Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many
Identifieur interne : 003E13 ( Main/Merge ); précédent : 003E12; suivant : 003E14Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many
Auteurs : John Kovaliski [Australie] ; Ron Sinclair [Australie] ; Greg Mutze [Australie] ; David Peacock [Australie] ; Tanja Strive [Australie] ; Joana Abrantes [Portugal, France] ; Pedro J. Esteves [France, Portugal] ; Edward C. Holmes [Australie]Source :
- Molecular Ecology [ 0962-1083 ] ; 2014-02.
Descripteurs français
- KwdFr :
- ARN viral (génétique), Analyse de séquence d'ADN, Animaux, Australie, Données de séquences moléculaires, Flux des gènes, Infections à Caliciviridae (médecine vétérinaire), Infections à Caliciviridae (virologie), Infections à Caliciviridae (épidémiologie), Lapins, Marqueurs génétiques, Phylogénie, Protéines virales structurales (génétique), Variation génétique, Virus de la maladie hémorragique du lapin (génétique), Épidémiologie moléculaire, Évolution moléculaire.
- MESH :
- génétique : ARN viral, Protéines virales structurales, Virus de la maladie hémorragique du lapin.
- médecine vétérinaire : Infections à Caliciviridae.
- virologie : Infections à Caliciviridae.
- épidémiologie : Infections à Caliciviridae.
- Analyse de séquence d'ADN, Animaux, Australie, Données de séquences moléculaires, Flux des gènes, Lapins, Marqueurs génétiques, Phylogénie, Variation génétique, Épidémiologie moléculaire, Évolution moléculaire.
- Wicri :
- geographic : Australie.
English descriptors
- KwdEn :
- Animals, Australia, Caliciviridae Infections (epidemiology), Caliciviridae Infections (veterinary), Caliciviridae Infections (virology), Evolution, Molecular, Gene Flow, Genetic Markers, Genetic Variation, Hemorrhagic Disease Virus, Rabbit (genetics), Molecular Epidemiology, Molecular Sequence Data, Phylogeny, RNA, Viral (genetics), Rabbits, Sequence Analysis, DNA, Viral Structural Proteins (genetics).
- MESH :
- chemical , genetics : RNA, Viral, Viral Structural Proteins.
- chemical : Genetic Markers.
- geographic : Australia.
- epidemiology : Caliciviridae Infections.
- genetics : Hemorrhagic Disease Virus, Rabbit.
- veterinary : Caliciviridae Infections.
- virology : Caliciviridae Infections.
- Animals, Evolution, Molecular, Gene Flow, Genetic Variation, Molecular Epidemiology, Molecular Sequence Data, Phylogeny, Rabbits, Sequence Analysis, DNA.
Abstract
Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16‐year period (1995–2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V‐351 and RHDV351INOC). Strikingly, despite more than 3000 rereleases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long‐term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia −4.0 (3.3–4.7) × 10−3 nucleotide substitutions per site per year – was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.
