{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:17:06Z","timestamp":1785417426482,"version":"3.56.0"},"reference-count":54,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T00:00:00Z","timestamp":1781654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-018278"],"award-info":[{"award-number":["INV-018278"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-036413"],"award-info":[{"award-number":["INV-036413"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-036379"],"award-info":[{"award-number":["INV-036379"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-018978"],"award-info":[{"award-number":["INV-018978"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"award":["INV-018278"],"award-info":[{"award-number":["INV-018278"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["INV-036413"],"award-info":[{"award-number":["INV-036413"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["INV-036379"],"award-info":[{"award-number":["INV-036379"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"publisher"}]},{"award":["INV-018978"],"award-info":[{"award-number":["INV-018978"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Pasteur Institute of C\u00f4te d\u2019Ivoire internal funds"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Endemic human coronaviruses (HCoVs) are important contributors to respiratory infections, yet genomic data from sub-Saharan Africa remain limited. We analyzed 13,530 nasopharyngeal samples collected through the national influenza sentinel surveillance network in C\u00f4te d\u2019Ivoire between 2022 and 2024 to characterize the circulation and genomic diversity of endemic HCoVs. A subset of 52 RT-qPCR-positive samples with Ct values \u2264 28 was selected for targeted hybrid-capture sequencing using the Twist Bioscience Respiratory Virus Research Panel. Genome recovery metrics were available for 28 samples, including HCoV-NL63 (n = 9), HCoV-229E (n = 8), HCoV-OC43 (n = 9), and HCoV-HKU1 (n = 2). Endemic HCoVs circulated throughout the study period, with temporal variation across species and increased detections during several rainy-season months. No co-presence of multiple endemic HCoV species was identified in the final analytical dataset. Genome recovery differed by species, with broader and more consistent coverage for HCoV-OC43 and HCoV-NL63 than for HCoV-229E and HCoV-HKU1. Phylogenetic analysis showed that all recovered HCoV-229E genomes clustered within genotype L6 and all recovered HCoV-HKU1 genomes within genotype A, whereas HCoV-OC43 and HCoV-NL63 were distributed across multiple genotypes among recovered genomes. To our knowledge, these findings provide the first genomic data on endemic HCoVs from C\u00f4te d\u2019Ivoire and support the feasibility and further targeted integration of targeted hybrid-capture sequencing into routine genomic surveillance of respiratory viruses.<\/jats:p>","DOI":"10.3390\/v18060678","type":"journal-article","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:49:42Z","timestamp":1781743782000},"page":"678","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Surveillance of Endemic Human Coronaviruses in C\u00f4te d\u2019Ivoire Using Targeted Hybrid-Capture Sequencing"],"prefix":"10.3390","volume":"18","author":[{"given":"Ange-Mich\u00e8le","family":"M\u2019bra","sequence":"first","affiliation":[{"name":"Department of Epidemic Viruses, Pasteur Institute of C\u00f4te d\u2019Ivoire, Abidjan 01 BP 490, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syndou","family":"Meite","sequence":"additional","affiliation":[{"name":"Molecular Biology Platform, Pasteur Institute of C\u00f4te d\u2019Ivoire, Abidjan 01 BP 490, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herve A.","family":"Kadjo","sequence":"additional","affiliation":[{"name":"Department of Epidemic Viruses, Pasteur Institute of C\u00f4te d\u2019Ivoire, Abidjan 01 BP 490, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luc Venance","family":"Kouakou","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Genetics, Peleforo Gon Coulibaly University, Korhogo BP 1328, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9354-8689","authenticated-orcid":false,"given":"Yakoura","family":"Ouattara","sequence":"additional","affiliation":[{"name":"Department of Epidemic Viruses, Pasteur Institute of C\u00f4te d\u2019Ivoire, Abidjan 01 BP 490, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mouhamed","family":"Kane","sequence":"additional","affiliation":[{"name":"Virology Department, Institut Pasteur de Dakar, 36 Avenue Pasteur, Dakar BP 220, Senegal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helene A.","family":"Kouassi","sequence":"additional","affiliation":[{"name":"Department of Epidemic Viruses, Pasteur Institute of C\u00f4te d\u2019Ivoire, Abidjan 01 BP 490, C\u00f4te d\u2019Ivoire"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ndeye Awa","family":"Ndiaye","sequence":"additional","affiliation":[{"name":"Virology 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