BACKGROUND: The @entity1707 -origin @entity778 (S-OIV) has come to the forefront since 2009 and was identified as a new reassortant strain. The @entity11230 (HA) glycoprotein mediates virus binding, contains antigenic regions recognized by neutralizing antibodies, and is associated with @entity1800 and adaption. The comparison study of codon usage preferences in influenza viral genomes was less extensive. In this study, we used codon usage pattern analyses to validate the adaption and origins of S-OIV. METHODS: Codon usage pattern was used to estimate the host adaption of S-OIVs. Phylogenetic analysis of the HA gene was conducted to understand the phylogeny of H1N1 viruses isolated from different hosts. @entity535 signature pattern on antigenic sites of HA was analyzed to understand the antigenic characteristics. RESULTS: Results of phylogenetic analyses of HA gene indicate that S-OIVs group in identical clusters. The synonymous codon usage pattern analyses indicate that the effective number of codons versus GC content at the third codon position in the HA1 gene slightly differ from those in @entity1707 H1N1 and gradually adapted to @entity1 . Our data indicate that S-OIV evolution occurred according to positive selection within these antigenic regions. A comparison of antigenic site @entity1522 reveals similar signature patterns between S-OIV and 1918 @entity1 influenza strains. CONCLUSION: This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.

Analysis of codon usage preference in hemagglutinin genes of the @entity1707 -origin XXXX .

@entity1 :: ('9606', 'Species') :: ['human'] @entity778 :: ('MESH:D015658', 'Disease') :: ['influenza A (H1N1) virus'] @entity1707 :: ('9823', 'Species') :: ['swine'] @entity1522 :: ('CHEBI:33709', 'Chemical') :: ['amino acids'] @entity535 :: ('CHEBI:33704', 'Chemical') :: ['Amino acid'] @entity1800 :: ('MESH:D014777', 'Disease') :: ['viral cross-species infection'] @entity11230 :: ('MESH:D006388', 'Chemical') :: ['hemagglutinin']
@entity778 :: (MESH:D015658,Disease) :: ['influenza A (H1N1) virus']
