Medicine / Special Report

Vol. 5, NO. 1 / April 2020

The Chemistry, Molecular Biology, or Virology of SARS⁠-⁠CoV⁠-⁠2

The Editors

← SARS-CoV-2: Research Guide

The following list of papers and articles will be updated regularly and is offered here as a resource for researchers and interested readers.


  • Dynamically Evolving Novel Overlapping Gene as a Factor in the SARS-CoV-2 Pandemic

    Chase W. Nelson et al. / October 1, 2020

    Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.

    Chase W. Nelson et al., "Dynamically Evolving Novel Overlapping Gene as a Factor in the SARS-CoV-2 Pandemic," eLife (2020), doi:10.7554/eLife.59633.

  • A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

    Hong Zhou et al. / June 8, 2020

    The unprecedented pandemic of pneumonia caused by a novel coronavirus, SARS-CoV-2, in China and beyond has had major public health impacts on a global scale. Although bats are regarded as the most likely natural hosts for SARS-CoV-2, the origins of the virus remain unclear. Here, we report a novel bat-derived coronavirus, denoted RmYN02, identified from a metagenomic analysis of samples from 227 bats collected from Yunnan Province in China between May and October 2019. Notably, RmYN02 shares 93.3% nucleotide identity with SARS-CoV-2 at the scale of the complete virus genome and 97.2% identity in the 1ab gene, in which it is the closest relative of SARS-CoV-2 reported to date. In contrast, RmYN02 showed low sequence identity (61.3%) to SARS-CoV-2 in the receptor-binding domain (RBD) and might not bind to angiotensin-converting enzyme 2 (ACE2). Critically, and in a similar manner to SARS-CoV-2, RmYN02 was characterized by the insertion of multiple amino acids at the junction site of the S1 and S2 subunits of the spike (S) protein. This provides strong evidence that such insertion events can occur naturally in animal betacoronaviruses.

    Hong Zhou et al., "A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein,"Cell (2020), doi:10.1016/j.cub.2020.05.023.

  • Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals (Preprint)

    Davide F. Robbiani et al. / May 15, 2020

    During the COVID-19 pandemic, SARS-CoV-2 infected millions of people and claimed hundreds of thousands of lives. Virus entry into cells depends on the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S). Although there is no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-2. Here we report on 68 COVID-19 convalescent individuals. Plasmas collected an average of 30 days after the onset of symptoms had variable half-maximal neutralizing titers ranging from undetectable in 18% to below 1:1000 in 78%, while only 3% showed titers >1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as few ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 without hospitalization do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

    Davide F. Robbiani et al., "Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals," bioRxiv (2020), doi:10.1101/2020.05.13.092619.

  • Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals

    Alba Grifoni et al. / May 14, 2020

    Understanding adaptive immunity to SARS-CoV-2 is important for vaccine development, interpreting coronavirus disease 2019 (COVID-19) pathogenesis, and calibration of pandemic control measures. Using HLA class I and II predicted peptide ‘megapools’, circulating SARS-CoV-2−specific CD8+ and CD4+ T cells were identified in ∼70% and 100% of COVID-19 convalescent patients, respectively. CD4+ T cell responses to spike, the main target of most vaccine efforts, were robust and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers. The M, spike and N proteins each accounted for 11-27% of the total CD4+ response, with additional responses commonly targeting nsp3, nsp4, ORF3a and ORF8, among others. For CD8+ T cells, spike and M were recognized, with at least eight SARS-CoV-2 ORFs targeted. Importantly, we detected SARS-CoV-2−reactive CD4+ T cells in ∼40-60% of unexposed individuals, suggesting cross-reactive T cell recognition between circulating ‘common cold’ coronaviruses and SARS-CoV-2.

    Alba Grifoni et al., "Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals," Cell (2020), doi:10.1016/j.cell.2020.05.015.

  • Outbreak of Kawasaki Disease in Children During COVID-19 Pandemic: a Prospective Observational Study in Paris, France (Preprint)

    Julie Toubiana et al. / May 14, 2020

    Background: Acute clinical manifestations of SARS-CoV-2 infection are less frequent and less severe in children than in adults. However, recent observations raised concerns about potential post-viral severe inflammatory reactions in children infected with SARS-CoV-2. Methods: We describe an outbreak of cases of Kawasaki disease (KD) admitted between April 27 and May 7, 2020, in the general paediatrics department of a university hospital in Paris, France. All children prospectively underwent nasopharyngeal swabs for SARS-CoV-2 RT-PCR, SARS-CoV-2 IgG serology testing, and echocardiography. The number of admissions for KD during the study period was compared to that observed since January 1, 2018, based on discharge codes, using Poisson regression. Results: A total of 17 children were admitted for KD over an 11-day period, in contrast with a mean of 1.0 case per 2-week period over 2018-2019 (Poisson incidence rate ratio: 13.2 [95% confidence interval: 7.3-24.1], p <0.001). Their median age was 7.5 (range, 3.7-16.6) years, and 59% of patients originated from sub-Saharan Africa or Caribbean islands. Eleven patients presented with KD shock syndrome (KDSS) requiring intensive care support, and 12 had myocarditis. All children had marked gastrointestinal symptoms at the early stage of illness and high levels of inflammatory markers. Fourteen patients (82%) had evidence of recent SARS-CoV-2 infection (positive RT-PCR 7/17, positive IgG antibody detection 14/16). All patients received immunoglobulins and some received corticosteroids (5/17). The clinical outcome was favourable in all patients. Moderate coronary artery dilations were detected in 5 cases (29%) during hospitalisation. Conclusions: The ongoing outbreak of KD in the Paris might be related to SARS-CoV2, and shows an unusually high proportion of children with gastrointestinal involvement, KDSS and African ancestry.

    Julie Toubiana et al., "Outbreak of Kawasaki Disease in Children During COVID-19 Pandemic: a Prospective Observational Study in Paris, France," medRxiv (2020), doi:10.1101/2020.05.10.20097394.

