Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts
Identifieur interne : 000028 ( France/Analysis ); précédent : 000027; suivant : 000029Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts
Auteurs : Shelley Cook [Royaume-Uni] ; Betty Y.-W. Chung [Royaume-Uni] ; David Bass [Royaume-Uni] ; Gregory Moureau [France] ; Shuoya Tang [Royaume-Uni] ; Erica Mcalister [Royaume-Uni] ; C. Lorna Culverwell [Royaume-Uni] ; Edvard Glücksman [Allemagne] ; Hui Wang [Royaume-Uni] ; T. David K. Brown [Royaume-Uni] ; Ernest A. Gould [France, Royaume-Uni] ; Ralph E. Harbach [Royaume-Uni] ; Xavier De Lamballerie [France] ; Andrew E. Firth [Royaume-Uni]Source :
- PLoS ONE [ 1932-6203 ] ; 2013.
Abstract
We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult
Url:
DOI: 10.1371/journal.pone.0080720
PubMed: 24260463
PubMed Central: 3832450
Affiliations:
- Allemagne, France, Royaume-Uni
- Angleterre, Angleterre de l'Est, Grand Londres, Provence-Alpes-Côte d'Azur
- Cambridge, Londres, Marseille
- Université de Cambridge
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000454
- to stream Pmc, to step Curation: 000453
- to stream Pmc, to step Checkpoint: 000182
- to stream Ncbi, to step Merge: 000283
- to stream Ncbi, to step Curation: 000283
- to stream Ncbi, to step Checkpoint: 000283
- to stream Main, to step Merge: 000215
- to stream Main, to step Curation: 000214
- to stream Main, to step Exploration: 000214
- to stream France, to step Extraction: 000028
Links to Exploration step
PMC:3832450Le document en format XML
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Chung</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Plant Sciences, University of Cambridge, Cambridge</wicri:regionArea><orgName type="university">Université de Cambridge</orgName><placeName><settlement type="city">Cambridge</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Angleterre de l'Est</region></placeName></affiliation></author><author><name sortKey="Bass, David" sort="Bass, David" uniqKey="Bass D" first="David" last="Bass">David Bass</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Life Sciences, Natural History Museum, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Moureau, Gregory" sort="Moureau, Gregory" uniqKey="Moureau G" first="Gregory" last="Moureau">Gregory Moureau</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. 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IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille</wicri:regionArea><placeName><region type="region">Provence-Alpes-Côte d'Azur</region><region type="old region">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Ecology & Hydrology, Wallingford, Oxfordshire</wicri:regionArea><wicri:noRegion>Oxfordshire</wicri:noRegion></affiliation></author><author><name sortKey="Harbach, Ralph E" sort="Harbach, Ralph E" uniqKey="Harbach R" first="Ralph E." last="Harbach">Ralph E. 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Chung</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Plant Sciences, University of Cambridge, Cambridge</wicri:regionArea><orgName type="university">Université de Cambridge</orgName><placeName><settlement type="city">Cambridge</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Angleterre de l'Est</region></placeName></affiliation></author><author><name sortKey="Bass, David" sort="Bass, David" uniqKey="Bass D" first="David" last="Bass">David Bass</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Life Sciences, Natural History Museum, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Moureau, Gregory" sort="Moureau, Gregory" uniqKey="Moureau G" first="Gregory" last="Moureau">Gregory Moureau</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille</wicri:regionArea><placeName><region type="region">Provence-Alpes-Côte d'Azur</region><region type="old region">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation></author><author><name sortKey="Tang, Shuoya" sort="Tang, Shuoya" uniqKey="Tang S" first="Shuoya" last="Tang">Shuoya Tang</name><affiliation wicri:level="4"><nlm:aff id="aff2"><addr-line>Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Plant Sciences, University of Cambridge, Cambridge</wicri:regionArea><orgName type="university">Université de Cambridge</orgName><placeName><settlement type="city">Cambridge</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Angleterre de l'Est</region></placeName></affiliation></author><author><name sortKey="Mcalister, Erica" sort="Mcalister, Erica" uniqKey="Mcalister E" first="Erica" last="Mcalister">Erica Mcalister</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Life Sciences, Natural History