Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity
Identifieur interne : 000252 ( Main/Exploration ); précédent : 000251; suivant : 000253Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity
Auteurs : Ka-Cheung Luk [États-Unis] ; Michael G. Berg [États-Unis] ; Samia N. Naccache [États-Unis] ; Beniwende Kabre [États-Unis] ; Scot Federman [États-Unis] ; Dora Mbanya [Cameroun] ; Lazare Kaptué [Cameroun] ; Charles Y. Chiu [États-Unis] ; Catherine A. Brennan [États-Unis] ; John Hackett [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Descripteurs français
- KwdFr :
- Cameroun, Co-infection (génétique), Donneurs de sang, Données de séquences moléculaires, Génome viral, Génotype, Humains, Métagénomique, Phylogénie, Recombinaison génétique, Séquençage nucléotidique à haut débit (), VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique), Variation génétique, Virus GB-C (génétique).
- MESH :
- génétique : Co-infection, VIH-1 (Virus de l'Immunodéficience Humaine de type 1), Virus GB-C.
- Cameroun, Donneurs de sang, Données de séquences moléculaires, Génome viral, Génotype, Humains, Métagénomique, Phylogénie, Recombinaison génétique, Séquençage nucléotidique à haut débit, Variation génétique.
- Wicri :
- geographic : Cameroun.
English descriptors
- KwdEn :
- MESH :
- geographic : Cameroon.
- genetics : Coinfection, GB virus C, HIV-1.
- methods : High-Throughput Nucleotide Sequencing.
- Blood Donors, Genetic Variation, Genome, Viral, Genotype, Humans, Metagenomics, Molecular Sequence Data, Phylogeny, Recombination, Genetic.
Abstract
Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.
Url:
DOI: 10.1371/journal.pone.0141723
PubMed: 26599538
PubMed Central: 4658132
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000027
- to stream Pmc, to step Curation: 000027
- to stream Pmc, to step Checkpoint: 000126
- to stream PubMed, to step Corpus: 000440
- to stream PubMed, to step Curation: 000440
- to stream PubMed, to step Checkpoint: 000440
- to stream Ncbi, to step Merge: 000908
- to stream Ncbi, to step Curation: 000908
- to stream Ncbi, to step Checkpoint: 000908
- to stream Main, to step Merge: 000252
- to stream Main, to step Curation: 000252
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity</title><author><name sortKey="Luk, Ka Cheung" sort="Luk, Ka Cheung" uniqKey="Luk K" first="Ka-Cheung" last="Luk">Ka-Cheung Luk</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Berg, Michael G" sort="Berg, Michael G" uniqKey="Berg M" first="Michael G." last="Berg">Michael G. Berg</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Naccache, Samia N" sort="Naccache, Samia N" uniqKey="Naccache S" first="Samia N." last="Naccache">Samia N. Naccache</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Kabre, Beniwende" sort="Kabre, Beniwende" uniqKey="Kabre B" first="Beniwende" last="Kabre">Beniwende Kabre</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Federman, Scot" sort="Federman, Scot" uniqKey="Federman S" first="Scot" last="Federman">Scot Federman</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Mbanya, Dora" sort="Mbanya, Dora" uniqKey="Mbanya D" first="Dora" last="Mbanya">Dora Mbanya</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Université de Yaoundé 1, Yaoundé, Cameroon</addr-line></nlm:aff><country xml:lang="fr">Cameroun</country><wicri:regionArea>Université de Yaoundé 1, Yaoundé</wicri:regionArea><wicri:noRegion>Yaoundé</wicri:noRegion></affiliation></author><author><name sortKey="Kaptue, Lazare" sort="Kaptue, Lazare" uniqKey="Kaptue L" first="Lazare" last="Kaptué">Lazare Kaptué</name><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>Université des Montagnes, Bangangté, Cameroon</addr-line></nlm:aff><country xml:lang="fr">Cameroun</country><wicri:regionArea>Université des Montagnes, Bangangté</wicri:regionArea><wicri:noRegion>Bangangté</wicri:noRegion></affiliation></author><author><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y." last="Chiu">Charles Y. Chiu</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff006"><addr-line>Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Brennan, Catherine A" sort="Brennan, Catherine A" uniqKey="Brennan C" first="Catherine A." last="Brennan">Catherine A. Brennan</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Hackett, John" sort="Hackett, John" uniqKey="Hackett J" first="John" last="Hackett">John Hackett</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26599538</idno><idno type="pmc">4658132</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658132</idno><idno type="RBID">PMC:4658132</idno><idno type="doi">10.1371/journal.pone.0141723</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000027</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000027</idno><idno