Url:
- https://api.istex.fr/document/228A244EBA717B1A9DEEB914F8A21B202E920845/fulltext/pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595043
DOI: 10.1111/mec.12596
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ISTEX:228A244EBA717B1A9DEEB914F8A21B202E920845Le document en format XML
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Holmes</name><affiliation wicri:level="4"><country xml:lang="fr">Australie</country><wicri:regionArea>Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, NSW, 2006, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region><settlement type="city">Sydney</settlement></placeName><orgName type="university">Université de Sydney</orgName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Australie</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Molecular Ecology</title><title level="j" type="alt">MOLECULAR ECOLOGY</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><biblScope unit="vol">23</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="408">408</biblScope><biblScope unit="page" to="420">420</biblScope><biblScope unit="page-count">13</biblScope><date type="published" when="2014-02">2014-02</date></imprint><idno type="ISSN">0962-1083</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0962-1083</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Australia</term><term>Caliciviridae Infections (epidemiology)</term><term>Caliciviridae Infections (veterinary)</term><term>Caliciviridae Infections (virology)</term><term>Evolution, Molecular</term><term>Gene Flow</term><term>Genetic Markers</term><term>Genetic Variation</term><term>Hemorrhagic Disease Virus, Rabbit (genetics)</term><term>Molecular Epidemiology</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>RNA, Viral (genetics)</term><term>Rabbits</term><term>Sequence Analysis, DNA</term><term>Viral Structural Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Australie</term><term>Données de séquences moléculaires</term><term>Flux des gènes</term><term>Infections à Caliciviridae (médecine vétérinaire)</term><term>Infections à Caliciviridae (virologie)</term><term>Infections à Caliciviridae (épidémiologie)</term><term>Lapins</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Protéines virales structurales (génétique)</term><term>Variation génétique</term><term>Virus de la maladie hémorragique du lapin (génétique)</term><term>Épidémiologie moléculaire</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term><term>Viral Structural Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Australia</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Caliciviridae Infections</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hemorrhagic Disease Virus, Rabbit</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Protéines virales structurales</term><term>Virus de la maladie hémorragique du lapin</term></keywords><keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr"><term>Infections à Caliciviridae</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Caliciviridae Infections</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à Caliciviridae</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Caliciviridae Infections</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à Caliciviridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Gene Flow</term><term>Genetic Variation</term><term>Molecular Epidemiology</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Rabbits</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Australie</term><term>Données de séquences moléculaires</term><term>Flux des gènes</term><term>Lapins</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Variation génétique</term><term>Épidémiologie moléculaire</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Australie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract">Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16‐year period (1995–2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V‐351 and RHDV351INOC). Strikingly, despite more than 3000 rereleases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long‐term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia −4.0 (3.3–4.7) × 10−3 nucleotide substitutions per site per year – was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.</div></front></TEI><double doi="10.1111/mec.12596"><ISTEX><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many</title><author><name sortKey="Kovaliski, John" sort="Kovaliski, John" uniqKey="Kovaliski J" first="John" last="Kovaliski">John Kovaliski</name></author><author><name sortKey="Sinclair, Ron" sort="Sinclair, Ron" uniqKey="Sinclair R" first="Ron" last="Sinclair">Ron Sinclair</name></author><author><name sortKey="Mutze, Greg" sort="Mutze, Greg" uniqKey="Mutze G" first="Greg" last="Mutze">Greg Mutze</name></author><author><name sortKey="Peacock, David" sort="Peacock, David" uniqKey="Peacock D" first="David" last="Peacock">David Peacock</name></author><author><name sortKey="Strive, Tanja" sort="Strive, Tanja" uniqKey="Strive T" first="Tanja" last="Strive">Tanja Strive</name></author><author><name sortKey="Abrantes, Joana" sort="Abrantes, Joana" uniqKey="Abrantes