August 2020 SHIC eNewsletter

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel and emerging swine disease for the benefit of US swine health. As a conduit of information and research, SHIC encourages sharing of its publications and research. Forward, reprint, and quote SHIC material freely. SHIC is funded by America’s pork producers to fulfill its mission to protect and enhance the health of the US swine herd. For more information, visit or contact Dr. Sundberg at [email protected].

SHIC Issues a Call for Proposals for Improved Oral Fluids PCR Sensitivity

Recent unpublished, observational research indicates oral fluids (OF), when collected by rope as an aggregate sample, could be a good sample for rapid detection of African swine fever virus (ASFv). However this experimental data also suggests that there is potential for false negative testing results.  Therefore, the Swine Health Information Center (SHIC) is calling for proposals to develop methods to improve the detection of low levels of nucleic acid in OF through enhancements to sample pre-extraction treatment(s) or through improved extraction methodologies compatible with the high throughput testing currently done in NAHLN laboratories.

With thousands of OF samples coming into diagnostic labs each month, the value of this type of testing for swine disease monitoring is irrefutable. The objective of this SHIC-funded research is to address concerns about OF testing sensitivity. Then, with this knowledge, the potential for an official option for ASF testing beyond whole blood, which is the antemortem sample presently proposed by USDA for surveillance, opens. Due to the urgency of preparing for ASF and other foreign animal disease testing protocols, SHIC will favor proposals reflecting this immediate need.

In a negative cohort study, no false positives for ASFv were reported. Experimental, unpublished, observational work indicated that ASFv may be detected in OF prior to onset of clinical signs even if only a small proportion of animals are infected. However, as the viral load, as measured by PCR CT comparison, was much lower in OF than individual tissue samples, the study indicated false negatives do occur. This limits the potential use of swine OF as an official monitoring and surveillance tool in the event of an ASF outbreak in the US without further study and refinement.

OF samples are widely used in swine surveillance for porcine reproductive and respiratory syndrome virus (PRRSV), Influenza A virus in Swine (IAV-S), and Mycoplasma hyopneumoniae (MHP) nucleic acids on US farms and have shown the potential for use in foreign animal disease (FAD) surveillance, as well. To date, more than 27 pig pathogens have been shown to produce detectable levels of nucleic acid in OF.  The proposed research could lead to increased sensitivity of PCR testing for these domestic and foreign animal diseases.

SHIC is currently sponsoring OF sensitivity research in Vietnam related to ASF as well. Building on those projects, it is hoped the research related to this new request for proposals will result in methods sensitive enough to support OF PCR diagnostic validation.

The following detailed points are included in SHIC’s request for proposal.

The deadline for submitting an RFP to SHIC for this project is August 25, 2020, at 5:00 pm CDT. For more information on the RFP process, please contact SHIC Executive Director Dr. Paul Sundberg at [email protected].

SHIC-Funded MSHMP Sequencing Project to Give Producers Edge in Responding to Emerging Virus Strains

Recent improvements have brought the Morrison Swine Health Monitoring Project (MSHMP)  closer to real-time monitoring of porcine reproductive and respiratory syndrome virus (PRRSV) sequence evolution and impact. Funded partially by the Swine Heath Information Center (SHIC), MSHMP has been adding capacity to capture diagnostic data from cooperating veterinary diagnostic labs (VDLs). The sequence acquisition process has been organized, and simplified, making sequence monitoring reality. Next, the real-time monitoring component will be developed. This data is being used to develop analytic methods for understanding PRRSV, giving producers the opportunity to respond to emerging, highly virulent strains.

Working closely with participating VDLs, MSHMP staff has been able to establish a methodology which increases PRRSV sequence update frequency. These frequent updates and virus classification into virus type, RFLP, and lineages has opened a great opportunity for the program from an added value standpoint. Maintaining an updated database has allowed MSHMP to quickly respond to sequence comparison requests from participants throughout the year during their outbreak investigations.

In the last fiscal year, MSHMP has been involved in 13 outbreak investigations. Of these, eight were requested in the current calendar year and corresponded to comparisons of 10 sequences to the MSHMP dataset. In all these cases, MSHMP staff were able to find similar sequences (>98% nucleotide identity) for all but one case. Similar sequences include sequences from the same systems which are conducting the outbreak investigation, in which case MSHMP shares all the details of the similar sequences including distance to farms. However, in cases where the sequence with the highest similarity includes another production system, a distance as a range is provided to preserve anonymity. This not only allows MSHMP to give back to participants, but also stimulates sharing of data making the program’s dataset more representative.

