cord-003490-swlkjtyo	2019	
cord-003767-9xbu4hnq	2019	The synthesis of the findings reveals a predictive virus evolution framework, based on the outerto inner-body changes in the interplay of host environment-transmission modes-organ system involvement-host cell infection cycle-virus genome. Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d . Pieced together on this basis was an outer-to inner-body line-up of viruses by organ system or combination of organ systems, guided by the one-to-four virus infiltration score, the corresponding virus organ system tropism, the matching virus transmission modes, length of the infection and shedding periods, infection severity level, and virus environmental survival rate, see Figure 3 and, also, Figure S1d .
cord-004578-x6uatd7j	2012	Although diseases such as influenza, tuberculosis and SARS are transmitted through an environmentally mediated mechanism, most modeling work on these topics is based on the concepts of infectious contact and direct transmission. In this paper we use a paradigm model to show that environmental transmission appears like direct transmission in the case where the pathogen persists little time in the environment. However, for obtaining results emerging from the first order expansion in the pathogen persistence time (e.g., the direct transmission model and its corresponding transmissibility formula) one may use the slow-fast dynamics formalism, a general technique of singular perturbation theory. In this work, we have shown using a paradigm model that direct transmission holds as an approximation for the environmental transmission mechanism in the case where the persistence time of the pathogen in the environment is short.
cord-004971-jwpb7862	2002	The home environment, particularly the kitchen and bathroom, serves as a reservoir of large numbers of microorganisms, particularly Enterobacteriacae,and infectious disease transmission has been demonstrated to occur in 6–60% of households in which one member is ill. Recent events, including widespread media coverage of foodborne outbreaks and increased marketing of a variety of antibacterial products for personal hygiene and hard surface disinfection, have resulted in a resurgence of interest and public concern about hygiene and cleanliness in the home. 17 In a study to evaluate the survival of bacteria and enteric viruses during washing and drying as performed in U.S. homes, sterile cotton swabs were inoculated with Mycobacterium fortuitum, Salmonella typhimurium, Staphylococcus aureus, E. This body of research suggests that a product containing an ingredient with disinfectant properties, such as alcohol, bleach or a phenolic, may be indicated for home use if a household member is ill with an infectious disease or in other high-risk situations.
cord-015884-mtpbzgr9	2013	The CDC, in cooperation with the Healthcare Infection Control Practices Advisory Committee (HICPAC), established Standard Precautions to address the prevention of the spread of infectious agents in healthcare settings and are the result of combining the key components from Universal Precautions and Body Substance Isolation along with the understanding that all blood and body fl uids, except sweat, are potentially infectious, and inanimate objects are potentially contaminated with infectious agents, therefore are capable of being reservoirs in the chain of transmission of infectious agents [ 11 , 12 ] . Standard Precautions group together infection prevention practices consisting of the use of Personal Protective Equipment (PPE), such as gowns, gloves, masks, goggles or face shields, and the performance of hand hygiene, washing hands with soap and water, especially when they are visibly soiled, or using an alcohol-based hand sanitizer.
cord-022103-4zk8i6qb	2017	
cord-022237-qxya4cs3	2013	The bird fits into the overall taxonomic scheme as follows: Specific pathogen-free (SPF) fertile eggs, day-old chicks, or Kingdom, Animal; Phylum, Chordata; Class, Aves; Order, 27 started pullets are available for use in research. A clear outline of the gen-free chickens or eggs come from breeding stock negative avian orders listing the common names of birds in each may be to diseases caused by mycoplasmas, Newcastle disease, infecfound in Steiner and Davis (1981) . Chickens, turkeys, and other birds require the six major nu trients: carbohydrates for energy, fats for energy and essential fatty acids, protein for meat and egg production, minerals for bones and shells, vitamins for chemical catalysts, and water. Fowl cholera, an acute septicémie disease of poultry, turkeys, waterfowl, and wild birds, is caused by Pasteurella multocida, a gram-negative, bipolar rod (Panigraphy and Glass, 1982) . Herpesvirus of turkeys (HVT) Marek''s vaccine should be administered to all birds at 1 day of age to prevent the disease.
