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

Abstract

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.

Keywords: Acute febrile illness; Amplicon sequencing; Flavivirus; Orthoflavivirus; PCR; West Nile virus.

Figure 1

Molecular phylogenetic analysis of full-length West Nile Virus (WNV) using the maximum-likelihood method with GTR+F+I+R2 model in IQ-TREE2. Analysis was completed for 211 representative WNV nucleotide sequences principally selected by Mencattelli et al. [11] to represent lineage 2 clade d, with individual clusters highlighted (1-5). Bootstrapping based on 1000 replications is shown next to each branch at a scale of 0.004, with bootstrap values below 70 omitted. Tree is midpoint rooted and silhouettes indicate viral sequence hosts.