Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020 Apr;5(4):536-544. PubMed: https://pubmed.gov/32123347. Full-text: https://doi.org/10.1038/s41564-020-0695-z
A consensus statement defining the place of SARS-CoV-2 (provisionally named 2019-nCoV) within the Coronaviridae family.
Analysis of 56 genomic sequences from distinct patients, showing high sequence similarity (>99%). A few variable genomic regions exist, mainly at the ORF8 locus (coding for accessory proteins).
Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar;579(7798):270-273. PubMed: https://pubmed.gov/32015507. Fulltext: https://doi.org/10.1038/s41586-020-2012-7
Full-length genome sequences from five patients at an early stage of the outbreak, showing 79.6% sequence identity to SARS-CoV and 96% to a bat coronavirus.
MacLean O, Orton RJ, Singer JB, et al. No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution. Full-text: https://doi.org/10.1093/ve/veaa034
Do not overinterpret genomic data! In this paper, authors discuss the difficulty in demonstrating the existence or nature of a functional effect of a viral mutation, and advise against overinterpretation.
Zhang X, Tan Y, Ling Y, et al. Viral and host factors related to the clinical outcome of COVID-19. Nature (2020). Full-text: https://doi.org/10.1038/s41586-020-2355-0
Viral variants do not affect outcome. This important study on 326 cases found at least two major lineages with differential exposure history during the early phase of the outbreak in Wuhan. Patients infected with these different clades did not exhibit significant differences in clinical features, mutation rates or transmissibility.
Day T, Gandon S, Lion S, et al. On the evolutionary epidemiology of SARS-CoV-2. Curr Biol 2020, June 11. Full-text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287426
Outstanding essay about what little is currently known about the evolution of SARS-CoV-2. At present, there is a lack of compelling evidence that any existing variants impact the progression, severity, or transmission of COVID-19.
Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. Proc Natl Acad Sci U S A. 2020 Jun 30;117(26):15193-15199. PubMed: https://pubmed.gov/32522874. Full-text: https://doi.org/10.1073/pnas.2008176117
This in-depth molecular analysis reconstructs key genomic features that differentiate SARS-CoV-2 from less pathogenic coronaviruses.
Korber B, Fischer WM, Gnanakaran S, et al. Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell July 02, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.06.043
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G (caused by an A-to-G nucleotide mutation at position 23,403 in the Wuhan reference strain) has become the most prevalent form in the global pandemic within a month, indicating a fitness advantage (better transmission).
Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature 2020, published 26. October. Full-text: https://doi.org/10.1038/s41586-020-2895-3
D614G enhances replication on human lung epithelial cells and primary human airway tissues through an improved infectivity of virions.
Yurkovetskiy L, Wang X, Pascal KE, et al. Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant. Cell 2020, published 15 September. Full-text: https://doi.org/10.1016/j.cell.2020.09.032
D614G is more infectious than the ancestral form on human lung cells, colon cells, and on cells expressing ACE.
Origin and hosts
Andersen KG, Rambaut A, Lipkin WA, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nature Medicine. Published: 17 March 2020. Fulltext: https://www.nature.com/articles/s41591-020-0820-9
Review on notable genomic features of SARS-CoV-2, compared to alpha- and beta-coronaviruses. Insights on the origin, clearly showing that this virus is not a laboratory construct or a purposefully manipulated virus.
Cui J, Li F, Shi ZL. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019 Mar;17(3):181-192. PubMed: https://pubmed.gov/30531947. Full-text: https://doi.org/10.1038/s41579-018-0118-9
SARS-CoV and MERS-CoV likely originated in bats, both jumping species to infect humans through different intermediate hosts.
Lam TT, Shum MH, Zhu HC, et al. Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins. Nature. 2020 Mar 26. PubMed: https://pubmed.gov/32218527. Fulltext: https://doi.org/10.1038/s41586-020-2169-0
Do Malayan pangolins act as intermediate hosts? Metagenomic sequencing identified pangolin-associated coronaviruses, including one with strong similarity to SARS-CoV-2 in the receptor-binding domain.
