1

Bovine Spongiform Encephalopathy (BSE) 

Ongoing Surveillance Plan 

July 20, 2006 
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Bovine Spongiform Encephalopathy Ongoing Surveillance Plan 

INTRODUCTION

The U.S. Department of Agriculture (USDA) has taken aggressive measures to prevent 

the introduction and potential spread of bovine spongiform encephalopathy (BSE), and 

has conducted surveillance since 1990 to monitor whether the disease was present. 

Surveillance was expanded in scope and intensity following the confirmation of BSE in 

an imported cow in December 2003. This expanded surveillance effort was designed to 

estimate the level of disease present in the United States and provide input for designing 

a long-term surveillance plan. 

The present plan is intended to inform and educate USDA’s partners and stakeholders on 

approaches to be employed in ongoing BSE surveillance. The plan retains the USDA’s 

ability to detect BSE at 1 infected animal per 1,000,000 adult cattle in the population with 

a high degree of confidence, maintains surveillance at levels that exceed international 

standards, emphasizes sample collection from cattle subpopulations where BSE is most 

likely to be detected, and retains sample collections from all important surveillance 

sources. 

The plan follows surveillance system design standards and guidelines established by the 

USDA’s Animal and Plant Health Inspection Service (APHIS), Veterinary Services (VS), 

National Surveillance Unit (NSU). These guidelines are intended to assist planners and 

managers in considering specific objectives, design strategies, reporting systems, 

implementation methods, and long-term system maintenance. The guidelines ensure that 

the objectives of the surveillance system are predefined, and that the collection, 

organization, and analysis of appropriate data are considered before implementation. 

Further, the guidelines provide a mechanism for review and evaluation to assure that the 

surveillance is providing the appropriate type and quality of information. 

Disease description 

Bovine spongiform encephalopathy, commonly known as “Mad Cow Disease”, is a 

transmissible neurodegenerative disease of adult cattle that emerged in Great Britain in 

1985,38 and has subsequently been identified in cattle of most European countries, 

Canada, the United States, and Japan. BSE belongs to the group of transmissible 

spongiform encephalopathies (TSEs), together with scrapie of sheep, chronic wasting 

disease of free-ranging and captive deer and elk, and Creutzfeldt-Jakob disease (CJD) of 

humans. TSEs have long latency periods, are untreatable, and currently cannot be 

prevented by vaccination since there is absence of a host immune response to infection. 

Most scientific evidence suggests that prions are the causative agent of TSEs;32 however, 

the nature of the prion remains undetermined. A unique characteristic of the prion is its 

resistance to inactivation by most conventional physical or chemical decontamination 

methods.37 The prion consists mostly of protein, largely comprised by a proteinaseresistant, disease-associated isoform (PrPres) of host-encoded prion protein (PrPC

).29,32 

The pathogenesis of the TSEs requires the formation of PrPres from PrPC

.

16 Interaction 
3

with PrPres leads to post-translational conformational modification of PrPC,

24,26,33 resulting 

in its conversion to PrPres.

14,19 The subsequent pathological accumulation of PrPres in 

certain tissues defines the TSEs.13,34 The pathogenesis of BSE appears to involve a much 

more restricted tissue distribution of PrPres accumulation than other animal TSEs, having 

reduced involvement of the lymphoreticular system. 

The origin of the BSE agent is unresolved. Theories have considered derivation from a 

TSE agent of another mammalian species, such as scrapie,40 or spontaneous genetic 

mutation of the bovid prion protein gene.31 The emergence of BSE coincided with 

reduced use of hydrocarbon solvents in the production of meat-and-bone meal (MBM) 

through carcass rendering.40

Transmission of BSE is thought to primarily occur through ingestion of feedstuff, 

especially ruminant-derived MBM, contaminated with the BSE agent.41,43 Calves born to 

infected cows have increased risk to develop BSE,44 especially if born around the time of 

disease onset in the dam.22 However, the risk is probably influenced by conserved 

management practices where both the dam and calf have been fed concentrated feedstuff 

containing MBM early in life.12 Horizontal transmission of BSE between cattle is not 

believed to occur. Most cattle become infected within the first 6 months of life.12 The 

mean incubation period for BSE is around 60 months, with clinical onset of disease 

occurring on average at 4-5 years of age.11 The age range of affected animals is very 

wide, although BSE is rarely confirmed in animals less than 30 months of age.4,48 

