Diversity, microevolution and within-host niche adaptation of Streptococcus equi

The objectives of this workwere to evaluate seroprevalence of the disease in Algeria, knowing that vaccination against equine flu is not mandatory in this country and to characterize new viral isolates from nasal swabs collected during 2010 and 2011. 397 sera from distinct horses have been collected, 297 sera were collected in 2009/2010 and 100 were collected during 2011. Serological analysis of equine sera was conducted using haemagglutination inhibition assays (HI), using H7N7/Prague/1956 and H3N8 equine influenza viruses (H3N8/Miami/1963; H3N8/Russie/1983; H3N8/Grosbois/2009). Nasal swabs were taken from horses showing signs of acute respiratory disease. Genotyping was performed by amplification and sequencing of the haemagglutinin gene (HA1) using RNA extracted directly from nasal swabs. Around 59% from 297 sera collected during 2009/2010 showed antibodies anti-H3N8 subtypes, this percentage rises to 81% for sera collected in 2011. Moreover, antibodies anti-H7N7 were found in 6 sera, those horses were imported from Europe and have been certainly vaccinated against equine influenza viruses with a vaccine containing H7N7 antigens. In the meantime, nasal swabs were collected from 7 sick horses showing fever and nasal discharge. Nasal swabs were found positive using a quantitative RT-PCR assay. Phylogenetic analysis using these HA1 sequences and some reference strains and others from GenBank grouped the viruses in different clusters: the Predivergent and American lineages with the Florida sublineage clades 1 and 2. Viruses from Algeria are members of the Florida sublineage Clade 2. In conclusion, the seroepidemiology study performed shows that equine influenza viruses from H3N8 subtypes are circulating in horse population from Algeria. Moreover, the virus characterized in this paper, named A/equine/H3N8/Tiaret/2011, is the first one to be characterized in Algeria since 1972.