  • Circulating Plasma Concentrations of Angiotensin-Converting Enzyme 2 in Men and Women with Heart Failure and Effects of Renin–Angiotensin–Aldosterone Inhibitors

    Iziah Sama et al. / May 10, 2020

    Aims: The current pandemic coronavirus SARS-CoV-2 infects a wide age group but predominantly elderly individuals, especially men and those with cardiovascular disease. Recent reports suggest an association with use of renin–angiotensin–aldosterone system (RAAS) inhibitors. Angiotensin-converting enzyme 2 (ACE2) is a functional receptor for coronaviruses. Higher ACE2 concentrations might lead to increased vulnerability to SARS-CoV-2 in patients on RAAS inhibitors.
    Methods: We measured ACE2 concentrations in 1485 men and 537 women with heart failure (index cohort). Results were validated in 1123 men and 575 women (validation cohort).
    Results: The median age was 69 years for men and 75 years for women. The strongest predictor of elevated concentrations of ACE2 in both cohorts was male sex (estimate = 0.26, P < 0.001; and 0.19, P < 0.001, respectively). In the index cohort, use of ACE inhibitors, angiotensin receptor blockers (ARBs), or mineralocorticoid receptor antagonists (MRAs) was not an independent predictor of plasma ACE2. In the validation cohort, ACE inhibitor (estimate = –0.17, P = 0.002) and ARB use (estimate = –0.15, P = 0.03) were independent predictors of lower plasma ACE2, while use of an MRA (estimate = 0.11, P = 0.04) was an independent predictor of higher plasma ACE2 concentrations.
    Conclusion: In two independent cohorts of patients with heart failure, plasma concentrations of ACE2 were higher in men than in women, but use of neither an ACE inhibitor nor an ARB was associated with higher plasma ACE2 concentrations. These data might explain the higher incidence and fatality rate of COVID-19 in men, but do not support previous reports suggesting that ACE inhibitors or ARBs increase the vulnerability for COVID-19 through increased plasma ACE2 concentrations.

    Iziah Sama et al., "Circulating Plasma Concentrations of Angiotensin-Converting Enzyme 2 in Men and Women with Heart Failure and Effects of Renin–Angiotensin–Aldosterone Inhibitors," European Heart Journal (2020), doi:10.1093/eurheartj/ehaa373.

  • Pediatric Multi-System Inflammatory Syndrome Potentially Associated with COVID-19

    Demetre Daskalakis / May 4, 2020

    A pediatric multi-system inflammatory syndrome, recently reported by authorities in the United Kingdom, is also being observed among children and young adults in New York City and elsewhere in the United States. Clinical features vary, depending on the affected organ system, but have been noted to include features of Kawasaki disease or features of shock; however, the full spectrum of disease is not yet known. Persistent fever and elevated inflammatory markers (CRP, troponin, etc.) have been seen among affected patients. Patients with this syndrome who have been admitted to pediatric intensive care units (PICUs) have required cardiac and/or respiratory support. Only severe cases may have been recognized at this time.

    Demetre Daskalakis, “Pediatric Multi-System Inflammatory Syndrome Potentially Associated with COVID-19,” NYC Health, 2020 Health Alert #13 (2020).

  • Profile of a Killer: The Complex Biology Powering the Coronavirus Pandemic

    David Cyranoski / May 4, 2020

    Scientists are piecing together how SARS-CoV-2 operates, where it came from and what it might do next — but pressing questions remain about the source of COVID-19.

    David Cyranoski, “Profile of a Killer: The Complex Biology Powering the Coronavirus Pandemic,” Nature (2020), doi:10.1038/d41586-020-01315-7.

  • Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

    Daniel Blanco-Melo et al. / May 4, 2020

    Viral pandemics, such as the one caused by SARS-CoV-2, pose an imminent threat to humanity. Because of its recent emergence, there is a paucity of information regarding viral behavior and host response following SARS-CoV-2 infection. Here, we offer an indepth analysis of the transcriptional response to SARS-CoV-2 as it compares to other respiratory viruses. Cell and animal models of SARS-CoV-2 infections, in addition to transcriptional and serum profiling of COVID-19 patients, consistently revealed a unique and inappropriate inflammatory response. This response is defined by low levels of Type I and III interferons juxtaposed to elevated chemokines and high expression of IL6. Taken together, we propose that reduced innate antiviral defenses coupled with exuberant inflammatory cytokine production are the defining and driving feature of COVID-19.

    Daniel Blanco-Melo et al., “Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19,” Cell (2020), doi:10.1016/j.cell.2020.04.026.

  • An 81 Nucleotide Deletion in SARS-COV-2 ORF7a Identified from Sentinel Surveillance in Arizona (Jan-Mar 2020)

    LaRinda Holland et al. / May 1, 2020

    On January 26 2020, the first Coronavirus Disease 2019 (COVID-19) case was reported in Arizona (3rd case in the US). Here, we report on early SARS-CoV-2 sentinel surveillance in Tempe, Arizona (USA). Genomic characterization identified an isolate encoding a amino acid in-frame deletion in accessory protein ORF7a, the ortholog of SARS-CoV immune antagonist ORF7a/X4.
    In anticipation of COVID-19 spreading in Arizona, we initiated a surveillance effort for local emergence of SARS-CoV-2 starting January 24 2020. We leveraged an ongoing influenza surveillance project at Arizona State University (ASU) Health Services in Tempe, Arizona. Individuals presenting with respiratory symptoms (ILI) were tested for influenza A and B virus (Alere BinaxNOW). Subsequently, we tested influenza-negative nasopharyngeal (NP) swabs for SARS-CoV-2. We extracted total nucleic acid using the bioMérieux eMAG automated platform and performed real-time RT-PCR (qRT-PCR) assays specific for SARS-CoV-2 N and E genes. Out of 382 NP swabs collected from January 24 to March 25, 2020, we detected SARS-CoV-2 in 5 swabs in the week of March 16 to 19. This corresponds to prevalence of 1.31%. Given the estimated 1– 14-day incubation period for COVID-19, the spike in cases might be related touniversity spring-break holiday travel (March 8 – 15) as previously seen in other outbreaks.
    To understand the evolutionary relationships and characterize the SARS-CoV-2 genomes, we performed next-generation sequencing (Illumina NextSeq, 2x76) directly on specimen RNA, thereby avoiding cell culture passage and potentially associated mutations. This generated an NGS dataset of 20.7 to 22.7 million paired-end reads per sample. We mapped quality-filtered reads to a reference SARS-CoV-2 genome (MN908947) using BBMap (version 39.64) to generate three full-length genomes: AZ-ASU2922 (376x coverage), AZ-ASU2923 (50x) and AZ- ASU2936 (879x) (Geneious prime version 2020.0.5). We aligned a total of 222 SARS-CoV-2 genome sequences comprising at least 5 representative sequences from phylogenetic lineages defined by Rambaut et al.. We performed phylogenetic reconstruction with BEAST (version 1.10.4, strict molecular clock, HKY + ? nucleotide substitution, exponential growth for coalescent model). The ASU sequences were phylogenetically distinct, indicating independent transmissions.
    Like SARS-CoV, the SARS-CoV-2 genome encodes multiple open reading frames in the 3' region. We found that the SARS-CoV-2 AZ-ASU2923 genome has an 81 nucleotide deletion in the ORF7a gene resulting in a 27 amino-acid in-frame deletion. The SARS-CoV ORF7a ortholog is a viral antagonist of host restriction factor BST-2/Tetherin and induces apoptosis. Based on the SARS-CoV ORF7a structure, the 27-aa deletion in SARS- CoV-2 ORF7a maps to the putative signal peptide (partial) and first two beta strands. To validate the deletion, we performed RT-PCR using primers spanning the region and verified by Sanger sequencing the amplicons. Similar deletions in SARS-CoV-2 genomes are emerging, notably in the ORF8 gene that may potentially reduce virus fitness. Hence, further experiments are needed to determine the functional consequences of the ORF7a deletion.
    Collectively, although global NGS efforts indicate that SARS-CoV-2 genomes are relatively stable, dynamic mutations can be selected in symptomatic individuals.

