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1.
Sci Rep ; 11(1): 24145, 2021 12 17.
Article in English | MEDLINE | ID: covidwho-1585802

ABSTRACT

Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus. Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46-7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.


Subject(s)
Alphacoronavirus/genetics , Betacoronavirus/genetics , COVID-19/transmission , Chiroptera/growth & development , SARS-CoV-2/genetics , Alphacoronavirus/classification , Animals , Asia, Southeastern/epidemiology , Betacoronavirus/classification , COVID-19/epidemiology , COVID-19/virology , Cambodia/epidemiology , Chiroptera/classification , Chiroptera/virology , Epidemics/prevention & control , Evolution, Molecular , Genome, Viral/genetics , Geography , Humans , Longitudinal Studies , Male , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/physiology , Species Specificity
2.
Viruses ; 13(10)2021 10 06.
Article in English | MEDLINE | ID: covidwho-1460085

ABSTRACT

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.


Subject(s)
Alphacoronavirus/isolation & purification , Betacoronavirus/isolation & purification , Chiroptera/virology , Genome, Viral/genetics , Metagenome/genetics , Alphacoronavirus/classification , Alphacoronavirus/genetics , Animals , Betacoronavirus/classification , Betacoronavirus/genetics , Chiroptera/genetics , Computational Biology/methods , Feces/virology , High-Throughput Nucleotide Sequencing , Metagenomics/methods , Moscow , Phycodnaviridae/classification , Phycodnaviridae/genetics , Phycodnaviridae/isolation & purification , Sequence Analysis, DNA
4.
PLoS Genet ; 16(12): e1009272, 2020 12.
Article in English | MEDLINE | ID: covidwho-1388879

ABSTRACT

The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Recombination, Genetic/genetics , Spike Glycoprotein, Coronavirus/genetics , Crossing Over, Genetic/genetics , Genes, Viral/genetics , Genome, Viral/genetics , Host Specificity/genetics , Models, Genetic , Polymorphism, Genetic , SARS-CoV-2/classification , SARS-CoV-2/genetics , Viral Tropism/genetics
6.
Microb Biotechnol ; 13(3): 607-612, 2020 05.
Article in English | MEDLINE | ID: covidwho-1319217

ABSTRACT

Another animal to human transmission of a coronavirus occurred in December 2019 on a live animal market in the Chinese city of Wuhan causing an epidemic in China, reaching now different continents. This minireview summarizes the research literature on the virological, clinical and epidemiological aspects of this epidemic published until end of February 2020.


Subject(s)
Betacoronavirus , Coronavirus Infections , Disease Outbreaks , Pandemics , Pneumonia, Viral , Animals , Betacoronavirus/classification , Betacoronavirus/physiology , COVID-19 , China , Coronavirus Infections/epidemiology , Coronavirus Infections/pathology , Coronavirus Infections/therapy , Coronavirus Infections/virology , Genome, Viral/genetics , Humans , Pneumonia, Viral/epidemiology , Pneumonia, Viral/pathology , Pneumonia, Viral/therapy , Pneumonia, Viral/virology , SARS-CoV-2
7.
Sci Rep ; 11(1): 14723, 2021 07 19.
Article in English | MEDLINE | ID: covidwho-1317811

ABSTRACT

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the spike protein receptor binding domain, but excluding the receptor binding motif, RhGB01 has a 77% (SARS-CoV-2) and 81% (SARS-CoV) amino acid homology. While apparently lacking hACE2 binding ability, and hence unlikely to be zoonotic without mutation, RhGB01 presents opportunity for SARS-CoV-2 and other sarbecovirus homologous recombination. Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection are underestimated. Preventing transmission of SARS-CoV-2 to bats is critical with the current global mass vaccination campaign against this virus.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/isolation & purification , Chiroptera/virology , Amino Acid Sequence , Animals , Europe , Genome, Viral , Metagenomics , Phylogeny , SARS Virus , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry
8.
Nat Commun ; 12(1): 2642, 2021 05 11.
Article in English | MEDLINE | ID: covidwho-1225505

