Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity

• DOI: 10.1371/journal.pone.0141723
• Publication Date: 2015-11-24T21:24:19Z
• Authors: 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
• Keywords: GB virus C

Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore utility of metagenomic NGS characterize divergent strains simultaneously screen other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads >4.4 log10 copies/ml were selected include a diverse representation group M strains. Random-primed libraries, prepared from plasma specimens, resulted greater than 90% genome coverage 88% specimens. Correct subtype designations based on concordant sub-region PCR data 31 35 (89%) cases. Complete genomes assembled 25 strains, including circulating recombinant forms relatively limited available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, CRF37_cpx), as well 9 unique forms. HPgV (formerly designated GBV-C) co-infection was detected (25%) which eight yielded complete genomes. The recovered formed cluster genotype sequences previously reported Ghana, Uganda, Japan. extensive obtained by improved accuracy confidence phylogenetic classification present study population relative conventional PCR. addition, these demonstrate analysis be used routine characterization identification co-infections.