BSE is invariably fatal. Clinical signs have an insidious onset and are largely 

nonspecific. Signs that may be associated with BSE include apprehension, ataxia, 

emaciation, hypersensitivity to touch or sound, head shyness, panic-stricken response, 

kicking in the milking parlor, reluctance to enter the milking parlor, abnormal ear 

movement or carriage, increased alertness behavior, reduced milk yield, bruxism, and 

change in temperament.35,43 The duration of clinical signs averages 1 to 2 months prior to 

death or slaughter, but may range from weeks to a year.43

Although live animal tests are under development, at present, none are available to 

reliably detect BSE. Diagnosis is achieved postmortem through examination of central 

nervous system (CNS) tissue, and is contingent on identification of characteristic 

histopathologic lesions, detection of PrPres, or electron microscopic visualization of 

scrapie-associated fibrils.6 Because PrPres is the only currently known disease-specific 

macromolecule, all commercially available diagnostic assays rely on its immunological 

detection.10 These assays have limited diagnostic sensitivity in that PrPres accumulation 

may not be detectable until late during the incubation period, within months prior to onset 

of clinical disease.27 Infected animals that are early in the incubation period can only be 

identified through demonstration of tissue infectivity using bioassay. The only lesions 

associated with BSE are found microscopically within CNS tissue.38,39 Lesions develop 

late in the disease process, roughly coinciding with the onset of clinical signs. These 

consist of non-inflammatory vacuolar degeneration, or spongiform change, of grey matter 

and neuronal cell bodies. Astrocytosis and cerebral amyloidosis, features of other TSEs, 

are unusual with BSE. 
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Breed-dependent differential susceptibility or incubation period has not been observed 

with BSE,42 and there is little variability in the bovine PrP gene.23 The consistent 

neuroanatomical lesion profile in the brains of cattle affected with BSE,36,39 and uniform 

glycoform ratios of PrPres as determined by immunoblotting,21,28 suggest the existence of 

a single strain of the BSE agent. However, a recently described atypical form of BSE, 

termed bovine amyloidotic spongiform encephalopathy (BASE), has modified glycoform

patterns similar to sporadic CJD in humans, and may represent an alternative strain of 

BSE agent.18

 

Although TSEs are usually confined to an individual species, concern has arisen for the 

potential of inter-species transmission of BSE. The BSE agent is widely recognized as 

the cause of variant CJD in humans, based on epidemiological and mouse inoculation 

studies,15,46 and biochemical PrPres characteristics.21 In addition, natural exposure to 

BSE agent has led to similar encephalopathic disease in captive wild ungulates and cats,25

and in domestic cats.47

Measures established by the United States to prevent new cases of BSE have included 

restrictions on the importation of ruminants and ruminant-derived products from 

countries affected with BSE or that present undue risk of BSE (9CFR Parts 93, 94, 95, 

96, and 98) and prohibition of feeding mammalian-derived proteins, with exceptions, to 

ruminants (21CFR589.2000). Mitigating measures have been considered to effectively 

reduce the likelihood of BSE introduction and amplification in U.S. cattle.20 Food-safety 

precautions implemented by the United States to protect the consumer have included the 

exclusion of non-ambulatory cattle from slaughter for human consumption, prohibitions 

on the use of specified risk material as human food, and prohibitions on the use of 

mechanically separated beef in human food (69 FR 1826, January 12, 2004; 69 FR 

42255, July 14, 2004); prohibition of the use of air-injection stunning devices to 

immobilize cattle during slaughter (69 FR 1885-1891); and prohibitions on the use of 

certain tissues in advanced meat recovery systems and additional process controls on 

these systems (69 FR 1874-1885). 

Purpose, rationale, and objectives of surveillance 

Animal and public health concerns have led to the establishment of active surveillance 

programs among other regulatory measures to monitor and prevent disease. Active 

surveillance for BSE was initiated in the United States in 1990. In response to 

identification of a BSE-affected imported dairy cow in December 2003, the U.S. 

Enhanced BSE Surveillance Program was implemented in June 2004. Through these 

efforts, 2 cases of BSE were identified through March 2006. Both cases were in beef 

cattle over ten years old (born before the feed ban of 1997), one located in Texas and one 

in Alabama. 

Based on data collected in the United States over the last seven years, including over a 

half million samples from the Enhanced Surveillance program, the USDA has developed 

an estimate of prevalence of BSE among U.S. cattle that was extremely low, projected at 
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less than 1 case per million animals in the standing adult cattle population at the 95% 

confidence level.1

 In addition, the USDA demonstrated that surveillance efforts to date 

far exceed the World Organization for Animal Health (Office Internationales des 

Epizooties [OIE]) “type A” surveillance requirements. Prevalence is expected to decline 

as long as mitigation efforts that maintain low risk for introduction and spread of the BSE 

agent among U.S. cattle are equivalent to or better than those evaluated by the Harvard 

Risk Assessment.20 The present plan details the objectives and methods considered 

pertinent and necessary for Ongoing BSE Surveillance. 

The principal purposes of Ongoing BSE Surveillance are: 

1. To continue to assess and monitor change in the BSE status of U.S. cattle. 

2. To provide mechanisms for detection of BSE prevalence if it were to increase 

above 1 infected animal per million adults. 

