1. Large-Scale Analysis of the Prevalence and Geographic Distribution of HIV-1 Non-B Variants in the United States
- Author
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Michael T. Pyne, John Hackett, David R. Hillyard, and Vera Holzmayer
- Subjects
Adult ,Male ,Microbiology (medical) ,Adolescent ,Genotype ,media_common.quotation_subject ,Molecular Sequence Data ,Immigration ,HIV Infections ,Drug resistance ,Biology ,Young Adult ,Virology ,Genetic variation ,Prevalence ,Cluster Analysis ,Humans ,Child ,Genotyping ,Aged ,media_common ,Aged, 80 and over ,Genetics ,Genetic diversity ,Infant, Newborn ,Genetic Variation ,Infant ,Sequence Analysis, DNA ,Middle Aged ,United States ,Subtyping ,Geographic distribution ,Phylogeography ,pol Gene Products, Human Immunodeficiency Virus ,Child, Preschool ,HIV-1 ,Female - Abstract
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 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 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.
- Published
- 2013