How to Prevent Contagious Diseases in Horses

By Dr Duncan Houston

Contagious disease control is not just for big racing yards, breeding farms, or veterinary hospitals.

If your horse travels, shares a barn, goes to shows, meets new horses, uses shared equipment, or lives on a property where horses come and go, biosecurity matters. One sick horse can quickly become a whole-yard problem if fever, nasal discharge, coughing, diarrhoea, swollen glands, or neurological signs are missed early.

The good news is that biosecurity does not need to be complicated. It needs to be consistent.

The real goal is simple: reduce the chance of disease entering your property, spot illness early, and stop one horse from infecting the rest of the barn.

Quick Answer

The best way to prevent contagious diseases in horses is to combine vaccination, quarantine for new or returning horses, twice-daily temperature monitoring during risk periods, no sharing of buckets or grooming gear, good hand hygiene, clean and disinfected equipment, and immediate isolation of any horse showing signs of illness. New and returning horses should be kept separate and monitored for at least 14 days, while some diseases or exposure events may require longer quarantine under veterinary guidance. A temperature above 101.5°F, coughing, nasal discharge, swollen lymph nodes, diarrhoea, neurological signs, or sudden dullness should prompt isolation and veterinary advice. (equinediseasecc.org)

What Is Biosecurity?

Biosecurity means the practical steps used to prevent infectious diseases from entering a horse population and to reduce spread when disease is already present.

That includes:

• Quarantine

• Isolation

• Vaccination

• Hygiene

• Equipment control

• Visitor control

• Travel precautions

• Temperature monitoring

• Disinfection

• Manure management

• Early veterinary testing

• Clear communication during outbreaks

AAEP defines biosecurity as practices intended to prevent the introduction and minimise the spread of infectious disease agents in equine populations. (AAEP)

In plain English: biosecurity is how you stop germs hitchhiking from one horse to the next.

Why Biosecurity Matters So Much in Horses

Horses are brilliant at sharing germs.

They sniff each other, drink from shared buckets, touch fences, travel in trailers, share airspace at shows, use common wash bays, and live in environments where people, dogs, vets, farriers, trainers, staff, and visitors move between animals.

A contagious disease can spread by:

• Direct nose-to-nose contact

• Coughing and respiratory droplets

• Nasal discharge

• Manure contamination

• Shared water buckets

• Shared feed tubs

• Grooming brushes

• Bits, bridles, halters, and lead ropes

• Thermometers

• Muck forks and wheelbarrows

• Hands, clothing, and boots

• Trailers

• Stalls

• Insects, depending on the disease

The mistake I see most often is owners thinking biosecurity starts once a diagnosis is confirmed. It does not. It starts the moment a horse looks “a bit off.”

By the time a lab result comes back, the horse may already have exposed others.

Which Contagious Diseases Are We Trying to Prevent?

Biosecurity does not target one disease. It reduces risk across many infectious problems.

Common contagious or outbreak-relevant equine diseases include:

Disease	Main concern	Why biosecurity matters
Equine influenza	Fever, cough, nasal discharge, rapid spread	Highly contagious respiratory virus
Equine herpesvirus	Respiratory disease, abortion, neurological disease	Can spread by contact, droplets, equipment, and carriers
Strangles	Fever, swollen lymph nodes, abscesses	Highly infectious and can persist through carrier horses
Equine coronavirus	Fever, dullness, diarrhoea, colic signs	Spreads mainly through manure contamination
Salmonella and other enteric infections	Diarrhoea, fever, dehydration, systemic illness	Can spread through manure and contaminated environments
Equine infectious anaemia	Serious blood-borne viral disease	Spread by blood-feeding insects and contaminated blood exposure
Ringworm and skin infections	Hair loss, crusting, skin lesions	Spread through direct contact and contaminated tack or grooming gear

EHV can cause fever, nasal discharge, swollen limbs, lethargy, abortion, neonatal disease, and neurological disease, and it can be spread through direct contact, respiratory secretions, contaminated clothing, and equipment. (equinediseasecc.org)

