EconomyEditor's PickImproving the ASF surveillance system

November 13, 2022

Iloilo province used to be “green” in so far as African swine fever (ASF) is concerned. But not since last month. On Oct. 17, the Provincial government of Iloilo implemented quarantine procedures and disease prevention and control measures against ASF-infected pigs, pork, and products derived from pork, declaring the town of Oton as the red zone. The spread of the virus was further confirmed with the issuance of Executive Order No. 460-A s. of 2022 including the town of San Miguel in the province’s ASF red zone.

That the fourth largest pig producing province of the country has been infected with the ASF virus is bad news for the industry, which has struggled to get rid of the ASF disease since 2019. The swine industry is economically significant. Agriculture sector growth has been stymied by the inability of the industry to restart itself. Worse, we now witness the proliferation of the ASF viral infection in the Visayas.

Private sector investments to restock the industry are hard to come by. The ASF viral infection, rather than contained, is expanding. Owners of commercial farms would be taking too much risk. In 2019, when the country had the first outbreak of the dreaded disease, thousands of sows had to be culled to contain the spread. Potential investors continue to face the same risk, and because of that the industry restart is not happening yet.

Government assistance is targeted to backyard farmers, leaving commercial farmers to fend for themselves. But because of the risk private investors face, the investments are not happening.

The assistance that the National Livestock Program provides the backyard farmers comes with the condition that they have to be organized into clusters for improved biosecurity. That calls for organizing backyard farmers into cooperatives, a task that is complicated. Add to that the challenge that cooperatives would have to have three years of experience before the government can provide financial assistance.

DETECTING ILLNESSThe country must revamp its approach in containing the spread of ASF. Those in charge of arresting the disease are passive, waiting for the clinical signs of the disease, i.e., the swine is already sick or suddenly died, before acting. Clinical signs indicate the disease is already in the farm.

We can understand their lack of proactiveness if there was no way to know if the virus is in the animal or not. But there are devices now that can be used by regulators — mobile polymerase chain reaction devices (mPCRs) are now available. These mPCRs can be used in onsite testing, with the same level of accuracy as the testing results of the qPCR or quantitative PCRs found in laboratories.

I suggest four improvements to our strategy of containing the spread of the ASF viral infection, and, hopefully, eradicating it all together.

1. We must use mPCRs to conduct on-site testing, instead of waiting to observe clinical signs of the presence of the virus. The onsite testing using an mPCR generates qualitative results, determining if the sample tested has or does not have the virus.

The application of the mPCR in ASF virus detection requires an appropriate testing kit. One such testing kit is the MLS ASFV PCR Detection System.* Accredited by the Bureau of Animal Industry until the end of this year, this product is a pre-mix material, ready to be used in onsite testing. Capable of being stored for three months (or for a year if refrigerated), a kit can test up to 350 samples in one run. It contains DNA extraction, PCR reagents, and DNA detection functionalities. The detection kit can be used with mPCRs as well as laboratory-based standard PCRs.

The device is capable of producing onsite results in at most two hours after testing. Sample preparation requires about half an hour. The polymerase chain reaction goes on for about 70 minutes and results come in 10 minutes. The detection kit is compatible with other portable and laboratory-based PCRs, which offers another advantage when there are more PCRs in the market.

2. Onsite ASF positive test results must be confirmed using qPCRs or real time PCRs, following the protocol of the World Animal Health Organization. Besides confirming the onsite positive test results, qPCRs or RTPCRs can count the viral load and virulence of the DNA of an infected sample. A negative onsite testing result from an mPCR is equivalent to a sample with zero viruses in a test using a qPCR.

An important functionality of the mPCR-ASFV PCR detection kit is that it can extract the DNA of the biological sample. At present, authorities transport biological samples suspected of being infected to laboratories to confirm presence of the virus and where other tests on the DNA are conducted. The current practice risks spreading the ASF virus into areas traveled by the sample. The switching of a bad with a good sample is possible, rendering the qPCR test useless.

Both metrics are used to describe the possible ASF risk levels. ASF negative animals are verified to have zero viral load. By defining threshold counts of viral load and virulence index, the virus containment system can divide the level of ASF viral infection into low and high, which in turn may be used to describe more refined risk levels.

A possible profile of ASF risk levels based on the viral load and virulence index and the risk management protocols may be shown in the table accompanying this article.

