{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T21:41:51Z","timestamp":1787953311502,"version":"build-2784847793"},"reference-count":37,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T00:00:00Z","timestamp":1721001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Coordination for the Improvement of Higher Education Personnel, Brazil (CAPES)","award":["U01 AI151698"],"award-info":[{"award-number":["U01 AI151698"]}]},{"name":"Coordination for the Improvement of Higher Education Personnel, Brazil (CAPES)","award":["CRP\/20\/03"],"award-info":[{"award-number":["CRP\/20\/03"]}]},{"name":"National Institutes of Health USA","award":["U01 AI151698"],"award-info":[{"award-number":["U01 AI151698"]}]},{"name":"National Institutes of Health USA","award":["CRP\/20\/03"],"award-info":[{"award-number":["CRP\/20\/03"]}]},{"name":"CRP-ICGEB RESEARCH GRANT 2020 Project CRP\/BRA20-03","award":["U01 AI151698"],"award-info":[{"award-number":["U01 AI151698"]}]},{"name":"CRP-ICGEB RESEARCH GRANT 2020 Project CRP\/BRA20-03","award":["CRP\/20\/03"],"award-info":[{"award-number":["CRP\/20\/03"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["U01 AI151698"],"award-info":[{"award-number":["U01 AI151698"]}]},{"name":"PON \u201cRicerca e Innovazione\u201d 2014\u20132020","award":["CRP\/20\/03"],"award-info":[{"award-number":["CRP\/20\/03"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Acute febrile illness (AFI) and severe neurological disorders (SNDs) often present diagnostic challenges due to their potential origins from a wide range of infectious agents. Nanopore metagenomics is emerging as a powerful tool for identifying the microorganisms potentially responsible for these undiagnosed clinical cases. In this study, we aim to shed light on the etiological agents underlying AFI and SND cases that conventional diagnostic methods have not been able to fully elucidate. Our approach involved analyzing samples from fourteen hospitalized patients using a comprehensive nanopore metagenomic approach. This process included RNA extraction and enrichment using the SMART-9N protocol, followed by nanopore sequencing. Subsequent steps involved quality control, host DNA\/cDNA removal, de novo genome assembly, and taxonomic classification. Our findings in AFI cases revealed a spectrum of disease-associated microbes, including Escherichia coli, Streptococcus sp., Human Immunodeficiency Virus 1 (Subtype B), and Human Pegivirus. Similarly, SND cases revealed the presence of pathogens such as Escherichia coli, Clostridium sp., and Dengue virus type 2 (Genotype-II lineage). This study employed a metagenomic analysis method, demonstrating its efficiency and adaptability in pathogen identification. Our investigation successfully identified pathogens likely associated with AFI and SNDs, underscoring the feasibility of retrieving near-complete genomes from RNA viruses. These findings offer promising prospects for advancing our understanding and control of infectious diseases, by facilitating detailed genomic analysis which is critical for developing targeted interventions and therapeutic strategies.<\/jats:p>","DOI":"10.3390\/genes15070922","type":"journal-article","created":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T18:17:32Z","timestamp":1721067452000},"page":"922","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach"],"prefix":"10.3390","volume":"15","author":[{"given":"Keldenn Melo Farias","family":"Moreno","sequence":"first","affiliation":[{"name":"Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virg\u00ednia Antunes","family":"de Andrade","sequence":"additional","affiliation":[{"name":"Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3629-8529","authenticated-orcid":false,"given":"Felipe Campos","family":"de Melo Iani","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory of the State of Minas Gerais, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5521-6448","authenticated-orcid":false,"given":"Vagner","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Department of Exact and Earth Sciences, University of the State of Bahia, Salvador 41150-000, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0830-3909","authenticated-orcid":false,"given":"Maur\u00edcio Teixeira","family":"Lima","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil"},{"name":"Ren\u00e9 Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3210-7342","authenticated-orcid":false,"given":"Emerson","family":"de Castro Barbosa","sequence":"additional","affiliation":[{"name":"Ren\u00e9 Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz Marcelo Ribeiro","family":"Tom\u00e9","sequence":"additional","affiliation":[{"name":"Ren\u00e9 Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nat\u00e1lia Rocha","family":"Guimar\u00e3es","sequence":"additional","affiliation":[{"name":"Ren\u00e9 Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1997-5786","authenticated-orcid":false,"given":"Hegger Machado","family":"Fritsch","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil"},{"name":"Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, University of Tours, 37032 Tours, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1471-0084","authenticated-orcid":false,"given":"Talita","family":"Adelino","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory of the State of Minas Gerais, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana","family":"Oliveira Fereguetti","sequence":"additional","affiliation":[{"name":"Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ma\u00edra Cardoso","family":"Aspahan","sequence":"additional","affiliation":[{"name":"Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tereza","family":"Gamarano Barros","sequence":"additional","affiliation":[{"name":"Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz Carlos Junior","family":"Alcantara","sequence":"additional","affiliation":[{"name":"Ren\u00e9 Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5849-7326","authenticated-orcid":false,"given":"Marta","family":"Giovanetti","sequence":"additional","affiliation":[{"name":"Department of Sciences and Technologies for Sustainable Development and One Health, Universit\u00e0 Campus Bio-Medico di Roma, 00128 Rome, Italy"},{"name":"Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Mbidde, E.K., Lutwama, J.J., Perniciaro, J.L., Nicholson, W.L., Bower, W.A., Bwogi, J., and Blaney, D.D. 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