Effective June 27, 2016, the USDA is implementing four changes to the Influenza A Virus (IAV-S) Surveillance Program in an effort to conserve spending and extend the program.
The USDA Influenza A Virus (IAV-S) Surveillance Program for the collection and characterization of virus isolates from case-compatible swine was initiated in 2009. The program supports both animal and public health objectives. Program goals include monitoring the evolution of the virus and providing isolates for 1) research, 2) the development of diagnostic reagents, and 3) updating diagnostic tests and vaccine seed stock products.
This voluntary surveillance program has been maintained with emergency money provided for surveillance of influenza in U.S. swine in response to the 2009 H1N1 human pandemic. Funding for this program is being rapidly depleted, with no currently identified funding sources to replace it in FY 2017.
With the impending depletion of funding APHIS reached out to stakeholders for input on program efficiencies that could be implemented to make the program more efficient, conserve spending of the remaining H1N1 funds, and extend the program. These efficiency measures were discussed in early May when APHIS convened a stakeholder meeting in Ames, IA. Meeting participants included personnel from pertinent APHIS staff, ARS collaborators, several NAHLN laboratories, representatives from several state animal health offices, academic researchers, and representatives from the AASV Influenza committee (including vaccine company personnel), NPB, NPPC and SHIC. Following 2 days of discussion, agreement was reached that the current stated goals of the program should remain the same.
Program efficiency alternatives that were discussed included 1) removal of oral fluids as a sample type; 2) require specific epidemiologic data for payment; 3) USDA reimbursement for only positive matrix PCRs; 4) discontinue USDA reimbursement for all matrix PCRs; 5) lower CT cutoff values for further reimbursable testing; 6) remove the subtyping PCR from the algorithm; 7) drop the M gene sequencing of viral isolates; 8) explore cost effectiveness of whole genome sequence technology versus 3 gene Sanger sequencing; and 9) reduce further testing from 2 samples to 1 sample per accession. Agreement for the adoption of three cost saving measures was reached at this meeting by attendees. Two additional measures also received support but required additional discussion. Further internal discussion later in May by the National Pork Board’s Swine Health Committee resulted in support for the four measures below.
- Lower the CT cutoff values for USDA funded further testing. Adopted. This measure suggested and supported by several NAHLN testing labs lowered the matrix PCR screening test CT cutoff values for reimbursement of further testing for nasal swabs and lung tissue samples to <25 (lowered from < 35) and for oral fluid samples to <20 (lowered from 30). These new cutoff values were established based on data provided by the University of Minnesota, and later verified by APHIS using recent USDA program data. This cutoff value reduction will increase the likelihood of acquiring an isolate from diagnostics that USDA funds. Further testing of samples not meeting these cut-offs may still be completed at the producer’s expense.
- Discontinue USDA reimbursement for NAHLN lab sequencing of the M gene. Adopted. This measure was suggested by ARS and supported by several diagnostic testing labs. The pandemic M gene has predominated in circulating swine influenza viruses for over 2 years. The M gene will continue to be monitored by NVSL through their current monthly whole genome sequencing isolates from the surveillance program. Reimbursement for sequencing of the H gene and N gene will continue for NAHLN laboratories.
- Reduce the number of samples per accession from 2 to 1 that will move forward for subtyping PCR’s. Adopted. This measure was suggested by several NAHLN labs and USDA. Two samples routinely yielded the same virus in each accession; only 5 percent of the subtyped accessions have resulted in a mixed virus detection. Cost savings can be achieved by only further testing 1 sample per accession with little loss to pertinent data.
- Discontinue USDA reimbursement for the Matrix PCR screening test. Adopted. This is one of two measures that were suggested by the AASV Influenza Committee based on USDA data. USDA data showed that only 37 percent of program accessions tested positive on the matrix PCR and only 10 percent of accessions yielded a virus isolate, yet this screening test consumes 50 percent of the NAHLN testing costs. Because the matrix PCR is a screening test for influenza that practitioners would typically request as part of a diagnostic work-up, dropping USDA payment for screening is not expected to adversely affect sample submissions a great deal. Stakeholders discussed an option for USDA reimbursement for only the positive matrix PCR tests, however this placed a heavy burden on the NAHLN labs to try to track and redirect the samples after matrix PCR testing. Consequently there was support to drop USDA reimbursement for the matrix PCR. USDA will maintain full cost coverage for subtyping PCRs, virus isolation and sequencing expenses on eligible samples, which directly support the cardinal goals for the program.
These program changes will help extend the surveillance program under current funding. They will take effect beginning June 27, 2016. Any samples received in the laboratory on or before June 27, 2016 will be tested in accordance with the current algorithm and billed to APHIS’s Veterinary Services (VS) program. Specific instructions for National Animal Health Laboratory Network Laboratories will be provided separately by the NAHLN Program Office.