolated to the lungs -a very short medical communication genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding anti-sars coronavirus c-like protease effects of isatis indigotica root and plant-derived phenolic compounds citrus fruits are rich in flavonoids for immunoregulation and potential targeting ace specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus broad-spectrum in vitro activity and in vivo efficacy of the antiviral protein griffithsin against emerging viruses of the family coronaviridae phenolic phytochemical displaying sars-cov papain-like protease inhibition from the seeds of psoralea corylifolia baicalin, a metabolite of baicalein with antiviral activity against dengue virus dual effect of glucuronidation of a pyrogallol-type phytophenol antioxidant: a comparison between scutellarein and scutellarin co-occurrence of nicotianamine and avenic acids in avena sativa and oryza sativa azetidine- -carboxylic acid derivatives from seeds of fagus silvatica l. and a revised structure for nicotianamine betulin and betulinic acid: triterpenoids derivatives with a powerful biological potential the griffithsin dimer is required for high-potency inhibition of hiv- : evidence for manipulation of the structure of gp as part of the griffithsin dimer mechanism research & consulting llc.the remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.copyright © beeraka, sadhu, madhunapantula, rao pragada, svistunov, nikolenko, mikhaleva and aliev. this is an open-access article distributed under the terms of the creative commons attribution license (cc by). the use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. no use, distribution or reproduction is permitted which does not comply with these terms. key: cord- -tk eturq authors: berrio, alejandro; gartner, valerie; wray, gregory a title: positive selection within the genomes of sars-cov- and other coronaviruses independent of impact on protein function date: - - journal: biorxiv doi: . / . . . sha: doc_id: cord_uid: tk eturq background the emergence of a novel coronavirus (sars-cov- ) associated with severe acute respiratory disease (covid- ) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. several recent studies of the sars-cov- genome have identified signals of conservation and positive selection within the gene encoding spike protein based on the ratio of synonymous to nonsynonymous substitution. such tests cannot, however, detect changes in the function of rna molecules. methods here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. results we recapitulate the finding that the gene encoding spike protein has been a target of both purifying and positive selection. in addition, we find other likely targets of positive selection within the genome of sars-cov- , specifically within the genes encoding nsp and nsp . homology-directed modeling indicates no change in either nsp or nsp protein structure relative to the most recent common ancestor. thermodynamic modeling of rna stability and structure, however, indicates that rna secondary structure within both genes in the sars-cov- genome differs from those of ratg , the reconstructed common ancestor, and pan-cov-gd (guangdong). these sars-cov- -specific mutations may affect molecular processes mediated by the positive or negative rna molecules, including transcription, translation, rna stability, and evasion of the host innate immune system. our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle. an important challenge in understanding zoonotic events is identifying the genetic changes that to identify branch specific positive selection, it is necessary to obtain a query and a reference alignment. we downloaded six high quality reference genomes from the subgenus sarbecovirus (table ). next, we used mafft (katoh & standley, ) (kearse et al., ) with default settings to build a sequence alignment. next, we refined the alignment using a gene by gene procedure. foreground branch is evolving at faster rates than the expectation from the background species. we performed a selection analysis on sliding windows of bp with a step of bp along a sequence alignment of reference genome sequences of coronaviruses of the subgenus sarbecovirus and two sequences of pangolin coronavirus recently published (liu, chen & chen, ; lam et al., ) . this procedure generates partitions where a tree topology can be fitted. to investigate the extent of positive selection or branches with long substitution rates along the sars-cov- genome, we used a branch-specific method known as adaptiphy that was initially pa_cov_guangxi_p l), (bat_cov_lyra , sars_cov)), bat_cov_bm ). this method is highly sensitive and specific and can differentiate between positive selection and relaxation of constraint. adaptiphy requires at least kb reference alignment for each species that is used as a putatively neutral proxy for computing substitution rates. viruses' genomes lack non-functional regions, therefore, the most reasonable proxy for neutral evolution has to be found in the regions outside the query window. to do this, we concatenated twenty regions of bp of the viral genome alignment that were drawn randomly with replacement from the entire genome alignment. then, for each query alignment, we built a reference alignment of kb as it produces a stable evolutionary standard of recombination rates. to control for the stochasticity of the evolutionary process, we run each query against ten bootstrapped samples of reference alignments. finally, we used a custom r script to compute the likelihood ratio, which was used as a test statistic for a chi-squared test with one degree of freedom to calculate a p-value for each query. then, we corrected the distribution of all p-values per query region using the p.adjust() r function with the fdr method. next, we classified a query window to be under positive selection if the p-adjusted value was < . . we were unable to successfully run adaptiphy on two windows because the outgroup species (bat_cov_bm ) contained a deletion of bp relative to sars-cov- , which spans the entire orf . next, we calculated the distribution of substitution rates for each branch and nodes in each query and reference sequence using phylofit (hubisz, pollard & siepel, (wong & nielsen, ) . to test for conservation, we used the phastcons computational method from phast (siepel et positive and negative selection are highly localized within coronavirus genomes we tested for branch-specific selection on nucleotide sequences in coronavirus genomes, the fourth signal is located in a segment encoding the s and s ' subunits that includes the boundary region between the s and the s subunits (fig ) , a region that includes the genes encoding nsp and nsp contain branch-specific signals of positive selection we also detected two shorter signals of positive selection within the sars-cov- genome that are located outside of the s gene, in orf a and orf b (fig a) . interestingly, both encode small proteins that contribute to viral replication. the first is nsp , which encodes a similarities to, but also notable differences from, that of sars-cov- (fig ) . in both species, s cov-ratg )))). recombination from a divergent species should produce an incongruent topology in one or more adjacent windows, revealing a recombined region and its approximate breakpoints. we identified regions where the topology differed from the expected (fig ) . of (fig c and a) . in contrast, signals of positive selection in sars-cov- and bat-cov-ratg are concentrated in the domain that mediates binding to the host receptor ace (fig c and a) . these distinct distributions suggest that modifications in different aspects of spike function took place as various coronaviruses adapted to novel hosts. in importantly, we also detected signals of positive selection in two additional regions of the sars-cov- genome, specifically within the genes encoding nsp and nsp (fig a) . of and rna structure (fig and ) . in the case of nsp protein, two nearly adjacent nonsynonymous substitutions at residues and occurred on the branch leading to sars-cov- ( fig b) . these both involve changing side chains with similar biochemical properties, respectively valine to alanine and valine to isoleucine. homology-directed modeling of protein structure suggests that these two amino acid substitutions have very little impact on either secondary or tertiary structure when comparing the sars-cov- protein orthologue to those of the other species examined (fig a) . in the case of nsp protein, no nonsynonymous substitutions evolved on the branch leading to sars-cov- . thus, the signal of positive selection within nsp is unlikely to reflect changes in protein structure or function, while the signal within nsp cannot affect either because the encoded polypeptide is identical. with