Undiagnosed West Nile virus lineage 2d infection in a febrile patient from South-west Uganda, 2018

This is the authors' abstract. We don't add key points for this paper.

• The first West Nile virus genome from a human infection since 1937 was discovered in Uganda. • Pan-genus polymerase chain reaction screening retrospectively detected the West Nile virus genome in immunoglobulin M-negative serum. • A novel 1200bp amplicon whole-genome sequencing scheme is presented. • Lineage 2d genome is closely related to the contemporary local vector-derived sequence. • Rural adult case with fever, headache, rash, vomiting, nausea, fatigue, and joint pain. We report the retrospective identification and subsequent recovery of a near-complete West Nile Virus lineage 2 genomes from a hospitalized patient with acute febrile illness in Uganda, using a combination of degenerate primer polymerase chain reaction screening and a novel 1200bp nanopore-based whole-genome amplicon sequencing scheme. This represents the first West Nile virus genome to be recovered from a human in Uganda since its discovery in 1937. Basic molecular rather than serological surveillance methods could be more widely deployed in the region to better diagnose febrile infections.