Wu H, Xing N, Meng K, et al. Nucleocapsid mutations R203K/G204R increase the infectivity, fitness and virulence of SARS-CoV-2. Cell Host Microbe November 12, 2021. https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(21)00511-4
R203K/G204R are co-occurring mutations in the N protein (another structural protein of the virion) that are rapidly increasing. Using the authentic virus, the authors showed that these mutations increase viral replication, that enhances the infectivity, fitness and virulence of SARS-CoV-2. R203K/G204R increase the sensitivity of virus to neutralizing antibodies, which may be complemented by immune resistance mutations, such as N501Y and E484K.
Giobbe GG, Bonfante F, Jones BC, et al. SARS-CoV-2 infection and replication in human gastric organoids. Nat Commun November 16, 12, 6610 (2021). https://www.nature.com/articles/s41467-021-26762-2
This study shows that the virus can efficiently infect the gastric epithelium, suggesting that the stomach might have an active role in fecal-oral SARS-CoV-2 transmission.
Van Cleemput J, van Snippenberg W, Lambrechts L, et al. Organ-specific genome diversity of replication-competent SARS-CoV-2. Nat Commun November 16, 2021, 12, 6612. https://www.nature.com/articles/s41467-021-26884-7
A detailed virological analysis of 13 post-mortem cases providing proof of viremia and presence of replication-competent SARS-CoV-2 in extrapulmonary organs of immunocompromised patients, including heart, kidney, liver, and spleen. In parallel, the authors found organ-specific SARS-CoV-2 genome diversity and mutations of concern in multiple organs.
Syed AM, Taha TY, Tabata T, et al. Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles. Science, November 4, 2021. https://www.science.org/doi/10.1126/science.abl6184
The authors present a new strategy for rapidly generating and analyzing SARS-CoV-2 virus-like particles that package and deliver exogenous mRNA. This approach allows examination of viral assembly, budding, stability, maturation, entry and genome uncoating involving all of the viral structural proteins without generating replication-competent virus.
Weigang S, Fuchs J, Zimmer G, et al. Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants. Nat Commun November 4, 2021, 12, 6405. https://www.nature.com/articles/s41467-021-26602-3
Virus genomic changes in an immunosuppressed kidney transplant recipient who acquired SARS-CoV-2 during the early phase of the COVID-19 pandemic. The patient had mild respiratory symptoms and tested positive for SARS-CoV-2 for more than 145 days. During this long period, viruses with multiple amino acid substitutions and deletions in the spike protein evolved.
Khan M, Yoo SJ, Clijsters M, et al. Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb. Cell November 02, 2021. https://doi.org/10.1016/j.cell.2021.10.027
SARS-CoV-2 does not appear to be a neurotropic virus. This cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling the authors to catch the virus while it was still replicating. They found that sustentacular cells are the major target cell type in the olfactory mucosa, but failed to find evidence for infection of olfactory sensory neurons. The parenchyma of the olfactory bulb was spared as well.
Han P, Su C, Zhang Y. et al. Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun October 20, 2021. https://doi.org/10.1038/s41467-021-26401-w
Important work, characterizing the hACE2-binding affinity and transduction efficiency of SARS-CoV-2 variants. The authors examined six different SARS-CoV-2 RBD variants, including Alpha, Beta and Gamma, and found that these dominant mutations result in enhanced binding affinity to hACE2 and/or enhancement of viral entry to human cells.
Vöhringer HS, Sanderson T, Sinnott M, et al. Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature October 14, 2021. https://www.nature.com/articles/s41586-021-04069-y
How (and when) Alpha and Delta entered England. Even though more than 90% of adults had antibodies against SARS-CoV-2 and close to 70% had received two doses of vaccination, England saw rising Delta variant cases in the first weeks of July 2021.
Zhang L, Cui Z, Li Q, et al. Ten emerging SARS-CoV-2 spike variants exhibit variable infectivity, animal tropism, and antibody neutralization. Commun Biol 4, 1196 (2021). Full text: https://www.nature.com/articles/s42003-021-02728-4
Insights into the importance of the E484K mutation. The authors compare the infectivity, host tropism and antigenicity of 10 SARS-CoV-2 variants using a VSV-based pseudovirus system. They suggest that “variants carrying E484K display the most significant reduction in sensitivity to neutralization, and may provide further insight into the development of relevant therapeutics for SARS-CoV-2 infection.”
Mendez AS, Ly M, Gonzáles-Sánchez AM, et al. The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression. Cell Reports 2021, 29 September. Full text: https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01305-X
SARS-CoV-2, like other viruses, relies on cellular ribosomes for protein synthesis and thus competes with endogenous mRNA for access to the translation machinery. In this article, find out more about host shut-off and how SARS-CoV-2 mRNA binding functionally alters the association of non-structural protein 1 (nsp1) with the ribosome, which might have implications for drug targeting.
Zhang Y, Huang K, Xie D. et al. In vivo structure and dynamics of the SARS-CoV-2 RNA genome. Nat Commun September 28, 12, 5695. https://www.nature.com/articles/s41467-021-25999-1
This study provides a global landscape of relationships between SARS-CoV-2 RNA structure and key processes of the viral life cycle, such as replication, discontinuous transcription and translation.
Patchett S, Ly Z, Rut W, et al. An A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease. Cell Rep September 20, 2021. https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01208-0
The SARS-CoV-2 papain-like protease (PLpro) is essential for processing viral polyproteins for replication and functions in host immune evasion by cleaving ubiquitin (Ub) and ubiquitin-like protein (Ubl) conjugates. This study gives insight into the ensemble of conformations that the highly conserved active site of PLpro can adopt.
Meyer B, Chiaravalli J, Gellenoncourt S, et al. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun September 21, 2021, 12, 5553. https://www.nature.com/articles/s41467-021-25796-w
An improved understanding of the exact ways in which proteolytic cleavage is regulated, modulates protein activity, and serves to benefit viral replication will be crucial for targeting cellular substrates of viral proteases as a therapeutic strategy. The authors applied mass spectrometry-based methods for N-terminomics to study proteolysis, enabling the identification of novel cleavage and processing sites within viral proteins. They discover that several of these novel viral cleavage sites show altered cleavage following treatment with the cathepsin/calpain inhibitor calpeptin.
Arbeitman CR, Rojas P, Ojeda-May P, et al. The SARS-CoV-2 spike protein is vulnerable to moderate electric fields. Nat Commun 12, 5407 (2021). https://www.nature.com/articles/s41467-021-25478-7
The spike protein of SARS-CoV-2 (and especially its RBD) is unusually vulnerable to external electric fields.
Shan KJ, Wei C, Wang Y, et al. Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process. The Innovation. August 30, 2021. https://www.cell.com/the-innovation/fulltext/S2666-6758(21)00084-9
Some data-driven support for the natural origin of SARS-CoV-2.
Holmes EC, Goldstein SA, Rasmussen AL, et al. The Origins of SARS-CoV-2: A Critical Review. Cell August 18, 2021. https://doi.org/10.1016/j.cell.2021.08.017
A “laboratory escape” scenario or zoonotic emergence? According to this comprehensive review, scientific evidence supports a zoonotic origin.
Resende PC, Naveca FG, Lins RD, et al. The Ongoing Evolution of Variants of Concern and Interest of SARS-CoV-2 in Brazil Revealed by Convergent Indels in the Amino (N)-Terminal Domain of the Spike Protein. Virus Evolution 2021, published 14 August. Full text: https://doi.org/10.1093/ve/veab069
The authors identified that SARS-CoV-2 lineages circulating in Brazil independently acquired convergent deletions and insertions in the amino (N)-terminal domain (NTD) of the S protein. They anticipate that ongoing widespread transmission of SARS-CoV-2 will generate new viral lineages that might be more resistant to antibody neutralization.
Liu Y, Liu J, Bryan AJ, et al. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. bioRxiv 2021, posted 12 August. Full text: https://doi.org/10.1101/2021.08.12.456173
The Delta spike mutation P681R could be a key mutation in enhancing Delta variant replication via increased S1/S2 cleavage. The authors suggest that Spike mutations that potentially affect furin cleavage efficiency should be closely monitored for future variant surveillance.
Mendonça L, Howe A, Gilchrist JB, et al. Correlative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress. Nat Commun 12, 4629 (2021). https://doi.org/10.1038/s41467-021-24887-y
The authors report a multi-modal, multi-scale cryo-correlative platform to image SARS-CoV-2 infection in Vero cells, describing viral RNA transport portals, virus assembly intermediates, viral egress pathway, and native virus spike structures, in the context of whole cell volumes revealing drastic cytopathic changes.
Scudellari M. How the coronavirus infects cells — and why Delta is so dangerous. Nature 2021, published 28 July. Full text: https://www.nature.com/articles/d41586-021-02039-y
Wendy Barclay, Imperial College London: “Two coronavirus variants, Alpha and Delta, have altered furin cleavage sites. In the Alpha variant, the initial proline amino acid is changed to a histidine (P681H); in the Delta variant, it is changed to an arginine (P681R). Both changes make the sequence less acidic, and the more basic the string of amino acids, the more effectively furin recognizes and cuts it.”
Hoffmann M, Pöhlmann S. How SARS-CoV-2 makes the cut. Nat Microbiol. 2021 Jul;6(7):828-829. PubMed: https://pubmed.gov/34194035. Full-text: https://doi.org/10.1038/s41564-021-00931-x
What allows the virus to evade innate antiviral defenses and what is required for transmission? Markus Hoffmann and Stefan Pöhlmann discuss the paper by Peacock TP, Goldhill DH, Zhou J, et al. The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat Microbiol. 2021 Jul;6(7):899-909. PubMed: https://pubmed.gov/33907312. Full-text: https://doi.org/10.1038/s41564-021-00908-w
Rapeport G, Smith E, Gilbert A, Catchpole A, McShane H, Chiu C. SARS-CoV-2 Human Challenge Studies – Establishing the Model during an Evolving Pandemic. N Engl J Med. 2021 Jul 21. PubMed: https://pubmed.gov/34289273. Full-text: https://doi.org/10.1056/NEJMp2106970
Can a SARS-CoV-2 human challenge research program be developed as part of the pandemic response? The authors report about the justification for such research and the management and minimization of risks.
Nicastro F, Sironi G, Antonello E, et al. Solar UV-B/A radiation is highly effective in inactivating SARS-CoV-2. Sci Rep 11, 14805 (2021). Full text: https://doi.org/10.1038/s41598-021-94417-9
In temperate regions of the Earth, summer solar radiation at noon is sufficient to inactivate 63% of virions in open-space concentrations in less than 2 min. The authors suggest implementing strategies of confinement during spring/summer months and fully implementing them during low solar irradiation periods.
Zhang Z, Zhang Y, Liu K, et al. The molecular basis for SARS-CoV-2 binding to dog ACE2. Nat Commun Jul 7, 2021, 12, 4195. https://www.nature.com/articles/s41467-021-24326-y
How can SARS-CoV-2 infect dogs? The present study solved the crystal structure of the RBD/dACE2 complex, and revealed the molecular basis for the recognition of SARS-CoV-2 receptor in dogs.
Kang L, He G, Sharp AK, et al. A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Cell July 06, 2021. https://www.cell.com/cell/fulltext/S0092-8674(21)00833-3
S protein residue 372 is critical for replication in human cells. The threonine-to-alanine change may have enabled the putative ancestral virus to replicate more efficiently in human cells, thus possibly enabling efficient human-to-human transmission.
Kang L, He G, Sharp AK, et al. A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation. Cell July 06, 2021. https://www.cell.com/cell/fulltext/S0092-8674(21)00833-3
S protein residue 372 is critical for replication in human cells. The threonine-to-alanine change may have enabled the putative ancestral virus to replicate more efficiently in human cells, thus possibly enabling efficient human-to-human transmission.
Zhang Q, Gefter J, Sneddon WB et al. ACE2 interaction with cytoplasmic PDZ protein enhances SARS-CoV-2 invasion. iScience June 23, 2021. https://www.cell.com/iscience/fulltext/S2589-0042(21)00738-0
This study bridges gaps in understanding SARS-CoV-2 entry into the cell. Intracellular factors are identified, involved in mediating SARS-CoV-2 internalization.
Puray-Chavez M, LaPak KM, Schrank TP. Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Cell Rep June 23, 2021. https://doi.org/10.1016/j.celrep.2021.109364
Screening several human lung and head & neck cancer cell lines expressing varying levels of ACE2 and TMPRSS2, the authors identified a human lung adenocarcinoma cell line as being naturally permissive to SARS-CoV-2 infection despite no evidence of detectable ACE2 and TMPRSS2 expression. The E484D spike substitution appears to be specifically required for viral entry into H522 cells.
Cao C, Cai Z, Xiao X, et al. The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun June 24, 2021, 12, 3917. https://www.nature.com/articles/s41467-021-22785-x
The authors developed a high-throughput approach for theoretically probing the in situ genome structure of any RNA virus. This RNA in situ conformation sequencing technology, named RIC-seq, allows unbiased mapping of RNA-RNA spatial interactions in living cells. In this study, the authors successfully applied the technology to probe the SARS-CoV-2 RNA genome structure in intact virions.
Meng B, Kemp SA, Papa G, et al. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the variant of concern lineage B.1.1.7. Cell Rep June 8, 2021. https://www.cell.com/cell-reports/fulltext/S2211-1247(21)00663-X
While ΔH69/V70 (a frequent deletion seen in many variants of concern) itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. H69/V70 does increase spike infectivity and compensates for an infectivity defect resulting from RBD mutations N439K and Y453F.
Hill KJ, Dewar K, Templeton K, et al. A multiregional evaluation of Ct values in SARS-CoV-2 VOC-20DEC-01 variant. J Inf Dis June 7, 2021, jiab303, https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiab303/6294643
A smaller difference in median Ct value between B.1.1.7 and wild type than previously reported. The authors “encourage the scientific community to also consider alternative reasons for the increased infectivity seen” with this variant.