Strangles is caused by Streptococcus equi and spreads through direct contact and contaminated surfaces. Carrier horses can also continue to shed bacteria after apparent recovery, which is why outbreak follow-up matters. (equinediseasecc.org)

Equine infectious anaemia is a viral, sometimes fatal disease of equids with no treatment, and it is reportable in all US states. It is not considered a threat to human health. (APHS)

The First Rule: Know Your Horse’s Normal Temperature

A thermometer is one of the cheapest and most useful biosecurity tools in the barn.

A fever is often one of the earliest signs of infectious disease. During higher-risk periods, such as after travel, after shows, after a new arrival, or during a suspected outbreak, take temperatures twice daily and record them.

The Equine Disease Communication Center advises that temperatures should be taken before giving fever-reducing medications, and that any temperature above 101.5°F, or above 101.0°F in a horse already on anti-inflammatory medication, should be reported to a veterinarian. (equinediseasecc.org)

Monitor for:

• Fever

• Reduced appetite

• Dullness

• Coughing

• Nasal discharge

• Swollen lymph nodes

• Diarrhoea

• Colic signs

• Limb swelling

• Neurological signs

• Sudden behaviour change

In practice, “he just seems quiet” plus a fever is enough reason to take the situation seriously.

Quarantine New and Returning Horses

New horses and returning horses are one of the biggest disease risks on a property.

This includes horses returning from:

• Shows

• Clinics

• Trail rides

• Racing or training centres

• Breeding farms

• Veterinary hospitals

• Sales

• Agistment or boarding facilities

• Transport with unknown horses

A practical minimum is to keep new or returning horses separate for at least 14 days, with twice-daily temperature checks and daily monitoring of appetite, water intake, manure, urination, and any signs of illness. The EDCC specifically recommends keeping new and returning horses separate and monitored for at least 14 days. (equinediseasecc.org)

For some situations, 14 days is not enough. EHV exposure, confirmed outbreaks, strangles, hospital return, or disease-specific risk may require longer quarantine and veterinary testing.

Merck notes that new horses or horses returning from other premises should be isolated for 21 days before mixing with resident horses, especially around pregnant mares, in the context of EHV prevention. (Merck Veterinary Manual)

The safest mindset is this: quarantine is not punishment. It is a health buffer.

How To Set Up a Proper Quarantine Area

A quarantine area should be separate enough that the new or returning horse does not share airspace, nose contact, water, feed, equipment, or handlers with the main herd.

A good quarantine setup includes:

• Separate stall or paddock

• No shared fence line if possible

• Dedicated water bucket

• Dedicated feed tub

• Dedicated grooming gear

• Dedicated muck fork and wheelbarrow

• Dedicated thermometer

• Separate hand-washing or sanitising supplies

• Clear signage

• Restricted visitor access

• Daily health log

If the same person must care for quarantine horses and resident horses, handle the healthy resident horses first and the quarantined horse last.

Do not use quarantine time to “just let them sniff over the fence.” That is how quarantine turns into a meet-and-greet for microbes.

Isolate Sick Horses Immediately

Quarantine is for horses that may be carrying disease.

Isolation is for horses showing signs of disease.

If a horse develops fever, cough, nasal discharge, diarrhoea, swollen lymph nodes, neurological signs, or sudden dullness, isolate that horse immediately and call your veterinarian.

EDCC advises immediately isolating horses showing clinical signs and isolating objects that have contacted the horse, including tack, grooming brushes, stall-cleaning tools, buckets, feeders, and water troughs. (equinediseasecc.org)

Isolation should include:

• No nose-to-nose contact

• No shared equipment

• No shared water

• No shared feed

• Restricted access

• Gloves or hand hygiene

• Dedicated clothing or coveralls where possible

• Boots or boot covers

• Separate manure handling

• Clear communication to all staff and owners

The worst thing to do is wait until “we know what it is.” If it looks contagious, act contagious until proven otherwise.

