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.

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Every year, several epizooties of equine influenza (EI) are reported worldwide. However, no EI case has been identified in France between 2015 and late 2018, despite an effective field surveillance of the pathogen and the disease. Vaccination against equine influenza virus (EIV) remains to this day one of the most effective methods to prevent or limit EI outbreaks and the lack of detection of the pathogen could be linked to vaccination coverage. The aim of this study was to evaluate EI immunity and vaccine coverage in France through a large-scale serological study. A total of 3004 archived surplus serums from French horses of all ages, breeds and sexes were selected from four different geographical regions and categories (i.e., sanitary check prior to exportation, sale, breeding protocol or illness diagnosis). EIV-specific antibody response was measured by single radial hemolysis (SRH) and an EIV-nucleoprotein (NP) ELISA (used as a DIVA test). Overall immunity coverage against EIV infection (i.e., titers induced by vaccination and/or natural infection above the clinical protection threshold) reached 87.6%. The EIV NP ELISA results showed that 83% of SRH positive serum samples from young horses (≤3 years old) did not have NP antibodies, which indicates that the SRH antibody response was likely induced by EI vaccination alone (the HA recombinant canarypoxvirus-based EI vaccine is mostly used in France) and supports the absence of EIV circulation in French horse populations between 2015 and late 2018, as reported by the French equine infectious diseases surveillance network (RESPE). Results from this study confirm a strong EI immunity in a large cohort of French horses, which provides an explanation to the lack of clinical EI in France in recent years and highlights the success of vaccination against this disease. However, such EI protection has been challenged since late 2018 by the incursion in the EU of a Florida Clade 1 sub-lineage EIV (undetected in France since 2009), which is also reported here.

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To evaluate the humoral immune response to mixed Equine Influenza vaccination, a common practice in the field, an experimental study was carried out on 42 unvaccinated thoroughbred weanling foals divided into six groups of seven. Three groups were vaccinated using a non-mixed protocol (Equilis® Prequenza-Te, Proteqflu-Te® or Calvenza-03®) and three other groups were vaccinated using a mix of the three vaccines mentioned previously. Each weanling underwent a primary EI vaccination schedule composed of two primary immunisations (V1 and V2) four weeks apart followed by a third boost immunisation (V3) six months later. Antibody responses were monitored until one-year post-V3 by single radial haemolysis (SRH). The results showed similar antibody responses for all groups using mixed EI vaccination and the group exclusively vaccinated with Equilis® Prequenza-TE, which were significantly higher than the other two groups vaccinated with Proteqflu-TE® and Calvenza-03®. All weanlings (100%) failed to seroconvert after V1 and 21% (9/42) still had low or no SRH antibody titres two weeks post-V2. All weanlings had seroconverted and exceeded the clinical protection threshold one month after V3. The poor response to vaccination was primarily observed in groups exclusively vaccinated with Proteqflu-Te® and Calvenza-03®. A large window of susceptibility (3–4.5-month duration) usually called immunity gap was observed after V2 and prior to V3 for all groups. The SRH antibody level was maintained above the clinical protection threshold for three months post-V3 for the groups exclusively vaccinated with Proteqflu-Te® and Calvenza-03®, and six months to one year for groups using mixed EI vaccination or exclusively vaccinated with Equilis® Prequenza-Te. This study demonstrates for the first time that the mix of EI vaccines during the primary vaccination schedule has no detrimental impact on the correlate of protection against EIV infection.

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Reasons for performing study Every year, several equine influenza (EI) epidemics are reported worldwide. Equine influenza vaccination is the most efficient method of prevention; however, not all horses develop sufficient immunity after EI immunisation, increasing the risk of infection, infectious virus excretion and the spread of the disease. Objectives This study aimed to better understand poor vaccine response mechanisms during the primary EI vaccination. Study design Cohort study. Methods The EI humoral immune response was measured in 118 Thoroughbred foals set in 3 different stud farms (SF#1 to SF#3) after the primary course of EI vaccination. All foals were immunised with a recombinant canarypox‐based EI vaccine, following the vaccine manufacturer's recommendations. The age at first vaccination was 4 to 8 months. Sera were tested by single radial haemolysis (SRH) against the A/equine/Jouars/4/2006 EIV strain (Florida clade 2) at the time of the first vaccination (V1), 2 weeks and 3 months after the second immunisation (V2), 2 days and 3 months after the third immunisation (V3). Results Short (V2 + 2 weeks) and mid‐term (V3 + 3 months) SRH antibody levels were statistically different between the stud farms (P‐value = 0.0011 and 0.003, respectively), with SF#1