Abstract
SummaryEquine influenza is a major cause of respiratory infections in horses and can spread rapidly despite the availability of commercial vaccines. In this study, we carried out molecular characterization of Equine Influenza Virus (EIV) isolated from the Malaysian outbreak in 2015 by sequencing of the HA and NA gene segments using Sanger sequencing. The nucleotide and amino acid sequences of HA and NA were compared with representative Florida clade 1 and clade 2 strains using phylogenetic analysis. The Florida clade 1 viruses identified in this outbreak revealed numerous amino acid substitutions in the HA protein as compared to the current OIE vaccine strain recommendations and representative strains of circulating Florida sub‐lineage clade 1 and clade 2. Differences in HA included amino acids located within antigenic sites which could lead to reduced immune recognition of the outbreak strain and alter the effectiveness of vaccination against the outbreak strain. Detailed surveillance and genetic information sharing could allow genetic drift of equine influenza viruses to be monitored more effectively on a global basis and aid in refinement of vaccine strain selection for EIV.
Highlights
Equine influenza virus (EIV), an influenza A virus belonging to the Orthomyxoviridae family, is a major cause of respiratory diseases in horses and can spread rapidly between naïve animals
The first EIV H3N8 virus was isolated during a widespread outbreak in Miami in 1963 (Scholtens et al, 1964; Waddell et al, 1963) and H3N8 viruses have continued to circulate till today (Favaro et al, 2018; Rash et al, 2017; Woodward et al, 2014)
The two genetic variants shared a nucleotide difference at position 808 that did not translate into any amino acid difference in the haem‐ agglutinin (HA) protein, while no sequence difference in the NA gene segment was identified between the two isolates
Summary
Equine influenza virus (EIV), an influenza A virus belonging to the Orthomyxoviridae family, is a major cause of respiratory diseases in horses and can spread rapidly between naïve animals. There are two major subtypes, H7N7 and H3N8, which have been isolated from horses (Scholtens, Steele, Dowdle, Yarbrough, & Robinson, 1964; Sovinona, Tumova, Pouska, & Nemec, 1958; Waddell, Teigland, & Sigel, 1963). The first EIV H3N8 virus was isolated during a widespread outbreak in Miami in 1963 (Scholtens et al, 1964; Waddell et al, 1963) and H3N8 viruses have continued to circulate till today (Favaro et al, 2018; Rash et al, 2017; Woodward et al, 2014). In the late 1980s, EIV diverged into two antigenically distinct lineages (Daly et al, 1996; Worobey, Han, & Rambaut, 2014), American and
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