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New, Unrelated Virus Strains Invade US Swine

07 April 2014
Genesus - The first power in genetics

US - At the recent American Association of Swine Veterinarians (AASV) meeting, an important topic was confirmation of the presence of multiple strains of Porcine Epidemic Diarrhoea Virus (PEDV) and Swine Delta Coronavirus (SDCV)in US swine, writes Pat Hoffmann, DVM, Director of Health and Biosecurity.

Two weeks ago, Genesus attended the American Association of Swine Veterinarians (AASV) Annual Meeting in Dallas, Texas. As one might imagine, there was a lot of discussion about PEDV… What can be done to minimize losses?... Can we contain it?... How do we prevent it?... How do we sanitize contaminated facilities and trucks?... etc. One of the hotter topics of discussion, though, was evidence that confirms the presence of multiple, unrelated strains of PEDV have been detected US swine in addition to a distant cousin, SDCV.

The Coronavirus family can be subdivided into four groups based on genetic sequencing and serologic properties some of which can infect pigs. These groups are known as Alpha, Beta, Gamma, and a fourth provisionally-assigned new group called Delta Coronaviruses. Until now, most of you probably have only heard of viruses from the Alpha group such as Transmissible Gastroenteritis virus (TGEV), Porcine Respiratory Corona Virus (PRCV) and of course, PEDV. However, as previously mentioned there is a new virus from the Delta group circulating among the US sow herd that virologists are currently calling Swine Delta Coronavirus (SDCV) that was confirmed in early 2014.

Today’s molecular diagnostic capabilities allow us to identify viruses based on their specific genetic sequence (DNA or RNA). Once we have the sequence we can search for genetically similar viruses in GenBank ®, a global collection of publicly available genetic sequences that have been identified and voluntarily submitted to the database. New sequences can also be added to a dendogram which is a family tree-style assortment used to illustrate the clustering of related viruses based on specific genes or entire sequences. This capability helps identify viruses detected in other regions of the world that closely match current strains in the US. In addition, it may assist practitioners, researchers and diagnosticians to form collaborations that aid in understanding clinical presentations associated with the new virus, or share available diagnostic tests, and potential treatments.

There was a Status Update on Swine Coronaviruses Recently Identified in US Swine released in February 2014 by a team of veterinary researchers and diagnosticians at Iowa State University’s Veterinary Diagnostic Laboratory (ISU VDL). Below is the current PEDV dendogram from the ISU VDL that includes both the original and variant strains of PEDV identified in US swine.

After evaluating the viral genotypes found in US swine, the ISU VDL has concluded that the two different PEDV clusters are probably not related through a genetic mutation. Thus, they conclude that more than one strain of PEDV has been introduced into the US either simultaneously or at different times since April, 2013. All of the strains at this point have been linked to other similar viruses detected in China.

The above hyerlinked article also starts to address Swine Delta Coronavirus (SDCV). All that is known about SDCV at this point is that it has been positively identified with a relatively high viral load on several farms experiencing acute diarrhea in sows and piglets that tested negative for PEDV and TGEV. There is still a lot to learn about the clinical significance related to SDCV and the level of mortality and morbidity associated with this deltacoronavirus.

Answering some of these questions about PEDV and SDCV will become easier as veterinary diagnostic laboratories work diligently to offer new tests. Currently, the presence of PEDV and SDCV can be detected via Polymerase Chain Reaction (PCR) and subsequently genotype variation (strains) can be identified though traditional or Next Generation Sequencing (NGS). We can also evaluate exposure to PEDV through the presence of antibodies in serum using an indirect Immunofluorescence Assay (IFA) and some recently available Enzyme-linked Immunosorbent Assay (ELISA) antibody tests. Not all veterinary diagnostic laboratories are currently offering all of these tests.

Identifying these viruses is one thing, but the bigger questions are 1) How did these viruses get into North America, and 2) What are we doing to prevent the next foreign virus from getting here (I never did accept that PEDV was properly labeled as “Transboundary Disease” instead of a “Foreign Animal Disease” like is… was). Genesus estimates that over half of the US sow inventory has been affected by PEDV resulting in over 5 million dead pigs to date. It is hard to believe, but this is nothing compared to the impact of a Foot and Mouth Disease (FMD) or Classical Swine Fever (CSF) outbreak that could devastate the US pork industry. These are scary times particularly for an industry that exports over 25 per cent of its production which would be shut down over night in the event that we break with FMD or CSF or any other foreign animal disease for that matter. Stay tuned as research continues to reveal more information regarding the pathogenesis, control, and detection of PEDV and SDCV.


To find out more about Genesus Genetics, please take the time to visit their website at www.genesus.com .



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