title: Genetic analysis of the matrix and non-structural genes of equine influenza virus (H3N8) from epizootic of 2008-2009 in India.
abstract: 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.
authors.affiliation: National Research Centre on Equines, Sirsa Road, Hisar 125 001, Haryana, India.
authors.forename: Nitin
authors.initials: N
authors.lastname: Virmani
authors.forename: B C
authors.initials: BC
authors.lastname: Bera
authors.forename: K
authors.initials: K
authors.lastname: Shanumugasundaram
authors.forename: B K
authors.initials: BK
authors.lastname: Singh
authors.forename: B R
authors.initials: BR
authors.lastname: Gulati
authors.forename: R K
authors.initials: RK
authors.lastname: Singh
authors.forename: R K
authors.initials: RK
authors.lastname: Vaid
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D002642:Chick Embryo; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D007194:India; D053123:Influenza A Virus, H3N8 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009976:Orthomyxoviridae Infections / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D014763:Viral Matrix Proteins / Q000235:genetics*; D017361:Viral Nonstructural Proteins / Q000235:genetics*
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; C085820:INS1 protein, influenza virus; C488936:M1 protein, Influenza A virus; D014763:Viral Matrix Proteins; D017361:Viral Nonstructural Proteins