Retrospective Analysis of Phefumula Cohort

Data and plasma from participants who were screened for the Phefumula cohort, a research bronchoscopy study described previously in Muema et al., 2020¹⁵ and Khuzwayo et al., 2021,¹⁶ were used for this retrospective analysis. Adult males or females (self-reported gender) living with and without HIV, between 18 and 50 years, who were otherwise healthy (no chronic medical conditions, no current or past tobacco use, no current TB symptoms) were recruited from KwaDabeka Community Health Clinic in peri-urban KwaZulu-Natal, South Africa. The HIV status of all participants was determined by fourth generation enzyme linked-immunosorbent assay (ELISA) testing and HIV RNA plasma viral load (Sigma–Aldrich). Participants living with HIV were newly diagnosed and had not initiated antiretroviral therapy (ART) at the time of enrolment; on the day of enrolment they received immediate referral for ART-initiation according to South African guidelines. No longitudinal data was collected after ART initiation. BCG and influenza vaccination status were not recorded.