Expected outcomes 

The results of Ongoing BSE Surveillance will be used for decision-making and policy 

development regarding design and implementation of future BSE surveillance programs 

and control efforts. Results will also be used to facilitate contingency plans for national 

BSE control and response programs and to evaluate the effectiveness of mitigations and 

control measures that have been implemented to reduce the risk of introduction and 

spread of BSE among U.S. cattle. The planned response to confirmed cases of BSE are 

described elsewhere.3,7 

Additionally, the implementation of a strong BSE surveillance strategy will help provide 

reassurance to consumers and international trading partners regarding our ability to detect 

a problem if one should arise. The results of the surveillance program will be an 

important component of documenting the BSE status of U.S. cattle. The USDA has 

designed this surveillance program to meet or exceed the internationally accepted 

surveillance practices recommended by the OIE. Compliance with OIE guidelines is an 

important component of assuring trading partners of the quality of our surveillance 

efforts.2

 USDA expects that this robust surveillance program will continue to provide the 

foundation for market confidence in the safety of U.S. cattle. 

Stakeholders and responsible parties 

Users of surveillance system information include policy makers within USDA, the U.S. 

livestock industry, consumer groups, trading partners, State Animal Health Offices, and 

data providers (sample collectors and veterinary diagnostic laboratories). In addition to 

information users, beneficiaries of the surveillance information include the public, the 

U.S. cattle industry, consumer groups, and industries engaged in export markets for 

cattle-derived products. 

Data collection will be performed by a variety of parties. Sample data will be collected 

by accredited veterinarians, Food Safety Inspection Service (FSIS) veterinarians and 

inspectors, veterinary diagnostic laboratory or public health laboratory personnel, and 
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qualified VS personnel (including animal health technicians and those involved with data 

entry). VS Area Offices will direct efforts for resolution of problematic data. 

Samples will be tested for BSE through cooperation of NVSL and contracted veterinary 

diagnostic laboratories. Positive samples will be confirmed by NVSL. American 

Association of Veterinary Laboratory Diagnosticians (AAVLD) accredited laboratories 

participating in the National Animal Health Laboratory Network (NAHLN) may be 

contracted by NVSL to perform BSE screening tests, provided quality assurance 

standards are met (as described by the most current version of NVSL protocols 

GPPISOP3501 and 3303). 

Training of sample collectors will be completed by Area Veterinarian in Charge (AVIC) 

office personnel with oversight by VS regional offices. Data entry training will be 

completed by these parties as well as the BSE Help Desk.a

Assessment of data quality, data analysis, and interpretation will be completed by the 

NSU, VS TSE program manager, and VS TSE epidemiologists. Reporting and 

dissemination of surveillance results will be primarily the responsibility of the NSU. In 

addition to standard Agricultural Marketing Service audit procedures, the NSU will 

conduct a review of the surveillance system’s effectiveness. NVSL will be responsible 

for quality assurance of laboratory results. 

POPULATION DESCRIPTION AND SAMPLING METHODS

Current OIE guidelines emphasize the development of ongoing surveillance programs 

that focus on obtaining quality samples from high risk subpopulations rather than on a 

target number of animals.2 As a result, if surveillance can be efficiently targeted to the 

highest risk subpopulations, meaningful surveillance can occur with a fairly low number 

of animals (for an example of how the OIE numbers are calculated, see the Summary of 

BSE Enhanced Surveillance in the United States).9 For this reason, an important focus of 

the Ongoing Surveillance will be obtaining samples from cattle that are “clinical 

suspects.” This subpopulation of cattle, particularly cattle over 30 months of age, has 

been found to exhibit the highest prevalence of BSE. Inferences derived from 

surveillance findings will be generalized to the adult U.S. cattle population (i.e. target or 

inference population), which consists of approximately 42 million adult cattle.5

Study (Targeted) Population 

Ongoing Surveillance will target subpopulations from the Enhanced Surveillance 

population with the highest probability of BSE detection. Because BSE is exceedingly 

uncommon among U.S. cattle, the chosen targeted population will create intentional bias 

in the sample frame which favors detection of disease. Cattle that are dead with unknown 

clinical history will be limited in the surveillance sampling strategy because they provide 

substantially less information than animals accompanied by clinical history. As used in 

this Ongoing Surveillance plan, “dead with unknown clinical history” refers to cattle that 

 

a

 Veterinary Services BSE Help Desk: (866) 370-6611, bse.help@aphis.usda.gov 
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are already dead prior to being presented for BSE sample collection and that have no 

known clinical history other than “dead of unknown cause.” Efforts for collecting 

clinical history data will be augmented for Ongoing Surveillance. At least one clinical 

sign must be identified for each sampled animal. Apparently healthy animals will not be 

targeted for surveillance. For those cattle without obvious CNS signs, sample collection 

on-farm will be preferred over other collection sites because the subtle and nonspecific 

nature of behavioral changes associated with BSE are best identified by those who handle 

cattle on a daily basis,2 and personnel on-farm are most suitable for providing this 

information. 

The targeted population for Ongoing Surveillance consists of cattle of any breed that fit 

one of the following clinical presentation criteria: 

1. Cattle of any age with CNS signs 

This category includes cattle exhibiting signs consistent with a central nervous 

system disorder (including rabies-negative cases from public health laboratories, 

and FSIS condemns for “CNS signs” or “rabies”). 