Museum, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Culverwell, C Lorna" sort="Culverwell, C Lorna" uniqKey="Culverwell C" first="C. Lorna" last="Culverwell">C. Lorna Culverwell</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Life Sciences, Natural History Museum, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Glucksman, Edvard" sort="Glucksman, Edvard" uniqKey="Glucksman E" first="Edvard" last="Glücksman">Edvard Glücksman</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>Department of General Botany, University Duisburg-Essen, Essen, Germany</addr-line></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of General Botany, University Duisburg-Essen, Essen</wicri:regionArea><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Hui" sort="Wang, Hui" uniqKey="Wang H" first="Hui" last="Wang">Hui Wang</name><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Ecology & Hydrology, Wallingford, Oxfordshire</wicri:regionArea><wicri:noRegion>Oxfordshire</wicri:noRegion></affiliation></author><author><name sortKey="Brown, T David K" sort="Brown, T David K" uniqKey="Brown T" first="T. David K." last="Brown">T. David K. Brown</name><affiliation wicri:level="4"><nlm:aff id="aff6"><addr-line>Department of Pathology, University of Cambridge, Cambridge, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Pathology, University of Cambridge, Cambridge</wicri:regionArea><orgName type="university">Université de Cambridge</orgName><placeName><settlement type="city">Cambridge</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Angleterre de l'Est</region></placeName></affiliation></author><author><name sortKey="Gould, Ernest A" sort="Gould, Ernest A" uniqKey="Gould E" first="Ernest A." last="Gould">Ernest A. Gould</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille</wicri:regionArea><placeName><region type="region">Provence-Alpes-Côte d'Azur</region><region type="old region">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="aff5"><addr-line>Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Centre for Ecology & Hydrology, Wallingford, Oxfordshire</wicri:regionArea><wicri:noRegion>Oxfordshire</wicri:noRegion></affiliation></author><author><name sortKey="Harbach, Ralph E" sort="Harbach, Ralph E" uniqKey="Harbach R" first="Ralph E." last="Harbach">Ralph E. Harbach</name><affiliation wicri:level="3"><nlm:aff id="aff1"><addr-line>Department of Life Sciences, Natural History Museum, London, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Life Sciences, Natural History Museum, London</wicri:regionArea><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="De Lamballerie, Xavier" sort="De Lamballerie, Xavier" uniqKey="De Lamballerie X" first="Xavier" last="De Lamballerie">Xavier De Lamballerie</name><affiliation wicri:level="3"><nlm:aff id="aff3"><addr-line>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France</addr-line></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille</wicri:regionArea><placeName><region type="region">Provence-Alpes-Côte d'Azur</region><region type="old region">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation></author><author><name sortKey="Firth, Andrew E" sort="Firth, Andrew E" uniqKey="Firth A" first="Andrew E." last="Firth">Andrew E. Firth</name><affiliation wicri:level="4"><nlm:aff id="aff6"><addr-line>Department of Pathology, University of Cambridge, Cambridge, United Kingdom</addr-line></nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Pathology, University of Cambridge, Cambridge</wicri:regionArea><orgName type="university">Université de Cambridge</orgName><placeName><settlement type="city">Cambridge</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Angleterre de l'Est</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult <italic>Anopheles maculipennis</italic> s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of <italic>Ochlerotatus caspius</italic> and <italic>Oc. detritus</italic> mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected. </p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Rosario, K" uniqKey="Rosario K">K Rosario</name></author><author><name sortKey="Breitbart, M" uniqKey="Breitbart M">M Breitbart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Crabtree, Mb" uniqKey="Crabtree M">MB Crabtree</name></author><author><name sortKey="Sang, Rc" uniqKey="Sang R">RC Sang</name></author><author><name sortKey="Stollar, V" uniqKey="Stollar V">V Stollar</name></author><author><name sortKey="Dunster, Lm" uniqKey="Dunster L">LM Dunster</name></author><author><name sortKey="Miller, Br" uniqKey="Miller B">BR