NAHLN Strategic and Transition Planning

The NAHLN Coordinating Council focused on two major activities in 2014. First, the committee updated the NAHLN Strategic Plan to reflect five strategic priorities and associated activities across the network for the next three years. The NAHLN Program Office will be developing the complementary Operational Plan next. Secondly, the Coordinating Council developed a transition plan for implementation of the NAHLN restructure, as proposed in the 2013 NAHLN Concept Paper.

The transition will occur in the following stages:

1. Self -Assessment (Completed September 2014): Each current NAHLN laboratory will be asked to provide their assessment of which level (Level 1, Level 2, Level 3, Affiliate, or Specialty as defined by the Concept Paper), they believe their lab best fit the established criteria, based on current capabilities, resources, commitment by State, and other relevant considerations.
2. External Review (Ongoing: September- December 2014): APHIS and NIFA will review the laboratory Self-Assessments, previous accomplishment reports, past performance, and other pertinent information to evaluate which level they potentially qualify for.
3. Needs Evaluation (Initiated: August 2014 - January 2015): A number of factors will be considered to determine the number of laboratories needed at each level. These factors will include, but are not limited to: geography, animal distribution, commodity demographics, farm gate values, pathway/risk assessments, capacity evaluations, etc.
4. Recommendations for Laboratory Distribution (Planned: March 2015): Based on all of the information gathered and analyses performed in Stages 1-3, APHIS and NIFA, in consultation with the NAHLN Coordinating Council will make recommendations on laboratory distribution to the VS and NIFA Deputy Administrators, with final restructuring to take effect in 2016 in accordance with USDA funding cycles.

Swine Enteric Coronavirus Diseases

Since its appearance in the United States in April 2013 and identification through NAHLN laboratory testing, porcine epidemic diarrhea virus (PEDv) has spread to over 30 States. In early 2014, an additional related coronavirus, porcine delta coronavirus (PDCoV), appeared in this country. These viruses are collectively referred to as swine enteric coronavirus diseases (SECD). Infections with novel SECD can cause significant morbidity and mortality, particularly in young piglets. Since April 2013, the swine producers, industry, veterinary diagnostic laboratories and Veterinary Services have been working to control the diseases.

In response to the mounting impact SECD continues to have on the U.S. pork industry, on June 5, 2014, the USDA issued a Federal Order requiring the reporting of SECD, implementation of herd monitoring, and management of Novel Swine Enteric Coronavirus Diseases. NAHLN laboratories are conducting the testing and reporting  results to the NAHLN Program Office for collation of results. Weekly laboratory testing reports were produced by the NAHLN Program Office in collaboration with the VS' Surveillance, Design and Analysis group since June 2013 and now accompany the weekly situation report. This combined report contains the field-based information entered into the Emergency Management Response System (EMRS). We've learned many lessons from SECD, and have made a number of advancements in collaborations, IT, and diagnostics across the network as a result of this outbreak.

 Laboratory Messaging

The network made significant advancements in secure communication mechanisms in the form of standardized, electronic messaging of test results. In 2013 and 2014, as a result of a close collaboration between the NAHLN Program Staff, VS' Office of the Chief Information Officer (OCIO) technical staff and the Surveillance, Design and Analysis Unit, the NAHLN IT system underwent a number of modifications and updates to increase functionality and is now known as the Laboratory Messaging Services (LMS). The LMS uses the same Health Level 7 (HL7) standards that the NAHLN IT system has used historically, but with a more general approach to accommodate messaging of any test results much more quickly. As a result, electronic messaging is now available for porcine epidemic diarrhea virus and porcine delta coronavirus, Influenza A in swine, foot and mouth disease and African Swine Fever. Input, user acceptance testing, and feedback from the NAHLN IT Committee has been essential. Furthermore, LMS has now been integrated with VS' Emergency Management Response System (EMRS 2.0) with the functionality operational in SECD reporting. Through this integration, we closed a long-identified gap for electronically integrating laboratory test results with field outbreak investigation data..

