Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.

Rousseau, C; Learn, G; Bhattacharya, T; Nickle, D; Heckerman, D; Chetty, S; Brander, C; Goulder, P; Walker, B; Kiepiela, P; Korber, B; Mullins, J

Journal article

Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.

Abstract:: Recombinant human immunodeficiency virus type 1 (HIV-1) strains containing sequences from different viral genetic subtypes (intersubtype) and different lineages from within the same subtype (intrasubtype) have been observed. A consequence of recombination can be the distortion of the phylogenetic signal. Several intersubtype recombinants have been identified; however, less is known about the frequency of intrasubtype recombination. For this study, near-full-length HIV-1 subtype C genomes from 270 individuals were evaluated for the presence of intrasubtype recombination. A sliding window schema (window, 2 kb; step, 385 bp) was used to partition the aligned sequences. The Shimodaira-Hasegawa test detected significant topological incongruence in 99.6% of the comparisons of the maximum-likelihood trees generated from each sequence partition, a result that could be explained by recombination. Using RECOMBINE, we detected significant levels of recombination using five random subsets of the sequences. With a set of 23 topologically consistent sequences used as references, bootscanning followed by the interactive informative site test defined recombination breakpoints. Using two multiple-comparison correction methods, 47% of the sequences showed significant evidence of recombination in both analyses. Estimated evolutionary rates were revised from 0.51%/year (95% confidence interval [CI], 0.39 to 0.53%) with all sequences to 0.46%/year (95% CI, 0.38 to 0.48%) with the putative recombinants removed. The timing of the subtype C epidemic origin was revised from 1961 (95% CI, 1947 to 1962) with all sequences to 1958 (95% CI, 1949 to 1960) with the putative recombinants removed. Thus, intrasubtype recombinants are common within the subtype C epidemic and these impact analyses of HIV-1 evolution.

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APA Style

Rousseau, C., Learn, G., Bhattacharya, T., Nickle, D., Heckerman, D., Chetty, S., Brander, C., Goulder, P., Walker, B., Kiepiela, P., Korber, B., & Mullins, J. (2007). Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. Journal of Virology, 81(9), 4492–4500.

MLA Style

Rousseau, C, et al. “Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections.” Journal of Virology, vol. 81, no. 9, 2007, pp. 4492–500.

Chicago Style

Rousseau, C, G Learn, T Bhattacharya, et al. 2007. “Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections.” Journal of Virology 81 (9): 4492–4500.
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