Browsing by Author "Pillay, Deenan"

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    High Rate of HIV Resuppression After Viral Failure on First-line Antiretroviral Therapy in the Absence of Switch to Second-line Therapy
    (Clinical infectious diseases, 2014) Gupta, Ravindra K.; Goodall, Ruth L.; Kityo, Cissy; Munderi, Paula; Lyagoba, Fred; Mugarura, Lincoln; Kaleebu, Pontiano; Pillay, Deenan
    In a randomized comparison of nevirapine or abacavir with zidovudine plus lamivudine, routine viral load monitoring was not performed, yet 27% of individuals with viral failure at week 48 experienced resuppression by week 96 without switching. This supports World Health Organization recommendations that suspected viral failure should trigger adherence counseling and repeat measurement before a treatment switch is considered.
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    Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis
    (Nature communications, 2019) Ratmann, Oliver tophe Fraser; Grabowski, M. Kate; Hall, Matthew; Golubchik, Tanya; Wymant, Chris; Abeler-Dörner, Lucie; Bonsall, David; Hoppe, Anne; Leigh Brown, Andrew; Oliveira, Tulio de; Gall, Astrid; Kellam, Paul; Pillay, Deenan; Kagaayi, Joseph; Kigozi, Godfrey; Quinn, Thomas C.; Wawer, Maria J.; Laeyendecker, Oliver; Serwadda, David; Gray, Ronald H.
    To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from a large population-based sample of infected individuals in Rakai District, Uganda, reconstruct partial transmission networks, and infer the direction of transmission within them at an estimated error rate of 16.3% [8.8–28.3%]. With this error rate, deep-sequence phylogenetics cannot be used against individuals in legal contexts, but is sufficiently low for population-level inferences into the sources of epidemic spread. The technique presents new opportunities for characterizing source populations and for targeting of HIV-1 prevention interventions in Africa.