Rees CA, Rostad CA, Mantus G, et al. Altered amino acid profile in patients with SARS-CoV-2 infection. PNAS June 22, 2021 118 (25) e2101708118; https://www.pnas.org/content/118/25/e2101708118
Low plasma arginine bioavailability has been implicated in endothelial dysfunction and immune dysregulation. Among 80 patients (28 controls, 32 adults with COVID-19, and 20 pediatric patients with COVID-19/MIS-C), mean plasma arginine and arginine bioavailability ratios were lower among adult and pediatric patients with COVID-19/MIS-C compared to controls.
Sender R, Bar-On YM, Gleizer S, et al. The total number and mass of SARS-CoV-2 virions. PNAS June 3, 2021. https://www.pnas.org/content/118/25/e2024815118
All SARS-CoV-2 virions currently in all human hosts have a mass of between 100 g and 10 kg. Although each infected person carries an estimated 1 billion to 100 billion virions during peak infection, their total mass is no more than 0.1 mg.
Chen J, Dai L, Barrett L et al. SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus. Commun Biol June 3, 2021, 4, 682. https://doi.org/10.1038/s42003-021-02220-z
New finding: SARS-CoV-2 encoded proteins and some anti-COVID-19 drugs currently used (e.g., azithromycin and nafamostat mesylate) induce lytic reactivation of human herpes virus 8, one of the major human oncogenic viruses. This may facilitate HHV-8 dissemination and initiate viral oncogenesis in immunosuppressed HHV-8+ patients exposed to and treated for COVID-19.
Wu C, Qavi AJ, Hachim A, et al. Characterization of SARS-CoV-2 N protein reveals multiple functional consequences of the C-terminal domain. iScience June 01, 2021. https://www.cell.com/iscience/fulltext/S2589-0042(21)00649-0
Insights into the nucleocapsid (N) encoded by SARS-CoV-2 that plays key roles in the replication cycle and is a critical serological marker. This work provides a biochemical description of SARS-CoV-2 N and highlights the value of using N domains as highly specific and sensitive diagnostic markers.
Maio N, Lafont BA, Sil D, et al. Fe-S cofactors in the SARS-CoV-2 RNA-dependent RNA polymerase are potential antiviral targets. Science 03 Jun 2021: eabi5224. https://science.sciencemag.org/content/early/2021/06/02/science.abi5224
The catalytic subunit of the RNA-dependent RNA polymerase (RdRp) has some metal binding sites that are essential for replication and for interaction with the viral helicase. Oxidation caused their disassembly, potently inhibited the RdRp, and blocked SARS-CoV-2 replication in cell culture.
Kamel W, Noerenberg M, Cerikan B, et al. Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection. Molecular Cell May 24, 2021. https://www.cell.com/molecular-cell/fulltext/S1097-2765(21)00407-X
A systematic and comprehensive analysis of protein-RNA interactions in SARS-CoV-2 infected cells. SARS-CoV-2 infection induces a pervasive remodelling of the “RBPome” (RNA-binding proteins) which involves the upregulation and downregulation of more than 300 RBPs. Dozens of cellular proteins interact with SARS-CoV-2 RNAs and appear to be promising therapeutic approaches.
Hsu JC, Laurent-Rolle M, Pawlak JB, et al. Translational shutdown and evasion of the innate immune response by SARS-CoV-2 NSP14 protein. PNAS June 15, 2021 118 (24) e2101161118. https://www.pnas.org/content/118/24/e2101161118
Another mechanism by which SARS-CoV-2 evades host antiviral responses: SARS-CoV-2 is able to shut down antiviral host protein synthesis. This is achieved by the SARS-CoV-2 nonstructural protein NSP14, a virus-encoded translation inhibitory factor.
Yiwen Zhang, Yingshi Chen, Yuzhuang Li, et al. The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι. PNAS May 21, 2021. https://www.pnas.org/content/118/23/e2024202118
This study shows how SARS-CoV-2 utilizes its open reading frame 8 (ORF8) protein to evade T cell responses. ORF8 (which shares the smallest homology with SARS-CoV among all viral proteins) directly interacts with major histocompatibility complex class Ι (MHC-Ι) molecules and mediates their down regulation. In ORF8-expressing cells, MHC-Ι molecules are selectively targeted for lysosomal degradation via autophagy. Thus, SARS-CoV-2–infected cells are much less sensitive to lysis by cytotoxic T lymphocytes.
Jones TC, Biele G, Mühlemann B, et al. Estimating infectiousness throughout SARS-CoV-2 infection course. Science 25 May 2021: eabi5273. https://science.sciencemag.org/content/early/2021/05/24/science.abi5273
Probably the most comprehensive study on infectiousness. Analyzing viral load, cell culture isolation, and genome sequencing data from 25,381 positive samples, the authors estimate 4.3 days from onset of shedding to peak viral load and cell culture isolation probability. Of note, among 2,228 (9%) highly-infectious subjects with a first-positive viral load of at least 9.0 log10, 804 (36.1%) were pre-, asymptomatic or mildly-symptomatic at the time of testing. B.1.1.7 subjects had mean log10 viral load 1.05 higher than non-B.1.1.7, with estimated cell culture replication probability 2.6 times higher.
Gao X, Zhu K, Qin B. et al. Crystal structure of SARS-CoV-2 Orf9b in complex with human TOM70 suggests unusual virus-host interactions. Nat Commun May 14, 2021, 12, 2843. https://doi.org/10.1038/s41467-021-23118-8
Orf9b is a unique accessory protein of SARS-CoV-2 and SARS-CoV. It is implicated in immune evasion by targeting mitochondria, where it associates with the versatile adapter TOM70. This study determined the crystal structure of SARS-CoV-2 Orf9b in complex with the cytosolic segment of human TOM70.
Yang Q, Saldi TK, Gonzales PK, et al. Just 2% of SARS-CoV-2−positive individuals carry 90% of the virus circulating in communities. PNAS May 11, 2021. 118 (21) e2104547118; https://doi.org/10.1073/pnas.2104547118
The vast majority of circulating virions in communities are found within the bodies of a small number of individuals. Testing more than 72,500 saliva samples by PCR from individuals who reported no symptoms on the day of collection, 1405 positive cases were identified. Regardless of symptomatic status, ∼ 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, with low viral loads in a range from which live virus has rarely been isolated. At any given time, only 2% of individuals carry 90% of the virions circulating within communities, serving as viral “super-carriers” and possibly also super-spreaders.
Bhatt PR, Scaiola A, Loughran G, et al. Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. Science May 12, 2021. https://science.sciencemag.org/content/early/2021/05/12/science.abf3546
This study provides a mechanistic description of frameshifting that occurs during translation of the SARS-CoV-2 genome and reveal the features that may be exploited by the virus to finely control the stoichiometry of viral proteins at different stages of infection.
Zhang L, Richards A, Barrasa I, et al. Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues. PNAS May 25, 2021 118 (21) e2105968118; https://doi.org/10.1073/pnas.2105968118
SARS-CoV-2 RNA can be reverse-transcribed and integrated into the genome of the infected cell and be expressed as chimeric transcripts fusing viral with cellular sequences. Importantly, such chimeric transcripts are detected in patient-derived tissues. Data suggest that, in some patient tissues, the majority of viral transcripts are derived from integrated sequences. This may help explain why patients can continue to produce viral RNA after recovery.
Hamed SM, Elkhatib WF, Khairalla AS et al. Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Sci Rep April 19, 2021, 11, 8435. https://www.nature.com/articles/s41598-021-87713-x
In this study, the metadata of 408,493 SARS-CoV-2 genomes submitted to GISAID EpiCoV database as of January 25, 2021 were analyzed. Most of the genomes belonged to one of seven major clades namely L, S, V, G, GH, GR or GV. Clade GR was the most frequently identified followed by GV and GH. Earlier in January, clade G characterized by spike D614G mutation was identified and rapidly predominated the pandemic. Some more data on geographic, age, and gender distribution.
Abdalhamid B, Iwen PC, Wiley MR, et al. Genome Analysis for Sequence Variants in SARS-CoV-2 Among Asymptomatic Individuals in a Long-term Care Facility. JAMA Netw Open April 9, 2021. 2021;4(4):e217939. https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2778345?resultClick=1
Early evidence of a reduced pathogenicity of the virus? In this small cohort of 7 individuals aged 75 years and older, 5 recovered without illness. In all cases, a new mutation in the spike protein was found (S:K854N) that could have reduced replication capacity. K854 may lead to a reduction of S protein binding ability to the ACE2 receptor. Good news, because we would highly welcome viruses of lower fitness.
Günther S, Reinke PY, Fernández-García Y, et al. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 02 Apr 2021: eabf7945. https://science.sciencemag.org/content/early/2021/03/31/science.abf7945
High-throughput X-ray crystallographic screen, revealing 43 compounds binding to Mpro, with seven compounds (calpeptin, ifenprodil, pelitinib, etc) showing antiviral activity against SARS-CoV-2. Structural evidence for interaction of these compounds at active and allosteric sites of Mpro is presented. Two allosteric binding sites represent attractive targets for drug development.
Jackson B, Rambaut A, Pybus OG, et al. Recombinant SARS-CoV-2 genomes involving lineage B.1.1.7 in the UK. Virological 2021, posted 17 March. Full text: https://virological.org/t/recombinant-sars-cov-2-genomes-involving-lineage-b-1-1-7-in-the-uk/658
The authors report SARS-CoV-2 genome sequences with some sections carrying mutations characteristic of B.1.1.7, while other sections carried mutations specific to another lineage. The timing, location, and genetic composition of the mosaic sequences provide evidence that they originated through recombination in co-infected individuals in the UK.
Braun KM, Moreno GK, Halfmann PJ, et al. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. PLOS Pathogens 2021, published 26 February. Full-text: https://doi.org/10.1371/journal.ppat.1009373
How is genetic variation generated and selected within and between individual hosts? Using domestic cats as a model, Thomas Friedrich, Katarina Braun and colleagues show that within-host SARS-CoV-2 genetic variation is predominantly influenced by genetic drift and purifying selection. In particular, they identified a notable variant at amino acid position 655 in spike (H655Y), which was previously shown to confer escape from human monoclonal antibodies. This variant arises rapidly and persists at intermediate frequencies in index cats.
Lythgoe KA, Hall M, Ferretti L, et al. SARS-CoV-2 within-host diversity and transmission. Science 09 Mar 2021: eabg0821 Full-text: https://doi.org/10.1126/science.abg0821
Katrina A. Lythgoe and colleagues deep-sequenced 1313 clinical samples from the UK. Interestingly, most samples harbored few intrahost variants, and estimated transmission bottleneck sizes were very small, with maximum likelihood estimates between 1 and 8 among household transmission pairs, meaning that if mutations do arise they will be prone to loss at the point of transmission. The results suggest that transmission-enhancing and/or immune-escape variants are likely to arise infrequently, but could spread rapidly if successfully transmitted.
Baggen J, Persoons L, Vanstreels E, et al. Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2. Nat Genet March 8, 2021. https://www.nature.com/articles/s41588-021-00805-2.pdf
Jim Baggen and colleagues from Belgium have identified two new host factors required for coronavirus infection. The lysosomal protein TMEM106B serves as an essential specific host factor for SARS-CoV-2 infection in multiple human cell lines. The phosphoinositide 3-kinase (PI3K) type 3 appears to be a common host factor for SARS-CoV-2 that could be targeted by small molecules.
Liu Y, Hu G, Wang Y, et al. Functional and genetic analysis of viral receptor ACE2 orthologs reveals a broad potential host range of SARS-CoV-2. PNAS March 23, 2021 118 (12) e2025373118; https://www.pnas.org/content/118/12/e2025373118
SARS-CoV-2 has the potential to infect a broad range of mammalian hosts, including domestic animals, pets, livestock, and animals commonly found in zoos and aquaria.
Schroeder S, Pott F, Niemeyer D, et al. Interferon antagonism by SARS-CoV-2: a functional study using reverse genetics. Lancet Microbe March 04, 2021. https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00027-6/fulltext
Do differences in receptor usage determine all the differences in disease presentation between SARS-CoV and SARS-CoV-2? This work by Christian Drosten and colleagues shows that SARS-CoV-2 suppresses cytokine induction and interferon signaling with lower efficiency than SARS-CoV, despite the shared genome architecture and expression of homologous viral proteins. Gene encoding protein 6 as a genetic marker of virulence varied between SARS-CoV and SARS-CoV-2, thus providing a target for genome-based surveillance of circulating strains of SARS-CoV-2. The authors recommend to monitor sequence evolution of SARS-CoV ORF6.
Murray CJ, Piot P. The Potential Future of the COVID-19 Pandemic. JAMA March 3, 2021. Full-text: https://jamanetwork.com/journals/jama/fullarticle/2777343
Will SARS-CoV-2 become a recurrent seasonal Infection? Peter Piot and Christopher Murray don’t know, how could they? According to their nice viewpoint, there is too much uncertainty about the probability and frequency of emergence of new variants, the reduction in vaccine efficacy for each variant, the critical question of cross-variant immunity, and the consistency of safe human behavior. However, the prospect of persistent and seasonal COVID-19 is real.
Phuong HVM, Tung TS, Trang UTH, et al. Novel mutation of SARS-CoV-2, Vietnam, July 2020. Emerg Infect Dis. 2021 May [date cited]. https://doi.org/10.3201/eid2705.210013
Now that the whole world is sequencing the virus, we are likely to see many such studies. A cluster in Danang, Vietnam, began July 25, 2020, and resulted in 551 confirmed cases and 35 deaths. The authors analyzed 26 sequences from this cluster and identified a novel shared mutation in non-structural protein 9, suggesting a single introduction into Vietnam. The single-nucleotide polymorphism, C835T, was not reported in any other sequences collected globally. However, it has no known associations with virulence or transmissibility.
