Background:  Although subtype B remains the predominant form of HIV-1 in the United States, limited data is available on the prevalence and distribution of non-subtype B strains or their trends over time. Due to increased international travel and immigration, the proportion of non-B subtypes is likely to increase. Genetic diversity of HIV-1 has significant implications for diagnosis, monitoring and clinical management of patients. Thus, it is important to be aware of the overall diversity of strains in the United States.

Methods:  Sequence data from 6955 samples submitted to ARUP Laboratories between 2004 and 2008 for HIV antiretroviral resistance genotyping were analyzed to determine subtype. The ViroSeq HIV-1 Genotyping System v 2.0 (Celera, Alameda, CA) was used to generate 1302 nucleotide sequences comprising codons 1 to 99 of the protease gene and 1 to 335 of the reverse transcriptase gene. Initial subtype characterization was performed with the REGA HIV-1 Subtyping Tool, Version 2.0 (Stanford University web site). For 370 sequences not successfully subtyped using the REGA tool, phylogeny was determined using PHYLIP software (v3.5c). Sequences were analyzed for recombination breakpoints with SimPlot (v3.5.1). Results were correlated to the patient’s age, gender, and geographic information.

Results:  The data set included samples submitted by clients in 41 states. The age of the patients ranged from newborn to 80, with an average age of 41 (median of 42), 69% male, and 31% female. Of 6955 sequences, 6764 (97.25%) were subtype B. The 191 non-B subtype samples included:  50 subtype A, 61 subtype C, 23 other subtypes (D, F, and G), 33 CRF02_AG, 8 other CRF (CRF09_cpx, CRF10_CD, CRF19_cpx, CRF21_A2D, CRF06_cpx, CRF12_BF), and 16 unique recombinant forms (URF_02A3, URF_A1D, URF_A1G, URF_A3G, URF_BC, URF_BF1, URF_BG). Non-B samples were received from 28 states. Subtype B varied from 100% in 2004 (n = 54), 98.90% in 2005 (n = 546), 97.86% in 2006 (n = 746), 97.34% in 2007 (n =2139), to 96.77% in 2008 (n = 3470). Subtypes A and C increased most dramatically during this period.

Conclusions:  The prevalence of diverse non-B subtypes and recombinants in the United States is steadily increasing and their geographic distribution is widespread. This study illustrates the ability to determine subtype from resistance genotyping sequences that are routinely obtained during patient treatment. Due to the potential effect on patient management, it is important to recognize the growing genetic diversity of HIV-1 in the United States.