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Co-infection with human T-cell lymphotropic virus types 1 and 2 (HTLV-1/2) and HIV is not routinely screened for, yet it may significantly influence clinical progression, mortality, and quality of life in affected individuals. This study aimed to estimate the prevalence of HTLV-1/2 co-infection among adults living with HIV and to identify associated epidemiological factors in the Peruvian Amazon. A cross-sectional study was conducted including patients receiving antiretroviral therapy through the multidisciplinary TARGA program in Iquitos, Peru, during the second quarter of 2013. Screening for HTLV-1/2 antibodies was performed using enzyme-linked immunosorbent assay, with reactive samples confirmed by Line Immunoassay. Demographic and behavioral variables were collected, and prevalence odds ratios with 95% confidence intervals were estimated using logistic regression models. Among the 284 patients included, 28 were co-infected with HIV and HTLV-1/2, resulting in a prevalence of 10% with a 95% confidence interval of 6.5 to 14.1. In multivariable analysis, age over 35 years and having more than 10 lifetime sexual partners were independently associated with co-infection, with prevalence odds ratios of 12.4 and 3.6, respectively. HTLV-1/2 co-infection was highly prevalent among people living with HIV in the Peruvian Amazon, and the main risk factors identified suggest that cumulative exposure and sexual behavior play a significant role in the joint transmission of both retroviruses, supporting the need to consider systematic HTLV screening in endemic settings.