Real-time Metagenomic Analysis of Undiagnosed Fever Cases Unveils a Yellow Fever Outbreak in Edo State, Nigeria
| Autor: | Philomena Eromon, Chikwe Ihekweazu, Oyewale Tomori, Stephen F. Schaffner, Samar B. Mehta, Fehintola V. Ajogbasile, Judith U. Oguzie, Onikepe A. Folarin, Katherine J. Siddle, Ephraim Ogbaini-Emovon, George O. Akpede, Kayvon Modjarrad, Sarah M. Winnicki, Pardis C. Sabeti, Christian T. Happi, Jessica N. Uwanibe, Bronwyn MacInnis, Ikponmwosa Odia, Nosa Akpede, Sylvanus Okogbenin, Paul E. Oluniyi |
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| Rok vydání: | 2020 |
| Předmět: |
Adult
Male 0301 basic medicine medicine.medical_specialty Adolescent Nigeria lcsh:Medicine Biology Undiagnosed Diseases Article Disease Outbreaks Young Adult 03 medical and health sciences 0302 clinical medicine Computer Systems Yellow Fever medicine Humans Child lcsh:Science Lassa fever Clade Phylogeny Likelihood Functions Multidisciplinary Public health Infectious-disease diagnostics lcsh:R Yellow fever Outbreak Middle Aged medicine.disease Unexplained fever Virology 3. Good health 030104 developmental biology Metagenomics Child Preschool Etiology Metagenome Female lcsh:Q Pathogens 030215 immunology |
| Zdroj: | Scientific Reports, Vol 10, Iss 1, Pp 1-6 (2020) Scientific Reports |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-020-59880-w |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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