Miller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sang, Rc" uniqKey="Sang R">RC Sang</name></author><author><name 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Mp" uniqKey="Seco M">MP Seco</name></author><author><name sortKey="Tenorio, A" uniqKey="Tenorio A">A Tenorio</name></author><author><name sortKey="Rizzoli, A" uniqKey="Rizzoli A">A Rizzoli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanchez Seco, Mp" uniqKey="Sanchez Seco M">MP Sánchez-Seco</name></author><author><name sortKey="Vazquez, A" uniqKey="Vazquez A">A Vázquez</name></author><author><name sortKey="Collao, X" uniqKey="Collao X">X Collao</name></author><author><name sortKey="Hernandez, L" uniqKey="Hernandez L">L Hernández</name></author><author><name sortKey="Aranda, C" uniqKey="Aranda C">C Aranda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Calzolari, M" uniqKey="Calzolari M">M Calzolari</name></author><author><name sortKey="Bonilauri, P" uniqKey="Bonilauri P">P Bonilauri</name></author><author><name sortKey="Bellini, R" uniqKey="Bellini R">R Bellini</name></author><author><name sortKey="Caimi, M" uniqKey="Caimi M">M Caimi</name></author><author><name sortKey="Defilippo, F" uniqKey="Defilippo F">F Defilippo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bolling, Bg" uniqKey="Bolling B">BG Bolling</name></author><author><name sortKey="Eisen, L" uniqKey="Eisen L">L Eisen</name></author><author><name sortKey="Moore, Cg" uniqKey="Moore C">CG Moore</name></author><author><name sortKey="Blair, Cd" uniqKey="Blair C">CD Blair</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Armitage, Pd" uniqKey="Armitage P">PD Armitage</name></author><author><name sortKey="Cranston, Ps" uniqKey="Cranston P">PS Cranston</name></author><author><name sortKey="Pinder, Lcv" uniqKey="Pinder L">LCV Pinder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Taylor, Dj" uniqKey="Taylor D">DJ Taylor</name></author><author><name sortKey="Bruenn, J" uniqKey="Bruenn J">J Bruenn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aswad, A" uniqKey="Aswad A">A Aswad</name></author><author><name sortKey="Katzourakis, A" uniqKey="Katzourakis A">A Katzourakis</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>France</li><li>Royaume-Uni</li></country><region><li>Angleterre</li><li>Angleterre de l'Est</li><li>Grand Londres</li><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Cambridge</li><li>Londres</li><li>Marseille</li></settlement><orgName><li>Université de Cambridge</li></orgName></list><tree><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Cook, Shelley" sort="Cook, Shelley" uniqKey="Cook S" first="Shelley" last="Cook">Shelley Cook</name></region><name sortKey="Bass, David" sort="Bass, David" uniqKey="Bass D" first="David" last="Bass">David Bass</name><name sortKey="Brown, T David K" sort="Brown, T David K" uniqKey="Brown T" first="T. David K." last="Brown">T. David K. Brown</name><name sortKey="Chung, Betty Y W" sort="Chung, Betty Y W" uniqKey="Chung B" first="Betty Y.-W." last="Chung">Betty Y.-W. Chung</name><name sortKey="Culverwell, C Lorna" sort="Culverwell, C Lorna" uniqKey="Culverwell C" first="C. Lorna" last="Culverwell">C. Lorna Culverwell</name><name sortKey="Firth, Andrew E" sort="Firth, Andrew E" uniqKey="Firth A" first="Andrew E." last="Firth">Andrew E. Firth</name><name sortKey="Gould, Ernest A" sort="Gould, Ernest A" uniqKey="Gould E" first="Ernest A." last="Gould">Ernest A. Gould</name><name sortKey="Harbach, Ralph E" sort="Harbach, Ralph E" uniqKey="Harbach R" first="Ralph E." last="Harbach">Ralph E. Harbach</name><name sortKey="Mcalister, Erica" sort="Mcalister, Erica" uniqKey="Mcalister E" first="Erica" last="Mcalister">Erica Mcalister</name><name sortKey="Tang, Shuoya" sort="Tang, Shuoya" uniqKey="Tang S" first="Shuoya" last="Tang">Shuoya Tang</name><name sortKey="Wang, Hui" sort="Wang, Hui" uniqKey="Wang H" first="Hui" last="Wang">Hui Wang</name></country><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Moureau, Gregory" sort="Moureau, Gregory" uniqKey="Moureau G" first="Gregory" last="Moureau">Gregory Moureau</name></region><name sortKey="De Lamballerie, Xavier" sort="De Lamballerie, Xavier" uniqKey="De Lamballerie X" first="Xavier" last="De Lamballerie">Xavier De Lamballerie</name><name sortKey="Gould, Ernest A" sort="Gould, Ernest A" uniqKey="Gould E" first="Ernest A." last="Gould">Ernest A. Gould</name></country><country name="Allemagne"><noRegion><name sortKey="Glucksman, Edvard" sort="Glucksman, Edvard" uniqKey="Glucksman E" first="Edvard" last="Glücksman">Edvard Glücksman</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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