Validation Studies in the NAHLN

Collaborative inter-laboratory comparison and negative cohort studies are a routine NAHLN function as a part of diagnostic assay validation. Overall, these studies provide data needed to determine if and how the assays should be used for a specific purpose (fit for purpose) and how the assay performs on the U.S.' negative population. Inter-laboratory comparison studies provide data about reproducibility and robustness of assay, while negative cohort studies provide specificity parameters and identify cross reactivity with other agents. The studies are designed to meet OIE guidelines for sample size numbers and geographic distribution representative of US livestock populations. The process for implementing these studies includes open communication with the stakeholders and approval by each participating State's Animal Health Official. This year, 13 NAHLN laboratories participated in inter-laboratory comparisons and negative cohorts for two different FMD serologic ELISAs. These studies were collaborations with NVSL's Foreign Animal Diagnostic Disease Laboratory and the Institute for Infectious Animal Diseases (IIAD). The statistical analysis is near completion and the dossier is being prepared for review by the MTWG in early 2015. In addition, five NAHLN laboratories participated in an inter-laboratory comparison and negative cohort study for an influenza A H5/H7 RT-PCR. Results will be presented in early 2015. The dossiers for the FMD milk PCR and FMD penside assays were also completed and reviewed by the MTWG for their recommendations to VS on the use of the assay.

Aquatic Pathogen Assays added to the NAHLN Scope

Adding aquatic animal testing to the NAHLN will enable VS to build our nation's capacity for accessible, timely, accurate, and consistent aquatic animal disease laboratory services. The NAHLN system will provide a framework for standards, including an implemented quality management system and adherence to standard operating procedures (SOPs). The goal is that through NAHLN, standardized reliable testing for targeted surveillance will be used for baseline and zonation studies (disease freedom); for monitoring of high-consequence aquatic diseases (of regulatory or industry concern); for responding to disease outbreaks; and for interstate and international movement and trade. Implementation will move forward in three phases. Phase 1 is underway.

Phase 1

NAHLN Methods Technical Working Group (MTWG) reviewed and approved the SOPs for infectious salmon anemia virus (ISAv) and viral hemorrhagic septicemia virus (VHSv) testing. Existing NAHLN laboratories were invited to choose to participate in Phase 1 by including ISAv and VHSv in their NAHLN testing capabilities, taking part in proficiency testing and reporting results as indicated in the SOPs. A total of 14 NAHLN laboratories are approved to test, with proficiency testing to begin in early 2015.

Phase 2

Federal and State non-NAHLN laboratories (e.g., U.S. Fish and Wildlife Fish Health Laboratories) and private aquatic animal health testing laboratories will be invited to consider applying for NAHLN approval and test for the approved aquatic diseases using standardized requirements. This phase will be implemented when the new Specialty laboratory category is implemented during the NAHLN Structure.

Phase 3

Additional aquatic animal pathogens identified by the Aquatic Animal Health Program in consultation with the Subcommittee on Aquatic Animal Health (SAAH), National Import Export Services (NIES), and NVSL will be added to the NAHLN disease testing list. The NAHLN Coordinating Council will evaluate and approve these prior to being added to the aquatic animal pathogen group within the NAHLN scope. The NAHLN MTWG will review the associated SOP.
 

The NAHLN Portal provides NAHLN laboratories a web-based mechanism to input and update their NAHLN-related information, resulting in more efficient communication with the NAHLN Program Staff and timely sharing of ideas and information through the various NAHLN work groups. Updates that were completed in 2014 include expanding and refining the functionality of the NAHLN laboratory directory. This resulted in mechanisms for receiving invitations to participate; registering participants and entering test results for proficiency tests (PT); accessing current standard operating procedures; providing electronic copies of accreditation documents and a means for monitoring assay performance. Phase one of the enhancement and expansion of the core functionality in the PT section has been completed. This included non-NAHLN, APHIS-approved PTs. Phase two, which is the addition of laboratories and personnel associated with non-NAHLN, APHIS-approved testing into the lab directory, is expected to be completed by early 2015. Phase three is expected to be completed by mid-2015 and will allow labs to receive non-NAHLN, APHIS-approved PT invitations, register participants and enter PT results using online forms. Additionally in 2014, the NAHLN Portal was integrated with the Laboratory Capacity Estimation Model (LCEM) eliminating the need for double entry of some information fields related to laboratory capacity that now automatically move into LCEM from the Portal.

Article submitted by Cindy Chard-Bergstrom, Microbiologist, NAHLN Program Office, USDA APHIS VS STAS NVSL, Ames, IA

Article submitted by Christina M. Loiacono, DVM, PhD, DACVP, Associate Coordinator, NAHLN Program Office,  USDA APHIS VS STAS NVSL, Ames, IA and Sarah M. Tomlinson, DVM, NAHLN Coordinator, USDA APHIS VS STAS NVSL, Fort Collins, CO

The NAHLN continues to collaborate with other groups in APHIS, such as the NVSL reference laboratories, Wildlife Services, Surveillance, Design and Analysis Unit, the Surveillance Response and Preparedness Services Unit to design and implement surveillance programs in domestic and feral species. In fiscal year 2014, NAHLN laboratories participated in APHIS surveillance programs for bovine spongiform encephalopathy (BSE), classical swine fever (CSF), scrapie, influenza A virus in swine

(IAV-S), and pseudorabies virus (PRV).