J" first="Joana" last="Abrantes">Joana Abrantes</name></author><author><name sortKey="Esteves, Pedro J" sort="Esteves, Pedro J" uniqKey="Esteves P" first="Pedro J." last="Esteves">Pedro J. Esteves</name></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C." last="Holmes">Edward C. Holmes</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:228A244EBA717B1A9DEEB914F8A21B202E920845</idno><date when="2014" year="2014">2014</date><idno type="doi">10.1111/mec.12596</idno><idno type="url">https://api.istex.fr/document/228A244EBA717B1A9DEEB914F8A21B202E920845/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000669</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">000669</idno><idno type="wicri:Area/Istex/Curation">000669</idno><idno type="wicri:Area/Istex/Checkpoint">000086</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000086</idno><idno type="wicri:doubleKey">0962-1083:2014:Kovaliski J:molecular:epidemiology:of</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Molecular epidemiology of <hi rend="fc">R</hi>abbit <hi rend="fc">H</hi>aemorrhagic <hi rend="fc">D</hi>isease <hi rend="fc">V</hi>irus in <hi rend="fc">A</hi>ustralia: when one became many</title><author><name sortKey="Kovaliski, John" sort="Kovaliski, John" uniqKey="Kovaliski J" first="John" last="Kovaliski">John Kovaliski</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, 5001, Adelaide, SA</wicri:regionArea><wicri:noRegion>SA</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, ACT, 2601, Canberra</wicri:regionArea><wicri:noRegion>Canberra</wicri:noRegion></affiliation></author><author><name sortKey="Sinclair, Ron" sort="Sinclair, Ron" uniqKey="Sinclair R" first="Ron" last="Sinclair">Ron Sinclair</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, 5001, Adelaide, SA</wicri:regionArea><wicri:noRegion>SA</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, ACT, 2601, Canberra</wicri:regionArea><wicri:noRegion>Canberra</wicri:noRegion></affiliation></author><author><name sortKey="Mutze, Greg" sort="Mutze, Greg" uniqKey="Mutze G" first="Greg" last="Mutze">Greg Mutze</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, 5001, Adelaide, SA</wicri:regionArea><wicri:noRegion>SA</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, ACT, 2601, Canberra</wicri:regionArea><wicri:noRegion>Canberra</wicri:noRegion></affiliation></author><author><name sortKey="Peacock, David" sort="Peacock, David" uniqKey="Peacock D" first="David" last="Peacock">David Peacock</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, 5001, Adelaide, SA</wicri:regionArea><wicri:noRegion>SA</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, ACT, 2601, Canberra</wicri:regionArea><wicri:noRegion>Canberra</wicri:noRegion></affiliation></author><author><name sortKey="Strive, Tanja" sort="Strive, Tanja" uniqKey="Strive T" first="Tanja" last="Strive">Tanja Strive</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, 2601, Canberra, ACT</wicri:regionArea><wicri:noRegion>ACT</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Black Mountain</wicri:regionArea><wicri:noRegion>Black Mountain</wicri:noRegion></affiliation></author><author><name sortKey="Abrantes, Joana" sort="Abrantes, Joana" uniqKey="Abrantes J" first="Joana" last="Abrantes">Joana Abrantes</name><affiliation wicri:level="1"><country xml:lang="fr">Portugal</country><wicri:regionArea>CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485‐661, Vairão</wicri:regionArea><wicri:noRegion>Vairão</wicri:noRegion></affiliation><affiliation wicri:level="4"><country xml:lang="fr">France</country><wicri:regionArea>INSERM, U892, Université de Nantes, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation></author><author><name sortKey="Esteves, Pedro J" sort="Esteves, Pedro J" uniqKey="Esteves P" first="Pedro J." last="Esteves">Pedro J. Esteves</name><affiliation wicri:level="4"><country xml:lang="fr">France</country><wicri:regionArea>INSERM, U892, Université de Nantes, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation><affiliation wicri:level="1"><country xml:lang="fr">Portugal</country><wicri:regionArea>CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra</wicri:regionArea><wicri:noRegion>Gandra</wicri:noRegion></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C." last="Holmes">Edward C. Holmes</name><affiliation wicri:level="4"><country xml:lang="fr">Australie</country><wicri:regionArea>Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, NSW, 2006, Sydney</wicri:regionArea><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region><settlement type="city">Sydney</settlement></placeName><orgName type="university">Université de Sydney</orgName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Australie</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Molecular Ecology</title><title level="j" type="alt">MOLECULAR ECOLOGY</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><biblScope unit="vol">23</biblScope><biblScope unit="issue">2</biblScope><biblScope unit="page" from="408">408</biblScope><biblScope unit="page" to="420">420</biblScope><biblScope unit="page-count">13</biblScope><date type="published" when="2014-02">2014-02</date></imprint><idno type="ISSN">0962-1083</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0962-1083</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16‐year period (1995–2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V‐351 and RHDV351INOC). Strikingly, despite more than 3000 rereleases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long‐term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia −4.0 (3.3–4.7) × 10−3 nucleotide substitutions per site per year – was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.