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Alcohol use has been shown to accelerate disease progression in experimental studies of simian immunodeficiency virus in macaques, but the results in observational studies of HIV have been conflicting.We conducted a prospective cohort study of the impact of unhealthy alcohol use on CD4 cell count among HIV-infected persons in southwestern Uganda not yet eligible for antiretroviral treatment (ART). Unhealthy alcohol consumption was 3-month Alcohol Use Disorders Identification Test—Consumption positive (≥3 for women, ≥4 for men) and/or phosphatidylethanol (PEth—an alcohol biomarker) ≥50 ng/mL, modeled as a time-dependent variable in a linear mixed effects model of CD4 count.At baseline, 43% of the 446 participants were drinking at unhealthy levels and the median CD4 cell count was 550 cells/mm3 (interquartile range 416–685). The estimated CD4 cell count decline per year was −14.5 cells/mm3 (95% confidence interval: −38.6 to 9.5) for unhealthy drinking vs. −24.0 cells/mm3 (95% confidence interval: −43.6 to −4.5) for refraining from unhealthy drinking, with no significant difference in decline by unhealthy alcohol use (P value 0.54), adjusting for age, sex, religion, time since HIV diagnosis, and HIV viral load. Additional analyses exploring alternative alcohol measures, participant subgroups, and time-dependent confounding yielded similar findings.Unhealthy alcohol use had no apparent impact on the short-term rate of CD4 count decline among HIV-infected ART naive individuals in Uganda, using biological markers to augment self-report and examining disease progression before ART initiation to avoid unmeasured confounding because of misclassification of ART adherence.