{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T14:08:23Z","timestamp":1790863703985,"version":"4.1.0"},"reference-count":63,"publisher":"American Society for Microbiology","issue":"9","license":[{"start":{"date-parts":[[2007,5,1]],"date-time":"2007-05-01T00:00:00Z","timestamp":1177977600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2007,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>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.<\/jats:p>","DOI":"10.1128\/jvi.02050-06","type":"journal-article","created":{"date-parts":[[2007,2,21]],"date-time":"2007-02-21T20:26:06Z","timestamp":1172089566000},"page":"4492-4500","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":60,"title":["Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections"],"prefix":"10.1128","volume":"81","author":[{"given":"Christine M.","family":"Rousseau","sequence":"first","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, Washington 98195-8070"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerald H.","family":"Learn","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, Washington 98195-8070"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanmoy","family":"Bhattacharya","sequence":"additional","affiliation":[{"name":"Los Alamos National Laboratory, Los Alamos, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David C.","family":"Nickle","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, Washington 98195-8070"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Heckerman","sequence":"additional","affiliation":[{"name":"Machine Learning and Applied Statistics Group, Microsoft Research, Redmond, Washington 98052"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Senica","family":"Chetty","sequence":"additional","affiliation":[{"name":"HIV Pathogenesis Program, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4015, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Brander","sequence":"additional","affiliation":[{"name":"Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip J. R.","family":"Goulder","sequence":"additional","affiliation":[{"name":"Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129"},{"name":"Nuffield Department of Medicine, The Peter Medawar Building for Pathogen Research, Oxford University, Oxford OX1 3SY, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce D.","family":"Walker","sequence":"additional","affiliation":[{"name":"Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02129"},{"name":"Howard Hughes Medical Institute, Chevy Chase, Maryland 20815"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Photini","family":"Kiepiela","sequence":"additional","affiliation":[{"name":"HIV Pathogenesis Program, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4015, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bette T.","family":"Korber","sequence":"additional","affiliation":[{"name":"Los Alamos National Laboratory, Los Alamos, New Mexico 87545"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James I.","family":"Mullins","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, Washington 98195-8070"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922200414938"},{"key":"e_1_3_2_3_2","first-page":"289","volume":"57","year":"1995","unstructured":"Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57:289-300.","journal-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing"},{"key":"e_1_3_2_4_2","unstructured":"Science"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.aids.0000131377.28694.04"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.16.10701-10708.2005"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2004.20.958"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti607"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-200401230-00003"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025808"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.13.8249-8261.2005"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.4.2587-2599.2003"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(04)15596-7"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922203322230941"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1086\/423940"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390235520"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922203771881220"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2006.22.599"},{"key":"e_1_3_2_19_2","first-page":"303","volume":"19","year":"2005","unstructured":"Hu, D. J., S. Subbarao, S. Vanichseni, P. A. Mock, A. Ramos, L. Nguyen, T. Chaowanachan, F. Griensven, K. Choopanya, T. D. Mastro, and J. W. Tappero. 2005. Frequency of HIV-1 dual subtype infections, including intersubtype superinfections, among injection drug users in Bangkok, Thailand. AIDS19:303-308.","journal-title":"AIDS"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1097\/00126334-199912010-00002"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.3.1234-1240.2000"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/418144a"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature03113"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-200301030-00004"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.288.5472.1789"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/156.3.1393"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2004.08.014"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.1.152-160.1999"},{"key":"e_1_3_2_29_2","unstructured":"MacClade: analysis of phylogeny and character evolution 2001"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1996.12.307"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00182389"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.24.12890-12899.2002"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.18.11693-11704.2005"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1069660"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.11.5435-5451.2002"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.5.4427-4432.1999"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.qai.0000214810.65292.73"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.1.353-363.2005"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922203322588350"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.241370698"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00163230"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1089\/08892220150217247"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/16.4.400"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jviromet.2006.04.009"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2006.22.171"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/156.2.879"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.75.21.10479-10487.2001"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026201"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.103.023382"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/123.3.603"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1001\/jama.292.10.1177"},{"key":"e_1_3_2_52_2","unstructured":"Reference deleted."},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-200301030-00004"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1530509100"},{"key":"e_1_3_2_55_2","unstructured":"PAUP* 4.0: phylogenetic analysis using parsimony (* and other methods) 1999"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2004.07.001"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/22.22.4673"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.19.10501-10506.2004"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1089\/08892220152644232"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922299311376"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0042-6822(03)00454-9"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.aids.0000131330.28762.0c"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.22.11273-11282.2002"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1089\/088922202320886370"}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.02050-06","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.02050-06","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T06:41:17Z","timestamp":1646462477000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.02050-06"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,5]]},"references-count":63,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2007,5]]}},"alternative-id":["10.1128\/JVI.02050-06"],"URL":"https:\/\/doi.org\/10.1128\/jvi.02050-06","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.1083780.536702","asserted-by":"object"}]},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,5]]},"assertion":[{"value":"2006-09-19","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2007-02-14","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2007-05-01","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}