Equine influenza (flu)

Picture of two horses looking down at camera.

What is equine influenza?

Equine influenza is a highly contagious respiratory disease of horses and other equidae. It is caused by two subtypes of the influenza A virus, which are related to, but distinct from, influenza viruses in other species. Equine influenza virus spreads easily through contact with infected horses and via contact with infected clothing, equipment, brushes, tack, etc. Some horses do not show any outward signs of infection, but can shed the virus and infect susceptible horses. Outbreaks result in significant economic losses to the equine industry, and are more likely to occur where large groups of horses gather, such as shows, races and events. Increased transportation of horses across state lines and between countries facilitates the spread of the virus.

Two types of influenza virus routinely circulate and cause seasonal flu epidemics in people: influenza A (which has multiple sub-types) and influenza B. Influenza A viruses are also found in animals and occasionally cross species barriers, causing serious illness and acting as the source of pandemics.

Strains of influenza A virus are named with H’s and N’s. H stands for hemagglutinin and N for neuraminidase. Both are proteins on the surface of the virus (antigens) that help it invade cells. There are 18 different H subtypes and 11 N subtypes, resulting in 198 possible combinations. Sometimes the strains trade genetic information, taking on new characteristics that our immune systems have never seen. This can lead to severe illness, and even death. Recent cross-species flu outbreaks include H5N1 “bird flu” and H1N1 “swine flu”, transmitted from birds to humans and pigs to humans, respectively.

Equine influenza sub-types are H7N7, which is thought to be extinct, and the current H3N8, which is spread widely throughout the world. The H3N8 subtype is further broken down into sublineages, with the Florida sublineage currently circulating. Clades 1 and 2 of this sublineage circulate in Europe. Clade 1 commonly circulates in North America (Figure 1). The H3N8 strain of equine influenza is not known to infect humans. This is partly due to the fact that there is minimal evolutionary pressure to generate strains with higher virulence, so the equine influenza virus evolves slowly in comparison to other influenza viruses.

Image showing sublineages of equine influenza.
Figure 1. Equine influenza H3N8 American and Eurasian sublineages.

What are the clinical signs of equine influenza?

Picture showing nasal discharge.
Nasal discharge is one of the potential signs of an equine influenza infection.

Equine influenza is a highly contagious respiratory disease with a high rate of transmission among horses and a short incubation time (1-3 days). It is spread by infected, coughing horses, contaminated buckets, brushes, tack, etc. Coughing horses aerosolize the organism and can spread the virus as far as 150 feet, quickly infecting an entire barn. Infected horses can shed the virus for up to 14 days post-infection. Humans can also spread the virus between horses through contaminated hands and clothing. Lastly, many horses are asymptomatic shedders of the virus, meaning that they are immune and won’t get sick, but the virus can still replicate and spread to other horses.

Similar to herpesviruses and Streptococcus equi subspecies equi (agent of strangles), greater incidence of infection is observed in colder months. Abrupt onset of clinical signs is common, and they usually last less than 3 days. Sick horses can exhibit fever, nasal discharge, cough, lethargy, loss of appetite and weakness. A cough is one of the most notable signs of equine flu. The virus causes destruction of cells in the throat and lungs, which take 3 weeks to regenerate. As a result, horses are particularly susceptible to secondary infections such as bacterial pneumonia during the first 2-3 weeks after infection.

How is equine influenza diagnosed?

Since respiratory signs of equine influenza are similar to those of other respiratory diseases, infection cannot be diagnosed based on clinical signs alone. The testing window is short in previously vaccinated horses. If samples are tested too late in the disease process, results may come back negative. Virus isolation is primarily performed by diagnostic testing laboratories on nasal swab samples collected from sick horses soon after infection. Diagnosis can also be determined through testing of serum samples.

The UC Davis Real-time PCR Research and Diagnostics Core Facility performs equine influenza A (H3N8) testing as part of an equine respiratory panel that also tests for equine herpesvirus 1 and 4, Streptococcus equi subspecies equi, equine rhinitis A virus, and equine rhinitis B virus. Quantitative PCR (qPCR) is quick (same day turnaround time), highly sensitive, accurate, and specific. This is the only laboratory that includes clade differentiation (identification of clade 1 vs. clade 2) in standard testing protocols. From 2017 to February 2019, the UC Davis facility tested 3475 samples, 273 (7.86%) of which tested positive by qPCR for EIV.

How is equine influenza treated?

Horses that do not develop complications are treated with rest and supportive care. Animals that are confirmed EIV positive should be on stall rest and taken out of training for a minimum of one week for every day of fever. If fever goes above 104oF (40oC), non-steroidal anti-inflammatories (NSAIDs) may be administered. In some cases, such as if fever persists, purulent nasal discharge is present, or if horses get pneumonia, antibiotics may be indicated. Horses should be returned to work gradually. As a general rule, they should have one week off for every day of fever. This allows adequate time for their lungs to recover following the infection.

What is the prognosis for equine influenza?

The prognosis for infected horses is good, with recovery occurring in approximately 2-3 weeks. Although equine influenza infection very rarely results in fatality, severely affected horses can be out of work for up to 6 months.

How can equine influenza be prevented?

Equine influenza is a virus that has significant impacts, but through proper vaccination and biosecurity, handlers do have some control over the outcome of infections. Owners, riders, grooms and trainers can minimize the risk of infection by following vaccination recommendations from the American Association of Equine Practitioners (AAEP), adhering to proper biosecurity protocols, working closely with their veterinarians, and being proactive (taking temperatures, isolating horses) when they notice possible signs of infection.

In the US, the equine influenza virus circulates at variable but relatively low levels throughout the year. Surges of activity can result in outbreaks, usually during the winter months (November – March). It is important to work closely with your veterinarian to ensure that your horse(s) is on an appropriate vaccination schedule.

Although vaccination is not a silver bullet, it is one of the best available defenses against this disease. In the event that a vaccinated horse becomes infected, disease is less severe and vaccinated horses shed the virus for fewer days. In a population of unvaccinated horses that have no prior exposure to the virus, infection rate is 100% and the virus can mutate quickly. The World Organization for Animal Health (OIE) recommendations specify that vaccines should contain contemporary strains (clades 1 & 2 of the Florida sublineage H3N8 EIV strains) unless it is a modified live vaccine. Immunity develops at different rates depending upon the type of vaccine that is administered, with the intranasal vaccination providing the quickest immune response. For competition horses that travel frequently, annual vaccination is recommended, with a booster every 6 months.

An increase in events and corresponding increases in transportation of horses lead to outbreaks of infectious diseases like equine influenza. Proper biosecurity measures, protocols to reduce pathogen transmission, and awareness of signs of illness are important prevention measures. Handlers should communicate with owners and veterinarians at event facilities to determine risk and reevaluate vaccination schedules as needed. Quarantine newly arrived horses away from the resident population for a sufficient amount of time to ensure that they are not bringing in any infectious diseases. Familiarize yourself with clinical signs of equine influenza and be on particular lookout for them during winter months. If flu is suspected, have your veterinarian collect appropriate samples and send them to a diagnostic laboratory for testing. Adequate precautions and increased awareness will minimize the spread of this highly infectious respiratory disease. 

*This article may not be reproduced without the written consent of the UC Davis Center for Equine Health. Please email requests to cehadmin@ucdavis.edu