Background:  The prevalence of transmitted drug resistance among persons newly diagnosed with HIV ranges from 12% to 16% in the US. Using national HIV surveillance data, we assessed prevalence and trends of transmitted drug resistance-associated mutations (TDRM) by duration of infection (recent vs long-standing) among persons newly diagnosed with HIV-1 infection during 2006 to 2009.

Methods:  HIV nucleotide sequences, BED HIV-1 Capture EIA results, and HIV testing and treatment history data were available from a convenience sample of persons newly diagnosed with HIV infection during 2006 to 2009, residing in 8 US jurisdictions at diagnosis, with no evidence of prior ARV use. Absent a BED result, persons with negative HIV test results ≤6 months before HIV diagnosis were classified as recent infections; those with AIDS ≤6 months after HIV diagnosis were classified as long-standing infections. We identified TDRM using the CDC HIV-1 surveillance mutation list. We used prevalence ratios (PR) and chi-square statistics to compare TDRM by duration of infection and assessed trends using the estimated annual percentage change.

Results:  Of 10,338 diagnosed infections, 1625 (15.7%) had sequences containing any TDRM, of which 1357 (83.5%) were single-drug class TDRM. By duration of infection, 2339 (22.6%) of the diagnoses were recent and 7999 (77.4%) were long-standing infections. Compared to long-standing, recent infections had higher prevalence of TDRM overall (PR = 1.29, 95% confidence interval = 1.17 to 1.43). Prevalence was also higher among recent versus LS infections for single-drug class TDRM (PR 1.24, CI 1.11 to 1.39), 2-drug class TDRM (PR 1.77, CI 1.34 to 2.35), and TDRM associated with NNRTI (PR 1.6, CI 1.39 to 1.84). Differences by duration of infection were seen for specific TDRM:  K103N, Y188H, M41L (p <0.01). During 2006 to 2009, the annual prevalence of TDRM among recent infections was consistently significantly higher than that for long-standing infections (p <0.05); no significant changes in the prevalence of TDRM by duration of infection were observed across years.

Conclusions:  In this analysis, 1 in 6 newly diagnosed HIV infections contained TDRM. Overall prevalence of TDRM was 1.3 times as high among recent compared to long-standing infections. These findings may be indicative of reversion of TDRM to wild type in long-standing infections or to TDRM presence below detectable levels, and suggest that the true overall TDRM prevalence in this sample may be underestimated.