More virus strains found in pigs

Second PED virus strain, deltacoronavirus present in some states
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U.S. pigs are infected with a second and possibly a third strain of a coronavirus that, by some estimates, has killed millions of the animals in the past year

Officials with the Ohio Department of Agriculture and Iowa State University each announced the discovery of at least one new strain of the porcine epidemic diarrhea virus, which has caused illnesses and deaths in at least 25 states since it was discovered in the U.S. in April 2013.

Electron photomicrograph showing a porcine epidemic diarrhea virus particle found in a fecal sample collected in 2013 during an outbreak on an Ohio farm. The scale bar is 50 nanometers. Reproduced with permission from Jung K, Wang Q, Scheuer KA, Lu Z, Zhang Y, Saif LJ. Pathology of US porcine epidemic diarrhea virus strain PC21A in gnotobiotic pigs [published online ahead of print]. Emerg Infect Dis doi: 10.3201/eid2004.131685. (Courtesy of the CDC)

And the Ohio authorities separately announced in February that a department virologist, Dr. Yan Zhang, had found an unrelated deltacoronavirus in samples taken from pigs that had clinical signs similar to those of PED and transmissible gastroenteritis.

Associated with milder signs

Officials at Iowa State University announced Jan. 30 that, among PED viruses isolated from 15 infections, five had substantial enough genetic differences that it was unlikely they evolved from the PED virus previously identified in the country. Yet those five were similar to one another.

“Determination of the entire genome sequences of these new PEDVs are in progress and will help determine the origin of the viruses,” the announcement states.

At about the same time, said Dr. Tony M. Forshey, Ohio’s state veterinarian, Dr. Zhang and others in the state agriculture department’s Animal Disease Diagnostic Laboratory had sequenced the genome of a new strain of PED virus. Dr. Zhang said he thinks the virus strains found by the Ohio and Iowa laboratories are the same virus.

Jianqiang Zhang, PhD, an assistant professor at the ISU laboratory, said he has not seen sequencing data from Ohio, and he did not know whether the laboratories had identified the same PED virus strain. Retrospective analysis showed that the PED virus strain sequenced at ISU was present in samples from at least six states and that the virus has been in the country at least since October 2013.

Dr. Forshey said the PED virus strain sequenced in Ohio was found in pigs that developed clinical signs of illness starting in late fall 2013. Unlike the original strain, which has been associated with high mortality rates among the youngest pigs, the outbreaks associated with this new strain caused milder clinical signs and lower mortality rates.

Deltacoronavirus also found

In other work, genetic sequencing indicates a swine deltacoronavirus initially found in Ohio is closely related to a deltacoronavirus discovered in 2012 in Hong Kong, Dr. Forshey said.  The U.S. deltacoronavirus was found in samples taken from pigs in response to outbreaks in January and February with swine having signs that were atypical for PED.

Clinical signs occurred in all ages of pigs, resulting in a mortality rate between 30 and 40 percent among the youngest pigs. Histologic lesions in samples from the pigs were indistinguishable from those caused by PED.

Of the four farms with pigs initially found to have the deltacoronavirus, three also had pigs positive for PED virus, Dr. Forshey said. However, none of the farms had pigs that were positive for transmissible gastroenteritis, which has similar clinical signs and is more familiar on U.S. farms.

Dr. Yan Zhang said the deltacoronavirus since has been detected in samples from Illinois, Indiana, Nebraska, Minnesota, Pennsylvania, and South Dakota.

Dr. Forshey noted that further research would reveal whether the deltacoronavirus causes disease by itself  or as part of a coinfection.

Complicating treatment

Dr. Tom Burkgren, executive director of the American Association of Swine Veterinarians, said the presence of multiple coronaviruses could complicate clinical work on farms. He noted that the discovery occurs as the swine industry is trying to control the original PED virus.

“It was troubling because we didn’t have all the answers with PED, and now we’ve got at least two other viruses out there on farms,” he said. “I don’t know if that makes it three times as troubling, but it certainly does complicate the clinical picture and increases the need for research,” he said.

Dr. Burkgren has heard differing opinions among virologists on whether the recently discovered PED virus strain or strains entered the U.S. whole or developed in the country through recombination. But the deltacoronavirus seems to have originated outside the U.S.

Dr. Burkgren said that, with the introduction of new viruses into U.S. pigs, the possibility that a pathway remains open for other diseases keeps him awake at night.

“If that pathway is still open, allowing new introductions, there’s a host of other viruses out there that could be utilizing that same pathway to get into the U.S. swine herd,” he said.

Swine veterinarians are focusing on biosecurity, including reducing risks from transportation, the people who enter farms, and the introduction of new animals. Some security actions may seem minute, he said, but their failure could result in an outbreak.

Dr. Burkgren said it is frustrating that “even in certain cases where bio­security has been very high and things have been very tightly run on the farm, some of those farms have still broken” with disease.

Dr. Forshey expects the discovery of the new viruses could bring comfort to the farm owners and veterinarians who have seen outbreaks that do not match the known patterns for PED. The discovery shows that someone knows about other viruses that could be circulating in U.S. swine and is learning more about them.

Harming millions

Estimates of the damage caused by the introduction of PED into the U.S. total in the millions of pigs.

Bo Manly, executive vice president and chief synergy officer for Smithfield Foods, said during a December 2013 earnings call that Smithfield’s livestock production subsidiary, Murphy-Brown, had PED virus infections in Midwestern and East Coast herds, according to information provided by a company spokeswoman. Manly estimated that, on the basis of industry figures on infected herds, the virus could affect up to 1 million sows throughout the industry, reducing the year’s production by 2 million to 3 million pigs.

Steve R. Meyer, PhD, president of Paragon Economics, and a consulting economist for the National Pork Board, said in early February he had heard an estimate that the PED virus had infected more than 1.7 million sows since June 2013, potentially causing millions of deaths among piglets. He said the pork industry was starting to see reductions in the numbers of pigs brought to market, and he expected those reductions would rise in spring and summer.

Related JAVMA content:

Pig disease has affected 20 states (Feb. 1, 2014)

Fighting a deadly pig disease (Aug. 15, 2013)