type="wicri:Area/Pmc/Curation">000027</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000027</idno><idno type="wicri:Area/Pmc/Checkpoint">000126</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000126</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000440</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000440</idno><idno type="wicri:Area/PubMed/Curation">000440</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000440</idno><idno type="wicri:Area/PubMed/Checkpoint">000440</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000440</idno><idno type="wicri:Area/Ncbi/Merge">000908</idno><idno type="wicri:Area/Ncbi/Curation">000908</idno><idno type="wicri:Area/Ncbi/Checkpoint">000908</idno><idno type="wicri:Area/Main/Merge">000252</idno><idno type="wicri:Area/Main/Curation">000252</idno><idno type="wicri:Area/Main/Exploration">000252</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity</title><author><name sortKey="Luk, Ka Cheung" sort="Luk, Ka Cheung" uniqKey="Luk K" first="Ka-Cheung" last="Luk">Ka-Cheung Luk</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Berg, Michael G" sort="Berg, Michael G" uniqKey="Berg M" first="Michael G." last="Berg">Michael G. Berg</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Naccache, Samia N" sort="Naccache, Samia N" uniqKey="Naccache S" first="Samia N." last="Naccache">Samia N. Naccache</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Kabre, Beniwende" sort="Kabre, Beniwende" uniqKey="Kabre B" first="Beniwende" last="Kabre">Beniwende Kabre</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Federman, Scot" sort="Federman, Scot" uniqKey="Federman S" first="Scot" last="Federman">Scot Federman</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Mbanya, Dora" sort="Mbanya, Dora" uniqKey="Mbanya D" first="Dora" last="Mbanya">Dora Mbanya</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Université de Yaoundé 1, Yaoundé, Cameroon</addr-line></nlm:aff><country xml:lang="fr">Cameroun</country><wicri:regionArea>Université de Yaoundé 1, Yaoundé</wicri:regionArea><wicri:noRegion>Yaoundé</wicri:noRegion></affiliation></author><author><name sortKey="Kaptue, Lazare" sort="Kaptue, Lazare" uniqKey="Kaptue L" first="Lazare" last="Kaptué">Lazare Kaptué</name><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>Université des Montagnes, Bangangté, Cameroon</addr-line></nlm:aff><country xml:lang="fr">Cameroun</country><wicri:regionArea>Université des Montagnes, Bangangté</wicri:regionArea><wicri:noRegion>Bangangté</wicri:noRegion></affiliation></author><author><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y." last="Chiu">Charles Y. Chiu</name><affiliation wicri:level="2"><nlm:aff id="aff002"><addr-line>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff003"><addr-line>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff006"><addr-line>Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Brennan, Catherine A" sort="Brennan, Catherine A" uniqKey="Brennan C" first="Catherine A." last="Brennan">Catherine A. Brennan</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Hackett, John" sort="Hackett, John" uniqKey="Hackett J" first="John" last="Hackett">John Hackett</name><affiliation wicri:level="2"><nlm:aff id="aff001"><addr-line>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Blood Donors</term><term>Cameroon</term><term>Coinfection (genetics)</term><term>GB virus C (genetics)</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Genotype</term><term>HIV-1 (genetics)</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Humans</term><term>Metagenomics</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cameroun</term><term>Co-infection (génétique)</term><term>Donneurs de sang</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Génotype</term><term>Humains</term><term>Métagénomique</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Séquençage nucléotidique à haut débit ()</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1) (génétique)</term><term>Variation génétique</term><term>Virus GB-C (génétique)</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>Cameroon</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coinfection</term><term>GB virus C</term><term>HIV-1</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Co-infection</term><term>VIH-1 (Virus de l'Immunodéficience Humaine de type 1)</term><term>Virus GB-C</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Blood Donors</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Genotype</term><term>Humans</term><term>Metagenomics</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cameroun</term><term>Donneurs