highly similar and identical protein structures predicted for nsp and nsp , respectively, in silico identification of conserved cis -acting rna elements in the sars- regulate antagonism of irf and nf-kappab signaling ubiquitination-mediated regulation of interferon responses coronavirus spike proteins in viral entry functional rna elements in the dengue virus genome recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission the vienna rna websuite membrane rearrangements mediated by coronavirus nonstructural proteins and . virology mobility and interactions of coronavirus nonstructural protein visualizing genomic data using gviz and bioconductor molecular biology promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution temporal dynamics in viral shedding and transmissibility of covid- structure of replicating sars-cov- polymerase a multibasic cleavage site in the spike protein of sars-cov- is essential for infection of human lung cells evidence of the recombinant origin of a bat severe acute respiratory syndrome (sars)-like coronavirus and its implications on the direct ancestor of sars discovery of a rich gene pool of bat sars-related coronaviruses provides new insights into the origin of sars coronavirus phast and rphast: phylogenetic analysis with space/time models coronavirus spike protein and tropism changes advances in virus research comprehensive in-vivo secondary structure of the sars-cov- genome reveals novel regulatory motifs and mechanisms. biorxiv : the preprint server for biology comprehensive in-vivo secondary structure of the sars-cov- genome reveals novel regulatory motifs and mechanisms. biorxiv : the preprint server for biology mafft multiple sequence alignment software version : improvements in performance and usability geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data the phyre web portal for protein modeling, prediction and analysis the architecture of sars-cov- tracking changes in sars-cov- spike: evidence that d g increases infectivity of the covid- raxml-ng: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference identifying sars-cov- -related coronaviruses in malayan pangolins severe acute respiratory syndrome (sars) horseshoe bats through recombination emergence of sars-cov- through recombination and strong purifying selection the divergence between sars-cov- and ratg might be overestimated due to the extensive rna modification viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (manis javanica) viennarna package . severe acute respiratory syndrome-associated coronavirus a protein forms an ion channel and modulates virus release cleavage inhibition of the murine coronavirus spike protein by a furin-like enzyme affects cell-cell but not virus-cell fusion downloaded from mechanism and structural diversity of exoribonuclease- resistant rna structures in flaviviral rnas coronavirus cis-acting rna elements the sars coronavirus papain like protease can inhibit irf at a post activation step that requires deubiquitination activity coronavirus non-structural protein : evasion, attenuation, and possible treatments the sars coronavirus a protein causes endoplasmic reticulum stress and induces ligand-independent downregulation of the type interferon receptor viral innate immune evasion and the pathogenesis of emerging rna virus infections the ratio of replacement to silent divergence and tests of neutrality topology and membrane anchoring of the coronavirus replication complex: not all hydrophobic domains of nsp and nsp are membrane spanning emerging sars-cov- mutation hot spots include a novel rna-dependent-rna polymerase variant structure of the human metapneumovirus polymerase phosphoprotein complex clinical progression and viral load in a community outbreak of coronavirus- associated sars pneumonia: a prospective study the coding region of the hcv genome contains a network of regulatory rna structures estimating variability in the transmission of severe acute respiratory syndrome to household contacts in hong kong hyphy: hypothesis testing using phylogenies hyphy . -a customizable platform for evolutionary hypothesis testing using phylogenies rna genome conservation and secondary structure in sars-cov- and sars-related viruses: a first look comparative analysis of coronavirus genomic rna structure reveals conservation in sars-like coronaviruses. biorxiv : the preprint server for biology in search of molecular darwinism evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes the nonstructural proteins directing coronavirus rna synthesis and processing the severe acute respiratory syndrome coronavirus a protein up-regulates expression of fibrinogen in lung epithelial cells on the origin and continuing evolution of sars-cov- structural insights into coronavirus entry sars-cov- genomic variations associated with mortality rate of covid- inhibition of irf -dependent antiviral responses by cellular and viral proteins positive selection of orf a and orf genes drives the evolution of sars-cov- during the enhanced receptor binding of sars-cov- through networks of hydrogen-bonding and hydrophobic interactions structural and functional basis of sars-cov- entry by using exploitation of glycosylation in enveloped virus pathobiology detecting selection in noncoding regions of nucleotide sequences cryo-em structure of the -ncov spike in the prefusion conformation cryo-em analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage fatcat: a web server for flexible structure comparison and structure similarity searching coronavirus open reading frame- a drives multimodal necrotic cell death the short- and long-range rna-rna interactome of sars-cov- co-first authors ribose '-o- methylation provides a molecular signature for the distinction of self and non-self mrna dependent on the rna sensor mda key: cord- -q d ysbo authors: liu, xue; liu, chao; liu, gang; luo, wenxin; xia, ningshao title: covid- : progress in diagnostics, therapy and vaccination date: - - journal: theranostics doi: . /thno. sha: doc_id: cord_uid: q d ysbo coronavirus disease (covid- ) caused by severe acute respiratory syndrome coronavirus (sars-cov- ) has recently become a pandemic. as the sudden emergence and rapid spread of sars-cov- is endangering global health and the economy, the development of strategies to contain the virus's spread are urgently needed. at present, various diagnostic kits to test for sars-cov- are available for use to initiate appropriate treatment faster and to limit further spread of the virus. several drugs have demonstrated in vitro activity against sars-cov- or potential clinical benefits. in addition, institutions and companies worldwide are working tirelessly to develop treatments and vaccines against covid- . however, no drug or vaccine has yet been specifically approved for covid- . given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for sars-cov- infection, helping to guide strategies to address the current covid- pandemic. the rapid spread of sars-cov- , a novel coronavirus that emerged in december , and the resulting disease, namely, coronavirus disease (covid- ) , has posed a serious global public health emergency. whole-genome sequencing results show that the causative agent is a novel coronavirus that was initially named -ncov by the world health organization (who) [ ] [ ] [ ] . covid- was subsequently recommended as the disease name. as the genomic sequence of the new virus is closely related to that of severe acute respiratory syndrome (sars) coronavirus (sars-cov), the international committee on taxonomy of viruses (ictv) officially designated the virus sars-cov- [ ] . patients infected by sars-cov- manifest a range of symptoms, such as dry cough, fever, headache and dyspnea, and are generally diagnosed with viral pneumonia [ , ] , but asymptomatic infections have also been reported [ , ] . coronaviruses, a genus in the coronaviridae family, are enveloped, positive-sense, single-stranded rna viruses with the largest known genomes (from to kb) among rna viruses [ , ] . coronavirinae is subdivided into four genera: alpha-, beta-, gamma-, and delta coronaviruses [ ] . phylogenetic analysis of coronavirus genomes has revealed that sars-cov- is a new member of the beta coronavirus genus, which includes sars-cov and middle east respiratory syndrome (mers) coronavirus (mers-cov), as well as other viruses that infect humans and diverse animal species. among the several coronaviruses that are pathogenic to humans, most are associated with mild clinical symptoms (e.g., hcov- e, hcov-nl , hcov-oc , and hcov-hku ) [ , ] , with three notable exceptions: sars-cov in november [ ] [ ] [ ] , mers-cov in april [ ] [ ] [ ] , and, more recently, sars-cov- causing covid- . sars-cov provoked a large-scale epidemic beginning in china and involving countries with