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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.
Afiliación
  • Oguzie JU; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
  • Petros BA; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Oluniyi PE; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Mehta SB; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, 02139, USA.
  • Eromon PE; Harvard/MIT MD-PhD Program, Boston, MA, 02115, USA.
  • Nair P; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
  • Adewale-Fasoro O; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
  • Ifoga PD; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Odia I; Chan Zuckerberg Biohub, San Francisco, CA, USA.
  • Pastusiak A; Department of Medicine, University of Maryland Medical Center, Baltimore, MA, USA.
  • Gbemisola OS; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Aiyepada JO; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
  • Uyigue EA; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
  • Edamhande AP; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Blessing O; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
  • Airende M; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Tomkins-Tinch C; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Qu J; Microsoft Premonition, Redmond, WA, USA.
  • Stenson L; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Schaffner SF; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Oyejide N; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Ajayi NA; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Ojide K; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Ogah O; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Abejegah C; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Adedosu N; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
  • Ayodeji O; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Liasu AA; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Okogbenin S; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Okokhere PO; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
  • Park DJ; Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.
  • Folarin OA; Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.
  • Komolafe I; Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria.
  • Ihekweazu C; Federal Medical Center, Owo, Ondo State, Nigeria.
  • Frost SDW; Federal Medical Center, Owo, Ondo State, Nigeria.
  • Jackson EK; Federal Medical Center, Owo, Ondo State, Nigeria.
  • Siddle KJ; Federal Medical Center, Owo, Ondo State, Nigeria.
  • Sabeti PC; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
  • Happi CT; Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
Nat Commun ; 14(1): 4693, 2023 08 04.
Article en En | MEDLINE | ID: mdl-37542071
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Virus / Fiebre de Lassa Tipo de estudio: Diagnostic_studies / Incidence_studies / Prognostic_studies / Screening_studies Límite: Humans País/Región como asunto: Africa Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2023 Tipo del documento: Article País de afiliación: Nigeria Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Virus / Fiebre de Lassa Tipo de estudio: Diagnostic_studies / Incidence_studies / Prognostic_studies / Screening_studies Límite: Humans País/Región como asunto: Africa Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2023 Tipo del documento: Article País de afiliación: Nigeria Pais de publicación: Reino Unido