ABSTRACT

Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding gene set, characterize evolutionary constraint, and prioritize functional mutations. We select 44 Sarbecovirus genomes at ideally-suited evolutionary distances, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for ORFs 3a, 6, 7a, 7b, 8, 9b, and a novel alternate-frame gene, ORF3c, whereas ORFs 2b, 3d/3d-2, 3b, 9c, and 10 lack protein-coding signatures or convincing experimental evidence of protein-coding function. Furthermore, we show no other conserved protein-coding genes remain to be discovered. Mutation analysis suggests ORF8 contributes to within-individual fitness but not person-to-person transmission. Cross-strain and within-strain evolutionary pressures agree, except for fewer-than-expected within-strain mutations in nsp3 and S1, and more-than-expected in nucleocapsid, which shows a cluster of mutations in a predicted B-cell epitope, suggesting immune-avoidance selection. Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations. Previously reported RNA-modification sites show no enrichment for conservation. Here we report a high-confidence gene set and evolutionary-history annotations providing valuable resources and insights on SARS-CoV-2 biology, mutations, and evolution.


Subject(s)
COVID-19/virology , Genome, Viral/genetics , Mutation , SARS-CoV-2/genetics , Betacoronavirus/classification , Betacoronavirus/genetics , Codon , Evolution, Molecular , Genes, Viral , Genetic Fitness , Genetic Variation , Open Reading Frames , Phylogeny , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/genetics
9.
Hum Genomics ; 15(1): 26, 2021 05 07.
Article in English | MEDLINE | ID: covidwho-1220117

ABSTRACT

BACKGROUND: Mathematical approaches have been for decades used to probe the structure of DNA sequences. This has led to the development of Bioinformatics. In this exploratory work, a novel mathematical method is applied to probe the DNA structure of two related viral families: those of coronaviruses and those of influenza viruses. The coronaviruses are SARS-CoV-2, SARS-CoV-1, and MERS. The influenza viruses include H1N1-1918, H1N1-2009, H2N2-1957, and H3N2-1968. METHODS: The mathematical method used is the slow feature analysis (SFA), a rather new but promising method to delineate complex structure in DNA sequences. RESULTS: The analysis indicates that the DNA sequences exhibit an elaborate and convoluted structure akin to complex networks. We define a measure of complexity and show that each DNA sequence exhibits a certain degree of complexity within itself, while at the same time there exists complex inter-relationships between the sequences within a family and between the two families. From these relationships, we find evidence, especially for the coronavirus family, that increasing complexity in a sequence is associated with higher transmission rate but with lower mortality. CONCLUSIONS: The complexity measure defined here may hold a promise and could become a useful tool in the prediction of transmission and mortality rates in future new viral strains.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Influenza A virus/classification , Influenza A virus/genetics , Models, Genetic , Betacoronavirus/physiology , Coronavirus Infections/mortality , Coronavirus Infections/transmission , Coronavirus Infections/virology , Evolution, Molecular , Humans , Influenza A virus/physiology , Influenza, Human/mortality , Influenza, Human/transmission , Influenza, Human/virology , Sequence Analysis, DNA , Species Specificity , Time Factors
10.
Comput Med Imaging Graph ; 90: 101921, 2021 06.
Article in English | MEDLINE | ID: covidwho-1201523

ABSTRACT

Novel corona-virus (nCOV) has been declared as a pandemic that started from the city Wuhan of China. This deadly virus is infecting people rapidly and has targeted 4.93 million people across the world, with 227 K people being infected only in Italy. Cases of nCOV are quickly increasing whereas the number of nCOV test kits available in hospitals are limited. Under these conditions, an automated system for the classification of patients into nCOV positive and negative cases, is a much needed tool against the pandemic, helping in a selective use of the limited number of test kits. In this research, Convolutional Neural Network-based models (one block VGG, two block VGG, three block VGG, four block VGG, LetNet-5, AlexNet, and Resnet-50) have been employed for the detection of Corona-virus and SARS_MERS infected patients, distinguishing them from the healthy subjects, using lung X-ray scans, which has proven to be a challenging task, due to overlapping characteristics of different corona virus types. Furthermore, LSTM model has been used for time series forecasting of nCOV cases, in the following 10 days, in Italy. The evaluation results obtained, proved that the VGG1 model distinguishes the three classes at an accuracy of almost 91%, as compared to other models, whereas the approach based on the LSTM predicts the number of nCOV cases with 99% accuracy.