approximately , cases and deaths [ ] ; mers-cov began in saudi arabia and caused a total of , mers cases with associated deaths as of the end of january [ ] . similar to sars-cov and mers-cov, the sars-cov- genome encodes nonstructural proteins (nsps, such as -chymotrypsin-like protease, papain-like protease, helicase, and rna-dependent rna polymerase), structural proteins and accessory proteins [ ] . sars-cov- has four structural proteins: the spike (s) protein, envelope (e) protein, membrane (m) protein, and nucleocapsid (n) protein. among these proteins, the trimeric s protein is indispensable for virus-cell receptor interactions during viral entry [ , ] . s protein comprises an n-terminal s subunit responsible for virus-receptor binding and a c-terminal s subunit responsible for virus-cell membrane fusion. s is further divided into an n-terminal domain (ntd) and a receptor-binding domain (rbd) [ , ] . sars-cov- targets cells through the s protein, which binds to the human angiotensin-converting enzyme (ace ) receptor and employs the cellular serine protease tmprss for s protein priming [ ] [ ] [ ] [ ] [ ] . such binding triggers a cascade of events leading to fusion between the cellular and viral membranes for cell entry. the viral rna genome is released into the cytoplasm after membrane fusion (see the sars-cov- lifecycle in figure ). polyproteins are subsequently synthesized to encode the viral replicase-transcriptase complex. the viral rna is then synthesized by rna-dependent rna polymerase. synthesis of structural proteins is followed by viral particle assembly and release [ , ] . these viral lifecycle steps provide potential targets for vaccines and therapeutics to prevent and treat sars-cov- infection. promising targets include nsps, which are involved in transcription and replication of the virus, as the key enzymes in the viral lifecycle. additional targets include viral entry and immune regulation pathways. for example, the s protein plays key roles in the induction of t cell responses and neutralizing antibodies (nabs), as well as protective immunity, during infection with sars-cov- . to elucidate the specific mechanisms of sars-cov- infection, the crystal structure of the sars-cov- spike rbd bound to the cell receptor ace at . Å resolution was recently determined [ ] . the overall binding mode of the sars-cov- rbd with ace is nearly identical to that of the sars-cov rbd, which also utilizes ace on the surface of host cells as a receptor. hela cells expressing ace are susceptible to sars-cov- infection, but cells without ace expression are not infected [ ] . in vitro binding experiments also show that the sars-cov- rbd has affinity for ace in the low nm range, indicating that the rbd is the key functional component of the s subunit responsible for the binding of ace to sars-cov- [ ] . more structural information at the atomic level would greatly enhance our understanding of the interaction between sars-cov- and host cells, providing precise targets for nabs, and assist us in urgently needed structure-based vaccine design in the ongoing fight against sars-cov- . in addition, research on cell modeling tools might promote insight into our understanding of infection mechanisms and speed up the development of therapeutic agents and vaccines for covid- [ ] . in this review, we aim to discuss the current status of diagnostics, therapeutics, and vaccines against covid- . as rapid diagnostics and development of drugs and vaccines for the virus are important interventions to control the outbreak, a review article that encompasses the current research on this topic may provide help for guiding strategies to address the current covid- pandemic. rapid and accurate detection of covid- is essential to initiate the appropriate treatment rapidly, to limit further spread of the virus and to ultimately eliminate the virus from circulation. covid- patients present a wide range of clinical symptoms (e.g., cough, fever, and dyspnea) that are similar to influenza or other respiratory infections and thus cannot be used for accurate diagnosis [ , ] . at present, accurate and rapid diagnosis has evolved as a tool for detecting this novel coronavirus ( table ) . molecular-based approaches are the first-line methods to confirm suspected cases. nucleic acid testing is the main technique for laboratory diagnosis. as with other emerging viruses, the development of methods to detect antibodies and viral antigens began after identification of the viral genome. in fact, the genomic sequence of sars-cov- was released to public databases on january , (genbank accession no. mn ), which facilitated the development of standardized laboratory pcr protocols for covid- in january of [ ] . this was followed by the launch of a range of commercial sars-cov- pcr-based assays in the last months [ ] [ ] [ ] [ ] [ ] [ ] [ ] . following entry of the virus into the host cell, viral genomic rna is released and translated into viral polymerase proteins. in this process, subgenomic (−) rnas are synthesized and used as a template to form subgenomic (+) messenger rnas (mrnas). the nucleocapsid (n) structural protein and viral rna are replicated, transcribed, and synthesized in the cytoplasm, whereas other viral structural proteins, including the s protein, membrane (m) protein and envelope (e) protein, are transcribed and then translated in the endoplasmic reticulum (er). the resulting structural proteins are further assembled into the nucleocapsid and viral envelope at the er-golgi intermediate compartment (ergic) to form a mature virion, followed by release of the nascent virion from the host cell. antigen-detection low complexity; rapid; easy to perform best used to identify acute or early infection; more prone to false negatives [ , , [ ] [ ] [ ] [ ] reverse transcription quantitative pcr (rt-qpcr) is the most common and straightforward method for the detection of sars-cov- owing to its advantages as a specific, sensitive and simple quantitative assay, which greatly helps in the diagnosis of early infection. as of may , a total of rt-qpcr tests to detect sars-cov- have been approved in china by the national medical products administration (nmpa) [ ] . although rt-qpcr assays using respiratory samples provided sensitive and specific diagnostic tests at the initial phase of the outbreak, these rt-qpcr test kits have many limitations [ ] . for example, this method is not efficient in rapidly screening a large number of individuals in places where thousands of people transit per hour. in addition, the performance of rt-qpcr depends on many factors, such as the sample type, stage of infection, skill of sample collection, and quality and consistency of the pcr assay being used [ , ] . these problems lead to a noteworthy delay in early diagnosis and subsequent management and pose a serious challenge to providing timely life-support treatment and preventive quarantine. notably, another powerful and promising tool involves clustered regularly interspaced short palindromic repeats (crispr) technology, which is being quickly deployed in the molecular diagnostics landscape. on may , sherlock biosciences received emergency use authorization (eua) from the us food and drug administration for its sherlock™ crispr sars-cov- kit for detection of the virus that causes covid- . based on the sherlock (specific high-sensitivity enzymatic reporter unlocking) method, the kit works by programming a crispr molecule to detect the presence of a specific genetic signature for sars-cov- [ ] . if the signature is found, the crispr enzyme generates a fluorescent glow. furthermore, mammoth biosciences has developed a rapid (< min), easy-to-implement and accurate crispr-based assay for the detection of sars-cov- from respiratory swab rna extracts called the sars-cov- dna endonuclease-targeted crispr trans reporter (detectr) [ ] . crispr-based diagnosis methods benefit from high sensitivity and specificity with efficiency and no requirement for elaborate instrumentation. as the assay uses similar specimen collection and nucleic acid extraction methods as the cdc and other rt-qpcr assays, it is subjected to the same potential limitations with regard to the availability of personal protective equipment, extraction kits and reagents. therefore, many clinicians have proposed that computed tomography (ct) scans should be a necessary auxiliary diagnostic method [ ] [ ] [ ] [ ] [ ] . to identify and quarantine patients at an early date, patients clinically diagnosed by chest ct with typical ground-glass lung opacities were also counted as confirmed cases beginning in early february [ ] [ ] [ ] [ ] . however, ct scans also have some shortcomings, such as the hysteresis of abnormal ct imaging and indistinguishability from other viral pneumonia presentations. accordingly, a