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

Author

Listed:
  • Judith U. Oguzie

    (Redeemer’s University
    Redeemer’s University)

  • Brittany A. Petros

    (Broad Institute of Harvard and MIT
    Harvard-MIT Program in Health Sciences and Technology
    Harvard/MIT MD-PhD Program
    Harvard Medical School)

  • Paul E. Oluniyi

    (Redeemer’s University
    Redeemer’s University
    Chan Zuckerberg Biohub)

  • Samar B. Mehta

    (University of Maryland Medical Center)

  • Philomena E. Eromon

    (Redeemer’s University)

  • Parvathy Nair

    (Howard Hughes Medical Institute)

  • Opeoluwa Adewale-Fasoro

    (Redeemer’s University
    Redeemer’s University)

  • Peace Damilola Ifoga

    (Redeemer’s University
    Redeemer’s University)

  • Ikponmwosa Odia

    (Irrua Specialist Teaching Hospital)

  • Andrzej Pastusiak

    (Microsoft Premonition)

  • Otitoola Shobi Gbemisola

    (Redeemer’s University)

  • John Oke Aiyepada

    (Irrua Specialist Teaching Hospital)

  • Eghosasere Anthonia Uyigue

    (Irrua Specialist Teaching Hospital)

  • Akhilomen Patience Edamhande

    (Irrua Specialist Teaching Hospital)

  • Osiemi Blessing

    (Irrua Specialist Teaching Hospital)

  • Michael Airende

    (Irrua Specialist Teaching Hospital)

  • Christopher Tomkins-Tinch

    (Broad Institute of Harvard and MIT
    Harvard University)

  • James Qu

    (Broad Institute of Harvard and MIT)

  • Liam Stenson

    (Broad Institute of Harvard and MIT)

  • Stephen F. Schaffner

    (Broad Institute of Harvard and MIT)

  • Nicholas Oyejide

    (Redeemer’s University)

  • Nnenna A. Ajayi

    (Alex Ekwueme Federal University Teaching Hospital)

  • Kingsley Ojide

    (Alex Ekwueme Federal University Teaching Hospital)

  • Onwe Ogah

    (Alex Ekwueme Federal University Teaching Hospital)

  • Chukwuyem Abejegah

    (Federal Medical Center)

  • Nelson Adedosu

    (Federal Medical Center)

  • Oluwafemi Ayodeji

    (Federal Medical Center)

  • Ahmed A. Liasu

    (Federal Medical Center)

  • Sylvanus Okogbenin

    (Irrua Specialist Teaching Hospital)

  • Peter O. Okokhere

    (Irrua Specialist Teaching Hospital)

  • Daniel J. Park

    (Broad Institute of Harvard and MIT)

  • Onikepe A. Folarin

    (Redeemer’s University
    Redeemer’s University)

  • Isaac Komolafe

    (Redeemer’s University
    Redeemer’s University)

  • Chikwe Ihekweazu

    (Nigeria Center for Disease Control)

  • Simon D. W. Frost

    (Microsoft Premonition
    London School of Hygiene and Tropical Medicine)

  • Ethan K. Jackson

    (Microsoft Premonition)

  • Katherine J. Siddle

    (Broad Institute of Harvard and MIT
    Brown University)

  • Pardis C. Sabeti

    (Broad Institute of Harvard and MIT
    Howard Hughes Medical Institute
    Harvard University
    Harvard T.H. Chan School of Public Health, Harvard University)

  • Christian T. Happi

    (Redeemer’s University
    Redeemer’s University
    Irrua Specialist Teaching Hospital
    Harvard T.H. Chan School of Public Health, Harvard University)

Abstract

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.

Suggested Citation

  • 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 & , 2023. "Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40247-4
    DOI: 10.1038/s41467-023-40247-4
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    Cited by:

    1. Zoë C. Levine & Aita Sene & Winnie Mkandawire & Awa B. Deme & Tolla Ndiaye & Mouhamad Sy & Amy Gaye & Younouss Diedhiou & Amadou M. Mbaye & Ibrahima M. Ndiaye & Jules Gomis & Médoune Ndiop & Doudou Se, 2024. "Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

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