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Background. Clinically, human immunodeficiency virus type 1 (HIV-1) pol sequences are used to evaluate for drug resistance. These data can also be used to evaluate transmission networks and help describe factors associated with transmission risk.Methods. HIV-1 pol sequences from participants at 5 sites in the CFAR Network of Integrated Clinical Systems (CNICS) cohort from 2000–2009 were analyzed for genetic relatedness. Only the first available sequence per participant was included. Inferred transmission networks (“clusters”) were defined as ≥2 sequences with ≤1.5% genetic distance. Clusters including ≥3 patients (“networks”) were evaluated for clinical and demographic associations.Results. Of 3697 sequences, 24% fell into inferred clusters: 155 clusters of 2 individuals (“dyads”), 54 clusters that included 3–14 individuals (“networks”), and 1 large cluster that included 336 individuals across all study sites. In multivariable analyses, factors associated with being in a cluster included not using antiretroviral (ARV) drugs at time of sampling (P < .001), sequence collected after 2004 (P < .001), CD4 cell count >350 cells/mL (P < .01), and viral load 10 000–100 000 copies/mL (P < .001) or >100 000 copies/mL (P < .001). In networks, women were more likely to cluster with other women (P < .001), and African Americans with other African Americans (P < .001).Conclusions. Molecular epidemiology can be applied to study HIV transmission networks in geographically and demographically diverse cohorts. Clustering was associated with lack of ARV use and higher viral load, implying transmission may be interrupted by earlier diagnosis and treatment. Observed female and African American networks reinforce the importance of diagnosis and prevention efforts targeted by sex and race.