cord-219107-klpmipaj	2020	For community transmission scenarios, our results demonstrate that mobility data adds the most value to risk predictions when case counts are low and spatially clustered. In each case, we use the Facebook mobility data that was available during the early stages of the outbreak to estimate future spatial patterns of relative transmission risk. For each of the three outbreak scenarios, we present the mobility-based estimates of the relative transmission risk distribution, and a time-varying correlation between our estimate and the case numbers ascertained through contact tracing and testing programs. Our results indicate that aggregate mobility data can be a useful tool in estimation of COVID-19 transmission risk diffusion from locations where active cases have been identified. A heat map (Supplemental Figure S1 ) of the average number of Facebook users present during the nighttime period (2am to 10am) as a proportion of the estimated resident population reported by the ABS (2018 [32] ) shows qualitative similarity to the spatial distributions of active cases and relative risk shown in Figure 5 
cord-245161-xbw72k4m	2020	Contaminated objects or surfaces, referred to as fomites, play a critical role in the spread of viruses, including SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Elucidating the physicochemical processes and surface science underlying the adsorption and transfer of virus between surfaces, as well as their inactivation, are important in understanding how the disease is transmitted, and in developing effective interception strategies. Three primary transmission routes have been found to contribute to the spread of respiratory viruses (e.g., SARS-CoV-1 and -2, measles, HCoV, rhinovirus, and influenza virus) ( Figure 1A ): 1) direct contact between individuals, 2) indirect contact via contaminated objects (fomites), 3) airborne transmission via droplets and aerosols. A study on SARS-CoV-2 infected patients in isolation rooms showed contamination of high-contact surfaces such as doorknobs and bedrails, as well as air outlet fans which indicated virus transfer from aerosols to a surface.
cord-253252-s8fm5rfa	2020	This review paper intends to outline the literature concerning the transmission of viral-laden droplets and aerosols in different environmental settings and demonstrates the behavior of droplets and aerosols resulted from a cough-jet of an infected person in various confined spaces. There have been myriads of hypotheses corroborating that certain threshold levels of humidity, temperature, sunlight, and ventilation will speed up the virus-laden droplet and aerosol transmission, aggravating the spread of the SARS-CoV disease (Morawska, 2006) . Nevertheless, the effectiveness of the use of masks for the control of SARS-CoV-2-laden aerosol transmission from an infected person to a susceptible host is uncertain and not fully conceivable. Researchers have speculated that both droplets and aerosols generated from non-violent and violent expirations of SARS-CoV-2-infected people may be responsible for the nonnosocomial and nosocomial transmission of COVID-19 disease.
cord-256543-7kfi2yvu	2016	Using a comparative approach including parasites, bacteria and viruses that transmit via the fecal-oral route, the meeting aimed at identifying the key drivers of sustained human-to-human transmission after a zoonotic event, taking into account the host, the pathogen and the interface (transmission amplifiers). Enteric pathogens can be transmitted between humans by the fecal-oral route via direct contact or indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites ( Figure 1 ). After shedding from the host enteric pathogens can be transmitted between humans by the fecal-oral route via direct contact between humans, or via indirect contact via contaminated fluids, including surface water, food, and carriers such as fomites. A human reservoir for non-typhoid Salmonella (NTS) transmission of multiple serotypes was demonstrated in a study of NTS-infected patients who continued to shed NTS for months up to years, and strains of these patients acquired antimicrobial resistance genes and virulence genes that possibly affected host-pathogen interactions [34 ] .
