Predictors of HIV seroconversion in Botswana: machine learning analysis in a representative, population-based HIV incidence cohort.

Objective: To identify predictors of HIV acquisition in Botswana.

Design: We applied machine learning approaches to identify HIV risk predictors using existing data from a large, well-characterized HIV incidence cohort.

Methods: We applied machine learning (randomForestSRC) to analyze data from a large population-based HIV incidence cohort enrolled in a cluster-randomized HIV prevention trial in 30 communities across Botswana. We sought to identify the most important risk factors for HIV acquisition, starting with 110 potential predictors.

Results: During a median 29-month follow-up of 8,551 HIV-negative adults, 147 (1.7%) acquired HIV. Our machine learning analysis found that for females, the most important variables for predicting HIV acquisition were the use of injectable hormonal contraception, frequency of sex in the prior 3 months with the most recent partner and residing in a community with HIV prevalence of 29% or higher. For the small proportion (0.3%) of females who had all three risk factors, their estimated probability of acquiring HIV during 29 months of follow-up was 34% (approximate annual incidence of 14%). For males, non-long-term relationships with the most recent partner and community HIV prevalence of 34% or higher were the most important HIV risk predictors. The 6% of males who had both risk factors had a 5.1% probability of acquiring HIV during the follow-up period (approximate annual incidence of 2.1%).

Conclusions: Machine learning approaches allowed us to analyze a large number of variables to efficiently identify key factors strongly predictive of HIV risk. These factors could help target HIV prevention interventions in Botswana.

Clinical trials registration: NCT01965470.