Tse H, Lung CD, Wong SC, et al. Emergence of a Severe Acute Respiratory Syndrome Coronavirus 2 virus variant with novel genomic architecture in Hong Kong. Clinical Infectious Diseases 02 March 2021, ciab198, https://doi.org/10.1093/cid/ciab198
SARS-CoV-2 lineages have emerged continuously, mostly through the genomic accumulation of substitutions. Herman Tse and colleagues highlight the considerable evolutionary potential of SARS-CoV-2. They report three infections caused by a variant with a novel genomic architecture resulting from deletion of an 882-nucleotide region spanning ORF6 to ORF8 together with duplication and transposition of a 57-nucleotide segment from the 5’-untranslated region (UTR). The tolerance of a major and unusual genomic arrangement led to the formation of ORF6x, which involved recruitment of typically non-coding sequences into the open reading frame. These events greatly increased the genetic diversity of SARS-CoV-2, thereby accelerating the evolution of new potentially advantageous genotypes and compensating for the relatively low mutation rates in coronaviruses. On a more immediate note, caution is warranted when using diagnostic assays targeting only accessory genes or proteins such as Orf8, given the risk of false-negative results.
Zhou D, Chan JF, Zhou B, et al. Robust SARS-CoV-2 Infection in Nasal Turbinates after Treatment with Systemic Neutralizing Antibodies. Cell Host Microbe February 24, 2021. Full-text: https://www.sciencedirect.com/science/article/pii/S1931312821000986?via%3Dihub
Viral infection in nasal turbinate may outcompete antibody treatment. Using a Syrian hamster model, the authors show that ZDY20, ZB8 and 2-15 (three of the most promising classes of RBD-specific human neutralizing Abs) prophylactic intraperitoneal or intranasal injection of individual HuNAb or DNA vaccination significantly reduced infection in the lungs but not in the nasal turbinates of hamsters intranasally challenged with SARS-CoV-2. Although post-challenge HuNAb therapy suppresses viral loads and lung damage, robust infection is observed in nasal turbinates treated within 1-3 days. This has significant implications for sub-protection, reinfection and vaccine.
Paper of the Day
Zhou B, Thi Nhu Thao T, Hoffmann D, et al. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature 26 February 2021. https://www.nature.com/articles/s41586-021-03361-1
Extensive study on the first update of SARS-CoV-2, namely the mutation at codon 614 (already partially dominant last spring in many countries). It is shown that the S-614G variant has enhanced binding to human host cell surface receptor ACE2, increased replication in primary human bronchial and nasal airway epithelial cultures as well as markedly increased replication and transmissibility in hamsters and ferrets. It will be interesting to see data on such in vivo competitive advantages with the new variants.
FT 2021026. The same covid-19 mutations are appearing in different places. Financial Times 2021, published 26 February. Link: https://www.economist.com/graphic-detail/2021/02/27/the-same-covid-19-mutations-are-appearing-in-different-places
Excellent ancestry tree of SARS-CoV-2. The Financial Times argues that convergent evolution might make travel restrictions redundant.
Bullock HA, Goldsmith CS, Zaki SR, Martines RB, Miller SE. Difficulties in differentiating coronaviruses from subcellular structures in human tissues by electron microscopy. Emerg Infect Dis, February 18, 2021 Apr [date cited]. https://wwwnc.cdc.gov/eid/article/27/4/20-4337_article
In attempts to attribute pathology directly to tissue damage caused by SARS-CoV-2, investigators have inaccurately reported subcellular structures, including coated vesicles, multivesicular bodies, and vesiculating rough endoplasmic reticulum, as coronavirus particles. Hannah A. Bullock from Atlanta and colleagues describe some morphologic features of coronavirus that distinguish it from subcellular structures.
Kim MC, Cui C, Shin KR, et al. Duration of Culturable SARS-CoV-2 in Hospitalized Patients with Covid-19. N Engl J Med. 2021 Feb 18;384(7):671-673. PubMed: https://pubmed.gov/33503337 . Full-text: https://doi.org/10.1056/NEJMc2027040
How long can we find culturable virus? Not beyond day 12. Min-Chul Kim and colleagues from Seoul, Korea, cultured SARS-CoV-2 in serial respiratory samples obtained from 21 hospitalized patients with COVID-19 to assess the duration of shedding of viable virus. The latest positive viral culture was 12 days after symptom onset (in one patient). Viral culture was positive only in samples with a cycle-threshold value of 28.4 or less.
Cao W, Dong C, Kim S, et al. Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction. Cell February 17, 2021. Full-text: https://www.cell.com/biophysj/fulltext/S0006-3495(21)00141-7
Using spectroscopy, the authors studied the interaction between the receptor-binding domain (RBD) at viral surface spike (S) protein of different coronaviruses and the angiotensin-converting enzyme 2 (ACE2) receptor expressed on many human cell types. The dissociate rate for RBD-CoV2−ACE2 and RBD-CoV1−ACE2 bonds or interactions were significantly different, possibly explaining the greater infectivity of SARS-CoV-2 vs SARS-CoV-1.
Kistler KE, Bedford T. Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e. Elife. 2021 Jan 19;10:e64509. PubMed: https://pubmed.gov/33463525. Full-text: https://doi.org/10.7554/eLife.64509
Kathryn Kistler and Trevor Bedford provide evidence that at least two of the seasonal coronaviruses, OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein that are exposed to human humoral immunity. This suggests that reinfection may be due, in part, to positively selected genetic changes in these viruses that enable them to escape recognition by the immune system.
Laue M, Kauter A, Hoffmann T, et al. Morphometry of SARS-CoV and SARS-CoV-2 particles in ultrathin plastic sections of infected Vero cell cultures. Sci Rep 11, 3515 (2021). https://doi.org/10.1038/s41598-021-82852-7
Profile of the criminal. Particle size: about 100 nm without spikes; maximal spike length: 23 nm; number of spikes per virus: 25.
Nanographics. High resolution renderings of SARS-CoV-2 Cryo-ET. Nanographics 2021, link: https://nanographics.at/projects/coronavirus-3d/
This is the first 3D image of SARS-CoV-2 made from a single scan of frozen virus particles. The authors used cryo-electron tomography scans and added colors to distinguish different parts of the virus. They release the image under Creative Commons Attribution license, so that everyone can use them freely in their work.
Paper of the Day
Greaney AJ, Loes AN, Crawford KHD, et al. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies. Cell 2021, 8 February. Full-text: https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(21)00082-2
Five weeks after the pre-print paper, now the publication in Cell Host Microbe. Jesse Bloom, Allison Greaney and colleagues comprehensively map how all mutations to the spike’s receptor-binding domain (RBD) reduce binding by antibodies in convalescent plasma. One major finding is that serum antibody binding is predominantly affected by mutations at just a few dominant epitopes in the RBD. The most important site is E484, where neutralization by some sera is reduced > 10-fold by several mutations. The authors’ approach doesn’t just consist in reactively characterizing mutations they observe in new lineages; rather, they prospectively map effects of all mutations so we can watch out for the next ones. Their bet for the future? The 443-450 loop in RBD, for example G446.
Ozono S, Zhang Y, Ode H, et al. SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nat Commun 12, 848 (2021). Full-text: https://www.nature.com/articles/s41467-021-21118-2
The D614G mutation increases cell entry by acquiring higher affinity to ACE2. The mutation does not affect neutralization by antisera against prototypic viruses.
Paper of the Day
Kemp SA, Collier DA, Datir RP, et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature 2021, published 5 February. Full-text: https://www.nature.com/articles/s41586-021-03291-y
In immune-suppressed patients, convalescent plasma therapy may lead to the emergence of viral variants with evidence of reduced susceptibility to neutralizing antibodies. Here, Ravinda Gupta, Steven Kemp and colleagues demonstrate that convalescent plasma therapy led to large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein.
McCarthy KR, Rennick LJ, Nambulli S, et al. Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape. Science 2021, published 3 January. Full-text: https://science.sciencemag.org/content/early/2021/02/02/science.abf6950
Coronaviruses acquire substitutions (variants) more slowly than other RNA viruses, due to a proofreading polymerase. In the spike glycoprotein, we find recurrent deletions overcome this slow substitution rate. In this adaptive evolution class, Paul Duprex, Kevin McCarthy and colleagues explain that deletion variants transmit efficiently, and are present in novel lineages, including those of current global concern. Deletions frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies.
Tegally H, Wilkinson E, Lessels RJ, et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med 2021, published 2 February. Full-text: https://doi.org/10.1038/s41591-021-01255-3
SARS-CoV-2 lineages from pre-variant times. Tulio de Oliveira, Houriiyah Tegally and colleagues analyzed 1,365 near whole genomes and report the identification of 16 new lineages isolated between March and August 2020. Most lineages had unique mutations that had not been identified elsewhere. The authors show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2.
Martin MA, VanInsberghe D, Koelle K. Insights from SARS-CoV-2 sequences. Science. 2021 Jan 29;371(6528):466-467. PubMed: https://pubmed.gov/33510015. Full-text: https://doi.org/10.1126/science.abf3995
In many ways, the SARS-CoV-2 pandemic offers a distinct opportunity for the field of phylodynamics. Methods development over the past 10 to 15 years, the widespread availability of sequencing technologies, open data sharing, and the tireless efforts of clinicians and scientists who collect these data mean that more can be learned from viral genomes than ever before.
Calisher CH, Childs JE, Field HE, Holmes KV, Schountz T. Bats: important reservoir hosts of emerging viruses. Clin Microbiol Rev. 2006 Jul;19(3):531-45. PubMed: https://pubmed.gov/16847084. Full-text: https://doi.org/10.1128/CMR.00017-06
Bats – more than 1000 species, 25% of all recognized species of mammals; living in HUGE communities (ideal for viral spread); flying dozens of kilometers while searching for food. Bats – fast reactors for viral evolution? Never forget this 2006 primer for emerging infectious diseases.
Starr TN, Greaney AJ, Addetia A. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science 25 Jan 2021:eabf9302. Full-text: https://doi.org/10.1126/science.abf9302
Incredible work, mapping how all mutations to SARS-CoV-2’s receptor-binding domain (RBD) affect binding by the antibodies from Regeneron and Lilly. There was not only a single amino acid mutation that fully escapes the REGN-COV2 cocktail but also mutations that were selected in a persistently infected patient treated with REGN-COV2, as well those already present in circulating SARS-CoV-2 strains. According to Tyler Starr and colleagues, it is “concerning that so many escape mutations impose little cost on RBD folding or receptor affinity, and that some are already present at low levels among circulating viruses”.
Johnson BA, Xie X, Bailey AL et al. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature January 25, 2021. Full-text: https://doi.org/10.1038/s41586-021-03237-4
SARS-CoV-2 has a furin cleavage site (PRRAR) in its spike protein that is absent in other CoVs. It has been postulated to be key to disease causing capability. To explore this, Bryan Johnson and colleagues from Texas generated a mutant SARS-CoV-2 deleting the furin cleavage site (ΔPRRA). SARS-CoV-2 ΔPRRA replicates had faster kinetics, improved fitness in Vero E6 cells, and reduced spike protein processing as compared to parental SARS-CoV-2. However, the ΔPRRA mutant had reduced replication in a human respiratory cell line and was attenuated in both hamster and K18-hACE2 transgenic mouse models of SARS-CoV-2 pathogenesis. Importantly, COVID-19 patient sera and RBD mAbs had lower neutralization values against the ΔPRRA mutant versus parental SARS-CoV-2.
Claro IM, da Silva Sales FC, Ramundo MS, Candido DS, Silva CAM, de Jesus JG, et al. Local transmission of SARS-CoV-2 lineage B.1.1.7, Brazil, December 2020. Emerg Infect Dis. January 25, 2021. Full-text: https://doi.org/10.3201/eid2703.210038
In December 2020, research surveillance detected the new SARS-CoV-2 variant B.1.1.7 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed two distinct introductions of the lineage. One patient reported no international travel. According to the authors, “there may be more infections with this lineage in Brazil than reported”. It would be surprising if not.
Mahase E. Covid-19: What new variants are emerging and how are they being investigated? BMJ. 2021 Jan 18;372:n158. PubMed: https://pubmed.gov/33462092. Full-text: https://doi.org/10.1136/bmj.n158
What do we know about the new variant emerging from Brazil? What do we know about the South African variant? Do the current vaccines work against the Brazilian, English, and South African variants? Could the virus still mutate to escape the vaccines? Elisabeth Mahase gives the preliminary answers.
Corum J, Zimmer C. Inside the B.1.1.7 Coronavirus Variant. The New York Times 2021, published 18 January. Full-text: https://www.nytimes.com/interactive/2021/health/coronavirus-mutations-B117-variant.html
Rambaut A, Loman N, Pybus O, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological 2020, Full-text: https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563/1
A paper we missed 4 weeks ago where Andrew Rambaut and colleagues describe the B117 lineage.
Tegally H, Wilkinson E, Giovanetti M, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Virological 2020, Full-text: doi: https://doi.org/10.1101/2020.12.21.20248640
Another paper we missed where Tulio de Oliveira, Houriiyah Tegally and colleagues describe the 501Y.V2 lineage characterized by eight mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa and spread rapidly, becoming the dominant lineage within weeks in the Eastern Cape and Western Cape Provinces.
Gravagnuolo AM, Faqih L, Cronshaw C, et al. Epidemiological Investigation of New SARS-CoV-2 Variant of Concern 202012/01 in England. medRxiv 2021, posted 15 January. Full-text: https://doi.org/10.1101/2021.01.14.21249386
The proportion in England of B117 (the new Variant of Concern) increased rapidly in December 2020 rising to over 70% of strong positive test results at the beginning of January 2021.
Cyranoski D. Alarming COVID variants show vital role of genomic surveillance. Nature 2021, published 15 January. Full-text: https://www.nature.com/articles/d41586-021-00065-4
2021 is shaping up to be the year of COVID-19 variants. In the past two months, scientists have identified several fast-spreading variants that have prompted government restrictions in many countries — and new variants are being detected more frequently.