Xiao K, Zhai J, Feng Y, et al. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature. 2020 May 7. PubMed: https://pubmed.gov/32380510. Full-text: https://doi.org/10.1038/s41586-020-2313-x
In a wildlife rescue center, authors found a coronavirus in 25 Malayan pangolins (some of them were very sick), showing 90-100% amino acid identity with SARS-CoV-2 in different genes. Comparative genomic analysis suggested that SARS-CoV-2 might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. As the RBD of Pangolin-CoV is virtually identical to that of SARS-CoV-2, the virus in pangolins presents a potential future threat to public health. Pangolins and bats are both nocturnal animals, eat insects, and share overlapping ecological niches, which make pangolins the ideal intermediate host. Stop the illegal pangolin trade!
Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 2020 Mar 13. PubMed: https://pubmed.gov/32197085. Fulltext: https://doi.org/10.1016/j.cub.2020.03.022
This study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs. Pangolin-CoV was 91.0% and 90.6% identical to SARS-CoV-2 and Bat-CoV RaTG13, respectively.
Zhou H, Chen X, Hu T, et al. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Curr Biol. 2020 May 11. PubMed: https://pubmed.gov/32416074. Full-text: https://doi.org/10.1016/j.cub.2020.05.023
A novel bat-derived coronavirus was identified from a metagenomics analysis of samples from 227 bats collected from Yunnan Province in 2019. Notably, RmYN02 shares 93.3% nucleotide identity with SARS-CoV-2 at the scale of the complete genome and 97.2% identity in the lab gene, in which it is the closest relative of SARS-CoV-2 reported to date. However, RmYN02 showed low sequence identity (61.3%) in the receptor binding domain and might not bind to ACE2.
Stability and transmission of the virus
Chin AW, Chu JT, Perera MR, et al. Stability of SARS-CoV-2 in different environmental conditions.The Lancet Microbe 2020, April 02. Full-text: https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(20)30003-3/fulltext
SARS-CoV-2 was highly stable at 4°C (almost no reduction on day 14) but sensitive to heat (70°C: inactivation 5 min, 56°: 30 min, 37°: 2 days). It also depends on the surface: No infectious virus could be recovered from print and tissue paper after 3 hours, from treated wood and cloth on day 2, from glass and banknotes on day 4, stainless steel and plastic on day 7. Strikingly, a detectable level of infectious virus (<0·1% of the original inoculum) was still present on the outer layer of a surgical mask on day 7.
Kim YI, Kim SG, Kim SM, et al. Infection and Rapid Transmission of SARS-CoV-2 in Ferrets. Cell Host Microbe. 2020 Apr 5. PubMed: https://pubmed.gov/32259477. Full-text: https://doi.org/10.1016/j.chom.2020.03.023.
Ferrets shed the virus in nasal washes, saliva, urine, and feces up to 8 days post-infection. They may represent an infection and transmission animal model of COVID-19 that may facilitate development of SARS-CoV-2 therapeutics and vaccines.
Leung NH, Chu Dk, Shiu EY. Respiratory virus shedding in exhaled breath and efficacy of face masks. Nature Med 2020, April 3. https://doi.org/10.1038/s41591-020-0843-2
This study from Hong Kong (performed 2013-16) quantified virus in respiratory droplets and aerosols in exhaled breath. In total, 111 participants (infected with seasonal coronavirus, influenza or rhinovirus) were randomized to wear or not to wear a simple surgical face mask. Results suggested that masks could be used by ill people to reduce onward transmission. In respiratory droplets, seasonal coronavirus was detected in 3/10 (aerosols: 4/10) samples collected without face masks, but in 0/11 (0/11) from participants wearing face masks. Influenza viruses were detected in 6/23 (8/23) without masks, compared to 1/27 (aerosol 6/27!) with masks. For rhinovirus, there were no significant differences at all. Of note, authors also identified virus in some participants who did not cough at all during the 30 min exhaled breath collection, suggesting droplet and aerosol routes of transmission from individuals with no obvious signs or symptoms.
Shi J, Wen Z, Zhong G, et al. Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS-coronavirus 2. Science. 2020 Apr 8. PubMed: https://pubmed.gov/32269068. Full-text: https://doi.org/10.1126/science.abb7015
SARS-CoV-2 replicates poorly in dogs, pigs, chickens, and ducks. However, ferrets and cats are permissive to infection and cats were susceptible to airborne infection. But cat owners can relax. Experiments were done in a small number of cats exposed to high doses of the virus, probably more than found in real-life. It also remains unclear if cats secrete enough coronavirus to pass it on to humans.
van Doremalen N, Bushmaker T, Morris DH, et al. Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. N Engl J Med. 2020 Mar 17. PubMed: https://pubmed.gov/32182409. Fulltext: https://doi.org/10.1056/NEJMc2004973
Stability of SARS-CoV-2 was similar to that of SARS-CoV-1, indicating that differences in the epidemics probably arise from other factors and that aerosol and fomite transmission of SARS-CoV-2 is plausible. The virus can remain viable and infectious in aerosols for hours and on surfaces up to days (depending on the inoculum shed).
