Evolution and Divergence of H3N8 Equine Influenza Viruses Circulating in the United Kingdom from 2013 to 2015

Abstract

Equine influenza viruses (EIV) are a major cause of acute respiratory disease in horses worldwide and occasionally also affect vaccinated animals. Like other influenza A viruses, they undergo antigenic drift, highlighting the importance of both surveillance and virus characterisation in order for vaccine strains to be kept up to date. The aim of the work reported here was to monitor the genetic and antigenic changes occurring in EIV circulating in the UK from 2013 to 2015 and to identify any evidence of vaccine breakdown in the field. Virus isolation, reverse transcription polymerase chain reaction (RT-PCR) and sequencing were performed on EIV-positive nasopharyngeal swab samples submitted to the Diagnostic Laboratory Services at the Animal Health Trust (AHT). Phylogenetic analyses were completed for the haemagglutinin-1 (HA1) and neuraminidase (NA) genes using PhyML and amino acid sequences compared against the current World Organisation for Animal Health (OIE)-recommended Florida clade 2 vaccine strain. Substitutions between the new isolates and the vaccine strain were mapped onto the three-dimensional structure protein structures using PyMol. Antigenic analyses were carried out by haemagglutination inhibition assay using a panel of post-infection ferret antisera. Sixty-nine outbreaks of equine influenza in the UK were reported by the AHT between January 2013 and December 2015. Forty-seven viruses were successfully isolated in eggs from 41 of the outbreaks. Only three cases of vaccine breakdown were identified and in each case the vaccine used contained a virus antigen not currently recommended for equine influenza vaccines. Nucleotide sequencing of the HA and NA genes revealed that all of the viruses belonged to the Florida clade 2 sub-lineage of H3N8 EIV. Phylogenetic and sequence analyses showed that the two sub-populations, previously identified within clade 2, continued to circulate and had accrued further amino acid substitutions. Antigenic characterisation using post-infection ferret antisera in haemagglutination inhibition assays however, failed to detect any marked antigenic differences between the isolates. These findings show that Florida clade 2 EIV continue to circulate in the UK and support the current OIE recommendation to include an example of Florida clade 2 in vaccines.

<p>Immunoinformatics and Vaccine Development: An Overview</p>

“…It involves several mechanisms including the varying of surface protein's phase, shifting and drifting of surface protein antigens and/or any other form of alteration of antigenic protein. 82 Antigenic variation plays significant roles in the pathogenicity of microorganisms by evasion of the host immune responses and establishment of re-infection. When a pathogen alters its surface antigens, it can evade the host's adaptive immunity and so reestablishes infection.…”

Isolation and characterization of equine influenza virus (H3N8) from an equine influenza outbreak in Malaysia in 2015

“…However, the equine H7N7 viruses are thought to be extinct as no H7N7 viruses have been isolated since 1979 (Webster, ). The first EIV H3N8 virus was isolated during a widespread outbreak in Miami in 1963 (Scholtens et al, ; Waddell et al, ) and H3N8 viruses have continued to circulate till today (Favaro et al, ; Rash et al, ; Woodward et al, ). In the late 1980s, EIV diverged into two antigenically distinct lineages (Daly et al, ; Worobey, Han, & Rambaut, ), American and Eurasian, and since then, the American lineage has further diverged into the Kentucky, South American and Florida sub‐lineage clades 1 and 2 (Bryant et al, ; Murcia, Wood, & Holmes, ).…”

“…For example, clade 1 viruses were responsible for the outbreaks in Japan and Australia in 2007 (Cowled, Ward, Hamilton, & Garner, ; Yamanaka, Niwa, Tsujimura, Kondo, & Matsumura, ) whereas clade 2 viruses were involved in the Mongolia outbreak in 2008 and the India outbreak in 2009 (Virmani et al, ; Yondon et al, ). Furthermore, in the 2014 equine influenza outbreaks, clade 1 viruses were detected in the USA (OIE, ; Sreenivasan et al, ) while clade 2 viruses were detected in France, Germany, Ireland, Sweden and the UK (Fougerolle et al, ; Gildea et al, ; Rash et al, ).…”

Outbreak of equine influenza in Croatia in 2015 and post outbreak epidemiological situation

“…Phylogenetically, the H3N8 subtype may be separated into six distinct clades, denoted as Pre-divergence, Eurasian and American lineages, with the American lineage further subdividing into the Kentucky, Argentinian/South American and Florida sublineages. The Florida sub-lineage has further divided into two clades (1 and 2) (BRYANT et al, 2009;RASH et al, 2017). Florida clade 1 and Florida clade 2 are now circulating worldwide, including Europe (AUTORINO et al, 2015;BACK et al, 2016;RASH et al, 2017).…”

“…The Florida sub-lineage has further divided into two clades (1 and 2) (BRYANT et al, 2009;RASH et al, 2017). Florida clade 1 and Florida clade 2 are now circulating worldwide, including Europe (AUTORINO et al, 2015;BACK et al, 2016;RASH et al, 2017). Vaccination is still the most important preventive measure for controlling EI infections.…”