Genomic epidemiology of equine influenza virus in the United Kingdom

The horse industry and its associated industries make a substantial contribution to the UK economy. Therefore, not only do equine infectious diseases pose a serious risk to horses, but also have the potential to significantly affect the National economy. Equine influenza (EI) is arguably the most important infectious disease of the horse (in economic terms). EI is endemic in the UK and many other countries around the world and is caused by equine influenza virus (EIV). As with other influenza viruses, EIV can acquire mutations in its genome and evade host immunity induced by vaccination. However, epidemiological information has shown that in the UK, EI affects mainly unvaccinated animals. Vaccination against EI is compulsory for competition horses. In 2019 the UK experienced one of the largest EI epidemics in history: over 200 outbreaks spread throughout all four Nations were reported. An important feature of this epidemic is that 26 of the outbreaks were reported among vaccinated horses. This led to a six-day closure of all horse competitions, causing significant economic losses. While the total losses incurred by the cancellation of equestrian events is currently unknown (but likely to have run into millions of pounds), the Horserace Betting Levy Board has confirmed that the betting levy alone (i.e. the tax raised on bets) that was lost was £1.5M over the 6 days. As the 2019 EIV epidemic was finally contained, we can use it to learn valuable insight to prevent and control future epidemics. Current advances in sequencing technologies allow us to characterise the entire EIV genome directly from a nasal swab obtained from a sick horse. In turn, virus genetic information, if linked with epidemiological data, can be used to track the spread of viral diseases in time and space. We propose to combine genetic information with epidemiological data to reconstruct the spread of EIV during the 2019 epidemic, identify the most likely origin of the epizootic virus, and determine the patterns of genetic change of EIV during the epidemic. To this end, we will sequence nearly 400 virus genomes, most of them from the 2019 UK epidemic, as well as viruses from other countries to put the epidemic in a global context. This is a joint project between the Centre for Virus Research (CVR) and the Animal Health Trust (AHT). The CVR is a National Centre for Virology and has extensive expertise in virus sequencing and sequence analyses. The AHT is the reference laboratory for EI and hosts Equiflunet, a UK-wide equine surveillance network specifically designed to monitor EI. Results from this project will help inform the design of improved intervention measures to prevent and control future EIV epidemics.