Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity
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...
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| Veröffentlicht in: | PloS one 2015-11, Vol.10 (11), p.e0141723-e0141723 |
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| creator | Luk, Ka-Cheung Berg, Michael G Naccache, Samia N Kabre, Beniwende Federman, Scot Mbanya, Dora Kaptué, Lazare Chiu, Charles Y Brennan, Catherine A Hackett, Jr, John |
| description | 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_str_mv | 10.1371/journal.pone.0141723 |
| format | Article |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0141723</identifier><identifier>PMID: 26599538</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acquired immune deficiency syndrome ; AIDS ; Analysis ; Blood Donors ; Cameroon ; Coinfection - genetics ; Drug resistance ; Epidemics ; GB virus C - genetics ; Gene sequencing ; Genetic aspects ; Genetic diversity ; Genetic Variation ; Genome, Viral ; Genomes ; Genomics ; Genotype ; Genotypes ; High-Throughput Nucleotide Sequencing - methods ; HIV ; HIV-1 - genetics ; Human immunodeficiency virus ; Humans ; Infections ; Infectious diseases ; Laboratories ; Medical screening ; Medicine ; Metagenomics ; Molecular Sequence Data ; Phylogeny ; Population ; Population studies ; Recombination, Genetic ; Risk factors ; Strains (organisms) ; Surveillance ; Viruses</subject><ispartof>PloS one, 2015-11, Vol.10 (11), p.e0141723-e0141723</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Luk et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Luk et al 2015 Luk et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-b46924586f71b89f36d405b57fe46e1519bafc8faeffe3072784ce15eb6aeadc3</citedby><cites>FETCH-LOGICAL-c692t-b46924586f71b89f36d405b57fe46e1519bafc8faeffe3072784ce15eb6aeadc3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658132/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658132/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,866,887,2106,2932,23875,27933,27934,53800,53802</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26599538$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Carr, Jean K</contributor><creatorcontrib>Luk, Ka-Cheung</creatorcontrib><creatorcontrib>Berg, Michael G</creatorcontrib><creatorcontrib>Naccache, Samia N</creatorcontrib><creatorcontrib>Kabre, Beniwende</creatorcontrib><creatorcontrib>Federman, Scot</creatorcontrib><creatorcontrib>Mbanya, Dora</creatorcontrib><creatorcontrib>Kaptué, Lazare</creatorcontrib><creatorcontrib>Chiu, Charles Y</creatorcontrib><creatorcontrib>Brennan, Catherine A</creatorcontrib><creatorcontrib>Hackett, Jr, John</creatorcontrib><title>Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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. 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of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity</title><author>Luk, Ka-Cheung ; Berg, Michael G ; Naccache, Samia N ; Kabre, Beniwende ; Federman, Scot ; Mbanya, Dora ; Kaptué, Lazare ; Chiu, Charles Y ; Brennan, Catherine A ; Hackett, Jr, John</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-b46924586f71b89f36d405b57fe46e1519bafc8faeffe3072784ce15eb6aeadc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Acquired immune deficiency syndrome</topic><topic>AIDS</topic><topic>Analysis</topic><topic>Blood Donors</topic><topic>Cameroon</topic><topic>Coinfection - genetics</topic><topic>Drug resistance</topic><topic>Epidemics</topic><topic>GB virus C - genetics</topic><topic>Gene sequencing</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Genetic Variation</topic><topic>Genome, 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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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26599538</pmid><doi>10.1371/journal.pone.0141723</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | PloS one, 2015-11, Vol.10 (11), p.e0141723-e0141723 |
| issn | 1932-6203 1932-6203 |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acquired immune deficiency syndrome AIDS Analysis Blood Donors Cameroon Coinfection - genetics Drug resistance Epidemics GB virus C - genetics Gene sequencing Genetic aspects Genetic diversity Genetic Variation Genome, Viral Genomes Genomics Genotype Genotypes High-Throughput Nucleotide Sequencing - methods HIV HIV-1 - genetics Human immunodeficiency virus Humans Infections Infectious diseases Laboratories Medical screening Medicine Metagenomics Molecular Sequence Data Phylogeny Population Population studies Recombination, Genetic Risk factors Strains (organisms) Surveillance Viruses |
| title | Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-03T09%3A47%3A23IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Utility%20of%20Metagenomic%20Next-Generation%20Sequencing%20for%20Characterization%20of%20HIV%20and%20Human%20Pegivirus%20Diversity&rft.jtitle=PloS%20one&rft.au=Luk,%20Ka-Cheung&rft.date=2015-11-23&rft.volume=10&rft.issue=11&rft.spage=e0141723&rft.epage=e0141723&rft.pages=e0141723-e0141723&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0141723&rft_dat=%3Cgale_plos_%3EA435602089%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1735663934&rft_id=info:pmid/26599538&rft_galeid=A435602089&rft_doaj_id=oai_doaj_org_article_cc2e10d5fb584d51a29731fe14c6c229&rfr_iscdi=true |