Abstract
Despite increasing access to antiretrovirals, HIV incidence in rural KwaZulu-Natal remains among the highest ever reported in Africa. While many epidemiological factors have been invoked to explain such high incidence, widespread human mobility and viral movement suggest that transmission between communities may be a major source of new infections. High cross-community transmission rates call into question how effective increasing the coverage of antiretroviral therapy locally will be at preventing new infections, especially if many new cases arise from external introductions. To help address this question, we use a phylodynamic model to reconstruct epidemic dynamics and estimate the relative contribution of local transmission versus external introductions to overall incidence in KwaZulu-Natal from HIV-1 phylogenies. By comparing our results with population-based surveillance data, we show that we can reliably estimate incidence from viral phylogenies once viral movement in and out of the local population is accounted for. Our analysis reveals that early epidemic dynamics were largely driven by external introductions. More recently, we estimate that 35 per cent (95% confidence interval: 20–60%) of new infections arise from external introductions. These results highlight the growing need to consider larger-scale regional transmission dynamics when designing and testing prevention strategies.
Highlights
While the HIV epidemic hit South Africa relatively late compared with other southern African nations, the epidemic grew explosively in the 1990s from an estimated 0.8 per cent prevalence in 1990 to over 20 per cent in 2000 (UNAIDS 2017)
To help situate the local epidemic in the Africa Health Research Institute (AHRI) study population within the larger context of the southern African HIV epidemic, an Maximum likelihood (ML) phylogeny was reconstructed from HIV-1 subtype C sequences sampled from 1,068 infected individuals in the AHRI population along with 11,289 sequences from a larger regional background dataset (Wilkinson et al 2016) sampled throughout southern Africa (Fig. 2A)
There are some larger clades composed predominantly of local viral samples which likely represent locally evolving sub-epidemics, the majority of samples from the AHRI are interspersed throughout clades composed predominantly of external samples, suggesting that many independent introduction events have occurred into the local population from elsewhere in South Africa or from other neighboring countries
Summary
While the HIV epidemic hit South Africa relatively late compared with other southern African nations, the epidemic grew explosively in the 1990s from an estimated 0.8 per cent prevalence in 1990 to over 20 per cent in 2000 (UNAIDS 2017). Many factors have been implicated in the explosive growth of the HIV epidemic in southern Africa and KZN in particular, but patterns of human movement in the region have long received special attention (Jochelson et al 1991; Quinn 1994; Lurie et al 1997). Beyond seeding local epidemics, increasing mobility and migrant labor may have played a larger role by placing individuals at an increased risk of infection (Lurie et al 2003; Welz et al 2007; Camlin et al 2010), possibly due to migrants engaging in riskier sexual behavior outside of their home communities (Coffee et al 2007)
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