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USDA Flu Surveillance Program – It’s a Good Thing

Article-USDA Flu Surveillance Program – It’s a Good Thing

For years, the USDA was planning a surveillance program for influenza virus in pigs. Unfortunately, the timing of the program announcement and launch coincided with the onset of the global pandemic of H1N1 influenza in people in the spring of 2009.

For years, the USDA was planning a surveillance program for influenza virus in pigs. Unfortunately, the timing of the program announcement and launch coincided with the onset of the global pandemic of H1N1 influenza in people in the spring of 2009. Participation in the program was effectively squelched by the flu pandemic, but the USDA and other organizations, such as the National Pork Board and the American Association of Swine Veterinarians, are encouraging producers to participate in the voluntary program.

How the Surveillance Program Works
Diagnostic samples for swine influenza (flu) virus testing submitted to any diagnostic laboratory that is a member of the USDA National Animal Health Laboratory Network (NAHLN) can be enrolled in the surveillance program. A list of the 36 NAHLN swine influenza virus (SIV) labs can be found at the following website: No cases will be enrolled into the voluntary program unless the submitting veterinarian or producer requests it.

Diagnostic cases can be enrolled into the program at two points in the diagnostic process:

  1. The submitting veterinarian can request to have the case be enrolled into the surveillance program when the samples are submitted if samples are from pigs with clinical signs of respiratory disease (cough, fever, lethargy, feed refusal, nasal discharge, difficulty breathing).

  2. The case can be enrolled into the surveillance program after influenza has been diagnosed at the diagnostic laboratory, if the submitting veterinarian or producer indicates they want the case enrolled.
After enrolling the case in the surveillance program, these two things happen:

  1. Diagnostic tests for influenza will be performed on each case and paid for by the USDA program. Test results are reported back to the submitting veterinarian with the case results. Tests include:

    a. Polymerase chain reaction (PCR) testing to detect influenza virus for up to 10 total nasal swabs or lung tissues per case.
    b. PCR testing to determine the subtype of the virus for at least two positive samples per case.
    c. Virus isolation for at least two positive samples per case.
    d. Gene sequencing of the virus for two positive samples per case.
  2. The diagnostic laboratory will report all influenza diagnostic results from the case to the USDA for inclusion in the surveillance database. No owner or specific location information is reported on any cases. The name of the submitting veterinarian is reported on cases that are positive for the 2009 pandemic H1N1 virus (2009pH1N1). These 2009pH1N1 positive cases will be posted on a website (
The information on the website includes the state in which the herd is located, but no owner information or further identification of the swine farm or herd veterinarian is listed.

Why Producers Should Participate
Producers and veterinarians were understandably reluctant to test for the 2009pH1N1 virus when officials couldn’t provide a clear explanation of what the consequences would be for a 2009pH1N1 positive herd. Now that 2009pH1N1 has been diagnosed in several herds, this uncertainty has largely been resolved and the reports of cases are becoming non-events in terms of media response.

This allows the swine industry to get back to work with day-to-day flu control. Characterizing flu viruses through subtyping and sequencing is an important tool for understanding and controlling the virus. With the USDA offering funds for such testing, there are several reasons why producers should consider participating in the surveillance program:

  1. Keep control strategies current – Vaccines remain an important tool for disease control. The past dozen years have taught us that, with influenza virus especially, we are shooting at a moving target. Both for applications of herd-specific autogenous vaccines and for development of licensed commercial vaccines, an understanding of virus changes and trends are crucial for maintaining vaccine effectiveness. We simply have to keep track of what’s going on with the virus in order to produce effective vaccines.

    Diagnostic tests also need to keep pace with virus changes. An accurate diagnosis is a key component of any disease control program. We are fortunate to have several very good diagnostic tests for influenza virus, but these tests must be tweaked occasionally in response to changes in the viruses that are circulating in swine herds. Cataloging the breadth of influenza virus diversity helps ensure our diagnostic tests are up to the task of detecting a virus that changes stripes readily.

  2. Develop effective, new control methods – As new methods or tools are developed for influenza control, they must be tested against a broad set of influenza viruses to ensure that the benefits extend to the full spectrum of viruses and how they affect pigs. But controlling flu in pigs could actually be good for more than just the pigs. That’s because flu is flu — more or less. Flu in pigs and people share many of the same features. The worldwide focus on ‘swine flu’ last year started a fire in the bellies of some agencies and now they want to increase flu research funding in many places. Research into new disease control methods that benefit people might really help pigs — and vice versa. Demonstrating a cooperative spirit by participating in a government-sponsored and funded surveillance program enhances the collaborations among research groups serving both the interests of pigs and people.

  3. One health – The human medical and public health communities are coming around to a clearer understanding of infectious diseases that move back and forth between people and animals, be they domesticated livestock, pets or wildlife. This has resulted in some increased funding for animal disease research and surveillance and has also increased scrutiny of many livestock production practices.

    Animal agriculture is learning how to deal with outside parties going beyond simply sticking their noses into our business. Outside detractors are feeding policymakers, politicians and voters a steady diet of misinformation about what, why and how we do things. If we believe that better information will improve the political and regulatory processes, then we have an opportunity and an obligation to take advantage of this high visibility and low risk surveillance program as a small step in that direction. This is definitely one of those situations where “it’s better to be at the table than wind up on the menu.”
Finally, it might be your nickel, but it’s their dime. Government funding of animal disease surveillance has been on the decline for many years. Renewed interest in and funding for livestock and poultry disease monitoring is obviously focused on its impact on human health, but information that is generated on influenza virus diversity is beneficial to our control efforts regardless of who signs the check.

Marie Gramer, DVM
[email protected]
Jerry Torrison, DVM
[email protected]
Minnesota Veterinary Diagnostic Laboratory