Subject(s)
Betacoronavirus/classification , Deep Learning , COVID-19/epidemiology , COVID-19/mortality , COVID-19/virology , Humans , Middle East Respiratory Syndrome Coronavirus/classification , Pneumonia, Viral/epidemiology , Pneumonia, Viral/mortality , Pneumonia, Viral/virology , SARS-CoV-2/classification
11.
Nat Commun ; 12(1): 1715, 2021 03 17.
Article in English | MEDLINE | ID: covidwho-1139739

ABSTRACT

The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry and the focus for development of protective antibodies and vaccines. Structural studies show exposed sites on the spike trimer that might be targeted by antibodies with cross-species specificity. Here we isolated two human monoclonal antibodies from immunized humanized mice that display a remarkable cross-reactivity against distinct spike proteins of betacoronaviruses including SARS-CoV, SARS-CoV-2, MERS-CoV and the endemic human coronavirus HCoV-OC43. Both cross-reactive antibodies target the stem helix in the spike S2 fusion subunit which, in the prefusion conformation of trimeric spike, forms a surface exposed membrane-proximal helical bundle. Both antibodies block MERS-CoV infection in cells and provide protection to mice from lethal MERS-CoV challenge in prophylactic and/or therapeutic models. Our work highlights an immunogenic and vulnerable site on the betacoronavirus spike protein enabling elicitation of antibodies with unusual binding breadth.


Subject(s)
Antibodies, Monoclonal, Humanized/immunology , Betacoronavirus/immunology , Epitopes/immunology , Spike Glycoprotein, Coronavirus/immunology , Animals , Antibodies, Monoclonal, Humanized/therapeutic use , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/therapeutic use , Antibodies, Viral/immunology , Betacoronavirus/classification , Camelus , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Cross Reactions , Epitopes/chemistry , Epitopes/genetics , Humans , Mice , Protein Conformation , Protein Subunits , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics
12.
Arch Microbiol ; 203(5): 1943-1951, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1118215

ABSTRACT

COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has put the global public health at its highest threat around the world. Previous epidemic caused by the acute respiratory syndrome coronavirus (SARS-CoV) in 2002 is also considered since both the coronaviruses resulted in the similar clinical complications. The outbreak caused by the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 had a low rate of disease transmission and death cases. Modes of entry by MERS and SARS coronaviruses are similar to that of SARS-CoV-2, except MERS-CoV utilize different receptor. They all belong to the lineage C of ß-coronavirus. Based on the information from the previous reports, the present review is mainly focused on the mechanisms of disease progression by each of these viruses in association to their strategies to escape the host immunity. The viral entry is the first step of pathogenesis associated with attachment of viral spike protein with host receptor help releasing the viral RNA into the host cell. Models of molecular pathogenesis are outlined with virus strategies escaping the host immunity along with the role of various inflammatory cytokines and chemokines in the process. The molecular aspects of pathogenesis have also been discussed.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/immunology , Coronavirus Infections/virology , Immune Evasion , Betacoronavirus/classification , Betacoronavirus/physiology , Coronavirus Infections/epidemiology , Cytokines/immunology , Disease Progression , Humans , Immunity, Innate , Species Specificity , Virus Internalization
13.
Viruses ; 12(12)2020 12 20.
Article in English | MEDLINE | ID: covidwho-1073490

ABSTRACT

Due to their need for living cells, viruses have developed adaptive evolutionary strategies to survive and perpetuate in reservoir hosts that play a crucial role in the ecology of emerging pathogens. Pathogenic and potentially pandemic betacoronaviruses arose in humans in 2002 (SARS-CoV, disappeared in July 2003), 2012 (MERS-CoV, still circulating in Middle East areas), and 2019 (SARS-CoV-2, causing the current global pandemic). As universally recognized, bats host ancestors of the above-mentioned zoonotic viruses. However, hedgehogs have been recently identified in Europe and Asia as possible reservoirs of MERS-CoV-like strains classified as Erinaceus coronavirus (EriCoV). To elucidate the evolution and genetics of EriCoVs, NGS (next generation sequencing) and Sanger sequencing were used to examine fecal samples collected in Northern Italy in 2018/2019 from 12 hedgehogs previously found EriCoV-positive by RT-PCR. By sequence analysis, eight complete EriCoV genomes, obtained by NGS, showed a high phylogenetic correlation with EriCoV strains previously reported in Eurasia. Interestingly, eight viral strains presented an additional ORF encoding for the CD200 ortholog located between the genes encoding for the Spike and the ORF3a proteins. The CD200 ortholog sequences were closely similar to the host CD200 protein but varying among EriCoVs. The result, confirmed by Sanger sequencing, demonstrates for the first time that CoVs can acquire host genes potentially involved in the immune-modulatory cascade and possibly enabling the virus to escape the host defence.