de sang</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Génotype</term><term>Humains</term><term>Métagénomique</term><term>Phylogénie</term><term>Recombinaison génétique</term><term>Séquençage nucléotidique à haut débit</term><term>Variation génétique</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Cameroun</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log<sub>10</sub> copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hemelaar, J" uniqKey="Hemelaar J">J Hemelaar</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Semaille, C" uniqKey="Semaille C">C Semaille</name></author><author><name sortKey="Barin, F" uniqKey="Barin F">F Barin</name></author><author><name sortKey="Cazein, F" uniqKey="Cazein F">F Cazein</name></author><author><name sortKey="Pillonel, J" uniqKey="Pillonel J">J Pillonel</name></author><author><name sortKey="Lot, F" uniqKey="Lot F">F Lot</name></author><author><name sortKey="Brand, D" uniqKey="Brand D">D Brand</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brennan, Ca" uniqKey="Brennan C">CA Brennan</name></author><author><name sortKey="Yamaguchi, J" uniqKey="Yamaguchi J">J Yamaguchi</name></author><author><name sortKey="Devare, Sg" uniqKey="Devare S">SG Devare</name></author><author><name sortKey="Foster, Ga" uniqKey="Foster G">GA Foster</name></author><author><name sortKey="Stramer, Sl" uniqKey="Stramer S">SL Stramer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="De Oliveira, Cf" uniqKey="De Oliveira C">CF de Oliveira</name></author><author><name sortKey="Diaz, Rs" uniqKey="Diaz R">RS Diaz</name></author><author><name sortKey="Machado, Dm" uniqKey="Machado D">DM Machado</name></author><author><name sortKey="Sullivan, Mt" uniqKey="Sullivan M">MT Sullivan</name></author><author><name sortKey="Finlayson, T" uniqKey="Finlayson T">T Finlayson</name></author><author><name sortKey="Gwinn, M" uniqKey="Gwinn M">M Gwinn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pyne, Mt" uniqKey="Pyne M">MT Pyne</name></author><author><name sortKey="Hackett, J" uniqKey="Hackett J">J Hackett</name></author><author><name sortKey="Holzmayer, V" uniqKey="Holzmayer V">V Holzmayer</name></author><author><name sortKey="Hillyard, Dr" uniqKey="Hillyard D">DR Hillyard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bobkov, Af" uniqKey="Bobkov A">AF Bobkov</name></author><author><name sortKey="Kazennova, Ev" uniqKey="Kazennova E">EV Kazennova</name></author><author><name sortKey="Selimova, Lm" uniqKey="Selimova L">LM Selimova</name></author><author><name sortKey="Khanina, Ta" uniqKey="Khanina T">TA Khanina</name></author><author><name sortKey="Ryabov, Gs" uniqKey="Ryabov G">GS Ryabov</name></author><author><name sortKey="Bobkova, Mr" uniqKey="Bobkova M">MR Bobkova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liitsola, K" uniqKey="Liitsola K">K Liitsola</name></author><author><name sortKey="Tashkinova, I" uniqKey="Tashkinova I">I Tashkinova</name></author><author><name sortKey="Laukkanen, T" uniqKey="Laukkanen T">T Laukkanen</name></author><author><name sortKey="Korovina, G" uniqKey="Korovina G">G Korovina</name></author><author><name sortKey="Smolskaja, T" uniqKey="Smolskaja T">T Smolskaja</name></author><author><name sortKey="Momot, O" uniqKey="Momot O">O Momot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hemelaar, J" uniqKey="Hemelaar J">J Hemelaar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barin, F" uniqKey="Barin F">F Barin</name></author><author><name sortKey="Lahbabi, Y" uniqKey="Lahbabi Y">Y Lahbabi</name></author><author><name sortKey="Buzelay, L" uniqKey="Buzelay L">L Buzelay</name></author><author><name sortKey="Lejeune, B" uniqKey="Lejeune B">B Lejeune</name></author><author><name sortKey="Baillou Beaufils, A" uniqKey="Baillou Beaufils A">A Baillou-Beaufils</name></author><author><name sortKey="Denis, F" uniqKey="Denis F">F Denis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Powell, Rl" uniqKey="Powell R">RL Powell</name></author><author><name sortKey="Urbanski, Mm" uniqKey="Urbanski M">MM Urbanski</name></author><author><name sortKey="Burda, S" uniqKey="Burda S">S Burda</name></author><author><name sortKey="Nanfack, A" uniqKey="Nanfack A">A Nanfack</name></author><author><name sortKey="Kinge, T" uniqKey="Kinge T">T Kinge</name></author><author><name sortKey="Nyambi, Pn" uniqKey="Nyambi P">PN Nyambi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brennan, Ca" uniqKey="Brennan C">CA Brennan</name></author><author><name sortKey="Bodelle, P" uniqKey="Bodelle P">P Bodelle</name></author><author><name sortKey="Coffey, R" uniqKey="Coffey R">R