Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.
Identifieur interne : 000440 ( PubMed/Corpus ); précédent : 000439; suivant : 000441Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.
Auteurs : Ka-Cheung Luk ; Michael G. Berg ; Samia N. Naccache ; Beniwende Kabre ; Scot Federman ; Dora Mbanya ; Lazare Kaptué ; Charles Y. Chiu ; Catherine A. Brennan ; John HackettSource :
- PloS one [ 1932-6203 ] ; 2015.
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.
DOI: 10.1371/journal.pone.0141723
PubMed: 26599538
Links to Exploration step
pubmed:26599538Le 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><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></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><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></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><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Kabre, Beniwende" sort="Kabre, Beniwende" uniqKey="Kabre B" first="Beniwende" last="Kabre">Beniwende Kabre</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Federman, Scot" sort="Federman, Scot" uniqKey="Federman S" first="Scot" last="Federman">Scot Federman</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Mbanya, Dora" sort="Mbanya, Dora" uniqKey="Mbanya D" first="Dora" last="Mbanya">Dora Mbanya</name><affiliation><nlm:affiliation>Université de Yaoundé 1, Yaoundé, Cameroon.</nlm:affiliation></affiliation></author><author><name sortKey="Kaptue, Lazare" sort="Kaptue, Lazare" uniqKey="Kaptue L" first="Lazare" last="Kaptué">Lazare Kaptué</name><affiliation><nlm:affiliation>Université des Montagnes, Bangangté, Cameroon.</nlm:affiliation></affiliation></author><author><name sortKey="Chiu, Charles Y" sort="Chiu, Charles Y" uniqKey="Chiu C" first="Charles Y" last="Chiu">Charles Y. 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Brennan</name><affiliation><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Hackett, John" sort="Hackett, John" uniqKey="Hackett J" first="John" last="Hackett">John Hackett</name><affiliation><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26599538</idno><idno type="pmid">26599538</idno><idno type="doi">10.1371/journal.pone.0141723</idno><idno type="wicri:Area/PubMed/Corpus">000440</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000440</idno></publicationStmt><sourceDesc><biblStruct><analytic><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><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></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><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></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><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Kabre, Beniwende" sort="Kabre, Beniwende" uniqKey="Kabre B" first="Beniwende" last="Kabre">Beniwende Kabre</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Federman, Scot" sort="Federman, Scot" uniqKey="Federman S" first="Scot" last="Federman">Scot Federman</name><affiliation><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Mbanya, Dora" sort="Mbanya, Dora" uniqKey="Mbanya D" first="Dora" last="Mbanya">Dora Mbanya</name><affiliation><nlm:affiliation>Université de Yaoundé 1, Yaoundé, Cameroon.</nlm:affiliation></affiliation></author><author><name sortKey="Kaptue, Lazare" sort="Kaptue, Lazare" uniqKey="Kaptue L" first="Lazare" last="Kaptué">Lazare Kaptué</name><affiliation><nlm:affiliation>Université des Montagnes, Bangangté, Cameroon.</nlm:affiliation></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><nlm:affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</nlm:affiliation></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><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></affiliation></author><author><name sortKey="Hackett, John" sort="Hackett, John" uniqKey="Hackett J" first="John" last="Hackett">John Hackett</name><affiliation><nlm:affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</nlm:affiliation></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015" type="published">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="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="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></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26599538</PMID><DateCreated><Year>2015</Year><Month>11</Month><Day>25</Day></DateCreated><DateCompleted><Year>2016</Year><Month>06</Month><Day>27</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>11</Issue><PubDate><Year>2015</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS ONE</ISOAbbreviation></Journal><ArticleTitle>Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.</ArticleTitle><Pagination><MedlinePgn>e0141723</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0141723</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Luk</LastName><ForeName>Ka-Cheung</ForeName><Initials>KC</Initials><AffiliationInfo><Affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berg</LastName><ForeName>Michael G</ForeName><Initials>MG</Initials><AffiliationInfo><Affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naccache</LastName><ForeName>Samia N</ForeName><Initials>SN</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kabre</LastName><ForeName>Beniwende</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Federman</LastName><ForeName>Scot</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mbanya</LastName><ForeName>Dora</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Université de Yaoundé 1, Yaoundé, Cameroon.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kaptué</LastName><ForeName>Lazare</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Université des Montagnes, Bangangté, Cameroon.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chiu</LastName><ForeName>Charles Y</ForeName><Initials>CY</Initials><AffiliationInfo><Affiliation>Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Brennan</LastName><ForeName>Catherine A</ForeName><Initials>CA</Initials><AffiliationInfo><Affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hackett</LastName><ForeName>John</ForeName><Initials>J</Initials><Suffix>Jr</Suffix><AffiliationInfo><Affiliation>Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList 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2014 Jun 19;370(25):2408-17</RefSource><PMID Version="1">24896819</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D001782" MajorTopicYN="N">Blood Donors</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002163" MajorTopicYN="N" Type="Geographic">Cameroon</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060085" MajorTopicYN="N">Coinfection</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029407" MajorTopicYN="N">GB virus C</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015497" MajorTopicYN="N">HIV-1</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056186" MajorTopicYN="Y">Metagenomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="N">Recombination, Genetic</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4658132</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>08</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>10</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>6</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26599538</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0141723</ArticleId><ArticleId IdType="pii">PONE-D-15-32792</ArticleId><ArticleId IdType="pmc">PMC4658132</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler 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