Emerging Animal Diseases: Actions Needed to Better Position USDA to Address Future Risks
Released: 2016-01-14T00:00:00

Letter

Background

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.

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

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.

USDA Did Not Take Regulatory Action During the Initial Response, Instead Playing a Supporting Role to Industry Efforts

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.

USDA Had Limited Information on SECD Geographic Distribution and Mode of Spread and Cannot Definitively Identify How the Diseases Entered the United States

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.

USDA Did Not Know the Initial Geographic Distribution of SECD Because Reporting Was Incomplete

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.

USDA Participated in Efforts to Understand Ways SECD Could Have Spread

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.

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

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.

USDA Subsequently Took Additional Actions to Manage SECD, with Mixed Results, and Identified Potential Preventive Strategies

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.

USDA Imposed Reporting and Planning Requirements and Provided Financial Assistance to Manage SECD

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.

USDA Announced Progress in Managing SECD, but Stakeholders We Interviewed Have Questioned the Usefulness of Some USDA Actions

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.

USDA Cited Several Achievements in Managing SECD

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.

Stakeholders We Interviewed Raised Concerns about the Usefulness of Some Aspects of USDA’s Efforts to Address SECD

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.

USDA Is Retrospectively Conducting Studies on Likely Sources of Entry for SECD and Identified a Strategy to Address Potential Biosecurity Gaps

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.

USDA Has Not Defined Key Aspects of Its Future Response to Emerging Animal Diseases

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.

USDA Has Drafted Guidance and an Associated List of Reportable Diseases to Improve Its Approach for Responding to Emerging Animal Diseases

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.

USDA Has Not Defined or Communicated Key Aspects of Its Approach for Responding to Emerging Animal Diseases

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.

Conclusions

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.

Recommendations for Executive Action

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.

Agency Comments and Our Evaluation

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.

Appendix I: GAO Review of Studies on the Spread of Porcine Epidemic Diarrhea

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.

Appendix II: Comments from the U.S. Department of Agriculture

Appendix III: GAO Contacts and Staff Acknowledgments

GAO Contacts

John Neumann, (202) 512-3841 or neumannj@gao.gov. Timothy M. Persons, (202) 512-6412 or personst@gao.gov.

Staff Acknowledgments

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.