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

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.

SUBMITTER: Oguzie JU

PROVIDER: S-EPMC10403498 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Oguzie Judith U JU Petros Brittany A BA Oluniyi Paul E PE Mehta Samar B SB Eromon Philomena E PE Nair Parvathy P Adewale-Fasoro Opeoluwa O Ifoga Peace Damilola PD Odia Ikponmwosa I Pastusiak Andrzej A Gbemisola Otitoola Shobi OS Aiyepada John Oke JO Uyigue Eghosasere Anthonia EA Edamhande Akhilomen Patience AP Blessing Osiemi O Airende Michael M Tomkins-Tinch Christopher C Qu James J Stenson Liam L Schaffner Stephen F SF Oyejide Nicholas N Ajayi Nnenna A NA Ojide Kingsley K Ogah Onwe O Abejegah Chukwuyem C Adedosu Nelson N Ayodeji Oluwafemi O Liasu Ahmed A AA Okogbenin Sylvanus S Okokhere Peter O PO Park Daniel J DJ Folarin Onikepe A OA Komolafe Isaac I Ihekweazu Chikwe C Frost Simon D W SDW Jackson Ethan K EK Siddle Katherine J KJ Sabeti Pardis C PC Happi Christian T CT

Nature communications 20230804 1

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 suspect ...[more]

PMID: 37542071

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Dataset Information

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

Publications

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

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