    LaRinda Holland et al., “An 81 Nucleotide Deletion in SARS-COV-2 ORF7a Identified from Sentinel Surveillance in Arizona (Jan-Mar 2020),” medRxiv (2020), doi:10.1128/JVI.00711-20.

  • Spike Mutation Pipeline Reveals the Emergence of a More Transmissible Form of SARS-CoV-2 (Preprint)

    Bette Korber et al. / April 30, 2020

    We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified fourteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.

    Bette Korber et al., “Spike Mutation Pipeline Reveals the Emergence of a More Transmissible Form of SARS-CoV-2,” bioRxiv (2020), doi:10.1101/2020.04.29.069054.

  • Structure of Replicating SARS-CoV-2 Polymerase (Preprint)

    Hauke Hillen et al. / April 27, 2020

    The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. Here we present the cryo-electron microscopic structure of the SARS-CoV-2 RdRp in its replicating form. The structure comprises the viral proteins nsp12, nsp8, and nsp7, and over two turns of RNA template-product duplex. The active site cleft of nsp12 binds the first turn of RNA and mediates RdRp activity with conserved residues. Two copies of nsp8 bind to opposite sides of the cleft and position the RNA duplex as it exits. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged ‘sliding poles’ that may enable processive replication of the long coronavirus genome. Our results will allow for a detailed analysis of the inhibitory mechanisms used by antivirals such as remdesivir, which is currently in clinical trials for the treatment of coronavirus disease 2019 (COVID-19).

    Hauke Hillen et al., “Structure of Replicating SARS-CoV-2 Polymerase,” bioRxiv (2020), doi:10.1101/2020.04.27.063180.

  • Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus -2 (SARS-CoV-2)

    Alberto Paniz-Mondolfi et al. / April 21, 2020

    Neurologic sequelae can be devastating complications of respiratory viral infections. We report the presence of virus in neural and capillary endothelial cells in frontal lobe tissue obtained at postmortem examination from a patient infected with Severe Acute Respiratory Syndrome Coronavirus?2. Our observations of virus in neural tissue, in conjunction with clinical correlates of worsening neurologic symptoms, pave the way to a closer understanding of the pathogenic mechanisms underlying CNS involvement.

    Alberto Paniz-Mondolfi et al., “Central Nervous System Involvement by Severe Acute Respiratory Syndrome Coronavirus ?2 (SARS?CoV?2),” Journal of Medical Virology (2020), doi:10.1002/jmv.25915.

  • SARS-CoV-2 Receptor ACE2 Is an Interferon-stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets Across Tissues

    Carly Ziegler et al. / April 20, 2020

    There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) which causes the disease COVID-19. SARS-CoV-2 spike (S)-protein binds ACE2, and in concert with host proteases, principally TMPRSS2, promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues, and the factors that regulate ACE2 expression, remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 amongst tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discover that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells, and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection

    Carly Ziegler et al., “SARS-CoV-2 Receptor ACE2 Is an Interferon-stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets Across Tissues,” Cell (2020), doi:10.1016/j.cell.2020.04.035.

  • CovProfile: Profiling the Viral Genome and Gene Expressions of SARS-COV-2 (Preprint)

    Yonghan Yu et al. / April 19, 2020

    The SARS-CoV-2 virus has infected more than one million people worldwide to date. Knowing its genome and gene expressions is essential to understand the virus' mechanism. Here, we propose a computational tool CovProfile to detect the viral genomic variations as well as viral gene expressions from the sequences obtained from Nanopore devices. We applied CovProfile to 11 samples, each from a terminally ill patient, and discovered that all the patients are infected by multiple viral strains, which might affect the reliability of phylogenetic analysis. Moreover, the expression of viral genes ORF1ab gene, S gene, M gene, and N gene are high among most of the samples. While performing the tests, we noticed a consistent abundance of transcript segments of MUC5B, presumably from the host, across all the samples.

    Yonghan Yu et al., “CovProfile: Profiling the Viral Genome and Gene Expressions of SARS-COV-2,” BioRxiv (2020), doi:10.1101/2020.04.05.026146.

  • Patient-derived Mutations Impact Pathogenicity of SARS-CoV-2 (Preprint)

    Hangping Yao et al. / April 19, 2020

    The sudden outbreak of the severe acute respiratory syndrome–coronavirus (SARS-CoV-2) has spread globally with more than 1,300,000 patients diagnosed and a death toll of 70,000. Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with functional changes in viral pathogenicity. We report functional characterizations of 11 patient-derived viral isolates. We observed diverse mutations in these viral isolates, including 6 different mutations in the spike glycoprotein (S protein), and 2 of which are different SNVs that led to the same missense mutation. Importantly, these viral isolates show significant variation in cytopathic effects and viral load, up to 270-fold differences, when infecting Vero-E6 cells. Therefore, we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity.

    Hangping Yao et al., “Patient-derived Mutations Impact Pathogenicity of SARS-CoV-2,” MedRxiv (2020), doi:10.1101/2020.04.14.20060160.

