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

Fehintola V. Ajogbasile, Judith U. Oguzie, Paul E. Oluniyi, Philomena E. Eromon, Jessica N. Uwanibe, Samar B. Mehta, Katherine J. Siddle, Ikponmwosa Odia, Sarah M. Winnicki, Nosa Akpede, George Akpede, Sylvanus Okogbenin, Ephraim Ogbaini-Emovon, Bronwyn L. MacInnis, Onikepe A. Folarin, Kayvon Modjarrad, Stephen F. Schaffner, Oyewale Tomori, Chikwe Ihekweazu, Pardis C. SabetiChristian T. Happi

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)3180
Number of pages1
JournalScientific reports
Issue number1
StatePublished - Feb 21 2020
Externally publishedYes

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria'. Together they form a unique fingerprint.

Cite this