combination of chest ct scans and repeated rt-qpcr tests may be helpful for individuals with a high clinical suspicion of sars-cov- infection but who are negative by rt-qpcr screening. compared to the currently used nucleic acid detection and ct scans, other methods, such as virus antigen or serological antibody testing, are advantageous with fast turn-around times, high throughput and reduced workload for the detection of novel coronavirus infection. currently, immunological identification technologies (point-of-care testing (poct) of igm/igg and enzyme-linked immunosorbent assay (elisa)) kits for sars-cov- have become available, with detection rates higher than those of nucleic acid detection approaches. one type of rapid diagnostic test based on host antibody detection has become available more recently [ ] [ ] [ ] [ ] . antibodies are produced over days to weeks after infection with the virus. antibody testing is easy to administer and only requires minimal training. it may be helpful as a complement to nucleic acid testing for the diagnosis of suspected covid- cases with negative rt-qpcr results as well as for the identification of asymptomatic infections [ ] . confirming suspected cases as early as possible with the benefit of antibody testing might reduce exposure to risk factors during repeated sampling and save valuable rt-qpcr tests. due to urgency and demand, many antibody test reagents are rapidly being developed and made available on the market to assist in the diagnosis of sars-cov- infection, including kits for testing total abs, igm antibody or igg antibody, by chemiluminescence, elisa or colloidal gold methods. on march , an anti-sars-cov- antibody test kit based on chemiluminescent particle immunoassay jointly developed by our team and beijing wantai biological pharmacy enterprise co., ltd. was approved for listing by the state drug administration for emergency approval and is the best performing commercial kit according to the latest who validation data [ ] . the kit is based on the double-antigen sandwich principle that detects total antibodies (including igm, igg, iga and other antibody types). specific testing for sars-cov- has great significance for public health and clinical practice, and evidence from studies further demonstrate that rt-qpcr detection combined with serological testing enhances diagnosis sensitivity while maintaining high specificity [ ] . another type of rapid diagnostic test (rdt) that detects the presence of viral antigens expressed by sars-cov- virus in a respiratory tract sample is of low complexity and may provide results typically within minutes [ , ] . the antigen(s) detected are expressed only when the virus is actively replicating; thus, such tests are best used to identify acute or early infection. monoclonal antibodies (mabs) against the nucleocapsid protein of sars-cov- have been developed and might constitute the basis of a future rapid antigen detection test. as of the time of this review, at least antigen-detection rdts were under evaluation (https://www.finddx.org/covid- / sarscov -eval-immuno/), though not all are ce marking approved or widely available. to date, there are no specific antiviral therapies or vaccines for covid- available for human use. given the urgency of treating these patients, rather than taking months to years to develop and test compounds from scratch, researchers are seeking to repurpose drugs that are already approved for other diseases and have acceptable safety profiles. small-molecule agents approved for other human diseases can exert their antiviral effect through multiple mechanisms, including blocking viral entry, inhibiting a virally encoded enzyme, targeting a host factor required for replication, or blocking virus particle formation [ ] . notably, some antivirals and antimalarials have shown promising abilities to treat patients and reduce the danger of covid- ( figure , table ). remdesivir (gs- ) is a nucleotide analog prodrug that shuts down viral replication by inhibiting a key viral enzyme, rna polymerase. a recent study reported that remdesivir potently blocks sars-cov- infection (ec = . μm) in vero e cells [ ] , and the first patient with confirmed sars-cov- infection in the united states recovered after receiving intravenous remdesivir in january [ ] . on april , a study reported clinical outcomes for compassionate use of remdesivir in a small cohort of patients with severe covid- . specifically, clinical improvement was observed in of patients ( %) [ ] . however, a trial (clinicaltrials.gov: nct ) found that compared with placebo, intravenous remdesivir did not provide significant clinical or antiviral effects in patients with serious covid- . ongoing trials with larger sample sizes will provide information on the efficacy of remdesivir for covid- [ ] . on may , the us food and drug administration granted emergency use authorization for remdesivir to treat covid- in adults and children hospitalized with severe disease. chloroquine (cq), a -aminoquinoline that is a widely used antimalarial and autoimmune disease drug, has recently been reported as a potential broad-spectrum antiviral drug [ ] . cq inhibits virus infection by increasing the endosomal ph required for virus/cell fusion, and a recent study reported its activity against covid- (ec = . μm) in vero e cells [ , ] . patients with covid- are being recruited in randomized trials (e.g., clinicaltrials.gov: nct , nct ) to determine the safety and efficacy of cq. although a few clinical trials have suggested some beneficial effects of cq for covid- , most of the reported data are preliminary [ , ] . furthermore, it is likely that the risk of adverse reactions to cq will hamper the successful treatment of patients with covid- . hydroxychloroquine (hcq), which exhibits an antiviral effect highly similar to that of chloroquine, might be a better therapeutic approach. studies have indicated that cq shows antagonism against sars-cov- in vitro. chen et al. partially confirmed the potential of hcq in patients with covid- (clinicaltrials.gov: chictr ) [ ] . although positive results from small studies have been reported for hydroxychloroquine, accumulating trial and observational evidence has prompted skepticism regarding whether there are any meaningful clinical benefits for patients with covid- . indeed, a study from france did not support the use of hcq in patients hospitalized with covid- who require oxygen [ ] . additionally, a randomized clinical trial (clinicaltrials.gov: chictr ) from china shows that hospitalized patients with mild to moderate persistent covid- who received hcq did not eliminate the virus more quickly than those receiving standard care. moreover, adverse events were higher among hcq recipients than nonrecipients [ ] . nonetheless, randomized clinical trials are needed to provide definitive causal evidence while offering an opportunity to continuously optimize the treatment plan. the lopinavir-ritonavir combination, which targets an enzyme that cleaves a long protein chain during the assembly of new viruses, can inhibit hiv protease [ , ] . the combination has been evaluated in patients with sars and mers, though the results are ambiguous [ ] [ ] [ ] [ ] . clinical trials (e.g., clinicaltrials.gov: nct , nct ) with covid- have been initiated to test the potency of the combination. recently, a randomized, controlled, open-label trial (clinicaltrials.gov: chictr ) involving patients with covid- was initiated, but no benefit beyond standard care was observed with lopinavir-ritonavir treatment. future trials including patients with severe illness may help to confirm or exclude the possibility of a treatment benefit. favipiravir (t- ), a purine nucleic acid analog approved for the treatment of influenza, can effectively inhibit the rna-dependent rna polymerase (rdrp) of rna viruses such as influenza, ebola and norovirus [ ] . studies in vero e cells have suggested that favipiravir can cripple the sars-cov- virus (ec = . μm) [ ] , and patients with covid- are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., clinicaltrials.gov: chictr , chictr ). camostat mesylate is a potent serine protease inhibitor that has been used primarily to treat pancreatitis and some types of cancer [ ] . sars-cov- uses ace for entry and the serine protease tmprss for s protein priming. utilizing research on sars-cov and the closely related sars-cov- cell entry mechanism, it has been demonstrated that camostat mesylate can block sars-cov- infection of lung cells [ ] . patients with covid- are being recruited in randomized trials (clinicaltrials.gov: nct , nct ) to determine whether this drug reduces sars-cov- viral load in early covid- disease. the antibody-mediated humoral response plays crucial roles in controlling viral infection. nabs, which can