key: cord-0870404-dfydh7sf
authors: Naqvi, Ahmad Abu Turab; Fatima, Kisa; Mohammad, Taj; Fatima, Urooj; Singh, Indrakant K.; Singh, Archana; Atif, Shaikh Muhammad; Hariprasad, Gururao; Hasan, Gulam Mustafa; Hassan, Md. Imtaiyaz
title: Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach
date: 2020-06-13
journal: Biochim Biophys Acta Mol Basis Dis
DOI: 10.1016/j.bbadis.2020.165878
sha: 5fc123cc606a6ac2a37dd7d215d58cc0d79af86b
doc_id: 870404
cord_uid: dfydh7sf

The sudden emergence of severe respiratory disease, caused by a novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), has recently become a public health emergency. Genome sequence analysis of SARS-CoV-2 revealed its close resemblance to the earlier reported SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). However, initial testing of the drugs used against SARS-CoV and MERS-CoV has been ineffective in controlling SARS-CoV-2. The present review looks to highlight the differences in genomic, proteomic, pathogenesis, and therapeutic strategies of SARS-CoV-2. We have carried out sequence analysis of potential drug target proteins in SARS-CoV-2 and, compared them with SARS-CoV-1 and MERS viruses. Analysis of mutations in the coding and non-coding regions, genetic diversity, and pathogenicity of SARS-CoV-2 has also been done. A detailed structural analysis of drug target proteins was performed to gain insights into the mechanism of pathogenesis, structure-function relationships, and the development of structure-guided therapeutic approaches. The cytokine profiling and inflammatory signalling are different in the case of SARS-CoV-2 infection. We also highlighted possible therapies and their mechanism of action followed by clinical manifestation. Our analysis suggests a minimal variation in the genome sequence of SARS-CoV-2, may be responsible for a drastic change in the structures of target proteins, makes available drugs ineffective.

Coronavirus disease is an infectious disease caused by a novel severe acute respiratory syndrome coronavirus (SARS-Cov-2) that initially started in Wuhan province in China and has now affected more than 200 countries worldwide and declared a Pandemic [1, 2] . The virus primarily affects the respiratory system causing flu-like illness with symptoms such as a cough, fever, and in more severe cases, difficulty breathing [3] . As per the statistics available, mortality is high in older age group individuals (more than 60 years of age) and people with other morbid conditions. In addition to acute respiratory distress syndrome and respiratory failure, coronavirus disease (COVID- 19) is now known to manifest as systemic inflammation, leading to sepsis, acute cardiac injury, and heart failure and multiorgan dysfunction in patients at high risk [4] .

COVID-19 has been declared a pandemic that has currently affected more than 200 countries across the world. As on the 8 th of June, 2020, more than 70 lakh people have been infected so far, with about 1 lakh cases infected every day (https://www.worldometers.info/coronavirus/). There have been more than 4 lakh deaths so far, at an average rate of 5000 deaths each day in the last three months.

While close to 35 lakh people have recovered completely, 32 lakh continues to be active cases and 53000 people in critical condition, requiring respiratory assistance.

The countries that have been affected the most have been the USA, Brazil, Russia, Spain, UK, India, and Italy, with more than 2.34 lakh infected cases each. While the USA has the greatest number of cases with over 20 lakhs being infected and has mortality with over 1 lakh deaths so far. China, the country where it all began in December, is now on the downslope reporting only single-digit cases and no deaths being reported. The majority of the countries around the world were in lockdown to halt human to human transmission of the virus to halt the spread of infection. As the number of COVID-19 cases is increasing, the World Health Organization has rightly J o u r n a l P r e -p r o o f 6 Design and development of SARS-CoV-2 specific direct-acting antiviral drugs can be made possible by targeting conserved enzymes such as 3C-like protease, papainlike protease, non-structural protein 12 (nsp12) and RNA-dependent RNA polymerase (RdRP) [14] . A comparative genomics-based approach can be used to understand the molecular basis of pathogenesis with possible implications in the development of a therapeutic strategy against COVID-19.

Out of the seven pathogenic CoVs, many of them including, HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1 cause mild clinical symptoms. SARS-CoV, MERS-CoV, and the newly identified SARS-CoV-2 infection causes severe respiratory illness and resulting in death in comorbid individuals. Potential adaptive mutations in the SARS-CoV-2 genome possibly made it highly pathogenic and difficult for drug and vaccine development [15] . This review provides comprehensive insights into the genome, proteome, structural features of potential drug targets, and molecular mechanisms of pathogenesis of these viruses in a comparative manner.