Subject(s)
Coronavirus Infections/virology , Coronavirus/classification , Coronavirus/genetics , Hedgehogs/virology , Animals , Base Composition , Betacoronavirus/classification , Betacoronavirus/genetics , COVID-19/virology , Chiroptera/virology , Evolution, Molecular , Genome, Viral , Middle East Respiratory Syndrome Coronavirus/genetics , Pandemics , Phylogeny , SARS-CoV-2/genetics , Sequence Alignment , Sequence Analysis , Spike Glycoprotein, Coronavirus/genetics
14.
Epidemiol. serv. saúde ; 29(5): e2020644, 2020. tab
Article in English, Portuguese | LILACS (Americas) | ID: covidwho-1015986

ABSTRACT

Objetivo: Descrever o perfil dos óbitos e a letalidade de síndrome respiratória aguda grave (SRAG) por COVID-19 em crianças e adolescentes hospitalizados no Brasil. Métodos: Estudo transversal, realizado com dados das fichas de notificação de SRAG de crianças e adolescentes (0 a 19 anos) com confirmação laboratorial para COVID-19. Foram incluídas as notificações com evolução completa de SRAG por COVID-19 até a 38ᵃ Semana Epidemiológica de 2020. Resultados: Foram investigadas 6.989 hospitalizações, das quais 661 evoluíram a óbito, perfazendo uma letalidade hospitalar de 9,5%. Observou-se maior letalidade entre menores de 1 ano de idade (14,2%), crianças e adolescentes do sexo feminino (9,7%), indígenas (23,0%) e residentes em zonas rurais (18,1%), como também nas regiões Nordeste (15,4%) e Norte (9,7%) do país. Conclusão: Foram observadas diferenças na letalidade hospitalar, conforme as características sociodemográficas e marcantes desigualdades regionais.


Objetivo: Describir el perfil de muertes y letalidad del Síndrome Respiratorio Agudo Severo (SRAS) por COVID-19 en niños y adolescentes hospitalizados en Brasil. Métodos: Estudio transversal realizado con datos de los formularios de notificación de SRAS de niños y adolescentes (0 a 19 años) confirmados en laboratorio para COVID-19. Se incluyeron notificaciones con evolución completa del SRAS por COVID-19, hasta la 38ª Semana Epidemiológica de 2020. Resultados: Se incluyeron 6.989 hospitalizaciones, 661 fallecidas, resultando en letalidad hospitalaria del 9,5%. Se observaron mayores tasas de letalidad entre los niños menores de un año (14,2%), niñas y adolescentes (9,7%), indígenas (23,0%) y residentes en zonas rurales (18,1%), así como en las regiones Nordeste (15,4%) y Norte (9,7%). Conclusión: Se observaron diferencias en la mortalidad hospitalaria según las características sociodemográficas y marcadas desigualdades regionales.


Objective: To describe the profile of deaths and the lethality of Severe Acute Respiratory Syndrome (SARS) due to COVID-19 in hospitalized children and adolescents in Brazil. Methods: This was a cross-sectional study conducted with data from the SARS notification forms of children and adolescents (0 to 19 years old) with laboratory-confirmed COVID-19. Notifications with complete progression of SARS due to COVID-19 were included, up to the 38th Epidemiological Week of 2020. Results: 6,989 hospitalizations were investigated, 661 died, resulting in 9.5% hospital lethality. Higher lethality rates were observed among children under 1 year of age (14.2%), female children and adolescents (9.7%), the indigenous (23.0%), and those living in rural areas (18.1 %), as well as in the Northeast (15.4%) and North (9.7%) regions of Brazil. Conclusion: Differences in hospital mortality were found according to sociodemographic characteristics and marked regional inequalities.