</div></front></TEI></ISTEX><PMC><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular epidemiology of Rabbit Haemorrhagic Disease Virus (RHDV) in Australia: when one became many</title><author><name sortKey="Kovaliski, John" sort="Kovaliski, John" uniqKey="Kovaliski J" first="John" last="Kovaliski">John Kovaliski</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Sinclair, Ron" sort="Sinclair, Ron" uniqKey="Sinclair R" first="Ron" last="Sinclair">Ron Sinclair</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Mutze, Greg" sort="Mutze, Greg" uniqKey="Mutze G" first="Greg" last="Mutze">Greg Mutze</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Peacock, David" sort="Peacock, David" uniqKey="Peacock D" first="David" last="Peacock">David Peacock</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Strive, Tanja" sort="Strive, Tanja" uniqKey="Strive T" first="Tanja" last="Strive">Tanja Strive</name><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3">CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, Black Mountain, ACT 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, Black Mountain, ACT 2601</wicri:regionArea><wicri:noRegion>ACT 2601</wicri:noRegion></affiliation></author><author><name sortKey="Abrantes, Joana" sort="Abrantes, Joana" uniqKey="Abrantes J" first="Joana" last="Abrantes">Joana Abrantes</name><affiliation wicri:level="1"><nlm:aff id="A4">CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos / Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos / Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão</wicri:regionArea><wicri:noRegion>4485-661 Vairão</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">INSERM, U892, Université de Nantes, Nantes, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INSERM, U892, Université de Nantes, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation></author><author><name sortKey="Esteves, Pedro J" sort="Esteves, Pedro J" uniqKey="Esteves P" first="Pedro J." last="Esteves">Pedro J. Esteves</name><affiliation wicri:level="4"><nlm:aff id="A5">INSERM, U892, Université de Nantes, Nantes, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INSERM, U892, Université de Nantes, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation><affiliation wicri:level="1"><nlm:aff id="A6">CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra</wicri:regionArea><wicri:noRegion>Gandra</wicri:noRegion></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C." last="Holmes">Edward C. Holmes</name><affiliation wicri:level="4"><nlm:aff id="A7">Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24251353</idno><idno type="pmc">4595043</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595043</idno><idno type="RBID">PMC:4595043</idno><idno type="doi">10.1111/mec.12596</idno><date when="2013">2013</date><idno 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type="wicri:Area/Ncbi/Checkpoint">001590</idno><idno type="wicri:doubleKey">0962-1083:2013:Kovaliski J:molecular:epidemiology:of</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular epidemiology of Rabbit Haemorrhagic Disease Virus (RHDV) in Australia: when one became many</title><author><name sortKey="Kovaliski, John" sort="Kovaliski, John" uniqKey="Kovaliski J" first="John" last="Kovaliski">John Kovaliski</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Sinclair, Ron" sort="Sinclair, Ron" uniqKey="Sinclair R" first="Ron" last="Sinclair">Ron Sinclair</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Mutze, Greg" sort="Mutze, Greg" uniqKey="Mutze G" first="Greg" last="Mutze">Greg Mutze</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Peacock, David" sort="Peacock, David" uniqKey="Peacock D" first="David" last="Peacock">David Peacock</name><affiliation wicri:level="1"><nlm:aff id="A1">NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide 5001</wicri:regionArea><wicri:noRegion>Adelaide 5001</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation></author><author><name sortKey="Strive, Tanja" sort="Strive, Tanja" uniqKey="Strive T" first="Tanja" last="Strive">Tanja Strive</name><affiliation wicri:level="1"><nlm:aff id="A2">Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3">CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, Black Mountain, ACT 2601, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, Black Mountain, ACT 2601</wicri:regionArea><wicri:noRegion>ACT 2601</wicri:noRegion></affiliation></author><author><name sortKey="Abrantes, Joana" sort="Abrantes, Joana" uniqKey="Abrantes J" first="Joana" last="Abrantes">Joana Abrantes</name><affiliation wicri:level="1"><nlm:aff