cord-261962-sfa9d1ux	2018	In this study, we proposed a comparative analysis approach and built a model to simulate outbreaks of 3 different in‐flight infections in a similar cabin environment, that is, influenza A H1N1, severe acute respiratory syndrome (SARS) coronavirus (CoV), and norovirus. • Our identification of the dominated routes, that is the close contact route (large droplet) for influenza, the fomite route for norovirus, and all 3 routes for SARS CoV, suggested the relative importance of different environment intervention for different infectious diseases in air cabins and probably also in other indoor environments. F I G U R E 1 Spatial distribution for 3 in-flight infection outbreaks, (A) norovirus, 26 (B) SARS CoV, 27 and (C) influenza A H1N1 28 of infectious pathogens from the index source passenger, which is also sometimes termed indirect contact route.
cord-263764-2ewz8ok4	2018	We here present an overview of the available data from experimental and observational studies on the transmission routes of respiratory viruses between humans, identify knowledge gaps, and discuss how the available knowledge is currently implemented in isolation guidelines in health care settings. Our observations underscore the urgent need for new knowledge on respiratory virus transmission routes and the implementation of this knowledge in infection control guidelines to advance intervention strategies for currently circulating and newly emerging viruses and to improve public health. Increasing numbers of studies focused on the detection and quantification of influenza viruses contained in droplets and aerosols expelled into the air through breathing, sneezing and coughing of infected individuals The SARS outbreak was primarily linked to healthcare settings, with 49% of the cases linked to hospitals [71] , most probably caused by aerosol-generating procedures on severely ill patients [72, 73] .
cord-264994-j8iawzp8	2019	
cord-269505-7g8lio9l	2010	For hantavirus pulmonary syndrome, a directly transmitted zoonotic disease, correlational and experimental studies have shown that a lower diversity of small mammals increases the prevalence of hantaviruses in their hosts, thereby increasing risk to humans (Box 2). Diversity has a similar effect for plant diseases, with species losses increasing the transmission of two fungal rust pathogens that infect perennial rye grass and other plant species 10 . This is because field studies like those on West Nile virus, hantaviruses and rye grass have typically not controlled for changes in host density that can result from changes in ''species richness'' (the number of species present in a community, which is a measure of taxonomic diversity). In sum, reducing biodiversity can increase disease transmission when the lost species are either not hosts for the pathogen or are suboptimal ones. In several case studies, the species most likely to be lost from ecological communities as diversity declines are those most likely to reduce pathogen transmission.
cord-271343-0rrhiw9m	2017	Long-standing guidance by public health agencies is that the primary transmission risk associated with air travel for most respiratory infectious diseases is associated with sitting within two rows of an infectious passenger. 1,2 Many instances of in-flight transmission have been documented, including cases of cholera, 3 influenza, 4-8 measles, 9, 10 meningococcal infections, 11 norovirus, 12 severe acute respiratory syndrome (SARS), 13, 14 shigellosis, 15 and tuberculosis. Longstanding guidance by public health agencies is that the primary transmission risk associated with air travel for most respiratory infectious diseases is associated with sitting within 2 rows of an infectious passenger. In this paper we document reports of in-flight transmission of respiratory infectious diseases by large droplets for which seat plans are given. k Authors reported data on 7 flights on which 9 passengers who were seated within AE2 rows of an infectious passenger became infected.
cord-276758-k2imddzr	2007	
cord-276916-j53i5xfs	2018	Some pathogens that were previously not considered to pose a general threat to human health have emerged at regional and global scales, such as Zika and Ebola Virus Disease. During emerging infectious disease outbreaks, empirical information and mathematical modelling techniques are now commonly used to characterise and predict the spatio-temporal dynamics of the spread of pathogens. Common spatiotemporal analyses of pathogen genomes focus on mapping and predicting virus lineage exchange among locations, with the underlying aim of reconstructing the pathways of disease introduction and spread, albeit at a coarse spatial resolution, and often retrospectively [2, 8, 33, 35, 37, 38] . In the recent yellow fever outbreak in southern Brazil, linking epidemiological, spatial and genomic data and techniques could provide insights into the transmission potential and risk of urban transmission [102] .
