Recombination analysis of full-length genomic sequences of novel influenza virus A/H1N1 in 2009 pandemic / 第二军医大学学报

ABSTRACT

Objective: To analyze the recombination of full-length genomic sequences of novel influenza virus A/H1N1 in 2009 pandemic. Methods: The full-length sequences of the novel A/H1N1 and reference sequences were downloaded from NCBI database. MEGA4.0 software was used to connect, align sequences, and analyze the similarity between the full-length sequences of the novel virus and each of the reference strains. Recombination was analyzed by Simplot software (version 3.5.1). Results: Simplot analysis indicated that the PB1 genes (polymerase B1, PB1) of the novel A/H1N1 viruses might evolve from human H3N2 virus (identity 93.7%); the PB2 genes (polymerase B2, PB2) and the PA genes (polymerase A, PA) might evolve from avian H5N1 viruses (identity 89.0%, 89.9%, respectively); the HA genes (hemagglutinin, HA), the NP genes (nucleoprotein, NP) and the NS genes (non-structural protein, NS) showed high similarities with those of swine H1N1 viruses isolated in North America (identity 91.7%, 93.1%, and 93.1%, respectively); and the NA genes (neuraminidase, NA) and the MP genes (matrix protein, MP) might evolve from European swine H1N1 viruses (identity 90.5%, 95.5%, respectively). The full-length sequence of the novel A/H1N1 viruses had a highest similarities with swine H1N1 viruses isolated in North America (identity 83.9%). Conclusion: The novel influenza virus A/H1N1 is a recombinant virus evolving from human H3N2 viruses, swine H1N1 from North America, swine H1N1 from Europe, and swine H5N1 from Asia.