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.

An outbreak of equine influenza (EI) was reported in Algeria between May and July, 2011. The outbreak started in Tiaret, in west province of Algeria, and spread to the other parts of the country affecting almost 900 horses in many provinces. The population studied was composed of 325 horses from different groups of age. Clinical sign expression was age dependent. Indeed, a morbidity rate of 14.9% was observed in horses under 15 months old and a rate of 4.95% in horses over 8 years old. Interestingly, the morbidity rate raised sharply to reach 100% in horses aged between 18 months and 7 years. The virus (H3N8) was detected in nasopharyngeal swabs (n = 11) from non-vaccinated horses using a qRT-PCR targeting a portion of the gene encoding the matrix protein (M). The virus isolates were identified as H3N8 by sequencing the haemagglutinin (HA) and neuraminidase (NA) genes and were named from A/equine/Tiaret/1/2011 to A/equine/Tiaret/10/2011. Alignment of HA1 amino acid sequence confirmed that viruses belong to Clade 2 of the Florida sublineage in the American lineage. Moreover, they are closely related to A/equine/Yokohama/aq13/2010, A/equine/Eyragues/1/2010, A/equine/Bokel/2011 and A/equine/Lichtenfeld/2012. Our data indicate that this strain was also circulating in the European horse population in 2010, 2011 and 2012.

SummaryIn 2009, a major outbreak of equine infectious anaemia (EIA) was reported in the south-east of France. This outbreak affected three premises located in the Var region where the index case, a 10-year-old mare that exhibited clinical signs consistent with EIA, occurred at a riding school. Overall, more than 250 horses were tested for EIAV (equine infectious anaemia virus) antibodies, using agar gel immunodiffusion test, and 16 horses were positive in three different holdings. Epidemiological survey confirmed that the three premises were related through the purchase/sale of horses and the use of shared or nearby pastures. Molecular characterization of viruses was performed by sequencing the full gag gene sequence (1,400 bp) of the proviral DNAs retrieved from the spleen of infected animals collected post-mortem. Phylogenetic analysis confirmed epidemiological data from the field, as viruses isolated from the three premises were clustering together suggesting a common origin whereas some premises were 50 km apart. Moreover, viruses characterized during this outbreak are different from European strains described so far, underlying the high genetic diversity of EIAV in Europe. K E Y W O R D Sepidemiology, equine infectious anaemia virus, France, horse, phylogeny

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