cord-277173-zdft23q8	2012	cases rather than the uninfected, but potentially susceptible bulk of the population, they can say little about the risk factors for infection or provide estimates of transmissibility in different contexts (e.g. households, schools or as a function of distance between a susceptible and an infected individual). We present a relatively generic statistical model for the estimation of transmission risk factors, and discuss algorithms to estimate its parameters for different levels of missing data. We present a relatively generic statistical model for the estimation of transmission risk factors, and discuss algorithms to estimate its parameters for different levels of missing data. For a directly transmitted disease, the first step to estimate transmission risk factors is usually to propose a model for transmission hazard l i!j ðtjQÞ from case i to subject j on day t, i.e. define l i!j ðtjQÞ as a function of the individual covariates z i (t) and z j (t) and a set of parameters Q.
cord-277818-8w15dz20	2018	
cord-279443-2e4gz2bo	2020	
cord-279520-zccd1mq5	2004	
cord-283432-od5nnxvg	2020	We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. We believe that the use of engineering controls in public buildings, including hospitals, shops, offices, schools, kindergartens, libraries, restaurants, cruise ships, elevators, conference rooms or public transport, in parallel with effective application of other controls (including isolation and quarantine, social distancing and hand hygiene), would be an additional important measure globally to reduce the likelihood of transmission and thereby protect healthcare workers, patients and the general public. While evidence for airborne transmission of COVID-19 is currently incomplete, several hospital-based studies have performed air-sampling for SARS-COV-2, including one published paper (Ong et al.
cord-283485-xit6najq	2020	
cord-285960-1zuhilmu	2020	
cord-288303-88c6qsek	2020	Classical Susceptible-Infected-Removed model with constant transmission rate and removal rate may not capture real world dynamics of epidemic due to complex influence of multiple external factors on the spread. Local interpretations of the model using perturbation method reveals local influence of different features on transmission rate which in turn is used to generate a set of generalized global interpretations. We experimented with available data of Covid-19 across multiple regions of USA and the model achieved 7.95% and 0.19% mean absolute percent error in terms of new infection cases in each locality and cumulative total infection cases across the country in a 10-day prediction period respectively. A long-term forecast using the trained model and modified recovery rate to satisfy disease-free equilibrium criteria reveals rapid damping of active infection cases to reach the baseline. The model predicts the transmission rate for a future time period for each pixel which in turn is used to calculate daily new infection cases ∆ + ( ) using equation 11.
cord-297625-eby014gm	2014	Our study confirms that rhinovirus infectiousness is related to the viral concentration in droplets and suggests that children represent the main transmission source, which occurs only rarely via adults. We conducted a series of experiments to assess the duration of human rhinovirus infectiousness duration on fingers, as well as the impact of viral concentration on survival rates. One hour after the deposit of disrupted droplets on the fingers of the six volunteers, infectious viruses could be detected by culture in all subjects contaminated with HC droplets (6/6), in four of the six volunteers with AC droplets, and none of the six volunteers with LC droplets, which confirmed the influence of concentration on survival (Fig. 1) . Our study showed that virus survival, and therefore infectiousness, was related to the viral concentration in droplets. Potential role of hands in the spread of respiratory viral infections: studies with human parainfluenza virus 3 and rhinovirus 14
cord-299720-f0ny4ur5	2017	title: Risk Factors for Transmission of Middle East Respiratory Syndrome Coronavirus Infection During the 2015 Outbreak in South Korea Transmission heterogeneity was observed during the 2015 Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Transmission heterogeneity was a significant characteristic of the 2015 South Korean outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection [1] . Epidemiological reports from the outbreak were evaluated to collect data regarding basic demographic characteristics, medical history, MERS-CoV exposure, symptoms and their onset date(s), sampling date(s), contact history, and post-exposure infection control. In the univariate analyses, transmission was associated with underlying respiratory disease, Ct value, interval from symptom onset to diagnosis, number of contacts, and pre-isolation hospitalization or ER visits. It appears that both host infectivity and the number of contacts influenced MERS-CoV transmission, whereas super-spreading events were mostly associated with a greater likelihood of encountering other people under diverse environmental conditions.
