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Governments are increasingly recognizing the need to focus limited HIV resources on specific geographic areas and specific populations to have a greater impact. Nigeria, with the second largest HIV epidemic in the world, is an important example of where more localized programming has the potential to improve the efficiency of the HIV response.Using Spectrum software we modelled the Nigerian HIV epidemic using two methods: First, we created national HIV estimates using trends in urban and rural areas. Second, we created national HIV estimates using trends from each of the 37 states in Nigeria and aggregated these results. In both instances we used HIV surveillance data from antenatal clinics and household surveys and aggregated the trends to determine the national epidemic.The state models showed divergent trends in the 37 states. Comparing the national results calculated from the two methods resulted in different conclusions. In the aggregated state files, adult HIV incidence in Nigeria was stable between 2005 and 2013 (change of −6%), whereas the urban and rural file suggested incidence was decreasing over the same time (change of −50%). This difference was also reflected in the HIV prevalence trends, although the two methods showed similar trends in AIDS-related mortality. The two models had similar adult HIV prevalence in 2013: 3.0% (2.0–4.5%) in the aggregated state files versus 3.2% (3.0–3.5%) in the urban/rural file.The state-level estimates provide insight into the variations of the HIV epidemic in each state and provide useful information for programme managers. However, the reliability of the results is highly dependent on the amount and quality of data available from each sub-national area.