The role of viral introductions in sustaining community-based HIV epidemics in rural Uganda: evidence from spatial clustering, phylogenics, and egocentric transmission models

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Background: It is often assumed that local sexual networks play a dominant role in HIV spread in sub-Saharan Africa. The aim of this study was to determine the extent to which continued HIV transmission in rural communities—home to two-thirds of the African population—is driven by intra-community sexual networks versus viral introductions from outside of communities.
Methods and Findings: We analyzed the spatial dynamics of HIV transmission in rural Rakai District, Uganda, using data from a cohort of 14,594 individuals within 46 communities. We applied spatial clustering statistics, viral phylogenetics, and probabilistic transmission models to quantify the relative contribution of viral introductions into communities versus community- and household-based transmission to HIV incidence. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7–3.7) times more likely to be HIV infected themselves compared to the population in general, but spatial clustering outside of households was relatively weak and was confined to distances <500 m. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified, of which 44% (42/95) were two individuals sharing a household. Among the remaining clusters, 72% (38/53) crossed community boundaries. Using the locations of self-reported sexual partners, we estimate that 39% (95% CI: 34%–42%) of new viral transmissions occur within stable household partnerships, and that among those infected by extra-household sexual partners, 62% (95% CI: 55%–70%) are infected by sexual partners from outside their community. These results rely on the representativeness of the sample and the quality of self-reported partnership data and may not reflect HIV transmission patterns outside of Rakai.
Grabowski MK, Lessler J, Redd AD, Kagaayi J, Laeyendecker O, Ndyanabo A, Nelson MI, Cummings DAT, Bwanika JB, Mueller AC, Reynolds SJ, Munshaw S, Ray SC, Lutalo T, Manucci J, Tobian AAR, Chang LW, Beyrer C, Jennings JM, Nalugoda F, Serwadda D, Wawer MJ, Quinn TC, Gray RH. The role of viral introductions in sustaining community-based HIV epidemics in rural Uganda: evidence from spatial clustering, phylogenetiics, and egocentric transmission models. PLoS Med. 2014;11(3): e1001610. PMID: 24595023
  • Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
  • NIH/NIAID, Bethesda, MD
  • Rakai Health Sciences Program, Kalisizo, Uganda
  • NIH/Fogarty International Center, Bethesda, MD
  • Makerere University, Kampala, Uganda