We further highlighted the cytokine profiles, inflammatory pathways, followed by the underlying mechanism of action of current therapeutics.

Like SARS-CoV and MERS-CoV, SARS-CoV-2 is also known to infect humans and cause severe respiratory disease. Whereas, other coronaviruses like HKU1, NL63, OC43, and 229E cause mild symptoms [16] . Virion particles enter the host cell via binding through the ACE2. Subsequently, its genome (ss RNA) gets attached to the host's ribosomes, resulting in the translation of 2 co-terminal and large polyproteins that are further processed by proteolytic enzymes/proteolysis [13, 17] . A brief outline of the virus life cycle is illustrated in Figure 1 . Proteolysis mediated by Coronavirus main protease (3CLpro) and papain-like protease (PLpro) [18, 19] , slices large polyproteins into smaller components for the folding and packaging of new virions, which consequently promotes the spread of infection. The main protease is a key J o u r n a l P r e -p r o o f 9 The genomic organization of the SARS-CoV-2 is in the form of a linear topology, sharing about 89% sequence identity with other CoVs (Figure 2A) . The translated sequences of SARS-CoV-2 proteins were retrieved from the GenBank (Accession ID: NC_045512.2)]. The whole genome of SARS-CoV-2 encodes about 7096 residues long polyprotein which consists of many structural and non-structural proteins (NSPs). The nucleotide content of the viral genome is held mainly by two non-structural proteins ORF1a and ORF1ab followed by structural proteins.

Polyproteins pp1a and pp1ab are encoded by ORFs 1a and 1b, where polyprotein pp1ab is encoded by the ribosomal frameshift mechanism of the gene 1b. These polyproteins are further processed by virally encoded proteinases and produce 16 proteins, which are well conserved in all CoVs belonging to the same family ( Figure   2B ). 

In addition to the capsid-forming structural proteins, the viral genome encodes many

NSPs that perform numerous roles in the replication and virus assembly processes [37] . These proteins participate in viral pathogenesis by modulating early transcription regulation, helicase activity, immunomodulation, gene transactivation, and countering the antiviral response [38] [39] [40] .

J o u r n a l P r e -p r o o f 11 We explored some of the major functions of NSPs in SARS-CoV-2 (Table 1) IUPred2A web servers [56] . These tools allowed us to identify disordered protein regions by predicting the residues which do not possess the tendency to form a structure in the native condition. Residues with a score of >0.5 thresholds were considered to be intrinsically disordered; whereas, residues with a score of between 0.2 and 0.5 were considered as flexible. The graph shows the disordering tendency of each residue in the SARS-CoV-2 polyprotein, where higher values correspond to a higher probability of disorder ( Figure 3) . The data analysis suggests that the SARS-CoV-2 has a chunk of intrinsically disordered regions that lack a well-defined tertiary structure under native conditions. The N-terminal region of Nsp3 (920-1020)

shows a higher tendency to be disordered as predicted by all four predictors.

Further, this analysis provides a brief insight into the non-structural proteome as well as the unstructured protein regions of the SARS-CoV-2 polyprotein that may be useful to understand the structural basis of infection, structure-based drug discovery and interaction of SARS-CoV-2 proteins with host proteins in different physiological conditions. 

The small machinery of proteins of human COVs as discussed in the preceding section contributes to the pathogenesis by helping the virus entry into the host cell 

Spike glycoprotein plays a significant role in pathogenesis by binding to the host cell through its RBD [58] . The S protein initiates the infection by sticking the virion to the host cell. It is composed of 1273 amino acid residues containing three subunits, namely S1, S2, and S2' which act differently during the process of adherence to the host cell. The S1 subunit is involved in the attachment of virions with the host cell membrane by interacting with human ACE2 that subsequently initiates the infection process [17] . During this process, S protein undergoes conformational changes induced upon its entry into the endosomes of the host cell [24] . The understanding of these conformational changes is essential for the process of vaccine development as dynamic changes in the target protein might affect immune responses [59] .

Mutations in the S protein seem to induce conformational changes, which may cause an altered antigenicity. Although several mutations have been found in the S1 receptor binding region of SARS-CoV-2, its interaction with ACE2 is preserved in humans, swine, civet, and bats, except for mouse ACE2 [60] [61] [62] .

