Publications

Scientific reports. 2020-02-21; 10.1: 3180.

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

Ajogbasile FV, Oguzie JU, Oluniyi PE, Eromon PE, Uwanibe JN, Mehta SB, Siddle KJ, Odia I, Winnicki SM, Akpede N, Akpede G, Okogbenin S, Ogbaini-Emovon E, MacInnis BL, Folarin OA, Modjarrad K, Schaffner SF, Tomori O, Ihekweazu C, Sabeti PC, Happi CT

PMID: 32081931

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.

This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project.

Metrics