Technology improves identification of common viruses

Bovine respiratory disease is usually considered the most important economic and costly disease of beef cattle.

Estimates vary, but up to 75 percent of the antimicrobial treatments and 50 percent of the mortality in feedlot cattle can be attributed to respiratory disease.

Stressors such as weaning, transport and mixing play an important role in the disease by compromising the animal’s immune system. Mixing and crowding may also play a role in the transmission of viruses and bacteria between animals.

There are a variety of bacteria and viruses associated with BRD and they often work in combination to cause respiratory disease.

Viruses may suppress parts of the normal defence mechanisms of the respiratory tract or alter the immune system, allowing various bacteria to colonize the lungs and cause pneumonia.

Bacteria commonly associated with respiratory disease include Mannheimia hemolytica, Pasteurella multocida, Histophilus somni and Mycoplasma bovis.

We have commercial vaccines available for all of these with the exception of Mycoplasma bovis. These vaccines are often included as part of the control strategy against respiratory disease in feedlot cattle.

Viruses commonly associated with respiratory disease include infectious bovine rhinotracheitis (IBR), parainfluenza 3 virus (PI3), bovine respiratory syncytial virus (BRSV) and bovine viral diarrhea virus (BVD). All four of these viruses are usually included in commercial vaccines given to feedlot cattle and to cows and calves in cow-calf herds.

Traditionally, researchers and diagnosticians would identify viruses from nasal swabs or tissue samples using a technique known as virus isolation. The virus would have to be grown on a special cell culture in the laboratory and then identified.

In some cases, researchers and veterinarians might use blood samples to identify antibodies in the blood to various viruses to demonstrate that an animal has been exposed to the virus. Both of these techniques are slow to give an answer and tend to be used only for targeted and specific viruses.

However, major advances now allow researchers to use a new technology known as “high throughput sequencing” where instead of growing viruses individually, they use the nasal swab to identify all of the DNA or RNA molecules present in the sample and sequence those molecules.

Researchers can then computationally sort through the vast amount of information and identify the genetic material that is associated with various viruses by sequencing these nucleic acid fingerprints. This rapidly evolving field of research and diagnostics is known as metagenomics.

A recent paper in the Transboundary and Emerging Diseases Journal was written by a group of researchers using these new techniques to explore the viruses associated with bovine respiratory disease in western Canadian feedlot cattle.

The research team included researchers from Prairie Diagnostic Services, the University of Saskatchewan, the University of Calgary and Agriculture Canada. They used metagenomics techniques to identify viruses from samples taken from 116 cattle from four southern Alberta feedlots.

The researchers sampled cattle that were identified as sick with respiratory disease and also sampled cattle that were healthy control animals.

The sick cattle were identified by pen checkers as having clinical signs of BRD and they were confirmed to have a fever as well as abnormal lung sounds and evidence of inflammatory markers in their blood.

Researchers also sampled an equal number of healthy animals. Samples including a deep nasal swab as well as a tracheal fluid aspirate.

The samples were taken for metagenomic sequencing to identify the genetic material associated with various viruses within the samples. It is important to remember that all of these cattle were vaccinated at arrival for IBR, BVD, PI3 and BRSV virus with a commercial vaccine.

The researchers identified a list of 21 viruses from these samples. However, when they compared the viruses identified in the sick cattle to the viruses identified in the healthy cattle, four suspects immediately stood out. The four viruses that seem to be associated with respiratory disease included influenza D virus, bovine rhinitis B virus, bovine respiratory syncytial virus (BRSV) and bovine coronavirus.

All four of these viruses were much more commonly seen in cases of respiratory disease than in the healthy controls, which could suggest that they might play a role in disease development.

It was interesting that only one of these four viruses (BRSV) was one of the usual suspects for which we currently have commercial vaccines. BRSV virus was identified in 17 percent of the case samples and two percent of the control samples. Bovine viral diarrhea virus and PI3 virus were identified in one or two samples and IBR virus was not identified at all. Perhaps this is because the vaccines we are using are fairly efficacious for these particular viruses.

However, a number of viruses were identified that seem to be potentially associated with respiratory disease for which we currently do not have vaccines. These included influenza D virus, which was found in 22 percent of case samples and five percent of healthy controls. Influenzas D virus was first identified in pigs in the United States. Several studies have since identified this virus as relatively common in cattle populations around the world. In the western Canadian study, almost all of the influenza D virus was found in the nasal swab samples and almost none in the samples from lower in the respiratory tract.

The other two viruses associated with respiratory disease were bovine rhinitis B virus and bovine coronavirus. Bovine coronaviruses have long been suspected of playing a role in bovine respiratory disease and this study provides further evidence of that, with 19 percent of the sick animals having the virus compared to three percent of the controls.

The bovine rhinitis B virus was seen in 28 percent of the cases and 10 percent of the healthy controls. This appears to be the first evidence of this particular virus being reported in Canadian cattle.

These results may eventually lead to a better understanding of the microbiome of the respiratory tract of cattle and the involvement of various viruses with respiratory disease. More research is required to assess the importance of some of these viruses, but it could eventually lead to the development of new vaccines.

John Campbell is a professor in the department of Large Animal Clinical Sciences at the University of Saskatchewan’s Western College of Veterinary Medicine.

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