Subject(s)
Humans , Male , Female , Infant , Child, Preschool , Child , Adolescent , Young Adult , Coronavirus Infections/complications , Coronavirus Infections/mortality , Coronavirus Infections/epidemiology , Severe Acute Respiratory Syndrome/mortality , Severe Acute Respiratory Syndrome/epidemiology , Hospitalization/statistics & numerical data , Brazil/epidemiology , Cross-Sectional Studies , Hospital Mortality , Pandemics/statistics & numerical data , Epidemiological Monitoring , Betacoronavirus/classification
15.
J Immunol ; 206(5): 923-929, 2021 03 01.
Article in English | MEDLINE | ID: covidwho-1004828

ABSTRACT

The Coronaviridae family includes the seven known human coronaviruses (CoV) that cause mild to moderate respiratory infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1) as well as severe illness and death (MERS-CoV, SARS-CoV, SARS-CoV-2). Severe infections induce hyperinflammatory responses that are often intensified by host adaptive immune pathways to profoundly advance disease severity. Proinflammatory responses are triggered by CoV entry mediated by host cell surface receptors. Interestingly, five of the seven strains use three cell surface metallopeptidases (CD13, CD26, and ACE2) as receptors, whereas the others employ O-acetylated-sialic acid (a key feature of metallopeptidases) for entry. Why CoV evolved to use peptidases as their receptors is unknown, but the peptidase activities of the receptors are dispensable, suggesting the virus uses/benefits from other functions of these molecules. Indeed, these receptors participate in the immune modulatory pathways that contribute to the pathological hyperinflammatory response. This review will focus on the role of CoV receptors in modulating immune responses.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/immunology , Coronavirus Infections/immunology , Immunomodulation , Metalloproteases/immunology , Receptors, Cell Surface/immunology , Receptors, Coronavirus/immunology , Angiotensin-Converting Enzyme 2/metabolism , Animals , Betacoronavirus/metabolism , Coronavirus Infections/virology , Cytokine Release Syndrome/immunology , Cytokine Release Syndrome/virology , Humans , Immunity , Interleukin-6/immunology , Virus Internalization
16.
Zool Res ; 41(6): 705-708, 2020 Nov 18.
Article in English | MEDLINE | ID: covidwho-982981

ABSTRACT

Since the first reported severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in December 2019, coronavirus disease 2019 (COVID-19) has become a global pandemic, spreading to more than 200 countries and regions worldwide. With continued research progress and virus detection, SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate. To meet the need for fast analysis of these genome sequences, the National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) has established an online coronavirus analysis platform, which includes de novoassembly, BLAST alignment, genome annotation, variant identification, and variant annotation modules. The online analysis platform can be freely accessed at the 2019 Novel Coronavirus Resource (2019nCoVR) (https://bigd.big.ac.cn/ncov/online/tools).


Subject(s)
Betacoronavirus/genetics , Computational Biology/methods , Coronavirus Infections/diagnosis , Genome, Viral/genetics , Genomics/methods , High-Throughput Nucleotide Sequencing/methods , Pneumonia, Viral/diagnosis , Animals , Betacoronavirus/classification , Betacoronavirus/physiology , COVID-19 , China , Computational Biology/organization & administration , Coronavirus Infections/virology , Genetic Variation , Humans , Internet , Molecular Sequence Annotation , Pandemics , Pneumonia, Viral/virology , SARS-CoV-2
17.
Disaster Med Public Health Prep ; 14(3): e25-e26, 2020 06.
Article in English | MEDLINE | ID: covidwho-950866

ABSTRACT

We investigated the adoption of World Health Organization (WHO) naming of COVID-19 into the respective languages among the Group of Twenty (G20) countries, and the variation of COVID-19 naming in the Chinese language across different health authorities. On May 7, 2020, we identified the websites of the national health authorities of the G20 countries to identify naming of COVID-19 in their respective languages, and the websites of the health authorities in mainland China, Hong Kong, Macau, Taiwan and Singapore and identify their Chinese name for COVID-19. Among the G20 nations, Argentina, China, Italy, Japan, Mexico, Saudi Arabia and Turkey do not use the literal translation of COVID-19 in their official language(s) to refer to COVID-19, as they retain "novel" in the naming of this disease. China is the only G20 nation that names COVID-19 a pneumonia. Among Chinese-speaking jurisdictions, Hong Kong and Singapore governments follow the WHO's recommendation and adopt the literal translation of COVID-19 in Chinese. In contrast, mainland China, Macau, and Taiwan refer to COVID-19 as a type of pneumonia in Chinese. We urge health authorities worldwide to adopt naming in their native languages that are consistent with WHO's naming of COVID-19.