cord-299828-fb84rtmx	2013	Despite the wealth of empirical WDM research, management outcomes can be difficult to predict because system-specific information is lacking for novel pathogens and many theoretical concepts in disease ecology (see Table 1 for a subset) have not been widely tested in the field, leading to uncertainty in their generality. Corridor vaccination can reduce disease in metapopulations; movement controls are unlikely to work for chronic infections Keeling & Eames (2005) Transmission increases with host density Host density reductions may reduce disease transmission, and density thresholds for disease persistence may exist Anderson & May (1979) Transmission increases with disease prevalence independent of host density Transmission associated with sexual interactions is more likely to cause host extinction, and non-selective culling may not reduce transmission Getz & Pickering (1983) Predation as a regulator of host population and disease We use a quantitative, case-based approach to provide a critical retrospective of WDM over the last four decades to: (i) quantify how frequently specific theoretical concepts from disease ecology have been applied in the literature, (ii) identify prevailing management objectives, groups and reported outcomes and (iii) assess taxonomic biases in WDM literature.
cord-303651-fkdep6cp	2020	
cord-304013-nzigx0k0	2020	
cord-305085-bv7udg9k	2011	
cord-306466-y4yg42p8	2020	
cord-307133-bm9z8gss	2016	Finally, we calibrated the model with the number of daily cases of severe acute respiratory syndrome (SARS) in Beijing in 2003, and the estimated parameters show that the control measures taken at that time were effective. A low level of heterogeneity results in dynamics similar to those predicted by the homogeneous-mixing model with a frequency-dependent transmission term, βSI N . The greatest difference is that at the overall level, the heterogeneity slows the transmission speed and decreases the peak sizes, which means milder disease outbreaks, because in the scenario with a high level of heterogeneity, only a small proportion of susceptible individuals have chances of coming into contact with infectious individuals and becoming infected, which results in a slower increase of the infected population. Our results show that, keeping other conditions identical, the higher is the level of heterogeneity in contact rates, the greater is the difference in the disease dynamics observed from those predicted using the homogeneous-mixing models.
cord-308089-q2w9fb0i	2005	This new germ theory is emphasizing how environments and human activities influence the characteristics of infectious agents and the broader role of infection as a cause of chronic diseases. The association between vector-borne transmission and virulence explains why diseases such as malaria, yellow fever, dengue, sleeping sickness, and visceral leishmaniasis are so severe, whereas most of the respiratory-tract pathogens of humans are relatively benign. Evolutionary management of the virulence of vector-borne diseases requires interventions that elevate the immobilization of hosts more costly to the infecting pathogens. Although sexually transmitted pathogens are molded by natural selection to be benign over the short run, this long-term persistence within hosts raises the possibility of long-term damage, even though there is low probability of severe damage during any small period of time during the first years of infection. The theoretical framework for understanding the evolution of virulence of sexually transmitted pathogens provides clues about which infectious agents are the most likely causes of these illnesses.
cord-308165-pk8d48hs	2020	
cord-311382-ioemd0ij	2019	For example, when the infectious dose (the number of infectious agents required to cause disease) of an organism is low, and where large numbers of pathogen-laden droplets are produced in crowded conditions with poor ventilation (in hospital waiting rooms, in lecture theatres, on public transport, etc.), explosive outbreaks can still occur, even with pathogens whose airborne transmission capacity is controversial, e.g. the spread of influenza in a grounded plane where multiple secondary cases were observed in the absence of any ventilation [11] . For example, tighter control of the environment may reduce or prevent airborne transmission by: 1) isolating infectious patients in a single-bed, negative pressure isolation room [25] ; 2) controlling environmental relative humidity to reduce airborne influenza survival [59] ; 3) reducing exposure from aerosols produced by patients through coughing, sneezing or breathing with the use of personal protective equipment (wearing a mask) on the patient (to reduce source emission) and/or the healthcare worker (to reduce recipient exposure) [60] ; 4) carefully controlling the use and exposure to any respiratory assist devices (high-flow oxygen masks, nebulizers) by only allowing their use in designated, containment areas or rooms [61] .