id="A4">CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos / Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos / Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661 Vairão</wicri:regionArea><wicri:noRegion>4485-661 Vairão</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="A5">INSERM, U892, Université de Nantes, Nantes, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INSERM, U892, Université de Nantes, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation></author><author><name sortKey="Esteves, Pedro J" sort="Esteves, Pedro J" uniqKey="Esteves P" first="Pedro J." last="Esteves">Pedro J. Esteves</name><affiliation wicri:level="4"><nlm:aff id="A5">INSERM, U892, Université de Nantes, Nantes, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>INSERM, U892, Université de Nantes, Nantes</wicri:regionArea><placeName><region type="region">Pays de la Loire</region><region type="old region">Pays de la Loire</region><settlement type="city">Nantes</settlement><settlement type="city">Nantes</settlement></placeName><orgName type="university">Université de Nantes</orgName></affiliation><affiliation wicri:level="1"><nlm:aff id="A6">CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal</nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra</wicri:regionArea><wicri:noRegion>Gandra</wicri:noRegion></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C." last="Holmes">Edward C. Holmes</name><affiliation wicri:level="4"><nlm:aff id="A7">Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006</wicri:regionArea><orgName type="university">Université de Sydney</orgName><placeName><settlement type="city">Sydney</settlement><region type="état">Nouvelle-Galles du Sud</region></placeName></affiliation></author></analytic><series><title level="j">Molecular ecology</title><idno type="ISSN">0962-1083</idno><idno type="eISSN">1365-294X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Australia</term><term>Caliciviridae Infections (epidemiology)</term><term>Caliciviridae Infections (veterinary)</term><term>Caliciviridae Infections (virology)</term><term>Evolution, Molecular</term><term>Gene Flow</term><term>Genetic Markers</term><term>Genetic Variation</term><term>Hemorrhagic Disease Virus, Rabbit (genetics)</term><term>Molecular Epidemiology</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>RNA, Viral (genetics)</term><term>Rabbits</term><term>Sequence Analysis, DNA</term><term>Viral Structural Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Australie</term><term>Données de séquences moléculaires</term><term>Flux des gènes</term><term>Infections à Caliciviridae (médecine vétérinaire)</term><term>Infections à Caliciviridae (virologie)</term><term>Infections à Caliciviridae (épidémiologie)</term><term>Lapins</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Protéines virales structurales (génétique)</term><term>Variation génétique</term><term>Virus de la maladie hémorragique du lapin (génétique)</term><term>Épidémiologie moléculaire</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term><term>Viral Structural Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Australia</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Caliciviridae Infections</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hemorrhagic Disease Virus, Rabbit</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Protéines virales structurales</term><term>Virus de la maladie hémorragique du lapin</term></keywords><keywords scheme="MESH" qualifier="médecine vétérinaire" xml:lang="fr"><term>Infections à Caliciviridae</term></keywords><keywords scheme="MESH" qualifier="veterinary" xml:lang="en"><term>Caliciviridae Infections</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à Caliciviridae</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Caliciviridae Infections</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à Caliciviridae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Gene Flow</term><term>Genetic Variation</term><term>Molecular Epidemiology</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Rabbits</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Australie</term><term>Données de séquences moléculaires</term><term>Flux des gènes</term><term>Lapins</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Variation génétique</term><term>Épidémiologie moléculaire</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Australie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (<italic>Oryctolagus cuniculus</italic>). We evaluated its evolution over a 16 year period (1995–2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared to those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V-351 and RHDV351INOC). Strikingly, despite more than 3000 re-releases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long-term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia – 4.0 (3.3 – 4.7) × 10<sup>−3</sup> nucleotide substitutions per site per year – was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.</p></div></front></TEI></PMC></double></record>Pour manipuler ce document sous Unix (Dilib)
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