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Effective programmatic responses to HIV epidemics require targeting the right people, in the right places, at the right time, in the right ways. We now have proven intervention strategies to prevent HIV acquisition for both concentrated and generalized epidemics. One limitation in achieving effectively targeted interventions is that average national HIV prevalence masks subnational variations. Although most tools currently used to estimate incidence and prevalence do not adequately capture this heterogeneity, new sources of geographical program data are becoming available to supplement traditional surveillance data, including population-based surveys, sentinel surveillance, and case reporting data. This makes it increasingly possible to account for epidemiological heterogeneity when producing HIV epidemic estimates. As it is time-consuming and expensive to collect detailed spatial data, it is important to get maximum benefit from available data.