Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana

Botswana is among the top three countries with the highest HIV burden globally. Since 2016, the country implemented the “Test and Treat all” program to reduce HIV transmission, however, targeted testing for people at a higher risk is still lacking. Botswana recently became one of the first three countries to reach the UNAIDS 95-95-95 targets, which are defined as 95% of people with HIV know they have HIV status, 95% of those people are on treatment and 95% of those on treatment have undetected virus (virally suppressed). One of the challenges towards eliminating HIV is identifying people living with HIV who are unaware of their status. As part of the Botswana Combination Prevention Project, 30 villages across Botswana were tested for HIV and monitored 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 study period. We conducted a study to evaluate factors associated with undiagnosed HIV infection using behavioral, sociodemographic data, and the changes in the genetic make-up of the HIV virus isolated from these individuals (HIV diversity).  We checked the changes in the virus genetic code to gauge how recent the infection was in newly tested individuals. Our results indicate that those with undiagnosed infections are likely to be young men and women who do not use condoms consistently. Among women, several factors were predictive: being married, educated, and testing frequently increased HIV risk. Men at risk were more difficult to identify. More than a third of undiagnosed infections were classified recently infected based changes in the genetic make-up of the virus. These tools can be used to identify persons newly infected and help with designing interventions to curb onward transmission.