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1.
J Proteome Res ; 19(4): 1351-1360, 2020 04 03.
Article in English | MEDLINE | ID: covidwho-688546

ABSTRACT

As the infection of 2019-nCoV coronavirus is quickly developing into a global pneumonia epidemic, the careful analysis of its transmission and cellular mechanisms is sorely needed. In this Communication, we first analyzed two recent studies that concluded that snakes are the intermediate hosts of 2019-nCoV and that the 2019-nCoV spike protein insertions share a unique similarity to HIV-1. However, the reimplementation of the analyses, built on larger scale data sets using state-of-the-art bioinformatics methods and databases, presents clear evidence that rebuts these conclusions. Next, using metagenomic samples from Manis javanica, we assembled a draft genome of the 2019-nCoV-like coronavirus, which shows 73% coverage and 91% sequence identity to the 2019-nCoV genome. In particular, the alignments of the spike surface glycoprotein receptor binding domain revealed four times more variations in the bat coronavirus RaTG13 than in the Manis coronavirus compared with 2019-nCoV, suggesting the pangolin as a missing link in the transmission of 2019-nCoV from bats to human.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Genome, Viral/genetics , Host-Pathogen Interactions , Models, Molecular , Pneumonia, Viral/virology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Amino Acid Sequence , Animals , Betacoronavirus/classification , Eutheria/virology , HIV-1/genetics , Humans , Metagenome , Pandemics , Protein Structure, Tertiary , Sequence Alignment , Sequence Analysis, Protein , Snakes/virology
2.
Vopr Virusol ; 65(1): 6-15, 2020.
Article in Russian | MEDLINE | ID: covidwho-533952

ABSTRACT

Results of analysis of phylogenetic, virological, epidemiological, ecological, clinical data of COVID-19 outbreaks in Wuhan, China (PRC) in comparison with SARS-2002 and MERS-2012 outbreaks allow to conclude: - the etiological agent of COVID-19 is coronavirus (2019-CoV), phylogenetically close to the SARS-CoV, isolated from human, and SARS-related viruses isolated from bats (SARS-related bat CoV viruses). These viruses belong to the Sarbecovirus subgenus, Betacoronavirus genus, Orthocoronavirinae subfamily, Coronaviridae family (Cornidovirinea: Nidovirales). COVID-19 is a variant of SARS-2002 and is different from MERS-2012 outbreak, which were caused by coronavirus belonged to the subgenus Merbecovirus of the same genus; - according to the results of phylogenetic analysis of 35 different betacoronaviruses, isolated from human and from wild animals in 2002-2019, the natural source of COVID-19 and SARS-CoV (2002) is bats of Rhinolophus genus (Rhinolophidae) and, probably, some species of other genera. An additional reservoir of the virus could be an intermediate animal species (snakes, civet, hedgehogs, badgers, etc.) that are infected by eating of infected bats. SARS-like coronaviruses circulated in bats in the interepidemic period (2003-2019); - seasonal coronaviruses (subgenus Duvinacovirus, Alphacoronavirus) are currently circulating (November 2019 - January 2020) in the European part of Russia, Urals, Siberia and the Far East of Russia, along with the influenza viruses A(H1N1)pdm09, A(H3N2), and В, as well as six other respiratory viruses (HPIV, HAdV, HRSV, HRV, HBoV, and HMPV).


Subject(s)
Betacoronavirus/classification , Coronavirus Infections/epidemiology , Pandemics , Phylogeny , Pneumonia, Viral/epidemiology , Respiratory Tract Infections/epidemiology , Animals , Betacoronavirus/genetics , Betacoronavirus/pathogenicity , China/epidemiology , Chiroptera/virology , Coronavirus Infections/diagnosis , Coronavirus Infections/physiopathology , Coronavirus Infections/transmission , Disease Reservoirs/virology , Epidemiological Monitoring , Hedgehogs/virology , Humans , Mustelidae/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/physiopathology , Pneumonia, Viral/transmission , Public Health/statistics & numerical data , Respiratory Tract Infections/diagnosis , Respiratory Tract Infections/physiopathology , Respiratory Tract Infections/transmission , Russia/epidemiology , Snakes/virology , Viverridae/virology
3.
J Med Virol ; 92(4): 433-440, 2020 04.
Article in English | MEDLINE | ID: covidwho-2245

ABSTRACT

The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission.


Subject(s)
Betacoronavirus/genetics , Chiroptera/virology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Disease Reservoirs , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Snakes/virology , Spike Glycoprotein, Coronavirus/genetics , Animals , Betacoronavirus/classification , Betacoronavirus/physiology , Bungarus/genetics , Bungarus/virology , Chiroptera/genetics , Codon Usage , Coronavirus Infections/epidemiology , Disease Outbreaks , Evolution, Molecular , Genome, Viral , Homologous Recombination , Host Specificity , Humans , Naja naja/genetics , Naja naja/virology , Phylogeny , Pneumonia, Viral/epidemiology , Snakes/genetics , Zoonoses
4.
J Med Virol ; 92(6): 595-601, 2020 06.
Article in English | MEDLINE | ID: covidwho-2181

ABSTRACT

From the beginning of 2002 and 2012, severe respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) crossed the species barriers to infect humans, causing thousands of infections and hundreds of deaths, respectively. Currently, a novel coronavirus (SARS-CoV-2), which has become the cause of the outbreak of Coronavirus Disease 2019 (COVID-19), was discovered. Until 18 February 2020, there were 72 533 confirmed COVID-19 cases (including 10 644 severe cases) and 1872 deaths in China. SARS-CoV-2 is spreading among the public and causing substantial burden due to its human-to-human transmission. However, the intermediate host of SARS-CoV-2 is still unclear. Finding the possible intermediate host of SARS-CoV-2 is imperative to prevent further spread of the epidemic. In this study, we used systematic comparison and analysis to predict the interaction between the receptor-binding domain (RBD) of coronavirus spike protein and the host receptor, angiotensin-converting enzyme 2 (ACE2). The interaction between the key amino acids of S protein RBD and ACE2 indicated that, other than pangolins and snakes, as previously suggested, turtles (Chrysemys picta bellii, Chelonia mydas, and Pelodiscus sinensis) may act as the potential intermediate hosts transmitting SARS-CoV-2 to humans.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Pandemics , Peptidyl-Dipeptidase A/chemistry , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Receptors, Virus/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Amino Acid Sequence , Animals , Betacoronavirus/classification , Betacoronavirus/pathogenicity , Binding Sites , China/epidemiology , Chiroptera/virology , Coronavirus Infections/virology , Eutheria/virology , Humans , Models, Molecular , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Phylogeny , Pneumonia, Viral/virology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Interaction Mapping , Receptors, Virus/genetics , Receptors, Virus/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Snakes/virology , Spike Glycoprotein, Coronavirus/classification , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Turtles/virology
5.
J Med Virol ; 92(4): 433-440, 2020 04.
Article in English | MEDLINE | ID: covidwho-17

ABSTRACT

The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission.


Subject(s)
Betacoronavirus/genetics , Chiroptera/virology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Disease Reservoirs , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Snakes/virology , Spike Glycoprotein, Coronavirus/genetics , Animals , Betacoronavirus/classification , Betacoronavirus/physiology , Bungarus/genetics , Bungarus/virology , Chiroptera/genetics , Codon Usage , Coronavirus Infections/epidemiology , Disease Outbreaks , Evolution, Molecular , Genome, Viral , Homologous Recombination , Host Specificity , Humans , Naja naja/genetics , Naja naja/virology , Phylogeny , Pneumonia, Viral/epidemiology , Snakes/genetics , Zoonoses
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