Two manuscripts are in the final stages of preparation regarding analysis performed with this data. The first one focuses on understanding whether sequences in the dataset clustered both in time and space. As expected, several clusters were identified in the dataset contained sequences with high similarity which highlighted the fact that a sequence (e.g. virus) disseminated throughout a region in a specific period of time. However, there were other instances in which clusters found contained multiple sequences clearly highlighting the fact that regional diversity continues to pose a risk from a biosecurity and pathogen evolution standpoint. The second manuscript comprises a description of all PRRSV type II sequences found in the MSHMP database. Characterization of the frequency of families of viruses (e.g. lineages) overt-time, their genetic difference to the first PRRSV type II isolated (e.g. VR 2332) which is also the parent strain for a commercial vaccine and the emergence and frequency of detection of the highly virulent 1-7-4 viruses over time will be part of the manuscript.

SHIC Sponsored Research in Vietnam Looks at Risk of ASF Transmission via Boar Studs

The common practice of artificial insemination (AI) in pork production often involves outside equipment, specialized crews, and off-site boar studs. Because AI has been linked to the spread of several pig disease outbreaks, the Swine Health Information Center (SHIC) is using USDA-FAS grant funds to sponsor research in Vietnam on the risk of introducing African swine fever (ASF) via this route. Specifically, the study will examine potential introduction of ASF to a sow farm as a result of semen movement from apparently healthy boar studs located in an ASF disease control area. Conducted by a team from the University of Minnesota with academic partners from the Vietnam National University of Agriculture, the study will include a pro-active risk assessment (RA) systematically evaluating the potential risk of semen movements during an outbreak. Resulting information will help the US swine industry continue to prepare for foreign animal disease issues as well as implement science-based prevention protocols.

This research will examine pathways of ASF introduction into boar studs and semen movement into sow farms. Researchers will also look at the simulated spread of ASF in a sow farm with multiple sows simultaneously exposed to ASF via the AI process. Present limitations on currently proposed surveillance protocols as they apply to boar studs, along with the inability to definitely show semen produced within an ASF control area is virus-free, create the necessity for research to determine what surveillance is needed, and how long semen should be held, to increase the likelihood of ASF detection.

The outcome from this project will be a completed RA of the likelihood of disease spread from the movement of semen from boars in an ASF disease control area. 

Hemorrhagic Tracheitis Standardized Submissions to Help Find Etiology Supported by SHIC

Hemorrhagic tracheitis syndrome (HTS) has been diagnosed in Canada for years, and recently increasingly recognized in the US. To date, no etiologic agent(s) has been definitively or consistently associated with the syndrome in the cases examined or reported. To investigate etiology, a joint project of the Iowa State University Veterinary Diagnostic Lab (ISU VDL), Animal Health Laboratory, University of Guelph (AHL-UG), and the Laboratoire de santé animale, MAPAQ,Québec has begun with support from SHIC. Diagnostic investigations at both ISU VDL and AHL-UG to date for tracheitis cases have been hampered by dependence on the submitter’s tissue sampling and diagnostic test selection. A standardized diagnostic test plan for swine tracheitis cases has been developed. This joint VDL project will facilitate thorough, consistent testing of these cases, allow staff to exclude common respiratory pathogens as the cause of tracheitis in individual animals and herds, and establish a tissue bank for future NGS to search for novel or emerging pathogens in those cases with no confirmed etiologic diagnosis.

This spring, the Swine Health Information Center (SHIC) and America Association of Swine Veterinarians co-hosted a webinar providing information on the syndrome, its signalments, tissues for postmortem assessment, and management. The webinar is available to view here.

Severe necrohemorrhagic tracheitis syndrome observed in finishing pigs and replacement breeding stock is characterized by severe erosive or ulcerative lesions. Transient outbreaks are reported, with herd resolution over a period of two to three weeks. Opportunistic bacterial infection is common among the tracheal lesions at the time of necropsy and evaluation. The temporal pattern, clinical signs, and gross and histologic lesions of severe necrohemorrhagic tracheitis, together with the failure to consistently identify any known respiratory pathogen in many of the cases, raises concern of either a novel infectious agent or a novel strain of a known infectious agent. Alternatively, the lesion may represent a stereotypic sequel to a variety of primary cause. Contribution of anatomic features (e.g. tracheal diameter, length) compressive effects of cervical lymphadenopathy, genetic factors, and environmental/air quality conditions to the development and severity of tracheitis must be considered.

