Emerging Animal Diseases: Actions Needed to Better Position USDA to Address Future Risks
Published: 2015-12-15T00:00:00

Fast Facts:

Highlights:
section_title: Why GAO Did This Study
paragraphs: Pork is consumed more than any other meat worldwide, and there are numerous other products made with ingredients from pigs, including medical products, such as insulin to treat diabetes. The United States is the world's third-largest producer of pork products. USDA estimated that U.S. pork exports in 2014 were valued at over $6 billion. Two lethal, highly contagious diseases in pigs emerged in the United States in 2013 and 2014, causing the deaths of millions of pigs. The two emerging diseases are collectively known as SECD.
GAO was asked to review federal actions to address SECD outbreaks. This report examines (1) the initial response to the SECD outbreaks, (2) USDA's subsequent actions to manage SECD, and (3) steps USDA has taken to improve its future response to emerging animal diseases. GAO analyzed USDA efforts to collect data about the number and location of infected herds; reviewed federal regulations and USDA animal disease response guidance; and interviewed USDA, state, and industry stakeholders involved in the response and control efforts.
section_title: What GAO Found
paragraphs: The U.S. Department of Agriculture (USDA) did not take regulatory action during the initial response to the outbreaks of Swine Enteric Coronavirus Diseases (SECD) beginning in May 2013, when an outbreak was first detected, because the agency did not believe then that such action was necessary. Instead, USDA initially supported swine industry-led efforts. Without regulatory action, such as requiring reporting of infected herds, USDA had limited information about the location of the first infected herds. In addition, USDA officials acknowledged that USDA did not follow its guidance that calls for conducting epidemiological investigations at the onset of outbreaks. As a result, USDA did not conduct timely investigations of the premises with the first infected herds, and the source of disease will likely never be determined. Further, USDA does not have a process to help ensure the guidance is followed. Without such a process, USDA lacks reasonable assurance that the guidance will be followed in the future.
In June 2014, amid concerns about the spread of SECD, USDA issued a federal order requiring reporting of newly infected herds. As a result, USDA has more accurate information about the number and location of such herds, and SECD have been confirmed in 28 U.S. states, as shown below. USDA also provided funding to help manage the diseases.
To help improve its future response to SECD and other emerging animal diseases—those not known to exist in the United States or which have changed to become a threat—USDA has drafted new guidance. However, it has not defined key aspects of its response such as roles and responsibilities, which according to its strategic plan, are key components of successful collaboration to protect animal health. Without a clearly defined response to such emerging animal diseases, response efforts could be slowed.
section_title: What GAO Recommends
paragraphs: GAO recommends that USDA develop a process to help ensure its guidance for investigation of animal diseases is followed and clarify and document how it will respond to emerging diseases, including defining roles and responsibilities. USDA generally agreed with GAO's recommendations.

section_title: Letter
paragraphs: Two lethal, highly contagious diseases in pigs—Porcine Epidemic  Diarrhea (PED) virus and Porcine Deltacoronavirus (PDCoV)—emerged  in the United States in 2013 and 2014 respectively. These diseases do  not directly affect public health but have resulted in the deaths of millions  of pigs. According to the U.S. Department of Agriculture (USDA), the  United States is the world’s third-largest producer and consumer of pork  and pork products. U.S. pork exports in 2014 were valued at over $6  billion, according to USDA’s Economic Research Service. Pork is  consumed more than any other meat worldwide, and there are numerous  other products made with ingredients from pigs, including medical  products, such as insulin to treat diabetes and manufacturing goods, such  as insulation and rubber.
PED and PDCoV are collectively known as Swine Enteric Coronavirus  Diseases (SECD). USDA currently categorizes SECD as emerging  animal diseases, which it defines, in part, as any animal disease  previously not known to exist in the United States, or any known animal  disease which has an unexpected and unexplained increase in morbidity  or mortality, or which has changed to become a threat to animal or public  health. SECD have also been identified in Canada, Mexico, South  America, Europe, and Asia according to USDA documents.
USDA has the authority to act to prevent the spread of animal diseases  under the Animal Health Protection Act. This act authorizes the  Secretary of Agriculture to carry out operations and measures to prevent,  detect, control, and eradicate diseases and pests of animals, including  emerging diseases, and recognizes that the prevention, detection,  control, and eradication of such diseases and pests are essential to  protect animal health, the health and welfare of people, economic  interests of livestock and related industries, the environment, and  interstate and foreign commerce in animals and other articles.
USDA uses an epidemiological approach to understand diseases and, if  appropriate, plans actions to control or manage them. Epidemiology  examines the spread of disease by time, place, and animal—by herd in  SECD context—as well as the mode of transmission and source of entry  of disease. In particular, it involves conducting outbreak investigations on  the premises where the disease is detected and identifying patterns of  geographic distribution to determine factors associated with the onset and  spread of disease.
You asked us to review SECD outbreaks and the federal actions taken to  address these diseases. This report examines (1) the initial response to  the SECD outbreaks; (2) USDA’s subsequent actions to manage SECD;  and (3) what steps, if any, USDA has taken to improve its future response  to emerging animal diseases.
To address all three objectives, we reviewed statutes, regulations, and  policies, as well as agency documents related to federal actions on  SECD. We also reviewed relevant documents from international animal  health organizations to learn about international requirements for SECD.
We interviewed officials from USDA’s Animal and Plant Health Inspection  Service’s Veterinary Services, which works to protect and improve animal  health; the Department of Health and Human Services’ Food and Drug  Administration’s (FDA) Center for Veterinary Medicine, which regulates  livestock feed; selected state animal health officials; and three industry  associations—American Association of Swine Veterinarians, National  Pork Board, and National Pork Producers Council—identified by USDA  officials as representing the commercial swine industry. These  associations represent the vast majority of the commercial industry, but  their views are not generalizable to all swine veterinarians and producers.  We interviewed state animal health officials from the 11 states that USDA  identified as having the highest number of positive tests for the SECD  virus during the initial response to the SECD outbreaks—specifically,  Illinois, Indiana, Iowa, Kansas, Michigan, Minnesota, Missouri, Nebraska,  North Carolina, Ohio, and Oklahoma. These states were also among the  highest pork producing states as of 2010 and received the highest level of  financial assistance to support their SECD activities. These officials’  views provide insights into how states perceived USDA’s actions to  address SECD, but these views cannot be generalized to all 50 states.
