Integrating Assisted Partner Services and Phylogenetics for HIV and HCV Prevention

Abstract: In sub-Saharan Africa and globally, many persons who inject drugs (PWID) are living with undiagnosed oruntreated HIV, experience high levels of poverty, food and housing instability, and discrimination, and haveincreased risk for health conditions that contribute to worse outcomes from COVID-19. It is also more challengingfor PWID to access healthcare when services have been limited by lockdowns and measures to ensure socialdistancing to prevent spread of respiratory viruses, such as SARS-CoV-2. We propose to recruit and follow acohort of 500 HIV-positive and 500 HIV-negative PWID and their partners, many of whom also have hepatitis C,to determine whether poorly controlled HIV infection, active drug use and other HIV- and PWID-specific riskfactors result in increased likelihood of COVID-19 acquisition, viral transmission, symptomatic disease andpoor clinical outcomes (AIM 1). We will also define transmission dynamics through phylogenetic analysesof SAR-CoV-2 sequences from symptomatic PWID (AIM 2) and determine whether HIV care and harmreduction service delivery disruptions are associated with poor compliance to ART and methadone, HIVviremia and other adverse outcomes (AIM 3). Our proposal is innovative in how it reaches PWID and partnersusing peer educators, employs targeted testing and symptom screening in this high-risk Kenyan population, anddefines COVID-19 transmission within and beyond local networks using phylogenetics. Participant recruitmentand enrollment will take place in drop-in centers and methadone clinics in Nairobi, Mombasa and Kilifi, Kenyaand follow-up visits will occur monthly for 6 months. In addition to collecting interview data and blood for SARS-CoV-2 antibodies, we will ask participants who have symptoms consistent with COVID-19 at any of the 7 visitsto self-collect a nasal swab specimen for SARS-CoV-2 polymerase chain reaction (PCR), followed by genomesequencing if positive. Laboratory assays for antibody and viral PCR testing will be conducted in Nairobi andpositive specimens will be shipped to Seattle for sequencing and phylogenetic analysis. We anticipate that ourresults will highlight the need for targeted testing among PWID and inform interventions and programs for HIVand addiction care and treatment across the globe for similar marginalized populations when confronted withCOVID-19 and other public health crises.