reduce viral infectivity by binding to the surface epitopes of viral particles and thereby blocking entry of the virus into host cells, are a promising approach to prevent and treat virus infection. passive antibody therapy, through transfusion of convalescent plasma from patients who have recovered from viral infections, can also be used as a treatment. importantly, this therapy offers the only short-term strategy of conferring immediate immunity to infected patients. the antibodies present in convalescent plasma can specifically bind to a given pathogen (e.g., an infectious virus), directly neutralizing its infectivity. other antibody-mediated pathways, such as antibody-dependent cellular cytotoxicity, complement activation, and/or phagocytosis, may also contribute to their therapeutic effect. there are numerous examples in which convalescent plasma therapy has been successfully applied to treat patients, as follows: sars; mers; h n (pandemic influenza a); h n (avian influenza a); several hemorrhagic fevers, such as ebola; and other viral infections [ ] [ ] [ ] [ ] [ ] . as no specific therapeutic agents or vaccines are available for covid- , this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as sars-cov- infection [ , ] . shen et al reported findings from a preliminary study of severely ill patients with covid- who were given plasma from recovered individuals [ ] . in this case series, the clinical status of all patients improved by approximately days after transfusion. in addition, the patients' specific nab titers increased following the transfusion, and respiratory samples became negative within days. although the limited case size and study design preclude a definitive statement about the potential efficacy of this treatment, the results provide some evidence to support the possibility of evaluating this therapy in more rigorous investigations involving patients with covid- . moreover, sophisticated technologies are devoted to identifying strongly neutralizing mabs that can be produced in large quantities. in coronaviruses, the viral component most frequently targeted by nabs is the surface-located envelope s protein [ ] [ ] [ ] . to this end, several potently neutralizing human mabs against sars-cov- have been developed using various approaches, including single-cell culturing methods of memory b cells isolated from sars-cov- patients, fusing b cells with an appropriate partner to produce hybridomas, selection of antibodies from phage-display libraries of human antibody fragments, and hybridoma fusion of b cells from immunized transgenic mice encoding human variable immunoglobulin domains [ ] [ ] [ ] [ ] [ ] . all of these antibodies were selected based on their in vitro neutralizing capacity, and most of them target the sars-cov- rbd. ju et al. isolated mabs specific for the sars-cov- rbd derived from single b cells of eight sars-cov- -infected individuals [ ] . using bioinformatic and biologic characterization, several mabs with potent binding and neutralizing activity against pseudovirus encoding the s protein and live sars-cov- have been identified. in particular, the most potent antibodies, p b- f and p c- f , out-competed ace with close to % efficiency, indicating that blocking the rbd and ace interaction is a useful surrogate for antibody neutralization. the results indicate that the humoral immune response is viral species specific and diverse and can produce potent nabs. wu et al. isolated mabs specific to sars-cov- rbd from a convalescent patient [ ] , and these antibodies effectively neutralized the sars-cov- , with two of them exhibiting additive inhibition effects. moreover, a therapeutic study in a mouse model validated that these antibodies can reduce virus titers in infected lungs. these antibodies will serve as the most promising candidates for the development of prophylactic and therapeutic interventions against sars-cov- . cd -spike protein, a receptor on host cells, is a novel route for sars-cov- invasion [ ] . meplazumab, an anti-cd antibody, effectively inhibited sars-cov- replication and virus-induced cytopathic effects in vero e cells; it also blocks cd , the receptor of the proinflammatory factor cypa, thus attenuating inflammation [ , ] . based on this evidence, the team designed an open-label, concurrent controlled trial (nct ) to assess the efficacy and safety of meplazumab in patients with covid- pneumonia. the data demonstrated that meplazumab efficiently improved the recovery of the patients, with a favorable safety profile. however, the results were limited by the absence of a parallel control and a small sample size. therefore, confirmation from a larger scale and randomized, double-blind trial is required to fully assess the efficacy of meplazumab in patients with covid- pneumonia. the s proteins of sars-cov- and sars-cov, which are structurally very similar, have an amino acid sequence identity of approximately % and commonly bind ace as a host receptor [ ] [ ] [ ] . to reduce the time that is required to develop sars-cov- -neutralizing antibodies de novo, researchers have assessed available sars-cov antibodies for cross-neutralization of sars-cov- , given the high degree of sequence similarity. for example, a sars-cov rbd-specific human nab (cr ) previously isolated from a convalescent sars patient is able to bind the sars-cov- rbd with high affinity (kd of . nm) and recognize an epitope on the rbd that does not overlap with the ace -binding site [ ] . however, cr does not neutralize sars-cov- in vitro, and it is possible that this epitope can confer in vivo protection [ ] . further studies will require suitable animal models, which have yet to be established. another anti-sars-cov antibody, d , was isolated from transgenic h l mice encoding the human immunoglobulin variable regions to generate antibodies that neutralize sars-cov- (and sars-cov). d binds a conserved epitope on the spike rbd, explaining its ability to cross-neutralize sars-cov and sars-cov- , with diverse mechanisms of action that are independent of receptor binding inhibition [ ] . this antibody offers potential for the prevention and treatment of covid- . although antibodies are generally beneficial and protective, in rare cases, pathogen-specific antibodies could promote pathology, resulting in a phenomenon known as antibody-dependent enhancement (ade) [ , ] . the ade phenomenon is documented for dengue virus and other viruses [ , ] . however, the neutralizing antibodies can be engineered of fc region with molecular precision to avoid the potential ade. vaccination can be used to prevent infection or to reduce disease severity, viral shedding and thereby transmission, thus helping to control sars-cov- outbreaks. multiple strategies have been employed to generate sars-cov- vaccines, including dna-and rna-based vaccines, viral vector vaccines, inactivated virus vaccines, live-attenuated virus vaccines and recombinant protein vaccines (figure ) . according to reports from the who, there are more than vaccines against sars-cov- at various stages of development. specifically, ten candidate vaccines are already in clinical evaluation ( table ) . mrna vaccines are an emerging new vaccine modality in which patients are treated with mrna oligonucleotides that encode either an antigen of interest or an antigen as well as its viral replication machinery [ ] . the potential advantages of the mrna approach to prophylactic vaccines include the ability to mimic natural infection to stimulate a more potent immune response, combining multiple mrnas into a single vaccine, rapid discovery to respond to emerging pandemic threats and manufacturing agility derived from the platform nature of mrna vaccine design and production [ ] . mrna vaccines have elicited potent immunity against infectious disease targets in animal models of infection with influenza virus, zika virus, rabies virus and others, especially in recent years, using lipid-encapsulated or naked forms of sequence-optimized mrna [ ] [ ] [ ] [ ] . after two doses, mrna- elicited neutralizing antibody titer levels at or above the levels in convalescent sera in all initial participants. to continue progress on this potential vaccine during the ongoing global public health emergency, moderna intends to work with the fda and other government and nongovernment organizations to be ready for phase and any subsequent trials, which are anticipated to include a large number of subjects and will seek to generate additional safety and immunogenicity data. furthermore, biontech and pfizer are jointly developing another mrna vaccine (bnt ), which has been approved for a phase / clinical trial to determine the optimal dose for further studies as well as to evaluate the safety and immunogenicity of the vaccine. the trial is the first clinical trial