Genetic evolution of equine influenza virus strains (H3N8) isolated in France from 1967 to 2015 and the implications of several potential pathogenic factors

Abstract

Equine influenza virus (EIV) is a major respiratory pathogen of horses despite the availability of equine influenza vaccines. This study aimed to determine genetic evolution of EIV strains in France between 1967 to present. A whole genome comparative analysis was also conducted on recent French strains in order to identify potential factors of pathogenicity. Comparison of French EIV sequences with vaccine and worldwide epidemic strains revealed amino acid substitutions in both haemagglutinin (HA) and neuraminidase, especially within the antigenic sites and/or close to receptor binding sites (HA). Amino acid substitutions were also identified in other genes, mainly the polymerase complex proteins and PB1-F2. Viruses belonging to Eurasian and American lineages have circulated until 2003 and Florida sub-lineage Clade 2 strains predominates since 2005. The last French strain (2015) displayed several specificities in HA suggesting the occurrence of antigenic drift with presence of pathogenic markers in the PA and PB1-F2 genes.

Whole‐genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey

“…50 A recent study of French EIV strains highlighted a potential pro-inflammatory motif in PB1-F2 of A/ equine/Belfond/6-2/2009, an FC1 strain. 51 However, the A/equine/ Ankara/1/2013 PB1-F2 sequence is similar to those of FC2 strains A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015 which possess a non-inflammatory motif (amino acid L62, H75 and Q79) ( Fig. S3.3).…”

“…It has been suggested that in addition to other non‐human influenza strains such as those of birds and pigs, EIV strains may act as donors of virulent PB1‐F2 to humans indicating a need for ongoing surveillance for genetic markers of virulence to improve pandemic preparedness . A recent study of French EIV strains highlighted a potential pro‐inflammatory motif in PB1‐F2 of A/equine/Belfond/6‐2/2009, an FC1 strain . However, the A/equine/Ankara/1/2013 PB1‐F2 sequence is similar to those of FC2 strains A/equine/Cambremer/1/2012 and A/equine/Saone et Loire/1/2015 which possess a non‐inflammatory motif (amino acid L62, H75 and Q79) (Fig.…”

Success and Limitation of Equine Influenza Vaccination: The First Incursion in a Decade of a Florida Clade 1 Equine Influenza Virus that Shakes Protection Despite High Vaccine Coverage

“…Such immune coverage in the French horse population studied could provide an explanation for a lack of detection of EIV and/or the disease between mid-2015 and late 2018, despite extensive surveillance by the RESPE and associated diagnostic laboratories (several hundreds of nasopharyngeal swab samples analyzed every year). Prior to this period, the last French EI outbreaks were reported in 2014 and 2015 but were limited in size and number (six and four, respectively) [13]. Other European countries with large equids population report EI cases every year [15,26].…”

“…The scale, number and duration of this epidemic had not been experienced in Europe since the late 1970s and 1980s. Sequencing results revealed that H3N8 EIV strains at the origin of the 2018-2019 French outbreaks (and EI outbreaks in other European countries, OIE ESP communication) belong to the FC1 sub-lineage, which was not isolated in France since 2009 [13] and was usually circulating in North and South Americas [17,20,32]. While several amino acids mutation were identified in the HA, results from the hemagglutination inhibition assay using mono-specific ferret sera and the associated antigenic cartography analyses indicate that FC1 EIV strains the origin of the 2018-2019 EI outbreaks were still antigenically closely related to the recommended FC1 EIV strains for inclusion in EI vaccine [33].…”

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

“…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, ).…”