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Background  Assessing patterns and trends in new infections is key to better understanding of HIV epidemics, and is best done through monitoring changes in incidence over time. In this study, we examined disparities in geographical trends of HIV epidemics among people who inject drugs (PWIDs), female sex workers (FSWs) and  hijra /transgender/male sex workers (H/MSWs), in Pakistan.    Methods  The UNAIDS Estimation and Projection Package (EPP) mathematical model was used to explore geographical trends in HIV epidemics. Four rounds of mapping and surveillance data collected among key populations (KPs) across 20 cities in Pakistan between 2005-2011 was used for modeling. Empirical estimates of HIV prevalence of each KP in each city were used to fit the model to estimate prevalence and incidence over time.    Results  HIV incidence among PWIDs in Pakistan reached its peak in 2011, estimated at 45.3 per 1000 person-years. Incidence was projected to continue to rise from 18.9 in 2015 to 24.3 in 2020 among H/MSWs and from 3.2 in 2015 to 6.3 in 2020 among FSWs. The number of people living with HIV in Pakistan was estimated to steadily increase through at least 2020. HIV incidence peak among PWIDs ranged from 16.2 in 1997 in Quetta to 71.0 in 2010 in Faisalabad (per 1000 person-years). Incidence among H/MSWs may continue to rise through 2020 in all the cities, except in Larkana where it peaked in the early 2000s. In 2015, model estimated incidence among FSWs was 8.1 in Karachi, 6.6 in Larkana, 2.0 in Sukkur and 1.2 in Lahore (per 1000 person-years).    Conclusions  There exists significant geographical heterogeneity in patterns and trends of HIV sub-epidemics in Pakistan. Focused interventions and service delivery approaches, different by KP and city, are recommended.

Heterogeneity in geographical trends of HIV epidemics among key populations in Pakistan: a mathematical modeling study of survey data