Chan KH, Sridhar S, Zhang RR, et al. Factors affecting stability and infectivity of SARS-CoV-2. J Hosp Infect. 2020 Jul 8. PubMed: https://pubmed.gov/32652214. Full-text: https://doi.org/10.1016/j.jhin.2020.07.009
Dry heat is bad, damp cold is good (for the virus). Dried SARS-CoV-2 virus on glass retained viability for over 3-4 days at room temperature and for 14 days at 4°C, but lost viability rapidly at 37°C. SARS-CoV-2 in solution remained viable for much longer under the same different temperature conditions.
Cell tropism, ACE expression
Chu H, Chan JF, Yuen TT, et al. Comparative tropism, replication kinetics, and cell damage profiling of SARS-CoV-2 and SARS-CoV with implications for clinical manifestations, transmissibility, and laboratory studies of COVID-19: an observational study. Lancet Microbe April 21, 2020. Full-text: https://doi.org/10.1016/S2666-5247(20)30004-5
An elegant study, explaining distinct clinical features of COVID-19 and SARS. Investigation of cell susceptibility, species tropism, replication kinetics, and virus-induced cell damage from both SARS-CoVs, using live infectious virus particles. SARS-CoV-2 replicated more efficiently in human pulmonary cells, indicating that SARS-CoV-2 has most likely adapted better to humans. SARS-CoV-2 replicated significantly less in intestinal cells (might explain lower diarrhea frequency compared to SARS) but better in neuronal cells, highlighting the potential for neurological manifestations.
Hou YJ, Okuda K, Edwards CE, et al. SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract. Cell, May 26, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.05.042
This study quantitated differences in ACE2 receptor expression and SARS-CoV-2 infectivity in the nose (high) vs the peripheral lung (low). If the nasal cavity is the initial site mediating seeding of the lung via aspiration, these studies argue for the widespread use of masks to prevent aerosol, large droplet, and/or mechanical exposure to the nasal passages.
Hui KPY, Cheung MC, Perera RAPM, et al. Tropism, replication competence, and innate immune responses of the coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures. Lancet Respir Med. 2020 May 7. PubMed: https://pubmed.gov/32386571. Full-text: https://doi.org/10.1016/S2213-2600(20)30193-4
More insights into the transmissibility and pathogenesis. Using ex vivo cultures, the authors evaluated tissue and cellular tropism of SARS-CoV-2 in human respiratory tract and conjunctiva in comparison with other coronaviruses. In the bronchus and in the conjunctiva, SARS-CoV-2 replication competence was higher than SARS-CoV. In the lung, it was similar to SARS-CoV but lower than MERS-CoV.
Shang J, Ye G, Shi K. Structural basis of receptor recognition by SARS-CoV-2. Nature 2020, March 30. Full-text: https://doi.org/10.1038/s41586-020-2179-y.
How well does SARS-CoV-2 recognize hACE2? Better than other coronaviruses. Compared to SARS-CoV and RaTG13 (isolated from bats), ACE2-binding affinity is higher. Functionally important epitopes in SARS-CoV-2 RBM are described that can potentially be targeted by neutralizing antibody drugs.
Sungnak W, Huang N, Bécavin C,et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nature Medicine, Published: 23 April 2020. Full-text: https://www.nature.com/articles/s41591-020-0868-6
Another elegant paper, confirming the expression of ACE2 in multiple tissues shown in previous studies, with added information on tissues not previously investigated, including nasal epithelium and cornea and its co-expression with TMPRSS2. Potential tropism was analyzed by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. These transcripts were found in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission.
Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res. 2020 Apr;176:104742. PubMed: https://pubmed.gov/32057769. Fulltext: https://doi.org/10.1016/j.antiviral.2020.104742
Identification of a peculiar furin-like cleavage site in the Spike protein of SARS-CoV-2, lacking in other SARS-like CoVs. Potential implication for the development of antivirals.