The other subunit of the S protein, S2 works as the fusion protein that helps in the fusion of virion with the mammalian cell membrane. During the process of fusion, the S2 protein appears in three main conformational states 1) pre-fusion native state, followed by 2) a pre-hairpin intermediate state, and 3) ensuing post-fusion hairpin state. It is interesting to understand how these dynamic conformation states orchestrate the mechanism of viral entry into the host cell membrane for this might lead to the development of effective therapeutics [59] . The remaining S2' cleaved subunit of the S protein functions as a fusion peptide [63] . The sequence of spike stalk S2 of SARS-CoV-2 is highly similar to bat SARS-like CoVs and human SARS- In the further analysis, we found that out of six residues of SARS-CoV2 critical for binding to ACE2 (Leu455, Phe486, Gln493, Ser494, Asn501, and Tyr505) of RBD, five differ from SARS-CoV, a feature that needs to be factored in drug design and development [16] .

Envelope membrane (E) proteins are a group of relatively small viral proteins that help the "assembly and release" of the virions [65] . Among the structural proteins of the SARS-CoV-2, E protein is considered as a potential drug target. The E protein is relatively small (75 aa), and play a significant role in the viral morphogenesis and assembly [66] . The E protein is known to act as viroporins that assemble into host membrane forming protein-lipid pores involved in ion transport. The sequences of E protein for all four strains are highly conserved regions among the BAT-CoV, SARS-CoV, and SARS-CoV-2 while exhibiting a slight variation in the sequence of MERS-CoV envelope proteins ( Figure 4B ).

M proteins are 222 amino acid long structural proteins that function in concurrence with E, N, and S proteins, and plays a major role in the RNA packaging [67] . The conserved stretch of amino acids suggests a common architecture for these proteins 

Nucleocapsid proteins (N) play an important role in the packaging of viral RNA into ribonucleocapsid [68] . N protein of SARS-CoV-2 is highly conserved across CoVs sharing ~90% sequence identity with that of SARS-CoV. It mediates viral assembly by interacting with the viral genome and M protein, which are helpful in the augmentation of viral RNA transcription and replication [69] . Thus, N proteins are considered as potential drug targets. The N proteins bind to viral RNA through its ~140 amino acid long RNA-binding domain in their core in a "bead on a string" manner [65] . MSA of N protein from the BAT-CoV, SARS-CoV, and SARS-CoV-2

show highly conserved regions ( Figure 4D ). Based on the high sequence similarity 

Replicase polyprotein is another essential enzyme that helps in the cleavage of host RNA and replication of the viral RNA [21] . As discussed earlier, the non-structural

ORFs 1a and 1ab share the majority of nucleotide content of the viral genome.

Replicase polyproteins are multifunctional proteins that can perform various tasks, contributing to the viral pathogenesis [70] . However, an in-depth description of the structure of target proteins at the active/binding site shows a larger variation.

The S protein is one of the most important drug/vaccine targets in CoV pathogenesis because the RBD of the S1 domain undergoes a hinge-like conformational movement and an important determinant of host cell receptor binding [7] . Such interactions help the virus to stick to the host cell ACE2 by the RBD [22, 72] .

Because of the vital function of the S protein, it is considered as an attractive target for antibody-mediated vaccine and drug development [62, 73] . Structure analysis revealed that the S1/S2 junction is present in a disordered, solvent-exposed loop which is not much conserved in other CoVs, causes a substantial effect on the structure or function [61] . RBD-directed monoclonal antibodies of SARS-CoV sharing common three epitopes were tested for SARS-CoV2, shows insignificant binding. Hence, a comparative structure analysis will enable the design and screening of a new class of small-molecule inhibitors which can interfere with the host fusion. Further, structural information will support to design a precise vaccine to accelerate therapeutic measures against COVID19. No significant difference was observed in the architecture of the E proteins ( Figure   S2 ). M protein does not show any significant difference in protein architecture ( Figure S3) . Similarly, nucleoprotein also shows a higher similarity in the core RNAbinding domain of the N protein ( Figure S4 ) conserved in most viral polymerases [75] .

The main protease is one of the most characterized drug targets of the CoVs as this enzyme is essential for processing the polyproteins required for viral assembly [76] . 

The innate immune response forms the first line of defense against viral infections.

