Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria

Judith U. Oguzie, Brittany A. Petros, Paul E. Oluniyi, Samar B. Mehta, Philomena E. Eromon, Parvathy Nair, Opeoluwa Adewale-Fasoro, Peace Damilola Ifoga, Ikponmwosa Odia, Andrzej Pastusiak, Otitoola Shobi Gbemisola, John Oke Aiyepada, Eghosasere Anthonia Uyigue, Akhilomen Patience Edamhande, Osiemi Blessing, Michael Airende, Christopher Tomkins-Tinch, James Qu, Liam Stenson, Stephen F. SchaffnerNicholas Oyejide, Nnenna A. Ajayi, Kingsley Ojide, Onwe Ogah, Chukwuyem Abejegah, Nelson Adedosu, Oluwafemi Ayodeji, Ahmed A. Liasu, Sylvanus Okogbenin, Peter O. Okokhere, Daniel J. Park, Onikepe A. Folarin, Isaac Komolafe, Chikwe Ihekweazu, Simon D.W. Frost, Ethan K. Jackson, Katherine J. Siddle, Pardis C. Sabeti, Christian T. Happi

Research output: Contribution to journalArticlepeer-review


Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.

Original languageEnglish (US)
Article number4693
JournalNature communications
Issue number1
StatePublished - Dec 2023
Externally publishedYes

ASJC Scopus subject areas

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy


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