{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T18:34:56Z","timestamp":1792002896148,"version":"4.4.0"},"reference-count":57,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2013,8,1]],"date-time":"2013-08-01T00:00:00Z","timestamp":1375315200000},"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 Clin Microbiol"],"published-print":{"date-parts":[[2013,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The genetic diversity of human immunodeficiency virus type 1 (HIV-1) has significant implications for diagnosis, vaccine development, and clinical management of patients. Although HIV-1 subtype B is predominant in the United States, factors such as global travel, immigration, and military deployment have the potential to increase the proportion of non-subtype B infections. Limited data are available on the prevalence and distribution of non-B HIV-1 strains in the United States. We sought to retrospectively examine the prevalence, geographic distribution, diversity, and temporal trends of HIV-1 non-B infections in samples obtained by ARUP Laboratories, a national reference laboratory, from all regions of the United States. HIV-1\n            <jats:italic>pol<\/jats:italic>\n            sequences from 24,386 specimens collected from 46 states between 2004 and September 2011 for drug resistance genotyping were analyzed using the REGA HIV-1 Subtyping Tool, version 2.0. Sequences refractory to subtype determination or reported as non-subtype B by this tool were analyzed by PHYLIP version 3.5 and Simplot version 3.5.1. Non-subtype B strains accounted for 3.27% (798\/24,386) of specimens. The 798 non-B specimens were received from 37 states and included 5 subtypes, 23 different circulating recombinant forms (CRFs), and 39 unique recombinant forms (URFs). The non-subtype B prevalence varied from 0% in 2004 (0\/54) to 4.12% in 2011 (201\/4,884). This large-scale analysis reveals that the diversity of HIV-1 in the United States is high, with multiple subtypes, CRFs, and URFs circulating. Moreover, the geographic distribution of non-B variants is widespread. Data from HIV-1 drug resistance testing have the potential to significantly enhance the surveillance of HIV-1 variants in the United States.\n          <\/jats:p>","DOI":"10.1128\/jcm.00880-13","type":"journal-article","created":{"date-parts":[[2013,6,13]],"date-time":"2013-06-13T03:53:26Z","timestamp":1371095606000},"page":"2662-2669","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":44,"title":["Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States"],"prefix":"10.1128","volume":"51","author":[{"given":"Michael T.","family":"Pyne","sequence":"first","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"John","family":"Hackett","sequence":"additional","affiliation":[{"name":"Abbott Diagnostics, Abbott Park, Illinois, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vera","family":"Holzmayer","sequence":"additional","affiliation":[{"name":"Abbott Diagnostics, Abbott Park, Illinois, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Hillyard","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA"},{"name":"University of Utah, Department of Pathology, Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm.2016"},{"key":"e_1_3_2_3_2","volume-title":"HIV Sequence Compendium 2011","author":"Kuiken C","year":"2011","unstructured":"KuikenC FoleyB LeitnerT ApetreiC HahnB MizrachiI MullinsJ RambautA WolinskyS KorberB (ed). 2011. HIV Sequence Compendium 2011. Los Alamos National Laboratory, Los Alamos, NM."},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.20599"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e328342ff93"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.8.3860-3868.2005"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0b013e31803260df"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jviromet.2007.02.013"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra0706737"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00685-10"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1155\/2012\/256982"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.23553"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00776-10"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0b013e3181b72539"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00578-12"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1537-2995.2011.03281.x"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2011.07.002"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2012.06.012"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-199712000-00015"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-200002180-00011"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.2807\/esm.09.10.00481-en"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1086\/519387"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1097\/00126334-200104010-00017"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1086\/644505"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1086\/430329"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.7326\/0003-4819-131-7-199910050-00004"},{"key":"e_1_3_2_27_2","first-page":"136","article-title":"Use of a drug resistance sequence database to determine the prevalence of non-subtype B HIV-1 infections in US and European clinical cohorts, abstr 177","volume":"5","author":"Wegner SA","year":"2000","unstructured":"WegnerSA LarderB HertogsK CarrJ McCutchanF. 2000. Use of a drug resistance sequence database to determine the prevalence of non-subtype B HIV-1 infections in US and European clinical cohorts, abstr 177. Antiviral Ther. 5(Suppl 3):136\u2013145.","journal-title":"Antiviral Ther"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1097\/00126334-200407010-00011"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1086\/430322"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.qai.0000200663.47838.f1"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1537-2995.2008.01935.x"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jir862"},{"key":"e_1_3_2_33_2","unstructured":"WheelerW\nMahleK\nBodnarU\nPienaizekD\nKlineR\nHallI\nMcKennaM US Variant Atypical and Resistant HIV Surveillance (VARHS) Group. 2007. Antiretroviral drug-resistance mutations and subtypes in drug-na\u00efve persons newly diagnosed with HIV-1 infection US March 2003 to October 2006. CDC Atlanta GA. http:\/\/www.retroconference.org\/2007\/PDFs\/648.pdf."},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.20971"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0b013e3181e0c3b3"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1086\/323601"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.20601"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAD.0b013e3283388742"},{"key":"e_1_3_2_39_2","unstructured":"United States Census Bureau. 2011. The newly arrived foreign-born population of the United States: 2010. United States Census Bureau U.S. Department of Commerce Suitland MD. http:\/\/www.census.gov\/prod\/2011pubs\/acsbr10-16.pdf."},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1537-2995.2000.40111399.x"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2013.03.013"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1994.10.625"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(95)92901-0"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1086\/314044"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1001\/jama.1996.03540020021012"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1086\/317649"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1086\/378280"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1089\/apc.2006.0172"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.qai.0000225871.87456.e7"},{"key":"e_1_3_2_50_2","unstructured":"PieniazekD\nZiebellR\nOcfemiaCB\nSaduvalaN\nKlineR\nPrejeanJ\nKimD\nHallHI US Variant Atypical and Resistant HIV Surveillance (VARHS) Group. 2012. Phylogenetic surveillance of HIV-1 non-B subtypes among US-born and foreign-born individuals living in the United States revealed similar viral genetic diversity but different race and male transmission patterns. CDC Atlanta GA. http:\/\/www.retroconference.org\/2012b\/PDFs\/516.pdf."},{"key":"e_1_3_2_51_2","unstructured":"Panel on Antiretroviral Guidelines for Adults and Adolescents. 2013. Guidelines for the use of antiretroviral agents in HIV-1 infected adults and adolescents. National Institutes of Health Rockville MD. http:\/\/aidsinfo.nih.gov\/ContentFiles\/AdultandAdolescentGL.pdf."},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2010.10.008"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1097\/01.qai.0000179430.34660.11"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0b013e31821438d9"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.42.6.2847-2849.2004"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02217-07"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01285-10"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2009.06.012"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.00880-13","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.00880-13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T11:46:01Z","timestamp":1646480761000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.00880-13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,8]]},"references-count":57,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2013,8]]}},"alternative-id":["10.1128\/JCM.00880-13"],"URL":"https:\/\/doi.org\/10.1128\/jcm.00880-13","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,8]]},"assertion":[{"value":"2013-04-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-06-05","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-07-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}