Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria

Abstract

Fifty patients with unexplained fever and poor outcomes presented at Irrua Specialist Teaching Hospital (ISTH) in Edo State, Nigeria, an area endemic for Lassa fever, between September 2018 - January 2019. After ruling out Lassa fever, plasma samples from these epidemiologically-linked cases were sent to the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria, where we carried out metagenomic sequencing which implicated yellow fever virus (YFV) as the etiology of this outbreak. Twenty-nine of the 50 samples were confirmed positive for YFV by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), 14 of which resulted in genome assembly. Maximum likelihood phylogenetic analysis revealed that these YFV sequences formed a tightly clustered clade more closely related to sequences from Senegal than sequences from earlier Nigerian isolates, suggesting that the YFV clade responsible for this outbreak in Edo State does not descend directly from the Nigerian YFV outbreaks of the last century, but instead reflects a broader diversity and dynamics of YFV in West Africa. Here we demonstrate the power of metagenomic sequencing for identifying ongoing outbreaks and their etiologies and informing real-time public health responses, resulting in accurate and prompt disease management and control.

Figure 1

Maximum likelihood phylogenetic trees for YFV, with bootstrap values shown for major branches. (a) 216 prM/E gene sequences (b) 2018 Nigerian YFV whole genome sequences and the West African whole genome sequences with which they most closely cluster. ID numbers for 2018 Nigerian sequences correspond to those given in Fig. 2; GenBank accession numbers are listed in Supplemental Table 1. Scale bars are in units substitutions per site. Trees were inferred using IQTREE and FigTree was used to view and annotate the trees. Cosmetic adjustments were made in Adobe Illustrator CC.

Figure 2

Virus detection by metagenomic sequencing. Heatmap shows the number of deduplicated read pairs that mapped to the indicated viral RefSeq genome; all viral species where at least one sample produced reads that aligned to a viral RefSeq genome are shown. Detected species were first filtered using Kraken. † samples from which we were subsequently able to assemble YFV genomes.