Biosecurity at Home

Home biosecurity should be routine, not something you invent in a panic.

Daily or weekly habits include:

• Check horses for appetite, attitude, cough, discharge, manure changes, and movement

• Keep individual feed and water buckets

• Avoid sharing grooming gear where possible

• Clean buckets and feed tubs regularly

• Store feed away from manure handling areas

• Wash hands or use sanitiser between horses when needed

• Keep sick-horse equipment separate

• Control visitors, especially those coming from other horse properties

• Ask farriers, bodyworkers, trainers, and visiting professionals to use clean tools and footwear

• Keep vaccination and health records current

For shared facilities, colour-coded equipment is useful. One horse, one bucket, one brush set, one labelled gear area. Not glamorous, but neither is a strangles outbreak.

Cleaning vs Disinfecting

Cleaning and disinfecting are not the same thing.

Cleaning removes visible dirt, manure, bedding, saliva, mucus, and organic material.

Disinfecting uses a chemical product to kill or reduce pathogens after cleaning.

This matters because disinfectants do not work properly on dirty surfaces. EDCC states that surfaces cannot be disinfected if organic matter is present, and recommends scrubbing with warm, soapy water before applying disinfectant. (equinediseasecc.org)

The correct order is:

1. Remove manure, bedding, feed, and visible dirt.

2. Wash with detergent or warm soapy water.

3. Rinse if needed.

4. Let the surface dry.

5. Apply the correct disinfectant at the correct dilution.

6. Allow the proper contact time.

7. Let it dry before reuse.

Do not spray disinfectant over manure and call it done. That is not biosecurity. That is perfume for pathogens.

What Should Be Disinfected?

During routine cleaning, focus on high-contact areas.

During illness or outbreak risk, increase cleaning and disinfection of:

• Water buckets

• Feed tubs

• Thermometers

• Stall doors

• Latches

• Cross ties

• Lead ropes

• Halters

• Bits

• Grooming tools

• Muck forks

• Wheelbarrow handles

• Wash bays

• Trailer dividers

• Trailer ties

• Stable walls

• Mats

• Door handles

• Shared equipment areas

EDCC lists bleach at 1 part bleach to 10 parts water, accelerated hydrogen peroxide, and phenolic products as possible disinfectants, while reminding owners to follow product label directions and safety precautions. (equinediseasecc.org)

Leather tack can be difficult to disinfect properly, so avoid sharing it during disease risk periods.

Biosecurity When Travelling

Travel increases disease risk because horses mix with unfamiliar horses, shared surfaces, shared airspace, and stressful environments.

Before travel:

• Check your horse’s temperature for several days before leaving

• Do not travel a horse that is coughing, febrile, dull, or off feed

• Check event health requirements

• Keep vaccination records current

• Confirm Coggins or EIA testing requirements where relevant

• Pack your own buckets, feed, hay, water, grooming gear, and thermometer

• Clean and disinfect the trailer before loading

• Avoid sharing transport with horses of unknown health status

At the event:

• Avoid nose-to-nose contact

• Do not share buckets

• Do not share hay nets

• Do not use communal water troughs if avoidable

• Keep your horse at your trailer or assigned stall

• Avoid letting strangers pet or feed your horse

• Wash or sanitise hands after touching other horses

• Do not graze in high-traffic manure-contaminated areas

• Monitor temperature and attitude daily

• Report sick horses to event management

After returning home:

• Quarantine or separate your horse from the main herd

• Check temperature twice daily

• Clean and disinfect travel gear

• Monitor appetite, manure, cough, discharge, and behaviour

• Do not rush straight back into the resident herd

EDCC recommends event isolation planning, and notes that recognised events should have isolation protocols for horses suspected of infectious disease. (equinediseasecc.org)

Vaccination Is Part of Biosecurity, Not a Replacement

Vaccination is essential, but it does not replace quarantine, hygiene, or disease monitoring.

