Background: HIV-1 is endemic in Botswana. The country’s primary challenge is identifying persons living with HIV who are unaware of their status. We evaluated factors associated with undiagnosed HIV infection using HIV-1 phylogenetic, behavioural, and demographic data.
Methods: As part of the Botswana Combination Prevention Project, 20% of adults residing in 30 villages were tested for HIV and followed from 2013 to 2018. A total of 12,610 participants were enrolled, 3,596 tested HIV-positive at enrolment, and 147 participants acquired HIV during the trial. Extensive socio-demographic and behavioural data were collected from participants and next-generation sequences were generated for HIV-positive cases. We compared three groups of participants: 1) those previously known to be HIV-positive at enrolment (n=2,995); 2) those newly diagnosed at enrolment (n=601) and 3) those who tested HIV-negative at enrolment but tested HIV-positive during follow-up (n=147). We searched for differences in demographic and behavioural factors between known and newly diagnosed group using logistic regression. We also compared the topology of each group in HIV-1 phylogenies and used a genetic diversity-based algorithm to classify infections as recent (<1 year) or chronic (≥1 year).
Results: Being male (aOR=2.23), younger than 35 years old (aOR=8.08), educated and married was associated with undiagnosed HIV infection (p<0.001). Inconsistent condom use (aOR=1.76), multiple sexual partners (aOR=1.73) and repeated HIV testing (aOR=3.96) increased the odds of having undiagnosed HIV infection, while knowledge of one’s partner’s positive HIV status decreased those odds as compared to knowing one’s partner to be negative (aOR=0.077, p<0.001). The genetic diversity-based algorithm classified most incident infections as recent (75.0%), but almost none of known infections (2.0%). The estimated proportion of recent infections among new diagnoses was 37.0% (p<0.001).
Conclusion: Our results indicate that those with undiagnosed infections are likely to be younger, educated, married, men who do not consistently use condoms with their partners. Notably, these men have been tested for HIV previously, and a sizeable proportion had recent infections based on a genetic diversity-based classifier, suggesting that they are aware of their risk. In the era of “test and treat all”, these identified predictors may help better prioritize groups for prevention and testing.