Watanabe Y, Allen JD, Wrapp D, McLellan JS, Crispin M. Site-specific glycan analysis of the SARS-CoV-2 spike. Science. 2020 May 4. PubMed: https://pubmed.gov/32366695. Full-text: https://doi.org/10.1126/science.abb9983
The surface of the envelope spike is dominated by host-derived glycans. These glycans facilitate immune evasion by shielding specific epitopes from antibody neutralization. SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer. Using a site-specific mass spectrometric approach, the authors reveal these glycan structures on a recombinant SARS-CoV-2 S immunogen.
Cai Y, Zhang J, Xiao T, et al. Distinct conformational states of SARS-CoV-2 spike protein. Science 21 Jul 2020. Full-text: https://doi.org/10.1126/science.abd4251
The authors report two cryo-EM structures, derived from a preparation of the full-length S protein, representing its pre-fusion (2.9Å resolution) and post-fusion (3.0Å resolution) conformations, respectively, and identify a structure near the fusion peptide – the fusion peptide proximal region (FPPR), which may play a critical role in the fusogenic structural rearrangements of S protein.
Ke Z, Oton J, Qu K, et al. Structures and distributions of SARS-CoV-2 spike proteins on intact virions. Nature 2020, published 17 August. Full-text: https://doi.org/10.1038/s41586-020-2665-2
More on how SARS-CoV-2 Spike (S) proteins function and how they interact with the immune system. This work extends the knowledge of the structures, conformations and distributions of S trimers within virions.
Toelzer C, Gupta K, Yadav SK, et al. Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein. Science 21 Sep 2020. Full-text: https://doi.org/10.1126/science.abd3255
The structure of the SARS-CoV-2 S glycoprotein. The RBDs tightly bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. The LA-binding pocket presents a promising target for future development of small molecule inhibitors that, for example, could irreversibly lock S in the closed conformation and interfere with receptor interactions.
Turoňová B, Sikora M, Schürmann C, et al. In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 2020, published 18 August. Full-text: https://science.sciencemag.org/content/early/2020/08/17/science.abd5223
This work shows that the stalk domain of S contains three hinges, allowing S to scan the host cell surface, shielded from antibodies by an extensive glycan coat.
Binding to ACE
Lan J, Ge J, Yu J, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. Published: 30 March 2020. Full-text: https://www.nature.com/articles/s41586-020-2180-5
To elucidate the SARS-CoV-2 RBD and ACE2 interaction at a higher resolution/atomic level, authors used X-ray crystallography. Binding mode was very similar to SARS-CoV, arguing for a convergent evolution of both viruses. The epitopes of two SARS-CoV antibodies targeting the RBD were also analysed with the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies.
Wang Q, Zhang Y, Wu L, et al. Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell. 2020 Apr 7. PubMed: https://pubmed.gov/32275855. Full-text: https://doi.org/10.1016/j.cell.2020.03.045
Atomic details of the crystal structure of the C-terminal domain of SARS-CoV-2 spike protein in complex with human ACE2 are presented. The hACE2 binding mode of SARS-CoV-2 seems to be similar to SARS-CoV, but some key residue substitutions slightly strengthen the interaction and lead to higher affinity for receptor binding. Antibody experiments indicated notable differences in antigenicity between SARS-CoV and SARS-CoV-2
Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science. 2020 Mar 27;367(6485):1444-1448. PubMed: https://pubmed.gov/32132184. Full-text: https://doi.org/10.1126/science.abb2762
Using cryo–electron microscopy, this paper shows how SARS-CoV-2 binds to human cells. The first step in viral entry is the binding of the viral trimeric spike protein to the human receptor angiotensin-converting enzyme 2 (ACE2). The authors present the structure of human ACE2 in complex with a membrane protein that it chaperones, B0AT1. The structures provide a basis for the development of therapeutics targeting this crucial interaction.
Starr TN, Greaney AJ, Hilton SK, et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell August 11, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.08.012
The authors have systematically changed every amino acid in the RBD and determine the effects of the substitutions on Spike expression, folding, and ACE2 binding. The work identifies structurally constrained regions that would be ideal targets for COVID-19 countermeasures and demonstrates that mutations in the virus which enhance ACE2 affinity can be engineered but have not, to date, been naturally selected during the pandemic.
