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

• Published in: IJID regions Vol. 13; p. 100462
• Main Authors: Byaruhanga, Timothy, Astbury, Stuart, Hill, Jack D., Tsoleridis, Theocharis, Chappell, Joseph G., Kayiwa, John T., Ataliba, Irene J., Nankya, Annet M., Ball, Jonathan K., Lutwama, Julius J., McClure, C. Patrick
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.12.2024; Elsevier
• Subjects: Acute febrile illness; Amplicon sequencing; Case Report; Flavivirus; Orthoflavivirus; PCR; West Nile virus; Orthoflavivirus; Acute febrile illness; Flavivirus; West Nile virus; Amplicon sequencing; PCR
• ISSN: 2772-7076; 2772-7076
• DOI: 10.1016/j.ijregi.2024.100462

•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.