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Phylogenetic Analysis and Functional Characterization of the Influenza A H5N1 PB 2 Gene
Author(s) -
Wei K.,
Liu X.
Publication year - 2017
Publication title -
transboundary and emerging diseases
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.392
H-Index - 63
eISSN - 1865-1682
pISSN - 1865-1674
DOI - 10.1111/tbed.12376
Subject(s) - phylogenetic tree , influenza a virus subtype h5n1 , biology , phylogenetics , gene , genetics , evolutionary biology , computational biology , virology , virus
Summary Highly pathogenic avian influenza ( HPAI ) H5N1 viruses are endemic in poultry and cause continued inter‐species transmission to human in Asia, such as China and Vietnam, leading to pandemic concerns and socio‐economic challenges. Phylogenetic analysis of H5N1 viruses isolated from China and Vietnam during 2001–2012 showed that several geographically distinct sublineages have become established in these two countries. Subsequently, we reassigned HPAI H5N1 viruses into three distinct groups to reveal the intrasubtype reassortment. Apart from six reassortants detected here, we found that several viral strains showed signals for homologous recombination within PB 2 and PB 1 genes, suggestive of the fluidity of the H5N1 virus gene pool. Furthermore, sequenced‐based analyses revealed that the viral polymerase displayed a higher level of genetic polymorphism but associated with lower substitution rate when compared with those of other gene segments. In addition, the selection pressure analysis indicated that purifying selection was predominant in eight genomic segments especially in the polymerase complex. However, the site‐by‐site analysis helped to detect 14 positively selected sites in the PB 1, PA , HA , NA , MP and NS proteins. Despite the fact that PB 2 protein of H5N1 viruses was highly conserved at the amino acid level, eleven adaptive mutations were still observed in the protein. Further comparative structural analysis of the K627E mutation indicated that there were no structural differences between the variants, which possessed either PB 2‐627E or PB 2‐627K. Transcriptomic analysis suggested the non‐mitochondrial PB 2 protein of H5N1 virus that forms a stable complex with the mitochondrial antiviral signalling protein ( MAVS , also known as IPS ‐1, VISA or Cardif) can induce interferon‐beta ( IFN ‐β) expression, but the substitution ( PB 2‐K627E) is not the sole determinant of the RIG ‐I‐like receptors ( RLR ) signalling components induction in Calu‐3 cells.