The mysterious illness occurred in one of the more remote spots in the horse world: a last-of-its-kind racetrack in rural Hokkaido, Japan, that serves as a venue for a sport known as draft-horse racing. Some 600 Ban’ei horses—a blend of Percheron, Belgian and other heavy breeds—were housed at the track, where they competed by pulling a heavily weighted sledge over a 200-meter course.

The first sign of trouble occurred in 2009, when a few Ban’ei horses—all aged to 2 to 4—became ill. Over the course of several months more and more horses were affected, always developing fevers and sometimes diarrhea. In all, 132 of the 600 horses at the track fell ill but all recovered within a few days. Japanese researchers isolated one potential pathogen from the manure of the sickened horses: equine coronavirus (ECoV), an organism previously associated with illness only in foals.

Later, in early 2011, Ron Vin, DVM, DACVIM, began receiving calls about horses with fever and diarrhea as part of his equine internal medicine consulting work with IDEXX Laboratories. “Those were sporadic cases, and I initially considered them as incidental findings with limited clinical significance,” he says. “My opinion changed when Anne Marie Ray [DVM] and Alice Lombard [DVM] from Washington State consulted with me on a small outbreak of horses with colic, diarrhea and fever they were treating.”

At about the same time, Nicola Pusterla, DVM, PhD, DACVIM, was seeing similar cases at the University of California–Davis. “We started to get reports of outbreaks in horses in 2011, in adult horses and generally horses that were part of large operations, show barns and boarding facilities,” he says. “Horses had relatively nonspecific signs—fever, going off their feed, acting depressed. It was very difficult to pinpoint which organ system was affected in these horses. There was no nasal discharge, no cough and no diarrhea.” Bloodwork showed only leukopenia (a drop in the number of white blood cells), which is a common finding in viral illnesses, and a few horses had mild colic or soft stools.

With only vague, generic signs to go by, researchers began by testing for more common viruses, such as equine herpesvirus-1 and influenza, but everything came up negative. So Pusterla widened the net: “Send us everything you can,” he instructed during the next outbreak. “Blood, nasal secretions, feces, urine, and we’ll test for all the organisms for which we have a test. And the only equine pathogen that was consistently detected was coronavirus.”

Back in New Hampshire, Vin came up with the same findings: “All the horses had consistent presentations and the typical pathology and hematology changes, and of course they were all positive for ECoV.” In total, the researchers tracked the illnesses of 161 U.S. horses in a total of four outbreaks on farms in California, Texas, Wisconsin and Massachusetts between November 2011 and April 2012. Four horses died or were euthanatized due to complications associated with the disease.

One troubling point remained. Before these outbreaks, ECoV had been considered a potential source of illness only in foals—but even that wasn’t certain. In one 2010 survey from Kentucky, ECoV was identified in the feces of 29 percent of foals with diarrhea, but the virus was also found in 27 percent of healthy foals. “The question is, How do you know that equine coronavirus is a true pathogen if it’s detected at the same rate between sick and healthy animals?” Pusterla says. “Plus, we’d never recognized it in adult horses.”

Was the presence of the ECoV in so many of the sick horses just a red herring, a fluke? Or is a new equine disease on the rise?

Pusterla and the other researchers remained cautious: “We knew we had to be careful, because you could also find coronavirus in healthy foals,” he says. So they took their testing one step further. In barns where outbreaks were occurring, they tested manure samples from healthy horses (96 in all) as well as sick ones (44 total). They found that 86 percent (38 out of 44) of the sick horses tested positive for the virus, while 93 percent of the healthy ones (89 out of 96) tested negative. In other words, the likelihood of the presence of ECoV corresponding with clinical signs of illness was 91 percent.

Equine coronavirus did indeed appear to be the sole cause of illness in each of the outbreaks.

Profile of a virus

Coronaviruses are members of the Coronaviridae family, which is known to cause intestinal and respiratory illness in people as well as a large number of domestic animals, including chickens, dogs, cats, pigs, camels and cattle. ECoV belongs to the subfamily called Betacoronavirus, a close relative to bovine coronavirus (BCV), which causes winter dysentery in cows and shipping fever in calves.

Although some coronaviruses spread throughout the body and cause systemic illness, many strains tend to attack only epithelial cells lining the respiratory tract or the intestinal wall, creating localized infections in those places. In the intestine, the viruses tend to damage the villi—the fingerlike projections that line the tract—leading to malabsorption and diarrhea.

Coronaviruses had long been suspected of causing gastrointestinal illness in foals, but there was little definitive proof. Not only was the virus found in healthy animals as well as those who were sick, in many cases the ill horses were also co-infected with rotavirus or other agents known to cause diarrhea.

The first case study of equine illness linked solely to a coronavirus was published in 2000: A Quarter Horse filly developed severe diarrhea at 2 days of age, but her samples were negative for all other known enteric pathogens. The foal deteriorated with multiple complications and was euthanatized. At necropsy, evidence of coronavirus infection was found in her intestinal wall. In this case, the virus was identified via cross-reactivity using the closely-related BCV.

That same year, a coronavirus identified in the feces of a 2-week-old Arabian foal with fever and diarrhea was analyzed genetically and determined to be approximately 90 percent similar to BCV but different enough to be considered a separate viral species, dubbed equine coronavirus, strain NC99. (In this case, the foal recovered from the illness after six days.)