In addition, for the first two objectives, we analyzed two USDA data  collection efforts to assess the number and location of infected herds.  These efforts included (1) initial voluntary positive testing results reported  by some diagnostic laboratories from 2013 to June 2014 and (2)  mandatory reports of confirmed cases of SECD from June 2014 through  September 2015 as reported by swine veterinarians or producers and  confirmed by a USDA official. To assess the quality of these two data  collection efforts, we reviewed agency documents and interviewed  officials responsible for collecting and analyzing these data. We found  significant problems of completeness with the voluntary positive testing  results. For example, the test samples did not consistently include  premises information. Without this information, USDA did not know if the  test samples were for diagnosing potentially newly infected herds or for  retesting herds that had previously been tested positive. However, we  found these data sufficiently reliable for the limited purpose of  characterizing the increase in SECD-positive testing results. We found  the mandatory reports of confirmed cases to be sufficiently reliable for the  limited purpose of characterizing the geographic distribution over time  within the United States. To understand the spread and source of these  diseases, we reviewed four studies from March 2013 to August 2015 in  peer-reviewed journals about factors that could contribute to the spread of  these diseases in the United States or lead to their entry into the United  States.
Further, for the first objective, we reviewed USDA’s response from the  initial identification of SECD in the United States in May 2013 up to its  subsequent approach to these diseases in June 2014. We compared  USDA’s actions with its guidance for investigating animal disease  outbreaks. We also interviewed agency officials from USDA’s Animal and  Plant Health Inspection Service’s Veterinary Services and industry  representatives from the American Association of Swine Veterinarians,  National Pork Board, and National Pork Producers Council to understand  the industry’s response to SECD.
For the second objective, we reviewed USDA’s actions to manage SECD  from June 2014 through September 2015, as well as information on  USDA funding for SECD research and actions during that period. We  compared these actions with USDA’s mission to help ensure the free flow  of agricultural trade by keeping U.S. agricultural industries free from pests  and diseases. We also compared them with federal standards for internal  control, in particular, the standards for monitoring to ensure that the  findings of reviews are promptly resolved. We interviewed USDA officials,  state veterinarians, and industry representatives—who are stakeholders  in USDA’s animal disease responses—to learn their views on the  usefulness of USDA’s actions. We met with academic researchers,  government officials, diagnostic laboratory officials, and swine  veterinarians in Colorado, Iowa, and Minnesota because these states  include key USDA offices or university laboratories that conducted the  majority of SECD diagnostic tests. The views of these stakeholders are  not generalizable, but they provide perspectives from researchers who  specialize in swine diseases, USDA officials who hold key roles in  addressing SECD, swine veterinarians with experience from a state that  produces a high number of swine, and diagnostic laboratory officials from  laboratories that conducted the majority of SECD diagnostic tests. We  also visited Ottawa, Canada, to interview Canadian government officials  and industry representatives and better understand the steps they have  taken in managing SECD, and to identify any differences from the steps  taken in the United States. We selected Canada because it has SECD  strains similar to those in the United States, is the largest exporter of live  pigs to the United States, and has been active at the national level in  managing SECD.
For the third objective, we also reviewed USDA’s policies and guidance  for investigating, reporting, and responding to animal diseases. We  compared information that USDA has communicated about its response  to emerging diseases with expectations for collaboration laid out in  USDA’s Animal and Plant Health Inspection Service’s Strategic Plan  2015-2019 and with federal standards for internal control, including  control activities and documentation.
We conducted this performance audit from October 2014 to December  2015 in accordance with generally accepted government auditing  standards. Those standards require that we plan and perform the audit to  obtain sufficient, appropriate evidence to provide a reasonable basis for  our findings and conclusions based on our audit objectives. We believe  that the evidence obtained provides a reasonable basis for our findings  and conclusions based on our audit objectives.
subsections: section_title: Background
paragraphs: According to USDA, SECD are characterized by an acute, rapidly  spreading viral diarrhea of pigs. No other species, including humans,  are known to be affected, and these diseases are not a direct public  health threat. Pigs develop varying degrees of diarrhea and loss of  appetite depending upon the age of the pig infected. Piglets are the most  severely affected and have the highest mortality rates (50 to 80 percent),  while growing and adult pigs have the lowest rates (approximately 1 to 3  percent).
PED was first recognized in England in 1971 and has been known to exist  in China since 1973. According to USDA’s SECD case definition  document, China has seen a large increase in outbreaks since 2010,  and the emergence of new strains of PED have been attributed to this  increase. USDA’s case definition document also provides information  about the presence or suspected presence of PED and PDCoV in the  United States and other countries. For example, the first outbreak of PED  in the United States was reported in May 2013. PED has also been  reported in Mexico and Canada, as of August 2013 and January 2014,  respectively. Further, as of June 2014, PED is thought to be widespread  throughout most regions of Western and Central Europe and Southeast  Asian countries. In addition, PED is suspected in parts of South  America. PDCoV is more recent and less widespread; it was first  reported in China in 2012, in the United States in January 2014, and later  in Canada according to the document.
USDA’s mission includes protecting and improving the health, quality, and  marketability of our nation’s animals and animal products by working to  prevent, control, or eliminate animal diseases, and by monitoring and  promoting animal health and productivity. USDA’s overall budget request  was $23 billion in fiscal year 2015, of which $287 million was budgeted for  the agency’s animal health efforts, including disease response. USDA  comprises multiple organizations that support its animal health mission;  see table 1 on the next page for selected organizations and their specific  missions and roles.
In carrying out its animal health mission, USDA participates in  surveillance and preparedness, as well as response efforts for animal  diseases. Surveillance activities can be conducted to monitor animal  health, or in response to a specific disease. Animal disease surveillance  consists of collecting, analyzing, and interpreting animal health data to  detect diseases early, enable rapid reporting and response during  disease outbreaks, and control the spread of disease. According to  USDA guidance, the agency also can use such data for accurate risk  analysis, which includes assessing present, future, and emerging threats  to animal health, and estimating the likelihood of a damaging event and  the resulting consequences.