cord-314325-nquov2i0	2008	Viral disease epidemiology has come to have a major role in clarifying the etiologic role of particular viruses and viral variants as the cause of specific diseases, in improving our understanding of the overall nature of specific viral diseases, and in determining factors affecting host susceptibility and immunity, in unraveling modes of transmission, in clarifying the interaction of viruses with environmental determinants of disease, in determining the safety, efficacy, and utility of vaccines and antiviral drugs, and especially in alerting and directing disease prevention and control actions. Epidemiology is also effective in (1) clarifying the role of particular viruses and viral variants as the cause of disease, (2) clarifying the interaction of viruses with environmental determinants of disease, (3) determining factors affecting host susceptibility, (4) unraveling modes of transmission, and (5) field testing of vaccines and antiviral drugs.
cord-315744-nr0fu2qb	2020	title: Reduction of secondary transmission of SARS-CoV-2 in households by face mask use, disinfection and social distancing: a cohort study in Beijing, China Conclusion The study confirms the highest risk of transmission prior to symptom onset, and provides the first evidence of the effectiveness of mask use, disinfection and social distancing in preventing COVID-19. Conclusion The study confirms the highest risk of transmission prior to symptom onset, and provides the first evidence of the effectiveness of mask use, disinfection and social distancing in preventing COVID-19. Given epidemic growth is dominated by household transmission, 5 6 studying the use of NPIs, such as face masks, social distancing and disinfection in the household setting, may inform community epidemic control and prevent transmission of COVID-19 in households. Transmission was significantly reduced BMJ Global Health by frequent use of chlorine or ethanol based disinfectant in households and family members (including the primary case) wearing a mask at home before the primary case developed the illness (table 4) .
cord-316126-j51dik7f	2020	title: SARS-CoV-2 and Health Care Worker Protection in Low-Risk Settings: a Review of Modes of Transmission and a Novel Airborne Model Involving Inhalable Particles Since the beginning of the COVID-19 pandemic, there has been intense debate over SARS-CoV-2''s mode of transmission and appropriate personal protective equipment for health care workers in low-risk settings. This review attempts to summarize current cumulative data on SARS-CoV-2''s modes of transmission and identify gaps in research while offering preliminary answers to the question on everyone''s mind: is the airborne route significant and should we modify our COVID-19 PPE recommendations for frontline workers in low-risk settings? Given that substantial disagreement persists on the importance of natural aerosol generation by COVID-19 patients, and consequently, the necessary level of respiratory protection in non-AGP contexts, our review will focus on transmission and PPE in low-risk health care settings.
cord-320560-yn3bbkdh	2020	[5] [6] [7] [8] [9] The lack of studies within the otorhinolaryngology field assessing the aerosol-generating potential of procedures involving mucosal surfaces pre-COVID-19 made it challenging to understand in an evidence-based fashion the potential risks of SARS-CoV-2 transmission associated with instrumentation of the upper airway; that is, whether these procedures may be infectious AGPs. At the early stages of the pandemic, based on the risks of exposure to high viral load mucosal surfaces, 10, 11 as well as on the lack of any immunity to SARS-CoV-2 and of any vaccines or effective treatments, an array of practice changes to protect health-care workers and patients were recommended and instituted for otorhinolaryngology procedures involving upper airway mucosal surfaces.
cord-327651-yzwsqlb2	2016	In infectious disease transmission network inference, Bayesian inference frameworks have been primarily used to integrate data such as dates of pathogen sample collection and symptom report date, pathogen genome sequences, and locations of patients [24] [25] [26] . Pathogen genomic data can capture within-host pathogen diversity (the product of effective population size in a generation and the average pathogen replication time [25, 26] ) and dynamics or provide information critical to understanding disease transmission such as evidence of new transmission pathways that cannot be inferred from epidemiological data alone [40, 41] . As molecular epidemiology and infectious disease transmission are areas in which network inference methods have been developed for bringing together multimodal data we use this review to investigate the foundational work in this specific field. In this section we briefly review multimodal integration methods for combining pathogen genomic data and epidemiological data in a single analysis, for inferring infection transmission trees and epidemic dynamic parameters.
