Next-generation sequencing survey of acute febrile illness in Senegal (2020–2022)

Abstract

Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): <i>Borrelia crocidurae</i> (N = 7), West Nile virus (N = 3), <i>Rickettsia felis</i> (N = 2), <i>Bartonella quintana</i> (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to <i>Plasmodium falciparum</i> were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.