of a covid- vaccine candidate to start in germany and is part of a global development program. dna vaccines are appropriate for emerging infectious diseases because they allow for the rapid design of multiple candidates for novel antigens [ ] . in addition, they are directly injected or otherwise inoculated into recipients. recently, various dna vaccine platforms have been developed to improve the efficacy of vaccines by using electroporation (ep) to deliver plasmids and adding adjuvants to enhance immune responses. inovio pharmaceuticals was the first to advance its vaccine (ino- ) against mers-cov [ ] , a related coronavirus, into evaluation in humans, and this company has developed a dna vaccine (ino- ) to prevent infection by sars-cov- . ino- induces t cell activation by delivering dna plasmids that express the sars-cov- s protein. the effects based on measuring functional antibodies and antigen-specific t cell responses in multiple animal models are particularly encouraging [ ] . inovio has also initiated an open-label trial (nct ) to evaluate the safety, tolerability and immunological profile of ino- administered by intradermal (id) injection followed by ep using a cellectra® device in healthy adult volunteers. viral vector vaccines, which function as viral gene expression and delivery systems, rely on a host viral genome, and an unrelated viral genome lacking packaging elements is engineered to encode antigenic components of the virus of interest to elicit an immune response. because viral vector vaccines persist in the host as genetic material, they directly infect antigen-presenting cells and have strong immunogenicity, efficiently inducing b cell-and t cell-mediated immune responses. furthermore, viral vector vaccines can result in high-titer nabs. several different virus vectors have been developed as sars-cov- vaccines. cansinobio and the beijing institute of biotechnology (bib) have collaborated to develop an adenovirus type vector-based novel coronavirus vaccine ("ad -ncov") that encodes the full-length s protein of sars-cov- . ad -ncov protects against sars-cov- infection by relying on a recombinant replication-defective human adenovirus type- vector to induce the immune response. the vaccine candidate is built upon cansinobio's adenovirus-based viral vector vaccine technology platform, which has also been successfully applied to develop a globally innovative vaccine against ebola virus infection. the results from preclinical studies of ad -ncov show that the vaccine candidate can induce a strong immune response in animal models, and preclinical animal safety studies demonstrate a good safety profile. this is currently the first novel coronavirus vaccine for covid- that has progressed to this stage in china. a first-in-human trial showed that the ad -ncov vaccine is tolerable and immunogenic in healthy adults [ ] , with specific humoral responses against sars-cov- peaking at day postvaccination and rapid specific t-cell responses noted at day . there is potential for further investigation of the ad -ncov vaccine for the control of the covid- outbreak. furthermore, university of oxford researchers have begun testing a new covid- vaccine called chadox ncov- ; it is derived from a virus (chadox ) that is an attenuated version of a common cold virus (adenovirus) causing infections in chimpanzees, but it has been genetically modified such that it is unable to proliferate in humans. the vaccine is based on an adenovirus vector (chadox ) and the sars-cov- s protein. the results showed that a single vaccination with chadox ncov- is effective for preventing lung damage upon high-dose challenge with sars-cov- ; however, all of the monkeys vaccinated with chadox ncov- became infected when challenged, and there was no difference in the amount of viral rna detected from nasal secretions in the vaccinated and unvaccinated monkeys [ ] . as of may , more than , volunteers participated in the trial, which aims to assess whether healthy people can be protected from covid- . it will also provide valuable information on the safety aspects of the vaccine and its ability to generate good immune responses against the virus. in addition to adenovirus, our team and the university of hong kong have used influenza virus vectors for the development of candidate sars-cov- vaccines that are in preclinical phases. inactivated virus vaccines use chemicals (such as formalin, β-propiolactone and diethylpyrocarbonate) or heat to render the viral genome noninfectious while maintaining the virion structure, thus preserving antigenicity but eliminating the potential to cause productive infection. thus, in theory, inactivated virus vaccines are easily prepared and antigenically similar to live viruses. such vaccines have been found to be effective and safe for the prevention of diseases caused by viruses such as poliovirus and influenza virus [ , ] [ ] . other vaccine approaches include liveattenuated vaccines that are produced by reducing or eliminating the virulence of a live virus, typically using chemical-driven or site-directed mutagenesis. thus, the virus is capable of productive infection, but the resulting disease is either diminished or eliminated. live-attenuated vaccines can elicit both innate and adaptive immune responses, and protection can be life-long. additionally, their production is inexpensive. codagenix and the serum institute of india are using viral deoptimization to synthesize "rationally designed", live-attenuated vaccines against the emergent coronavirus. recombinant-protein-based vaccines are advantageous over other types of vaccines in that they are safe and have few side effects, inducing the immune system without the introduction of infectious viruses. one example is the nvx-cov vaccine developed by novavax, which is in the clinical stage [ ] . it was created using recombinant nanoparticle technology to generate antigen derived from the s protein and contains matrix-m™ adjuvant to enhance the immune response and stimulate high levels of neutralizing antibodies. a trial of clover's s-trimer vaccine developed by clover biopharmaceuticals will be recruiting healthy adults in australia, and this vaccine will be widely available upon confirmation of its safety and efficacy. in addition, lv-smenp-dc and pathogen-specific aapc vaccines from shenzhen geno-immune medical institute are in phase clinical trials to evaluate safety and immune reactivity [ , ]. despite tremendous efforts to prevent the spread of sars-cov- worldwide, the high mortality and person-to-person transmission pose a significant threat to global public health. diagnostics are important for dealing with virus outbreaks because they can enable healthcare workers to direct efforts to patients with covid- . remarkably, various diagnostic kits to test for covid- are available. several drugs have demonstrated in vitro activity against the sars-cov- virus or potential clinical benefits in observational or small, nonrandomized studies. additionally, researchers are evaluating several different technologies, and more than vaccines are under development against sars-cov- worldwide. specifically, ten candidate vaccines have already been administered to volunteers in safety trials; others have started testing in animals. however, as the development of vaccines for human use can take years, their development will likely come too late to impact the first wave of the pandemic. these challenges will remain in the long term. clearly, there is an urgent need for effective antiviral therapy and vaccines for this emerging global threat. there are a series of patient-associated and virologic factors that pose major clinical challenges to the development of anti-sars-cov- drugs. sars-cov- is a virus with diversity that becomes mutated, and novel sars-cov- mutants are likely to emerge repeatedly at unpredictable times [ , ] . therefore, most drugs that specifically target the existing sars-cov- may not be effective against a mutant sars-cov- . the lag time between mutant emergence and the development of new prophylactic treatments is of concern. thus, there is an urgent need for the development of new, broad-spectrum drugs that target conserved sites to prepare for future outbreaks involving mutants. recent studies have reported that lipopeptide ek c shows exceptional promise to be developed as the first pan-cov fusion inhibitor-based antiviral therapeutic or prophylactic for treatment or prevention of infection by the currently circulating sars-cov- and mutants or emerging sars-related covs [ ] [ ] [ ] . in addition, combining the advanced knowledge of bioinformatics and immunology to screen and confirm the conserved dominant epitopes of sars-cov- , it will be helpful to develop therapeutic antibodies with broadspectrum neutralization activity