Background: A new pandemic influenza A (H1N1) emerged in April 2009, causing considerable morbidity and mortality. Since mutations in the haemagglutinin (HA) may influence the antigenicity and pathogenicity of the virus, continued epidemiological and molecular characterization for the effective control of pandemic flu and developing of more appropriate vaccine is crucial.
Objective: To monitor the molecular evolution of A (H1N1) pdm09 viruses in a specific time period in Shiraz, Southern Iran.
Methods: A total of 200 samples were collected from February-April 2013. HA gene of the isolates was amplified and sequenced. Phylogenetic analysis of the HA gene was performed.
Results: Out of 200 samples, a total of 77 (38.5%) samples were confirmed as A (H1N1) pdm09 virus using Real-time PCR method. Nucleotide similarity of our study strains with respect to reference strain A/California/07/2009 (H1N1) was 97.5%-98.5%. Phylogenetic analysis of our study strains indicated that the dominant A (H1N1) pdm09 clade was clade 7 and the dominant genetic group in circulating strains in Shiraz was genetic group 6. Some of our study strains showed substitutions at or in the vicinity of the antigenic sites of the HA1 region which may affect the efficacy of the vaccine.
Conclusion: Our study strains showed a high homology to the vaccine strain. Our findings confirm the genetic variability of influenza A (H1N1) pdm09 and highlight the necessity of continuous molecular study of the virus for effective management of influenza.