Chen Y, Li S, Wu W, Geng S, Mao M. Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent global expansion. bioRxiv 2021, published 8 January. Full-text: https://doi.org/10.1101/2021.01.05.425339
Mao Mao, Yan Chen and colleagues analyzed 4013 full-length SARS-CoV-2 genomes from different continents over a 14-week timespan since the outbreak in Wuhan. 2954 unique nucleotide substitutions were identified with 31 of the 4013 genomes remaining as ancestral type, and 952 (32,2%) mutations recurring in more than one genome. The authors used the same approach to analyze 261.350 full-length SARS-CoV-2 genomes available in the GISAID database as of 25 December 2020. They suggest that viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures.
Zahradnik J, Marciano S, Shemesh M, et al. SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor. bioRxiv 2021, posted 8 January. Full-text: https://www.biorxiv.org/content/10.1101/2021.01.06.425392v2
SARS-CoV-2 is constantly evolving, with more contagious mutations spreading rapidly, in particular in England and South Africa. Here, Gideon Schreiber, Jiří Zahradník and colleagues show that the naturally selected mutations S477N, E484K, and N501Y of the Spike protein RBD, which show higher infectivity, were also selected by yeast surface display affinity maturation already in the first round, giving rise to the South African, E484K, N501Y, and British variants that bind ACE2 13 and 3,5-fold tighter than RBD-WT.
Greaney AJ, Loes AN, Crawford KHD, et al. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies. bioRxiv 2021, posted 4 January. Full-text: https://doi.org/10.1101/2020.12.31.425021
Jesse Bloom, Allison Greaney and colleagues comprehensively mapped how mutations to the SARS-CoV-2 RBD affected binding by the antibodies in convalescent human serum. One major finding is that serum antibody binding is predominantly affected by mutations at just a few dominant epitopes in the RBD. The most important site is E484, where neutralization by some sera is reduced > 10-fold by several mutations, including one in emerging viral lineages in South Africa and Brazil. Don’t miss this pre-print paper.
Andreano E, Piccini G, Licastro D, et al. SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma. bioRxiv. 2020 Dec 28:2020.12.28.424451. PubMed: https://pubmed.gov/33398278. Full-text: https://doi.org/10.1101/2020.12.28.424451
If constantly pressured, SARS-CoV-2 virus has the ability to escape even a potent polyclonal serum targeting multiple neutralizing epitopes. By Rino Rappuoli, Emanuele Andreano and colleagues.
Lauring AS, Hodcroft EB. Genetic Variants of SARS-CoV-2—What Do They Mean? JAMA 2021, published 6 January. Full-text: https://doi.org/10.1001/jama.2020.27124
The emergence of the new “UK variant”—lineage B.1.1.7—has raised widespread concern. Adam Lauring and Emma Hodcroft explain virus evolution and the genomic epidemiology of SARS-CoV-2. They conclude that it is possible that mutations in spike that are “good” for the virus right now could also make it less fit in the context of population-level immunity in the future. Defining these dynamics, and their potential influence on vaccine effectiveness, will require large-scale monitoring of SARS-CoV-2 evolution and host immunity for a long time to come.
Mahase E. Covid-19: What have we learnt about the new variant in the UK? BMJ 2020, published 23 December. Full-text: https://doi.org/10.1136/bmj.m4944
The new SARS-CoV-2 variant has evoked scenes reminiscent of the early days of COVID-19 when much of the world banned travel to and from Wuhan, China. With large parts of south-east England locked down, Elisabeth Mahase looks at what we know so far.
Li T, Liu D, Yang Y, et al. Phylogenetic supertree reveals detailed evolution of SARS-CoV-2. Sci Rep 10, 22366 (2020), published 22 December. Full-text: https://doi.org/10.1038/s415
The origin of SARS-CoV-2 and its evolutionary relationship is still being discussed. Here, Jie Feng, Tingting Li and colleagues applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2.
Schoof M, Faust B, Saunders RA, et al. An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike. Science 2020, Vol. 370, Issue 6523, pp. 1473-1479. Full-text: https://doi.org/10.1126/science.abe3255
Monoclonal antibodies that target SARS-CoV-2 must be produced in mammalian cells and need to be delivered intravenously. By contrast, nanobodies can be produced in bacteria or yeast, and their stability may enable aerosol delivery. Here, Aashish Manglik, Michael Schoof and colleagues describe nanobodies that disrupt the interaction between the SARS-CoV-2 Spike protein and the host cell receptor angiotensin-converting enzyme 2 (ACE2). Cryo–electron microscopy (cryo-EM) revealed that one nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains locked into their inaccessible down state, incapable of binding ACE2.
Xiang Y, Nambulli S, Xiao Z, et al. Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Science 2020, Vol. 370, Issue 6523, pp. 1479-1484. Full-text: Full-text: https://doi.org/10.1126/science.abe4747
In yet another paper on nanobodies, Yi She, Yufei Xiang and colleagues describe neutralizing nanobodies (Nbs) with picomolar to femtomolar affinities that inhibit viral infection at concentrations below the nanograms-per-milliliter level. The authors determined a structure of one of the most potent Nbs in complex with the RBD. Multivalent constructs of selected nanobodies achieved even more potent neutralization.
Pickering BS, Smith G, Pinette MM, et al. Susceptibility of domestic swine to experimental infection with severe acute respiratory syndrome coronavirus 2. Emerg Infect Dis December 17, 2020. Full-text: https://doi.org/10.3201/eid2701.200339
Domestic swine are susceptible to low levels of SARS-CoV-2 viral infection. Among 16 experimentally inoculated animals, 5 (31,3%) displayed some level of exposure or elicited an immune response to the virus. Only 1 pig in the study retained live virus, but 2 other animals had detectible RNA measured in nasal wash, and another 2 developed antibodies. Of note, Brad Pickering from the Canadian Food Inspection Agency and colleagues used a 10-fold higher viral dose for experimental infection than was used in previous studies.
Miao G, Zhao H, Li Y, et al. ORF3a of the COVID-19 virus SARS-CoV-2 blocks HOPS complex-mediated assembly of the SNARE complex required for autolysosome formation. Development Cell December 16, 2020. Full-text: https://doi.org/10.1016/j.devcel.2020.12.010
Have no clue what HOPS and SNARE complexes are? Never mind. Autophagy acts as a cellular surveillance mechanism to combat invading pathogens. Viruses have evolved various strategies to block autophagy and even subvert it for their replication and release. This study reveals a mechanism by which SARS-CoV-2 evades lysosomal destruction. ORF3a, an accessory protein specific to SARS-CoV-2, greatly impairs the formation of degradative autolysosomes.
Liu K, Tan S, Niu S, et al. Cross-species recognition of SARS-CoV-2 to bat ACE2. PNAS December 16, 2020. 118 (1). Full-text: https://doi.org/10.1073/pnas.2020216118
SARS-CoV-2 may infect bats, and the extensive species diversity of bats may have profound effects on SARS-CoV-2 evolution. However, SARS-CoV-2 receptor binding domain (RBD) binds to bACE2-Rm with lower affinity than that to human ACE2 receptor (hACE2).
Baric RS. Emergence of a Highly Fit SARS-CoV-2 Variant. NEJM December 16, 2020. Full-text: https://doi.org/10.1056/NEJMcibr2032888
Brief overview on the genetic and molecular evidence for enhanced fitness of the G614 variant over ancestral strains by Ralph S. Baric, one of the world‘s leading experts in the field. Fortunately, the new variant is as sensitive to the serum specimens as the D614 strain and thus should allay fears that it might escape vaccine-elicited immunity. However, there remains a critical need for proactive, rather than reactive, tracking of SARS-CoV-2 and other potential emerging coronaviruses.
Lu M, Uchil PD, Li W, et al. Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles. Cell Host Microbe. 2020 Dec 9;28(6):880-891.e8. PubMed: https://pubmed.gov/33242391. Full-text: https://doi.org/10.1016/j.chom.2020.11.001
More on the mechanisms of S (SARS-CoV-2 spike) recognition and conformations for immunogen design. The authors apply single-molecule fluorescence (Förster) resonance energy transfer (smFRET) imaging to observe conformational dynamics of S on viral particles, showing transitions from a closed ground state to the open receptor-accessible conformation via an on-path intermediate.
See also the comment by Serrão VHB, Lee JE. FRETing over SARS-CoV-2: Conformational Dynamics of the Spike Glycoprotein. Cell Host Microbe 2020, published 9 December. Full-text: https://doi.org/10.1016/j.chom.2020.11.008
Swann H, Sharma H, Preece B, et al. Minimal system for assembly of SARS-CoV-2 virus like particles. Sci Rep 10, 21877 (2020). Full-text: https://doi.org/10.1038/s41598-020-78656-w
Non-infectious virus-like particles (VLPs) displaying essential viral proteins can be used to study the structural properties of the SARS-CoV-2 virions and because of their maximum immunogenicity are also vaccine candidates. Here, Saveez Saffarian, Heather Swann and colleagues demonstrate that non-infectious SARS-CoV-2 virus-like particles (VLPs) can be assembled by co-expressing the viral proteins S, M and E in mammalian cells.
Wang K, Chen W, Zhang Z, et al. CD147-spike protein is a novel route for SARS-CoV-2 infection to host cells. Sig Transduct Target Ther 5, 283 (2020). Full-text: https://doi.org/10.1038/s41392-020-00426-x
Might there be a hitherto clandestine loophole for SARS-CoV-2 to enter into human cells? Here, Zhi-Nan Chen, Ke Wang and co-authors wonder that although angiotensin-converting enzyme 2 (ACE2) – the receptor which mediates the infection of cells by binding to the spike protein – is expressed in the lung, kidney, and intestine, its expressing levels are rather low, especially in the lung. They describe an interaction between the host cell receptor CD147 and the SARS-CoV-2 spike protein. The loss of CD147 or blocking CD147 in Vero E6 and BEAS-2B cell lines by anti-CD147 antibody meplazumab inhibited SARS-CoV-2 amplification. The authors suggest that a novel viral entry route via the CD147-spike protein might provide a new target for developing drugs against SARS-CoV-2.
Popa A, Genger JW, Nicholson MD. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Science Translational Medicine 23 November 2020: eabe2555. Full-text: https://doi.org/10.1126/scitranslmed.abe2555
Alexandra Popa, Andreas Bergthaler and colleagues from Vienna identified major SARS-CoV-2 clusters during the first wave of infections in Austria and performed deep whole-genome sequencing of 572 virus samples. Their genomic epidemiology analysis enabled the retrospective identification of SARS-CoV-2 chains of transmission and international hotspots. Taking advantage of a well-described and independently confirmed transmission network with 39 transmission events, the authors also found that the number of viral particles transmitted from one individual to another that contributed productively to the infection was on average higher than 1000. This suggests that social distancing and mask wearing may be effective even when they cannot prevent the spread of all viral particles.
Hammer AS, Quaade ML, Rasmussen TB, Fonager J, Rasmussen M, Mundbjerg K, et al. SARS-CoV-2 transmission between mink (Neovison vison) and humans, Denmark. Emerg Infect Dis Nov 18, 2020. 2021 Feb. Full-text: https://doi.org/10.3201/eid2702.203794
Anne Sophie Hammer and colleagues describe the outbreaks on three Danish mink farms. A high proportion of mink were infected within a few days, which may provide major virus exposure to persons working with mink. Full-length virus genome sequencing revealed novel viral variants in mink. These variants subsequently appeared within the local human community.
Volz E, Hill V, McCrone JT, et al. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell November 18, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.11.020
Investigating the hypothesis for positive selection of Spike D614G in more than 25.000 whole genome SARS-CoV-2 sequences from the UK, not all approaches showed a conclusive signal of positive selection. However, population genetic analysis indicated that 614G increased in frequency relative to 614D in a manner consistent with a selective advantage. 614G was also associated with higher viral load and younger age of patients.
Klein S, Cortese M, Winter SL, et al. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat Commun 11, 5885 (2020). Full-text: https://doi.org/10.1038/s41467-020-19619-7
How is the unusually large SARS-CoV-2 genome incorporated into the virion? Find the answer in this paper by Petr Chlanda, Ralf Bartenschläger, Steffen Klein and colleagues. The authors characterized the viral replication compartment and report critical insights into the budding mechanism of SARS-CoV-2.
Relman DA. Opinion: To stop the next pandemic, we need to unravel the origins of COVID-19. PNAS first published November 3, 2020. Full-text: https://doi.org/10.1073/pnas.2021133117
Important comment. According to David A. Relman from Stanford, “a more complete understanding of the origins of COVID-19 clearly serves the interests of every person in every country on this planet. It will limit further recriminations and diminish the likelihood of conflict; it will lead to more effective responses to this pandemic, as well as efforts to anticipate and prevent the next one. It will also advance our discussions about risky science. And it will do something else: Delineating COVID-19’s origin story will help elucidate the nature of our very precarious coexistence within the biosphere.”
Zheng J, Wong LR, Li K et al. COVID-19 treatments and pathogenesis including anosmia in K18-hACE2 mice. Nature (2020). Full-text: https://doi.org/10.1038/s41586-020-2943-z
SARS-CoV-2-infected K18-hACE2 mice developed dose-dependent lung disease with features similar to severe human COVID-19, including diffuse alveolar damage, inflammatory cell infiltration, tissue injury, lung vascular damage, and death. Remarkably, K18-hACE2 mice also support SARS-CoV-2 replication in the and associated with this pathology develop anosmia, a common feature of human disease.
Zhang Q. Chen, CZ, Swaroop M, et al. Heparan sulfate assists SARS-CoV-2 in cell entry and can be targeted by approved drugs in vitro. Cell Discov 6, 80 (2020). https://doi.org/10.1038/s41421-020-00222-5
The authors report that entry of SARS-CoV and CoV-2 requires the cell surface heparan sulfate (HS) as an assisting cofactor and that ablation of genes involved in HS biosynthesis or incubating cells with a HS mimetic inhibit Spike-mediated viral entry. After screening of approved drugs they identified various inhibitors: Mitoxantrone, Sunitinib and 7-benzylidenenaltrexone (BNTX).
