Quantifying prevalence and risk factors of HIV multiple infection in Uganda from population-based deep-sequence data
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People living with HIV can be simultaneously infected with genetically distinct variants. This can occur either at the time of initial infection (“coinfection”) or at a later time-point (“superinfection”). Multiple infection provides the necessary conditions for the generation of novel recombinant forms of HIV and may worsen clinical outcomes and increase the rate of transmission to HIV seronegative sexual partners. To date, studies of HIV multiple infection have relied on insensitive bulk-sequencing, labor intensive single genome amplification protocols, or deep-sequencing of short genome regions. Here, we identified multiple infections in whole-genome or near whole-genome HIV RNA deep-sequence data generated from plasma samples of 2,029 people living with viremic HIV who participated in the population-based Rakai Community Cohort Study. We estimated individual- and population-level probabilities of being multiply infected and assessed epidemiological risk factors using the novel Bayesian deep-phylogenetic multiple infection model ( deep-phyloMI ) which accounts for bias due to partial sequencing success and false-negative and false-positive detection rates. We estimated that between 2010 and 2020, 5.79% (95% highest posterior density interval (HPD) 4.56% - 7.07%) of sequenced participants with viremic HIV had a multiple infection at time of sampling. Participants living in high-HIV prevalence communities along Lake Victoria were 2.22-fold (95% HPD 1.28 - 3.43) more likely to harbor a multiple infection compared to individuals in lower prevalence neighboring communities. This work introduces a high-throughput surveillance framework for identifying people with multiple HIV infections and quantifying population-level prevalence and risk factors of multiple infection for clinical and epidemiological investigations.
Author summary
HIV exists as a population of genetically distinct viral variants among people living with HIV. People living with HIV can be infected with genetically distinct variants. Identification of these mixed infections requires generating viral genomic data from people living with HIV. In the past, the approaches used to identify multiple infections from viral genomic data have had poor sensitivity or required labor intensive protocols that are prohibitive in application to large data sets. Prior work has also only utilized data generated from only small portions of the viral genome and the statistical procedures used to generate population-level estimates from sequencing data generated from individual infections has not accounted for incomplete sampling of the within-host viral population or sources of sequencing error, which may confound multiple infection estimates. Here, we develop a statistical model that addresses these limitations and allows for the identification of multiple infections and the estimation of population-level risk of multiple infection from deep-sequence data. We fit this model to population-based HIV genomic data from people living with HIV in southern Uganda and estimate that approximately 6% of viremic participants harbor a multiple infection at a given point in time. We show that the prevalence of multiple infections is higher in key populations with high HIV prevalence. These findings inform our understanding of the sexual risk networks that give rise to multiple infections and aid in efforts to model HIV epidemiological dynamics and evolution during a period of incidence declines and shifting transmission dynamics across Eastern and Southern Africa.