As part of the agency’s preparedness and response efforts, USDA has  identified certain animal diseases that pose a risk and must be reported if  they occur in the United States. Data collected on these diseases are  used to estimate their geographic distribution and severity, which inform  officials’ response efforts. For example, USDA established program  diseases to control or eradicate specific diseases that must be reported to  federal and state animal health officials. The agency works with federal- state-industry stakeholders to control or eradicate these diseases. USDA  describes program diseases as serious zoonotic diseases, diseases that  are economically important, or diseases of concern to the livestock,  poultry, or aquaculture industries.
Among these program diseases, some are designated as foreign animal  diseases, which, in addition to being reported to USDA must be reported  to the international community. USDA defines a foreign animal disease as  a terrestrial animal disease or pest, or an aquatic animal disease or pest,  not known to exist in the United States or its territories. A foreign animal  disease may involve livestock, poultry, wildlife, or other animals. The  World Organisation for Animal Health (formerly known as the Office of  International Epizooties or, more commonly by its previous acronym, OIE)  develops the list of internationally reportable animal diseases. This list is  used by OIE’s 180 member countries when determining trade restrictions  on animals or animal products that pose a risk to their agricultural  industries. According to USDA’s guidance about animal diseases, one  of the most immediate and severe consequences of an incident of an  OIE-Listed animal disease in the United States is the loss of export  markets. For example, according to the USDA’s Economic Research  Service website, as a result of the current outbreak of highly pathogenic  avian influenza—an OIE-Listed disease—as of June 2015, 15 countries,  including China, Russia, and South Korea, have banned poultry imports  from the United States with many other countries placing bans on U.S.  states or regions.
Rapid response to diseases can prevent or limit sudden, negative  consequences for animal health, economic security, and food security.  Additionally, a rapid response can help normal production to resume as  quickly as possible. When deciding on and implementing actions to  respond to outbreaks of animal disease, USDA collaborates with other  federal agencies, state officials, and with industry. For example, USDA  works with
FDA, which, among other things, is responsible for ensuring the safety  of feed, to investigate potential feed contamination; state animal health officials and state departments of agriculture to  assist in disease control efforts such as data collection; and  industry to implement biosecurity practices that are critical to limiting  disease entry and spread. For example, diseases can be introduced  or spread to healthy animals via footwear and outerwear, but  biosecurity practices such as changing or covering these items before  entering premises can help prevent the introduction of disease.  Similarly, changing or covering these items after working with infected  animals can prevent the spread of disease.
According to USDA’s Animal and Plant Health Inspection Service’s  strategic plan, collaborative efforts are thought to produce more public  value than any single agency could produce. Components of these efforts  include the identification of roles and responsibilities and mutually agreed  upon common outcomes, such as the control or eradication of a  disease, as well as joint strategies for achieving the agreed-upon  outcome.
section_title: USDA Did Not Take Regulatory Action During the Initial Response to the SECD Outbreak, Limiting Its Understanding of the Geographic Distribution, Spread, and Source of the Diseases
paragraphs: USDA did not take regulatory action during the initial response to the  SECD outbreak, beginning in May 2013 when the PED virus was first  detected, because it did not believe then that such action was necessary  to manage the outbreak. By not taking regulatory action, USDA had  limited information about the initial geographic distribution of the  diseases; their modes of spread; and the locations of the first infected  herds, which could have helped identify the source of entry of the  diseases in the United States.
subsections: section_title: USDA Did Not Take Regulatory Action During the Initial Response, Instead Playing a Supporting Role to Industry Efforts
paragraphs: USDA did not take regulatory action during the initial response when  SECD were identified in May 2013. According to USDA officials, the  agency was reluctant—and did not believe it was necessary—to take  regulatory action, such as requiring reporting of infected herds or  restricting the movement of pigs. Such action could have had negative  financial impacts on the swine industry, according to USDA documents.  Instead, the agency initially supported swine industry-led efforts to  address SECD.
Moving Pigs   Pigs are often moved among multiple  premises at different stages of their life spans  to accommodate their growth in size.  Typically, pigs are moved by truck and trailer  as shown in the picture below. Additionally,  the U.S. Department of Agriculture (USDA)  estimates that more than 600,000 pigs are  transported to slaughter on any given day in  the United States.   According to industry representatives and  USDA, movement restrictions such as a  quarantine lasting more than a week could  potentially result in euthanasia of hundreds of  thousands or millions of animals, depending  on how long the quarantine was in place,  since premises may not be able to humanely  house pigs larger than they customarily  handle.
The agency’s decision not to take regulatory action took into account  several factors, including that these diseases were not listed as  internationally reportable animal diseases, do not pose a threat to people,  and were not lethal to all pigs. If USDA had designated these as foreign  animal diseases within the United States, the agency might have been  expected to impose quarantines, and other countries might have  restricted the importation of pigs or pig products. According to USDA  guidance for reportable and foreign animal diseases, import restrictions  could potentially have severe consequences because U.S. animal  agricultural industries are becoming more dependent on exports, and the  long-term strategic plans of these industries call for increasing the amount  of goods sold abroad.
Porcine Epidemic Diarrhea Virus (PED)  Strains   The U.S. Department of Agriculture and other  researchers have reported on more than one  strain of PED presently in the United States.  According to recent research, two strains  identified in the United States closely resemble  the strains of PED virus circulating in China;  however, genetic resemblance does not  indicate how the virus arrived in the United  States.
USDA officials told us that, at that time of their decision, varying strains  of PED were known and active around the world, and the agency and  the swine industry were aware of how PED spread (via fecal  contamination). At that time, USDA believed the best course of action  was for industry to manage SECD according to an agency  announcement about the diseases. USDA officials explained that  industry was already leading the response to other swine diseases,  such as transmissible gastroenteritis.
The initial response by industry and USDA to the SECD outbreak  included efforts to learn more about these diseases. Within 3 months of  the first PED diagnosis, one of the main swine industry associations— the National Pork Board—made $800,000 available for research to  learn about PED and potential ways to control the disease, such as  through promoting maternal (sow) immunity. USDA provided support  and collaborated with industry associations in the response. Initial  agency support included providing diagnostic support through its National Veterinary Services  Laboratories to the National Animal Health Laboratory Network; providing funding for and participating with industry associations in  investigations of herds that became infected without an obvious  reason, such as a newly infected herd in a remote area that had no  clear connections to another infected herd; and compiling and reporting to industry associations positive testing  results (indicating infected herds) that were voluntarily reported by  veterinarians or producers to the National Animal Health Laboratory  Network laboratories.
