Prospective surveillance of acute febrile illness in two tertiary health facilities in Nigeria, March 2021-September 2022

Background: Most infectious diseases present as acute febrile illness (AFI). Diagnostic gaps in most resource-constrained countries contribute to disproportionate disease burden, antimicrobial misuse, and poor epidemic preparedness. Understanding the etiology and epidemiology of AFI improves early warning systems for epidemic-prone pathogens and supports routine updates of the priority pathogen list. We describe the results of sentinel AFI surveillance in Nigeria. Methods: Hospital-based sentinel surveillance was implemented at Asokoro District Hospital, Abuja, and Nnamdi Azikiwe University Teaching Hospital, Anambra, from 29 March 2021 to 29 September 2022. Blood specimens from patients ≥2 years old with a temperature≥37.5°C or self-reported fever for 2-7 days of unknown etiology were tested using AFI TaqMan® Array Card (TAC) assays to detect 36 pathogens. Results: In this exploratory phase, only 393 of 2,155 specimens were tested due to limited funding and high TAC cost. The majority (62%) of participants tested were adults (246/393), and 52% were female (205/393). The top ten ranked pathogens of the 32 identified were West Nile virus (39%), Zika virus (17%), SARS-CoV-2 (16%), adenovirus (16%), Brucella (8%), Chikungunya virus (7%), Burkholderia (6%), Plasmodium vivax (6%), Plasmodium falciparum (6%), and Crimean Congo Hemorrhagic Fever virus (4%). Coinfections were detected in 45% (178/393) of patients; 24% (94/393) had two pathogens, 21% (84/393) had three or more, and one patient had eight. Conclusion: This pilot study of AFI etiologies in Nigeria suggests emerging and re-emerging viruses are more common than malaria parasites. Co-infection in nearly half of cases warrants further investigation and supports investment in multiplex testing to address diagnostic gaps. The utility of TAC for exploratory studies in low-income settings may be limited by its prohibitive cost. These findings emphasize the need for continued investment in cost-effective diagnostic technologies and enhanced multi-pathogen surveillance systems, essential to early detection and response to epidemic-prone infections.