Genomic Surveillance of Endemic Human Coronaviruses in Côte d’Ivoire Using Targeted Hybrid-Capture Sequencing

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 Côte d’Ivoire 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 ≤ 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 Côte d’Ivoire and support the feasibility and further targeted integration of targeted hybrid-capture sequencing into routine genomic surveillance of respiratory viruses.