Murugan NA, Kumar S, Jeyakanthan J, et al. Searching for target-specific and multi-targeting organics for Covid-19 in the Drugbank database with a double scoring approach. Sci Rep 10, 19125 (2020). https://doi.org/10.1038/s41598-020-75762-7
Next study on the use of computational screening approaches to identify lead drug-like compounds for Covid-19. The harvest (selection): Baloxavir marboxil, Phthalocyanine, Tadalafil, Lonafarnib, Nilotinib, Dihydroergotamine.
Shang J, Han N, Chen Z, et al. Compositional diversity and evolutionary pattern of coronavirus accessory proteins. Briefings in Bioinformatics, October 30, 2020, bbaa262. Full-text: https://doi.org/10.1093/bib/bbaa262
Accessory proteins play important roles in the interaction between coronaviruses and their hosts. The authors developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. This tool builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.
Han Y, Duan X, Yang L, et al. Identification of SARS-CoV-2 Inhibitors using Lung and Colonic Organoids. Nature 2020, October 28. Full-text: https://doi.org/10.1038/s41586-020-2901-9
The authors developed a lung organoid model using human pluripotent stem cells (hPSC-LOs). The hPSC-LOs, particularly alveolar type II-like cells, were permissive to SARS-CoV-2 infection, and showed robust induction of chemokines upon SARS-CoV-2 infection, similar to what is seen in COVID-19 patients. The authors also generated complementary hPSC-derived colonic organoids (hPSC-COs) to explore the response of colonic cells to SARS-CoV-2 infection. Both cell models can serve as disease models to study SARS-CoV-2 infection and provide a valuable resource for drug screening to identify candidate COVID-19 therapeutics.
V’kovski P, Kratzel A, Steiner S, et al. Coronavirus biology and replication: implications for SARS-CoV-2. Nat Rev Microbiol 2020, published 28 October. Full-text: https://doi.org/10.1038/s41579-020-00468-6
In contrast to the SARS-CoV epidemic of almost 20 years ago, improved technologies, such as transcriptomics, proteomics, single-cell RNA sequencing, global single-cell profiling of patient samples, advanced primary 3D cell cultures and rapid reverse genetics, have been valuable tools to understand and tackle SARS-CoV-2 infections. Follow the authors on a 13-page review of the first discoveries that shape our current understanding of SARS-CoV-2 infection throughout the intracellular viral life cycle and relate that to our knowledge of coronavirus biology.
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
The spike protein mutation D614G has become dominant in the current SARS-CoV-2 pandemic. Now, Pei-Yong Shi, Jessica Plante and colleagues show that D614G enhances replication on human lung epithelial cells and primary human airway tissues through an improved infectivity of virions. The mutation might also enhance viral loads in the upper respiratory tract of COVID-19 patients and increase transmission. The authors suggest that therapeutic antibodies should be tested against the circulating G614 virus. Discover why the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19.
Wei J, Alfajaro MM, DeWeirdt PC, et al. Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection. Cell October 20, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.10.028
Using genome-wide CRISPR screens in Vero-E6 cells, Jin Wei and colleagues have found some new host genes that affect infection by SARS-CoV-2 and other pandemic coronaviruses. In addition, the authors discovered pro-viral genes and pathways including HMGB1 which seems to have an epigenetic role in regulating ACE2 expression and thus susceptibility (HMGB1 is a pleiotropic protein that binds nucleosomes regulating chromatin in the nucleus and functions as a secreted alarmin in response to virus infection).
McNamara RP, Caro-Vegas C, Landis JT, et al. High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States. Cell Rep October 20, 2020. Full-text: https://doi.org/10.1016/j.celrep.2020.108352
The D614G mutation now dominates over the initial human strain defined by the SARS-CoV-2/human/CHN/Wuhan-01/2019 isolate. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern US region, showing that now 57% of strains carry the spike D614G variant, which was associated with higher genome copy numbers. Given the increasing abundance of D614G, further research into its role in pathogenicity and clinical outcomes is warranted.
Du P, Song C, Li R, et al. Specific re-distribution of SARS-CoV-2 variants in the respiratory system and intestinal tract, Clinical Infectious Diseases, ciaa1617. Full-text: https://doi.org/10.1093/cid/ciaa1617
Two distinct variants in a patient: Pengcheng Du and colleagues from Beijing report on a young male patient with mild symptoms who seemingly had a dual-infection of two SARS-CoV-2 variants. Of note, they also observed changes in the distribution of these variants in specimens collected from the respiratory and intestinal tracts during the course of the infection.
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
For many viruses, tissue tropism is determined by the availability of virus receptors and entry co-factors on the surface of host cells. Here, Mikael Simons, Ludovico Cantuti-Castelvetri and colleagues report that 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. Another potential target for antiviral intervention.
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
Again, neuropilin-1. Step-by-step: 1) SARS-CoV-2 uses the viral Spike (S) protein for host cell attachment and entry. 2) The host protease furin cleaves the full-length precursor S glycoprotein into two associated polypeptides: S1 and S2. 3) Cleavage of S generates a polybasic Arg-Arg-Ala-Arg C-terminal sequence on S1, which conforms to a C-end rule (CendR) motif that 4) binds to cell surface neuropilin-1 (NRP1) and neuropilin-2 (NRP2) receptors. Now Yohei Yamauchi, James Daly and colleagues show that the S1 CendR motif directly binds NRP1. Blocking this interaction, using RNAi or selective inhibitors, reduced SARS-CoV-2 entry and infectivity in cell culture. NRP1 binding to the CendR peptide in S1 is thus likely to play a role in the increased infectivity of SARS-CoV-2 compared with SARS-CoV. The authors conclude that the ability to target this specific interaction might provide a route for COVID-19 therapies.
Rattanapisit K, Shanmugaraj B, Manopwisedjaroen S. et al. Rapid production of SARS-CoV-2 receptor binding domain (RBD) and spike specific monoclonal antibody CR3022 in Nicotiana benthamiana. Sci Rep 10, 17698 (2020). Full-text: https://doi.org/10.1038/s41598-020-74904-1
This study demonstrates the rapid production of the RBD of SARS-CoV-2 and mAb CR3022 in Nicotiana benthamiana using a transient expression system. The plant-produced RBD showed specific binding to the receptor of SARS-CoV-2 (ACE2), confirming its structural integrity. Further, the plant-produced mAb CR3022 exhibited binding to SARS-CoV-2, but it failed to neutralize the virus in vitro. Overall, this study provides a proof-of-principle for the rapid production of SARS-CoV-2 antigens or monoclonal antibodies in a plant expression system in order to produce diagnostic reagents, vaccines and therapeutics.
Lu S, Zhao Y, Yu W, et al. Comparison of nonhuman primates identified the suitable model for COVID-19. Signal Transduct Target Ther. 2020 Oct 19;5(1):157. PubMed: https://pubmed.gov/32814760. Full-text: https://doi.org/10.1038/s41392-020-00269-6
The authors characterized SARS-CoV-2 infection in three non-human primate species: Old World monkeys Macaca mulatta (M. mulatta) and Macaca fascicularis (M. fascicularis) and New World monkey Callithrix jacchus (C. jacchus). Susceptibilities of Old World and New World monkeys to SARS-CoV-2 differed markedly. Macaca mulatta seemed to be the most suitable for modeling COVID-19.
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
Nevan Krogan, David Gordon and colleagues – a group of 200 researchers – uncovered molecular processes used by coronaviruses MERS, SARS-CoV1 and SARS-CoV2 to manipulate host cells. The researchers from six countries found 73 human proteins with which components of all three types of the virus enter into bonds and thus influence the survival of infected cells in culture. Host factors that functionally impinge on coronavirus proliferation include Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 Orf9b. The consortium also discovered cell surface molecules that are influenced by all three coronaviruses and that bind to already approved drugs, for example an antipsychotic and an anti-inflammatory drug.
Riddell S, Goldie S, Hill A, et al. The effect of temperature on persistence of SARS-CoV-2 on common surfaces. Virol J 17, 145 (2020). Full-text: https://doi.org/10.1186/s12985-020-01418-7
It might seem that SARS-CoV-2 could remain infectious for longer time periods than generally considered until recently. Shane Riddell et al. measured the survival rates of infectious SARS-CoV-2 on several common surface types. They incubated the inoculated surfaces at 20 °C, 30 °C and 40 °C and sampled at various time points. The authors report isolation of viable virus for up to 28 days at 20 °C from common surfaces such as glass, stainless steel and both paper and polymer banknotes. A temperature of 40 °C, however, didn’t seem to suit the virus: it survived less than 24 h.
Note of the Editor: After more than 6 months living in the new SARS-CoV-2 world, this study might not change my behavior.
Vann KR, Tencer AH, Kutateladze TG. Inhibition of translation and immune responses by the virulence factor Nsp1 of SARS-CoV-2. Sig Transduct Target Ther 5, 234 (2020). Full-text: https://doi.org/10.1038/s41392-020-00350-0
A major virulence factor of SARS-CoV is the non-structural protein 1 (Nsp1) which suppresses host gene expression by ribosome association (see our July 18 CR Top 10: Thoms M, Buschauer R, Ameismeier M, et al. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science 17 Jul 2020: eabc8665. Full-text: https://doi.org/10.1126/science.abc8665). The authors briefly review Nsp1’s ability to downregulate the innate immune responses. A new drug target?
Bruchez A, Sha K, Johnson J, et al. MHC class II transactivator CIITA induces cell resistance to Ebola virus and SARS-like coronaviruses. Science 2020, published 9 October. Full-text: https://doi.org/10.1126/science.abb3753
The concerted efforts of antiviral factors within cells are central to host cell defense. Without these factors, the cell remains defenseless against potentially harmful pathogens (Wells 2020). Here, the authors show that the major histocompatibility complex (MHC) class II transactivator (CIITA) has antiviral activity against Ebola virus (EBOV). They show that CIITA induces resistance by up-regulation of the p41 isoform of CD74, which blocks cathepsin-mediated cleavage of viral GPs, thereby preventing viral fusion. CD74 p41 can also block the endosomal entry pathway of coronaviruses, including SARS-CoV-2.
See also the comment by Wells, AI, Coyne CB. Inhibiting Ebola virus and SARS-CoV-2 entry. Science 2020, published 9 October. Full-text: https://doi.org/10.1126/science.abe2977
Cheng MH, Zhang S, Porritt RA, et al. Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. PNAS first published September 28, 2020. Full-text: https://doi.org/10.1073/pnas.2010722117
Mary Hongying Cheng and colleagues from Pittsburgh show that SARS-CoV-2 spike contains sequence and structure motifs highly similar to those of a bacterial superantigen and may directly bind T cell receptors. They also report a skewed T cell receptor repertoire in COVID-19 patients with severe hyperinflammation, in support of such a superantigenic effect. Notably, the superantigen-like motif is not present in other SARS family coronaviruses, which may explain the unique potential for SARS-CoV-2 to cause both MIS-C and the cytokine storm observed in adult COVID-19.
Rosas-Lemus M, Minasov G, Shuvalova L, et al. High-resolution structures of the SARS-CoV-2 2′-O-methyltransferase reveal strategies for structure-based inhibitor design. Science Signaling, September 29: Vol. 13, Issue 651, eabe1202. Full-text: https://doi.org/10.1126/scisignal.abe1202
The components of the replication-transcription complex include enzymes that regulate mRNA and genomic RNA synthesis, proofreading, and mRNA maturation. Enzymes such as nsp16 are critical for capping viral mRNAs, a tactic used by multiple RNA viruses to avoid immune detection. Monica Rosas-Lemus and colleagues performed an x-ray crystallographic study of the SARS-CoV-2 nsp16-nsp10 2′-O-methyltransferase complex, which methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. They solved crystal structures for the methyltransferase in complex with various combinations of its methyl donor and cap structure substrates, a reaction product, and an inhibitor. These structures suggest potential treatment strategies by disrupting the formation of the active enzyme complex or blocking its catalytic activity.
Brooke GN Prischi F. Structural and functional modelling of SARS-CoV-2 entry in animal models. Sci Rep 10, 15917 (2020). Full-text: https://doi.org/10.1038/s41598-020-72528-z
Greg Brooke and Filippo Prischi compared the ACE2 receptor, and TMPRSS2 and Furin proteases usage of the SARS-CoV-2 Spike glycoprotein in human and in a panel of animal models (guinea pig, dog, cat, rat, rabbit, ferret, mouse, hamster, macaque) and find that ACE2, but not TMPRSS2 or Furin, has a higher level of sequence variability in the Spike protein interaction surface, which greatly influences Spike protein binding mode. The authors also show that the Spike (S) protein recognizes macaque, hamster, and ferret in a comparable way to human ACE2. However, there were substantial differences in the binding mode of the SARS-CoV and SARS-CoV-2 S protein to guinea pigs, mice and rats ACE2.
Muñoz-Fontela C, Dowling WE, Funnell SGP, et al. Animal models for COVID-19. Nature. 2020 Sep 23. PubMed: https://pubmed.gov/32967005. Full-text: https://doi.org/10.1038/s41586-020-2787-6
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. According to this review (performed by a huge international collaboration), however, no murine model at present recapitulates all aspects of human COVID-19, especially unusual features such as the pulmonary vascular disease observed in adults and hyperinflammatory syndromes in children.
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
This group from Bristol, UK determined the structure of the SARS-CoV-2 S glycoprotein by cryo-EM. The receptor binding domains (RBDs) tightly bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. At least four molecular features mediating LA binding to SARS-CoV-2 were identified. 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.
