Background: Against a background of security challenges, Nigeria conducted recently the largest population-based HIV survey in the world to ascertain the burden of the HIV disease in the country. We evaluated the main outcomes of the survey and the level of success using participation/response indicators. Methods: The survey was conducted from July 2018 to December 2018 by over 6,000 field staff across Nigeria in six consecutive webs, using two-stage cluster sampling. This analysis was restricted to adults (15-64 years old) from randomly selected households. We estimated the prevalence of HIV, hepatitis B and hepatitis C in the entire country and by conflict zone status. Adjusted odds ratios (OR) and 95% confidence intervals (CI) from survey logistic regression models were used to compare the likelihood of test positivity for the three infections between zones. Findings: A total of 186,405 adults were interviewed from 97,250 households in 3,848 census enumeration areas. Although household response rate was lower in conflict compared to non-conflict areas (68·76% versus 89·83%; p < 0·01), rates of interview response (92·43% versus 91·61%) and blood draw acceptance (94·71% versus 92·91%) were higher in conflict zones. The overall HIV, hepatitis B and hepatitis C positivity rates were 1·55%, 7·63% and 1·73%, respectively. The prevalence of HIV, hepatitis B and C infection was significantly greater in conflict than non-conflict zones (HIV: 1·75% versus 1·0%; hepatitis B: 9·9% versus 7·3%; and hepatitis C: 3·2% versus 0·3%; p < 0·01 in all cases). Individuals living in conflict zones were about three times as likely to test positive for HIV (OR = 2·80, 95% CI = 2·08,3·60) and nearly six times as likely to test positive for hepatitis C (OR = 5·90, 95% CI = 2·17,16·67). Interpretation: Large population-based surveys are feasible, even in armed conflict settings. The burden of HIV, hepatitis B and hepatitis C was significantly higher in areas of conflict in Nigeria, highlighting the need for reinforced public health control measures in these settings in order to attain UNAIDS’ 95-95-95 targets of controlling the HIV epidemic in sub-Saharan Africa by 2030. Funding Statement: President’s Emergency Plan for AIDS Relief (PEPFAR), The US Centers for Disease Control and Prevention, The Global Fund. Declaration of Interests: All authors attest that there is no conflict of interest to be declared Ethics Approval Statement: The protocol for the survey was approved by the Nigeria National Health Research Ethics Committee (NHREC) and the Institutional Review Boards at the CDC and the University of Maryland.
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