Respiratory Pathogen Detection Among Febrile Inpatients in Northern Tanzania, 2016-2019.

Background: Febrile illness is a common reason for hospital admission in sub-Saharan Africa, yet the illness etiology often remains unknown. To address these knowledge gaps, we conducted respiratory pathogen testing in a cohort of febrile inpatients in northern Tanzania. Methods: We enrolled a prospective cohort of febrile pediatric and adult inpatients within 24 hours after admission to 2 hospitals in northern Tanzania. Nasopharyngeal/oropharyngeal specimens were collected for detection of 19 pathogens with polymerase chain reaction. Participants were stratified by age (<10 or and ≥10 years) and categorized into the following 3 groups: severe acute respiratory infection (SARI), non-SARI respiratory illness, or no respiratory illness. Results: Among the 1132 participants enrolled, 930 (82.1%) had nasopharyngeal/oropharyngeal specimens tested. Their median (interquartile range) age was 22.3 (2.1-44.0) years, 432 (46.5%) were female, and 378 (40.7%) had SARIs. We observed 410 pathogen detections in 359 participants (38.6%), in 256 (67.2%) of 381 in the <10-year age group and 103 (18.8%) of 549 in the older group (≥10 years old). Of the 301 pathogen detections among participants <10 years old, the most common were rhinovirus (RV)/enterovirus (EV) (n = 80 [26.6%]), influenza (n = 60 [19.9%]) and adenovirus (n = 45 [15.0%]). Of the 109 pathogen detections in participants ≥10 years old, the most common were RV/EV (n = 41 [37.6%]), influenza (n = 37 [33.9%]), and respiratory syncytial virus (RSV) (n = 6 [5.5%]). Among SARIs, the most common pathogens were influenza (n = 71 [18.8%]), RV/EV (n = 66 [17.5%]), and RSV (n = 37 [9.8%]). Conclusions: RV/EV, influenza and RSV were commonly detected among febrile inpatients in Tanzania, including in participants with SARIs. These findings have implications for vaccine development and implementation in low- and middle-income countries.