Vaccines reduce the risk, severity, and spread of some diseases, but they do not create a magic force field around the horse.

AAEP divides vaccines into core and risk-based categories. Core vaccines are recommended because of severity, public health relevance, regional endemic risk, or broad patient benefit. Risk-based vaccines depend on exposure, travel, geography, age, use, and individual horse risk. (AAEP)

Core and risk-based discussions may include:

• Tetanus

• Rabies where relevant

• Eastern and Western equine encephalomyelitis

• West Nile virus

• Equine influenza

• EHV-1 and EHV-4

• Strangles

• Potomac horse fever

• Botulism

• Equine viral arteritis

• Rotavirus in breeding settings

• Other region-specific diseases

For influenza, AAEP notes that horses at increased risk of exposure may be revaccinated every 6 months, and that some facilities or competitions require vaccination within the previous 6 months. (AAEP)

For EHV, vaccines can help reduce respiratory disease signs and abortion risk, but EDCC notes that there is currently no vaccine labelled to prevent the neurological form, EHM. (equinediseasecc.org)

The practical message is: vaccinate properly, but still quarantine properly.

Risk Framework: How Worried Should You Be?

Low Risk

Low risk means your horse is bright, eating, afebrile, has no cough, no nasal discharge, no diarrhoea, no swollen lymph nodes, no neurological signs, and has not recently mixed with unknown horses.

Action: Continue routine monitoring, vaccination planning, hygiene, and sensible equipment management.

Moderate Risk

Moderate concern includes recent travel, a new arrival, return from hospital, mild cough, mild clear nasal discharge, slight dullness, or exposure to a horse from an unknown health background.

Action: Separate the horse, monitor temperature twice daily, avoid sharing equipment, and contact your vet if signs persist, worsen, or fever appears.

High Risk

High concern includes fever above 101.5°F, thick nasal discharge, coughing, swollen lymph nodes, diarrhoea, reduced appetite, multiple horses showing signs, recent exposure to a confirmed infectious disease, or a horse returning from a high-risk facility.

Action: Isolate immediately and call your veterinarian. Testing, quarantine, and movement restrictions may be needed.

Critical Risk

Critical concern includes neurological signs, inability to stand, severe respiratory distress, severe diarrhoea, dehydration, colic signs with fever, suspected EHV neurological disease, suspected strangles outbreak with multiple horses affected, or sudden severe illness in several horses.

Action: Treat this as urgent. Stop horse movement, isolate affected horses, call your vet, and follow disease-control instructions.

What Else Could Look Like a Contagious Disease?

Not every cough or fever is an outbreak, but every possible outbreak deserves respect until proven otherwise.

Important rule-outs include:

• Dust irritation

• Equine asthma

• Seasonal allergies

• Dental disease causing nasal discharge

• Sinus disease

• Choke

• Pneumonia

• Viral respiratory disease

• Strangles

• EHV

• Influenza

• Equine coronavirus

• Salmonella

• Clostridial diarrhoea

• Potomac horse fever in relevant regions

• Parasites

• Heat stress

• Transport stress

• Toxicity

• Colic unrelated to infection

• Neurological trauma or spinal disease

• Tick-borne or vector-borne disease depending on region

The key is not guessing. The key is separating the horse first, then working with your vet to decide what needs testing.

When Is This an Emergency?

Call a veterinarian urgently if your horse has:

• Temperature above 101.5°F with dullness or other signs

• Coughing with fever

• Thick yellow, green, bloody, or foul nasal discharge

• Swollen or painful lymph nodes

• Difficulty breathing

• Not eating

• Severe diarrhoea

• Colic signs

• Dehydration

• Abnormal gum colour

• Sudden hindlimb weakness

• Incoordination

• Urine dribbling

• Loss of tail tone

• Recumbency or inability to stand

• Abortion

• Sudden severe illness after travel

• Multiple horses sick on the same property

• Known exposure to EHV, influenza, strangles, or another reportable disease

EHV neurological disease can involve incoordination, hind-end weakness, urine dribbling, reduced tail tone, recumbency, and in severe cases paralysis. EDCC notes that testing and quarantine are primary disease-control tools for EHV. (equinediseasecc.org)

If neurological signs appear, do not move the horse unless directed by a veterinarian. Movement can create more risk and spread exposure.

