SPF shrimp in Aquaculture

Facts, truths, and myths about SPF shrimp in Aquaculture

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By: Victoria Alday-Sanz, James Brock, Timothy W. Flegel, Robins McIntosh, Melba G. Bondad-Reantaso, Marcela Salazar and Rohana Subasinghe *

This article, developed by a group of shrimp farming specialists, seeks to clarify the meanings of new terms that are frequently used within the international shrimp farming industry when talking about SPF shrimp (Free of Specific Pathogens) and their correlation with each other. The correct understanding of these terms can reduce the risk of disease outbreaks for global shrimp production and increase this important aquaculture sector’s benefits and profits.

The concept of specific pathogen-free (SPF) animal stocks, and the technology to create and manage them originated in the early 1940s and lies within the scope of laboratory animal medicine.

Specifically, specific pathogen-free (SPF) chicken eggs were developed for vaccine production. After that, over the subsequent 30–40 years, SPF technology was adopted, developed, and applied to commercial poultry, and in the 1960s, extended to swine and other domestic animal production systems.

“It was also used in veterinary applications to produce and maintain standardized and genetically inbred animal stocks to serve as ‘white mice’ for medical and research.”

The United States Marine Shrimp Farming Program was formed in 1984, with the objective of increasing local production while decreasing the importation. After having its breeding program hit by a disease outbreak, the response of this initiative was towards designing, developing, and implementing an integrated SPF management program.

SPF shrimp in Aquaculture

The first commercial program for domestication and genetic improvement of penaeid shrimp was initiated using Pacific white leg shrimp (Penaeus vannamei) in 1989. The program adopted the breeding and selection concepts from the livestock and poultry industries to establish specific pathogen-free (SPF) stocks of shrimp that would provide high health and genetically improved postlarvae.

The stocks were obtained by rigorous screening of captured wild shrimp for selection of individuals naturally free from pathogens that it would be possible to permanently exclude from the stock under strict quarantine conditions in a nucleus breeding center (NBC) housing many founder families.

“These stocks could then be subjected to a domestication and genetic improvement program. Better performing families from each generation could be used to produce postlarvae destined to become SPF broodstock in an adequately biosecure broodstock multiplication center (BMC).”

The broodstock would be supplied to commercial hatcheries where postlarvae would be produced for farmers to stock in ponds. In parallel, several programs were carried out.

In Venezuela, a mass selection program began in 1990 to produce shrimp well-adapted to the local rearing conditions. In Colombia, producers selected TSV resistant shrimp in the early 1990s. These early efforts later developed into fully-fledged family selection breeding programs that resulted in some improved local industry populations.

SPF shrimp in Aquaculture

The programs in Latin America were based on the concept that the populations should be adapted to local conditions and should be resistant or tolerant to the major disease problems endemic in the region.

Thus, a major dichotomy in breeding strategies emerged in the 1990s, with selection, maintenance, and multiplication of populations in essentially disease-free conditions under the SPF protocols of the USMSFP while other programs used populations selected in the presence of multiple disease pressures that are common in commercial production.

A significant impetus for the eventual wide adoption of the SPF shrimp concept was the emergence and spread of white spot disease (WSD) of shrimp, caused by white spot syndrome virus (WSSV) in the mid-1990s. At that time, Penaeus monodon was the main cultivated shrimp species in Asia, and it was soon realized that the major source of WSSV in shrimp grow-out ponds was infected postlarvae derived from captured WSSV-carrying broodstock.

“The main reason behind the importation of P. vannamei to Asia was the perceived poor performance, slow growth rate, and disease susceptibility of P. chinensis and P. monodon. Because of the benefits of using domesticated and genetically improved SPF stocks of P. vannamei to produce healthy PLs for farmers to use in stocking their ponds, the term SPF in Asia began to be related to stocks with higher disease resistance or tolerance.”

The opposite situation occurred in Latin America where SPF shrimp were stocked in ponds with no pathogen exclusion biosecurity, leading to mass mortalities and farmer’s perception that SPF status implied higher disease susceptibility.

This perception was incorrect. SPF only indicates the sanitary status of a stock and does not indicate its susceptibility, resistance, or tolerance to infection and disease.

Major definitions

Concerning pathogen status, the only technical terminology used for terrestrial animals is specific pathogenfree (SPF) stocks. That definition can be applied to all animals.

