March 11, 2020


Single-cell RNA expression profiling shows that ACE2, the putative receptor of COVID-2019, has significant expression in nasal and mouth tissue, and is co-expressed with TMPRSS2 and not co-expressed with SLC6A19 in the tissues.


A novel coronavirus (COVID-2019) was first identified in Wuhan, Hubei Province, and then spreads to the other Provinces of China. COVID-2019 was reported to share the same receptor, Angiotensin-converting enzyme 2 (ACE2), with SARS-CoV. But the infection rate of COVID-2019 is much higher than SARS-CoV. The biophysical and structural evidence showed that the COVID-2019 binds ACE2 with 10~20 times affinity than SARS-CoV. TMPRSS2 cleaves ACE2 and facilitates the entry of the virus into host cells. The presence of SLC6A19 may block the access of TMPRSS2 to the cutting site on ACE2 and weaken the entry of COVID-2019 into host cells. Here based on the public single-cell RNA-Seq datasets, we analyzed the ACE2 expression in the nasal, mouth, lung, and colon tissues. We find that the number of ACE2-expressing cells in the nasal and mouth tissues is comparable to the number of ACE2-expressing cells in the lung and colon tissues. We also find that ACE2 tends to be co-expressed with TMPRSS2 and not co-expressed with SLC6A19 in the nasal and mouth tissues. With the results, we infer that nasal and mouth tissues may be the first host cells of COVID-2019 infection. In our previous report in medRxiv and a recurrent report in New England Journal of Medicine, the COVID-2019 load tends to be higher in the nasal-swabs than in throat-swabs. We believe the roles of nasal and mouth tissues in COVID-2019 infection should be investigated, and we need to pay more attention to protect nose and mouth from COVID-2019 infection.

March 11, 2020 


Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China


An in-depth annotation of the newly discovered coronavirus (2019-nCoV) genome has revealed differences between 2019-nCoV and severe acute respiratory syndrome (SARS) or SARS-like coronaviruses. A systematic comparison identified 380 amino acid substitutions between these coronaviruses, which may have caused functional and pathogenic divergence of 2019-nCoV.


March 9, 2020


Structure, Function, and Antigenicity of the SARSCoV-2 Spike Glycoprotein


SARS-CoV-2, a newly emerged pathogen spreading worldwide, binds with high affinity to human ACE2 and uses it as an

entry receptor to invade target cells. Cryo-EM structures of the SARS-CoV-2 spike glycoprotein in two distinct

conformations, along with inhibition of spike-mediated entry by SARS-CoV polyclonal antibodies provide a blueprint for the design of vaccines and therapeutics.

March 9, 2020 


Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1


A novel human coronavirus, now named severe acute respiratory syndrome coronavirus (SARS-CoV-2, referred to as HCoV-19 here) that emerged in Wuhan, China in late 2019 is now causing a pandemic. Here, we analyze the aerosol and surface stability of HCoV-19 and compare it with SARS2-CoV-1, the most closely related human coronavirus. We evaluated the stability of HCoV-19 and SARS-CoV-1 in aerosols and on different surfaces and estimated their decay rates using a Bayesian regression

model (see Supplementary Appendix). All experimental measurements are reported as mean across 3 replicates.

March 6, 2020 


Simple Strategy for Rapid and Sensitive Detection of 2019 Novel Coronavirus Based on Antibody


Since December 2019, acute respiratory disease due to 2019 novel coronavirus emerged in Wuhan city and rapidly spread throughout China. Real-time RTPCR

is widely deployed in diagnostic virology. However, the positive detection rates of RTPCR are only 30% to 50%. Therefore, we propose a simple strategy for rapidly and sensitively detecting the IgM/IgG antibody against 2019-nCoV using a colloidal gold-based immunochromatographic strip test.

March 6, 2020 


A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2


Effective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (SARS-CoV-2) require the development of data and tools to understand and monitor its spread and immune responses to it. However, little information is available about the targets of immune responses to SARS-CoV-2. We used the Immune Epitope Database and Analysis Resource (IEDB) to catalog available data related to other coronaviruses. This includes SARSCoV, which has high sequence similarity to SARS-CoV-2 and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in SARS-CoV-2 that have high homology to the SARS-CoV virus. Parallel bioinformatic predictions identified a priori potential B and T cell epitopes for SARS-CoV-2. The independent identification of the same regions using two approaches reflects the high probability that these regions are promising targets for immune recognition of SARS-CoV-2. These predictions can facilitate effective vaccine design against this virus of high priority.


March 5, 2020 


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


The emerging SARS-coronavirus (SARS-CoV-2) threatens public health. Hoffmann and coworkers show that SARS-CoV-2 infection depends on the

host cell factors ACE2 and TMPRSS2 and can be blocked by a clinically proven protease inhibitor. These findings might

help to establish options for prevention and treatment.