However, when the immune response is dysregulated, it will result in excessive inflammation, and even death [79] . During the CoV infections, the innate immune responses have been involved in driving a cytokine storm and altering the adaptive immune responses [80] . [90] [91] [92] [93] . Increased concentrations of IL-6 are associated with increased viral load and the recruitment of inflammatory monocytes [94] . Suppressor of cytokine signalling 3 (SOCS3) regulates the negative feedback mechanism of IL-6, which is found to be reduced in the patients with COVID-19 [95] . Plasma TNF-α was found to be moderately regulated in SARS-CoV patients [96] . In summary, the three diseases have marginal differences in terms of innate immune responses but greatly differ in terms of morbidity and mortality.

Therapies available for CoVs are mainly divided into either acting on targets of the human immune system or human cells, or another one is the virus itself. Figure 8 shows the target sites for different drugs in the life cycle of the virus. The major attention of the scientific community has now shifted towards the SARS-CoV-2, leaving various essential projects in limbo [97] . The identification of available antiviral drugs as potential candidates through drug repurposing [98, 99] , state of the art in silico methods to discover novel drugs [100, 101] , allowing the use of antiinflammatory for treating COVID-19 [102] . As we have discussed, subtle structural differences in the target proteins lead to possible hurdles in the process of identifying effective therapeutics using the aforementioned strategies.

Management of COVID-19 patients has been symptomatic approach, and the severe cases are provided with ventilation assistance. Prevention is achieved by propagating the importance of regular hand washing, avoiding touching of the face, and adopting social distancing where individuals are asked to maintain one-meter distance from each other. Also, several drug molecules have been tried in the last couple of months as a treatment strategy. Some of the studies relating to the treatment of COVID-19 has been highlighted in Table 2 . Inhibition of JAK2 inhibits phosphorylation of STAT 3 and 5, which prevents cell division and induces apoptosis.

[107]

Protease inhibitor have in vitro antiviral activity against SARS associated coronavirus Inhibition of coronavirus main proteinase interferes in the processing of polypeptide translation products.

[106]

Oseltamivi 

Janus kinase (JAK) inhibitor

May block viral entry by inhibiting adaptor-associated protein kinase 1 and cyclin Gassociated kinase [114] 12.

Inhibition of IL-6 may attenuate pulmonary inflammation by controlling cytokine storm.

[110]

Anti TNF alpha agents TNF alpha TNF-α promotes the production of other chemokine and cytokines, controls endotoxin-induced septic shock [114] The existing broad-spectrum antiviral drugs used to treat pneumonia-like symptoms, interferons, ribavirin, and cyclophilin are the first line of the therapeutic option [115] .

Remdesivir, an analog of adenosine, is what seems to have a more promising future.

Remdesivir is an adenosine analog terminates the synthesis of viral RNA chains by incorporating in place of real nucleotide. In a recent study, it was shown that remdesivir binds to RdRp and inhibits its activity [75] . This drug has been effective against single-stranded RNA viruses including MERS and SARS-CoV. Encouraged by these results, remdesivir is being advocated for the treatment of SARS-CoV-2 [104] . Remdesivir, as a single agent drug, was used for individual cases of COVID-19 in Italy and the Czech Republic, in March 2020. But the outcomes of these trials still need to be verified before it is declared as being successful. Remdesivir along with chloroquine effectively inhibited SARS-CoV-2 in vitro. Further studies and clinical trials in humans will be required before it is declared as being effective against COVID-19 [116] .

In the frantic search for drug molecules against SARS-CoV-2, repurposing of antimalarials drugs for COVID-19 shown some positive impact [117] . Among these, chloroquine has been gaining a lot of attention in the last few weeks as an option to treat COVID-19 [118, 119] . Chloroquine has antiviral effects by increasing endosomal and lysosomal pH causes an impaired release of the virus from the endosome or lysosome and thus recommended to handle severe COVID-19 patients [120] . Hydroxy-chloroquine, a less toxic derivative of chloroquine, also found is effective in inhibiting SARS-CoV-2 infection [121] . Anti-inflammatory drugs like ibuprofen or cortisone sometimes recommended controlling the infection [122] .