Coffey</name></author><author><name sortKey="Devare, Sg" uniqKey="Devare S">SG Devare</name></author><author><name sortKey="Golden, A" uniqKey="Golden A">A Golden</name></author><author><name sortKey="Hackett, J" uniqKey="Hackett J">J Hackett</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Carr, Jk" uniqKey="Carr J">JK Carr</name></author><author><name sortKey="Wolfe, Nd" uniqKey="Wolfe N">ND Wolfe</name></author><author><name sortKey="Torimiro, Jn" uniqKey="Torimiro J">JN Torimiro</name></author><author><name sortKey="Tamoufe, U" uniqKey="Tamoufe U">U Tamoufe</name></author><author><name sortKey="Mpoudi Ngole, E" uniqKey="Mpoudi Ngole E">E Mpoudi-Ngole</name></author><author><name sortKey="Eyzaguirre, L" uniqKey="Eyzaguirre L">L Eyzaguirre</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chiu, Cy" uniqKey="Chiu C">CY Chiu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Henn, Mr" uniqKey="Henn M">MR Henn</name></author><author><name sortKey="Boutwell, Cl" uniqKey="Boutwell C">CL Boutwell</name></author><author><name sortKey="Charlebois, P" uniqKey="Charlebois P">P Charlebois</name></author><author><name sortKey="Lennon, Nj" uniqKey="Lennon N">NJ Lennon</name></author><author><name sortKey="Power, Ka" uniqKey="Power K">KA Power</name></author><author><name sortKey="Macalalad, Ar" uniqKey="Macalalad A">AR Macalalad</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Malboeuf, Cm" uniqKey="Malboeuf C">CM Malboeuf</name></author><author><name sortKey="Yang, X" uniqKey="Yang X">X Yang</name></author><author><name sortKey="Charlebois, P" uniqKey="Charlebois P">P Charlebois</name></author><author><name sortKey="Qu, J" uniqKey="Qu J">J Qu</name></author><author><name sortKey="Berlin, Am" uniqKey="Berlin A">AM Berlin</name></author><author><name sortKey="Casali, M" uniqKey="Casali M">M Casali</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simons, Jn" uniqKey="Simons J">JN Simons</name></author><author><name sortKey="Leary, Tp" uniqKey="Leary T">TP Leary</name></author><author><name sortKey="Dawson, Gj" uniqKey="Dawson G">GJ Dawson</name></author><author><name sortKey="Pilot Matias, Tj" uniqKey="Pilot Matias T">TJ Pilot-Matias</name></author><author><name sortKey="Muerhoff, As" uniqKey="Muerhoff A">AS Muerhoff</name></author><author><name sortKey="Schlauder, Gg" uniqKey="Schlauder G">GG Schlauder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bhattarai, N" uniqKey="Bhattarai N">N Bhattarai</name></author><author><name sortKey="Stapleton, Jt" uniqKey="Stapleton J">JT Stapleton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giret, Mt" uniqKey="Giret M">MT Giret</name></author><author><name sortKey="Kallas, Eg" uniqKey="Kallas E">EG Kallas</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sahni, H" uniqKey="Sahni H">H Sahni</name></author><author><name sortKey="Kirkwood, K" uniqKey="Kirkwood K">K Kirkwood</name></author><author><name sortKey="Kyriakides, Tc" uniqKey="Kyriakides T">TC Kyriakides</name></author><author><name sortKey="Stapleton, J" uniqKey="Stapleton J">J Stapleton</name></author><author><name sortKey="Brown, St" uniqKey="Brown S">ST Brown</name></author><author><name sortKey="Holodniy, M" uniqKey="Holodniy M">M Holodniy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brennan, Ca" uniqKey="Brennan C">CA Brennan</name></author><author><name sortKey="Bodelle, P" uniqKey="Bodelle P">P Bodelle</name></author><author><name sortKey="Coffey, R" uniqKey="Coffey R">R Coffey</name></author><author><name sortKey="Harris, B" uniqKey="Harris B">B Harris</name></author><author><name sortKey="Holzmayer, V" uniqKey="Holzmayer V">V Holzmayer</name></author><author><name sortKey="Luk, Kc" uniqKey="Luk K">KC Luk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mourez, T" uniqKey="Mourez T">T Mourez</name></author><author><name sortKey="Simon, F" uniqKey="Simon F">F Simon</name></author><author><name sortKey="Plantier, Jc" uniqKey="Plantier J">JC Plantier</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Lihana, Rw" uniqKey="Lihana R">RW Lihana</name></author><author><name sortKey="Ssemwanga, D" uniqKey="Ssemwanga D">D Ssemwanga</name></author><author><name sortKey="Abimiku, A" uniqKey="Abimiku A">A Abimiku</name></author><author><name sortKey="Ndembi, N" uniqKey="Ndembi N">N Ndembi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Konings, Fa" uniqKey="Konings F">FA Konings</name></author><author><name sortKey="Haman, Gr" uniqKey="Haman G">GR Haman</name></author><author><name sortKey="Xue, Y" uniqKey="Xue Y">Y Xue</name></author><author><name sortKey="Urbanski, Mm" uniqKey="Urbanski M">MM Urbanski</name></author><author><name sortKey="Hertzmark, K" uniqKey="Hertzmark