USDA also funded SECD-related research through the regular annual  grant cycle of its National Institute of Food and Agriculture, as well as  within the Agriculture Research Service. According to several federal,  state, industry, and academic stakeholders we interviewed, research  funding is important. Several stakeholders explained both industry and  federal funding are important to promote research because they typically  have different objectives. Generally, industry focuses on research with  near-term applicability for producers, such as identifying which  disinfectants are most effective in killing viruses. USDA generally  supports research that is more broadly intended to further understanding  of animal diseases. For example, past USDA work led to a diagnostic tool  that was used to confirm the first identification of PED in the United  States. The protocol for this tool was provided to the National Animal  Health Laboratory Network. This protocol helped veterinary diagnostic  laboratories participating in this network develop faster diagnostic tools,  which they currently use to identify SECD.
section_title: USDA Had Limited Information on SECD Geographic Distribution and Mode of Spread and Cannot Definitively Identify How the Diseases Entered the United States
paragraphs: Because USDA did not take regulatory action, the agency had limited  information about the initial geographic distribution of the diseases; their  modes of spread; and the locations of the first infected herds, which could  have helped identify the source of entry of the diseases in the United  States. Further, in part because USDA did not have information about  locations of the first infected herds, it did not investigate the first outbreak  of SECD at the onset, and the source of entry of SECD into the United  States will likely never be determined.
subsections: section_title: USDA Did Not Know the Initial Geographic Distribution of SECD Because Reporting Was Incomplete
paragraphs: At the onset of SECD in the United States, USDA did not know the  geographic distribution because disease reporting was incomplete. State  veterinary diagnostic laboratories and swine veterinarians initially  identified these diseases and provided USDA with limited information on  their geographic distribution by state, but not by premises. According to  USDA’s Chief Epidemiologist, location information is an important  component in understanding how the disease is spread and how to  prevent diseases and mitigate their spread. However, USDA did not  initially require reporting of infected herds or the exact location of these  herds, and swine producers were reluctant to voluntarily share this  information with USDA. USDA officials, swine veterinarians, and industry  representatives that we interviewed believed that producers’ reluctance  stemmed partly from concern about whether USDA had the ability or  procedures in place to maintain confidentiality of this information. Swine  veterinarians we interviewed told us that producers were also concerned  about public perception of these diseases based on past experience with  other diseases. Specifically, in 2009, a novel influenza virus with origins in  pigs caused a worldwide epidemic and led to substantial losses in pork  sales when consumers mistakenly believed they could become infected  by eating pork.
Swine Enteric Coronavirus Diseases  (SECD) Spread   GAO’s review of literature found that there are  multiple likely modes for the spread of SECD.  Specifically, these studies found that SECD  could likely be spread by transport vehicles,  people, feed, and air. For example, people  involved in transporting pigs can potentially  spread virus on their clothing and boots from  one location to another. In addition,  employees and veterinarians in direct contact  with pigs, service people delivering feed or  water, maintenance workers, and others who  visit premises can carry the virus onto and off  of the premises, spreading it inadvertently. As  demonstrated in the image below, the  National Pork Board recommends biosecurity  practices such as changing outerwear and  footwear before entering premises with pigs to  help mitigate the risk of spreading diseases.  For further discussion of the literature review,  see appendix I.
According to USDA’s summary of SECD testing results, the information  USDA received voluntarily from laboratories in the early outbreak of PED,  and later for PDCoV, was not useful for determining the number of  infected herds. In particular, swine producers did not consistently share  information on the location of their premises when submitting samples for  testing, and some producers submitted multiple samples at various times  from the same premises in an effort to determine if SECD had been  eradicated. Without complete location information, USDA did not know if  these test samples were for diagnosing potentially newly infected herds,  or for retesting herds that had previously tested positive. Additionally, in  some cases, the results reported to USDA contained inaccuracies, such  as incorrect state locations of the infected herds. For example, USDA  officials explained that a swine-producing company could be based in one  state, but the premises on which the sample was collected might have  been in another state. Further, test samples provided by producers to  diagnostic laboratories did not identify the type of swine infected, such as  breeding sows, piglets, or pigs ready for slaughter—information useful for  understanding the type of animal most susceptible and the impact of  these diseases on industry. The laboratories also did not report to USDA  the results of negative tests until November 2013, which could have  demonstrated where the diseases were not occurring or where the  disease occurrence might have been declining.
The limited information USDA received, while incomplete, suggested that  the diseases were quickly spreading to multiple states. Specifically, PED  was initially diagnosed in 3 states (Indiana, Iowa, and Ohio) in May 2013.  The laboratories then diagnosed PED in 10 additional states through  June 2013 and in about 30 states total through May 2014. Similarly, the  limited information for PDCoV suggested that it was present in the same  3 original states as PED in January 2014 (Indiana, Iowa, and Ohio) and  had spread to at least 11 additional states through May 2014.
section_title: USDA Participated in Efforts to Understand Ways SECD Could Have Spread
paragraphs: Beginning in May 2013, USDA collaborated with universities and industry  associations on various efforts to understand how SECD may have  spread in the United States. In one instance, USDA personnel provided  statistical and technical support for university-based research on the  possible airborne transmission of PED and geographic clustering of  positive sites. In another effort, USDA personnel contributed to  questionnaire development and analysis for a nationwide survey by swine  veterinarians of selected swine producers with PED-infected herds; this  effort found feed could have been a potential factor in the spread of the  disease. In addition, for PDCoV, USDA participated with industry in  investigations in April 2014 at premises where the disease was diagnosed  in the United States.
Porcine Epidemic Diarrhea Virus (PED) in  Canada   PED was first reported in Canada in January  2014, 8 months after it was first reported in  the United States. Canadian provincial and  federal government officials, with help from  private swine veterinarians, conducted an  immediate epidemiological investigation on  the source of the PED and found an  association between cases of PED in Canada  and a feed ingredient (spray-dried porcine  blood plasma) from a U.S. feed distributor.  According to Canadian federal government  officials, the feed distributor voluntarily  removed this feed from the market and the  officials believe this change helped reduce the  spread of PED in Canada.
