**1. Introduction**

Equine influenza (EI) is an important equine respiratory pathogen and a high‐priority disease for the equine industry globally. It is highly contagious and spreads rapidly in horse population by direct contact; clinical signs associated with the infection are characterized by pyrexia, dyspnoea, dry hacking cough and serous nasal discharge that can become mucopurulent in the case of secondary bacterial infections [1]. The causative agent, equine influenza virus (EIV), has a global distribution; it is endemic in many countries and there are occasional incursions in

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Japan, South Africa and Hong Kong, with only Australia, New Zealand and Iceland being considered free.

**Figure 1.** Phylogenetic analysis of the HA1 nucleotide sequences encoded by 90 EIV, subtype H3N8 isolated since 1963 and prototype strains of the different lineages and clades. Sequences are coloured by date of isolation for the years 2011 (red), 2010 (green) and 2009 (blue), with older strains in black. Current OIE recommended vaccine strains are highlighted in yellow [1].

EIV is belonging to the family of the *Orthomyxoviridae*, genus *Influenzavirus*, type A and is a major cause of respiratory diseases in horses. Only two antigenic subtypes of EIV (H7N7 and H3N8) have been isolated from horses, although highly pathogenic avian influenza virus (H5N1) was isolated from donkeys in Egypt [2]. The equine H7N7 virus first isolated in Prague (Czechoslovakia) in 1956 [3] and has not been isolated in horses since 1979 [4], but serological evidence for its circulation in unvaccinated horses has been recorded at the end of the 1980s in India [5] and at the beginning of the 1990s in Croatia and USA [6, 7]. Since then, the equine H3N8 virus, first isolated in 1963 after an important outbreak in Miami (Florida, USA) [8], has persisted [9, 10] and only has been isolated from sick horses [11–15]. Phylogenetic studies have shown that H3N8 virus evolved in the late 1980s, into the American and the Eurasian lineages [16]. The Eurasian lineage strains, were almost exclusively isolated from horses in Europe and Asia, represented by Newmarket/2/93, continue to form a single clade, but have rarely been isolated in recent years [17]. The American lineage strains, were predominantly isolated from horses on the continent of America, further evolved into three sublineages, South American, Kentucky and Florida [18]. The original American lineage strains, represented by Newmarket/ 1/93 and Kentucky/1994, have not been completely superseded, with isolations of strains from this clade in the United Kingdom [17] and Chile [19] in 2006. The evolution of the Florida sublineage resulted in the emergence of two groups of viruses that differ in their HA sequences referred as Clade 1 viruses that have been isolated in North America since 2003 (e.g. Ohio/ 2003) and are distinct from the Florida Clade 2 strains that spread to Europe (Newmarket/ 5/03) [17]. Clade 1 viruses predominate on the American continent; nevertheless, they have caused large outbreaks in Africa, Asia, Australia, Europe and South America [20–27]. Similarly, Clade 2 viruses predominate in Europe but also have been isolated in Asia and North Africa [15, 28–32]. The phylogenetic analysis points to sporadic incursions of virus from North America into Europe and other regions, as happened around 1993 and 2003, followed by a period of more localized divergent evolution (**Figure 1**).

Japan, South Africa and Hong Kong, with only Australia, New Zealand and Iceland being

20 Epidemiology of Communicable and Non-Communicable Diseases - Attributes of Lifestyle and Nature on Humankind

**Figure 1.** Phylogenetic analysis of the HA1 nucleotide sequences encoded by 90 EIV, subtype H3N8 isolated since 1963 and prototype strains of the different lineages and clades. Sequences are coloured by date of isolation for the years 2011 (red), 2010 (green) and 2009 (blue), with older strains in black. Current OIE recommended vaccine strains are

EIV is belonging to the family of the *Orthomyxoviridae*, genus *Influenzavirus*, type A and is a major cause of respiratory diseases in horses. Only two antigenic subtypes of EIV (H7N7 and H3N8) have been isolated from horses, although highly pathogenic avian influenza virus

considered free.

highlighted in yellow [1].

The use of the molecular tools is of a high interest in epidemiology. The interest of the association of these techniques and the classical epidemiological analyses will be illustrated by considering the example of equine influenza viruses. The determination and the compari‐ son of the nucleotide sequences allow to characterize the virus strains more precisely than the classical methods and are useful to analyze the evolution of the equine influenza viruses. These methods are also useful to select the relevant strains that will be used in the vaccines. The possible reasons for the infection of horses despite intensive vaccination are currently being investigated and may shed new light on the epidemiology of equine influenza [33].

Influenza is a classic example of a (re‐)emerging infection. Vaccines against influenza have been used in man since the 1940s [34] and became available for use in horses 20 years later. However, the existence of a reservoir of virus in aquatic birds and the highly variable nature of the virus mean that influenza defies worldwide eradication. The prevention and control of influenza are closely related measures of vaccination and livestock management. Vaccination is to date the most average usual to limit the spread of the virus in the horse population. Vaccines against equine influenza must contain subtypes and, inside thereof, the antigenic variants circulating in the horse population. Every year, the expert surveillance panel (ESP) of the World Organization for Animal Health (OIE) recommends influenza virus strains to be contained equine vaccines. The fact that H7N7 viruses and Eurasian H3N8 viruses are no longer required, current vaccines should include the antigenic variants of viruses representing each of Clades 1 and 2 of the Florida sublineage. The Clade 1 is represented by A/equine/South Africa/4/2003‐like or A/equine/Ohio/2003‐like viruses. The Clade 2 is represented by A/equine/ Richmond/1/2007‐like viruses.
