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.

Equine influenza (EI) is an important viral disease of the horse and is endemic in the UK and many other countries despite the availability of vaccines. The UK experienced one of the largest EI epizootics in 2019, with more than 200 outbreaks reported throughout the whole country. An unusual feature of the 2019 epizootic was that a large number of outbreaks (n=26) affected previously vaccinated horses. This led to the suspension of all equestrian events for 6 days, causing significant economic losses.
We propose to apply a phylodynamic framework to link EI epidemic processes with EIV evolution during the 2019 epizootic. To this end we will (i) sequence a large number of complete equine influenza virus (EIV) genomes obtained during the UK 2019 epizootic and (ii) combine sequencing data with epidemiological information to reconstruct the spatial and temporal dynamics of the 2019 EIV epizootic; iii) characterise the evolutionary dynamics of EIV during the 2019 epizootic; and iv) compare patterns of virus diversity associated with immunological status.
A large number of viral samples (i.e. qPCR positive nasal swabs) and epidemiological data have been collected by the Animal Health Trust, the OIE National reference laboratory for EI. We will use the Illumina platform to generate deep sequencing whole-genome data from all UK EIV outbreak locations. We will also sequence ~140 EIV genomes from other countries collected in 2018/19 to increase the robustness of phylogenetic inferences at the global level. Virus sequencing and data analyses will be carried out at the Centre for Virus Research.
Results from this project will help inform the design of intervention strategies to control EI and also provide new insights on the phylodynamic patterns of influenza viruses. Given the amount of sequencing data and the quality of epidemiological data obtained, we are confident that our results will help the development of new methodologies to study disease transmission.

This research will benefit the horserace and associated industries, animal health officials, veterinarians, virology researchers, and researchers interested in influenza evolution and modelling. Indirectly, this research will benefit researchers interested in developing new algorithms to analyse big data, as well as the vaccine industry. An important output from this project will be a novel state-of-the-art analytical pipeline that will integrate full genome EIV data with epidemiological data to track EIV for the first time. The availability of this pipeline will benefit:
-The horserace industry, who invests heavily in disease surveillance via the Horserace Betting Levy Board.
-The World Organisation for Animal Health (OIE) will benefit from the analysis of EIV genomes which will reveal the most likely geographical source of the epizootic virus as well as the routes it followed to spread within the UK. Dr Elton, Co-investigator in the project, is a member of the OIE Expert Surveillance Panel (OIE/ESP), who are responsible for compiling and presenting the surveillance data each year and discussing with other members of the panel (this includes the three OIE reference labs [UK, Ireland, USA], World Influenza Centre at the Crick Institute, experts in antigenic cartography [Dr Nicola Lewis, RVC] plus international collaborating labs from Japan, China, India, France, Sweden, Argentina and Germany). Results from this research will enable future modelling work aimed at testing different epizootic scenarios as well as the impact of intervention measures. Both the CVR and the AHT have a track record of collaborative work with modellers and we will continue that approach.
This research will also provide information about the mutations that appeared in EIV during the 2019 epizootic (including mutations resulting in altered antigenicity if present). This information will be of value to:
-UK and international researchers working on influenza viruses as it will inform future experiments that will include candidate mutations associated with changes in influenza infection biology.
-OIE/ESP will be interested in whether or not observed mutations are likely to change antigenicity. This will inform their recommendations on vaccine strains and whether they are updated or not.
-Industrial partners with an interest in equine infectious diseases and we will communicate our results to them directly through bi-annual industry meetings hosted by AHT to provide updates on matters of infectious diseases.
-Our results will also benefit researchers working on the evolutionary biology of influenza (and other) viruses.
All the data generated in this project will be publicly available (see DMP) and accessible to all. We will communicate our results in an openly accessible and timely manner (see Pathways to Impact and DMP). Data generated will be amenable to the development of new algorithms to infer transmission, selection, variation, etc. For example, datasets from previous studies carried out by us have been used by others to develop methods to analyse virus genetic variation; infer transmission; and explore the clonal structure of viruses.
This project will benefit the PDRA involved in it because the project itself is a training opportunity. On top of that, we want to use this research as a platform for career development. To this end, this project will result in publishable outputs that will enhance the PDRA's CV. We will encourage the use of career development workshops and mentorship programs available at the University of Glasgow, aligned to the Researcher Development Concordat. We have a PhD studentship available(starting October 2020) at the CVR to study influenza transmission dynamics. The PDRA will co-supervise this student, thus gaining crucial supervisory experience. This will also benefit the PhD student as he/she will compare and contrast results from this project that involve natural field transmission, with experimental work.