What Should You Do If You Suspect a Contagious Disease?

1. Stop movement

Do not take the horse to a show, clinic, trail ride, breeding farm, or another property.

Do not move other horses off the property unless your veterinarian says it is safe.

2. Isolate the horse

Move the horse to a pre-planned isolation area if safe. If not, treat the current stall or paddock as the isolation zone.

3. Call your veterinarian

Give your vet:

• Temperature

• Heart rate and breathing rate if known

• Appetite

• Manure changes

• Cough or nasal discharge details

• Swollen lymph node details

• Travel history

• New horse arrivals

• Recent events attended

• Number of horses exposed

• Number of horses showing signs

• Vaccination history

4. Use dedicated equipment

Immediately separate:

• Buckets

• Feed tubs

• Thermometer

• Grooming tools

• Halter and lead

• Muck fork

• Wheelbarrow

• Towels

• Rugs or blankets

• Cleaning supplies

5. Handle sick horses last

Healthy horses first. Sick or exposed horses last.

Then wash hands, change clothing if possible, and clean footwear.

6. Start a health log

Record twice daily:

• Temperature

• Appetite

• Water intake

• Manure

• Cough

• Nasal discharge

• Swollen glands

• Behaviour

• Limb swelling

• Neurological signs

• Medications given

7. Wait for veterinary guidance before ending isolation

Different diseases require different release criteria. For example, strangles may require follow-up testing to identify carrier status, and EHV or influenza outbreaks may require specific isolation periods after clinical signs resolve. AAEP strangles guidance notes that guttural pouch lavage PCR combined with endoscopy is the test of choice for determining recovered animal status. (AAEP)

Common Mistakes Horse Owners Make

Waiting for a diagnosis before isolating

Isolation should start when contagious disease is suspected, not after a lab report confirms it.

Sharing thermometers

Rectal thermometers can spread infectious material if not properly disinfected. Use individual thermometers where possible.

Letting horses touch noses at shows

A quick sniff can be enough contact to matter, especially around respiratory disease.

Using communal water sources

Shared troughs and buckets are easy disease-transfer points.

Forgetting returning horses

Your own horse can bring disease home after travel. Familiar horse does not mean low-risk horse.

Cleaning without disinfecting, or disinfecting without cleaning

Both matter. Disinfectant on top of manure is not effective biosecurity.

Ending quarantine too early

A horse may look normal before the risk is over. Some diseases require longer isolation or testing.

Not telling other owners

During a suspected outbreak, silence spreads disease. Clear communication protects the whole yard.

How To Prevent Disease Spread at Shows and Events

A good travel biosecurity kit should include:

• Digital thermometer

• Disposable gloves

• Hand sanitiser

• Disinfectant wipes

• Spray disinfectant

• Own buckets

• Own feed tubs

• Own hay net

• Own grooming kit

• Own mucking tools if practical

• Paper towels

• Rubbish bags

• Copy of vaccination records

• Coggins or EIA paperwork where required

• Emergency vet contact details

At shows, keep your horse’s bubble boring.

That means no shared buckets, no random nose contact, no communal water, no borrowed brushes, no mystery treats from friendly strangers, and no casual handshakes between every horse in the aisle. Horses do not need networking events. Their immune systems are already busy enough.

