Background: Influenza viruses have high mutation rates and cause serious health problems worldwide. In our population, no study has examined mutations and their variation relative to the wild-type and vaccine strains.

Objective: Study focused on whole-genome sequencing to characterize the virus, construct phylogenetic trees, analyze mutations, and assess nucleotide diversity.

Study design: Nasal swabs were collected from 170 patients with RTI (SARI or ILI) in Baghdad and Wasit from November 2024 to March 2025, and tested for influenza A virus detection and typing by real-time reverse transcription polymerase chain reaction. The 14 positive viral genomes were sequenced using the MinION nanopore platform.

Results: 49 influenza viral genomes were identified as positive cases, comprising 48 A/H1N1 and 1 A/H3N2 strain. Nine complete A/H1N1 were sequenced, revealing nonsynonymous mutations, especially in the hemagglutinin (HA), neuraminidase (NA), and nonstructural protein 1 (NS1) genes. Nucleotide diversity analysis revealed negative selection in certain A/H1N1 genes. Mutations were detected in antigenic and functional regions of HA and NA, indicating ongoing antigenic drift in circulating strains. Phylogenetic analysis showed that the Iraqi isolates were closely related to contemporary regional and global strains reported from neighboring countries such as Iran and Saudi Arabia, and were partially genetically related to recent vaccine strains such as A/Wisconsin/67/2022 and A/Missouri/11/2025. By contrast, the older vaccine strains suggest that Iraqi influenza viruses are evolving slowly, accumulating mutations continuously, while the important internal proteins are conserved.

Conclusion: Mutations across all eight genome segments will be crucial for elucidating the genetic evolution of influenza A viruses in Iraq.