March 4, 2020


An Investigation of the Expression of 2019 Novel Coronavirus Cell Receptor Gene ACE2 in a Wide Variety of Human Tissues


The 2019 novel coronavirus (2019-nCoV) has affected more than 72,000 people worldwide and caused more than 1,800 deaths so far. 2019-nCoV uses the angiotensinconverting enzyme 2 (ACE2) as the cell receptor to invade the human host and primarily causes pneumonia. Thus, ACE2 is the key to understanding the mechanism of 2019-nCoV infection.

March 1, 2020


Molecular immune pathogenesis and diagnosis of COVID-19


Coronavirus disease 2019 (COVID-19) is a kind of viral pneumonia with an unusual outbreak in Wuhan, China, in December 2019, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The emergence of SARS-CoV-2 has been marked as the third introduction of a highly pathogenic coronavirus into the human population after the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV) in the twenty-first century. In this minireview, we provide a brief introduction of the general features of SARS-CoV-2 and discuss current knowledge of molecular immune pathogenesis, diagnosis and treatment of COVID-19 on the base of the present understanding of SARS-CoV and MERS-CoV infections, which may be helpful in offering novel insights and potential therapeutic targets for combating the SARS-CoV-2 infection.

March 1, 2020 


Evidence of the COVID-19 Virus Targeting the CNS: Tissue Distribution, Host−Virus Interaction, and Proposed Neurotropic Mechanisms


The recent outbreak of coronavirus infectious disease 2019 (COVID-19) has gripped the world with apprehension and has evoked a scare of epic proportion regarding its potential to spread and infect humans worldwide. As we are in the midst of an ongoing pandemic of COVID-19, scientists are struggling to understand how it resembles and differs from the severe acute respiratory syndrome coronavirus (SARSCoV) at the genomic and transcriptomic level. In a short time following the outbreak, it has been shown that, similar to SARS-CoV, COVID-19 virus exploits the angiotensinconverting enzyme 2 (ACE2) receptor to gain entry inside the cells. This finding raises the curiosity of investigating the expression of ACE2 in neurological tissue and determining the possible contribution of neurological tissue damage to the morbidity and mortality caused by COIVD-19. Here, we investigate the density of the expression levels of ACE2 in the CNS, the host−virus interaction and relate it to the pathogenesis and complications seen in the recent cases resulting from the COVID-19 outbreak. Also, we debate the need for a model for staging COVID-19 based on neurological tissue involvement.

February 29, 2020 


Infection with Novel Coronavirus (SARS-CoV-2) Causes Pneumonia in the Rhesus Macaques


SARS-CoV–2 caused acute localized-to-widespread pneumonia as proved by pathological studies in all animals studied, although without obvious clinical symptoms of respiratory disease. This animal model has confirmed the causal relationship between SARS-CoV–2 and respiratory disease in RM reminiscent of the mild respiratory disease or non-symptomatic cases in COVID–19 already reported in humans, thus fulfilling Koch’s postulates. The model enables detailed studies of the pathogenesis of this illness and may play a critical role in the evaluation of therapeutic drugs and vaccines.

February 26, 2020 


Structural basis for receptor recognition by the novel coronavirus from Wuhan


A novel SARS-like coronavirus (2019-nCoV) recently emerged from Wuhan, China and is quickly spreading in humans. A key to tackling this epidemic is to understand the virus’s receptor recognition mechanism, which regulates its infection, pathogenesis, and host range. 2019-nCoV and SARS-CoV recognize the same host receptor ACE2. Here we determined the crystal structure of 2019-nCoV receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex of human ACE2.

February 26, 2020 


COVID-19 Spike-Host Cell Receptor GRP78 Binding Site Prediction


Coronaviruses have been circulating between animals and humans repeatedly. A novel human coronavirus, named COVID-19, has recently emerged in Hubei Province, China. Within the first two months, more than 2200 deaths have been confirmed, and there have been more than 79,000 hospitalized patients, mainly in China. Understanding the virus mode of host cell recognition may help to fight the disease and save lives. The spike protein of coronaviruses is the main driving force for host cell recognition. In this study, the COVID-19 corona viral spike binding site to the cell-surface receptor (Glucose Regulated Protein 78 (GRP78)) is predicted using combined molecular modeling docking and structural bioinformatics. The cyclic peptide Pep42 (CTVALPGGYVRVC) was reported earlier to be the docking platform of GRP78 in cancer cells. The COVID-19 spike protein is modeled using its counterpart, the SARS spike. Sequence and structural alignments show that four regions, in addition to its cyclic nature (the S-S bond), have sequence and physicochemical similarities to the cyclic Pep42. Protein-protein docking was performed to

test the four regions of the spike that fit tightly in the GRP78 Substrate Binding Domain β (SBDβ). The docking pose revealed the involvement of the SBDβ of GRP78 and the receptor-binding domain of the coronavirus spike protein in recognition of the host cell receptor. We reveal that the binding is more favorable between regions III (C391-C525) and IV (C480-C488) of the spike protein model and GRP78. Region IV is the main driving force for GRP78 binding with the predicted binding affinity of -9.8 kcal/mol. These nine residues (region IV) of the spike can be used to develop therapeutics specific against COVID-19.


