Detection and characterisation of primary (acute and early) HIV-1 infections in an HIV hyper-endemic area

Abstract

South Africa (SA) has the highest number of HIV infections worldwide. Acute HIV infection (AHI) refers to the time of virus acquisition until the appearance of HIV-specific antibodies, usually at 3 – 12 weeks. Early (primary) HIV infection, which includes AHI, is the interval between virus acquisition and the establishment of viral load (VL) set-point. Early HIV infection is characterized by high VL in the blood and genital secretions. Thus, infected individuals are highly infectious during this stage. Most rapid tests often misdiagnose individuals with early HIV infection as antibodies are the last diagnostic marker to appear in the blood after infection. This study aimed to detect and characterize early HIV infections in an HIV hyper-endemic area. This was a diagnostic study that enrolled 10 287 individuals who tested negative on rapid HIV tests from five HIV counselling and testing (HCT) clinics in the Tshwane district of SA. We collected HIV risk behaviour on a questionnaire at enrolment, and used pooled nucleic acid testing (NAAT) to detect HIV in plasma samples, followed by serological characterization in positive samples. NAAT-positive participants were recalled to the clinics for further management and follow-up samples were obtained from them. In-house polymerase chain reaction was designed for amplifying the complete polymerase gene of HIV, followed by Sanger and deep sequencing. Pregnant participants were followed up to assess vertical transmission. The INSTI rapid HIV test was later evaluated at two antenatal clinics. The first dataset reported on newly diagnosed HIV-infected individuals with early or chronic infection who were misdiagnosed by rapid tests at all study sites. We showed that follow-up rapid tests done within a 4 week interval detected early and chronic HIV infections initially missed at point-of-care (POC) facilities. In the second dataset, we showed that majority of sexually active people in the Tshwane district had high risk exposure to HIV as they were unaware of their partner’s HIV status and had high prevalence of unprotected sex. We showed that a questionnaire that captures HIV risk behaviour would be useful during HCT to ensure that there is a systematic way of identifying HIV risk factors and that counselling is optimised for each individual. In the third dataset, we reported on transmitted HIV drug-resistance among individuals with early HIV infection. Illumina deep sequencing detected a higher rate of transmitted antiretroviral (ARV) drug-resistance mutations; and showed emergence of minority variants in some sample pairs without ARV drug pressure, highlighting their potential clinical relevance. The fourth dataset reported on vertical transmission of HIV among pregnant participants who were initially misdiagnosed by the rapid HIV tests at the antenatal clinics. We observed that most pregnant women presented late for antenatal care (ANC), and found transmitted HIV in three babies whose mothers were started on ARV treatment during ANC. In the fifth dataset, we reported on the field performance of the INSTI rapid HIV test, which had 100% sensitivity, specificity and negative predictive value for detection of HIV antibodies.