Yang J, Petitjean SJL, Koehler M. Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor. Nat Commun 11, 4541 (2020). Full-text: https://doi.org/10.1038/s41467-020-18319-6
How the receptor binding domain serves as the binding interface within the S-glycoprotein with the ACE2 receptor. Kinetic and thermodynamic properties of this binding pocket.
Hoffmann M, Kleine-Weber H, Schroeder S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020 Mar 4. PubMed: https://pubmed.gov/32142651. Fulltext: https://doi.org/10.1016/j.cell.2020.02.052
This work shows how viral entry happens. SARS-CoV-2 uses the SARS-CoV receptor ACE2 for entry and the serine protease TMPRSS2 for S protein priming. In addition, sera from convalescent SARS patients cross-neutralized SARS-2-S-driven entry.
Letko M, Marzi A, Munster V. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses. Nat Microbiol. 2020 Apr;5(4):562-569. PubMed: https://pubmed.gov/32094589. Full-text: https://doi.org/10.1038/s41564-020-0688-y
Important work on viral entry, using a rapid and cost-effective platform which allows to functionally test large groups of viruses for zoonotic potential. Host protease processing during viral entry is a significant barrier for several lineage B viruses. However, bypassing this barrier allows several coronaviruses to enter human cells through an unknown receptor.
Ou X, Liu Y, Lei X, et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun. 2020 Mar 27;11(1):1620. PubMed: https://pubmed.gov/32221306. Fulltext: https://doi.org/10.1038/s41467-020-15562-9
More on viral entry and on (the limited) cross-neutralization between SARS-CoV and SARS-CoV-2.
Yuan M, Wu NC, Zhu X, et al. A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV. Science. 2020 Apr 3. PubMed: https://pubmed.gov/32245784. Full-text: https://doi.org/10.1126/science.abb7269
Insights into antibody recognition and how SARS-CoV-2 can be targeted by the humoral response, revealing a conserved epitope shared between SARS-CoV and SARS-CoV-2. This epitope could be used for vaccines and the development of cross-protective antibodies.
Zhang L, Lin D, Sun X, et al. Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science. 2020 Mar 20. PubMed: https://pubmed.gov/32198291. Fulltext: https://doi.org/10.1126/science.abb3405
Description of the X-ray structures of the main protease (Mpro, 3CLpro) of SARS-CoV-2 which is essential for processing the polyproteins that are translated from the viral RNA. A complex of Mpro and an optimized protease α-ketoamide inhibitor is also described.
Cantuti-Castelvetri L, Ojha R, Pedro LD, et al. Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science 2020, published 20 October. Full-text: https://doi.org/10.1126/science.abd2985
Neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, an effect blocked by a monoclonal blocking antibody against NRP1.
Daly JL, Simonetti B, Klein K, et al. Neuropilin-1 is a host factor for SARS-CoV-2 infection. Science 2020, published 20 October. Full-text: https://doi.org/10.1126/science.abd3072
More on how S binds to cell surface neuropilin-1 (NRP1) and neuropilin-2 (NRP2) receptors.
RNA-dependent RNA polymerase (RdRp)
Gao Y, Yan L, Huang Y, et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 15 May 2020: Vol. 368, Issue 6492, pp. 779-782. Full-text: https://doi.org/10.1126/science.abb7498
Using cryogenic electron microscopy, the authors describe the structure of the RNA-dependent RNA polymerase, another central enzyme of the viral replication machinery. It is also shown how remdesivir and sofosbuvir bind to this polymerase. The authors determined a 2.9-angstrom-resolution structure of the RNA-dependent RNA polymerase (also known as nsp12), which catalyzes the synthesis of viral RNA, in complex with two cofactors, nsp7 and nsp8.
Hillen HS, Kokic G, Farnung L et al. Structure of replicating SARS-CoV-2 polymerase. Nature 2020. Full-text: https://doi.org/10.1038/s41586-020-2368-8
The cryo-electron microscopic structure of the SARS-CoV-2 RdRp in active form, mimicking the replicating enzyme. Long helical extensions in nsp8 protrude along the exiting RNA, forming positively charged ‘sliding poles’. These sliding poles can account for the known processivity of the RdRp that is required for replicating the long coronavirus genome. A nice video provides an animation of the replication machine.
Chen J, Malone B, Llewellyn E, et al. Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex. Cell 2020, 27 July, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.07.033
A cryo-electron microscopic structure of the SARS-CoV-2 holo-RdRp with an RNA template-product with two molecules of the nsp13 helicase and identify a new potential target for future antiviral drugs.
