{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T14:15:47Z","timestamp":1789654547264,"version":"4.0.1"},"reference-count":45,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,3,13]],"date-time":"2025-03-13T00:00:00Z","timestamp":1741824000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Africa Pathogen Genomics Initiative funds","award":["4306-22-EIPHLSSGENOMICS"],"award-info":[{"award-number":["4306-22-EIPHLSSGENOMICS"]}]},{"name":"Africa Pathogen Genomics Initiative funds","award":["CZZ3209"],"award-info":[{"award-number":["CZZ3209"]}]},{"DOI":"10.13039\/501100011061","name":"Agence Fran\u00e7aise de D\u00e9veloppement","doi-asserted-by":"publisher","award":["4306-22-EIPHLSSGENOMICS"],"award-info":[{"award-number":["4306-22-EIPHLSSGENOMICS"]}],"id":[{"id":"10.13039\/501100011061","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011061","name":"Agence Fran\u00e7aise de D\u00e9veloppement","doi-asserted-by":"publisher","award":["CZZ3209"],"award-info":[{"award-number":["CZZ3209"]}],"id":[{"id":"10.13039\/501100011061","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ANRS|Maladies infectieuses \u00e9mergentes in partnership with Institut Pasteur and IRD","award":["4306-22-EIPHLSSGENOMICS"],"award-info":[{"award-number":["4306-22-EIPHLSSGENOMICS"]}]},{"name":"ANRS|Maladies infectieuses \u00e9mergentes in partnership with Institut Pasteur and IRD","award":["CZZ3209"],"award-info":[{"award-number":["CZZ3209"]}]},{"name":"Institut Pasteur de Dakar internal funds","award":["4306-22-EIPHLSSGENOMICS"],"award-info":[{"award-number":["4306-22-EIPHLSSGENOMICS"]}]},{"name":"Institut Pasteur de Dakar internal funds","award":["CZZ3209"],"award-info":[{"award-number":["CZZ3209"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Orthobunyaviruses are a diverse group of segmented RNA viruses with significant but underexplored public and veterinary health implications. This study provides a genomic, phylogenetic, and ecological analysis of neglected Orthobunyaviruses using next-generation sequencing and computational predictions. We identified unique phylogenetic relationships, with Tanga virus forming a distinct lineage linked to zoonotic, human-associated, or non-vertebrate viruses across segments. GC content analysis revealed segment-specific patterns: higher GC content in the S segment suggests genomic stability and immune evasion, while lower GC content in the L segment reflects host-vector adaptation. Phylogenetic ties to well-characterized pathogenic viruses, such as Ilesha virus with Cache Valley virus and Bwamba virus with California encephalitis virus, indicate potential neurotropism. Ingwavuma virus clustered with Oropouche virus, suggesting risks of systemic febrile illnesses. Within the Simbu serogroup, Sango and Sabo viruses show teratogenic risks to livestock. Vector and host predictions implicate rodents, artiodactyls, and primates in Orthobunyavirus transmission, emphasizing complex ecological dynamics and zoonotic potential. These findings advance the understanding of Orthobunyavirus diversity, linking genomic features to pathogenicity and ecological adaptation, while providing a foundation for future surveillance and intervention strategies targeting these neglected viruses.<\/jats:p>","DOI":"10.3390\/v17030406","type":"journal-article","created":{"date-parts":[[2025,3,13]],"date-time":"2025-03-13T04:18:32Z","timestamp":1741839512000},"page":"406","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genomic Insights into Neglected Orthobunyaviruses: Molecular Characterization and Phylogenetic Analysis"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8559-2161","authenticated-orcid":false,"given":"Safi\u00e9tou","family":"Sankhe","sequence":"first","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"},{"name":"Animal Biology Department, Faculty of Sciences and Techniques, Cheikh Anta Diop University of Dakar, Dakar BP 5005, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8584-5592","authenticated-orcid":false,"given":"Idrissa","family":"Dieng","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6489-7244","authenticated-orcid":false,"given":"Mouhamed","family":"Kane","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"},{"name":"Animal Biology Department, Faculty of Sciences and Techniques, Cheikh Anta Diop University of Dakar, Dakar BP 5005, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8584-9972","authenticated-orcid":false,"given":"Amadou","family":"Diallo","sequence":"additional","affiliation":[{"name":"Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ndeye Awa","family":"Ndiaye","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ndeye Marieme","family":"Top","sequence":"additional","affiliation":[{"name":"Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-9911-0176","authenticated-orcid":false,"given":"Moussa","family":"Dia","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ousmane","family":"Faye","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amadou Alpha","family":"Sall","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3478-1322","authenticated-orcid":false,"given":"Oumar","family":"Faye","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pape Mbacke","family":"Sembene","sequence":"additional","affiliation":[{"name":"Animal Biology Department, Faculty of Sciences and Techniques, Cheikh Anta Diop University of Dakar, Dakar BP 5005, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9582-4197","authenticated-orcid":false,"given":"Cheikh","family":"Loucoubar","sequence":"additional","affiliation":[{"name":"Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3207-6344","authenticated-orcid":false,"given":"Martin","family":"Faye","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5461-5623","authenticated-orcid":false,"given":"Moussa Moise","family":"Diagne","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,13]]},"reference":[{"key":"ref_1","unstructured":"(2024, December 09). International Committee on Taxonomy of Viruses ICTV. [En ligne]. Disponible sur. Available online: https:\/\/ictv.global\/taxonomy."