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Deciphering multiplicity of HIV-1C infection : transmission of closely related multiple viral lineages

dc.contributor.authorNovitsky, Vlad
dc.contributor.authorMoyo, Sikhulile
dc.contributor.authorWang, Rui
dc.contributor.authorGaseitsiwe, Simani
dc.contributor.authorEssex, M.
dc.date.accessioned2017-10-12T10:04:24Z
dc.date.available2017-10-12T10:04:24Z
dc.date.issued2016
dc.identifier.citationNovitsky, V., et al. 2016. Deciphering multiplicity of HIV-1C infection : transmission of closely related multiple viral lineages. PLoS ONE, 11(11):e0166746, doi:10.1371/journal.pone.0166746
dc.identifier.issn1932-6203 (online)
dc.identifier.otherdoi:10.1371/journal.pone.0166746
dc.identifier.urihttp://hdl.handle.net/10019.1/102315
dc.descriptionCITATION: Novitsky, V., et al. 2016. Deciphering multiplicity of HIV-1C infection : transmission of closely related multiple viral lineages. PLoS ONE, 11(11):e0166746, doi:10.1371/journal.pone.0166746.
dc.descriptionThe original publication is available at http://journals.plos.org/plosone
dc.description.abstractBackground: A single viral variant is transmitted in the majority of HIV infections. However, about 20% of heterosexually transmitted HIV infections are caused by multiple viral variants. Detection of transmitted HIV variants is not trivial, as it involves analysis of multiple viral sequences representing intra-host HIV-1 quasispecies. Methodology: We distinguish two types of multiple virus transmission in HIV infection: (1) HIV transmission from the same source, and (2) transmission from different sources. Viral sequences representing intra-host quasispecies in a longitudinally sampled cohort of 42 individuals with primary HIV-1C infection in Botswana were generated by single-genome amplification and sequencing and spanned the V1C5 region of HIV-1C env gp120. The Maximum Likelihood phylogeny and distribution of pairwise raw distances were assessed at each sampling time point (n = 217; 42 patients; median 5 (IQR: 4–6) time points per patient, range 2–12 time points per patient). Results: Transmission of multiple viral variants from the same source (likely from the partner with established HIV infection) was found in 9 out of 42 individuals (21%; 95 CI 10–37%). HIV super-infection was identified in 2 patients (5%; 95% CI 1–17%) with an estimated rate of 3.9 per 100 person-years. Transmission of multiple viruses combined with HIV super-infection at a later time point was observed in one individual. Conclusions: Multiple HIV lineages transmitted from the same source produce a monophyletic clade in the inferred phylogenetic tree. Such a clade has transiently distinct sub-clusters in the early stage of HIV infection, and follows a predictable evolutionary pathway. Over time, the gap between initially distinct viral lineages fills in and initially distinct sub-clusters converge. Identification of cases with transmission of multiple viral lineages from the same source needs to be taken into account in cross-sectional estimation of HIV recency in epidemiological and population studiesen_ZA
dc.description.urihttp://journals.plos.org/plosone
dc.format.extent15 pages
dc.language.isoen_ZAen_ZA
dc.publisherPublic Library of Science
dc.subjectHIV infectionsen_ZA
dc.titleDeciphering multiplicity of HIV-1C infection : transmission of closely related multiple viral lineagesen_ZA
dc.typeArticleen_ZA
dc.description.versionPublisher's version
dc.rights.holderAuthors retain copyright


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