Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States

ARUP Institute for Clinical and Experimental Pathology®, 500 Chipeta Way, Salt Lake City, Utah 84108, USA.
Journal of clinical microbiology (Impact Factor: 3.99). 06/2013; 51(8). DOI: 10.1128/JCM.00880-13
Source: PubMed


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 is available on the prevalence and distribution of non-B HIV-1 strains in the U.S. 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 pol 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 v3.5 and Simplot v3.5.1. 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). Non-subtype B prevalence varied from 0% in 2004 (0/54) to 4.12% in 2011 (201/4884). This large-scale analysis reveals that 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 surveillance of HIV-1 variants in the United States.

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Available from: Michael Pyne, Sep 22, 2014
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