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Windhaber, S., Xin, Q., and Lozach, P.Y. (2021). Orthobunyaviruses: From Virus Binding to Penetration into Mammalian Host Cells. Viruses, 13.","DOI":"10.3390\/v13050872"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nrmicro3332","article-title":"Orthobunyaviruses: Recent genetic and structural insights","volume":"12","author":"Elliott","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"5627","DOI":"10.1128\/JVI.02448-05","article-title":"Batai and Ngari viruses: M segment reassortment and association with severe febrile disease outbreaks in East Africa","volume":"80","author":"Briese","year":"2006","journal-title":"J. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Toure, C.T., Dieng, I., Sankhe, S., Kane, M., Dia, M., Mhamadi, M., Ndiaye, M., Faye, O., Sall, A.A., and Diagne, M.M. (2024). Genomic Characterization of a Bata\u00ef Orthobunyavirus, Previously Classified as Ilesha Virus, from Field-Caught Mosquitoes in Senegal, Bandia 1969. Viruses, 16.","DOI":"10.3390\/v16020261"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Sakkas, H., Bozidis, P., Franks, A., and Papadopoulou, C. (2018). Oropouche Fever: A Review. Viruses, 10.","DOI":"10.3390\/v10040175"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.micinf.2017.11.013","article-title":"Oropouche fever, an emergent disease from the Americas","volume":"20","author":"Escobar","year":"2018","journal-title":"Microbes Infect."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"199318","DOI":"10.1016\/j.virusres.2024.199318","article-title":"Oropouche virus: A neglected global arboviral threat","volume":"341","author":"Zhang","year":"2024","journal-title":"Virus Res."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Edridg, A.W.D., and van der Hoek, L. (2020). Emerging orthobunyaviruses associated with CNS disease. PLoS Negl. Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008856"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1743-422X-5-25","article-title":"La Crosse virus infectivity, pathogenesis, and immunogenicity in mice and monkeys","volume":"5","author":"Bennett","year":"2008","journal-title":"Virol. J."},{"key":"ref_11","first-page":"303","article-title":"California encephalitis virus, a newly described agent","volume":"77","author":"Hammon","year":"1952","journal-title":"Calif. Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"8922","DOI":"10.1128\/JVI.78.16.8922-8926.2004","article-title":"Ngari virus is a Bunyamwera virus reassortant that can be associated with large outbreaks of hemorrhagic fever in Africa","volume":"78","author":"Gerrard","year":"2004","journal-title":"J. Virol."},{"key":"ref_13","first-page":"12","article-title":"Ngari virus (Bunyaviridae: Bunyavirus). First isolation from humans in Senegal, new mosquito vectors, its epidemiology","volume":"89","author":"Zeller","year":"1996","journal-title":"Bull. Soc. Pathol. Exot. (1990)"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"183","DOI":"10.4269\/ajtmh.19-0596","article-title":"Identification of Bunyamwera and Possible Other Orthobunyavirus Infections and Disease in Cattle during a Rift Valley Fever Outbreak in Rwanda in 2018","volume":"103","author":"Dutuze","year":"2020","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1111\/zph.12621","article-title":"Cache Valley virus: A scoping review of the global evidence","volume":"66","author":"Waddell","year":"2019","journal-title":"Zoonoses Public Health"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1093\/jme\/tjad058","article-title":"Cache Valley virus: An emerging arbovirus of public and veterinary health importance","volume":"60","author":"Hughes","year":"2023","journal-title":"J. Med. Entomol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/0035-9203(94)90297-6","article-title":"Ilesha virus: A new aetiological agent of haemorrhagic fever in Madagascar","volume":"88","author":"Morvan","year":"1994","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_18","first-page":"88","article-title":"Isolation of 2 human strains of Ilesha virus in the Central African Republic","volume":"14","author":"Chippaux","year":"1969","journal-title":"Bull. Soc. Med. Afr. Noire Lang. Fr."},{"key":"ref_19","first-page":"223","article-title":"Recent data from serological surveys on the prevalence of arbovirus infections in Africa, with special reference to yellow fever","volume":"43","year":"1970","journal-title":"Bull. World Health Organ."},{"key":"ref_20","first-page":"24","article-title":"Isolations of Bwamba virus from south central Uganda and north eastern Tanzania","volume":"2","author":"Lutwama","year":"2002","journal-title":"Afr. Health Sci."