  • How Does Coronavirus Kill? Clinicians Trace a Ferocious Rampage Through the Body, from Brain to Toes

    Meredith Wadman et al. / April 17, 2020

    On rounds in a 20-bed intensive care unit one recent day, physician Joshua Denson assessed two patients with seizures, many with respiratory failure and others whose kidneys were on a dangerous downhill slide. Days earlier, his rounds had been interrupted as his team tried, and failed, to resuscitate a young woman whose heart had stopped. All shared one thing, says Denson, a pulmonary and critical care physician at the Tulane University School of Medicine. “They are all COVID positive.”
    As the number of confirmed cases of COVID-19 surges past 2.2 million globally and deaths surpass 150,000, clinicians and pathologists are struggling to understand the damage wrought by the coronavirus as it tears through the body. They are realizing that although the lungs are ground zero, its reach can extend to many organs including the heart and blood vessels, kidneys, gut, and brain.

    Meredith Wadman et al., “How Does Coronavirus Kill? Clinicians Trace a Ferocious Rampage Through the Body, from Brain to Toes,” Science (2020).

  • Temporal Dynamics in Viral Shedding and Transmissibility of COVID-19

    Xi He et al. / April 15, 2020

    We report temporal patterns of viral shedding in 94 patients with laboratory-confirmed COVID-19 and modeled COVID-19 infectiousness profiles from a separate sample of 77 infector–infectee transmission pairs We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset We estimated that 44% (95% confidence interval, 25–69%) of secondary cases were infected during the index cases’ presymptomatic stage, in settings with substantial household clustering, active case finding and quarantine outside the home. Disease control measures should be adjusted to account for probable substantial presymptomatic transmission.

    Xi He et al., “Temporal Dynamics in Viral Shedding and Transmissibility of COVID-19,” Nature Medicine (2020), doi:10.1038/s41591-020-0869-5.

  • O-GlcNAc Transferase Promotes Influenza a Virus–induced Cytokine Storm by Targeting Interferon Regulatory Factor–5

    Qiming Wang et al. / April 15, 2020

    In this study, we demonstrated an essential function of the hexosamine biosynthesis pathway (HBP)–associated O-linked β-N-acetylglucosamine (O-GlcNAc) signaling in influenza A virus (IAV)–induced cytokine storm. O-GlcNAc transferase (OGT), a key enzyme for protein O-GlcNAcylation, mediated IAV-induced cytokine production. Upon investigating the mechanisms driving this event, we determined that IAV induced OGT to bind to interferon regulatory factor–5 (IRF5), leading to O-GlcNAcylation of IRF5 on serine-430. O-GlcNAcylation of IRF5 is required for K63-linked ubiquitination of IRF5 and subsequent cytokine production. Analysis of clinical samples revealed that IRF5 is O-GlcNAcylated, and higher levels of proinflammatory cytokines correlated with higher levels of blood glucose in IAV-infected patients. We identified a molecular mechanism by which HBP-mediated O-GlcNAcylation regulates IRF5 function during IAV infection, highlighting the importance of glucose metabolism in IAV-induced cytokine storm.

    Qiming Wang et al., “O-GlcNAc Transferase Promotes Influenza a Virus–induced Cytokine Storm by Targeting Interferon Regulatory Factor–5,” Science Advances 6, no. 16 (2020): eaaz7086, doi:10.1126/sciadv.aaz7086.

  • Antibody Points to Possible Weak Spot on Novel Coronavirus

    Francis Collins / April 14, 2020

    Researchers are working hard to produce precise, 3D molecular maps to guide the development of safe, effective ways of combating the coronavirus disease 2019 (COVID-19) pandemic. While there’s been a lot of excitement surrounding the promise of antibody-based tests and treatments, this map highlights another important use of antibodies: to inform efforts to design a vaccine.

    Francis Collins, “Antibody Points to Possible Weak Spot on Novel Coronavirus,” NIH Director’s Blog (2020).

  • CoV Genome Tracker: Tracing Genomic Footprints of Covid-19 Pandemic (Preprint)

    Saymon Akther et al. / April 14, 2020

    Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular targets of clinical interventions.

    Saymon Akther et al., "CoV Genome Tracker: Tracing Genomic Footprints of Covid-19 Pandemic," bioRxiv (2020)

  • Loss of Smell and Taste in Combination with Other Symptoms Is a Strong Predictor of COVID-19 Infection (Preprint)

    Cristina Menni et al. / April 7, 2020

    Importance: A strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive biospecimen testing.
    Objectives: Here we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases.
    Design: Community survey.
    Setting and Participants: Subscribers of RADAR COVID-19, an app that was launched for use among the UK general population asking about COVID-19 symptoms.
    Main Exposure: Loss of smell and taste.
    Main Outcome Measures: COVID-19.
    Results: Between 24 and 29 March 2020, 1,573,103 individuals reported their symptoms via the app; 26% reported suffering from one or more symptoms of COVID-19. Of those, n=1702 reported having had a RT-PCR COVID-19 test and gave full report on symptoms including loss of smell and taste; 579 were positive and 1123 negative. In this subset, we find that loss of smell and taste were present in 59% of COVID-19 positive individuals compared to 18% of those negative to the test, yielding an odds ratio (OR) of COVID-19 diagnosis of OR[95%CI]=6.59[5.25; 8.27], P= 1.90x10-59 . We also find that a combination of loss of smell and taste, fever, persistent cough, fatigue, diarrhoea, abdominal pain and loss of appetite is predictive of COVID-19 positive test with sensitivity 0.54[0.44; 0.63], specificity 0.86[0.80; 0.90], ROC-AUC 0.77[0.72; 0.82] in the test set, and cross-validation ROC-AUC 0.75[0.72; 0.77]. When applied to the 410,598 individuals reporting symptoms but not formally tested, our model predicted that 13.06%[12.97%;13.15] of these might have been already infected by the virus.
    Conclusions and Relevance: Our study suggests that loss of taste and smell is a strong predictor of having been infected by the COVID-19 virus. Also, the combination of symptoms that could be used to identify and isolate individuals includes anosmia, fever, persistent cough, diarrhoea, fatigue, abdominal pain and loss of appetite. This is particularly relevant to healthcare and other key workers in constant contact with the public who have not yet been tested for COVID-19.

    Cristina Menni et al., “Loss of Smell and Taste in Combination with Other Symptoms Is a Strong Predictor of COVID-19 Infection,” medRxiv (2020), doi:10.1101/2020.04.05.20048421.

