The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments
Identifieur interne : 001841 ( Main/Exploration ); précédent : 001840; suivant : 001842The Role of Viral Population Diversity in Adaptation of Bovine Coronavirus to New Host Environments
Auteurs : Monica K. Borucki ; Jonathan E. Allen ; Haiyin Chen-Harris ; Adam Zemla ; Gilda Vanier ; Shalini Mabery ; Clinton Torres ; Pamela Hullinger ; Tom SlezakSource :
- PLoS ONE [ 1932-6203 ] ; 2013.
Descripteurs français
- KwdFr :
- Alignement de séquences, Animaux, Bovins (virologie), Coronavirus bovin (), Coronavirus bovin (génétique), Coronavirus bovin (physiologie), Données de séquences moléculaires, Génome viral, Humains, Infections à coronavirus (médecine vétérinaire), Infections à coronavirus (virologie), Lignée cellulaire, Modèles moléculaires, Mutation ponctuelle, Phylogénie, Protéines virales (), Protéines virales (génétique), Pénétration virale, Structure tertiaire des protéines, Séquence consensus, Séquence d'acides aminés, Séquençage nucléotidique à haut débit, Taux de mutation, Variation génétique.
- MESH :
- génétique : Coronavirus bovin, Protéines virales.
- médecine vétérinaire : Infections à coronavirus.
- physiologie : Coronavirus bovin.
- virologie : Bovins, Infections à coronavirus.
- Alignement de séquences, Animaux, Coronavirus bovin, Données de séquences moléculaires, Génome viral, Humains, Lignée cellulaire, Modèles moléculaires, Mutation ponctuelle, Phylogénie, Protéines virales, Pénétration virale, Structure tertiaire des protéines, Séquence consensus, Séquence d'acides aminés, Séquençage nucléotidique à haut débit, Taux de mutation, Variation génétique.
English descriptors
- KwdEn :
- Amino Acid Sequence, Animals, Cattle (virology), Cell Line, Consensus Sequence, Coronavirus Infections (veterinary), Coronavirus Infections (virology), Coronavirus, Bovine (chemistry), Coronavirus, Bovine (genetics), Coronavirus, Bovine (physiology), Genetic Variation, Genome, Viral, High-Throughput Nucleotide Sequencing, Humans, Models, Molecular, Molecular Sequence Data, Mutation Rate, Phylogeny, Point Mutation, Protein Structure, Tertiary, Sequence Alignment, Viral Proteins (chemistry), Viral Proteins (genetics), Virus Internalization.
- MESH :
- chemical , chemistry : Viral Proteins.
- chemistry : Coronavirus, Bovine.
- genetics : Coronavirus, Bovine, Viral Proteins.
- physiology : Coronavirus, Bovine.
- veterinary : Coronavirus Infections.
- virology : Cattle, Coronavirus Infections.
- Amino Acid Sequence, Animals, Cell Line, Consensus Sequence, Genetic Variation, Genome, Viral, High-Throughput Nucleotide Sequencing, Humans, Models, Molecular, Molecular Sequence Data, Mutation Rate, Phylogeny, Point Mutation, Protein Structure, Tertiary, Sequence Alignment, Virus Internalization.
Abstract
The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.