3. The technology that the surveillance system uses is only as good as how a province is organized to fight ASF, as well as the human resources using it. A province like Iloilo must be organized for the purpose of allocating the tasks to monitor, investigate, and manage the ASF disease into three groups, or Tiers.

Farms, businesses, or pork value chain compartments with an address in the town/city are grouped under Tier 1. Compartments that do businesses in more than one town/city — such as feed mills, large slaughterhouses, or businesses at the border — are grouped under Tier 2 (the province). In general, all compartments fall under Tier 1 unless the municipal/city government claims that the businesses located in their respective territories shall be grouped as Tier 2 to be monitored by the Provincial government.

No businesses are monitored by Tier 3 or the Department of Agriculture (DA) Regional Field Unit. Instead, it provides audit services in the province or all provinces of the region to ensure the integrity of the surveillance system.

The bulk of the disease monitoring is conducted by Tier 1 authorities. The mayor of the municipality or city deploys Testing Field Units (TFUs). A unit is made up of two personnel, the head and an assistant. The TFU head performs the test. The assistant helps conduct of the test and reports the results to the Office of the Provincial Veterinarian (the Tier 2 head).

Tier 2 takes over the task of monitoring and investigating the disease in samples with positive ASF viral presence. While it conducts on-site testing in businesses offering their services or products in several towns such as feed mills, abattoirs, or meat cutting facilities, its major responsibility is in disease investigation and management and in analyzing the results and updating the geo-mapping of ASF risks in the province as results are submitted by TFUs.

When a positive sample is reported by a TFU, the Provincial Veterinarian creates the ASF Task Force in coordination with the TFU of the municipality where the infected sample is located. The Task Force validates the finding using mPCRs and confirms the presence of the virus, determines the viral load, and describing the virulence of the virus using a qPCR in a laboratory if there is one in the province, or in one which it sets up at the Office of the Provincial Veterinarian.

It maintains a server where all testing results are stored. It analyzes the results, producing a distribution of them based on risk levels as defined by the viral load. The distribution is geo-mapped to determine which areas belong to red, pink, and green zones.

The complete onsite testing task of the FTU, including the extraction of DNA extracts, on a sample of farms or other value chain businesses, is a testing event. The results of a testing event are assigned a unique numerical code.

Testing results codes are respectively paired with the unique identification codes of the sample tested. Each value chain compartment in the province is assigned a code with six levels of coordinates: 1.) name of the owner of the compartment, 2.) type of business, whether a farm or downstream business like a meat cutting facility; 3.) address in terms of the 4.) barangay, municipality/city, 5.) province and 6.) region. A sample taken from a farm or other pork value chain components takes the identification code of the component.

4. An ICT application is to be developed to send the testing results, paired with the identification code of the farm or pork value chain component from the field, in real time and these are stored in the ASF Server of the Office of the Provincial Veterinarian.

The surveillance system geo-maps the ASF virus risk levels in the province. Onsite testing results are sent from mobile phones or computers onsite by TFUs to the ASF server controlled by the Office of the Provincial Veterinarian. At regular periods, the accumulated results are sorted by the smallest geographical area — such as a town, barangay, or a cluster of barangays which can be digitally mapped — of the province, and then segregated further based on viral loads, virulence indices, or a composite of both, with negative ASF presence (green zone), and positive-ASF areas, which in turn are further segregated by their respected viral loads and virulence indices.

Areas with lower viral loads are grouped as the buffer zone (pink areas) and areas with higher viral loads are designated as red zones. A geographical area where the majority of farms are tested to be Risk Level 2, is a pink zone. The farms in red zones are tested to be Risk Level 3, 4, and 5. The majority of farms in a green zone are ASF-free farms (Risk Level 1).

The zoning is dynamic. In regular periods corresponding to the frequency of disease monitoring by the TFUs, Tier 2 authorities recompute the distribution of results and update the geo-map of ASF risks. This gives authorities information on the state of the ASF infection in the province, and the direction and intensity of the spread of the virus through time.

* MLS stands for Microbiome Life Sciences, Inc., a company registered in Singapore, which has been used by KMP Pig Farm in Bulan, Indonesia.

Ramon L. Clarete is a professor at the University of the Philippines School of Economics.

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