{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T12:40:39Z","timestamp":1778676039016,"version":"3.51.4"},"reference-count":95,"publisher":"American Society for Microbiology","issue":"24","license":[{"start":{"date-parts":[[2012,12,15]],"date-time":"2012-12-15T00:00:00Z","timestamp":1355529600000},"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":[[2012,12,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Simian immunodeficiency virus (SIV) infection of rhesus macaques causes immune depletion and disease closely resembling human AIDS and is well recognized as the most relevant animal model for the human disease. Experimental investigations of viral pathogenesis and vaccine protection primarily involve a limited set of related viruses originating in sooty mangabeys (SIVsmm). The diversity of human immunodeficiency virus type 1 (HIV-1) has evolved in humans in about a century; in contrast, SIV isolates used in the macaque model evolved in sooty mangabeys over millennia. To investigate the possible consequences of such different evolutionary histories for selection pressures and observed diversity in SIVsmm and HIV-1, we isolated, sequenced, and analyzed 20 independent isolates of SIVsmm, including representatives of 7 distinct clades of viruses isolated from natural infection. We found SIVsmm diversity to be lower overall than HIV-1 M group diversity. Reduced positive selection (i.e., less diversifying evolution) was evident in extended regions of SIVsmm proteins, most notably in Gag p27 and Env gp120. In addition, the relative diversities of proteins in the two lineages were distinct: SIVsmm Env and Gag were much less diverse than their HIV-1 counterparts. This may be explained by lower SIV-directed immune activity in mangabeys relative to HIV-1-directed immunity in humans. These findings add an additional layer of complexity to the interpretation and, potentially, to the predictive utility of the SIV\/macaque model, and they highlight the unique features of human and simian lentiviral evolution that inform studies of pathogenesis and strategies for AIDS vaccine design.<\/jats:p>","DOI":"10.1128\/jvi.01862-12","type":"journal-article","created":{"date-parts":[[2012,10,11]],"date-time":"2012-10-11T09:01:29Z","timestamp":1349946089000},"page":"13217-13231","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":31,"title":["Distinct Evolutionary Pressures Underlie Diversity in Simian Immunodeficiency Virus and Human Immunodeficiency Virus Lineages"],"prefix":"10.1128","volume":"86","author":[{"given":"Will","family":"Fischer","sequence":"first","affiliation":[{"name":"Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristian","family":"Apetrei","sequence":"additional","affiliation":[{"name":"University of Pittsburgh Center for Vaccine Research, Pittsburgh, Pennsylvania, USA"},{"name":"Tulane National Primate Research Center, Covington, Louisiana, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario L.","family":"Santiago","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingying","family":"Li","sequence":"additional","affiliation":[{"name":"Departments of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajeev","family":"Gautam","sequence":"additional","affiliation":[{"name":"Tulane National Primate Research Center, Covington, Louisiana, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivona","family":"Pandrea","sequence":"additional","affiliation":[{"name":"University of Pittsburgh Center for Vaccine Research, Pittsburgh, Pennsylvania, USA"},{"name":"Tulane National Primate Research Center, Covington, Louisiana, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George M.","family":"Shaw","sequence":"additional","affiliation":[{"name":"Departments of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA"},{"name":"Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beatrice H.","family":"Hahn","sequence":"additional","affiliation":[{"name":"Departments of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA"},{"name":"Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norman L.","family":"Letvin","sequence":"additional","affiliation":[{"name":"Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary J.","family":"Nabel","sequence":"additional","affiliation":[{"name":"Vaccine Research Center, Bethesda, Maryland, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bette T.","family":"Korber","sequence":"additional","affiliation":[{"name":"Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, USA"},{"name":"The Santa Fe Institute, Santa Fe, New Mexico, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00281-07"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.14.8991-9005.2005"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002721"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10766"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm.2089"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.178.12.8002"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0023092"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1097\/COH.0b013e32834dde01"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2010-12-325936"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20040874"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.3159089"},{"key":"e_1_3_3_13_2","unstructured":"DelportW\nPoonA\nFrostSD\nKosakovsky PondSL. 2011. 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Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. thesis.The University of Texas at Austin Austin TX."}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.01862-12","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.01862-12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T10:28:09Z","timestamp":1646476089000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.01862-12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12,15]]},"references-count":95,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2012,12,15]]}},"alternative-id":["10.1128\/JVI.01862-12"],"URL":"https:\/\/doi.org\/10.1128\/jvi.01862-12","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.717963034.793465083","asserted-by":"object"}]},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12,15]]},"assertion":[{"value":"2012-07-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-09-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-01-19","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}