Yao H, Song Y, Chen Y, et al. Molecular architecture of the SARS-CoV-2 virus. Cell 2020, published 14 September. Full-text: https://doi.org/10.1016/j.cell.2020.09.018
How does a virus pack its ∼30 kb long single-segmented RNA in a ∼80 nm diameter lumen? Here, Sai Li, Lanjuan Li and Hangping Yao report the molecular assembly of the authentic SARS-CoV-2 virus using cryo-electron tomography and subtomogram averaging. From ~2300 intact virions, the authors provide molecular insights into the structures of spikes in the pre- and post-fusion conformations, the ribonucleoproteins and how they assemble on the authentic virus. They also analyzed the detailed glycan compositions of the native spikes.
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
The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide in a matter of months, suggesting that the mutation confers a replication advantage. Here, the authors show that D614G is more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs, while not altering S protein synthesis, processing, or incorporation into SARS-CoV-2 particles. Remember that the D614G variant is not associated with more severe COVID-19.
Benton DJ, Wrobel AG, Xu P, et al. Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion. Nature (2020). https://doi.org/10.1038/s41586-020-2772-0
After investigating the binding of ACE2 to the furin-cleaved form of SARS-CoV-2 S by cryoEM, Steven Gamblin, Donald Benton and colleagues propose mechanistic suggestions for the early stages of SARS-CoV-2 infection of cells. The authors classified ten different molecular species including the unbound, closed spike trimer, the fully open ACE2-bound trimer, and dissociated monomeric S1 bound to ACE2.
Shannon A, Selisko B, Le N. Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis. Nat Commun 11, 4682 (2020). https://doi.org/10.1038/s41467-020-18463-z
The SARS-CoV-2 RNA-dependent-RNA-polymerase (RdRp) is a promising therapeutic target for polymerase inhibitors. Here, Bruno Canard, Ashleigh Shannon and colleagues propose that favipiravir could exert an antiviral effect through lethal mutagenesis. They also suggest that the RdRp complex might be an Achilles heel for SARS-CoV-2. Hopefully SARS-CoV-2 has more than just one Achilles heel.
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
What do we know about the dynamics of the binding of the spike (S) glycoprotein to the ACE2 receptor at the single-molecule level? Try atomic force microscopy. David Alsteens, Jinsung Yang and colleagues demonstrate, both on model surfaces and on living cells, that the receptor binding domain serves as the binding interface within the S-glycoprotein with the ACE2 receptor and extract the kinetic and thermodynamic properties of this binding pocket. Then they examined how several ACE2-derived peptide fragments could interfere with the S1–ACE2 complex formation. Peptides mimicking the N-terminal helix of the ACE2 receptor showed the best results. New therapeutic candidates?
Finkel Y, Mizrahi O, Nachshon A, et al. The coding capacity of SARS-CoV-2. Nature 2020, published 9 September. Full-text: https://doi.org/10.1038/s41586-020-2739-1
Eight months into the COVID-19 pandemic, do we know everything about SARS-CoV-2? Maybe not, say Noam Stern-Ginossar, Yaara Finkel and colleagues and delineate a new highly complex landscape of translation products, including translation of 23 novel viral open reading frames (ORFs) and revealed the relative production of canonical viral proteins. The functional significance and antigenic potential of these ORFs will soon be explored.
Unchwaniwala N, Ahlquist P. Coronavirus dons a new crown. Science 2020, published 11 September. Full-text: https://doi.org/10.1126/science.abe0322
Nuruddin Unchwaniwala and Paul Ahlquist discuss the paper by Montserrat Bárcena, Georg Wolff et al. [Wolff G, Limpens RWAL, Zevenhoven-Dobbe JC, et al. A molecular pore spans the double membrane of the coronavirus replication organelle. Science. 2020 Aug 6:eabd3629. PubMed: https://pubmed.gov/32763915. Full-text: https://doi.org/10.1126/science.abd3629] tried to understand how progeny (+)RNA genomes are released from double-membrane vesicles.
Callaway E. The coronavirus is mutating — does it matter? Nature 2020, published 8 September. Full-text: https://www.nature.com/articles/d41586-020-02544-6
Is there evolutionary pressure on the virus to spread better? Maybe later, but not now. At a time when nearly everyone on the planet is susceptible, “every single person that it comes to is a good piece of meat (William Hanage)”. Follow Ewen Callaway on a ‘Current Knowledge Tour’ about SARS-CoV-2 mutations
O’Leary VB, Ovsepian SV. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Trends in Genetics. Published August 26, 2020. Full-text: https://doi.org/10.1016/j.tig.2020.08.014
Brief review of the genome of SARS-CoV-2. Valerie Bríd O’Leary and Saak Victor Ovsepian also provide a fun fact you should know before you die: The SARS-CoV-2 non-structural protein 3 has a 46% similarity to a protein also found in a ray-finned fish Labrus bergylta (Ballan wrasse), a protogynous hermaphrodite, that begins life as a female yet with territorial dominance becomes male. If you are tempted to try CoV-2-protein: wrasses have firm meat and taste excellent.
Sardar R, Satish D, Birla S. Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction, pathogenesis and clues for novel therapies. Heliyon August 20, 2020. Full-text: https://doi.org/10.1016/j.heliyon.2020.e04658
Integrative analysis of SARS-CoV-2 genome sequences from different countries, confirming unique features absent in other evolutionarily related coronavirus family genomes, which presumably confer unique infection, transmission and virulence capabilities to the virus. This work explores the functional impact of the virus mutations on its proteins and interaction of its genes with host antiviral mechanisms.
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, complicating model development. Sometimes it is better to modify the virus (vs the mouse): Kenneth H. Dinnon et al. altered the SARS-CoV-2 receptor binding domain allowing viral entry via mACE, using reverse genetics to remodel the interaction between S and mACE2. This resulted in a recombinant virus (SARS-CoV-2 MA) that could utilize mACE2 for entry. SARS-CoV-2 MA replicated in both the upper and lower airways of both young adult and aged standard lab mice. Importantly, disease was more severe in aged mice, and showed more clinically relevant phenotypes than those seen in HFH4-hACE2 transgenic mice. This model may be helpful in studying COVID-19 pathogenesis.
To KK, Hung IF, Ip JD, et al. COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing. Clinical Infectious Diseases, 25 August 2020, ciaa1275. Full-text: https://doi.org/10.1093/cid/ciaa1275
The first case of re-infection? During recent weeks, there has been probably no other case report gaining so much media attention as this 33-year old gentleman residing in Hong Kong. By the end of March, a mildly symptomatic SARS-CoV-2 infection was confirmed by a positive posterior oropharyngeal saliva PCR on March 26, 2020. On August 15, 142 days later, the patient returned to Hong Kong from Spain via the United Kingdom and was tested positive by SARS-CoV-2 RT-PCR on the posterior oropharyngeal saliva taken for entry screening at the Hong Kong airport. Of note, the patient remained asymptomatic during the second episode but had elevated CRP, relatively high viral load with gradual decline, and seroconversion of SARS-CoV-2 IgG during the second episode, suggesting that this was a genuine episode of acute infection. Viral genomes from first and second episodes belonged to different clades/lineages. Kwok-Yung Yuen, Kelvin Kai-Wang To and colleagues discuss several implications of this case.
Damas J, Hughes GM, Keough KC, et al. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. PNAS August 21, 2020 Full-text: https://doi.org/10.1073/pnas.2010146117
Joana Damas and colleagues utilized a unique dataset of ACE2 sequences from 410 vertebrate species, including 252 mammals, to study the conservation of ACE2 and its potential to be used as a receptor by SARS-CoV-2. A large number of mammals were identified that can potentially be infected by SARS-CoV-2 via their ACE2 proteins. Species with the highest risk for SARS-CoV-2 infection were wildlife and endangered species. However, the authors urge caution not to overinterpret their predictions, given the limited infectivity data for the species studied.
Wang Z, Zhang L, Wu M. Human-viral chimera: a novel protein affecting viral virulence and driving host T-cell immunity. Sig Transduct Target Ther 5, 167 (2020). Full-text: https://doi.org/10.1038/s41392-020-00272-x
Zhenling Wang, Li Zhang and Min Wu discuss the paper by Ho et al. (see below) which shows that RNA viruses like influenza A can produce previously unrecognized chimeric proteins containing both viral and human genetic information, which can then affect virulence and modulate T cell responses in hosts. They conclude that this finding could lend critical insight into designing novel approaches to control emerging viral infections, such as SARS-CoV-2. (Ho JSY, Angel M, Ma Y, et al. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell. 2020 Jun 25;181(7):1502-1517.e23. PubMed: https://pubmed.gov/32559462. Full-text: https://doi.org/10.1016/j.cell.2020.05.035)
Latinne A, Hu B, Olival KJ et al. Origin and cross-species transmission of bat coronaviruses in China. Nat Commun 11, 4235 (2020). Full-text: https://www.nature.com/articles/s41467-020-17687-3
All coronaviruses (CoV) known to infect humans are zoonotic, or of animal origin, with many thought to originate in bat hosts. Now Peter Daszak, Alice Latinne and colleagues analyze their macroevolution, cross-species transmission and dispersal and present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in bats of the genus Rhinolophus. They also show that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs and is more highly constrained by phylogenetic distance for beta-CoVs. The authors identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance.
Zhao P, Praissman JL, Grant OC, et al. Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor. bioRxiv. 2020 Jul 24:2020.06.25.172403. PubMed: https://pubmed.gov/32743578. Full-text: https://doi.org/10.1101/2020.06.25.172403
A detailed understanding of SARS-CoV-2 Spike binding to ACE2 is critical for elucidating the mechanisms of viral binding and entry, as well as for the rational design of effective therapeutics. Here Lance Wells, Peng Zhao and colleagues utilize glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer Spike mimetic immunogen and for a soluble version of human ACE2. The authors generate molecular dynamics simulations of each glycoprotein alone and interacting with one another. Their data and related similar findings might provide a framework to facilitate the production of immunogens, vaccines, antibodies, and inhibitors as well as providing additional information regarding mechanisms by which glycan microheterogeneity is achieved.
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
Fully understanding how SARS-CoV-2 Spike (S) proteins function and how they interact with the immune system, requires knowledge of the structures, conformations and distributions of S trimers within virions. Now John Briggs and colleagues collect viral particles from infected cells and determine the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface. They express optimism that cryo-electron microscopy can be used to study antibody binding to S in the context of the viral surface. Such studies would provide insights into how neutralizing antibodies block virus infection, particularly for antibodies against membrane-proximal regions of S, and could thus inform design of immunogens for vaccination.
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
If you are not a virologist, cryo electron tomography, sub-tomogram averaging and molecular dynamics simulations may all be Greek to you. To structurally analyze the SARS-CoV-2 Spike (S) protein in situ, Martin Beck, Jacomina Locker, Gerhard Hummer and colleagues did exactly that. They show that the stalk domain of S contains three hinges, giving the head unexpected orientational freedom, and propose that the hinges allow S to scan the host cell surface, shielded from antibodies by an extensive glycan coat.
Sarkar M, Saha S. Structural insight into the role of novel SARS-CoV-2 E protein: A potential target for vaccine development and other therapeutic strategies. PLoS ONE August 13, 15(8). Full-text: https://doi.org/10.1371/journal.pone.0237300 Full-text:
Coronaviruses have four main structural proteins: Nucleocapsid protein (N), Spike protein (S), Membrane protein (M), and Envelope protein (E). The E protein is the smallest and is involved in a wide spectrum of functional repertoire. Using the bioinformatics and structural modelling approach, the authors modelled the structure of E and give insights into the functional role of this protein that has a low disparity and low mutability.
Lau SKP, Wong ACP, Luk HKH, Li KSM, Fung J, He Z, et al. Differential tropism of SARS-CoV and SARS-CoV-2 in bat cells. Emerg Infect Dis. 2020 Dec [date cited]. Full-text: https://doi.org/10.3201/eid2612.202308
SARS-CoV-2 did not replicate efficiently in 13 bat cell lines, whereas SARS-CoV replicated efficiently in kidney cells of its ancestral host, the Rhinolophus sinicus bat, suggesting different evolutionary origins. Structural modeling showed that RBD/RsACE2 binding may contribute to the differential cellular tropism. Although SARS-CoV-2 is closely related to SARS-CoVs in bats and pangolins, none of the existing animal viruses represents the immediate ancestor of SARS-CoV-2.
Alm E, Broberg EK, Connor T. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance Volume 25, Issue 32, 13/Aug/2020. Full-text: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.32.2001410
How do genetic clades distribute between European countries? Erik Alm and colleagues have applied the available nomenclatures to describe broad geographical and temporal trends in the distribution of SARS-CoV-2 genetic clades and discuss potential genomic surveillance objectives at the European level.
Sun Z, Cai X, Gu C et al. Survival of SARS-COV-2 under liquid medium, dry filter paper and acidic conditions. Cell Discov 6, 57 (2020). Full-text: https://doi.org/10.1038/s41421-020-00191-9
Zhenghong Yuan, Youhua Xie, Di Qu and colleagues show that SARS-COV-2 can survive for 3 days in liquid medium or on dry filter paper. At high titers, the virus might also be able to survive under acidic conditions that mimic the gastric environment.
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 receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. These researchers from Seattle 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.
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. Using cellular electron cryo-microscopy, the authors visualized 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.
Huang Y, Yang C, Xu X et al. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin 2020, published 3 August. Full-text: https://www.nature.com/articles/s41401-020-0485-4
The spike protein of SARS-CoV-2 plays a key role in the receptor recognition and cell membrane fusion process. In this review, Shu-wen Liu, Wei Xu and colleagues from Southern Medical University, Guangzhou, China, highlight recent research advances in the structure, function and development of antiviral drugs targeting the S protein. Six pages, 86 references.
