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

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

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. Schaffner, Nicholas 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 () and Christian T. Happi ()
Additional contact information
Judith U. Oguzie: Redeemer’s University
Brittany A. Petros: Broad Institute of Harvard and MIT
Paul E. Oluniyi: Redeemer’s University
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
Peace Damilola Ifoga: 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
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
Isaac Komolafe: Redeemer’s University
Chikwe Ihekweazu: Nigeria Center for Disease Control
Simon D. W. Frost: Microsoft Premonition
Ethan K. Jackson: Microsoft Premonition
Katherine J. Siddle: Broad Institute of Harvard and MIT
Pardis C. Sabeti: Broad Institute of Harvard and MIT
Christian T. Happi: Redeemer’s University

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-40247-4

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