Shrimp interactions with viral pathogens are not fully understood. Unlike vertebrates, they do not produce antibodies, and it is well known that survivors from disease outbreaks with a normally lethal virus may remain infected at a low level for up to a lifetime, without showing any gross signs of disease.

In this state, they maintain the potential to transmit the pathogen to their offspring and naïve shrimp. The phenomenon of tolerating infectious viral pathogens for long periods of time without disease signs has been called viral accommodation, but the mechanisms underlying it are still unclear.

SPF shrimp in Aquaculture

Shrimp stocks tolerant to TSV but uninfected with TSV have been developed using genetic selection. When these stocks are challenged with lethal isolates of TSV, they become infected but show no gross signs of disease. However, they carry the deadly virus and can transmit it to naïve, susceptible shrimp.

Thus, shrimp stocks that tolerate and carry viral pathogens may lack gross signs of disease (including histological lesions) and may negatively affect molecular detection methods of low sensitivity, which constitutes a special danger that must be guarded against in the transboundary movement of shrimp stocks for aquaculture. It also has consequences for stocks labeled with the terms defined below.

These terms must be clearly defined and understood to avoid confusion that unscrupulous individuals might use to take advantage of shrimp farmers.

Pathogen-free (PF) stocks (new term)

These are stocks that are free from any known or unknown pathogen. Since the definition includes ‘unknown pathogens,’ it is evident that PF cannot refer to any actual animal stock, and that it must be reserved only for theoretical discussions.

Specific pathogen-free (SPF) stocks (an existing, defined term)

SPF animal stocks must come from a population that has tested negative for specific pathogens for at least two consecutive years; it has been raised in highly biosecure facilities (to qualify as highly biosecure facilities, the risk of introduction of pathogens needs to be negligible) following stringent biosecurity management measures; and has been fed with biosecure feeds.

“SPF stocks are not necessarily free of all pathogens. A list of pathogens from which the animals are claimed to be free should always accompany them.”

Any shrimp stock claimed to be SPF should be free from Vibrio isolates that cause acute hepatopancreatic necrosis disease (AHPND), Hepatobacter penaei that causes necrotising hepatopancreatitis (NHP), infectious hypodermal and haematopoietic necrosis virus (IHHNV), infectious myonecrosis virus (IMNV), Taura syndrome virus (TSV), white spot syndrome virus (WSSV) and yellow head virus (YHV – genotype 1).

We currently accept that there are two ways to generate SPF shrimp stocks. One way is to find a geographical area where major shrimp pathogens are known to be absent or at low prevalence, to capture and screen wild shrimp from that area, and to select individuals that are shown to be naturally free of a specified list of pathogens for at least two consecutive years.

SPF shrimp in Aquaculture

A stock generated in this fashion could be called a ‘natural SPF stock.’ Another way to generate an SPF stock is to choose a shrimp farming area where major shrimp pathogens such as WSSV, TSV, and IHHNV are present and to use a process of continuous screening to select individuals that are shown to be free of a specified list of pathogens for a period of at least 2 consecutive years.

A stock generated in this fashion could be called a ‘cleansed SPF stock.’ For geneticists, resistance is defined as the ability to limit the burden of a pathogen in an infected animal, while tolerance is defined as the ability to limit the severity of disease induced by a given pathogen burden.

Both traits are quantitative. It has long been understood that the disease state arises from an interaction of host (genetics), pathogen, and environmental factors. So, from the sanitary point of view, resistance is the ability to be refractory to infection (qualitative trait), while tolerance is the ability to reduce the expression of disease (quantitative trait).

Specific pathogen resistant (SPR) stocks (new term)

These are animal stocks that remain refractory to infection without showing gross signs of infection and/or disease, even after challenge with a lethal dose of one or more specific pathogens.

Specific pathogen tolerant (SPT) stocks (new term)

These are stocks that are susceptible to infection by a specific pathogen but do not normally develop clear signs of disease as a result of such infection, i.e., they are tolerant to disease expression in a quantitative manner dependent on their genetics, on the pathogen strain, and on environmental conditions that influence the disease.

Tolerance may be specific to a pathogen, to a strain of a pathogen, or to a group of pathogens.

Combined SPF and SPR or SPT stocks (new terms)

While SPF refers to animal health status (backed up by a 2- year stock history at a certified rearing facility for the absence of specific pathogens), it is possible and logical to combine SPF health status with genetic status SPF+SPR, SPF+SPT, or SPF+SPT+SPR stocks.