cord-334021-ex4z2b75	2020	Early evidence indicated that schools were low risk and children were unlikely to be very infectious, but it is becoming clear that children and youth can acquire and transmit COVID-19 in school settings and that transmission clusters and outbreaks can be large. Total cluster size is the number of students who are ultimately infected in class (or in both classes in the high school), including the index case. This pattern continues; with a highly infectious index case in a higher-risk room (fourth row): in the baseline protocol in which the main intervention is that symptomatic individuals do not attend, cluster sizes range from 0 to over 20 students in a single classroom (median=4, sympt. We illustrate this by showing results on cluster size for a high school with pre-COVID structure: four 1.25 hour classes every day with largely different students in each.
cord-336687-iw3bzy0m	2015	Here, we fitted a mathematical model of dengue virus transmission to spatial time-series data from Pakistan and compared maximum-likelihood estimates of ''mixing parameters'' when disaggregating data across an urban–rural gradient. Accounting for differences in mobility by incorporating two fine-scale, density-dependent covariate layers eliminates differences in mixing but results in a doubling of the estimated transmission potential of the large urban district of Lahore. In no application of the TSIR model to date has the potential for variation in these parameters been assessed, leaving the extent to which inhomogeneity of mixing varies across space and time as an open question in the study of infectious disease dynamics. To assess the potential for spatial variation in the inhomogeneity of mixing as it pertains dengue transmission, we performed an analysis of district-level time series of dengue transmission in the Punjab province of Pakistan using a TSIR model with separate mixing parameters for urban and rural districts.
cord-340357-gyvvcnuf	2020	
cord-345504-4d6rq9qj	2020	title: Transmission routes of SARS-CoV-2 journal: J Dent Sci However, the authors make inaccurate references to the established transmission routes of SARS-CoV-2. The authors state that the novel coronavirus is spread via aerosols and the faecal-oral route, in spite of a largely undeveloped evidence-base in support of these pathways. 2 Indeed, aerosol-generating procedures (AGPs) are implied in facilitating airborne transmission but limited evidence is available to support this for SARS-CoV-2. The authors imply confirmation of the faecal-oral route and reference a paper by Meng and colleagues however this seems to have been misinterpreted. Although the suggested infection control measures for oral healthcare settings seem practical, a thorough awareness of transmission routes is pre-requisite to devising effective advice. Oral healthcare during the COVID-19 pandemic Coronavirus disease 2019 (COVID-19): emerging and future challenges for dental and oral medicine COVID-19: faecaleoral transmission? Please cite this article as: Patel J, Transmission routes of SARS-CoV-2
cord-347262-q88g1561	2020	
cord-347351-emdj66vj	2020	
cord-348192-ibohbjfb	2020	
cord-350519-3h5ipcwn	2020	From adjusted logistic models, we observed increased odds of any household transmission with longer testing delays for the index case compared to 0-day (i.e., the individual was tested on the same day as their symptom onset) testing delays (ORs: 1-day delay=2·02, 2-day delay=1·96, 3-day delay=2·36, 4-day delay=2·64, ≥5-day delay=3·02) (Figure 3 , Supplementary Table S4 ). In this retrospective study of 26,152 confirmed cases of COVID-19 residing in 21,226 private households, we found that longer testing delays and male sex were associated with greater odds of household secondary transmission, while being a healthcare worker or linked to a known outbreak was associated with lower odds of household transmission. Adjusted odds ratios and 95% confidence intervals for the associations between index case delay metrics and odds of household transmission 269 cases were excluded from the testing delay models that had COVID-19 symptoms flagged in provincial reportable disease systems but were missing symptom onset date.
cord-351225-dq0xu85c	2004	
cord-351905-tjcyvkcv	2020	
cord-354254-89vjfkfd	2020	
cord-355024-v5lahyw4	2016