Additionally, this category includes cattle highly suspicious for BSE as indicated 

by VS Memo 580.16, which includes: 1) cattle affected by illnesses that are 

refractory to treatment (including anorexia, loss of condition in spite of good 

appetite, pneumonia, decreased milk yield) and are displaying progressive 

behavioral changes that are not of an acute nature (including apprehension, 

nervousness, excitability, aggression, head shyness, hypermetria, kicking when 

milked, difficulty in rising, excessive nose scratching, or hesitation at 

gates/barriers); 2) cattle displaying progressive neurological signs that cannot be 

attributed to infectious illness and are not responsive to treatment. 

2. Cattle ≥ 30 months of ageb

 that are condemned during antemortem inspection 

or are excluded from slaughter due to poor health status (nonambulatory, 

unhealthy, or dead) 

This category includes: 

a) Cattle that are condemned by FSIS at antemortem inspection for any 

reason (other than “CNS signs” or “rabies,” which are covered above 

under “Cattle of any age with CNS signs”). 

b) Cattle without a history of CNS signs for which sample collection occurs 

on-farm, at veterinary clinics, or at livestock sale or auction barns and that 

are dead, nonambulatory, or have clinical signs that may be associated 

with BSE. For those cattle that are dead prior to arrival of sampling 

 

b Age of 30 months or older is evidenced by the eruption of at least one of the second set of permanent 

incisors. 
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personnel on-farm, additional clinical history must be available other than 

“dead of unknown cause.” 

c) Cattle presented to veterinary diagnostic laboratories for necropsy or for 

ancillary diagnostics without a history of CNS signs but which had clinical 

signs that may be associated with BSE. 

d) Cattle from renderers or 3D/4D facilities (up to a maximum of 5,000) that 

are dead, nonambulatory, or sick. Collection of clinical history is 

preferable for these samples but is not required. 

The Enhanced Surveillance data provide information on the number of clinical suspects 

and the number of nonambulatory, unhealthy, or dead animals over 30 months classified 

by collection site.9

 We expect that collection sites yielding the highest proportion of 

clinical suspects relative to the number of animals sampled will continue to do so. 

Accordingly, because renderers and 3D/4D facilities produced the most samples but 

proportionately the fewest clinical suspects in the Enhanced Surveillance program, we 

will limit samples from these facilities to 5,000 animals. 

Sample Points and Numbers to Meet OIE Surveillance Standards 

APHIS is committed to maintaining BSE surveillance that at least meets OIE guidelines. 

The OIE BSE surveillance guidelines recommend a target number of surveillance points 

for Type A surveillance based on the size of a country’s cattle population. These points 

are accrued over 7 consecutive years, and are weighted according to the surveillance 

stream and age of the animal sampled. For a large cattle population, using the design 

prevalence of 1 case per 100,000 adult cattle and 95% confidence, 300,000 total points 

over 7 years, or 42,857 points per year are required for Type A surveillance.2

The four surveillance streams identified in the OIE Code are clinical suspects; casualty 

slaughter; fallen stock; and healthy slaughter. OIE guidelines recommend sampling from 

at least three of the four surveillance streams. BSE surveillance efforts in the US have 

always focused on the three surveillance streams where BSE is more likely to be found – 

clinical suspects, casualty slaughter, and fallen stock. During the 7 consecutive years 

prior to March 17, 2006, the United States collected 735,213 BSE samples from these 

surveillance streams and accumulated 2,973,804 OIE points.9

 

If the Ongoing Surveillance plan maintains similar sample numbers from these 

surveillance streams, approximately 10,500 cattle per year would be sufficient to meet the 

OIE minimum number of sample points for Type A surveillance. 

2,973,804 points ÷ 735,213 samples = 4.1 points per sample 

and 

42,857 points required per year ÷ 4.1 points per sample = 10,453 samples per year 
9

The Ongoing Surveillance plan targets relatively few of the lowest value samples (i.e., 

only 5,000 renderer and 3D-4D origin samples as compared to over 1⁄2 million during 

Enhanced Surveillance). Thus, the point value per sample will be higher than 4.1, and 

10,453 samples from Ongoing Surveillance will easily exceed the OIE requirements. 

Sample Points and Sample Size for BSE Prevalence Estimates

The OIE minimum number of samples as outlined would be sufficient for a design 

prevalence of 1 case per 100,000 adult cattle. In the interest of maintaining confidence in 

previous BSE prevalence estimates, a more sensitive design prevalence of 1 case per 

1,000,000 adult cattle will be adopted for Ongoing Surveillance. 

The point tables described by OIE surveillance guidelines were designed using the 

BSurvE model to represent the most conservative scenario of the characteristics of the 

cattle populations of all its member States. These conservative demographic 

characteristics describe a population that culls cattle very rapidly (mean age of 

approximately 4 years) and results in point values that are that are much lower than the 

BSurvE model would calculate for cattle in most countries. The United States has 

relevant demographic data pertaining to the adult cattle population that indicate 25% of 

the adult cattle population of approximately 42 million are dairy production type and 

75% are beef cattle.30 While the U.S. dairy population undergoes rapid culling similar to 

the conservative characteristics used to develop the OIE table, beef cattle generally 

remain in the herd to a much older age until they no longer produce calves. 

