The Modern Equine Vet
September 2026
Vol 16 Issue 9 2026
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Experts warn ‘Super’ El Niño could bring surge in mosquito-borne equine infections

By Adam Marcus

By Adam Marcus

Equine health experts are raising the alarm about a potential surge in mosquito-borne infections as heavy rains predicted to accompany the so-called “super El Niño” arrive in the coming months.

El Niños are weather and climate events that emerge from warm currents in the Pacific Ocean and typically bring heavier-than-normal precipitation to the Southern and Eastern parts of the United States. According to the National Oceanic and Atmospheric Administration, the country is already experiencing a rapidly developing El Niño that is highly likely to become a “super El Niño” this fall. Super El Niños are marked by ocean temperatures at least 2 °C warmer than normal.

Although the effects of El Niños are unpredictable, the increased rainfall and warmer temperatures they often generate are ideal conditions for the mosquitoes that transmit arboviruses such as eastern equine encephalitis (EEE) and West Nile virus (WNV).

The mortality rate for unvaccinated horses that contract EEE is nearly 100%, while the rate for West Nile is roughly 45%. Fully vaccinated animals, on the other hand, rarely get sick and almost never experience life-threatening illness.

“Properly vaccinated, there’s no mortality with these infections, but owners need to keep up with annual boosters,” said Maureen T. Long, DVM, PhD, DACVIM, an emeritus professor in the College of Veterinary Medicine at the University of Florida, in Gainesville.

Although most horse owners vaccinate their animals, some may skip years because of cost, Dr. Long explained. Next spring is not the time to cut back, she added. “No year is a year to skip, but this coming season may be a particularly bad one to do so,” she said.

Chrissie Pariseau, DVM, MS, DABVP, a senior equine professional services veterinarian at Merck Animal Health, which recently issued an alert about climate-related threats to horses, said the ideal time to vaccinate against EEE, Western equine encephalitis (WEV) and WNV is just before the start of mosquito season, which can vary depending on geography. “We want to boost a horse’s immunity before they’re going to be exposed. Most of the time that’s early spring, but it can be a little later in some Northern areas,” she said.

Outside of the Southeastern United States, the recommendation is annual vaccination, but in the Southeast, mosquitoes are particularly active even in non-El Niño periods, and they have a longer feeding season. As a result, many veterinarians advise a booster dose within the same calendar year. Texas may also experience a surge in arbovirus diseases, as some areas of the state are prone to flooding,
Dr. Long noted.

The AAEP recommends that adult horses not vaccinated against EEE or WNV receive an initial 2-dose course of injections spaced 4 to 6 weeks apart, although some manufacturers may have different instructions on their labels, Dr. Pariseau noted.

For foals, which likely have some maternally conferred antibodies, the guidance calls for a 3-dose series, with the first 2 shots given when a foal is between 4 and 6 months old, followed by the third injection given between 10 and 12 months of age. “That usually puts the third dose of the initial series just before the start of mosquito season,” Dr. Pariseau said.

Dr. Pariseau stressed that imported horses sometimes fall through the cracks and are not adequately immunized. “Sometimes those horses come with the history of being ‘fully vaccinated’, but what’s fully vaccinated in another country might be different from what we consider fully vaccinated in the United States,” she said. “They should be treated as naive horses. They need that initial 2-dose series.”

The effects of El Niños on mosquito populations often extend well beyond the immediate cycle. Studies of previous events show elevated mosquito activity—and increases in associated infectious diseases—for 2 to 3 years after the El Niño came and went.

Long-term problem
As a result, Dr. Long said, equine veterinarians should expect more arboviruses to circulate in areas hit by increased rainfall until 2029. “Veterinarians should work with their clients to make vaccination as accessible as possible, especially over the next couple of years,” she added.

Beyond promoting vaccination against arboviral infections, Dr. Long said equine veterinarians should also be vigilant about reporting cases of such diseases when they see them. “In addition to wanting to prevent these infections, we need to be reporting them and following up on them,” she said. “It’s part of our responsibility as veterinarians.”

Farm management to decrease mosquito breeding sites is also key, Dr. Long said. “Remove debris and any standing water, and vessels with water such as stock tanks and water buckets should be cleaned frequently,” she said. MeV

 

This illustration depicts a silhouette of a mosquito that was in the process of obtaining its blood meal from its warm-blooded host. After inserting its flexible, straw-like proboscis through the skin and piercing an arteriole, the blood travels up the proboscis into the mouth. However, while obtaining blood, microorganisms travel back through the proboscis (green arrow) into the host’s blood supply, acting as a vector for diseases such as West Nile virus, Mosquito-borne equine infections, horses, equine medicine

This illustration depicts a silhouette of a mosquito that was in the process of obtaining its blood meal from its warm-blooded host. After inserting its flexible, straw-like proboscis through the skin and piercing an arteriole, the blood travels up the proboscis into the mouth. However, while obtaining blood, microorganisms travel back through the proboscis (green arrow) into the host’s blood supply, acting as a vector for diseases such as West Nile virus.
Source Credit: CDC

Mosquito-borne equine infections, horses, equine medicine