  • Evolutionary Origins of the SARS-CoV-2 Sarbecovirus Lineage Responsible for the COVID-19 Pandemic (Preprint)

    Maciej Boni et al. / March 31, 2020

    There are outstanding evolutionary questions on the recent emergence of coronavirus SARS-CoV-2/hCoV-19 in Hubei province that caused the COVID-19 pandemic, including (1) the relationship of the new virus to the SARS-related coronaviruses, (2) the role of bats as a reservoir species, (3) the potential role of other mammals in the emergence event, and (4) the role of recombination in viral emergence. Here, we address these questions and find that the sarbecoviruses – the viral subgenus responsible for the emergence of SARS-CoV and SARS-CoV-2 – exhibit frequent recombination, but the SARS-CoV-2 lineage itself is not a recombinant of any viruses detected to date. In order to employ phylogenetic methods to date the divergence events between SARS-CoV-2 and the bat sarbecovirus reservoir, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were consistent for all three recombination-free alignments and robust to two different prior specifications based on HCoV-OC43 and MERS-CoV evolutionary rates. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% HPD: 1879-1999), 1969 (95% HPD: 1930-2000), and 1982 (95% HPD: 1948-2009). Despite intensified characterization of sarbecoviruses since SARS, the lineage giving rise to SARS-CoV-2 has been circulating unnoticed for decades in bats and been transmitted to other hosts such as pangolins. The occurrence of a third significant coronavirus emergence in 17 years together with the high prevalence and virus diversity in bats implies that these viruses are likely to cross species boundaries again.

    Maciej Boni et al., “Evolutionary Origins of the SARS-CoV-2 Sarbecovirus Lineage Responsible for the COVID-19 Pandemic,” BioRxiv doi:10.1101/2020.03.30.015008.

  • Structural Basis of Receptor Recognition by SARS-CoV-2

    https://doi.org/10.1038/s41586-020-2179-y / March 30, 2020

    A novel SARS-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans. A key to tackling this epidemic is to understand the virus’s receptor recognition mechanism, which regulates its infectivity, pathogenesis and host range. SARS-CoV-2 and SARS-CoV recognize the same receptor — human ACE2 (hACE2). Here we determined the crystal structure of the SARS-CoV-2 receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex with hACE2. Compared with the SARS-CoV RBD, a hACE2-binding ridge in SARS-CoV-2 RBD takes a more compact conformation; moreover, several residue changes in SARS-CoV-2 RBD stabilize two virus-binding hotspots at the RBD/hACE2 interface. These structural features of SARS-CoV-2 RBD enhance its hACE2-binding affinity. Additionally, we show that RaTG13, a bat coronavirus closely related to SARS-CoV-2, also uses hACE2 as its receptor. The differences among SARS-CoV-2, SARS-CoV and RaTG13 in hACE2 recognition shed light on potential animal-to-human transmission of SARS-CoV-2. This study provides guidance for intervention strategies targeting receptor recognition by SARS-CoV-2.

    Jian Shang et al., “Structural Basis of Receptor Recognition by SARS-CoV-2,” Nature (2020), doi:10.1038/s41586-020-2179-y.

  • Might the Many Positive COVID19 Subjects in Italy Have Been Caused by Resident Bat–Derived Zoonotic β–Coronaviruses Instead of the Wuhan (China) Outbreak?

    Salvatore Chirumbolo / March 27, 2020

    In a recent article by Lai et al., published on the Journal of Medical Virology, the authors attempted a mathematical reconstruction of the evolutionary dynamics of the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) outbreak occurred in Wuhan (China), by analyzing 52 SARS-CoV2 genomes provided at GISAID on 4 February 2020. This evaluation is fundamental to make authorities aware about spreading characteristics of SARS-CoV2 in the Italian population and to earn insightful clues about the presumptive hypothesis that the current viral spreading in Italy surely comes from a Wuhan–borne genotype and/or a Chinese outbreak. The same authors concluded that the SARS-CoV2 in Italy might be present at least since September and October 2019, much before the claimed Wuhan outbreak.1 According to the World Health Organization evaluation, SARS-CoV2 outbreaks in Europe occurred much before in Germany and France respect to Italy. Therefore, it might be presumed that a significant proportion of Italians were infected by SARS-CoV2 in times greatly preceding the Government dispositions upon the cases enumeration. The daily differences between cases in the highest emergence period, that is, 1 to 9 March 2020, plotted a linear rather than an exponential trend. As x increases (1 day each), y values (cases number) increases by the same amount (1.2 or +20%) (Shapiro–Wilk’s exp test P = .442857). This possibly suggests that rhinopharyngeal swabs are catching homogeneous clusters of cases from dating back homogeneously, normally distributed preinfected population, depending also on an established maximal number of analyzed swabs for the day.

    Salvatore Chirumbolo, “Might the Many Positive COVID19 Subjects in Italy Have Been Caused by Resident Bat–Derived Zoonotic Β–Coronaviruses Instead of the Wuhan (China) Outbreak?” Journal of Medical Virology (2020), doi:10.1002/jmv.25777.

  • Genotyping Coronavirus SARS-CoV-2: Methods and Implications (Preprint)

    Changchuan Yin / March 24, 2020

    The emerging global infectious COVID-19 coronavirus disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December 2019 in China. The virus has gone through various pathways of evolution. For understanding the evolution and transmission of SARS-CoV-2, genotyping of virus isolates is of great importance. We present an accurate method for effectively genotyping SARS-CoV-2 viruses using complete genomes. The method employs the multiple sequence alignments of the genome isolates with the SARS-CoV-2 reference genome. The SNP genotypes are then measured by Jaccard distances to track the relationship of virus isolates. The genotyping analysis of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations are the predominated mutation type during the current epidemic. Our method serves a promising tool for monitoring and tracking the epidemic of pathogenic viruses in their gradual and local genetic variations. The genotyping analysis shows that the genes encoding the S proteins and RNA polymerase, RNA primase, and nucleoprotein, undergo frequent mutations. These mutations are critical for vaccine development in disease control.

    Changchuan Yin, “Genotyping Coronavirus SARS-CoV-2: Methods and Implications,” arXiv:2003.10965 (2020).

  • Temporal Profiles of Viral Load in Posterior Oropharyngeal Saliva Samples and Serum Antibody Responses During Infection by SARS-CoV-2: An Observational Cohort Study

    Kelvin Kai-Wang To et al. / March 23, 2020

    Coronavirus disease 2019 (COVID-19) causes severe community and nosocomial outbreaks. Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available. Nasopharyngeal and throat swabs are usually obtained for serial viral load monitoring of respiratory infections but gathering these specimens can cause discomfort for patients and put health-care workers at risk. We aimed to ascertain the serial respiratory viral load of SARS-CoV-2 in posterior oropharyngeal (deep throat) saliva samples from patients with COVID-19, and serum antibody responses.