A new urgency

Research on ECoV continued after those cases were published in 2000, but efforts to understand the virus took on a new urgency after the outbreaks occurred among adult horses in 2010. In the years since the first four outbreaks described in Pusterla’s paper, 12 more have been studied in the United States, and one more has occurred at the same racetrack in Japan, involving a strain (ECoV-Tokachi09) different from the one found in the United States. Slowly, researchers are piecing together a clearer picture of the disease.

“Coronavirus infects a wide range of ages, typically middle-aged horses in a boarding facility, and it can affect up to 50 percent of horses with a morbidity rate of 20 to 57 percent,” Pusterla says. Once infected with the virus, the time until signs of illness appear is relatively short—48 to 72 hours.

“Clinical presentation is pretty general—you have a horse that is febrile, with a temperature of 101 to 105 degrees, they’ll go off their feed, they’ll be depressed,” says Pusterla. “In the majority of horses it’s self-limiting. Generally they get better in two to four days with treatment using anti-inflammatories and, if they haven’t been eating or drinking, giving them fluids via nasogastric tubes or intravenously.”

Only a few horses grow more seriously ill. “We started seeing a small percentage of horses, 10 to 15 percent, that would go on to develop gastrointestinal signs, mainly colic but also changes in fecal character, cowpie to watery diarrhea,” Pusterla says. But even those horses generally recover without incident.

However, approximately 7 percent of all horses ill with coronavirus develop fatal complications, such as shock and multiple organ failure. Some exhibit signs of neurological impairment, including circling, head pressing and recumbency. How and why this happens isn’t known, says Pusterla: “One of the theories we have is the virus in some cases can cause such severe pathology in the small intestine that the intestinal wall is breached.”

If the protective mucosal barrier is compromised, bacteria and waste products may leak out of the intestines. Bacteria that reach the bloodstream can cause septicemia, while waste products such as ammonia, a known neurotoxin, can build up in the blood and eventually reach the central nervous system, causing encephalopathy.

So far there’s no evidence that ECoV directly infects the central nervous system in horses. But other coronaviruses do cause encephalitis in cats and mice, so it is a possibility. “I truly hope that our experience with neurological disease in horses affected by equine coronavirus remains minimal,” says Vin, “but efforts to continue investigating the cause of these complications should persist.”

Defensive measures

No vaccine is available to protect a horse from ECoV, and the only treatment is supportive care to manage the signs while he recovers. One bit of good news is that ECoV infection can be diagnosed readily using polymerase chain reaction (PCR), a technique that confirms the presence of a pathogen by identifying nucleic acids. Many laboratories now include this test as part of their standard panel for equine diarrhea, and veterinarians are becoming more aware of ECoV and consider it a possibility when evaluating a horse with fever, anorexia and lethargy, whether or not he’s experiencing changes in manure consistency.

For now, the best way to stop the spread of coronavirus is to keep sick horses isolated in quarantine. The illness clearly passes readily from horse to horse, and because sick animals shed the virus in their manure, it is assumed that it spreads via the fecal-to-oral route—when a horse consumes feed or water contaminated with the virus.

Your veterinarian can help you establish a quarantine strategy that meets your needs, but the general principle is to prevent any contact between ill and healthy horses. Specific measures might include:

• Move the ill horse to a remote stall away from traffic in the aisle. Ideally, you’d have one empty stall between the ill horse and any others in the barn.
• Turn out the ill horse in a separate paddock that does not share a fence with other pastures. In a pinch, you can erect temporary fencing to cordon off a separate portion of the main paddock, but use double fences spaced at least 10 feet apart to prevent any direct contact.
• Designate one person to care for the ill horse who can avoid all contact with the healthy ones. If that’s not possible, then the sole caretaker needs to finish all chores with the healthy horses before approaching the one in isolation.
• Wear protective clothing to avoid spreading contamination. One way to do this is to designate one pair of boots, gloves and coveralls that are washed immediately after caring for the ill horse. You can also buy disposable gowns, gloves and shoe covers like those worn by health-care workers.
• Use a separate set of buckets, halters, grooming brushes and stall-cleaning tools only for the isolated horse. Remember that pathogens can travel on tractor and wheelbarrow tires, so they may need to be scrubbed with a bleach solution after each trip.
• Implement footbaths, shallow trays with a beach solution placed outside the stall. Anyone going in or out of the stall needs to step in it to kill pathogens on their boots.
• Wash hands or use a skin sanitizer after handling each horse, sick or not.

During an outbreak of coronavirus, these measures need to be kept up for at least two, preferably three, weeks after the last ill horse recovers. “We know that horses continue to shed the virus in their feces up to 14 days after complete resolution of clinical signs,” Vin says.

For now the research continues. “We’re still gathering epidemiological information, establishing tests and doing genetic work,” Pusterla says. “Down the road, once we characterize the virus, we may be able to develop more specific preventative measures.”

In a few short years, coronavirus has gone from virtually unknown to the average horse owner to an increasing source of concern. But even as research continues into the nature of this pathogen, we can take steps to protect our horses.

As coronavirus illness becomes easier to recognize, diagnosis can be made more swiftly and sensible biosecurity measures can be put in place to prevent outbreaks from spreading throughout equine populations.

This article first appeared in EQUUS issue #454, July 2015.