and vaccines that can induce a broad-spectrum antiviral immune response. currently, there are a limited number of animal models available for infections caused by sars-cov- . normally, antiviral therapy or vaccines enter into human trials after tests for safety and effectiveness in appropriate animal models. however, the virus does not grow in wild-type mice and induces only mild disease in transgenic animals expressing human ace [ , ] . the limited availability of mouseadapted virus strains and ace transgenic mice remains a major obstacle to testing anti-sars-cov- drugs or vaccines. other potential animal models include ferrets and nonhuman primates (nhps), for which pathogenicity studies are ongoing. in addition, understanding how the immune system interacts with the pathogen and the vaccine itself is crucial for avoiding pitfalls, such as ade phenomenon, a process in which a virus leverages antibodies to promote infection. the viral load curve of covid- is similar to that of influenza, and the viral load is very high at the time of presentation [ , ] . experience from the treatment of influenza patients, in this case of high-viral load patients, suggested that the combination of multiple antiviral drugs is more effective than single drug treatments [ ] [ ] [ ] . indeed, the combination of appropriate antiviral drugs might rapidly suppress the high initial viral load, improve the clinical parameters, and reduce the risk to medical staff by controlling the spread of the virus. a multicenter randomized open-label phase trial (chictr ) showed that triple antiviral therapy with interferon beta- b, lopinavir-ritonavir, and ribavirin was safe and superior to lopinavirritonavir alone in alleviating symptoms, suppressing shedding of sars-cov- , and facilitating discharge of patients with mild to moderate covid- [ ] . there are also many other studies investigating combination therapy; these smaller clinical studies examining virologic endpoints may be sufficient to identify which combinations can be used for large studies in risk groups or hospitalized patients. for combinations involving immunomodulatory interventions, the challenges may be great because the goal is disease amelioration by regulating the host complex responses. regardless, it is certain that as our continuous in-depth understanding of the immune response dynamics and the disease pathogenesis of sars-cov- deepens, combination therapy involving immunomodulation, vaccines or other immunotherapies will have great potential. the outbreak has emphasized the urgent need for renewed efforts to develop specific antiviral therapies or vaccines to combat sars-cov- . we need well-developed emergency plans that allow us to develop, test, produce, and distribute agents or vaccines as quickly as possible. such endeavors would require tight coordination among governments, regulatory agencies, pharmaceutical companies, and the who, as well as novel approaches and clinical trial design. a pneumonia outbreak associated with a new coronavirus of probable bat origin a new coronavirus associated with human respiratory disease in china a novel coronavirus from patients with pneumonia in china coronaviridae study group of the international committee on taxonomy of v. the species severe acute respiratory syndrome-related coronavirus: classifying -ncov and naming it sars-cov- clinical features of patients infected with novel coronavirus in wuhan pathological findings of covid- associated with acute respiratory distress syndrome clinical features of covid- clinical characteristics of asymptomatic and symptomatic patients with mild covid- coronavirus pathogenesis and the emerging pathogen severe acute respiratory syndrome coronavirus coronavirus diversity, phylogeny and interspecies jumping properties of coronavirus and sars-cov- genetic recombination, and pathogenesis of coronaviruses molecular evolution of human coronavirus genomes identification of a novel coronavirus in patients with severe acute respiratory syndrome a novel coronavirus associated with severe acute respiratory syndrome description and clinical treatment of an early outbreak of severe acute respiratory syndrome (sars) in guangzhou, pr china isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome coronavirus: what do we know? sars and mers: recent insights into emerging coronaviruses summary of probable sars cases with onset of illness from therapeutic options for the novel coronavirus ( -ncov) structure, function, and antigenicity of the sars-cov- spike glycoprotein genomic characterisation and epidemiology of novel coronavirus: implications for virus origins and receptor binding the spike protein of sars-cov--a target for vaccine and therapeutic development mers-cov spike protein: a key target for antivirals sars-cov- pandemic and research gaps: understanding sars-cov- interaction with the ace receptor and implications for therapy sars-cov- cell entry depends on ace and tmprss and is blocked by a clinically proven protease inhibitor characterization of spike glycoprotein of sars-cov- on virus entry and its immune cross-reactivity with sars-cov characterization of the receptor-binding domain (rbd) of novel coronavirus: implication for development of rbd protein as a viral attachment inhibitor and vaccine functional assessment of cell entry and receptor usage for sars-cov- and other lineage b betacoronaviruses emerging coronaviruses: genome structure, replication, and pathogenesis coronavirus infection, er stress, apoptosis and innate immunity structure of the sars-cov- spike receptor-binding domain bound to the ace receptor bioengineering tools to speed up the discovery and preclinical testing of vaccines for sars-cov- and therapeutic agents for covid- comparative review of respiratory diseases caused by coronaviruses and influenza a viruses during epidemic season detection of novel coronavirus ( -ncov) by real-time rt-pcr laboratory readiness and response for novel coronavirus ( -ncov) in expert laboratories in eu/eea countries molecular diagnosis of a novel coronavirus ( -ncov) causing an outbreak of pneumonia improved molecular diagnosis of covid- by the novel, highly sensitive and specific covid- -rdrp/hel real-time reverse transcription-pcr assay validated in vitro and with clinical specimens positive rt-pcr test results in patients recovered from covid- epidemiologic features and clinical course of patients infected with sars-cov- in singapore coronavirus and the race to distribute reliable diagnostics primer design for quantitative real-time pcr for the emerging coronavirus sars-cov- correlation of chest ct and rt-pcr testing in coronavirus disease (covid- ) in china: a report of cases sars-cov- viral load in upper respiratory specimens of infected patients a familial cluster of pneumonia associated with the novel coronavirus indicating person-to-person transmission: a study of a family cluster multiplexed and portable nucleic acid detection platform with cas , cas a, and csm crispr-cas -based detection of sars-cov- ct scans of patients with novel coronavirus (covid- ) pneumonia ct quantification of pneumonia lesions in early days predicts progression to severe illness in a cohort of covid- patients multicenter cohort study demonstrates more consolidation in upper lungs on initial ct increases the risk of adverse clinical outcome in covid- patients association of clinical and radiographic findings with the outcomes of patients with covid- in wuhan risk factors for adverse clinical outcomes with covid- in china: a multicenter, retrospective, observational study patients with rt-pcr-confirmed covid- and normal chest ct chest ct findings in coronavirus disease- (covid- ): relationship to duration of infection time course of lung changes on chest ct during recovery from novel coronavirus (covid- ) pneumonia clinical characteristics of hospitalized patients with novel coronavirus-infected pneumonia in wuhan fast, portable tests come online to curb coronavirus pandemic molecular and serological investigation of -ncov infected patients: implication of multiple shedding routes antibody responses to sars-cov- in patients of novel coronavirus disease development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis developing antibody tests for sars-cov- temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov- : an observational cohort study fast, portable tests come online to curb coronavirus pandemic towards effective diagnostic assays for covid- : a review diagnosing covid- : the disease and tools for detection ct screening for early diagnosis of sars-cov- infection false negative chest x-rays in patients affected by covid- pneumonia and corresponding chest ct findings molecular immune pathogenesis and diagnosis of covid- evaluation of a high-speed but low-throughput rt-qpcr system