Isolation and sequence analysis of hemagglutinin gene of Influenza A H1N1 virus from Iranian clinical samples during 2009 pandemic flu

Influenza virus is a globally important respiratory pathogen causing high degree of morbidity and mortality annually. The novel Influenza virus (A/H1N1) which involved many populations of the world in 2009 is a sort of triple reassortment between swine، bird and human viruses. Given the important role of hemagglutinin in the infectivity of influenza virus، genome sequencing of this protein and investigation of its changes seems necessary. In this experimental study، the viral genome was extracted from clinical throat swab samples، in which the presence of swine influenza genome has been confirmed by Real-time PCR according to WHO protocol in Influenza Research Lab، Pasteur Institute of Iran. Full-length of HA genome was amplified using specific primers by one step-RT-PCR، cloned into pGEM-T Easy vector followed by identification with restriction enzyme analysis and sequencing. Full genome of novel influenza A/H1N1 from clinical samples was amplified by PCR and the expected 1777 bp segment PCR product was visualized by electrophoresis، gel purified، cloned into pGEM-TEasy vector and then sequenced. Analysis of sequencing was accomplished by chromas software (version 1. 45-Australia) and the nucleotide sequence data was deposited in GenBank database under the accession number: “HQ419001. 1”. The result of sequencing was well-matched with the recommended vaccine strain and other registered sequences in NCBI.