In other words, a stock characterized as SPF based on health status can be subjected to a subsequent genetic selection
designed to identify, characterize and select for genetic attributes in the stock population that could lead to specific disease resistance and/or tolerance for one or more pathogens.

Uncharacterized, selected survivor (USS) stocks (new term)

These are animal stocks that have been produced by selecting survivors (based on size and gross health appearance) from several successive generations under non-biosecure farming conditions in a region where several known and unknown pathogens occur.

Such stocks have previously been referred to as ‘all pathogen exposed’ (APE) stocks. However, ‘all’ pathogens do not occur in every geographical region, and those known and unknown in any particular region are not always present in every pond.

We propose that the term ‘APE stock’ be regarded as unacceptable by the shrimp industry and replaced by ‘USS stock’ as defined herein.

High health (HH) stocks (new term)

It is a commercial term frequently used but not clearly defined. It often refers to descendants of an SPF stock. Since it does not specify the pathogens, genetic, epigenetic, or rearing conditions or status, the use of the term ‘HH stock’ should be avoided. Instead, one of the above terms describing health status and pathogen response should be used to characterize a stock.

Validation and maintenance of SPF status

The validation and maintenance of the SPF status for shrimp is a time consuming and expensive process. It requires that the facility, the biosecurity standard operating procedures (SOPs), and the shrimp within the facility conform to standards to ensure that the shrimp housed in the facility can be maintained as SPF. Stated differently, the validation is for the facility as well as for a specific lot of shrimps.

The risk of exogenous pathogen contamination is reduced considerably for an SPF facility located inland, away from the coastal zone and utilizing recirculation technology with appropriate biosecurity practices.

Problems confirming SPF status

Although internationally approved procedures are in place to detect most of the important pathogens of shrimp that should be included in an SPF program, the issue of endogenous viral elements (EVEs) has become a scientific challenge for confirming and certifying the SPF status of a shrimp stock.

Although many EVE originate from retroviuses, nonretroviral EVE was first reported in shrimp for two EVEs of IHHNV.

However, at the time, the term EVE did not exist and was not coined until discovering previously unknown and unexpected, non-retroviral EVE in vertebrates. Subsequently, many more EVE for IHHNV were reported for P. monodon and P. vannamei, and many of them gave false-positive PCR test results for IHHNV, even though the shrimp were not infected with IHHNV.

Such false-positive test results for an infectious virus could have international severe trade implications for shrimp breeders.

Importance and benefits of SPF shrimp

Naturally derived SPF P. vannamei from Hawaii was first introduced (imported) to Thailand in 2002. Following this introduction, shrimp production was revolutionized in Asia, with P. vannamei almost completely replacing P. monodon. In 2003, a company in Thailand started its SPF breeding program with high biosecurity protocols.

This program contributed significantly to the industry’s exponential growth in Southeast Asia for nearly a decade, until a new disease, acute hepatopancreatic necrosis disease (AHPND), emerged in 2009.


SPF refers to a shrimp stock’s health status, while SPR and SPT statuses refer to defined genetic characteristics of stocks in response to pathogens and disease. The objective is to avoid negative impacts on production, transmission among species, and trade barriers that might arise from pathogen detection in shrimp and shrimp products.

“The designation ‘USS stock’ alone does not indicate either the specific health status or specific genetic characteristics of a shrimp stock concerning pathogen and disease response. It is also possible to combine strategies such as SPF+SPR, SPF+SPT, or SPF+SPR+SPT to help shrimp farmers prevent disease outbreaks in grow-out ponds.”

The success of these approaches may depend on the biosecurity strategy defined for each facility. Farmers must also consider other aspects of stock performance, such as growth and survival, that may be related to stock health status and genetic status.

We recommend that farmers cooperate with one another in the critical evaluation of stocks provided by commercial suppliers. Over time, this process should reveal the most reliable stock suppliers’ identity with respect to overall stock performance.

This is a synthesized version developed by Ph.D. Carlos Rangel Davalos, professor, and researcher at the Department of Marine and Coastal Sciences of the Autonomous University of Baja California Sur, of the article: “Facts, truths, and myths about SPF shrimp in Aquaculture” written by Victoria Alday-Sanz, James Brock, Timothy W. Flegel, Robins McIntosh, Melba G. Bondad-Reantaso, Marcela Salazar, and Rohana Subasinghe.
The article was originally published in volume 12 of the journal Reviews in Aquaculture (2020).
The original version can be found through Wiley’s online library at the following link: https://onlinelibrary.wiley.com/doi/full/10.1111/raq.12305

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