Wolff G, Limpnes RW, Zevenhoven-Dobbe JC, et al. A molecular pore spans the double membrane of the coronavirus replication organelle. Science 06 Aug 2020: eabd3629. Full-text: https://doi.org/10.1126/science.abd3629
Coronavirus replication is associated with virus-induced cytosolic double-membrane vesicles, which may provide a tailored micro-environment for viral RNA synthesis in the infected cell. Visualization of a molecular pore complex that spans both membranes of the double-membrane vesicle and would allow export of RNA to the cytosol. Although the exact mode of function of this molecular pore remains to be elucidated, it would clearly represent a key structure in the viral replication cycle that may offer a specific drug target.
Animals and animal models
In transgenic mice bearing human ACE2 and infected with SARS-CoV-2, the pathogenicity of the virus was demonstrated. This mouse model will be valuable for evaluating antiviral therapeutics and vaccines as well as understanding the pathogenesis of COVID-19.
Chan JF, Zhang AJ, Yuan S, et al. Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility. Clin Infect Dis. 2020 Mar 26. PubMed: https://pubmed.gov/32215622. Fulltext: https://doi.org/10.1093/cid/ciaa325
A readily available hamster model as an important tool for studying transmission, pathogenesis, treatment, and vaccination against SARS-CoV-2.
Chandrashekar A, Liu J, Martinot AJ, et al. SARS-CoV-2 infection protects against rechallenge in rhesus macaques. Science. 2020 May. PubMed: https://pubmed.gov/32434946. Full-text: https://doi.org/10.1126/science.abc4776
No re-infection in macaques. Following initial viral clearance, 9 rhesus macaques were re-challenged on day 35 with the same doses of virus that were utilized for the primary infection. Very limited viral RNA was observed in BAL on day 1 after re-challenge, with no viral RNA detected at subsequent timepoints. These data show that SARS-CoV-2 infection induced protective immunity against re-exposure in nonhuman primates.
Halfman PJ, Hatta M, Chiba S, et al. Transmission of SARS-CoV-2 in Domestic Cats. NEJM May 13, 2020. Full-text: https://www.nejm.org/doi/full/10.1056/NEJMc2013400
Three domestic cats were inoculated with SARS-CoV-2. One day later, an uninfected cat was cohoused with each of the inoculated cats. All six cats became infected and developed antibody titers but none showed any symptoms. Cats may be a silent intermediate host.
Rockx B, Kuiken T, Herfst S, et al. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model. Science 17 Apr 2020. Full text: https://science.sciencemag.org/content/early/2020/04/16/science.abb7314
Macaques may serve as a model to test therapeutic strategies. Virus was excreted from nose and throat in the absence of clinical signs, and was detected in type I and II pneumocytes in foci of diffuse alveolar damage and in ciliated epithelial cells of nasal, bronchial, and bronchiolar mucosae. In SARS-CoV infection, lung lesions were typically more severe, while they were milder in MERS-CoV infection, where virus was detected mainly in type II pneumocytes.
Munster VJ, Feldmann F, Williamson BN, et al. Respiratory disease in rhesus macaques inoculated with SARS-CoV-2. Nature 2020. Full-text: https://doi.org/10.1038/s41586-020-2324-7
SARS-CoV-2 caused respiratory disease in 8 rhesus macaques, lasting 8-16 days. High viral loads were detected in swabs as well as in bronchoalveolar lavages. This “model” recapitulates COVID-19, with regard to virus replication and shedding, the presence of pulmonary infiltrates, histological lesions and seroconversion.
Sia SF, Yan L, Chin AWH. et al. Pathogenesis and transmission of SARS-CoV-2 in golden hamsters. Nature 2020. Full-text: https://doi.org/10.1038/s41586-020-2342-5
In most cases, you don’t need monkeys. Golden Syrian hamsters may also work. SARS-CoV-2 transmitted efficiently from inoculated hamsters to naïve hamsters by direct contact and via aerosols. Transmission via fomites in soiled cages was less efficient. Inoculated and naturally-infected hamsters showed apparent weight loss, and all animals recovered with the detection of neutralizing antibodies.
