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PLoS One. 2015 Nov 23;10(11):e0141723. doi: 10.1371/journal.pone.0141723. eCollection 2015.

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

Author information

1
Abbott Diagnostics, Infectious Disease Research, Abbott Park, Illinois, United States of America.
2
Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America.
3
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America.
4
Université de Yaoundé 1, Yaoundé, Cameroon.
5
Université des Montagnes, Bangangté, Cameroon.
6
Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America.

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.

PMID:
26599538
PMCID:
PMC4658132
DOI:
10.1371/journal.pone.0141723
[Indexed for MEDLINE]
Free PMC Article

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