Diversity and characterization of HIV-1 subtypes in the United States, 2008–2016

Abstract

Purpose: This article describes subtype diversity among diagnosed HIV-1 infections in the United States during 2008–2016 by demographic or risk group and over time. Methods: HIV-1 polymerase sequences reported to the National HIV Surveillance System for persons in 17 U.S. states with HIV infection diagnosed during 2008–2016 were subtyped using COMET, an automated subtyping tool, and National HIV Surveillance System demographic data were analyzed. Results: Subtype B was identified in 93.6% of 121,793 reported sequences. The most common non-B subtypes and circulating recombinant forms (CRFs) were C, CRF02_AG, A, CRF01_AE, and G. Elevated percentages of non-B subtypes or CRFs were found in persons who were female, aged less than 13 years at diagnosis, Asian, or had transmission attributable to heterosexual contact (females only) or perinatal exposure. Foreign-born persons had a higher percentage of non-B subtypes. The prevalence of non-B subtypes and CRFs increased from 5.0% in 2008 to 8.5% in 2016; among specific subtypes and CRFs, subtype G and CRF01_AE increased. Conclusions: Subtype B remains the predominant strain in the United States. Non-B subtypes and CRFs were not widespread, but diversity and numbers increased from 2008 through 2016, which could have consequences for clinical management, diagnostic testing, and vaccine development.