Xiong X, Qu K, Ciazynska KA, et al. A thermostable, closed SARS-CoV-2 spike protein trimer. Nat Struct Mol Biol. 2020 Jul 31. PubMed: https://pubmed.gov/32737467. Full-text: https://doi.org/10.1038/s41594-020-0478-5
The spike (S) protein which mediates receptor binding and cell entry exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor-binding site and, subsequently, from pre-fusion to post-fusion conformations to mediate fusion of viral and cellular membranes. John Briggs, Xiaoli Xiong and colleagues now design mutations in the spike protein to allow the production of thermostable, disulfide-bonded S-protein trimers that are trapped in the closed, pre-fusion state. Furthermore, they demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. They anticipate a wide array of potential applications as a reagent for serology, virology and as an immunogen.
Shin D, Mukherjee R, Grewe D et al. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 2020, published 29 July. Full-text: https://doi.org/10.1038/s41586-020-2601-5
The papain-like protease PLpro, an essential coronavirus enzyme required for generating a functional replicase complex, is also implicated in evasion mechanisms against host anti-viral immune responses. Now Ivan Dikic and colleagues from Frankfurt Goethe University show that SCoV2-PLpro attenuates type I interferon responses and that inhibition of SCoV2-PLpro with the naphthalene-based inhibitor GRL-0617 impairs virus-induced cytopathogenic effects, fosters the anti-viral interferon pathway and reduces viral replication in infected cells. The authors conclude that targeting of SCoV2-PLpro could suppress SARS-CoV-2 infection and promote anti-viral immunity.
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
The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with accessory factors such as the nsp13 helicase. Elizabeth A. Campbell, Seth A. Darst and colleagues now present 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.
Viswanathan T, Arya S, Chan SH, et al. Structural basis of RNA cap modification by SARS-CoV-2. Nat Commun 11, 3718 (2020). Full-text: https://doi.org/10.1038/s41467-020-17496-8
Does SARS-CoV-2 use an alarm code to enter cells without bells going off? That’s the proposal by Yogesh K. Gupta and colleagues who explain that the virus possesses the code to waltz right in. The authors report the high-resolution structure of a ternary complex of SARS-CoV-2 nsp16 and nsp10 (nps = nonstructural protein) in the presence of cognate RNA substrate analogue and methyl donor, S-adenosyl methionine. The nsp16/nsp10 heterodimer is captured in the act of 2′-O methylation of the ribose sugar of the first nucleotide of SARS-CoV-2 mRNA. A perfect camouflage: SARS-CoV-2 avoids the induction of the innate immune response mediated by interferon stimulated genes. As a result of these modifications, viral messenger RNA is considered as part of the cell’s own code and not foreign. As genetic disruption of SARS-CoV nsp16 markedly reduces (by 10-fold) the synthesis of viral RNA, the authors speculate that the ablation of nsp16 activity should trigger an immune response to SARS-CoV-2 infection and limit pathogenesis. They go on to describe a distantly located ligand-binding site in nsp16/10 capable of accommodating small molecules outside of the catalytic pocket. A new class of antiviral drugs on the horizon? Remember that these developments take years.
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. Discover why the study raises potential concerns about current vaccine strategies.
Pollock DD, Castoe TA, Perry BW, et al. Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Mol Biol Evol. 2020 Jul 13. PubMed: https://pubmed.gov/32658964 . Full-text: https://doi.org/10.1093/molbev/msaa178
No, dogs are not intermediate hosts. The authors clearly refute the conclusions of another group that dogs are a likely intermediate host of a SARS-CoV-2 ancestor, highlighting major flaws in the inference process and analysis.
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 (within one day) at 37°C. SARS-CoV-2 in solution remained viable for much longer under the same different temperature conditions. Commonly used fixatives, nucleic acid extraction methods and heat inactivation were found to significantly reduce viral infectivity.
Wang X, Xu W, Hu G, et al. Retraction Note to: SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion. Cell Mol Immunol (2020). Full-text: https://doi.org/10.1038/s41423-020-0498-4
The authors have retracted this article (which has been discussed in the Virology chapter of the 4th issue of covidreference.com) after it came to the authors’ attention that in order to support the conclusions of the study, the authors should have used primary T cells instead of T cell lines. In addition, there were concerns that the flow cytometry methodology applied here was flawed. These points resulted in the conclusions being considered invalid. The question remains why the reviewers (a highly ranked Cell journal would have at least 2-4 for each paper) did not see this. But again, good news: bad science will not stand the test of time.
Abritis A, Marcus A, Oransky I. An ‘alarming’ and ‘exceptionally high’ rate of COVID-19 retractions? Account Res. 2020 Jul 7. PubMed: https://pubmed.gov/32634321. Full-text: https://doi.org/10.1080/08989621.2020.1793675
While we’re at it: See the title. The authors say no. It should also be noted that COVID-19 papers are being subjected to a high rate of scrutiny, which means that flaws are being detected more frequently than they might otherwise.
Wong YC, Lau SY, Wang KK, et al. Natural transmission of bat-like SARS-CoV-2ΔPRRA variants in COVID-19 patients. Clin Infect Dis July 10, 2020. Full-text: https://doi.org/10.1093/cid/ciaa953
SARS-CoV-2 contains the furin cleavage PRRA motif in the S1/S2 region, which enhances viral pathogenicity but is absent in closely related bat and pangolin coronaviruses. It remains unknown if bat-like coronaviral variants without PRRA (ΔPRRA) can establish natural infection in humans. In this study, these variants were readily detected among acute patients, including a family cluster showing that these variants exist naturally and are currently transmitting in COVID-19 patients. Although these variants only consisted of a very small fraction in the wild type viral challenge stock, they were also consistently detected in intranasally inoculated hamsters.
Sharma A, Garcia G, Arumugaswami V, Svendsen CN. Human iPSC-Derived Cardiomyocytes are Susceptible to SARS-CoV-2 Infection. bioRxiv. 2020 Apr 21:2020.04.21.051912. PubMed: https://pubmed.gov/32511402. Full-text: https://doi.org/10.1101/2020.04.21.051912
In this study, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) were used as a model to examine the mechanisms of cardiomyocyte-specific infection by SARS-CoV-2. Microscopy and RNA-sequencing demonstrated that SARS-CoV-2 can enter hiPSC-CMs via ACE2. Viral replication and cytopathic effect induce hiPSC-CM apoptosis and cessation of beating after 72 hours of infection.
Qian Q, Fan L, Liu W, et al. Direct evidence of active SARS-CoV-2 replication in the intestine. Clin Inf Dis 2020, July 8. Full-text: https://doi.org/10.1093/cid/ciaa925
The virus is not only in the heart but also in the rectum. In this case report, quantitative RT-PCR was performed on rectal tissue specimens obtained from surgical resection in a COVID-19 patient with rectal adenocarcinoma. RNA of SARS-CoV-2 was detected in surgically resected rectal specimens, but not in samples collected 37 days after discharge. Notably, coinciding with rectal tissues of surgical specimens nucleic acid positive for SARS-CoV-2, typical coronavirus virions in rectal tissue were observed under electron microscopy. Moreover, abundant lymphocytes and macrophages (some are SARS-CoV-2 positive) infiltrating the lamina propria were found with no significant mucosal damage.
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
Based on 28,576 sequences until May 29, 2020, the authors show that 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. G614 has replaced D614 as the dominant pandemic form and the consistent increase of G614 at regional levels may indicate a fitness advantage. Moreover, G614 is associated with lower RT-PCR CT in the upper respiratory tract, suggestive of higher viral loads in patients. The G614 variant also grows to higher titers as pseudotyped virions. However, there was no association between G614 and disease severity.
Grubaugh ND, Hanage WP, Rasmussen AL. Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear. Cell July 02, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.06.040
Comment on the above work. Main message = title. While clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, vaccine and therapeutic development are largely unknown. As these forces can work in tandem, it’s often hard to differentiate when a virus mutation becomes common through fitness or by chance. It is even harder to determine if a single mutation will change the outcome of an infection, or a pandemic.
Barr IG, Rynehart C, Whitney P, et al. SARS-CoV-2 does not replicate in embryonated hen’s eggs or in MDCK cell lines. Eurosurveillance Volume 25, Issue 25, 25/Jun/2020. Full-text: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.25.2001122
This study showed that even if a clinical sample, containing both human influenza and SARS-CoV-2, was inoculated into substrates used to prepare seeds for influenza vaccine production (embryonated chicken eggs or MDCK-based cell lines), SARS-CoV-2 would be unlikely to be propagated and would be undetectable after a small number of passages. This finding reassures influenza vaccine production staff and laboratory scientists who might be concerned about potential exposure to SARS-CoV-2 and also suggests that loss of potentially important influenza candidate vaccine viruses or final vaccine lots due to SARS-CoV-2 contamination is unlikely.
Wu KE, Fazal FM, Parker KR, et al. RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. Cell Systems, June 20, 2020. Full-text: https://doi.org/10.1016/j.cels.2020.06.008
SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell’s machinery. But where is the viral RNA localized in the cell? Computational modeling of SARS-CoV-2 viral RNA subcellular residency across eight subcellular neighborhoods, predicted the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus. The authors interpret the mitochondrial residency signal as an indicator of intracellular RNA trafficking with respect to double-membrane vesicles, a critical stage in the coronavirus life cycle.
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 ll (Outstanding)
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 in an adaptive manner. The authors discuss the potential evolutionary routes that SARS-CoV-2 might take and dispel some of the current misinformation that is circulating in the media.
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, SARS-CoV and MERS-CoV from less pathogenic coronaviruses. Exploring the regions identified within the nucleocapsid that predict the high case fatality rate of coronaviruses, the authors found that these deletions and insertions result in substantial enhancement of motifs that determine nuclear localization. The deletions, insertions, and substitutions in the N proteins of the high-CFR coronaviruses map to two monopartite nuclear localization signals. These findings imply an important role of the subcellular localization of the nucleocapsid protein in coronavirus pathogenicity.
Wang H, Zhang Y, Huang B, et al. Development of an inactivated vaccine candidate, BBIBP-CorV, with potent protection against SARS-CoV-2. Cell 2020, June 06. Full-text: https://doi.org/10.1016/j.cell.2020.06.008
Will this be the first vaccine? Compared with the adenovirus-vectored and the DNA vaccine, inactivated vaccine development and production is a conventional and mature technology (main pro: large amounts of vaccine doses can be easily manufactured, main con: safety issues, including an antibody-dependent worsening of the infection). BBIBP-CorV, an inactivated SARS-CoV-2 vaccine, induced high levels of neutralizing antibody in several animal models, including 8 rhesus macaques, protecting them against SARS-CoV-2 infection. There was no observable antibody-dependent infection enhancement or immunopathological exacerbation. A Phase I clinical trial of BBIBP-CorV is currently in progress and a Phase II clinical trial has recently been initiated.
Cyranoski D. The biggest mystery: what it will take to trace the coronavirus source. Nature 2020, June 05. Full-text: https://www.nature.com/articles/d41586-020-01541-z
Elegant article summarizing the current (and limited) knowledge of the origin of SARS-CoV-2. Most researchers say the more likely explanation is that bats passed it to an intermediate animal, which then spread it to people. However, this finding will be tricky, as will calming speculations of a “lab escape”. This would require a forensic investigation, looking for viruses that matched the genetic sequence of SARS-CoV-2 and. Authorities would need to take samples from the lab, interview staff, review lab books and records of safety incidents, and see what types of experiment researchers had done.
Sun SH, Chen Q, Gu HJ, et al. A Mouse Model of SARS-CoV-2 Infection and Pathogenesis. Cell Host Microbe. 2020 May 27:S1931-3128(20)30302-4. PubMed: https://pubmed.gov/32485164. Full-text: https://doi.org/10.1016/j.chom.2020.05.020
Human ACE2 knockin mice were generated by using CRISPR-Cas9 technology. Bottom line: SARS-CoV-2 led to robust replication in the lung, trachea, and brain. SARS-CoV-2 caused interstitial pneumonia and elevated cytokines. A high dose of virus could establish infection via an intragastric route.
Jamrozik E, Selgelid MJ. COVID-19 human challenge studies: ethical issues. Lancet Infect Dis. 2020 May 29:S1473-3099(20)30438-2. PubMed: https://pubmed.gov/32479747. Full-text: https://doi.org/10.1016/S1473-3099(20)30438-2
Human challenge studies could accelerate vaccine development, helping to test multiple candidate vaccines. This personal view on ethical issues explains why this will be difficult. This is bad news. However, this is also somewhat good news (exception today!), as the authors argue that human challenge studies can “reasonably be considered ethically acceptable insofar as such studies are accepted internationally and by the communities in which they are done, can realistically be expected to accelerate or improve vaccine development, have considerable potential to directly benefit participants, are designed to limit and minimise risks to participants, and are done with strict infection control measures to limit and reduce third-party risks.”
Peng Q, Peng R, Yuan B, et al. Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from SARS-CoV-2. Cell Reports. May 30, 2020. Full-text: https://10.1016/j.celrep.2020.107774
The replication of coronavirus is operated by a set of non-structural proteins (nsps) encoded by the open-reading frame 1a (ORF1a) and ORF1ab in its genome, which are initially translated as polyproteins followed by proteolysis cleavage for maturation. These proteins assemble into a multi-subunit polymerase complex to mediate the transcription and replication of viral genome. Among them, nsp12 is the catalytic subunit with RNA-dependent RNA polymerase (RdRp) activity. The nsp12 itself is capable of conducting polymerase reaction with extremely low efficiency, whereas the presence of nsp7 and nsp8 cofactors remarkably stimulates its polymerase activity. Using cryo-EM, near-atomic resolution structure of SARS-CoV-2 nsp12-nsp7-nsp8 core polymerase complex is described.
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. 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.
Park A, Iwasaki A. Type I and Type III Interferons – Induction, Signaling, Evasion, and Application to Combat COVID-19. Cell Host Microbe. 2020 Jun 10;27(6):870-878. PubMed: https://pubmed.gov/32464097. Full-text: https://doi.org/10.1016/j.chom.2020.05.008 l (Important)
The interferon (IFN) response constitutes the major first line of defense against viruses. This complex host defense strategy can, with accurate understanding of its biology, be translated into safe and effective antiviral therapies. In their comprehensive review, authors describe the recent progress in our understanding of both type I and type III IFN-mediated innate antiviral responses against human coronaviruses and discuss the potential use of IFNs as a treatment strategy.
