{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T08:48:19Z","timestamp":1791967699729,"version":"4.3.4"},"update-to":[{"DOI":"10.12688\/openresafrica.13406.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000}}],"reference-count":52,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["openresearchafrica.org"],"crossmark-restriction":false},"short-container-title":["Open Res Africa"],"abstract":"<ns5:p>\n                    The clinical importance of non-malaria febrile acute illness (NM-AFI) in patients with a negative parasitological test has become apparent, with the progressive reduction in malaria transmission in endemic regions. Bacterial pathogens, for example\n                    <ns5:italic>Streptococcus pneumoniae<\/ns5:italic>\n                    and\n                    <ns5:italic>Haemophilus influenzae<\/ns5:italic>\n                    , which contribute disproportionally to febrile illness, are now preventable by vaccines. However, there are no vaccines, and little is known about viral NM-AFI prevalence, proliferation, virulence, and transmission chains between hosts. Although the predominant viral causes of NM-AFI are established, it is unclear if there are other NM-AFI associated emerging infectious viral pathogens that previously remained undetectable by conventional diagnostic strategies, for example severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Presumptive broad-spectrum antibiotic prescriptions to aparasitaemic patients not only drive drug resistance, but also lead to poor treatment outcomes. We hypothesized that insights on NM-AFI etiology, and consequently case management, could be improved by exploiting viral sequence diversity to identify viral pathogens present within metagenomics samples. We exploited simulated and existing infectious disease (Ebola, hepatitis C, chikungunya, and mosquito-borne arboviruses) metagenomic datasets to determine the composition of viral pathogens present, by implementing profile Hidden Markov Models derived from Swiss-Prot viral reference sequences for accurate pathogen detection and classification. Our analysis identified a combination of sequences from multiple viral etiological agents within the same disease sample. This approach provides a granular perspective of multiple viral etiological agents present within a single intra-host disease episode. It highlights prevalent viral strains that can subsequently be routinely detected using directed diagnostic tests to improve disease surveillance in endemic regions.\n                  <\/ns5:p>","DOI":"10.12688\/openresafrica.13406.2","type":"journal-article","created":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T08:04:23Z","timestamp":1791965063000},"page":"24","update-policy":"https:\/\/doi.org\/10.12688\/openresafrica.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["NOMAD: metagenomic characterisation of the viral pathogen composition in outbreaks of non-malaria acute febrile illness cases"],"prefix":"10.12688","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6825-1832","authenticated-orcid":false,"given":"Benard W.","family":"Kulohoma","sequence":"first","affiliation":[{"name":"Centre for Biotechnology and Bioinformatics Nairobi University of Nairobi"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ibrahim","family":"Ng'eno","sequence":"additional","affiliation":[{"name":"Nairobi International Centre for Insect Physiology and Ecology"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2025,12,1]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0007792","article-title":"Global knowledge gaps in acute febrile illness etiologic investigations: a scoping review.","volume":"13","author":"C Rhee","year":"2019","journal-title":"PLoS Negl Trop Dis."},{"key":"ref-2","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-019-4185-y","article-title":"Diversity of infectious aetiologies of acute undifferentiated febrile illnesses in south and Southeast Asia: a systematic review.","volume":"19","author":"K Wangdi","year":"2019","journal-title":"BMC Infect 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openresafrica.14554.r30054, Sophana Chea, International Center of Excellence in Research, National Institutes of Health, Phnom Penh, 11 Aug 2023, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/openresearchafrica.org\/articles\/5-24\/v1#referee-response-30054","order":0,"name":"referee-response-30054","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openresafrica.17523.r33186, Gerald Mboowa, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 27 Dec 2025, version 2, indexed","URL":"https:\/\/openresearchafrica.org\/articles\/5-24\/v2#referee-response-33186","order":1,"name":"referee-response-33186","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"BK received a GeMVi Research Fellowship. This work was supported by the National Institute for Health Research (NIHR) (project references 17\/63\/82) using UK aid from the UK Government to support global health research. The views expressed in this publication are those of the author (s) and do not necessarily reflect those of the UK government\u2019s official policies. BK is an Affiliate Fellow of the African Academy of Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":2,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}