The BSurvE model can be used to determine sample point values based on a particular 

population’s demographics. Because actual U.S. data are available regarding population 

characteristics, and because this population differs significantly from that used for the 

conservative OIE estimates, it is appropriate to base the sample size estimates on the 

points calculated through BSurvE given U.S. demographics (these points are hereafter 

referred to as “analytical points”). The higher average age at which beef cattle are culled 

influences the BSurvE output and results in substantially higher point values. Hence, 

sample values calculated with BSurvE from actual U.S. data result in higher point values 

than the conservative OIE estimates . Each analytical point calculated by BSurvE 

corresponds to a single non-targeted sample.45 

According to OIE, BSurvE and Cannon and Roe17calculations, the required number of 

non-targeted samples needed to detect a prevalence of 1 case per million adult cattle with 

95% confidence (given a population size of 42 million adult cattle) is 3,000,000, 

2,995,730, and 2,891,389, respectively. Conservatively using the value of 3 million, we 

calculate that we will need to accumulate 428,571 analytical points (with negative 

results) per year across a period of 7 years to meet this objective. 

3,000,000 analytical points ÷ 7 years = 428,571 analytical points per year 
10

The prevalence analysis conducted on U.S. surveillance data collected from March, 1999 

through March 2006 reports 6,745,010 points resulting from 735,213 samples. The 

average sample was worth 9.5 analytical points.1

6,745,010 analytic points ÷ 735,213 samples = 9.5 analytic points per sample 

If USDA maintained an equivalent mix of surveillance streams during Ongoing 

Surveillance, then approximately 45,113 samples per year would be required to meet this 

objective. 

428,571 analytical points per year ÷ 9.5 analytical points per sample = 45,113 

samples per year 

However, greater than one half million of the samples from Enhanced Surveillance were 

collected from fallen stock – the surveillance stream that produced the lowest point 

values. Sampling efforts can be focused on higher value surveillance streams – clinical 

suspects and casualty slaughter – with a limited number of samples obtained from the 

fallen stock surveillance stream. This will increase the average point value per sample. 

Therefore, we estimate that 40,000 samples collected from these 3 surveillance streams – 

with a focus on clinical suspects and casualty slaughter - will exceed the number of 

points necessary to maintain confidence that prevalence is less than 1 infected animal per 

million adult cattle. Further, since the data are analyzed over 7 consecutive years, the 

estimate of sample size may be adjusted each year as appropriate to assure a robust 

prevalence estimate. 

Study Area Under Surveillance 

The collection sites for this sampling plan have been selected to include animals from all 

sections of the United States and comprise nationally representative avenues through 

which cattle exit production. In combination, these data sources provide the opportunity 

for cattle residing in any part of the country or segment of industry to be sampled: 

• Slaughter facilities are located throughout the United States and service every 

constituent of the production industry. Additionally, western States that 

practice open range grazing and do not have access to renderers, or may not 

observe animal deaths, will still ship cull cattle to FSIS-inspected facilities in 

other States. 

• Rendering facilities or 3D/4D facilities are located throughout the United 

States. Some of these facilities draw from the same populations as the 

slaughter facilities, as they are the disposal facility for offal and condemned 

animals from the slaughter facilities. Focusing on these facilities, and on 

rendering facilities in geographic locations with only limited disposal 

alternatives will help ensure a broad geographical representation. The 

inclusion of these facilities ensures access to the fallen stock surveillance 

stream. 

• On-farm sample collection allows that samples will be collected wherever 

cattle reside. Efforts will be made across the nation to encourage the 
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participation of veterinary professionals and paraprofessionals in on-farm 

sample collection. 

• There are no areas in the nation that cannot submit fresh whole cattle brain to 

a public health or veterinary diagnostic laboratory. 

A qualitative, not quantitative, analysis of sample origin and collection site will be 

employed for Ongoing Surveillance sampling.c With increased emphasis on the 

importance of obtaining samples from high risk subpopulations, establishing and meeting 

a specific numeric target for the total number of cattle sampled becomes relatively less 

important. The results of Enhanced Surveillance allowed us to identify the collection 

sites that are more likely to yield clinical suspects. Nevertheless, it is important to obtain 

coverage of all potential streams at all collection sites in order to maximize the likelihood 

that we will obtain samples from clinical suspects. 

OIE Guidelines and Surveillance Streams 

Samples will be assigned to the surveillance streams described in Article 3.8.4.2 of the 

OIE Terrestrial Animal Health code. The stream to which a sample is assigned will be 

based on clinical signs that are provided, sample source, and condemnation code data. 

Note that samples within the “Routine Slaughter” stream (from Article 3.8.4.2) will not 

be collected during Ongoing Surveillance. The OIE surveillance streams and the criteria 

by which samples will be assigned to them are listed below. 

1. Clinical suspect – cattle displaying behavioral or clinical signs consistent 

with BSE. 

Article 3.8.4.2 of the OIE Terrestrial Animal Health code describes this group as 

follows: “Cattle affected by illnesses that are refractory to treatment, and 

displaying progressive behavioral changes such as excitability, persistent kicking 

when milked, changes in herd hierarchical status, hesitation at doors, gates and 

barriers, as well as those displaying progressive neurological signs without signs 

of infectious illness are candidates for examination. These behavioral changes, 

being very subtle, are best identified by those who handle animals on a daily 

basis.” 

