Strengthening Respiratory Virus Surveillance in Sub-Saharan Africa: Integrated Epidemiological and Genomic Monitoring...

Following WHO recommendations issued in 2019 and 2022, the National Influenza Center (NIC) of Côte d'Ivoire initiated the integration of Respiratory Syncytial Virus (RSV) and SARS-CoV-2 surveillance into its existing sentinel influenza surveillance to strengthen the monitoring of respiratory viruses.

The national influenza sentinel surveillance protocol was revised to include specific requirement of RSV and SARS-CoV-2. Nasopharyngeal swabs were collected between January 2022 and December 2023 for all three viruses and were tested by real time RT-PCR. Only PCR-positive samples with Ct value < 28 and adequate sample volume were selected for sequencing. CDC Flu SC2 multiplex rRT-PCR assay and Oxford Nanopore MinION Mk1C were used; influenza sequencing was performed at CDC Atlanta. Phylogenetic analyses were conducted to identify genotypes, lineages, and assess genetic relatedness to global strains.

Between January 2022 and December 2023, 8316 samples were tested; 12.6% (n = 1044) were positive for at least one of the three viruses. RSV (5.63%) detection in severe acute respiratory infection (SARI) cases increased significantly from 3.4% in 2022 to 8.4% in 2023 (p < 0.0001). Similarly, influenza (3.71%) detection in SARI cases rose from 1.3% to 2.6% (p = 0.0057). SARS-CoV-2 (3.22%) detection was significantly associated with age (p = 0.002). All three viruses circulated year-round with distinct seasonal peaks. Genomic analysis showed that A(H3N2) viruses belonged to clade 3C.2a1b.2a.2, A(H1N1) pdm09 to clade 6B.1A.5a.2 and B/Victoria to clade V1A.3a.2, all aligning with global trends. Among SARS-CoV-2 cases, BA.2 and BA.5 sublineages of Omicron predominated in 2022 while XBB and XBB.1.5 sublineages emerged in 2023. Whole genome sequencing revealed RSV A strains as genotype A.D.5.1 and RSV B as genotype B.D.E.1.

Integration of RSV and SARS-CoV-2 into influenza sentinel surveillance has enabled continuous detection and genomic characterization, reinforcing the critical role of integrated sentinel surveillance for timely response to respiratory virus threats.