title: Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity.
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.
authors.affiliation: Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.
authors.forename: Ka-Cheung
authors.initials: KC
authors.lastname: Luk
authors.affiliation: Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.
authors.forename: Michael G
authors.initials: MG
authors.lastname: Berg
authors.affiliation: Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.
authors.forename: Samia N
authors.initials: SN
authors.lastname: Naccache
authors.affiliation: Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.
authors.forename: Beniwende
authors.initials: B
authors.lastname: Kabre
authors.affiliation: Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.
authors.forename: Scot
authors.initials: S
authors.lastname: Federman
authors.affiliation: Université de Yaoundé 1, Yaoundé, Cameroon.
authors.forename: Dora
authors.initials: D
authors.lastname: Mbanya
authors.affiliation: Université des Montagnes, Bangangté, Cameroon.
authors.forename: Lazare
authors.initials: L
authors.lastname: Kaptué
authors.affiliation: Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.|UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.|Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Charles Y
authors.initials: CY
authors.lastname: Chiu
authors.affiliation: Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Brennan
authors.affiliation: Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.
authors.forename: John
authors.initials: J
authors.lastname: Hackett
mesh_terms: D001782:Blood Donors; D002163:Cameroon; D060085:Coinfection / Q000235:genetics; D029407:GB virus C / Q000235:genetics*; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D056186:Metagenomics; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic