Genomic surveillance of SARS-CoV-2 in Cote d’Ivoire, 2024 - 2025; diversification of JN.1 derived lineages and detection of the recombinant XFJ.1

Abstract Although the COVID-19 public health emergency ended in 2023, SARS-CoV-2 continues to circulate and diversify. Genomic surveillance therefore remains essential, particularly in regions underrepresented in global databases. We characterized the SARS-CoV-2 lineages circulating in Côte d’Ivoire in 2024-2025. Nasopharyngeal samples were collected from patients with influenza-like illness or severe acute respiratory infection within the national sentinel surveillance network. SARS-CoV-2 RNA was detected by multiplex real-time RT-qPCR, and specimens with a cycle threshold ≤ 30 underwent targeted sequencing of the Spike (S) gene on the Oxford Nanopore platform. Consensus sequences were assigned to Nextstrain clades with Nextclade. Of 9,622 specimens tested, 207 were positive (2.1% in 2024; 2.2% in 2025), and 158 yielded high-quality S-gene sequences. All belonged to BA.2.86/JN.1 descendants. Clade 24A predominated in 2024 (70.4%) and was replaced in 2025 by clades 24H (44.2%) and 25H (23.4%). The recombinant XFJ.1 became the most frequent lineage in 2025 (23.4%). Lineage diversity was highest in 2025 and lowest in 2024. These results show a continued diversification of JN.1-derived lineages and support sustained, geographically expanded genomic surveillance in West Africa. Keywords: SARS-CoV-2, genomic surveillance, JN.1, recombinant XFJ.1, Côte d’Ivoire