Samples will be assigned to this surveillance stream if they are from cattle defined 

as highly suspicious as outlined in VS Memorandum 580.16, were tested negative 

for rabies at a public health or veterinary diagnostic laboratory, had CNS signs or 

were condemned by FSIS for CNS signs or rabies, or if the likelihood ratio for 

clinical signs associated with BSE is above an appropriate cutoff value (methods 

for these determinations are described elsewhere).9

 Most of these samples are 

 

c

 A quantitative analysis of geographical representation is difficult to interpret since cattle movement in the 

United States is poorly defined, and a sample’s site of collection site may not correspond to where the 

animal was born or resided most of its life (i.e., the area where BSE transmission would have occurred). 

Statistical comparison of geographic regions in the Enhanced Surveillance analysis and the paucity of 

positive cases provide no evidence that BSE prevalence varies by region within the United States. 
12

anticipated to be derived from samples collected on-farm. A substantial number 

will also be contributed by FSIS, veterinary diagnostic laboratories, and public 

health laboratories. 

2. Casualty slaughter –cattle over 30 months of age that are non-ambulatory, 

recumbent, unable to rise or to walk without assistance, sent for emergency 

slaughter, or condemned at antemortem inspection. 

Samples will be assigned to this surveillance stream if the likelihood ratio for 

clinical signs being associated with BSE is below an appropriate cutoff value, and 

if the sample meets the OIE criteria for this stream. Most of these samples are 

anticipated to be derived from FSIS-inspected slaughter plants. However, a 

considerable number will be contributed by other data sources such as on-farm 

and veterinary diagnostic laboratories. 

3. Fallen stock – cattle over 30 months of age that are found dead on farm, or 

during transport to or at an abattoir. 

Samples will be assigned to this surveillance stream if the likelihood ratio for clinical 

signs being associated with BSE is below an appropriate cutoff value, and if the sample 

meets the OIE criteria for this stream. These samples are anticipated to contribute a 

negligible portion of total points. 

Table 2. OIE point values for each surveillance stream by cattle age 

Clinical 

suspect 

Casualty 

slaughter 

Fallen 

stock 

Routine 

slaughter 

(Apparently Healthy)

Age ≥ 1 year and < 2 years N/A 0.4 0.2 0.01 

Age ≥ 2 years and < 4 years 260 0.4 0.2 0.1 

Age ≥ 4 years and < 7 years 750 1.6 0.9 0.2 

Age ≥ 7 years and < 9 years 220 0.7 0.4 0.1 

Age ≥ 9 years 45 0.2 0.1 0.0 

Sample collection sites 

The following sites have been selected based on observations from Enhanced 

Surveillance including relative quality of data collected, average point value per sample, 

and total sample numbers. Additionally, these collection sites comprise nationally 

representative avenues through which cattle may exit the adult cattle population and be 

available for sampling. Cattle meeting the targeted criteria will be sampled from the 

following sites: 

1. On-Farm

These samples may be collected by accredited veterinarians, Federal or State 

employees (including animal health technicians), or VS-approved dead stock 

haulers. Under VS Area Office oversight, sample collectors with other 
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qualifications may be enlisted when resources preclude the participation of 

aforementioned sample collectors in a given area. Although these samples may 

have a higher cost relative to other data sources, they are anticipated to have 

higher value to surveillance since the accuracy, quantity, and perceived validity of 

clinical history is superior relative to other data sources. 

 

2. Veterinary Diagnostic Laboratories

Cattle submitted for necropsy, or fresh whole brainstem submitted for ancillary 

diagnostics to veterinary diagnostic laboratories, including those not involved in 

BSE testing, will be sampled by laboratory personnel. Such samples are usually 

accompanied by significant clinical history and thus are of high value to 

surveillance. 

3. Public Health Laboratories

Samples from cattle that are rabies suspects and test negative for rabies will be 

submitted for BSE testing by laboratory personnel. All samples derived from this 

data source can be characterized as clinically suspicious for BSE, and thus are of 

high value to surveillance. 

4. Slaughter (FSIS)

Cattle 30 months or older condemned at antemortem inspection, and cattle of any 

age condemned for “CNS signs” or “rabies,” will be sampled by FSIS employees 

or designated off-site sample collection facilities. 

5. Facilities contracted to collect samples from cattle condemned by FSIS at 

antemortem inspection

Samples derived from animals condemned by FSIS personnel at antemortem 

inspection may be collected by personnel of a contracted rendering or 3D/4D 

facility, or other APHIS approved facility. Under these circumstances, 

communication of condemnation codes, clinical signs, and condemnation tag 

numbers (Z-tags) to the contracted facility is imperative. 

6. Rendering or 3D/4D facilities 

In order to represent the “fallen stock” surveillance stream and a wide variety of 

data sources, 5,000 samples will be collected over a 12-month period from 

targeted cattle presented to rendering or 3D/4D facilities. A quota is selectively 

applied to this collection site type since these samples tend to lack adequate 

clinical history, making them a less reliable source for clinical suspect animals. 