Url:
DOI: 10.1371/journal.pone.0052752
PubMed: 23308119
PubMed Central: 3538757
Affiliations:
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Le document en format XML
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Borucki</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Allen, Jonathan E" sort="Allen, Jonathan E" uniqKey="Allen J" first="Jonathan E." last="Allen">Jonathan E. 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(chemistry)</term><term>Coronavirus, Bovine (genetics)</term><term>Coronavirus, Bovine (physiology)</term><term>Genetic Variation</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Mutation Rate</term><term>Phylogeny</term><term>Point Mutation</term><term>Protein Structure, Tertiary</term><term>Sequence Alignment</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term><term>Virus Internalization</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences</term><term>Animaux</term><term>Bovins (virologie)</term><term>Coronavirus bovin ()</term><term>Coronavirus bovin (génétique)</term><term>Coronavirus bovin (physiologie)</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus (médecine vétérinaire)</term><term>Infections à coronavirus (virologie)</term><term>Lignée cellulaire</term><term>Modèles moléculaires</term><term>Mutation ponctuelle</term><term>Phylogénie</term><term>Protéines virales ()</term><term>Protéines virales (génétique)</term><term>Pénétration virale</term><term>Structure tertiaire des protéines</term><term>Séquence consensus</term><term>Séquence d'acides aminés</term><term>Séquençage nucléotidique à haut débit</term><term>Taux de mutation</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Coronavirus, Bovine</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus, Bovine</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus bovin</term><term>Protéines virales</term></keywords><keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Coronavirus bovin</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Coronavirus, Bovine</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Bovins</term><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Cattle</term><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Cell Line</term><term>Consensus Sequence</term><term>Genetic Variation</term><term>Genome, Viral</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Mutation Rate</term><term>Phylogeny</term><term>Point Mutation</term><term>Protein Structure, Tertiary</term><term>Sequence Alignment</term><term>Virus Internalization</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Animaux</term><term>Coronavirus bovin</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>Lignée cellulaire</term><term>Modèles moléculaires</term><term>Mutation ponctuelle</term><term>Phylogénie</term><term>Protéines virales</term><term>Pénétration virale</term><term>Structure tertiaire des protéines</term><term>Séquence consensus</term><term>Séquence d'acides aminés</term><term>Séquençage nucléotidique à haut débit</term><term>Taux de mutation</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Woolhouse, Mej" uniqKey="Woolhouse M">MEJ Woolhouse</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Elena, Sf" uniqKey="Elena S">SF Elena</name></author><author><name sortKey="Carrasco, P" uniqKey="Carrasco P">P Carrasco</name></author><author><name sortKey="Daros, J A" uniqKey="Daros J">J-A Daros</name></author><author><name sortKey="Sanjuan, R" uniqKey="Sanjuan R">R Sanjuan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Domingo, E" uniqKey="Domingo E">E Domingo</name></author><author><name 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Stabel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cho, Ko" uniqKey="Cho K">KO Cho</name></author><author><name sortKey="Hasoksuz, M" uniqKey="Hasoksuz M">M Hasoksuz</name></author><author><name sortKey="Nielsen, Pr" uniqKey="Nielsen P">PR Nielsen</name></author><author><name sortKey="Chang, Ko" uniqKey="Chang K">KO Chang</name></author><author><name sortKey="Lathrop, S" uniqKey="Lathrop S">S Lathrop</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tamura, K" uniqKey="Tamura K">K Tamura</name></author><author><name sortKey="Peterson, D" uniqKey="Peterson D">D Peterson</name></author><author><name sortKey="Peterson, N" uniqKey="Peterson N">N Peterson</name></author><author><name sortKey="Stecher, G" uniqKey="Stecher G">G Stecher</name></author><author><name sortKey="Nei, M" uniqKey="Nei M">M Nei</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Allen, Jonathan E" sort="Allen, Jonathan E" uniqKey="Allen J" first="Jonathan E." last="Allen">Jonathan E. Allen</name><name sortKey="Borucki, Monica K" sort="Borucki, Monica K" uniqKey="Borucki M" first="Monica K." last="Borucki">Monica K. Borucki</name><name sortKey="Chen Harris, Haiyin" sort="Chen Harris, Haiyin" uniqKey="Chen Harris H" first="Haiyin" last="Chen-Harris">Haiyin Chen-Harris</name><name sortKey="Hullinger, Pamela" sort="Hullinger, Pamela" uniqKey="Hullinger P" first="Pamela" last="Hullinger">Pamela Hullinger</name><name sortKey="Mabery, Shalini" sort="Mabery, Shalini" uniqKey="Mabery S" first="Shalini" last="Mabery">Shalini Mabery</name><name sortKey="Slezak, Tom" sort="Slezak, Tom" uniqKey="Slezak T" first="Tom" last="Slezak">Tom Slezak</name><name sortKey="Torres, Clinton" sort="Torres, Clinton" uniqKey="Torres C" first="Clinton" last="Torres">Clinton Torres</name><name sortKey="Vanier, Gilda" sort="Vanier, Gilda" uniqKey="Vanier G" first="Gilda" last="Vanier">Gilda Vanier</name><name sortKey="Zemla, Adam" sort="Zemla, Adam" uniqKey="Zemla A" first="Adam" last="Zemla">Adam Zemla</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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