Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda
Adam A. Capoferri, Susanna L. Lamers, M. Kate Grabowski, Rebecca Rose, Maria J. Wawer, David Serwadda, Ronald H. Gray, Thomas C. Quinn, Godfrey Kigozi, Joseph Kagaayi, Oliver Laeyendecker, Lucie Abeler‐Dörner, Helen Ayles, David Bonsall, Rory Bowden, Vincent Cálvez, Myron S. Cohen, A. Mitchison Denis, Daniel Frampton, Túlio de Oliveira, Max Essex, Sarah Fidler, Christophe Fraser, Tanya Golubchik, Richard Hayes, Joshua T. Herbeck, Anne Hoppé, Pontiano Kaleebu, Paul Kellam, Cissy Kityo, Andrew Brown, Jairam R. Lingappa, Vladimir Novitsky, Nick Paton, Deenan Pillay, Andrew Rambaut, Oliver Ratmann, Janet Seeley, Deogratius Ssemwanga, Frank Tanser
Abstract
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset ( n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.