Sit TH, Brackman CJ, Ip SM et al. Infection of dogs with SARS-CoV-2. Nature 2020. Full-text: https://www.nature.com/articles/s41586-020-2334-5
Two out of fifteen dogs (one Pomeranian and one German Shepherd) from households with confirmed COVID-19 cases in Hong Kong were found to be infected. Both dogs remained asymptomatic but later developed antibody responses detected using plaque reduction neutralization assays. Genetic analysis suggested that the dogs caught the virus from their owners. It still remains unclear whether infected dogs can transmit the virus to other animals or back to humans.
Dinnon KH, Leist SR, Schäfer A et al. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature, August 27, 2020. Full-text: https://doi.org/10.1038/s41586-020-2708-8
Unfortunately, standard laboratory mice do not support infection with SARS-CoV-2 due to incompatibility of the S protein to the murine ortholog (mACE2) of the human receptor. This work has developed a recombinant virus (SARS-CoV-2 MA) that could utilize mACE2 for entry. This model may be helpful in studying COVID-19 pathogenesis.
Mice, hamsters, ferrets, minks, cats, pigs, fruit bats, monkeys: a variety of murine models for mild and severe COVID-19 have been described or are under development. All will be useful for vaccine and antiviral evaluation and some share features with the human disease. Review (performed by a huge international collaboration).
Vaccine (see also Immunology)
Le TT, Andreadakis Z, Kumar A, et al. The COVID-19 vaccine development landscape. Nature reviews drug discovery. 09 April 2020. Full-text: https://www.nature.com/articles/d41573-020-00073-5.
Brief data-driven overview by seven experts. The conclusion is that efforts are unprecedented in terms of scale and speed and that there is an indication that vaccine could be available by early 2021. As of 8 April 2020, the global vaccine landscape includes 115 candidates, of which the 5 most advanced candidates have already moved into clinical development, including mRNA-1273 from Moderna, Ad5-nCoV from CanSino Biologics, INO-4800 from Inovio, LV-SMENP-DC and pathogen-specific aAPC from Shenzhen Geno-Immune Medical Institute. The race is on!
Callaway E. The race for coronavirus vaccines: a graphical guide, Eight ways in which scientists hope to provide immunity to SARS-CoV-2. Nature 2020, 28 April 2020. 580, 576-577. Full-text: https://doi.org/10.1038/d41586-020-01221-y
Fantastic graphic review on current vaccine development. Easy to understand, it explains different approaches such as virus, viral-vector, nucleic-acid and protein-based vaccines.
Zhu FC, Li YH, Guan XH. Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. Lancet May 22, 2020. Full-text: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)31208-3/fulltext
Open label Phase I trial of an Ad5 vectored COVID-19 vaccine, using the full-length spike glycoprotein. A total of 108 healthy adults aged between 18 and 60 years from Wuhan, China, were given three different doses. ELISA antibodies and neutralising antibodies increased significantly and peaked 28 days post-vaccination. Specific T cell response peaked at day 14 post-vaccination. Follow up is still short and authors are going to follow up the vaccine recipients for at least 6 months, so more data will be obtained. Of note, adverse events were relatively frequent, encompassing pain at injection sites (54%), fever (46%), fatigue (44%) and headache (39%). Phase II studies are underway.
Blanco-Melo D, Nilsson-Payant BE, Liu WC, et al. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell May 15, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.04.026
Incredible in-depth analysis of host response to SARS-CoV-2 and other human respiratory viruses in cell lines, primary cell cultures, ferrets, and COVID-19 patients. Data consistently revealed a unique and inappropriate inflammatory response to SARS-CoV-2 which is imbalanced with regard to controlling virus replication versus activation of the adaptive immune response. It is defined by low levels of type I and III interferons juxtaposed to elevated chemokines and high expression of IL-6. The authors propose that reduced innate antiviral defenses coupled with exuberant inflammatory cytokine production are the defining and driving features of COVID-19. Given this dynamic, treatments for COVID-19 have less to do with the IFN response and more to do with controlling inflammation.
Bordoni V, Sacchi A, Cimini E. An inflammatory profile correlates with decreased frequency of cytotoxic cells in COVID-19. Clinical Infectious Diseases 2020, May 15. Full-text: https://doi.org/10.1093/cid/ciaa577
The increase in inflammatory mediators is correlated with a reduction of innate and adaptive cytotoxic antiviral function. The authors found a lower perforin+ NK cell number in 7 intensive care unit (ICU) patients compared to 41 non-ICU patients, suggesting an impairment of the immune cytotoxic arm as a pathogenic mechanism.