K">K Hertzmark</name></author><author><name sortKey="Nanfack, A" uniqKey="Nanfack A">A Nanfack</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Delaugerre, C" uniqKey="Delaugerre C">C Delaugerre</name></author><author><name sortKey="De Oliveira, F" uniqKey="De Oliveira F">F De Oliveira</name></author><author><name sortKey="Lascoux Combe, C" uniqKey="Lascoux Combe C">C Lascoux-Combe</name></author><author><name sortKey="Plantier, Jc" uniqKey="Plantier J">JC Plantier</name></author><author><name sortKey="Simon, F" uniqKey="Simon F">F Simon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simon, F" uniqKey="Simon F">F Simon</name></author><author><name sortKey="Mauclere, P" uniqKey="Mauclere P">P Mauclere</name></author><author><name sortKey="Roques, P" uniqKey="Roques P">P Roques</name></author><author><name sortKey="Loussert Ajaka, I" uniqKey="Loussert Ajaka I">I Loussert-Ajaka</name></author><author><name sortKey="Muller Trutwin, Mc" uniqKey="Muller Trutwin M">MC Muller-Trutwin</name></author><author><name sortKey="Saragosti, S" uniqKey="Saragosti S">S Saragosti</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plantier, Jc" uniqKey="Plantier J">JC Plantier</name></author><author><name sortKey="Leoz, M" uniqKey="Leoz M">M Leoz</name></author><author><name sortKey="Dickerson, Je" uniqKey="Dickerson J">JE Dickerson</name></author><author><name sortKey="De Oliveira, F" uniqKey="De Oliveira F">F De Oliveira</name></author><author><name sortKey="Cordonnier, F" uniqKey="Cordonnier F">F Cordonnier</name></author><author><name sortKey="Lemee, V" uniqKey="Lemee V">V Lemee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vallari, A" uniqKey="Vallari A">A Vallari</name></author><author><name sortKey="Holzmayer, V" uniqKey="Holzmayer V">V Holzmayer</name></author><author><name sortKey="Harris, B" uniqKey="Harris B">B Harris</name></author><author><name sortKey="Yamaguchi, J" uniqKey="Yamaguchi J">J Yamaguchi</name></author><author><name sortKey="Ngansop, C" uniqKey="Ngansop C">C Ngansop</name></author><author><name sortKey="Makamche, F" uniqKey="Makamche F">F Makamche</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Keele, Bf" uniqKey="Keele B">BF Keele</name></author><author><name sortKey="Van Heuverswyn, F" uniqKey="Van Heuverswyn F">F Van Heuverswyn</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Bailes, E" uniqKey="Bailes E">E Bailes</name></author><author><name sortKey="Takehisa, J" uniqKey="Takehisa J">J Takehisa</name></author><author><name sortKey="Santiago, Ml" uniqKey="Santiago M">ML Santiago</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Peeters, M" uniqKey="Peeters M">M Peeters</name></author><author><name sortKey="D Arc, M" uniqKey="D Arc M">M D'Arc</name></author><author><name sortKey="Delaporte, E" uniqKey="Delaporte E">E Delaporte</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Heuverswyn, F" uniqKey="Van Heuverswyn F">F Van Heuverswyn</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Bailes, E" uniqKey="Bailes E">E Bailes</name></author><author><name sortKey="Neel, C" uniqKey="Neel C">C Neel</name></author><author><name sortKey="Lafay, B" uniqKey="Lafay B">B Lafay</name></author><author><name sortKey="Keele, Bf" uniqKey="Keele B">BF Keele</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Heuverswyn, F" uniqKey="Van Heuverswyn F">F Van Heuverswyn</name></author><author><name sortKey="Li, Y" uniqKey="Li Y">Y Li</name></author><author><name sortKey="Neel, C" uniqKey="Neel C">C Neel</name></author><author><name sortKey="Bailes, E" uniqKey="Bailes E">E Bailes</name></author><author><name sortKey="Keele, Bf" uniqKey="Keele B">BF Keele</name></author><author><name sortKey="Liu, W" uniqKey="Liu W">W Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Naccache, Sn" uniqKey="Naccache S">SN Naccache</name></author><author><name sortKey="Federman, S" uniqKey="Federman S">S Federman</name></author><author><name sortKey="Veeraraghavan, N" uniqKey="Veeraraghavan N">N Veeraraghavan</name></author><author><name sortKey="Zaharia, M" uniqKey="Zaharia M">M Zaharia</name></author><author><name sortKey="Lee, D" uniqKey="Lee D">D Lee</name></author><author><name sortKey="Samayoa, E" uniqKey="Samayoa E">E Samayoa</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Greninger, Al" uniqKey="Greninger A">AL Greninger</name></author><author><name sortKey="Chen, Ec" uniqKey="Chen E">EC Chen</name></author><author><name sortKey="Sittler, T" uniqKey="Sittler T">T Sittler</name></author><author><name sortKey="Scheinerman, A" uniqKey="Scheinerman A">A Scheinerman</name></author><author><name sortKey="Roubinian, N" uniqKey="Roubinian N">N Roubinian</name></author><author><name