Influenza and other respiratory viruses · 2026
Strengthening Respiratory Virus Surveillance in Sub-Saharan Africa: Integrated Epidemiological and Genomic Monitoring in Côte d'Ivoire.
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Kadjo Hervé A, Coulibaly Daouda, Ouattara Yakoura Karidja, Aboubacar Sylla, Maxime Diané, Konan Nguessan, Luc-Venance Kouakou, Helene Kouassi, Marc Mboua Jean, Bertin Kouakou, Marius Adagba, Adjogoua Edgard, Daniel Ekra, Syndou Meite
Аннотация
BACKGROUND: 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.
METHODS: 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.
RESULTS: 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.
CONCLUSION: 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.
METHODS: 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.
RESULTS: 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.
CONCLUSION: 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.