Sentinel Surveillance of Influenza A in Libya: Subtyping and Genomic Analysis During Recent Seasons (2022–2024)

Influenza sentinel surveillance in Libya was formally established in 2022 by the Libyan National Center for Disease Control (NCDC), initially comprising a single sentinel site in Tripoli. By the end of 2025, the network had expanded to 15 sites across five cities nationwide. Between 2022 and 2024, a total of 1,864 nasopharyngeal specimens were collected from patients presenting with influenza-like illness and tested using the GeneXpert for influenza A virus, influenza B virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and respiratory syncytial virus (RSV). Influenza A virus was detected in 21.1% (393/1,864) of samples and influenza B virus in 5.4% (100/1,864). SARS-CoV-2 and RSV were identified in 11.6% (216/1,864) and 4.1% (77/1,864) of specimens, respectively. A subset of 29 influenza A–positive samples was randomly selected for confirmatory testing and further molecular characterization. Real-time RT-PCR subtyping identified 13 A(H1N1)pdm09 and five A(H3N2) viruses. Whole-genome sequencing was successfully performed for 13 isolates, followed by phylogenetic analysis. Genetic characterization revealed that all A(H1N1)pdm09 viruses belonged to clade 6B.1A.5a.2a (5a.2a), while A(H3N2) viruses clustered within clade 3C.2a1b.2a.2a.3a.1 (2a.3a.1) based on hemagglutinin gene mutations. No neuraminidase mutations associated with antiviral resistance were detected. This study represents the first molecular and phylogenetic characterization of circulating human influenza viruses in Libya, with sequence data submitted to the Global Initiative on Sharing All Influenza Data (GISAID). These findings establish baseline genetic data for influenza viruses in Libya and support the strengthening of national respiratory virus surveillance.