sortKey="Yu, G" uniqKey="Yu G">G Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sorber, K" uniqKey="Sorber K">K Sorber</name></author><author><name sortKey="Chiu, C" uniqKey="Chiu C">C Chiu</name></author><author><name sortKey="Webster, D" uniqKey="Webster D">D Webster</name></author><author><name sortKey="Dimon, M" uniqKey="Dimon M">M Dimon</name></author><author><name sortKey="Ruby, Jg" uniqKey="Ruby J">JG Ruby</name></author><author><name sortKey="Hekele, A" uniqKey="Hekele A">A Hekele</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Hall, Rj" uniqKey="Hall R">RJ Hall</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author><author><name sortKey="Todd, Ak" uniqKey="Todd A">AK Todd</name></author><author><name sortKey="Bissielo, Ab" uniqKey="Bissielo A">AB Bissielo</name></author><author><name sortKey="Yen, S" uniqKey="Yen S">S Yen</name></author><author><name sortKey="Strydom, H" uniqKey="Strydom H">H Strydom</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Montavon, C" uniqKey="Montavon C">C Montavon</name></author><author><name sortKey="Vergne, L" uniqKey="Vergne L">L Vergne</name></author><author><name sortKey="Bourgeois, A" uniqKey="Bourgeois A">A Bourgeois</name></author><author><name sortKey="Mpoudi Ngole, E" uniqKey="Mpoudi Ngole E">E Mpoudi-Ngole</name></author><author><name sortKey="Malonga Mouellet, G" uniqKey="Malonga Mouellet G">G Malonga-Mouellet</name></author><author><name sortKey="Butel, C" uniqKey="Butel C">C Butel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Luk, Kc" uniqKey="Luk K">KC Luk</name></author><author><name sortKey="Holzmayer, V" uniqKey="Holzmayer V">V Holzmayer</name></author><author><name sortKey="Yamaguchi, J" uniqKey="Yamaguchi J">J Yamaguchi</name></author><author><name sortKey="Swanson, P" uniqKey="Swanson P">P Swanson</name></author><author><name sortKey="Brennan, Ca" uniqKey="Brennan C">CA Brennan</name></author><author><name sortKey="Ngansop, C" uniqKey="Ngansop C">C Ngansop</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilbe, K" uniqKey="Wilbe K">K Wilbe</name></author><author><name sortKey="Casper, C" uniqKey="Casper C">C Casper</name></author><author><name sortKey="Albert, J" uniqKey="Albert J">J Albert</name></author><author><name sortKey="Leitner, T" uniqKey="Leitner T">T Leitner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thomson, Mm" uniqKey="Thomson M">MM Thomson</name></author><author><name sortKey="Casado, G" uniqKey="Casado G">G Casado</name></author><author><name sortKey="Posada, D" uniqKey="Posada D">D Posada</name></author><author><name sortKey="Sierra, M" uniqKey="Sierra M">M Sierra</name></author><author><name sortKey="Najera, R" uniqKey="Najera R">R Najera</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Powell, Rl" uniqKey="Powell R">RL Powell</name></author><author><name sortKey="Zhao, J" uniqKey="Zhao J">J Zhao</name></author><author><name sortKey="Konings, Fa" uniqKey="Konings F">FA Konings</name></author><author><name sortKey="Tang, S" uniqKey="Tang S">S Tang</name></author><author><name sortKey="Ewane, L" uniqKey="Ewane L">L Ewane</name></author><author><name sortKey="Burda, S" uniqKey="Burda S">S Burda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Muerhoff, As" uniqKey="Muerhoff A">AS Muerhoff</name></author><author><name sortKey="Dawson, Gj" uniqKey="Dawson G">GJ Dawson</name></author><author><name sortKey="Desai, Sm" uniqKey="Desai S">SM Desai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Archer, J" uniqKey="Archer J">J Archer</name></author><author><name sortKey="Weber, J" uniqKey="Weber J">J Weber</name></author><author><name sortKey="Henry, K" uniqKey="Henry K">K Henry</name></author><author><name sortKey="Winner, D" uniqKey="Winner D">D Winner</name></author><author><name sortKey="Gibson, R" uniqKey="Gibson R">R Gibson</name></author><author><name sortKey="Lee, L" uniqKey="Lee L">L Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bimber, Bn" uniqKey="Bimber B">BN Bimber</name></author><author><name sortKey="Dudley, Dm" uniqKey="Dudley D">DM Dudley</name></author><author><name sortKey="Lauck, M" uniqKey="Lauck M">M Lauck</name></author><author><name sortKey="Becker, Ea" uniqKey="Becker E">EA Becker</name></author><author><name sortKey="Chin, En" uniqKey="Chin E">EN Chin</name></author><author><name sortKey="Lank, Sm" uniqKey="Lank S">SM Lank</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Redd, Ad" uniqKey="Redd A">AD Redd</name></author><author><name sortKey="Collinson Streng, A" uniqKey="Collinson Streng A">A Collinson-Streng</name></author><author><name sortKey="Martens, C" uniqKey="Martens C">C Martens</name></author><author><name