Disease-Specific Notes Owners Should Know

Equine influenza

Equine influenza spreads rapidly through respiratory secretions, droplets, contaminated surfaces, and close horse contact. EDCC states that prevention includes isolation and increased biosecurity for 14 days after clinical signs resolve. (equinediseasecc.org)

Equine herpesvirus

EHV can cause respiratory disease, abortion, neonatal disease, and neurological disease. Horses can carry EHV without clinical signs and may shed virus. Vaccines can reduce respiratory disease signs and abortion risk, but they do not guarantee prevention of neurological EHV. (equinediseasecc.org)

Strangles

Strangles is highly infectious and can spread through direct horse contact or contaminated surfaces. Carrier horses can continue shedding intermittently, which is why testing and veterinary-directed release from isolation are important after outbreaks. (equinediseasecc.org)

Equine infectious anaemia

EIA is blood-borne and can be spread by blood-feeding insects and contaminated blood exposure. Testing requirements vary by region, but many events and movements require proof of a recent negative Coggins test. (APHS)

Equine coronavirus and diarrhoeal disease

Gut-based infectious diseases require especially careful manure control, dedicated mucking tools, gloves, and cleaning before disinfecting. Shared wheelbarrows, forks, boots, and dirty hands can spread manure contamination faster than people realise.

Prevention Checklist for Horse Properties

A strong prevention plan includes:

• Current vaccination plan made with your vet

• Written quarantine policy

• Isolation area identified before it is needed

• Twice-daily temperature monitoring during high-risk periods

• No shared buckets for new, returning, or sick horses

• Dedicated equipment for quarantine and isolation

• Clear visitor policy

• Hand hygiene stations

• Clean footwear policy

• Event return protocol

• New horse arrival protocol

• Trailer cleaning protocol

• Manure management plan

• Staff and boarder communication plan

• Emergency vet contact list

• Records for vaccines, travel, temperatures, and illness

If you manage a boarding barn or training facility, write the protocol down. A biosecurity plan that lives only in someone’s head will disappear the moment everyone panics.

FAQs

How long should I quarantine a new horse?

At least 14 days is a common minimum for new or returning horses, with twice-daily temperature checks and daily health monitoring. Higher-risk situations, EHV exposure, strangles risk, or hospital return may require longer quarantine under veterinary guidance. (equinediseasecc.org)

What temperature is a fever in a horse?

A temperature above 101.5°F should be reported to a veterinarian, especially if the horse is dull, coughing, off feed, recently travelled, or has been exposed to sick horses. Temperature should be taken before giving fever-reducing medications. (equinediseasecc.org)

Should horses share water buckets at shows?

No. Shared water buckets and troughs increase disease risk. Bring your own buckets and avoid communal water sources whenever possible.

Can vaccination prevent all contagious diseases?

No. Vaccination reduces risk and severity for some diseases, but it does not replace quarantine, hygiene, isolation, and monitoring. Risk-based vaccines should be selected with your veterinarian based on your horse’s travel, location, age, use, and exposure risk. (AAEP)

What should I do first if my horse starts coughing after a show?

Take the temperature, isolate the horse from others, stop travel, monitor appetite and nasal discharge, and call your veterinarian if there is fever, dullness, thick discharge, worsening cough, or other horses showing signs.

Final Thoughts

Biosecurity is not about being paranoid. It is about being prepared.

Most contagious disease outbreaks do not start with chaos. They start with one horse that is a little quiet, one shared bucket, one borrowed brush, one new arrival turned out too quickly, or one fever that was not checked until three days later.

The best protection is not one dramatic action. It is a boring, consistent system: vaccinate properly, quarantine new and returning horses, isolate sick horses early, stop sharing equipment, clean before disinfecting, monitor temperatures, and communicate quickly when something looks wrong.

One horse getting sick is sometimes unavoidable.

Letting that one horse infect the whole barn is often preventable.

---

If you are unsure whether your horse’s cough, fever, nasal discharge, diarrhoea, swollen glands, travel exposure, or outbreak risk needs isolation or veterinary testing, ASK A VET™ can help you decide what can be monitored, what needs a vet visit, and what should be treated as urgent.