Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates

Coinfection ofa single cell with two or more HIVstrains may produce recombinant viruses upon template switching by the replication machinery. We applied a hierarchical multiple change point model to simultaneously infer inter-subtype recombination breakpoints and spatial variation in the recombination rate along the HIV-1 genome. We examined thousands of publicly available HIV-1 sequences representing the worldwide epidemic andfocused on 544 unique recombinants with 1, 701 recombination breakpoints. Estimates ofper site recombination rate revealed the presence ofa novel hotspot in the pol gene, surrounded by a cluster of mutations associated with resistance to reverse transcriptase inhibitors. We also confirm the presence ofa known hotspot in the env gene and a previously hypothesized hotspot in the gag gene.

• Type: Conference
• Year: 2007
• Where: BIBE
• Authors: Misha L. Rajaram, Vladimir N. Minin, Marc A. Suchard, Karin S. Dorman
• Keywords: BIBE 2007, Bioinformatics, Inter-subtype Recombination Breakpoints, Ofa Single Cell, Recombination Breakpoints