Background: Transmitted drug resistance (TDR) is critical to managing HIV-1–infected individuals and being a public health concern. We report on TDR prevalence and include analyses of phylogenetic clustering of HIV-1 in a predominantly men who have sex with men cohort diagnosed during acute/recent HIV-1 infection in New York City.
Methods: Genotypic resistance testing was conducted on plasma samples of 600 individuals with acute/recent HIV-1 infection (1995–2010). Sequences were used for resistance and phylogenetic analyses. Demographic and clinical data were abstracted from medical records. TDR was defined according to International AIDS Society–USA and Stanford HIV database guidelines. Phylogenetic and other analyses were conducted using PAUP*4.0 and SAS, respectively.
Results: The mean duration since HIV-1 infection was 66.5 days. TDR prevalence was 14.3% and stably ranged between 10.8% and 21.6% (Ptrend = 0.42). Nucleoside reverse transcriptase inhibitors resistance declined from 15.5% to 2.7% over the study period (Ptrend = 0.005). M41L (3.7%), T215Y (4.0%), and K103N/S (4.7%) were the most common mutations. K103N/S prevalence increased from 1.9% to 8.0% between 1995 and 2010 (Ptrend = 0.04). Using a rigorous definition of clustering, 19.3% (112 of 581) of subtype B viral sequences cosegregated into transmission clusters and clusters increased over time. There were fewer and smaller transmission clusters than had been reported in a similar cohort in Montreal but similar to reports from elsewhere.
Conclusions: TDR is stable in this cohort and remains a significant concern to both individual patient management and the public health.