Virologia

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N. N.

Questo capitolo è sotto costruzione. Il nome dell’autore sarà presto comunicato. Nel frattempo, controlla il testo inglese su www.CovidReference.com/virology.

Bibliografia

(in lingua inglese)

Taxonomy

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.

Ceraolo C, Giorgi FM. Genomic variance of the 2019-nCoV coronavirus. J Med Virol. 2020 May;92(5):522-528. PubMed: https://pubmed.gov/32027036. Full-text: https://doi.org/10.1002/jmv.25700

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.

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 betacoronaviruses. 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. pii: 10.1038/s41586-020-2169-0. 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.

Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol. 2020 Mar 13. pii: S0960-9822(20)30360-2. 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.

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. DOI:https://doi.org/10.1016/S2666-5247(20)30003-3. 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 printing and tissue papers 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. pii: S1931-3128(20)30187-6. 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. pii: science.abb7015. 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).

Cell tropism

Chu H, Chan JF, Wang Y, et al. Comparative replication and immune activation profiles of SARS-CoV-2 and SARS-CoV in human lungs: an ex vivo study with implications for the pathogenesis of COVID-19. Clin Infect Dis. 2020 Apr 9. pii: 5818134. PubMed: https://pubmed.gov/32270184

Cell experiments on replication capacity and immune activation profile of SARS-CoV-2 and SARS-CoV infection in human lung tissues. Both viruses were similar in cell tropism, with both targeting types I and II pneumocytes, and alveolar macrophages. SARS-CoV-2 generated 3.20 times more infectious virus particles than that of SARS-CoV from infected lung tissues.

Wang X, Xu W, Hu G, et al. SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion. Cell Mol Immunol. 2020 Apr 7. pii: 10.1038/s41423-020-0424-9. PubMed: https://pubmed.gov/32265513. Full-text: https://doi.org/10.1038/s41423-020-0424-9

It remains unclear whether SARS-CoV-2 can also infect T cells, resulting in lymphocytopenia. Using a model with pseudoviruses, authors showed that SARS-CoV-2 infects (but does not replicate in) T cells through S protein-mediated membrane fusion. T-cell lines were significantly more sensitive to SARS-CoV-2 infection when compared with SARS-CoV. Of note, a very low expression level of hACE2 was found, indicating that a novel receptor might mediate SARS-CoV-2 entry into T cells.

Spike protein and cell entry

Chu H, Chan JF, Wang Y, et al. Comparative replication and immune activation profiles of SARS-CoV-2 and SARS-CoV in human lungs: an ex vivo study with implications for the pathogenesis of COVID-19. Clin Infect Dis. 2020 Apr 9. pii: 5818134. PubMed: https://pubmed.gov/32270184.

Cell experiments on replication capacity and immune activation profile of SARS-CoV-2 and SARS-CoV infection in human lung tissues. Both viruses were similar in cell tropism, with both targeting types I and II pneumocytes, and alveolar macrophages. SARS-CoV-2 generated 3.20 folds more infectious virus particles than that of SARS-CoV from infected lung tissues.

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.

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. pii: S0092-8674(20)30229-4. 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.

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.

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.

Monteil V, Kwon H, Patricia Prado P, et al. Inhibition of SARS-CoV-2 infections in engineered human tissues using clinical-grade soluble human ACE2. Cell 2020. DOI: 10.1016/j.cell.2020.04.004. https://www.cell.com/pb-assets/products/coronavirus/CELL_CELL-D-20-00739.pdf.

This study shows that human recombinant soluble ACE2 (hrsACE2) blocks SARS-CoV-2 infections of different cells, human blood vessel organoids and human kidney organoids. In ARDS patients, hrsACE2 was ineffective but safe at a broad range of doses. Apeiron Biologics plans a randomized study on 200 COVID-19 patients in April.

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.

Shang J, Ye G, Shi K. Structural basis of receptor recognition by SARS-CoV-2. Nature 2020, March 30. 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.

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. pii: S0092-8674(20)30338-X. 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, it is shown 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). 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.

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. pii: science.abb7269. 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.

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. 2020 Apr 10. pii: science.abb7498. PubMed: https://pubmed.gov/32277040. Full-text: https://doi.org/10.1126/science.abb7498

Using cryogenic electron microscopy, 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.

Other key papers

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.

Le TT, Andreadakis Z, Kumar A, et al. The COVID-19 vaccine development landscape. Nature reviews drug discovery. 09 April 2020. doi: 10.1038/d41573-020-00073-5. 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!

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. pii: 5815743. 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.