USDA officials explained that there were other actions the agency could  have taken to potentially limit the spread. For example, the agency could  have imposed a temporary quarantine, restricting movement for a few  days. However, these officials told us that, in their opinions, quarantine,  depending on its length, could have had negative financial consequences  to swine producers. Further, the officials told us that agency actions, such  as quarantine, may not have been able to prevent the spread based on  the pig industry’s reliance on movement. The diseases are highly  infectious and, by the time the first SECD was identified in May 2013,  diagnostic laboratories later determined that PED had already been  spreading, and multiple herds were infected as early as April 2013. After  observing what happened in the United States, officials in at least one  Canadian province worked with producers to establish voluntary  movement restrictions to limit the spread in Canada, according to  Canadian swine industry and government officials. Additionally, several  Canadian provinces required reporting of infected herds including  premises identification numbers. In the United States, these numbers  serve as a way to track a farm (or premises) without using specific  location information, such as longitude and latitude coordinates or a  postal address, to help protect the privacy of the producer.
section_title: USDA Did Not Investigate the First Outbreak at the Onset, and the Source of Entry of SECD into the United States Will Likely Never Be Determined
paragraphs: USDA officials told us they missed an opportunity to conduct in-depth  epidemiological outbreak investigations at the premises where PED was  first diagnosed. Such investigations can help identify how a disease may  have entered specific premises and, thus, may help determine how the  disease entered the United States. USDA’s investigation guidance for  emerging animal disease incidents in effect during the first outbreak  stated that collecting and analyzing epidemiological information is a  critical element to an investigation. Had USDA followed this guidance, it  would have conducted key steps of an outbreak investigation at the onset  of the first cases, such as interviewing persons for incident history on the  first infected premises near the time of the initial diagnosis and collecting  and analyzing other epidemiological data for those incidents. Such an  investigation does not guarantee that the source of the outbreak will be  determined, but it typically provides some information necessary for such  a determination. USDA’s Chief Epidemiologist told us that timely outbreak  investigations at the first infected premises would have been helpful in  collecting more information on the source of entry. Because USDA did not  follow its investigation guidance, the source of entry of PED into the  United States will likely never be determined.
When asked why USDA did not conduct a timely outbreak investigation at  the premises where PED was first diagnosed, senior USDA officials told  us that the agency did not have information about locations of the first  infected herds—information that would have been gained through  regulatory action to require reporting. In addition, agency officials said  USDA learned about the disease after it was identified by a laboratory.  Officials explained that typically USDA applies its investigation guidance  when the agency is contacted to help identify an unknown disease on the  premises. One senior USDA official explained that, in the case of PED,  USDA chose not to follow its investigation guidance since the disease  was already identified—even though the guidance does not provide for an  exception in such cases.
USDA’s investigation guidance states that employees may not deviate  from the directions provided without appropriate justification and  supervisory concurrence. USDA officials acknowledged that they did not  follow the guidance. USDA currently does not have a process in place  that would help ensure this guidance is followed. According to federal  standards for internal control, internal control activities help ensure that  management directives, such as those incorporated in the investigation  guidance, are carried out. The control activities should be effective and  efficient in accomplishing the agency’s control objectives. One example of  a control activity would be establishing a process for documentation of the  justification and approval of any deviation from the directions. Without  appropriate control activities, USDA cannot have reasonable assurance  that the guidance will be followed in future outbreaks.
section_title: USDA Subsequently Took Additional Actions to Manage SECD, with Mixed Results, and Identified Potential Preventive Strategies
paragraphs: Amid mounting concerns about the spread of the diseases and the  associated economic losses, USDA took additional actions to manage  SECD beginning in June 2014. In particular, USDA issued a federal order  imposing reporting and planning requirements, and it provided financial  assistance to states and producers. USDA cites progress in addressing  SECD, but stakeholders we interviewed have questioned the usefulness  of some of USDA’s actions. In addition, USDA is retrospectively  conducting a study of potential ways PED could have entered the United  States and has identified potential preventive strategies based on its  findings.
subsections: section_title: USDA Imposed Reporting and Planning Requirements and Provided Financial Assistance to Manage SECD
paragraphs: In June 2014, USDA issued a federal order to help manage the diseases.  According to USDA documents, the order followed a winter in which  SECD appeared to spread at increasing rates, leading to mounting  producer concerns about economic losses from pig deaths. The order  includes two basic requirements that remain in place at the time of this  report. First, it requires anyone with knowledge of the diseases, including  producers, veterinarians, and diagnostic laboratories to report all new  SECD incidents to USDA or state animal health officials, providing  specific information, including premises identification numbers. It also  requires that, before a herd is considered confirmed positive for SECD,  the herd with positive testing results also has at least one case of a pig  with a history of clinical signs consistent with SECD. According to  USDA, routine, standard reporting for SECD helps determine the  magnitude of the diseases in the United States and documents progress  in managing the diseases. Second, the order requires producers reporting  SECD incidents to work with a veterinarian—either their herd  veterinarians, or USDA or state animal health officials—to develop herd  management plans. These herd management plans, which must be  submitted to USDA, list biosecurity practices that the producers will follow  to control the spread of disease.
USDA also provided approximately $26 million for a variety of activities to  help manage SECD. This funding was budgeted for, among other things,  cooperative agreements with state animal health offices to support  SECD management and control activities related to required  reporting; financial assistance for diagnostic testing to determine the presence  or absence of SECD;  financial assistance for veterinarians developing the required herd  management plans—specifically, reimbursement of $150 per plan;  financial assistance to producers for biosecurity practices, specifically  for purchasing disinfectants for transportation trucks and premises; efforts to develop vaccines; genomic sequencing of the viruses that cause SECD to better  understand their characteristics; and  internal USDA SECD-related activities, such as staff time for SECD  reporting and working with stakeholders.
section_title: USDA Announced Progress in Managing SECD, but Stakeholders We Interviewed Have Questioned the Usefulness of Some USDA Actions
paragraphs: Following its regulatory actions and provision of funding related to SECD,  USDA announced progress in managing these diseases. However,  stakeholders we interviewed raised concerns about the usefulness of  some aspects of USDA’s efforts to address SECD. USDA officials  explained that, in response to some of these concerns, they have shifted  funding to activities that stakeholders found more useful.
subsections: section_title: USDA Cited Several Achievements in Managing SECD
paragraphs: In December 2014, USDA announced in a public statement that it had  made progress addressing SECD and was receiving more accurate and  timely information about SECD-infected herds and their locations.  According to USDA’s announcement, this information allowed animal  health officials to better understand how the diseases spread and what  measures have been most effective in containing them. More  specifically, USDA noted that it had achieved the following in reporting  and managing SECD:  received information quickly and electronically through an improved  information technology network with the laboratories, allowing federal  and state health officials to better understand the spread of an animal  disease outbreak in nearly real time; increased the number of diagnostic tests submitted that include the  premises identification number, allowing for more accurate monitoring  of current disease incidence and spread; granted two conditional licenses for vaccines developed for SECD;  improved its ability to detect new viruses and changes to existing  viruses through genomic sequencing.