To understand the SARS-CoV-2 infection at the molecular level, it is essential to know the renin-angiotensin-aldosterone system (RAAS) hormone system that is central to SARS-CoV-2 infection (Figure 9 ). The angiotensinogen is converted into angiotensin I by plasma renin released by the liver which is subsequently converted to angiotensin II by the ACE found on the surface of vascular endothelial cells of lungs. Angiotensin II acts on the AT1 receptor to cause vasoconstriction and also stimulates the secretion of the hormone aldosterone, which increases the reabsorption of sodium, thereby increasing blood pressure. Angiotensin I and II are degraded by ACE2 to angiotensin (1-9) and angiotensin (1-7), respectively. These molecules act on the Mas receptor to effect vaso-dilation thereby counteracting the effects of angiotensin II. SARS-CoV-2 infection requires the binding of the virus to the membrane-bound form of ACE2 and internalization of the S protein of the virus to the extracellular domain of ACE2, a membrane receptor, with a high affinity of 15nM to be internalized by the host cell [24, 123] .

In the last few months, the following hypothesis has emerged about COVID19 infection and cardiovascular diseases. Whether or not RAS blockers would be beneficial to COVID-19 cases is still controversial. Many patients with hypertension or other cardiovascular diseases are routinely treated with RAAS blockers and statins. However, clinical concerns remain whether these patients are at greater risk for SARS-CoV-2 infection due to enhanced ACE2 expression [124] . However, this has been argued against Huang and his group [125] who have shown that ACE inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) have few effects on increasing the clinical severe conditions of COVID-19. It would, therefore, be fair J o u r n a l P r e -p r o o f 30 to conclude here that more laboratory and clinical evidence are required to establish the roles of antihypertensive agents, ACE2 expression outcomes of COVID-19 in patients with cardiovascular disease [126] . Many different approaches have been adopted to tide over the COVID-19 pandemic [127] [128] [129] [130] [131] [132] . Few of therapeutics used and their lacunae have been enumerated: (i) chloroquine phosphate: acute poisoning and death [133] ; (ii) Lopinavir/ritonavir combination: randomized control trial not conducted [134] ; (iii) Ibuprofen: safety concerns [135] ; (iv) hydroxyl-chloroquine: randomized control trial not conducted [62] ; (v) umbilical cord mesenchymal stem cells: still under study [136] , (vi) Tilorone:

broad-spectrum anti-viral (not specific) [137] , (vii) losartan (ACE2 receptor blocker):

hypothetical proposition [138] , and (viii) Intravenous immunoglobulin collected from recovered coronavirus patients: SARS-CoV-2 contamination [139] , (ix) blood purification therapy in reducing cytokine storm as a late complication of the disease J o u r n a l P r e -p r o o f 31 [140] . SARS-CoV-2 vaccine pipeline holds a lot of promises that include whole virus vaccines, recombinant protein subunit vaccines, and nucleic acid vaccines. All these vaccines are currently under evaluation [141] .

Even as the pandemic is growing in proportion and affecting millions across the world, there have been certain misconceptions about drug therapies for certain comorbid conditions in COVID19 patients [142] . The most important one pertains to the notion that NSAIDs cause an aggravation of COVID19 infection. But with a lack of robust evidence, COVID-19 patients have been advised against self-medication with NSAIDs [143] . Also, paracetamol, an NSAID, is the choice of drug for fever, NSAIDs generally have no specific role in suppressing SAS-CoV-2. In terms of targeting the human immune system, the innate immune system is mostly recommended because it controls the replication and infection of CoVs [144] . In this regard, blocking the interferon signaling is expected to enhance the immune response. Also, blocking the signal pathways of human cells involved in virus replication was shown to have an effective antiviral effect.

In the quest to find a cure for COVID-19, WHO has conceptualized "SOLIDARITY", an international clinical trial as a common global platform. The advantages of this trial are manifold: (i) reduces the time taken by 80%, as compared to other trials; (ii) helps facilitate the rapid worldwide comparison of unproven treatments; (iii) overcome the risk of multiple small trials not generating the strong evidence needed to determine the relative effectiveness of potential treatments, and (iv) it looks to involve developers and companies to collaborate on ensuring affordability and availability of the treatment options if they prove effective. Based on the evidence so far from laboratories, animal studies and preliminary clinical studies, the treatment options of Remdesivir, Lopinavir/Ritonavir, Lopinavir/Ritonavir, Lopinavir/Ritonavir with Interferon beta-1a, have now been initiated [113, 127, 145] .

