Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event
Identifieur interne : 000621 ( Main/Exploration ); précédent : 000620; suivant : 000622Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event
Auteurs : D. Paraskevis [Grèce] ; E. G. Kostaki [Grèce] ; G. Magiorkinis [Grèce] ; G. Panayiotakopoulos [Grèce] ; G. Sourvinos [Grèce] ; S. Tsiodras [Grèce]Source :
- Infection, Genetics and Evolution [ 1567-1348 ] ; 2020.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Betacoronavirus.
- virology : Coronavirus Infections, Pneumonia, Viral.
- Genome, Viral, High-Throughput Nucleotide Sequencing, Pandemics, Phylogeny, Recombination, Genetic.
Abstract
A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.
Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods.
Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5′-part spanning the first 11,498 nucleotides and the last 3′-part spanning 24,341–30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3′-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch.
The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.
Url:
DOI: 10.1016/j.meegid.2020.104212
PubMed: 32004758
PubMed Central: 7106301
Affiliations:
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Paraskevis</name><affiliation wicri:level="3"><nlm:aff id="af0005">Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Kostaki, E G" sort="Kostaki, E G" uniqKey="Kostaki E" first="E. G." last="Kostaki">E. G. Kostaki</name><affiliation wicri:level="3"><nlm:aff id="af0005">Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Magiorkinis, G" sort="Magiorkinis, G" uniqKey="Magiorkinis G" first="G." last="Magiorkinis">G. Magiorkinis</name><affiliation wicri:level="3"><nlm:aff id="af0005">Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Panayiotakopoulos, G" sort="Panayiotakopoulos, G" uniqKey="Panayiotakopoulos G" first="G." last="Panayiotakopoulos">G. Panayiotakopoulos</name><affiliation wicri:level="3"><nlm:aff id="af0010">National Public Health Organization (NPHO), Athens, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>National Public Health Organization (NPHO), Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author><author><name sortKey="Sourvinos, G" sort="Sourvinos, G" uniqKey="Sourvinos G" first="G." last="Sourvinos">G. Sourvinos</name><affiliation wicri:level="1"><nlm:aff id="af0015">Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion</wicri:regionArea><wicri:noRegion>Heraklion</wicri:noRegion></affiliation></author><author><name sortKey="Tsiodras, S" sort="Tsiodras, S" uniqKey="Tsiodras S" first="S." last="Tsiodras">S. Tsiodras</name><affiliation wicri:level="3"><nlm:aff id="af0020">Medical School, National and Kapodistrian University of Athens, Athens, Greece</nlm:aff><country xml:lang="fr">Grèce</country><wicri:regionArea>Medical School, National and Kapodistrian University of Athens, Athens</wicri:regionArea><placeName><settlement type="city">Athènes</settlement><region nuts="2" type="region">Attique (région)</region></placeName></affiliation></author></analytic><series><title level="j">Infection, Genetics and Evolution</title><idno type="ISSN">1567-1348</idno><idno type="eISSN">1567-7257</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Betacoronavirus (genetics)</term><term>Coronavirus Infections (virology)</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Pandemics</term><term>Phylogeny</term><term>Pneumonia, Viral (virology)</term><term>Recombination, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Génome viral</term><term>Infections à coronavirus (virologie)</term><term>Pandémies</term><term>Phylogénie</term><term>Pneumopathie virale (virologie)</term><term>Recombinaison génétique</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term><term>Pneumopathie virale</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term><term>Pneumonia, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Pandemics</term><term>Phylogeny</term><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome viral</term><term>Pandémies</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.</p></sec><sec><title>Methods</title><p>Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods.</p></sec><sec><title>Results</title><p>Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5′-part spanning the first 11,498 nucleotides and the last 3′-part spanning 24,341–30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3′-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch.</p></sec><sec><title>Conclusions</title><p>The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alagaili, A N" uniqKey="Alagaili A">A.N. Alagaili</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="World Health Organization" uniqKey="World Health Organization">World Health Organization</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Babcock, G J" uniqKey="Babcock G">G.J. Babcock</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cui, J" uniqKey="Cui J">J. Cui</name></author><author><name sortKey="Li, F" uniqKey="Li F">F. Li</name></author><author><name sortKey="Shi, Z L" uniqKey="Shi Z">Z.L. Shi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drosten, C" uniqKey="Drosten C">C. 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Swofford</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="World Health Organization" uniqKey="World Health Organization">World Health Organization</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zaki, A M" uniqKey="Zaki A">A.M. Zaki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, P" uniqKey="Zhou P">P. Zhou</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhu, N" uniqKey="Zhu N">N. Zhu</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Grèce</li></country><region><li>Attique (région)</li></region><settlement><li>Athènes</li></settlement></list><tree><country name="Grèce"><region name="Attique (région)"><name sortKey="Paraskevis, D" sort="Paraskevis, D" uniqKey="Paraskevis D" first="D." last="Paraskevis">D. Paraskevis</name></region><name sortKey="Kostaki, E G" sort="Kostaki, E G" uniqKey="Kostaki E" first="E. G." last="Kostaki">E. G. Kostaki</name><name sortKey="Magiorkinis, G" sort="Magiorkinis, G" uniqKey="Magiorkinis G" first="G." last="Magiorkinis">G. Magiorkinis</name><name sortKey="Panayiotakopoulos, G" sort="Panayiotakopoulos, G" uniqKey="Panayiotakopoulos G" first="G." last="Panayiotakopoulos">G. Panayiotakopoulos</name><name sortKey="Sourvinos, G" sort="Sourvinos, G" uniqKey="Sourvinos G" first="G." last="Sourvinos">G. Sourvinos</name><name sortKey="Tsiodras, S" sort="Tsiodras, S" uniqKey="Tsiodras S" first="S." last="Tsiodras">S. Tsiodras</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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