Genetic analysis of the matrix and non-structural genes of equine influenza virus (H3N8) from epizootic of 2008–2009 in India

• Published in: Veterinary microbiology 2011-08, Vol.152 (1), p.169-175
• Main Authors: Virmani, Nitin, Bera, B.C., Shanumugasundaram, K., Singh, B.K., Gulati, B.R., Singh, R.K., Vaid, R.K.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amino Acid Substitution; amino acids; Animals; Biological and medical sciences; Chick Embryo; cluster analysis; Equine influenza; Equine influenza virus; Fundamental and applied biological sciences. Psychology; genes; Hemagglutinin Glycoproteins, Influenza Virus - genetics; India; Influenza A virus; Influenza A Virus, H3N8 Subtype - classification; Influenza A Virus, H3N8 Subtype - genetics; Influenza A Virus, H3N8 Subtype - isolation & purification; Matrix; Microbiology; Miscellaneous; Molecular Sequence Data; Non-structural; nucleotide sequences; Orthomyxoviridae Infections - veterinary; Orthomyxoviridae Infections - virology; Phylogenetic analysis; Phylogeny; proteins; Selection, Genetic; sequence analysis; Sequence Analysis, RNA; Viral Matrix Proteins - genetics; Viral Nonstructural Proteins - genetics; Virology; viruses
• ISSN: 0378-1135; 1873-2542
• DOI: 10.1016/j.vetmic.2011.04.011

India faced an epizootic of equine influenza in 2008–2009. The isolated viruses were typed as H3N8 and grouped with the clade 2 viruses of Florida sublineage on the basis of haemagglutinin (HA) gene sequence analysis. This report describes the genetic analysis and selection pressure of matrix (M) and non-structural 1 (NS1) genes of the Indian isolates. All isolates shared 98.41% and 99.54% homology with other clade 2 viruses of Asian origin for M1 and M2 amino acid (aa) sequences, respectively. There were 3 and 4 unique aa residue changes respectively in M1 and M2 proteins in all Asian isolates. Phylogenetic analysis revealed clustering of Indian and Chinese isolates in a separate group designated here as Asian clade for M gene. Indian and Chinese isolates shared homology ranging from 98.17% to 99.08% at aa level. The M and NS1 genes were under negative selection pressure with estimated magnitude of pressure ( ω) 0.054, 0.581 and 0.30 for M1, M2 and NS1, respectively.