NAHLN laboratories play a critical role in VS surveillance programs by providing rapid standardized testing and results reporting for the above-mentioned diseases that are targeted in national animal disease surveillance initiatives.

Testing data provided in The NAHLN Update are based on results data that are available at the time of release of the newsletter. Testing numbers may change in future reports as new information is received and testing data are updated (for reference, see article in Volume 3, No. 2 edition titled, "Data dynamics within the SIV Surveillance Program, Why do the reports change?").

Bovine Spongiform Encephalopathy (BSE) Surveillance

The USDA has conducted surveillance for BSE since 1990. In 2004, following the December 2003 detection of BSE in an imported cow, USDA implemented an enhanced BSE surveillance program to more accurately determine the prevalence of the disease in the U.S. cattle population.

USDA concluded that the prevalence of BSE in the United States is extremely low (less than 1 case per million adult cattle), and in 2006, transitioned to an ongoing BSE surveillance program that tests at a level more commensurate with this extremely low level of risk. Ongoing BSE surveillance exceeds guidelines set forth by the World Organization for Animal Health (OIE), providing testing at a level 10 times that which is recommended by OIE.

On May 29, 2013, Agriculture Secretary Tom Vilsack released a statement regarding notification received from the World Organization for Animal Health (OIE) upgrading the United States' risk classification for bovine spongiform encephalopathy (BSE) to negligible risk. This was a significant achievement and it demonstrates OIE's belief that both our surveillance for, and safeguards against, BSE are strong.

The NAHLN laboratories have provided BSE surveillance testing since 2004. Currently, six NAHLN laboratories provide diagnostic testing for the BSE surveillance program. These laboratories continue to conduct testing to detect BSE at the very low level of less than 1 case per million adult cattle, assess any change in the BSE status of U.S. cattle, and identify any rise in BSE prevalence in this country. The NVSL Pathobiology Laboratory in Ames, Iowa, serves as the national reference laboratory and performs surveillance and confirmatory testing on all samples identified as suspect (potential positive) for BSE by the NAHLN laboratories.

The chart below shows sample testing performed, by quarter, for BSE by NAHLN laboratories (not including NVSL) in Federal fiscal years (FY) 2013 and 2014. The total number of animals tested for BSE by NAHLN laboratories in FY 2013 (October 2012 through September 2013) was 40,699 and in FY2014, 38,936 animals were tested (not including NVSL).

 

 

 

Classical Swine Fever Surveillance 

 

The CSF surveillance program was initiated in 2006 to rapidly detect CSF virus and monitor the risk of introduction of the virus in the U.S. swine herd. The surveillance program targets five specific swine populations for testing:

• Sick pig submissions to veterinary diagnostic laboratories (VDLs)
• Slaughter swine with a high probability for CSF exposure
• Feral swine
• Swine populations (including waste feeding operations) with a high probability for CSF exposure in Florida, Texas, and Puerto Rico
• Swine highly suspicious for CSF and entered into a Foreign Animal Disease Investigation

NAHLN laboratories conduct CSF surveillance testing and NVSL's Foreign Animal Disease Diagnostic Laboratory (FADDL) is the CSF reference and confirmatory laboratory. In FY 2014, 15 NAHLN laboratories provided diagnostic testing for the CSF surveillance program.

 

The table below shows the number of animals tested for CSF by NAHLN laboratories in two target surveillance populations in FY 2013 and the first three quarters of FY 2014. Feral swine test counts are not included here and waste feeder/high probability for exposure data is not available.

 

        
 

Scrapie Surveillance

USDA initiated the National Accelerated Scrapie Eradication Program in 2001 with the goal of eradicating scrapie from the U.S. sheep and goat populations. Since 2003, surveillance for the program has been conducted primarily through the Regulatory Scrapie Slaughter Surveillance (RSSS) program, which targets sheep and goat populations that have been recognized as having higher than average scrapie prevalence.

 

Other scrapie surveillance also targets scrapie-exposed and potentially exposed sheep and goats found through investigations of infected animals; clinical-suspect animals and other mature sheep and goats submitted to veterinary diagnostic laboratories; rabies-suspect animals that test negative for rabies; and voluntary on-farm testing of flocks with risk factors for scrapie or as part of the Scrapie Flock Certification Program.