Sampling progress will be monitored on a monthly basis. If the results differ 

considerably from expectations, the sampling strategy may be adjusted. For example, 

should we find that our expectations of sites most likely to yield clinical suspects are not 

met, we may refocus sampling efforts to other collection sites. Similarly should we find 

there are substantially large numbers of non-clinical-suspect cattle being sampled, we 

may reduce the intensity of our sampling in these categories. Such restrictions may 

involve reducing or stopping the collection of samples on-farm, at veterinary clinics, or 
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auction barns or reducing or stopping the collection of cattle condemned by FSIS. 

However, samples will be collected without restriction throughout the sampling period 

from cattle with CNS signs, rabies suspects, those considered highly suspicious for BSE, 

or cattle condemned by FSIS for CNS disorders or rabies regardless of the avenue 

through which they present to surveillance, and regardless of the degree with which 

sampling goals have been met. 

Sample points derived from Enhanced Surveillance have provided a substantial cushion 

for potential deficiency during Ongoing Surveillance. Since international standards allow 

points to be included in surveillance analysis over a 7-year time period, there is 

considerable time to adjust Ongoing Surveillance to meet surveillance needs with the 

most cost-efficient methods of sampling. 

COLLECTION METHODS 

Data Collection Methods 

Data collection methods will utilize the structures and processes established in the 

Enhanced Surveillance program. Sample data should be collected using the forms 

employed by Enhanced Surveillance: USDA BSE Surveillance Submission Form and 

USDA BSE Surveillance Data Collection Form. Forms are completed by the sample 

collector either by hand (paper forms) or electronically, through the NAHLN Web site 

(nahln.aphis.usda.gov/nahln/jsp/login.jsp). If the collection site cannot complete data 

entry electronically, paper copies must be forwarded to a designated USDA:VS office or 

the BSE Helpdesk for data entry. Training of data entry is overseen by VS area and 

regional offices, and the BSE Help Desk. 

A hard copy of the BSE Surveillance Submission Form must be submitted to the 

diagnostic laboratory. If samples are not accompanied by the appropriate submission 

forms with all necessary information, it is the responsibility of the diagnostic laboratories 

to contact the sample collection site. Diagnostic laboratories may report collection sites 

that are repeatedly problematic to the appropriate AVIC for correctional efforts. 

The USDA BSE Surveillance Submission Form must be completed for each set of 

samples from a particular collection site and date. The USDA BSE Surveillance Data 

Collection Form must be completed for each animal sampled. All types of ID present on 

the animal must be provided, including silver tag number, owner ear tag number, 

vaccination tag number, condemnation tag number, back tag number, bangle tag number, 

ear tattoo, brands, or microchip. In the case of samples from cattle condemned at 

antemortem inspection, the “Z” tag (FSIS condemnation tag number) must be recorded. 

A “Primary Reason for Submission,” is used to assure the sample collector that the 

animal being sampled is appropriate for surveillance (i.e. is a member of the targeted 

population). It is imperative that the clinical signs section be completed as thoroughly 

and accurately as possible because data from this section of the form are used for 

allocation of samples into appropriate surveillance streams during data analysis. 
15

Data relevant to the results of laboratory testing are entered through the NALHN 

interface by diagnostic laboratory personnel. Results can include any of the following:

• Not Detected – negative by ELISA or IHC 

• Not detected, not obex* – negative by ELISA; although the sample appeared 

to be brainstem, the laboratory technician could not identify the sample as 

obex tissue 

• Not tested* – sample not tested because sample could not be recognized as 

brainstem by the laboratory technician 

• Initial reactor – positive on first screening (ELISA) test 

• Inconclusive – following a positive on the first screening test, at least one 

additional test is positive when the screening test is repeated in duplicate 

• IHC Inconclusive – sample with equivocal immunohistochemistry results 

• Positive – samples positive either by IHC or immunoblotting 

*For these selections, the reason for the result must be further specified as one of the 

following: 

• Advanced tissue decomposition 

• Wrong anatomic location 

• Tissue disrupted preventing anatomic orientation 

Sample Collection Methods 

Samples may be collected by authorized Federal or State personnel, accredited 

veterinarians, APHIS-contracted employees, or diagnostic laboratory personnel. 

Animal identification items (drawings or digital pictures of brands, removed tattooed 

hide, ear tags, etc.) should be collected from each animal sampled, bagged, labeled with 

the sample number, attached to a copy of the USDA BSE Surveillance Submission Form, 

and saved by the sample collector until negative results are received. 

Brainstem samples may be collected through the foramen magnum, using a brain spoon 

or other extraction techniques (such as water extraction or compressed air), after 

disarticulation of the atlanto-occipital joint. Alternatively, a brainstem sample may be 

collected by dismantling the calvarium (e.g. when retrieving the whole brain for rabies 

diagnosis). An appropriate brainstem sample includes obex with little contamination or 

postmortem decomposition. Samples with post-mortem or post-collection decomposition 

such that they cannot be recognized as brainstem will not be tested by the diagnostic 

laboratory. Sample collectors should submit samples that have questionable testability 

and allow laboratory technicians to decide if tissue integrity precludes testing. 

