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A1 Pairwise diversity and tMRCA as potential markers of HIV infection recency

Year: 2018
Type: article
Abstract: Intra-host HIV-1 diversity increases linearly over time. We assessed the extent to which mean pairwise distances and the time to the most recent common ancestor (tMRCA) inferred from intra-host HIV-1 C env sequences were associated with the estimated time of HIV infection. Data from a primary HIV-1 C infection study in Botswana were used for this analysis (N = 42). A total of 2,540 HIV-1 C env gp120 V1C5 viral sequences were generated by single genome amplification and sequencing, with an average of sixty-one viral sequences per participant and eleven sequences per time point per participant. Raw pairwise distances were calculated for each time point and participant using the ape package in R software. The tMRCA was estimated using phylogenetic inference implemented in BEAST v1.8.2. Pairwise distances and tMRCA were significantly associated with the estimated time since HIV infection (both P < 0.001). Taking into account multiplicity of HIV infection strengthened these associations. HIV-1 C env-based pairwise distances and tMRCA can be used as potential markers for HIV recency. However, the tMRCA estimates demonstrated no advantage over the pairwise distances estimates.
DOI: 10.1093/ve/vey010
Authors: Sikhulile Moyo, Eduan Wilkinson, Alain Vandormael, Rui Wang, Jia Weng, Kenanao P Kotokwe, Simani Gaseitsiwe, Rosemary Musonda, Joseph Makhema, Max Essex, Susan Engelbrecht, Tulio de Oliveira, Vladimir Novitsky
Institutions: Stellenbosch University, Botswana Harvard AIDS Institute Partnership, University of KwaZulu-Natal, Harvard University, National Health Laboratory Service, University College London
Language: English
Subfield: Virology
Open Access status: gold
Estimated APC paid: $3,304
OpenAlex ID: W2802254661
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