 

Currently, 17 NAHLN laboratories are approved to conduct diagnostic testing for scrapie surveillance. The NVSL Pathobiology Laboratory in Ames, Iowa serves as the national reference laboratory and performs surveillance and confirmatory testing on all samples identified as suspect (potential positive) by the NAHLN laboratories.

 

In FY 2013, 42,342 animals were tested, and in FY2014, 45,670 animals were tested by NAHLN laboratories for scrapie. The charts below show the number of animals, by quarter, tested for scrapie by the NAHLN laboratories in FY 2013 and FY 2014 (not including NVSL).

 

 

 

 

Influenza A Virus in Swine Surveillance

The goals of the IAV-S surveillance program are (1) to monitor the genetic evolution of endemic swine influenza A virus to better understand endemic and emerging influenza virus ecology, (2) make IAV-S isolates and associated epidemiologic data available for research and analysis, and (3) select proper isolates for the development of relevant diagnostic reagents, updating diagnostic assays, and vaccine seed stock products. The program was initiated in May 2009 with a focus on monitoring the pandemic H1N1 2009 [pH1N1 (2009)] virus in swine. As the human health threat of pH1N1 (2009) declined in 2010, IAV-S surveillance efforts were re-focused on monitoring all current circulating IAV in swine. Also in 2010, an anonymous submission protocol was adopted to encourage more industry participation and increase the number of samples available for monitoring IAV-S in the U.S. swine herd. The IAV-S surveillance efforts are targeted towards these three swine populations:

• Case-compatible sick pig submissions to VDLs
• Swine exhibiting influenza-like illness at first points of concentration or commingling events i.e., markets, fairs
• Swine populations that are epidemiologically linked to confirmed human cases involving IAV-S.

NAHLN laboratories conduct IAV-S surveillance for the above-mentioned streams. The NVSL Diagnostic Virology Laboratory in Ames, Iowa is the IAV-S confirmatory laboratory.

 

 

IAV-S testing results reported by NAHLN laboratories

in FY 2013 and FY 2014

The table below shows the number of accessions tested, number of influenza-positive accessions, and number of accessions with virus subtyping results reported in FY 2013 and the first three quarters of FY 2014.

  *Influenza-positive accessions are those with samples with positive matrix assay results

  

 

Pseudorabies Virus Surveillance

The PRV surveillance program was initiated in 2009 as an extension of USDA's successful PRV eradication efforts. The program gathers surveillance data to support three specific objectives: (1) rapidly detect PRV entry and infection in U.S. commercial swine, (2) demonstrate freedom from PRV in commercial herds, and (3) monitor domestic sources of PRV.

 

Targeted Populations (surveillance streams)

• Investigation and diagnosis of suspicious PRV cases
• Sick pig submissions to veterinary diagnostic laboratories (VDLs)
• Herds participating in routine serology and herd profiling
• Herds classified as high probability for exposure
• Herds with reported exposure to feral swine
• Cull sow-boars at slaughter
• Market swine at slaughter
• Feral swine

PRV-approved NAHLN laboratories test serologic samples from domestic swine for four targeted PRV surveillance populations: sick pig submissions, routine serology and herd profiling, swine populations with a high probability for exposure, and swine with known feral swine exposure. NAHLN laboratories also conduct PRV testing for domestic swine samples that are submitted as part of epidemiologic trace back investigations. Fourteen NAHLN laboratories currently conduct PRV surveillance sample testing in domestic swine. The NVSL Diagnostic Virology Laboratory serves as the national reference laboratory and performs confirmatory testing for suspect and positive submissions for PRV.

 

In FY 2013, 274,252 swine were tested under the PRV surveillance program in the following streams: diagnostic laboratory serologic submissions, sow-boar slaughter, and market slaughter. NAHLN laboratories tested 23,598 swine for the PRV diagnostic laboratory stream in FY 2013 and 25,360 swine in the first three quarters of FY 2014.

 

 

The surveillance information in this article has been provided by the responsible USDA APHIS offices.

 

Charts in this article are based on information and test results available at the time of report generation.  Numbers are subject to change due to later reporting of test results and updates in the database(s).

 

Below you will find various NAHLN Procedure Manuals, the date of the latest version, and either a weblink or contact where they are available:

Classical Swine Fever Surveillance Procedure Manual, latest version dated April 2007

Pseudorabies Surveillance Procedure Manual, Version 1.3, latest version dated October 2010

Procedure Manual for Vesicular Stomatitis Viruses (VSV), latest version dated January 2008

Influenza Surveillance in Swine Procedures Manual, latest version dated July 2010