Morbidity ranges from <1% to 10 to 50%, depending on the herd, with consistently low mortality (<1-3%). Clinical signs resolve over seven to 10 days, sometimes in response to antibiotic and/or anti-inflammatory therapy; however, resolution was noted in some herds with no or minimal treatment or interventions.

The following represents desired submissions for the HTS study at participating VDLs to develop a diagnostic investigation protocol and establishment of a tissue bank. Samples should be sent using each facility’s particular submission forms.

Clinical history
Percent morbidity/mortality, approximate weight of hogs, herd genetics
Gross images
Cervical region and pluck at time of necropsy
Intact plucks
Trachea from larynx to bifurcation, both lungs, from affected pigs
Tracheas should be partially opened during the field necropsy to confirm lesions compatible with necrohemorrhagic tracheitis
Further dissection and sampling of trachea and lung for diagnostic testing and lesion documentation will be done at the VDLs
Lymph nodes
Bilateral caudal deep cervical and costo-axillary lymph nodes
Intact, fresh, and labelled (right and left, anatomic site).
Control animals
Plucks and lymph nodes as above from two or three unaffected herdmates dying or euthanized during the same timeframe, potentially due to other causes, and without gross lesions of necrohemorrhagic tracheitis
Systemic samples
Fresh AND formalin-fixed: spleen, stomach, ileum, and heart
Oral fluids
From all affected pens, two unaffected pens in affected barn, and two pens in unaffected barns
From five animals in each of one representative affected pen, one unaffected pen, and one pen in an unaffected barn.

Additionally, environmental control records for affected barns for two weeks prior to outbreak, targeting sudden fluctuations in temperature or humidity are requested, including comments regarding barn air quality.

Tissues submitted towards this study should be clearly labeled with “SHIC Hemorrhagic Tracheitis Project,” or similar verbiage, and directed towards the attention of the diagnostician associated with this project at the respective institution (see below).

VDL Address Submission Form Link Attending Diagnostician
Iowa State University
Veterinary Diagnostic Laboratory
Iowa State University
1850 Christensen Dr
Ames, IA 50011-1134
Please use “Pathology Request Form”
under “Cases WITH tissue”

Alyona Michael
University of Guelph
Animal Health Laboratory
University of Guelph
Address: Building 89, 419 Gordon St.
Guelph, Ontario Canada N1G 2W1
Josepha DeLay
(519-824-4120 ext 54576)
Laboratoire de santé animale :
2650, rue Einstein
Québec (Québec) G1P 4S8
Isabelle St-Pierre
418-643-6140 ext. 2626
[email protected]

SHIC Launches Podcast to Share Timely Swine Health Information

The Swine Health Information Center has created a podcast to share timely and relevant swine health information. The first episode of SHIC Talk features our interview with Dr. Joe Connor of Carthage Veterinary Services. He is a member of SHIC’s Monitoring and Analysis Working Group and tells us about test-and-remove protocols being followed in China for African swine fever eradication. 

Be watching for SHIC Talk to be available where you get your podcasts including Apple Play, Google Podcasts, and PodBean.

August Swine Disease Monitoring Reports

As the world deals with the COVID-19 pandemic, SHIC continues to focus efforts on prevention, preparedness, and response to novel
and emerging swine disease for the benefit of US swine health.

Domestic Disease Monitoring Report

This month’s Domestic Swine Disease Monitoring Report shows a moderate decrease of porcine reproductive and respiratory syndrome virus (PRRSV) cases in July compared to June, down substantially in wean-to-market category. Porcine epidemic diarrhea virus (PEDV)-positive cases were down moderately in July compared to June as well and within expected boundaries for this time of year. Detection of porcine delta coronoavirus (PDCoV) was also within the expected boundaries for this time of year. Mycoplasma hyopneumoniae (MHP)-positive cases in July were similar June and also within expected boundaries.

Global Swine Disease Monitoring Report

In this month’s Global Swine Disease Monitoring Report, read about the first African swine fever (ASF) reports in Latvia and Slovakia where new cases were found in domestic pigs. The ASF outbreak expands in Nigeria where nine states have reported the disease. Foot-and-mouth disease has been diagnosed in Rwanda for the first time since 2017. The report also includes information on an OIE and FAO joint initiative for an ASF global control strategy.