    Kelvin Kai-Wang To et al., “Temporal Profiles of Viral Load in Posterior Oropharyngeal Saliva Samples and Serum Antibody Responses During Infection by SARS-CoV-2: An Observational Cohort Study,” The Lancet: Infectious Diseases (2020), doi:10.1016/S1473-3099(20)30196-1.

  • Prolonged Presence of SARS-CoV-2 Viral RNA in Faecal Samples

    Yongjian Wu et al. / March 19, 2020

    We present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR results of all respiratory and faecal samples from patients with coronavirus disease 2019 (COVID-19) at the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China, throughout the course of their illness and obligated quarantine period. Real-time RT-PCR was used to detect COVID-19 following the recommended protocol. Patients with suspected SARS-CoV-2 were confirmed after two sequential positive respiratory tract sample results. Respiratory and faecal samples were collected every 1–2 days (depending on the availability of faecal samples) until two sequential negative results were obtained. We reviewed patients’ demographic information, underlying diseases, clinical indices, and treatments from their official medical records. The study was approved by the Medical Ethical Committee of The Fifth Affiliated Hospital of Sun Yat-sen University (approval number K162-1) and informed consent was obtained from participants. Notably, patients who met discharge criteria were allowed to stay in hospital for extended observation and health care.

    Yongjian Wu et al., “Prolonged Presence of SARS-CoV-2 Viral RNA in Faecal Samples,” The Lancet: Gastroenerology & Hepatology (2020), doi:10.1016/S2468-1253(20)30083-2.

  • Comparative Pathogenesis of COVID-19, MERS and SARS in a Non-Human Primate Model (Preprint)

    Barry Rockx et al. / March 17, 2020

    A novel coronavirus, SARS-CoV-2, was recently identified in patients with an acute respiratory syndrome, COVID-19. To compare its pathogenesis with that of previously emerging coronaviruses, we inoculated cynomolgus macaques with SARS-CoV-2 or MERS-CoV and compared with historical SARS-CoV infections. In SARS-CoV-2-infected macaques, virus was excreted from nose and throat in absence of clinical signs, and detected in type I and II pneumocytes in foci of diffuse alveolar damage and mucous glands of the nasal cavity. 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. These data show that SARS-CoV-2 can cause a COVID-19-like disease, and suggest that the severity of SARS-CoV-2 infection is intermediate between that of SARS-CoV and MERS-CoV.

    Barry Rockx et al., “Comparative Pathogenesis of COVID-19, MERS and SARS in a Non-Human Primate Model,” bioRxiv (2020), doi:10.1101/2020.03.17.995639.

  • Pay Attention to SARS-CoV-2 Infection in Children

    Zhengde Xie / March 17, 2020

    The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been prevalent for nearly two months. The first case of COVID-19 was reported in Wuhan, Hubei Province, China in mid-December 2019. On January 9, 2020, Chinese scientists isolated and obtained the genome sequence of the new virus; they shared the genome information on relevant international websites one day later. Announcement No. 1 of the National Health Commission of the People’s Republic of China (on January 20, 2020) has categorized COVID-19 as a Class B infectious disease, in accordance with the Law of the People’s Republic of China on the Prevention and Treatment of Infectious Diseases; however, the announcement ur ged public health authorities to undertake prevention and control appropriate for a Class A infectious disease. As of January 31, 2020, there were 9720 confirmed cases of COVID-19 in China and a total of 9826 cases have been reported globally, involving 19 countries. WHO declared the outbreak to be a public health emergency of international concern on January 31 2020.4 Thus far, the SARS-CoV-2 outbreak has not been well controlled and requires close attention.
    Coronavirus (CoV) belongs to the family Coronavirinae of the order Nidovirales. Based on analysis of their genomic structure and phylogenetics, CoVs are divided into four genera: α, β, γ, and δ. Both α and β CoVs only infect mammals, whereas γ and δ CoVs mainly infect birds and rarely infect mammals. The genome of CoV is a complete single-stranded positive-sense RNA of approximately 30 kb in length, which is the largest of all RNA viruses. It also exhibits typical characteristics of RNA viruses, including a 5’ cap and 3’ poly-A tail.

    Zhengde Xie, “Pay Attention to SARS-CoV-2 Infection in Children,” Pediatric Investigation 4, no. 1 (2020): 1–4, doi:10.1002/ped4.12178.

  • Genetic Evolution Analysis of 2019 Novel Coronavirus and Coronavirus from Other Species

    Chun Li, Yanling Yang, and Linzhu Ren / March 10, 2020

    The Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a Public Health Emergency of International Concern. However, so far, there are still controversies about the source of the virus and its intermediate host. Here, we found the novel coronavirus was closely related to coronaviruses derived from five wild animals, including Paguma larvata, Paradoxurus hermaphroditus, Civet, Aselliscus stoliczkanus and Rhinolophus sinicus, and was in the same branch of the phylogenetic tree. However, genome and ORF1a homology show that the virus is not the same coronavirus as the coronavirus derived from these five animals, whereas the virus has the highest homology with Bat coronavirus isolate RaTG13.

    Chun Li, Yanling Yang, and Linzhu Ren, “Genetic Evolution Analysis of 2019 Novel Coronavirus and Coronavirus from Other Species,” Infection, Genetics and Evolution (2020) doi:10.1016/j.meegid.2020.104285.

  • Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding

    Roujian Lu et al. / February 22, 2020

    We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.
    The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.

    Roujian Lu et al., “Genomic Characterisation and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding,” The Lancet 395, no. 10,224 (2020): 565–74, doi:10.1016/S0140-6736(20)30251-8.

  • The Spike Glycoprotein of the New Coronavirus 2019-nCoV Contains a Furin-like Cleavage Site Absent in CoV of the Same Clade

    Bruno Coutard et al. / February 10, 2020

    In 2019, a new coronavirus (2019-nCoV) infecting Humans has emerged in Wuhan, China. Its genome has been sequenced and the genomic information promptly released. Despite a high similarity with the genome sequence of SARS-CoV and SARS-like CoVs, we identified a peculiar furin-like cleavage site in the Spike protein of the 2019-nCoV, lacking in the other SARS-like CoVs. In this article, we discuss the possible functional consequences of this cleavage site in the viral cycle, pathogenicity and its potential implication in the development of antivirals.

    Bruno Coutard et al., “The Spike Glycoprotein of the New Coronavirus 2019-nCoV Contains a Furin-like Cleavage Site Absent in CoV of the Same Clade,” Antiviral Research 176, no. 104,742 (2020), doi:10.1016/j.antiviral.2020.104742.

