{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T12:28:57Z","timestamp":1774787337744,"version":"3.50.1"},"reference-count":36,"publisher":"American Society for Microbiology","issue":"24","license":[{"start":{"date-parts":[[2009,12,15]],"date-time":"2009-12-15T00:00:00Z","timestamp":1260835200000},"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":[[2009,12,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Human immunodeficiency virus type 1 (HIV-1) genetic diversity, due to its high evolutionary rate, has long been identified as a main cause of problems in the development of an efficient HIV-1 vaccine. However, little is known about differences in evolutionary rate between different subtypes. In this study, we collected representative samples of the main epidemic subtypes and circulating recombinant forms (CRFs), namely, sub-subtype A1, subtypes B, C, D, and G, and CRFs 01_AE and 02_AG. We analyzed separate data sets for\n            <jats:italic>pol<\/jats:italic>\n            and\n            <jats:italic>env<\/jats:italic>\n            . We performed a Bayesian Markov chain Monte Carlo relaxed-clock phylogenetic analysis and applied a codon model to the resulting phylogenetic trees to estimate nonsynonymous (dN) and synonymous (dS) rates along each and every branch. We found important differences in the evolutionary rates of the different subtypes. These are due to differences not only in the dN rate but also in the dS rate, varying in roughly similar ways, indicating that these differences are caused by both different selective pressures (for dN rate) and the replication dynamics (for dS rate) (i.e., mutation rate or generation time) of the strains. CRF02_AG and subtype G had higher rates, while subtype D had lower dN and dS rates than the other subtypes. The dN\/dS ratio estimates were also different, especially for the\n            <jats:italic>env<\/jats:italic>\n            gene, with subtype G showing the lowest dN\/dS ratio of all subtypes.\n          <\/jats:p>","DOI":"10.1128\/jvi.01022-09","type":"journal-article","created":{"date-parts":[[2009,10,1]],"date-time":"2009-10-01T00:49:47Z","timestamp":1254358187000},"page":"12917-12924","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":83,"title":["Quantifying Differences in the Tempo of Human Immunodeficiency Virus Type 1 Subtype Evolution"],"prefix":"10.1128","volume":"83","author":[{"given":"Ana B.","family":"Abecasis","sequence":"first","affiliation":[{"name":"Instituto Gulbenkian de Cie\u0302ncia, Oeiras, Portugal"},{"name":"Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium"}]},{"given":"Anne-Mieke","family":"Vandamme","sequence":"additional","affiliation":[{"name":"Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","first-page":"2","year":"2007","unstructured":"Abecasis, A., A.-M. Vandamme, and P. Lemey. 2007. Sequence alignment in HIV computational analysis, p. 2-16. In T. Leitner, B. Foley, B. Hahn, P. Marx, F. McCutchan, J. Mellors, S. Wolinsky, and B. Korber (ed.), HIV sequence compendium 2006\/2007. Theoretical Biology and Biophysics Group, Los Alamos, NM.","journal-title":"HIV sequence compendium 2006\/2007"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00463-07"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1086\/512682"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.4.1962-1970.2004"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti607"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0040088"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/161.3.1307"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2148-7-214"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi103"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0705329104"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.aids.0000247564.73009.bc"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1126531"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1086\/527416"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.288.5472.1789"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.0030029"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00985-07"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/1743-422X-5-160"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-3-40"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1059128"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi009"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti079"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1246"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.20.11193-11200.2003"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.11.6359-6366.2003"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.288.5463.55d"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-004-0206-5"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1096\/fj.00-0449fje"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1995.11.1423"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.3.502"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.1.115"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj021"},{"key":"e_1_3_2_33_2","unstructured":"PAUP* 4.0\u2014phylogenetic analysis using parsimony (*and other methods). 1998"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/22.22.4673"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2004.06.011"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature07390"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1038\/35400"}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.01022-09","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.01022-09","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T12:41:32Z","timestamp":1646484092000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.01022-09"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12,15]]},"references-count":36,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2009,12,15]]}},"alternative-id":["10.1128\/JVI.01022-09"],"URL":"https:\/\/doi.org\/10.1128\/jvi.01022-09","relation":{},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,12,15]]},"assertion":[{"value":"2009-05-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2009-09-24","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2009-12-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}