Subject(s)
Betacoronavirus/classification , Coronavirus Infections/classification , Internationality , Language , Names , Pandemics/classification , Pneumonia, Viral/classification , COVID-19 , Humans , SARS-CoV-2
18.
Viruses ; 12(11)2020 11 16.
Article in English | MEDLINE | ID: covidwho-927371

ABSTRACT

The Betacoronavirus genus of mammal-infecting viruses includes three subgenera (Sarbecovirus, Embecovirus, and Merbecovirus), in which most known human coronaviruses, including SARS-CoV-2, cluster. Coronaviruses are prone to host shifts, with recombination and positive selection possibly contributing to their high zoonotic potential. We analyzed the role of these two forces in the evolution of viruses belonging to the Betacoronavirus genus. The results showed that recombination has been pervasive during sarbecovirus evolution, and it is more widespread in this subgenus compared to the other two. In both sarbecoviruses and merbecoviruses, recombination hotspots are clearly observed. Conversely, positive selection was a less prominent force in sarbecoviruses compared to embecoviruses and merbecoviruses and targeted distinct genomic regions in the three subgenera, with S being the major target in sarbecoviruses alone. Overall, the results herein indicate that Betacoronavirus subgenera evolved along different trajectories, which might recapitulate their host preferences or reflect the origins of the presently available coronavirus sequences.


Subject(s)
Betacoronavirus/classification , Betacoronavirus/genetics , Evolution, Molecular , Genetic Variation , Recombination, Genetic , Selection, Genetic , Animals , Coronavirus Infections/virology , Genome, Viral , Genomics , Host Microbial Interactions , Humans , Phylogeny , Viral Zoonoses
19.
PLoS One ; 15(11): e0240345, 2020.
Article in English | MEDLINE | ID: covidwho-917985

ABSTRACT

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.


Subject(s)
Betacoronavirus/genetics , Genetic Variation , Genome, Viral , Betacoronavirus/classification , Betacoronavirus/isolation & purification , COVID-19 , China , Coronavirus Infections/pathology , Coronavirus Infections/virology , Evolution, Molecular , Humans , Pandemics , Phylogeny , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Polyproteins , Protein Structure, Tertiary , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Viral Proteins/chemistry , Viral Proteins/genetics
20.
Sci Rep ; 10(1): 18289, 2020 10 26.
Article in English | MEDLINE | ID: covidwho-892042

ABSTRACT

The World Health Organization characterized COVID-19 as a pandemic in March 2020, the second pandemic of the twenty-first century. Expanding virus populations, such as that of SARS-CoV-2, accumulate a number of narrowly shared polymorphisms, imposing a confounding effect on traditional clustering methods. In this context, approaches that reduce the complexity of the sequence space occupied by the SARS-CoV-2 population are necessary for robust clustering. Here, we propose subdividing the global SARS-CoV-2 population into six well-defined subtypes and 10 poorly represented genotypes named tentative subtypes by focusing on the widely shared polymorphisms in nonstructural (nsp3, nsp4, nsp6, nsp12, nsp13 and nsp14) cistrons and structural (spike and nucleocapsid) and accessory (ORF8) genes. The six subtypes and the additional genotypes showed amino acid replacements that might have phenotypic implications. Notably, three mutations (one of them in the Spike protein) were responsible for the geographical segregation of subtypes. We hypothesize that the virus subtypes detected in this study are records of the early stages of SARS-CoV-2 diversification that were randomly sampled to compose the virus populations around the world. The genetic structure determined for the SARS-CoV-2 population provides substantial guidelines for maximizing the effectiveness of trials for testing candidate vaccines or drugs.


Subject(s)
Betacoronavirus/genetics , Polymorphism, Genetic , Betacoronavirus/classification , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/epidemiology , Coronavirus Infections/pathology , Coronavirus Infections/virology , Coronavirus Nucleocapsid Proteins , Genotype , Humans , Nucleocapsid Proteins/genetics , Pandemics , Phosphoproteins , Phylogeny , Pneumonia, Viral/epidemiology , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics , Viral Nonstructural Proteins/genetics , Viral Proteins/genetics
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