Several state, industry, and federal stakeholders we interviewed told us  that providing financial assistance for diagnostic testing and requiring  reporting were the most important USDA actions for helping to manage  these diseases. Several stakeholders also said that these actions  improved information available about the geographic distribution of  SECD. According to USDA’s Chief Epidemiologist, frequent diagnostic  testing demonstrated whether biosecurity practices to reduce the risk of  spread were working. The federal order’s requirement to report positive  SECD incidents requiring specific information, including premises  identification numbers, has resulted in USDA having more accurate data  on the frequency and date of new SECD incidents, and on the location of  infected herds. According to a USDA report on these diseases, the  agency can use premises identification numbers to identify whether a  herd was previously reported as infected to avoid double counting  infected herds, and USDA officials commented that the required  information also assists officials in contacting producers to confirm clinical  signs of illness. USDA can now more accurately report on the number of  new infections and on infections by state. As shown in figures 1 and 2 on  the next pages, from June 5, 2014, through September 5, 2015, PED- infected premises have been confirmed in 28 U.S. states and 1 U.S.  territory and PDCoV-infected premises have been confirmed in 15 U.S.  states.
USDA reported in September 2015 that, since June 2014, cumulatively,  1,599 premises have been confirmed as having herds infected with  SECD. More specifically, within these premises 1,468 herds have been  infected with PED, 73 herds have been infected with PDCoV, and 58  herds have been infected with both PED and PDCoV. From June 2014  through September 2015, about 40 percent of infected U.S. herds were  in Iowa, the top swine-producing state. Using industry estimates, USDA  reported in June 2014, that these diseases have caused approximately  7 million pig deaths, mainly among piglets, in the United States, with  PED causing the majority of these deaths.
section_title: Stakeholders We Interviewed Raised Concerns about the Usefulness of Some Aspects of USDA’s Efforts to Address SECD
paragraphs: Some aspects of USDA’s efforts to address SECD were not as well  received as the financial assistance for diagnostic testing and the  reporting requirements, according to stakeholders in our review. For  example, stakeholders we interviewed told us veterinarians did not seek  the $150 dollar financial assistance USDA offered for each herd  management plan developed to help control the spread of disease on  premises with SECD-infected herd because the effort associated with  obtaining the assistance was not worth the amount received. According to  data provided by USDA, less than 16 percent of the funds originally  budgeted for reimbursing veterinarians had been obligated as of August  2015. Additionally, according to several state officials and industry  representatives and a USDA official responsible for the funds, many  producers were not applying for financial assistance for their biosecurity  practices. As of August 2015, less than $1 million of the $11.2 million  initially budgeted for biosecurity payments had been obligated according  to the data USDA provided. State officials and industry representatives  explained that producers were not seeking this assistance for various  reasons, including that the effort associated with obtaining financial  assistance was not worth the amount received; the assistance was limited  to purchasing disinfectants; and the assistance was available only to  producers with herds that tested positive after the federal order was  issued.
USDA officials explained that they, therefore, shifted funds from this  category to cover other activities, such as diagnostic testing, in response  to stakeholder concerns. USDA initially budgeted $2.4 million for  diagnostic testing. However, according to USDA officials, laboratories and  industry representatives requested that the agency treat SECD diagnostic  testing similar to testing for other reportable animal diseases and  reimburse diagnostic laboratories for all tests, not only tests with positive  results for infection. As a result, USDA increased the amount of financial  assistance available for diagnostic testing within a few weeks of  announcing its funding for SECD activities and, as of August 2015, about  $10 million has been obligated for diagnostic testing. See table 2 for the  initial funding amounts for SECD activities and obligated amounts by  activity as of August 2015.
Regarding other USDA actions, nonfederal stakeholders—including  industry representatives, private veterinarians, and academics—told us  that further work is needed for the conditionally approved PED vaccines  to be effective in preventing new herds from getting infected. As a result,  some stakeholders we interviewed said these conditional vaccines are  used on a limited basis or in conjunction with a traditional disease control  method known as “feedback.” However, immunity from feedback or  vaccines is not lifelong, and reoccurrences may occur. In addition, some  state animal health officials noted that it would be helpful if USDA’s  information system for tracking infected herds automatically notified them  of new infections in their state, similar to how USDA’s officials are  notified. Some of these state officials explained that automatic notification  could assist them in conducting their disease response activities. For  example, officials may need to collect additional information from  producers of infected herds to complete documentation of herd  management plans and obtain additional samples to monitor herds’  disease status. Currently, after the first incident in the state, to learn about  subsequent incidents, a state official could either access USDA’s  information system to check if there have been any new incidents within  the state or could contact each laboratory to request direct notification of  new incidents, according to USDA officials we interviewed.
section_title: USDA Is Retrospectively Conducting Studies on Likely Sources of Entry for SECD and Identified a Strategy to Address Potential Biosecurity Gaps
paragraphs: While USDA was unable to definitively identify how either PED or PDCoV  entered the United States, in September 2015, USDA released a  retrospective study of numerous potential ways SECD could have entered  the United States. This retrospective root cause study began almost a  year after laboratories diagnosed PED in the first known infected herd.