  • Persistence of Coronaviruses on Inanimate Surfaces and Their Inactivation with Biocidal Agents

    Günter Kampf et al. / February 6, 2020

    Currently, the emergence of a novel human coronavirus, SARS-CoV-2, has become a global health concern causing severe respiratory tract infections in humans. Human-to-human transmissions have been described with incubation times between 2-10 days, facilitating its spread via droplets, contaminated hands or surfaces. We therefore reviewed the literature on all available information about the persistence of human and veterinary coronaviruses on inanimate surfaces as well as inactivation strategies with biocidal agents used for chemical disinfection, e.g. in healthcare facilities. The analysis of 22 studies reveals that human coronaviruses such as Severe Acute Respiratory Syndrome (SARS) coronavirus, Middle East Respiratory Syndrome (MERS) coronavirus or endemic human coronaviruses (HCoV) can persist on inanimate surfaces like metal, glass or plastic for up to 9 days, but can be efficiently inactivated by surface disinfection procedures with 62–71% ethanol, 0.5% hydrogen peroxide or 0.1% sodium hypochlorite within 1 minute. Other biocidal agents such as 0.05–0.2% benzalkonium chloride or 0.02% chlorhexidine digluconate are less effective. As no specific therapies are available for SARS-CoV-2, early containment and prevention of further spread will be crucial to stop the ongoing outbreak and to control this novel infectious thread.

    Günter Kampf et al., “Persistence of Coronaviruses on Inanimate Surfaces and Their Inactivation with Biocidal Agents,” Journal of Hospital Infection 104, no. 3 (2020): 246–51, doi:10.1016/j.jhin.2020.01.022.

  • Detection and Full Genome Characterization of Two Beta CoV Viruses Related to Middle East Respiratory Syndrome from Bats in Italy

    Ana Moreno et al. / December 19, 2017

    Middle East respiratory syndrome coronavirus (MERS-CoV), which belongs to beta group of coronavirus, can infect multiple host species and causes severe diseases in humans. Multiple surveillance and phylogenetic studies suggest a bat origin. In this study, we describe the detection and full genome characterization of two CoVs closely related to MERS-CoV from two Italian bats, Pipistrellus kuhlii and Hypsugo savii.

    Ana Moreno et al., “Detection and Full Genome Characterization of Two Beta CoV Viruses Related to Middle East Respiratory Syndrome from Bats in Italy,” Virology Journal 14, no. 239 (2017), doi:10.1186/s12985-017-0907-1.

  • The Detection and Characterisation of Coronavirus and Astrovirus in Chiroptera in Cambodia and Laos

    Audrey Lacroix / December 1, 2017

    Zoonoses are important public health issues, and represent 60% of emerging infectious diseases. Most of zoonotic pathogens originate from wildlife, such as the Human Immunodeficiency Virus, Influenza Virus or Ebola Virus. Chiroptera have been recognized as an important reservoir of zoonotic viruses, such as the lyssavirus or the coronavirus responsible for the pandemic of severe acute respiratory syndrome (SARS) in 2003-2004. Southeast Asia is a hotspot for emerging diseases. Bats represent 30% of the biodiversity and are in close contact with human populations, due to the exploitation of the same environment and the use of bats as food in subsistence hunting. So far, there has been a lack of knowledge and understanding concerning the viruses circulating in the bat population in this region, especially in Cambodia and Lao P.D.R. The work presented in this thesis is dedicated to this problematic, with a special focus on the detection and molecular characterization of coronaviruses and astroviruses in bat populations in these two countries. The aim was also to depict environmental aspects which increase the risk of potential transmission from bats to humans.

    Audrey Lacroix, “La détection et la caractérisation de coronavirus et astrovirus chez les chiroptères au Cambodge et au Laos” (PhD thesis, Université Montpellier, 2016).

  • Jumping Species—A Mechanism for Coronavirus Persistence and Survival

    Vineet Menachery, Rachel Graham, and Ralph Baric / March 21, 2017

    Zoonotic transmission of novel viruses represents a significant threat to global public health and is fueled by globalization, the loss of natural habitats, and exposure to new hosts. For coronaviruses (CoVs), broad diversity exists within bat populations and uniquely positions them to seed future emergence events. In this review, we explore the host and viral dynamics that shape these CoV populations for survival, amplification, and possible emergence in novel hosts.

    Vineet Menachery, Rachel Graham, and Ralph Baric, “Jumping Species—A Mechanism for Coronavirus Persistence and Survival,” Current Opinion in Virology 23 (2017): 1–7, doi:10.1016/j.coviro.2017.01.002.

  • A SARS-like Cluster of Circulating Bat Coronaviruses Shows Potential for Human Emergence

    Vineet Menachery et al. / November 9, 2015

    The emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome (MERS)-CoV underscores the threat of cross-species transmission events leading to outbreaks in humans. Here we examine the disease potential of a SARS-like virus, SHC014-CoV, which is currently circulating in Chinese horseshoe bat populations1. Using the SARS-CoV reverse genetics system2, we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that group 2b viruses encoding the SHC014 spike in a wild-type backbone can efficiently use multiple orthologs of the SARS receptor human angiotensin converting enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments demonstrate replication of the chimeric virus in mouse lung with notable pathogenesis. Evaluation of available SARS-based immune-therapeutic and prophylactic modalities revealed poor efficacy; both monoclonal antibody and vaccine approaches failed to neutralize and protect from infection with CoVs using the novel spike protein. On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations.

    Vineet Menachery et al., “A SARS-like Cluster of Circulating Bat Coronaviruses Shows Potential for Human Emergence,” Nature Medicine 21, no. 12 (2015): 1,508–13, doi:10.1038/nm.3985.

  • Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat

    Victor Corman et al. / July 14, 2014

    The emerging Middle East respiratory syndrome coronavirus (MERS-CoV) causes lethal respiratory infections mainly on the Arabian Peninsula. The evolutionary origins of MERS-CoV are unknown. We determined the full genome sequence of a CoV directly from fecal material obtained from a South African Neoromicia capensis bat (NeoCoV). NeoCoV shared essential details of genome architecture with MERS-CoV. Eighty-five percent of the NeoCoV genome was identical to MERS-CoV at the nucleotide level. Based on taxonomic criteria, NeoCoV and MERS-CoV belonged to one viral species. The presence of a genetically divergent S1 subunit within the NeoCoV spike gene indicated that intraspike recombination events may have been involved in the emergence of MERS-CoV. NeoCoV constitutes a sister taxon of MERS-CoV, placing the MERS-CoV root between a recently described virus from African camels and all other viruses. This suggests a higher level of viral diversity in camels than in humans. Together with serologic evidence for widespread MERS-CoV infection in camelids sampled up to 20 years ago in Africa and the Arabian Peninsula, the genetic data indicate that camels act as sources of virus for humans rather than vice versa. The majority of camels on the Arabian Peninsula is imported from the Greater Horn of Africa, where several Neoromicia species occur. The acquisition of MERS-CoV by camels from bats might have taken place in sub-Saharan Africa. Camelids may represent mixing vessels for MERS-CoV and other mammalian CoVs.

    Victor Corman et al., “Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat,” Journal of Virology 88, no. 19 (2014): 11,297–303, doi:10.1128/JVI.01498-14.

  • Isolation and Characterization of a Bat SARS-like Coronavirus That Uses the ACE2 Receptor

    Xing-Yi Ge et al. / November 28, 2013

    The 2002–3 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV) was one of the most significant public health events in recent history. An ongoing outbreak of Middle East respiratory syndrome coronavirus suggests that this group of viruses remains a key threat and that their distribution is wider than previously recognized. Although bats have been suggested to be the natural reservoirs of both viruses, attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. Diverse SARS-like coronaviruses (SL-CoVs) have now been reported from bats in China, Europe and Africa, but none is considered a direct progenitor of SARS-CoV because of their phylogenetic disparity from this virus and the inability of their spike proteins to use the SARS-CoV cellular receptor molecule, the human angiotensin converting enzyme II (ACE2). Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs. They also highlight the importance of pathogen-discovery programs targeting high-risk wildlife groups in emerging disease hotspots as a strategy for pandemic preparedness.

    Xing-Yi Ge et al., “Isolation and Characterization of a Bat SARS-like Coronavirus That Uses the ACE2 Receptor,” Nature 503, no. 7,477 (2013): 535–38, doi:10.1038/nature12711.

  • A Case for the Ancient Origin of Coronaviruses

    https://doi.org/10.1128/jvi.03273-12 / May 28, 2013

    Coronaviruses are found in a diverse array of bat and bird species, which are believed to act as natural hosts. Molecular clock dating analyses of coronaviruses suggest that the most recent common ancestor of these viruses existed around 10,000 years ago. This relatively young age is in sharp contrast to the ancient evolutionary history of their putative natural hosts, which began diversifying tens of millions of years ago. Here, we attempted to resolve this discrepancy by applying more realistic evolutionary models that have previously revealed the ancient evolutionary history of other RNA viruses. By explicitly modeling variation in the strength of natural selection over time and thereby improving the modeling of substitution saturation, we found that the time to the most recent ancestor common for all coronaviruses is likely far greater (millions of years) than the previously inferred range.

    Joel Wertheim et al., “A Case for the Ancient Origin of Coronaviruses,” Journal of Virology (2013), doi:10.1128/JVI.03273-12.

  • Coronavirus Nonstructural Protein 16 Is a Cap-0 Binding Enzyme Possessing (Nucleoside-2′O)-Methyltransferase Activity

    Etienne Decroly et al. / July 28, 2008

    The coronavirus family of positive-strand RNA viruses includes important pathogens of livestock, companion animals, and humans, including the severe acute respiratory syndrome coronavirus that was responsible for a worldwide outbreak in 2003. The unusually complex coronavirus replicase/transcriptase is comprised of 15 or 16 virus-specific subunits that are autoproteolytically derived from two large polyproteins. In line with bioinformatics predictions, we now show that feline coronavirus (FCoV) nonstructural protein 16 (nsp16) possesses an S-adenosyl-l-methionine (AdoMet)-dependent RNA (nucleoside-2'O)-methyltransferase (2'O-MTase) activity that is capable of cap-1 formation. Purified recombinant FCoV nsp16 selectively binds to short capped RNAs. Remarkably, an N7-methyl guanosine cap (7MeGpppAC3-6) is a prerequisite for binding. High-performance liquid chromatography analysis demonstrated that nsp16 mediates methyl transfer from AdoMet to the 2'O position of the first transcribed nucleotide, thus converting 7MeGpppAC3-6 into 7MeGpppA2'OMeC3-6. The characterization of 11 nsp16 mutants supported the previous identification of residues K45, D129, K169, and E202 as the putative K-D-K-E catalytic tetrad of the enzyme. Furthermore, residues Y29 and F173 of FCoV nsp16, which may be the functional counterparts of aromatic residues involved in substrate recognition by the vaccinia virus MTase VP39, were found to be essential for both substrate binding and 2'O-MTase activity. Finally, the weak inhibition profile of different AdoMet analogues indicates that nsp16 has evolved an atypical AdoMet binding site. Our results suggest that coronavirus mRNA carries a cap-1, onto which 2'O methylation follows an order of events in which 2'O-methyl transfer must be preceded by guanine N7 methylation, with the latter step being performed by a yet-unknown N7-specific MTase.

    Etienne Decroly et al., “Coronavirus Nonstructural Protein 16 Is a Cap-0 Binding Enzyme Possessing (Nucleoside-2′O)-Methyltransferase Activity,” Journal of Virology 82, no. 16 (2008): 8,071–84, doi:10.1128/JVI.00407-08.

  • The Severe Acute Respiratory Syndrome-Coronavirus Replicative Protein nsp9 Is a Single-Stranded RNA-Binding Subunit Unique in the RNA Virus World

    Marie-Pierre Egloff et al. / March 16, 2004

    The recently identified etiological agent of the severe acute respiratory syndrome (SARS) belongs to Coronaviridae (CoV), a family of viruses replicating by a poorly understood mechanism. Here, we report the crystal structure at 2.7-Å resolution of nsp9, a hitherto uncharacterized subunit of the SARS-CoV replicative polyproteins. We show that SARS-CoV nsp9 is a single-stranded RNA-binding protein displaying a previously unreported, oligosaccharide/oligonucleotide fold-like fold. The presence of this type of protein has not been detected in the replicative complexes of RNA viruses, and its presence may reflect the unique and complex CoV viral replication/transcription machinery.

    Marie-Pierre Egloff et al., “The Severe Acute Respiratory Syndrome-Coronavirus Replicative Protein nsp9 Is a Single-Stranded RNA-Binding Subunit Unique in the RNA Virus World,” Proceedings of the National Academy of Sciences of the United States of America 101, no. 11 (2004): 3,792–96, doi:10.1073/pnas.0307877101.

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