sortKey="Ricklefs, S" uniqKey="Ricklefs S">S Ricklefs</name></author><author><name sortKey="Mullis, Ce" uniqKey="Mullis C">CE Mullis</name></author><author><name sortKey="Manucci, J" uniqKey="Manucci J">J Manucci</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Simen, Bb" uniqKey="Simen B">BB Simen</name></author><author><name sortKey="Braverman, Ms" uniqKey="Braverman M">MS Braverman</name></author><author><name sortKey="Abbate, I" uniqKey="Abbate I">I Abbate</name></author><author><name sortKey="Aerssens, J" uniqKey="Aerssens J">J Aerssens</name></author><author><name sortKey="Bidet, Y" uniqKey="Bidet Y">Y Bidet</name></author><author><name sortKey="Bouchez, O" uniqKey="Bouchez O">O Bouchez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yin, L" uniqKey="Yin L">L Yin</name></author><author><name sortKey="Liu, L" uniqKey="Liu L">L Liu</name></author><author><name sortKey="Sun, Y" uniqKey="Sun Y">Y Sun</name></author><author><name sortKey="Hou, W" uniqKey="Hou W">W Hou</name></author><author><name sortKey="Lowe, Ac" uniqKey="Lowe A">AC Lowe</name></author><author><name sortKey="Gardner, Bp" uniqKey="Gardner B">BP Gardner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Deng, X" uniqKey="Deng X">X Deng</name></author><author><name sortKey="Linsuwanon, P" uniqKey="Linsuwanon P">P Linsuwanon</name></author><author><name sortKey="Bangsberg, D" uniqKey="Bangsberg D">D Bangsberg</name></author><author><name sortKey="Bwana, Mb" uniqKey="Bwana M">MB Bwana</name></author><author><name sortKey="Hunt, P" uniqKey="Hunt P">P Hunt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, J" uniqKey="Yang J">J Yang</name></author><author><name sortKey="Yang, F" uniqKey="Yang F">F Yang</name></author><author><name sortKey="Ren, L" uniqKey="Ren L">L Ren</name></author><author><name sortKey="Xiong, Z" uniqKey="Xiong Z">Z Xiong</name></author><author><name sortKey="Wu, Z" uniqKey="Wu Z">Z Wu</name></author><author><name sortKey="Dong, J" uniqKey="Dong J">J Dong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Archer, J" uniqKey="Archer J">J Archer</name></author><author><name sortKey="Pinney, Jw" uniqKey="Pinney J">JW Pinney</name></author><author><name sortKey="Fan, J" uniqKey="Fan J">J Fan</name></author><author><name sortKey="Simon Loriere, E" uniqKey="Simon Loriere E">E Simon-Loriere</name></author><author><name sortKey="Arts, Ej" uniqKey="Arts E">EJ Arts</name></author><author><name sortKey="Negroni, M" uniqKey="Negroni M">M Negroni</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Magiorkinis, G" uniqKey="Magiorkinis G">G Magiorkinis</name></author><author><name sortKey="Paraskevis, D" uniqKey="Paraskevis D">D Paraskevis</name></author><author><name sortKey="Vandamme, Am" uniqKey="Vandamme A">AM Vandamme</name></author><author><name sortKey="Magiorkinis, E" uniqKey="Magiorkinis E">E Magiorkinis</name></author><author><name sortKey="Sypsa, V" uniqKey="Sypsa V">V Sypsa</name></author><author><name sortKey="Hatzakis, A" uniqKey="Hatzakis A">A Hatzakis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Law, J" uniqKey="Law J">J Law</name></author><author><name sortKey="Jovel, J" uniqKey="Jovel J">J Jovel</name></author><author><name sortKey="Patterson, J" uniqKey="Patterson J">J Patterson</name></author><author><name sortKey="Ford, G" uniqKey="Ford G">G Ford</name></author><author><name sortKey="O Keefe, S" uniqKey="O Keefe S">S O'Keefe</name></author><author><name sortKey="Wang, W" uniqKey="Wang W">W Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wilson, Mr" uniqKey="Wilson M">MR Wilson</name></author><author><name sortKey="Naccache, Sn" uniqKey="Naccache S">SN Naccache</name></author><author><name sortKey="Samayoa, E" uniqKey="Samayoa E">E Samayoa</name></author><author><name sortKey="Biagtan, M" uniqKey="Biagtan M">M Biagtan</name></author><author><name sortKey="Bashir, H" uniqKey="Bashir H">H Bashir</name></author><author><name sortKey="Yu, G" uniqKey="Yu G">G Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grard, G" uniqKey="Grard G">G Grard</name></author><author><name sortKey="Fair, Jn" uniqKey="Fair J">JN Fair</name></author><author><name sortKey="Lee, D" uniqKey="Lee D">D Lee</name></author><author><name sortKey="Slikas, E" uniqKey="Slikas E">E Slikas</name></author><author><name sortKey="Steffen, I" uniqKey="Steffen I">I Steffen</name></author><author><name sortKey="Muyembe, Jj" uniqKey="Muyembe J">JJ Muyembe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Swei, A" uniqKey="Swei A">A Swei</name></author><author><name sortKey="Russell, Bj" uniqKey="Russell B">BJ Russell</name></author><author><name sortKey="Naccache, Sn" uniqKey="Naccache S">SN Naccache</name></author><author><name