Diagnostic laboratories will be compensated for efforts related to determining sample 

testability. 

Samples may be held prior to submission to the diagnostic laboratory, provided they are 

refrigerated (e.g., for sending multiple samples in one shipment). These should be 
16

submitted as soon as possible, but may be held for no longer than 7 days. Samples 

should not be frozen. 

Fresh brainstem samples are individually packaged in plastic tubes labeled with a unique 

BSE sample identification bar code supplied by the USDA. Samples are enclosed with 

cold packs in insulated packages and are shipped by overnight contract delivery service 

(e.g. Federal Express), same-day courier service, or by hand delivery to a NALHN 

laboratory that offers BSE test service the following business day. Once shipped, delivery 

of samples to diagnostic laboratories should be completed within 24 hours so as to 

preserve sample integrity. If samples are received by a diagnostic laboratory on a nonoperating weekday, samples will be held under refrigeration by the diagnostic laboratory 

and subsequently tested on the next operating weekday. If test results are urgently 

needed, the AVIC office may dictate that samples be redirected to an operating diagnostic 

laboratory. For samples with “inconclusive” test results, all remaining tissue must be 

immediately forwarded to NVSL (per the most current version of NVSL protocol 

GPPISOP0029). The timeline of procedures and reporting that occur in response to a 

positive case are described elsewhere.3,7

The diagnostic laboratory is responsible for entering test results into the NAHLN 

database and for notifying the sample submitter of test results electronically, by phone, or 

in writing. This should be completed within 24-48 hours of test completion. Additional 

parties, including the AVIC and State veterinary office, may also be notified of results 

given that an arrangement has been agreed upon between the diagnostic laboratory and 

additional party. APHIS Animal Identification Coordinators (AIC) may assist with 

sample delivery verification and troubleshooting. Training of sample collectors is 

completed by AVIC offices and VS regional offices, and, at their discretion, state 

veterinary offices. It is the responsibility of the AVIC offices to monitor sample 

collectors in the relevant area for habitual poor sample collection technique. 

Animal Disposal 

Carcasses from negative animals are disposed of in compliance with Federal, State, and 

local laws. Carcasses and offal from “inconclusive” or positive animals may be disposed 

of by one of the following: rendering for non-animal feed use by dedicated facilities, 

burial in a landfill, burial on-farm, alkaline digestion, or incineration. Rendering 

facilities may refrigerate or freeze carcasses, or may proceed with rendering and hold 

batches of final products, pending test results. Should a positive animal occur with the 

latter method, an indemnity would be supplied for the disposed batches of products. 

Clinical Case Definition

Clinical case definitions are not applicable to the present surveillance methods. Because 

clinical signs have such poor specificity and sensitivity for BSE diagnosis, and because 

the diagnostic assays used for BSE diagnosis are considered to have near perfect analytic 

sensitivity and specificity (i.e. cattle with detectable disease are reliably differentiated 

from cattle without detectable disease), BSE diagnosis is solely based on laboratory 
17

criteria. The case definition used for surveillance is the laboratory case definition for 

BSE as defined by the most current version of NVSL document GPISOP0034. 

Laboratory Criteria for Diagnosis

The diagnostic strategy implemented for BSE surveillance is described elsewhere (most 

current versions of NVSL protocols GPPISOP0027 and GPPISOP0034). 

ANALYSIS, REPORTING, AND PRESENTATION

The NSU is the party primarily responsible for data analysis and reporting. Reports 

produced by the NSU for the Deputy Administrator of VS and his designates will include 

monthly reports used for program monitoring and oversight, and an annual summary 

report analogous to that produced at the conclusion of the Enhanced Surveillance 

program. The annual summary report is intended to tally surveillance points derived 

from BSE surveillance efforts over the last 7 years using the OIE Code. Additionally, 

this report will provide an estimate of BSE prevalence, and/or demonstrate freedom from 

disease in U.S. cattle. The information provided by the annual report may be further 

tabulated for public consumption at the request of the Deputy Administrator; however 

monthly reports are anticipated to remain for internal USDA use only. Measures that will 

be portrayed by the monthly reports, in tabular and graphical format, include monthly and 

cumulative numbers of targeted samples, non-targeted samples, “not detected, not obex” 

samples, and total samples stratified by collection site type, submission reason, and 

geographical area. Monthly reports will be used to assess progress toward national 

sampling goals with respect to point totals. 

Data analysis will be performed throughout the Ongoing Surveillance to assess sampling 

progress. Data quality will be monitored periodically using an error-checking routine to 

identify information that is outside expected values or for key data that are missing. 

Samples that do not meet the targeted sampling criteria will be identified, and feedback 

will be provided through appropriate channels to sample collectors that submit nontargeted samples. Many mechanisms are already in place in the existing BSE database 

that prevent common data entry errors and that require recording of important sample 

data. 
18

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