Grifoni A, Weiskopf D, Ramirez SI, et al. Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals. Cell 2020. Full-text: https://doi.org/10.1016/j.cell.2020.05.015
Cellular response is a major knowledge gap. This important study identified circulating SARS-CoV-2−specific CD8 and CD4 T cells in 70-100% of 20 COVID-19 convalescent patients, respectively. CD4 T cell responses to spike protein were robust and correlated with the magnitude of IgG titers. Of note, the authors detected SARS-CoV-2−reactive CD4 T cells in 40-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating seasonal coronaviruses and SARS-CoV-2.
Li H, Liu L, Zhang D, et al. SARS-CoV-2 and viral sepsis: observations and hypotheses. Lancet. 2020 May 9;395(10235):1517-1520. PubMed: https://pubmed.gov/32311318. Full-text: https://doi.org/10.1016/S0140-6736(20)30920-X
Brief but nice review and several hypotheses about SARS-CoV-2 pathogenesis. What happens during the second week – when resident macrophages initiating lung inflammatory responses are unable to contain the virus after SARS-CoV-2 infection and when both innate and adaptive immune responses are inefficient to curb the viral replication so that the patient would recover quickly?
Shen B, Yi X, Sun Y, et al. Proteomic and Metabolomic Characterization of COVID-19 Patient Sera. Cell May 27, 2020. Full-text: https://www.sciencedirect.com/science/article/pii/S0092867420306279
Molecular insights into the pathogenesis of SARS-CoV-2 infection. The authors applied proteomic and metabolomic technologies to analyze the proteome and metabolome of sera from COVID-19 patients and several control groups. Pathway analyses and network enrichment analyses of the 93 differentially expressed proteins showed that 50 of these proteins belong to three major pathways, namely activation of the complement system, macrophage function and platelet degranulation. It was found that 80 significantly changed metabolites were also involved in the three biological processes revealed in the proteomic analysis.
Tay MZ, Poh CM, Rénia L et al. The trinity of COVID-19: immunity, inflammation and intervention. Nat Rev Immunol (2020). Full-text: https://www.nature.com/articles/s41577-020-0311-8
Brilliant overview of the pathophysiology of SARS-CoV-2 infection. How SARS-CoV-2 interacts with the immune system, how dysfunctional immune responses contribute to disease progression and how they could be treated.
Vabret N, Britton GJ, Gruber C, et al. Immunology of COVID-19: current state of the science. Immunity 2020, May 05. Full-text: https://www.cell.com/immunity/fulltext/S1074-7613(20)30183-7
Fantastic review on the current knowledge of innate and adaptive immune responses elicited by SARS-CoV-2 infection and the immunological pathways that likely contribute to disease severity and death.
Other key papers
Monto AS, DeJonge P, Callear AP, et al. Coronavirus occurrence and transmission over 8 years in the HIVE cohort of households in Michigan. J Infect Dis. 2020 Apr 4. PubMed: https://pubmed.gov/32246136. Full-text: https://doi.org/10.1093/infdis/jiaa161
It’s not clear whether SARS-CoV-2 behaves like other human coronaviruses (hCoVs). A longitudinal surveillance cohort study of children and their households from Michigan found that hCoV infections were sharply seasonal, showing a peak for different hCoV types (229E, HKU1, NL63, OC43) in February. Over 8 years, almost no hCoV infections occurred after March.
Thao TTN, Labroussaa F, Ebert N, et al. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform. Nature. 2020 May 4. PubMed: https://pubmed.gov/32365353. Full-text: https://doi.org/10.1038/s41586-020-2294-9
An important technical advance, enabling the rapid generation and functional characterization of evolving RNA virus variants. The authors show the functionality of a yeast-based synthetic genomics platform to genetically reconstruct diverse RNA viruses (which are cumbersome to clone and manipulate due to size and instability). They were able to engineer and resurrect chemically-synthetized clones of SARS-CoV-2 only a week after receipt of the synthetic DNA fragments.
Gordon DE, Hiatt J, Bouhaddou M, et al. (Total: 200 authors) Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 2020, published 15 October. Full-text: https://doi.org/10.1126/science.abe9403
A group of 200 researchers uncovers molecular processes used by coronaviruses MERS, SARS-CoV1 and SARS-CoV2 to manipulate host cells.