This retrospective root cause study indicates that the use of transport  carrier totes is the most plausible potential source of entry based on the  criteria the agency used when evaluating how PED may have entered the  United States. These totes are large, flexible sacks with a capacity of  more than 1,000 pounds that are used to carry dry products. USDA  determined that these totes were generally not cleaned before being  reused for a number of purposes, including distributing pet food treats  and shipping pig feed ingredients, such as organic soybeans, to the  United States. The study explained that organic soybeans are a product  imported from China that can be fertilized with swine manure and are  frequently shipped in totes. Because the study identified totes as a  potential gap in U.S. border biosecurity, USDA has initiated further  research into totes to provide evidence to support the study’s findings.  Specifically, USDA is conducting tests to confirm that cross contamination  between the totes and feed ingredients can occur and that the virus can  survive during long transit times. According to a USDA official, the results  demonstrate that the PED virus can survive on the totes for at least 5  weeks at room temperature and at least 10 weeks at 39 degrees  Fahrenheit. According to the retrospective root cause study, the agency is  also working with the Department of Homeland Security’s U.S. Customs  and Border Protection to test samples of organic soybean shipments to  determine whether they are a possible source of PED virus.
The retrospective root cause study also identified two preventive  strategies that could mitigate the potential risk related to totes: (1) not  reusing these totes or (2) identifying appropriate cleaning and disinfection  procedures for the totes before their reuse to transport products into the  United States. USDA has communicated findings of the study to FDA,  which, among other things, is responsible for ensuring the safety of feed,  and to stakeholders in the feed and swine industry, who, according to  USDA, could mitigate risks prior to exposure of animals.
section_title: USDA Has Not Defined Key Aspects of Its Future Response to Emerging Animal Diseases
paragraphs: To improve its future response to emerging animal diseases, USDA has  drafted new guidance and a proposed list of reportable diseases but has  not defined key aspects of its response. More specifically, USDA has  drafted guidance for responding to emerging animal diseases and has  proposed a comprehensive list of animal diseases that must be reported  by anyone with knowledge of the diseases. However, USDA has not  defined roles and responsibilities or criteria for actions that are included in  its response to emerging diseases.
subsections: section_title: USDA Has Drafted Guidance and an Associated List of Reportable Diseases to Improve Its Approach for Responding to Emerging Animal Diseases
paragraphs: USDA has drafted new guidance for responding to emerging animal  diseases; according to a USDA summary document, the agency  developed this guidance as a result of its experience with SECD and to  improve the agency’s response to future diseases. USDA made this  guidance available for public comment from October 16, 2014, through  January 16, 2015. The draft guidance describes USDA’s goals for  addressing emerging diseases as (1) undertake global awareness of,  assessment of, and preparedness for animal diseases or pathogens not  currently in the United States that may be of animal or public health  concern or have trade implications; (2) detect, identify, and characterize  disease events; (3) communicate findings and inform stakeholders; and  (4) respond quickly to minimize the impact of disease events. This draft  guidance also refers to existing USDA guidance for conducting  investigations and reporting results for emerging animal disease events.
In conjunction with the draft guidance, USDA also released a “Proposed  National List of Reportable Animal Diseases.” According to USDA’s  description of the proposed list, it is intended to, among other things,  facilitate the response to an emerging animal disease in the United  States. In the list, USDA identifies specific animal diseases and their  proposed monitoring and reporting requirements, which would also apply  to emerging animal diseases either currently on the list or newly  identified. Any individuals, including producers and laboratory personnel,  who have any knowledge of an incident of any of the listed diseases that  USDA categorizes as “notifiable” would be required to comply with these  reporting requirements; currently no individuals beyond accredited  veterinarians are specifically required to report to USDA, according to the  list. Agency officials we interviewed told us that expanding the reporting  requirement to all knowledgeable individuals closes a reporting gap for  disease incidents where no accredited veterinarian examined the animal  or conducted the testing.
section_title: USDA Has Not Defined or Communicated Key Aspects of Its Approach for Responding to Emerging Animal Diseases
paragraphs: USDA’s draft guidance has not defined or communicated key aspects of  its response to emerging diseases, including when the agency would take  a lead role, what the agency’s responsibilities would be, and examples of  what circumstances may trigger actions such as euthanasia or  quarantines. In contrast, USDA has defined and communicated such  aspects of its response to foreign animal diseases. For example, USDA’s  guidance for responding to foreign animal diseases provides information  on roles and responsibilities, the scope of regulatory intervention, the  criteria used in the selection of a response strategy, and examples of  actions taken under different strategies. In addition, for several foreign  animal diseases, USDA has created specific response plans that include  examples of different types of responses to different levels of outbreaks.
According to a senior USDA official who was involved in the drafting of  the emerging diseases draft guidance, this guidance is intended to be  broadly applicable and not as detailed as the guidance for foreign animal  diseases. In addition, the characteristics of each emerging disease could  vary dramatically, and creating a decision tree, for example, to show what  actions to take could be difficult because of a high number of different  potential scenarios. We recognize that defining the response to every  emerging disease can be challenging because of the many unknowns.  However, in its draft guidance, the agency has not included general  information on key aspects of its response to emerging diseases, such as  roles and responsibilities of the various involved stakeholders, potential  response strategies, and what may trigger different types of actions. This  information could facilitate rapid, effective decision making.
USDA’s Animal and Plant Health Inspection Service stated in its 2015- 2019 Strategic Plan that protecting the health, welfare, and value of  America’s agriculture and natural resources requires coordinated and  collaborative efforts, and that identifying roles and responsibilities is a key  component of successful collaboration. Agency officials we interviewed  agreed that they believe developing additional information on roles and  responsibilities, potential response strategies, and what may trigger  different types of actions would be feasible and useful. In a summary  document that USDA released about its draft guidance on responding to  emerging diseases, USDA noted that, for SECD, the options for  responding to these diseases and how decisions would be made were not  clear. Industry representatives we interviewed said that they did not  know how USDA would address the diseases and what role industry  would have, which led to concerns about sharing information about SECD  incidents with USDA and how USDA would use this information. Without  more information on USDA’s approach, the representatives said they may  not be receptive to USDA taking the lead in addressing future emerging  animal diseases. The National Pork Board announced in November 2014  that it would provide $15 million for a swine health information center to  better prepare industry for the next emerging swine disease.
