Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants.

TitleDetection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants.
Publication TypeJournal Article
Year of Publication2011
AuthorsGianella S, Delport W, Pacold ME, Young JA, Choi J Y, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM
JournalJ Virol
Volume85
Issue16
Pagination8359-67
Date Published2011 Aug
ISSN1098-5514
KeywordsAdult, Anti-HIV Agents, Base Sequence, Drug Resistance, Viral, env Gene Products, Human Immunodeficiency Virus, Female, gag Gene Products, Human Immunodeficiency Virus, Genes, env, Genes, gag, Genes, pol, Genetic Variation, HIV Infections, HIV-1, Humans, Male, Middle Aged, pol Gene Products, Human Immunodeficiency Virus, RNA, Viral, Sequence Analysis, RNA, Treatment Outcome
Abstract

Reports of a high frequency of the transmission of minority viral populations with drug-resistant mutations (DRM) are inconsistent with evidence that HIV-1 infections usually arise from mono- or oligoclonal transmission. We performed ultradeep sequencing (UDS) of partial HIV-1 gag, pol, and env genes from 32 recently infected individuals. We then evaluated overall and per-site diversity levels, selective pressure, sequence reproducibility, and presence of DRM and accessory mutations (AM). To differentiate biologically meaningful mutations from those caused by methodological errors, we obtained multinomial confidence intervals (CI) for the proportion of DRM at each site and fitted a binomial mixture model to determine background error rates for each sample. We then examined the association between detected minority DRM and the virologic failure of first-line antiretroviral therapy (ART). Similar to other studies, we observed increased detection of DRM at low frequencies (average, 0.56%; 95% CI, 0.43 to 0.69; expected UDS error, 0.21 ± 0.08% mutations/site). For 8 duplicate runs, there was variability in the proportions of minority DRM. There was no indication of increased diversity or selection at DRM sites compared to other sites and no association between minority DRM and AM. There was no correlation between detected minority DRM and clinical failure of first-line ART. It is unlikely that minority viral variants harboring DRM are transmitted and maintained in the recipient host. The majority of low-frequency DRM detected using UDS are likely errors inherent to UDS methodology or a consequence of error-prone HIV-1 replication.

DOI10.1128/JVI.02582-10
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/21632754?dopt=Abstract
PMCPMC3147985
Alternate JournalJ. Virol.
PubMed ID21632754