February 26, 2020 


Characterization of Codon Usage Pattern in Novel Coronavirus 2019-nCoV


The outbreak of viral pneumonia in China due to a novel coronavirus 2019-nCoV poses significant threats to international health. In this study we perform bioinformatic analysis to take a snapshot of the codon usage pattern of 2019-nCoV and uncover that this novel coronavirus has a relatively low codon usage bias. The information from this research may not only be helpful to get new insights into the evolution of 2019-nCoV, but also have potential value for developing coronavirus vaccines.

February 19, 2020


Novel Antibody Epitopes Dominate the Antigenicity of Spike Glycoprotein in SARS-CoV-2 Compared to SARS-CoV


In our study, we found the SARS-CoV-2 spike protein had approximately 24.5% amino acid (a.a.) sequence non-conserved to that of SARS-CoV (Supplementary Fig. 1). Because of the divergence of spike proteins, the non-conserved regions of spike proteins might have the main responsibility for the antigenic

difference. Thus, to solve the problem, we conducted antibody epitope analysis that focused on the comparison of the conserved and non-conserved regions of spike glycoproteins between MERSCoV, SRAS-CoV, and SARS-CoV-2.

February 19, 2020 


Characterization of Spike Glycoprotein of 2019-nCoV On Virus Entry And Its Immune Crossreactivity With Spike Glycoprotein of SARS-CoV


Since beginning of this century, there have already been three zoonotic outbreaks caused by beta coronaviruses (CoV), SARS-CoV in 2002-2003, MERS-CoV in 2012, and the newly identified 2019-nCoV in late 2019, Wuhan, China. As to Feb 10th, 2020, there are over 40,000 confirmed cases and over 900 deaths. However, little is known about the biology of this newly emerged virus. Here we developed a lentiviral based pseudovirus system for S protein of 2019-nCoV to study virus entry in BSL2 settings. First, we confirmed that human angiotensin converting enzyme 2 (hACE2) is the main entry receptor for 2019-nCoV. Second, we found that 2019-nCoV S protein mediated entry on 293/hACE2 cells was mainly through endocytosis, and PIKfyve, TPC2, and cathepsin L are critical for virus entry. Third, 2019-nCoV S protein is less stable than SARS-CoV, and it could trigger protease independent and receptor dependent cell-cell fusion, which might help virus rapidly spread from cell to cell. Finally and more importantly, polyclonal anti-SARS S1 antibodies T62 effectively inhibited entry of SARS-CoV S pseudovirions, but almost had no effect on entry of 2019-nCoV S pseudovirions. Further studies using sera from one recovered SARSCoV patient and five 2019-nCoV patients showed that there was only limited crossneutralization activities between SARS-CoV and 2019-nCoV sera, suggesting that recovery from one infection might not protect against the other. Our results present potential targets for development of drugs and vaccines for 2019-nCoV.

February 18, 2020


Single-cell RNA Expression Profiling of ACE2, the Putative Receptor of Wuhan 2019-nCoV, in the Nasal Tissue


A novel coronavirus (2019-nCoV) was first identified in Wuhan, Hubei Province, and then spreads to the other Provinces of China. WHO decides to determine a Public Health Emergency of International Concern (PHEIC) of 2019-nCoV. 2019-nCov was reported to share the same receptor, Angiotensin-converting enzyme 2 (ACE2), with SARS-Cov. Here based on the public single-cell RNA-Seq datasets, we analyzed the ACE2 RNA expression profile in the tissues at different locations of the respiratory tract. The result indicates that the ACE2 expression appears in nasal epithelial cells. We found that the size of this population of ACE2-expressing nasal epithelial cells is comparable with the size of the population of ACE2-expression type II alveolar cells (AT2) in the Asian sample reported by Yu Zhao et al. We further detected 2019-nCoV by polymerase chain reaction (PCR) from the nasal-swab and throat-swab of seven suspected cases. We found that 2019-nCoV tends to have a higher concentration in the nasal-swab comparing to the throat-swab, which could attribute to the ACE2-expressing nasal epithelial cells. We hope this study could be informative for virus-prevention strategy development, especially the treatment of nasal mucus.






January  29, 2020

     

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


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. 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin- converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.