In addition to discussed therapies, mesenchymal stem cell (MSC) therapy is a promising option currently implicated in the treatment of COVID-19 [146, 147] convalescent plasma emerged as a potential therapy for severe COVID-19 patients [132] . The use of convalescent plasma as a treatment was recommended by WHO during the outbreak of the Ebola virus in 2014. In the strategy, the convalescent plasma is retrieved from the fully recovered patients of viral disease and is transfused in the infected person as a treatment strategy. During the time of the COVID-19 pandemic, the successful application of this therapy is effective in some of the patients [149] .

Tocilizumab is a monoclonal antibody against the Interleukin-6. During recent months, as the severity of COVID-19 elevates globally, it has been used as an alternative treatment strategy for COVID-19 patients [129] . The rationale for using tocilizumab, an Interleukin-6 inhibitor, is that in most COVID-19 affected persons the activation of T lymphocytes and mononuclear macrophages occurs in large numbers resulting in the secretion of interleukin-6 [128] . Excessive presence of Interleukin-6 causes cytokine storm and other inflammatory responses in the lungs and other organs [150] . The tocilizumab administration is used to control the elevated levels of Interleukin-6. The studies suggest that successful application of tocilizumab treatment in COVID-19 patients shows enhanced improvement in the condition of the patients with an average of 15 days from the start of treatment and resulted in decreased mortality [151] .

As far as the drug resistance in coronaviruses is concerned, there are very few available studies that deal with the subject with intricate depth [152] . However, the studies conducted so far suggest the role of various mutations in the target proteins of the coronaviruses associated mutations to the drug resistance [153, 154] . Despite suggested studies, there is still a need to conduct more studies focusing specifically on gene mutations that are responsible for drug resistance in coronavirus related maladies [155] . The best approach for the development of drugs for SARS-CoV-2 may be the use of available marketed drugs, validated through a well-defined pipeline of drug repurposing [156] [157] [158] . Recently, we have shown that FDA approved drugs, glecaprevir and maraviroc may be implicated as Inhibitors of the main protease of SARS-CoV-2 to address COVID-19 therapy [159] . Once the efficacy of J o u r n a l P r e -p r o o f 33 such drugs in the case of COVID-19 is determined, rapid clinical treatment of patients will be available.

The sudden emergence of pandemic SARS-CoV-2 has caused widespread fear and concern and has threatened global health security. The scientific community all over the globe is working rigorously to find an effective vaccine of drugs against the novel coronavirus. The genomic features of SARS-CoV-2 discussed in this study provide a possible hypothesis for the pathogenesis and transmission of the disease in humans.

Efforts in the short term should be focused on developing a vaccine or inhibitors that help to prevent the infection by targeting the major viral proteins such as S protein, E, M, N, and proteases. The three diseases have marginal differences in terms of innate immune responses but greatly differ in terms of morbidity and mortality. The insights that we presented in the various sections of this review might help pave the way for understating how the novel coronavirus differs in its modus operandi compared to previously known strains. Our comparative study provides answers to some key critical questions relating to pathogenic mechanisms of SARS-CoV-2, in the context of developing potent drugs and vaccines against protein targets for better approaches in COVID-19 therapy.

All authors of the manuscript declare to have no conflicts of interest. 

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China, The Lancet

Early transmission dynamics in Wuhan, China, of novel coronavirusinfected pneumonia

SARS-CoV-2 viral load in upper respiratory specimens of infected patients

Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in

Emerging novel coronavirus (2019-nCoV)-current scenario, evolutionary perspective based on genome analysis and recent developments

Pathological findings of COVID-19 associated with acute respiratory distress syndrome, The Lancet respiratory medicine

Emerging coronaviruses: genome structure, replication, and pathogenesis

Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China

Coronaviruses: an overview of their replication and pathogenesis

Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts, The Lancet Global Health

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

Pathogenesis of severe acute respiratory syndrome

Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target

Coronaviruses -drug discovery and therapeutic options

Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV

The proximal origin of SARS-CoV-2

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors

Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: possible implication in COVID-19 therapy

SARS coronavirus replicase proteins in pathogenesis

Structural basis of receptor recognition by SARS-CoV-2

Drug targets in severe acute respiratory syndrome (SARS) virus and other coronavirus infections

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV

A new coronavirus associated with human respiratory disease in China

Complete genome sequence of Middle East respiratory syndrome coronavirus (MERS-CoV) from the first imported MERS-CoV case in China

Characterization of a novel coronavirus associated with severe acute respiratory syndrome

