Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.
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 si...
| Hauptverfasser: | , , , , , , , , , , , |
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| Format: | Journal article |
| Sprache: | English |
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2007
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| _version_ | 1826293613715259392 |
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| author | Rousseau, C Learn, G Bhattacharya, T Nickle, D Heckerman, D Chetty, S Brander, C Goulder, P Walker, B Kiepiela, P Korber, B Mullins, J |
| author_facet | Rousseau, C Learn, G Bhattacharya, T Nickle, D Heckerman, D Chetty, S Brander, C Goulder, P Walker, B Kiepiela, P Korber, B Mullins, J |
| author_sort | Rousseau, C |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T03:32:50Z |
| format | Journal article |
| id | oxford-uuid:bb4c133b-9d9f-4d6b-8b24-3ccf4c5038fc |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:32:50Z |
| publishDate | 2007 |
| record_format | dspace |
| spelling | oxford-uuid:bb4c133b-9d9f-4d6b-8b24-3ccf4c5038fc2022-03-27T05:15:58ZExtensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:bb4c133b-9d9f-4d6b-8b24-3ccf4c5038fcEnglishSymplectic Elements at Oxford2007Rousseau, CLearn, GBhattacharya, TNickle, DHeckerman, DChetty, SBrander, CGoulder, PWalker, BKiepiela, PKorber, BMullins, JRecombinant 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. |
| spellingShingle | Rousseau, C Learn, G Bhattacharya, T Nickle, D Heckerman, D Chetty, S Brander, C Goulder, P Walker, B Kiepiela, P Korber, B Mullins, J Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. |
| title | Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. |
| title_full | Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. |
| title_fullStr | Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. |
| title_full_unstemmed | Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. |
| title_short | Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. |
| title_sort | extensive intrasubtype recombination in south african human immunodeficiency virus type 1 subtype c infections |
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