for sars-cov- detection combination of rt-qpcr testing and clinical features for diagnosis of covid- facilitates management of sars-cov- outbreak the crispr tool kit for genome editing and beyond sars-cov- detection with crispr diagnostics development of crispr as an antiviral strategy to combat sars-cov- and influenza development and clinical application of a rapid igm-igg combined antibody test for sars-cov- infection diagnosis antibody responses to sars-cov- in patients with covid- comparing the analytical performance of three sars-cov- molecular diagnostic assays antibody detection and dynamic characteristics in patients with covid- rapid detection and monitoring of human coronavirus infections immunofluorescence assay for detection of the nucleocapsid antigen of the severe acute respiratory syndrome (sars)-associated coronavirus in cells derived from throat wash samples of patients with sars a highly specific rapid antigen detection assay for on-site diagnosis of mers diagnosis of acute respiratory syndrome coronavirus infection by detection of nucleocapsid protein. medrxiv coronaviruses -drug discovery and therapeutic options remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus ( -ncov) in vitro first case of novel coronavirus in the united states compassionate use of remdesivir for patients with severe covid- remdesivir in adults with severe covid- : a randomised, double-blind, placebo-controlled, multicentre trial effects of chloroquine on viral infections: an old drug against today's diseases? efficacy of hydroxychloroquine in patients with covid- : results of a randomized clinical trial breakthrough: chloroquine phosphate has shown apparent efficacy in treatment of covid- associated pneumonia in clinical studies treating covid- with chloroquine hydroxychloroquine and azithromycin as a treatment of covid- : results of an open-label non-randomized clinical trial clinical efficacy of hydroxychloroquine in patients with covid- pneumonia who require oxygen: observational comparative study using routine care data hydroxychloroquine in patients with mainly mild to moderate coronavirus disease : open label, randomised controlled trial comparative efficacy and safety of second-line antiretroviral therapy for treatment of hiv/aids: a systematic review and network meta-analysis optimizing use of theranostic nanoparticles as a life-saving strategy for treating covid- patients comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings consideration of highly active antiretroviral therapy in the prevention and treatment of severe acute respiratory syndrome screening of an fda-approved compound library identifies four small-molecule inhibitors of middle east respiratory syndrome coronavirus replication in cell culture favipiravir (t- ), a broad spectrum inhibitor of viral rna polymerase a phase / trial to evaluate the pharmacokinetics, safety, and efficacy of ni- in patients with chronic pancreatitis: study protocol for a randomized controlled trial on the assessment of camostat treatment in chronic pancreatitis (tactic) experimental drugs poised for use in ebola outbreak mechanism of inhibition of ebola virus rna-dependent rna polymerase by remdesivir chloroquine is a potent inhibitor of sars coronavirus infection and spread sars-cov- : recent reports on antiviral therapies based on lopinavir/ritonavir, darunavir/umifenovir, hydroxychloroquine, remdesivir, favipiravir and other drugs for the treatment of the new coronavirus hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov- infection in vitro pharmacologic treatments for coronavirus disease (covid- ): a review experimental treatment with favipiravir for covid- : an open-label control study. engineering (beijing) favipiravir: pharmacokinetics and concerns about clinical trials for -ncov infection effectiveness of favipiravir (t- ) against wild-type and oseltamivir-resistant influenza b virus in mice convalescent plasma for ebola virus disease treatment with convalescent plasma for influenza a (h n ) infection sars: systematic review of treatment effects feasibility of using convalescent plasma immunotherapy for mers-cov infection, saudi arabia convalescent plasma treatment reduced mortality in patients with severe pandemic influenza a (h n ) virus infection convalescent plasma to treat covid- : possibilities and challenges treatment with convalescent plasma for critically ill patients with sars-cov- infection treatment of critically ill patients with covid- with convalescent plasma perspectives on therapeutic neutralizing antibodies against the novel coronavirus sars-cov- potent neutralization of severe acute respiratory syndrome (sars) coronavirus by a human mab to s protein that blocks receptor association potent cross-reactive neutralization of sars coronavirus isolates by human monoclonal antibodies identification of human single-domain antibodies against sars-cov- a human neutralizing antibody targets the receptor binding site of sars-cov- neutralizing antibodies against sars-cov- and other human coronaviruses potent human neutralizing antibodies elicited by sars-cov- infection a noncompeting pair of human neutralizing antibodies block covid- virus binding to its receptor ace function of hab g/cd in invasion of host cells by severe acute respiratory syndrome coronavirus sars-cov- invades host cells via a novel route: cd -spike protein receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus angiotensin-converting enzyme (ace ) as a sars-cov- receptor: molecular mechanisms and potential therapeutic target angiotensin converting enzyme : sars-cov- receptor and regulator of the renin-angiotensin system a highly conserved cryptic epitope in the receptor-binding domains of sars-cov- and sars-cov potent binding of novel coronavirus spike protein by a sars coronavirus-specific human monoclonal antibody a human monoclonal antibody blocking sars-cov- infection the potential danger of suboptimal antibody responses in covid- modelling the impact of antibody-dependent enhancement on disease severity of zika virus and dengue virus sequential and co-infection antibody-dependent enhancement of virus infection and disease immune response to dengue and zika unlocking the potential of vaccines built on messenger rna mrna vaccines -a new era in vaccinology modified mrna vaccines protect against zika virus infection safety and immunogenicity of a mrna rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase clinical trial nucleoside-modified mrna immunization elicits influenza virus hemagglutinin stalk-specific antibodies moderna announces positive interim phase data for its mrna vaccine (mrna- ) against novel coronavirus. revised engineering dna vaccines against infectious diseases safety and immunogenicity of an anti-middle east respiratory syndrome coronavirus dna vaccine: a phase , open-label, single-arm, dose-escalation trial immunogenicity of a dna vaccine candidate for covid- safety, tolerability, and immunogenicity of a recombinant adenovirus type- vectored covid- vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial chadox ncov- vaccination prevents sars-cov- pneumonia in rhesus macaques safety of trivalent inactivated influenza vaccines in adults: background for pandemic influenza vaccine safety monitoring inactivated poliovirus vaccine: past and present experience safety and immunogenicity study of inactivated vaccine for prophylaxis of sars cov- infection (covid- ) novavax initiates phase / clinical trial of covid- vaccine. revised international expansion of a novel sars-cov- mutant attenuated sars-cov- variants with deletions at the s /s junction inhibition of sars-cov- (previously -ncov) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion a pan-coronavirus fusion inhibitor targeting the hr domain of human coronavirus spike fusion mechanism of -ncov and fusion inhibitors targeting hr domain in spike protein the pathogenicity of sars-cov- in hace transgenic mice pathogenesis of sars-cov- in transgenic mice expressing human angiotensin-converting enzyme . cell. in press triple combination of interferon beta- b, lopinavir-ritonavir, and ribavirin in the treatment of patients admitted to hospital with covid- : an open-label, randomised, phase trial medical treatment of viral pneumonia including sars in immunocompetent adult investigating different mechanisms of action in combination therapy for influenza international severe acute r, emerging infection c. antiviral combinations for severe influenza efficacy of clarithromycin-naproxen-oseltamivir combination in the treatment of patients hospitalized for influenza a(h n ) infection: an open-label randomized, controlled, phase iib/iii trial this work was supported by the xiamen science and technology major project the authors have declared that no competing interest exists.