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

Bats are natural reservoirs of SARS-like coronaviruses

Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China

Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats

Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

Infection of dogs with SARS-CoV-2

Structural disorder in viral proteins

Membrane binding proteins of coronaviruses

Helicase of Type 2 Porcine Reproductive and Respiratory Syndrome Virus Strain HV Reveals a Unique Structure

Broad-spectrum antiviral activity of the eIF4A inhibitor silvestrol against corona-and picornaviruses

Novel betabarrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus

Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity

Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites

Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage

Structure of the C-terminal domain of nsp4 from feline coronavirus

Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain

Structural genomics of the severe acute respiratory syndrome coronavirus: nuclear magnetic resonance structure of the protein nsP7

Insights into SARS-CoV transcription and replication from the structure of the nsp7-nsp8 hexadecamer

The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world

Crystal structure of nonstructural protein 10 from the severe acute respiratory syndrome coronavirus reveals a novel fold with two zinc-binding motifs

A reevaluation of the higher taxonomy of viruses based on RNA polymerases

Crystal structure of the superfamily 1 helicase from Tomato mosaic virus

The predicted metalbinding region of the arterivirus helicase protein is involved in subgenomic mRNA synthesis, genome replication, and virion biogenesis

mRNA cap-1 methyltransferase in the SARS genome

PONDR (predicators of natural disorder regions)

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

The SARS Coronavirus 3a protein binds calcium in its cytoplasmic domain

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Improved molecular diagnosis of COVID-19 by the novel, highly sensitive and specific COVID-19-RdRp/Hel real-time reverse transcriptionpolymerase chain reaction assay validated in vitro and with clinical specimens

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike

Coronaviruses: an overview of their replication and pathogenesis

Regulation of the ER Stress Response by the Ion Channel Activity of the Infectious Bronchitis Coronavirus Envelope Protein Modulates Virion Release, Apoptosis, Viral Fitness, and Pathogenesis

Coronavirus membrane fusion mechanism offers as a potential target for antiviral development

Supramolecular Architecture of the Coronavirus Particle

Nucleocapsid protein recruitment to replicationtranscription complexes plays a crucial role in coronaviral life cycle

Potential Inhibitors Targeting RNA-Dependent RNA Polymerase Activity (NSP12) of SARS-CoV-2

Recent Advances in the Structure-Based Drug Design and Discovery

Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV

Unexpected receptor functional mimicry elucidates activation of coronavirus fusion

Structure of the hemagglutinin precursor cleavage site, a determinant of influenza pathogenicity and the origin of the labile conformation

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs

pH-dependent conformational flexibility of the SARS-CoV main proteinase (Mpro) dimer: molecular dynamics simulations and multiple X-ray structure analyses

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

Recent human genetic errors of innate immunity leading to increased susceptibility to infection

Innate Immunity of the Lung

Coronavirus infection, ER stress, apoptosis and innate immunity

SARS coronavirus pathogenesis: host innate immune responses and viral antagonism of interferon, Current opinion in virology

SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the MAVS/TRAF3/TRAF6 signalosome

Forty years with coronaviruses

Regulation of RIG-I-like receptor signaling by host and viral proteins

Cytokine systems approach demonstrates differences in innate and pro-inflammatory host responses between genetically distinct MERS-CoV isolates

MERS-CoV papain-like protease has deISGylating and deubiquitinating activities

Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus

Immunopathogenesis of coronavirus infections: implications for SARS

Dysregulated type I interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in SARS-CoV-infected mice

Lianhuaqingwen exerts anti-viral and antiinflammatory activity against novel coronavirus (SARS-CoV-2)

COVID-19 infection: the perspectives on immune responses

COVID-19: immunopathology and its implications for therapy

Interleukin-6 is a potential biomarker for severe pandemic H1N1 influenza A infection

Cytokine regulation in SARS coronavirus infection compared to other respiratory virus infections

Modulation of TNF-α-converting enzyme by the spike protein of SARS-CoV and ACE2 induces TNF-α production and facilitates viral entry

Coronavirus shuts down trials of drugs for multiple other diseases

Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases

Could chloroquine /hydroxychloroquine be harmful in Coronavirus Disease 2019 (COVID-19) treatment?

Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study

Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus

The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China

The spike protein of SARS-CoV -a target for vaccine and therapeutic development

Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro

Chloroquine and hydroxychloroquine as available weapons to fight COVID-19

A systematic review on the efficacy and safety of chloroquine for the treatment of COVID-19

TH17 responses in cytokine storm of COVID-19: An emerging target of JAK2 inhibitor Fedratinib

Antivirals and antiviral strategies

The COVID-19 epidemic

Updated approaches against SARS-CoV-2

Ribavirin in the treatment of SARS: A new trick for an old drug?

Anti-HCV, nucleotide inhibitors, repurposing against COVID-19, Life sciences

Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study

COVID-19, cytokines and immunosuppression: what can we learn from severe acute respiratory syndrome?

Coronaviruses-drug discovery and therapeutic options

Remdesivir in adults with severe COVID-19: a randomised, double-blind

Repurposing antimalarials and other drugs for COVID-19

Treating COVID-19 with Chloroquine

Combating COVID-19 with Chloroquine

Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies

Hydroxychloroquine, a less toxic derivative of chloroquine, is effective in inhibiting SARS-CoV-2 infection in vitro

Misguided drug advice for COVID-19

High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa

COVID-19, ACE2, and the cardiovascular consequences

Angiotensin-converting enzyme inhibitors and angiotensin receptor blockers decrease the incidence of atrial fibrillation: a meta-analysis

Association of inpatient use of angiotensin converting enzyme inhibitors and angiotensin II receptor blockers with mortality among patients with hypertension hospitalized with COVID-19

COVID-19: immunopathology and its implications for therapy

Effective treatment of severe COVID-19 patients with tocilizumab

Mesenchymal Stem Cell Therapy for COVID-19: Present or Future

Treatment of 5 Critically Ill Patients With COVID-19 With Convalescent Plasma

Convalescent plasma as a potential therapy for COVID-19

The Trial of Chloroquine in the Treatment of Corona Virus Disease 2019 COVID-19 and Its Research Progress in Forensic Toxicology

Lopinavir/ritonavir combination therapy amongst symptomatic coronavirus disease 2019 patients in India: Protocol for restricted public health emergency use

Covid-19: European drugs agency to review safety of ibuprofen

Expanded Umbilical Cord Mesenchymal Stem Cells (UC-MSCs) as a Therapeutic Strategy in Managing Critically Ill COVID-19 Patients: The Case for Compassionate Use

Tilorone: a Broad-Spectrum Antiviral Invented in the USA and Commercialized in Russia and beyond

Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics

Could Intravenous Immunoglobulin Collected from Recovered Coronavirus Patients Protect against COVID-19 and Strengthen the Immune System of New Patients?

Potential effect of blood purification therapy in reducing cytokine storm as a late complication of severe COVID-19

The SARS-CoV-2 Vaccine Pipeline: an Overview

Misguided drug advice for COVID-19

NSAIDs in patients with viral infections, including Covid-19: victims or perpetrators?

Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: a retrospective cohort study

Comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against MERS-CoV

The potential of mesenchymal stem cell therapy for chronic lung disease, Expert review of respiratory medicine

Expanded umbilical cord mesenchymal stem cells (UC-MSCs) as a therapeutic strategy in managing critically ill COVID-19 patients: The case for compassionate use

Transplantation of ACE2(-) Mesenchymal Stem Cells Improves the Outcome of Patients with COVID-19 Pneumonia

Effectiveness of convalescent plasma therapy in severe COVID-19 patients

The cytokine release syndrome (CRS) of severe COVID-19 and Interleukin-6 receptor (IL-6R) antagonist Tocilizumab may be the key to reduce the mortality

Tocilizumab treatment in COVID-19: A single center experience

Homology-Based Identification of a Mutation in the Coronavirus RNA-Dependent RNA Polymerase That Confers Resistance to Multiple Mutagens

Study on the resistance of severe acute respiratory syndromeassociated coronavirus

Coronaviruses resistant to a 3C-like protease inhibitor are attenuated for replication and pathogenesis, revealing a low genetic barrier but high fitness cost of resistance

Mutations in the Spike Protein of Middle East Respiratory Syndrome Coronavirus Transmitted in Korea Increase Resistance to Antibody-Mediated Neutralization

Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods

Repurposing of clinically approved drugs for treatment of coronavirus disease 2019 in a 2019-novel coronavirus (2019-nCoV) related coronavirus model

Drug repurposing for viral infectious diseases: how far are we?

Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: possible implication in COVID-19 therapy

MIH thanks to the Department of Science and Technology and Indian Council of Medical Research for financial support.