Absence of a clearly defined agency response to emerging animal  diseases is also inconsistent with federal standards for internal control.  USDA guidance primarily lists the goals of USDA in responding to  emerging diseases and does little to explain how these goals will be  achieved. Under these federal standards, control activities are the  policies, procedures, techniques, and mechanisms that enforce  management’s directives; these activities help ensure that actions are  taken to address risks. Appropriate documentation is an example of a  control activity. The standards state that internal control needs to be  clearly documented, and the documentation should be readily available  for examination. The documentation should appear in management  directives, administrative policies, or operating manuals. Without a  clearly defined and documented response to emerging animal diseases,  response efforts could be slowed as agency staff and other stakeholders  may not be able to quickly identify the appropriate actions to take.
section_title: Conclusions
paragraphs: The recent outbreaks of SECD have heightened awareness of the need  to better prepare for emerging animal diseases. USDA, the states, and  the swine industry are making considerable efforts to ensure that, in the  future, the response to such diseases will be swift and effective—which  can be paramount for preventing or limiting sudden, negative  consequences for animal health, economic security, and food security.  While much has been accomplished, opportunities remain to improve  USDA’s ability to respond to the risks posed by emerging animal  diseases. In particular, unless USDA clarifies how it intends to respond to  such diseases, stakeholders may not be receptive to USDA leadership  and agency staff may not know their options for managing future  outbreaks or how to decide among these options. Additionally, USDA  currently does not have a process in place that, consistent with standards  for internal control, would help ensure its guidance for investigation of  foreign or emerging animal diseases is followed. Until USDA develops  such a process, it cannot have reasonable assurance that the guidance  will be followed in future outbreaks.
section_title: Recommendations for Executive Action
paragraphs: To improve USDA’s ability to respond to and protect against future  emerging animal diseases, we recommend that the Secretary of  Agriculture direct the Administrator of the Animal and Plant Health  Inspection Service to take the following two actions:
Clarify and document how the agency will respond to emerging  diseases including defining key aspects of its response, such as roles  and responsibilities, potential response strategies, and what may  trigger different types of actions.
Develop a process to help ensure that its guidance for investigation of  foreign or emerging animal diseases is followed, such as a process  for documentation of the justification and approval of any deviation  from the directions.
section_title: Agency Comments and Our Evaluation
paragraphs: We provided a draft of this report to USDA for review and comment.  USDA provided written comments, which are summarized below and  reproduced in appendix II. In its comments, USDA agreed with the intent  of our recommendations and described actions or plans to address them.
More specifically, to clarify and document how the agency will respond to  emerging diseases, USDA noted that its new draft guidance for  responding to emerging animal diseases was made available for public  comment and stated that it will revise this guidance as needed. USDA  also stated that, for each of the goals within this guidance, APHIS is  developing further direction to clarify roles and responsibilities, potential  responses, and possible triggers.
To develop a process to help ensure that its guidance for investigation of  foreign or emerging diseases is followed, USDA stated that the intended  refinement and expansion of the guidance for responding to emerging  animal diseases will address when and how emerging diseases may be  investigated differently from the procedures in its current investigation  guidance.
In our draft, we also included a recommendation to develop a process to  address deficiencies identified by USDA’s root cause retrospective study  or demonstrate the findings do not warrant management action to reduce  the likelihood of entry of future animal diseases into the United States.  We have removed this recommendation because, in its written  comments, USDA provided new information on actions it has recently  taken to address it. Specifically, USDA identified two approaches to  mitigate potential risks identified in the study. First, USDA stated that,  prior to the release of the study, APHIS consulted with FDA, which has  regulatory jurisdiction over feed and feed facilities, to discuss potential  regulatory controls under the Food Safety and Modernization Act. In  particular, USDA noted a rule FDA enacted in September 2015 to  implement provisions of this act that requires registered animal food  facilities to develop a food safety plan, perform an analysis on hazards  associated with the animal food and the facility, and implement measures  to control these hazards. USDA stated that these regulatory controls are  believed to address the risks identified in the study related to the entry of  animal diseases into the United States. We believe that this is a  reasonable assessment of the new regulatory controls. Second, USDA  has communicated findings of the study to stakeholders in the feed and  swine industry, who, according to USDA, could mitigate risks prior to  exposure of animals. USDA provided us with documentation supporting  its statement about meeting recently with FDA and industry, and we  verified with a senior swine industry official that USDA presented findings  of its study to the swine industry prior to its release. In light of these  recent activities, we no longer believe that there is a need for a  recommendation to develop a process to address deficiencies identified  in the root cause analysis report, and we removed it accordingly.
As agreed with your office, unless you publicly announce the contents of  this report earlier, we plan no further distribution until 30 days from the  report date. At that time, we will send copies to the appropriate  congressional committees, the Secretary of Agriculture, and other  interested parties. In addition, the report will be available at no charge on  the GAO website at http://www.gao.gov.
If you or your staff members have any questions about this report, please  contact John Neumann at (202) 512-3841 or neumannj@gao.gov, or  Timothy M. Persons at (202) 512-6412 or personst@gao.gov. Contact  points for our Offices of Congressional Relations and Public Affairs may  be found on the last page of this report. GAO staff who made key  contributions to this report are listed in appendix III.
section_title: Appendix I: GAO Review of Studies on the Spread of Porcine Epidemic Diarrhea
paragraphs: We identified and reviewed four studies published between March 2013  and August 2015 in peer-reviewed journals that examined factors that  may have contributed to the spread of Porcine Epidemic Diarrhea (PED)  in the United States. University researchers, swine veterinarians, and  pork producers collaborated on these studies. None of the four studies we  reviewed found evidence of a definitive cause of PED spread. However,  the studies showed that it is plausible for PED viruses to be spread by air,  feed, transport vehicles, or people. See table 3 below for a summary of  the studies.
section_title: Appendix II: Comments from the U.S. Department of Agriculture
section_title: Appendix III: GAO Contacts and Staff Acknowledgments
subsections: section_title: GAO Contacts
paragraphs: John Neumann, (202) 512-3841 or neumannj@gao.gov.  Timothy M. Persons, (202) 512-6412 or personst@gao.gov.
section_title: Staff Acknowledgments
paragraphs: In addition to the individual named above, Mary Denigan-Macauley  (Assistant Director), Sushil Sharma (Assistant Director), Leslie  Ashton, Kevin Bray, Mark Braza, Allen Chan, Barbara El Osta,  Cynthia Norris, Dan Royer, Amber Sinclair, and Elaine Vaurio made  key contributions to this report.