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 its active form, mimicking the replicating enzyme. Long helical extensions in nsp8 protrude along 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.
Zhang X, Tan Y, Ling Y, et al. Viral and host factors related to the clinical outcome of COVID-19. Nature. 2020 May 20. PubMed: https://pubmed.gov/32434211. Full-text: https://doi.org/10.1038/s41586-020-2355-0 ll (Outstanding)
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 difference in clinical features, mutation rate or transmissibility. Lymphocytopenia, especially a reduced CD4+ and CD8+ T cell counts upon admission, was predictive of disease progression. High levels of IL-6 and IL-8 during treatment were observed in patients with severe or critical disease and correlated with decreased lymphocyte count. The determinants of disease severity seemed to stem mostly from host factors such as age, lymphocytopenia, and its associated cytokine storm.
Yu J, Tostanoski LH, Peter L, et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science 20 May 2020. Full-text: https://doi.org/10.1126/science.abc6284
A series of different DNA vaccine candidates expressing different forms of the spike protein were evaluated in 35 rhesus macaques. Vaccinated animals (especially those receiving a vaccine encoding the full-length spike protein) developed humoral and cellular immune responses, including neutralizing antibody titers comparable to those found in convalescent humans. Protection was likely not sterilizing but instead appeared to be mediated by rapid immunologic control following challenge.
Chandrashekar A, Liu J, Martinot AJ, et al. SARS-CoV-2 infection protects against rechallenge in rhesus macaques. Science. 2020 May 20:eabc4776. PubMed: https://pubmed.gov/32434946. Full-text: https://doi.org/10.1126/science.abc4776 l (Important)
No re-infection in macaques. Following initial viral clearance and on day 35 following initial viral infection, 9 rhesus macaques were re-challenged with the same doses of virus that were utilized for the primary infection. Very limited viral RNA was observed in bronchoalveolar lavage on day 1, with no viral RNA detected at subsequent timepoints. These data show that SARS-CoV-2 infection induced protective immunity against re-exposure in non-human primates.
Munster VJ, Feldmann F, Williamson BN, et al. Respiratory disease in rhesus macaques inoculated with SARS-CoV-2. Nature 2020. https://doi.org/10.1038/s41586-020-2324-7 l (Important)
SARS-CoV-2 caused respiratory disease in 8 infected rhesus macaques, lasting 8-16 days. Pulmonary infiltrates were visible in lung radiographs. High viral loads were detected in swabs as well as in bronchoalveolar lavages. Taken together, this rhesus macaque “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. https://doi.org/10.1038/s41586-020-2342-5
In most cases, you don’t need monkeys. Golden Syrian hamsters may also work as an animal model. 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.
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
Another study analyzing the RNA synthesizing machine. Using cryoelectron microscopy, 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.
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 l (Important)
More insights into transmissibility and pathogenesis. Using ex-vivo cultures, authors evaluated tissue and cellular tropism of SARS-CoV-2 in the 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.
Corey L, Mascola JR, Fauci AS, Collins FS. A strategic approach to COVID-19 vaccine R&D. Science Policy Forum, May 11, 2020. Full-text https://science.sciencemag.org/content/early/2020/05/08/science.abc5312
The full development pathway for an effective vaccine for SARS-CoV-2 will require that industry, government, and academia collaborate in unprecedented ways, each adding their individual strengths. Authors discuss one such collaborative program that has recently emerged: the ACTIV (Accelerating COVID-19 Therapeutic Interventions and Vaccines) public-private partnership.
Bost P, Giladi A, Liu Y, et al. Host-viral infection maps reveal signatures of severe COVID-19 patients. Cell May 07, 2020. Full-text: https://doi.org/10.1016/j.cell.2020.05.006
A computational method is proposed that globally scans unmapped scRNA-seq data for the presence of viral RNA, enabling transcriptional cell sorting of infected versus bystander cells. It is shown how SARS-CoV-2 infects epithelial cells and alters the immune landscape in patients with severe disease.
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 SARS-CoV-2 infection and when both innate and adaptive immune responses are insufficient to curb the viral replication and the patient doesn’t recover quickly.
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 May 8;368(6491):630-633. PubMed: https://pubmed.gov/32245784. Full-text: https://doi.org/10.1126/science.abb7269
Molecular insights into how SARS-CoV-2 can be targeted by the humoral immune response. The authors determined the crystal structure of CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient, in complex with the receptor binding domain of the SARS-CoV-2 spike protein.
Zhou H, Chen X, Hu T. A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein. Current Biology 2020, May 10. 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 between May and October 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 1ab 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.
Enserink M, Cohen J. Fact-checking Judy Mikovits, the controversial virologist attacking Anthony Fauci in a viral conspiracy video. Science 2020, May 8. Full-text: https://www.sciencemag.org/news/2020/05/fact-checking-judy-mikovits-controversial-virologist-attacking-anthony-fauci-viral
The pandemic has resulted in numerous conspiracy theories and misinformation, mainly spread through social media. WHO has declared an “infodemic” of incorrect information about the virus, which poses risks to global health. In a video that has exploded on social media in the past few days, virologist Judy Mikovits claims the virus is being wrongly blamed for many deaths. Fortunately, there are intelligent science journalists who take the time to refute this crap.
Bao L, Deng W, Huang B, et al. The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature. 2020 May 7. PubMed: https://pubmed.gov/32380511. Full-text: https://doi.org/10.1038/s41586-020-2312-y
In transgenic mice bearing human ACE2 and infected with SARS-CoV-2, 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.
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 l (Important)
In a wildlife rescue center, authors found coronavirus in 25 Malayan pangolins (some of whom 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 illegal pangolin trade!
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 in only a week after receipt of the synthetic DNA fragments.
Cyranoski D. Profile of a killer: the complex biology powering the coronavirus pandemic. Nature. 2020, 581, 22-26. Full-text: https://www.nature.com/articles/d41586-020-01315-7
Fantastic, a thrilling feature on what we know about how the virus operates, where it came from and what it might do next. Leading scientists are asked about their hypotheses and current research projects on the origin and on the heterogeneity of the clinical course of COVID-19.
Lau SY, Wang P, Mok BW, et al. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction. Emerg Microbes Infect. 2020 Dec;9(1):837-842. PubMed: https://pubmed.gov/32301390. Full-text: https://doi.org/10.1080/22221751.2020.1756700
Viral variants which contain 15-30-bp deletions (Del-mut) or point mutations respectively at the S1/S2 junction are described. Some of them were less pathogenic in a hamster model. It would be interesting to see the prevalence of these variants in asymptomatic infected cases. The potential of the Del-mut variants as an attenuated vaccine or laboratory tool should also be evaluated.
Gordon DE, Jang GM, Bouhaddou M, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Apr 30. PubMed: https://pubmed.gov/32353859. Full-text: https://doi.org/10.1038/s41586-020-2286-9
A blueprint for future therapies. This heroic work, emerging from a world-wide collaboration (> 100 co-authors!), systematically maps the interaction landscape between SARS-CoV-2 proteins and human proteins. The authors cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and analyzed the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), identifying 332 high-confidence SARS-CoV-2-human protein-protein interactions (PPIs). In total 66 human proteins or host factors targeted by 69 compounds (29 FDA approved drugs, 12 drugs in clinical trials, and 28 preclinical compounds) were found. Screening a subset of these in multiple viral assays identified two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the Sigma1 and Sigma2 receptors.
Yin W, Mao C, Luan X. Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by Remdesivir. Science 01 May 2020. Full-text: https://science.sciencemag.org/content/early/2020/04/30/science.abc1560
Convincing data from clinical trials are still lacking (mostly rumours and press releases). However, this work shows how remdesivir inhibits the SARS-CoV-2 RdRp activity in theory. The authors describe the structure of the SARS-CoV-2 RdRp complex in the apo form and in the complex with a template-primer RNA and the active form of remdesivir. The cryo-EM structures reveal how the template-primer RNA is recognized by the enzyme and how chain elongation is inhibited by remdesivir (and why other nucleotides such as EIDD-2801 may be more potent).
Lamers MM, Beumer J, van der Vaart J, et al. SARS-CoV-2 productively infects human gut enterocytes. Science 01 May 2020. Full-text: https://science.sciencemag.org/content/early/2020/04/30/science.abc1669
SARS-CoV and SARS-CoV-2 infected enterocyte lineage cells in a human intestinal organoid model. Similar infection rates of enterocyte-precursors and enterocytes were observed and low levels of ACE2 may be sufficient for viral entry. This study explains why gastrointestinal symptoms are observed in a subset of patients and why viral RNA can be found in rectal swabs, even after nasopharyngeal testing has turned negative.
Tang Y, Wu C, Li X. On the origin and continuing evolution of SARS-CoV-2. National Science Review 2020, March 03. https://doi.org/10.1093/nsr/nwaa036. Full-text: https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463
Authors from China report on a SARS-CoV-2 subtype which seems to be more aggressive and to spread more quickly. This paper has gained much attraction in the media.
MacLean O, Orton RJ, Singer JB, et al. No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, veaa034, https://doi.org/10.1093/ve/veaa034. Full-text: https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veaa034/5827470?searchresult=1
In this paper, Scottish researches now demonstrate very clearly that Tang et al. were wrong and that the major conclusions of that paper cannot be substantiated. Using examples from other viral outbreaks, the authors discuss the difficulty in demonstrating the existence or nature of a functional effect of a viral mutation, and advise against overinterpretation of genomic data during the pandemic. Although rapid publication is critical for unfolding disease outbreaks, thorough and independent peer review should not be bypassed to get results published quickly.
Tay MZ, Poh CM, Rénia L et al. The trinity of COVID-19: immunity, inflammation and intervention. Nat Rev Immunol (2020). https://doi.org/10.1038/s41577-020-0311-8. Full-text: https://www.nature.com/articles/s41577-020-0311-8#citeas
A 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.
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. https://doi.org/10.1038/d41586-020-01221-y
Fantastic graphical review on current vaccine development. Easy to understand, it explains different approaches such as virus, viral-vector, nucleic-acid and protein-based vaccines.
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 l (Important)
An elegant study explaining distinct clinical features of COVID-19 and SARS. Authors investigated 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.
Huang H, Koyuncu OO, Enquist LW. Pseudorabies Virus Infection Accelerates Degradation of the Kinesin-3 Motor KIF1A. J Virol. 2020 Apr 16;94(9). PubMed: https://pubmed.gov/32075931. Full-text: https://doi.org/10.1128/JVI.01934-19
Pseudorabies virus (PRV), an alphaherpesvirus, is sorted and transported in axons in the anterograde direction by the kinesin-3 motor KIF1A. Why is this of interest? Because it’s currently (April 28, 2020, 7:15 a.m. CET) the headline article of the Journal of Virology, the Journal of the American Society of Microbiology (Impact Factor 4.3). No work, no link on COVID-19, nothing on their website. This journal aims for “reporting important new discoveries and pointing to new directions in research”. Just saying.
Cohen J. COVID-19 vaccine protects monkeys from new coronavirus, Chinese biotech reports. Science April 23, 2020. Full-text: https://www.sciencemag.org/news/2020/04/covid-19-vaccine-protects-monkeys-new-coronavirus-chinese-biotech-reports
Preliminary results of an old-fashioned vaccine consisting of a chemically inactivated version of the virus (which could be produced easily and in huge quantities). The vaccine worked in 8 rhesus macaques, while no obvious side effects were observed. Sinovac Biotech, an experienced vaccine maker from China, has now started Phase I clinical trials in 144 healthy volunteers to evaluate safety.
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 l (Important)
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.
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: eabb7314. Full text: https://science.sciencemag.org/content/early/2020/04/16/science.abb7314 l (Important)
This animal study was performed to understand the pathogenesis, showing SARS-CoV-2-infected macaques provide a new model to test therapeutic strategies. Virus was excreted from nose and throat in the absence of clinical signs, and 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.
Monteil V, Kwon H, Prado P, et al. Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2. Cell. 2020 May 14;181(4):905-913.e7. PubMed: https://pubmed.gov/32333836. Full-text: https://doi.org/10.1016/j.cell.2020.04.004
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.
Gao Y, Yan L, Huang Y, et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 2020 Apr 10. PubMed: https://pubmed.gov/32277040. Full-text: https://doi.org/10.1126/science.abb7498 l (Important)
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.
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. PubMed: https://pubmed.gov/32270184. Full-text: https://doi.org/10.1093/cid/ciaa410
Cell experiments on replication capacity and the 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 x more infectious virus particles than SARS-CoV from the infected lung tissues.
Cao X. COVID-19: immunopathology and its implications for therapy. Nat Rev Immunol. 2020 Apr 9. PubMed: https://pubmed.gov/32273594. Full-text: https://doi.org/10.1038/s41577-020-0308-3
Some thoughts on the immunopathological changes in patients with COVID-19 and how this may provide potential targets for drug discovery and may be important for clinical management.
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 l (Important)
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 indicate notable differences in antigenicity between SARS-CoV and SARS-CoV-2.
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 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 not representing real-life. It remains also unclear if cats secrete enough coronavirus to pass it on to people.
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. 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.
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.
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
Let’s pray that SARS-CoV-2 remembers its origins. And that it 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. Will SARS-CoV-2 remember this? It’s April….
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 ll (Outstanding)
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.
Lan J, Ge J, Yu J, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020 May;581(7807):215-220. PubMed: https://pubmed.gov/32225176. Full-text: https://doi.org/10.1038/s41586-020-2180-5 ll (Outstanding)
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 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.
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 l (IMPORTANT)
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.
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).
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 l (Important)
Consensus statement (a little wordy), defining the place of SARS-CoV-2 (provisionally named 2019-nCoV) within the Coronaviridae.
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 with 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.