sortKey="Kabre, B" uniqKey="Kabre B">B Kabre</name></author><author><name sortKey="Veeraraghavan, N" uniqKey="Veeraraghavan N">N Veeraraghavan</name></author><author><name sortKey="Pilgard, Ma" uniqKey="Pilgard M">MA Pilgard</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schwarze Zander, C" uniqKey="Schwarze Zander C">C Schwarze-Zander</name></author><author><name sortKey="Blackard, Jt" uniqKey="Blackard J">JT Blackard</name></author><author><name sortKey="Rockstroh, Jk" uniqKey="Rockstroh J">JK Rockstroh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ghai, Rr" uniqKey="Ghai R">RR Ghai</name></author><author><name sortKey="Sibley, Sd" uniqKey="Sibley S">SD Sibley</name></author><author><name sortKey="Lauck, M" uniqKey="Lauck M">M Lauck</name></author><author><name sortKey="Dinis, Jm" uniqKey="Dinis J">JM Dinis</name></author><author><name sortKey="Bailey, Al" uniqKey="Bailey A">AL Bailey</name></author><author><name sortKey="Chapman, Ca" uniqKey="Chapman C">CA Chapman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Beerenwinkel, N" uniqKey="Beerenwinkel N">N Beerenwinkel</name></author><author><name sortKey="Gunthard, Hf" uniqKey="Gunthard H">HF Gunthard</name></author><author><name sortKey="Roth, V" uniqKey="Roth V">V Roth</name></author><author><name sortKey="Metzner, Kj" uniqKey="Metzner K">KJ Metzner</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Naccache, Sn" uniqKey="Naccache S">SN Naccache</name></author><author><name sortKey="Greninger, Al" uniqKey="Greninger A">AL Greninger</name></author><author><name sortKey="Lee, D" uniqKey="Lee D">D Lee</name></author><author><name sortKey="Coffey, Ll" uniqKey="Coffey L">LL Coffey</name></author><author><name sortKey="Phan, T" uniqKey="Phan T">T Phan</name></author><author><name sortKey="Rein Weston, A" uniqKey="Rein Weston A">A Rein-Weston</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Delwart, E" uniqKey="Delwart E">E Delwart</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Firth, C" uniqKey="Firth C">C Firth</name></author><author><name sortKey="Lipkin, Wi" uniqKey="Lipkin W">WI Lipkin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Cameroun</li><li>États-Unis</li></country><region><li>Californie</li><li>Illinois</li></region></list><tree><country name="États-Unis"><region name="Illinois"><name sortKey="Luk, Ka Cheung" sort="Luk, Ka Cheung" uniqKey="Luk K" first="Ka-Cheung" last="Luk">Ka-Cheung Luk</name></region><name sortKey="Berg, Michael G" sort="Berg, Michael G" uniqKey="Berg M" first="Michael G." last="Berg">Michael G. Berg</name><name sortKey="Brennan, Catherine A" sort="Brennan, Catherine A" uniqKey="Brennan C" first="Catherine A." last="Brennan">Catherine A. Brennan</name><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y." last="Chiu">Charles Y. Chiu</name><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y." last="Chiu">Charles Y. Chiu</name><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y." last="Chiu">Charles Y. Chiu</name><name sortKey="Federman, Scot" sort="Federman, Scot" uniqKey="Federman S" first="Scot" last="Federman">Scot Federman</name><name sortKey="Federman, Scot" sort="Federman, Scot" uniqKey="Federman S" first="Scot" last="Federman">Scot Federman</name><name sortKey="Hackett, John" sort="Hackett, John" uniqKey="Hackett J" first="John" last="Hackett">John Hackett</name><name sortKey="Kabre, Beniwende" sort="Kabre, Beniwende" uniqKey="Kabre B" first="Beniwende" last="Kabre">Beniwende Kabre</name><name sortKey="Kabre, Beniwende" sort="Kabre, Beniwende" uniqKey="Kabre B" first="Beniwende" last="Kabre">Beniwende Kabre</name><name sortKey="Naccache, Samia N" sort="Naccache, Samia N" uniqKey="Naccache S" first="Samia N." last="Naccache">Samia N. Naccache</name><name sortKey="Naccache, Samia N" sort="Naccache, Samia N" uniqKey="Naccache S" first="Samia N." last="Naccache">Samia N. Naccache</name></country><country name="Cameroun"><noRegion><name sortKey="Mbanya, Dora" sort="Mbanya, Dora" uniqKey="Mbanya D" first="Dora" last="Mbanya">Dora Mbanya</name></noRegion><name sortKey="Kaptue, Lazare" sort="Kaptue, Lazare" uniqKey="Kaptue L" first="Lazare" last="Kaptué">Lazare Kaptué</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/SidaGhanaV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000252 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000252 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= SidaGhanaV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:4658132
|texte= Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26599538" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a SidaGhanaV1
| This area was generated with Dilib version V0.6.31. |  |