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...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4658132?pdf=render |
| _version_ | 1818957443857645568 |
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| author | Ka-Cheung Luk Michael G Berg Samia N Naccache Beniwende Kabre Scot Federman Dora Mbanya Lazare Kaptué Charles Y Chiu Catherine A Brennan John Hackett |
| author_facet | Ka-Cheung Luk Michael G Berg Samia N Naccache Beniwende Kabre Scot Federman Dora Mbanya Lazare Kaptué Charles Y Chiu Catherine A Brennan John Hackett |
| author_sort | Ka-Cheung Luk |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-20T11:09:56Z |
| format | Article |
| id | doaj.art-cc2e10d5fb584d51a29731fe14c6c229 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T11:09:56Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-cc2e10d5fb584d51a29731fe14c6c2292022-12-21T19:42:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011011e014172310.1371/journal.pone.0141723Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.Ka-Cheung LukMichael G BergSamia N NaccacheBeniwende KabreScot FedermanDora MbanyaLazare KaptuéCharles Y ChiuCatherine A BrennanJohn HackettGiven 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.http://europepmc.org/articles/PMC4658132?pdf=render |
| spellingShingle | Ka-Cheung Luk Michael G Berg Samia N Naccache Beniwende Kabre Scot Federman Dora Mbanya Lazare Kaptué Charles Y Chiu Catherine A Brennan John Hackett Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. PLoS ONE |
| title | Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. |
| title_full | Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. |
| title_fullStr | Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. |
| title_full_unstemmed | Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. |
| title_short | Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity. |
| title_sort | utility of metagenomic next generation sequencing for characterization of hiv and human pegivirus diversity |
| url | http://europepmc.org/articles/PMC4658132?pdf=render |
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