Abstract
Equine influenza virus (EIV) is considered the most important respiratory pathogen of horses as outbreaks of the disease lead to substantial economic losses. The H3N8 EIV has caused respiratory disease in horses across the world, including South American countries. Nucleotide and deduced amino acid sequences for the complete haemagglutinin gene of the H3N8 EIV detected in South America since 1963 were analyzed. Phylogenetic and Bayesian coalescent analyses were carried out to study the origin, the time of the most recent common ancestors (tMRCA), the demographic and the phylogeographic patterns of the H3N8 EIV. The phylogenetic analysis demonstrated that the H3N8 EIV detected in South America grouped in 5 well-supported monophyletic clades, each associated with strains of different origins. The tMRCA estimated for each group suggested that the virus was circulating in North America at least one year before its effective circulation in the South American population. Phylogenetic and coalescent analyses revealed a polyphyletic behavior of the viruses causing the outbreaks in South America between 1963 and 2012, possibly due to the introduction of at least 4 different EIVs through the international movement of horses. In addition, phylodynamic analysis suggested South America as the starting point of the spread of the H3N8 EIV in 1963 and showed migration links from the United States to South America in the subsequent EIV irruptions. Further, an increase in the relative genetic diversity was observed between 2006 and 2007 and a subsequent decline since 2009, probably due to the co-circulation of different lineages and as a result of the incorporation of the Florida clade 2 strain in vaccines, respectively. The observed data highlight the importance of epidemiological surveillance and the implementation of appropriate quarantine procedures to prevent outbreaks of the disease.
Highlights
Equine influenza (EI) is one of the major infectious respiratory diseases of horses and is considered severely damaging in economic terms
The time-scaled maximum clade credibility (MCC) tree inferred by Bayesian coalescent analysis displayed a similar phylogenetic pattern (Figure 1) [38]
Three of the twelve groups (VI, VII and IX) were not observed in the maximum likelihood (ML) tree obtained with the partial HA data set, probably due to a lower phylogenetic signal in the partial HA data set compared to the complete HA data set
Summary
Equine influenza (EI) is one of the major infectious respiratory diseases of horses and is considered severely damaging in economic terms. This is due to the highly contagious nature of the virus which. The H7N7 was identified in 1956 during an outbreak of respiratory disease in horses in Czechoslovakia [4], and the H3N8 subtype was first detected in 1963 during a major epizootic of respiratory disease in horses in Florida, United States (USA) [5,6]. Both subtypes of viruses co-circulated for around 25 years; the H7N7 has not been isolated since 1979 and is considered to be extinct [7], and since that time, all outbreaks of EI worldwide have been caused by the H3N8 subtype
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