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"75","DOI":"10.4269\/ajtmh.1941.s1-21.75","article-title":"Bwamba Fever and Its Causative Virus","volume":"21","author":"Smithburn","year":"1941","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"251","DOI":"10.4269\/ajtmh.1974.23.251","article-title":"Ingwavuma virus in Thailand. Infection of domestic pigs","volume":"23","author":"Top","year":"1974","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/s13337-023-00808-z","article-title":"Vector competence of three species of mosquitoes to Ingwavuma virus (Manzanilla orthobunyavirus), a new bunyavirus found circulating in India","volume":"34","author":"Kumar","year":"2023","journal-title":"Virusdisease"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Oluwayelu, D., Wernike, K., Adebiyi, A., Cadmus, S., and Beer, M. (2018). Neutralizing antibodies against Simbu serogroup viruses in cattle and sheep, Nigeria, 2012\u20132014. BMC Vet. Res., 14.","DOI":"10.1186\/s12917-018-1605-y"},{"key":"ref_25","first-page":"69","article-title":"Isolation of Sango viruses from Israeli symptomatic cattle","volume":"7","author":"Golender","year":"2021","journal-title":"Int. J. Vet. Sci. Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1080\/00034983.1972.11686835","article-title":"Isolations of Simbu-group viruses in Ibadan, Nigeria 1964\u201369, including the new types Sango, Shamonda, Sabo and Shuni","volume":"66","author":"Causey","year":"1972","journal-title":"Ann. Trop. Med. Parasitol."},{"key":"ref_27","first-page":"512","article-title":"The M\u2019Poko virus (BA 365), new prototype of arbovirus isolated in the Centrafrican Republic","volume":"119","author":"Digoutte","year":"1970","journal-title":"Ann. Inst. Pasteur"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"223","DOI":"10.4269\/ajtmh.1961.10.223","article-title":"Immunological studies relating two recently isolated viruses, Germiston virus from South Africa and Ilesha virus from West Africa, to the Bunyamwera group","volume":"10","author":"Okuno","year":"1961","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"ofab655","DOI":"10.1093\/ofid\/ofab655","article-title":"Detection of Rift Valley Fever Virus Lineage H From South Africa Through the Syndromic Sentinel Surveillance Network in Senegal","volume":"9","author":"Bob","year":"2022","journal-title":"Open Forum Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinforma. Oxf. Engl."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/s12985-024-02426-7","article-title":"An amplicon-based sequencing approach for Usutu virus characterization","volume":"21","author":"Ndione","year":"2024","journal-title":"Virol. J."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol. J. Comput. Mol. Cell Biol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Grubaugh, N.D., Gangavarapu, K., Quick, J., Matteson, N.L., De Jesus, J.G., Main, B.J., Tan, A.L., Paul, L.M., Brackney, D.E., and Grewal, S. (2019). An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. Genome Biol., 20.","DOI":"10.1186\/s13059-018-1618-7"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_36","unstructured":"(2024, December 09). Molecular Evolution, Phylogenetics and Epidemiology. Consult\u00e9 le: 5 Janvier 2025. [En Ligne]. Disponible sur. Available online: http:\/\/tree.bio.ed.ac.uk\/."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1126\/science.aap9072","article-title":"Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes","volume":"362","author":"Babayan","year":"2018","journal-title":"Science"},{"key":"ref_38","unstructured":"(2024, December 09). Viral Host Predictor Website. Consult\u00e9 le: 9 Octobre 2024. [En ligne]. Disponible sur. Available online: http:\/\/host-predict.cvr.gla.ac.uk\/."},{"key":"ref_39","unstructured":"(2024, December 09). R: The R Project for Statistical Computing. Consult\u00e9 le: 3 Janvier 2025. [En Ligne]. Disponible sur. Available online: https:\/\/www.r-project.org\/."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). Data Analysis. ggplot2: Elegant Graphics for Data Analysis, Springer International Publishing.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"giac079","DOI":"10.1093\/gigascience\/giac079","article-title":"The complexity landscape of viral genomes","volume":"11","author":"Silva","year":"2022","journal-title":"GigaScience"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1128\/JVI.72.2.1122-1130.1998","article-title":"Silencing homologous RNA recombination hot spots with GC-rich sequences in brome mosaic virus","volume":"72","author":"Nagy","year":"1998","journal-title":"J. Virol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"451","DOI":"10.3201\/eid0703.010316","article-title":"The first reported case of California encephalitis in more than 50 years","volume":"7","author":"Eldridge","year":"2001","journal-title":"Emerg. Infect. Dis."},{"key":"ref_44","first-page":"119","article-title":"Serological and clinical evidence of a teratogenic Simbu serogroup virus infection of cattle in Israel, 2001\u20132003","volume":"40","author":"Brenner","year":"2004","journal-title":"Vet. Ital."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Kapuscinski, M.L., Bergren, N.A., Russell, B.J., Lee, J.S., Borland, E.M., Hartman, D.A., King, D.C., Hughes, H.R., Burkhalter, K.L., and Kading, R.C. (2021). Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses. PLoS Pathog., 17.","DOI":"10.1371\/journal.ppat.1009315"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/3\/406\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:52:45Z","timestamp":1760028765000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/3\/406"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,13]]},"references-count":45,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["v17030406"],"URL":"https:\/\/doi.org\/10.3390\/v17030406","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3,13]]}}}