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"Confusion" about the rapid diagnosis RT-PCR? - click here

Dr Colin Fink's offer to help with FMD testing and Fred Landeg's reasons - "his unfortunate failure to grasp the basics is not reassuring" - for refusal


Tuesday 24 April 2001

At a meeting held in the House of Lords on Tuesday 24 April 2001 at 4.0 pm ( convened by Mrs Alicia Eykyn at the invitation of the Countess of Mar), members of the government's science group for foot and mouth discussed the situation with other interested parties, most notably the acknowledged world expert , Professor Fred Brown OBE, FRS, Visiting Scientist to Plum Island. In spite of his unique experience, the UK government had not asked for his help or his advice. Dr Simon Barteling from Holland, formally head of the European Community Coordinating Institute for Foot and Mouth Vaccines, who had particular knowledge of the FMD virus, was also there.

John Wilesmith, to the surprise of those outside the science group, disclosed that it had previously been unanimously agreed by the science group that the vaccination route should have been adopted by the government. However, it had been overruled by the Chief Veterinary Officer, Jim Scudamore, and by MAFF and NFU leaders. No other farmers (including NFU subscription-paying members), farming bodies, tourist organisations, or animal welfare groups had been given any accurate information or asked for their views.

Professor Brown and Dr Barteling questioned much of the government policy including why Pirbright had turned down the possible use of the RT-PCR device. They also asked why it was taking so long to produce the results of blood tests. When Dr Paul Kitching said that Pirbright was finding it hard to cope with the overwhelming number of samples, Colin Fink of Warwick Science Park reminded them that he had offered the services of his laboratory and had been ignored. It was then agreed to make arrangements to avail him of the fixed virus necessary for him to start to help. At an earlier meeting that day, hosted by the CLA, Lindsay Harris ( a policy advisor to MAFF) had agreed to do the same.

May 11th 2001

A Parliamentary Question was put by Baroness Mallalieu Q.C. on May 11th 2001

May 2001

In a letter which was sent just after MAFF withdrew from its threatened legal action against the Thomas Everards in Dulverton, a letter, Dr Fink wrote

Chris Stockdale, in his thesis on FMD for the Cirencester Royal Agriculture College, asked why Dr. Colin Fink's offer to produce a rapid viral assay, although initially accepted, was then overruled by Mr. Fred Landeg. He also wondered why Biosecurity Level (BL) 4 was required for this virus when the Institute of Animal Health (I.A.H.) Pirbright had been working on genetic modification of FMD at BL 2, 3 and 4

The Health and Safety Executive papers on the work describe the DNA insert as of 'human origin', and expressed concern should a leak of experimental material occur as it could be 'environmentally persistent'" (Bird, 2001).

Mr David Curry, Chairman of the EFRA Select Committee, with Professor David King and Dr Alex Donaldson on April 25th 2001.

(The question is about the use of the Real-Time PCR device)

398. I will ask a strictly scientific question now. On 9 March, Dr Alex Donaldson received an e-mail from Roger Breeze, who is the Assistant to the Head of the USDA in America, Floyd Hall, asking if he could co-operate with Pirbright, using a machine which he describes as a "real-time PCR", which, as I understand it, and I am not a scientist, is a machine which will identify a virus in the saliva, or from a nasal swab, of animals that are infected with foot and mouth before they show symptoms. Now this I was told yesterday by Professor Fred Brown, from Plum Island, who was over here for a day; and, as I understand it, he received no reply. If this machine is as accurate as Professor Brown told me, he said it is 99 per cent accurate, could it not have saved this huge, vast, expensive cull of mainly healthy animals?

(Professor King) Could I answer this, first of all, and then, of course, I will ask Dr Donaldson to deal with your specific query. The question of the so-called 'smart cycler' is one that was brought to my attention in a discussion I had, very early on, with Fred Brown; so, here, I am simply telling you that, as Chief Scientist, I got on the telephone and 'phoned the experts around the world, and Fred Brown was one of those. And Fred Brown told me about the development of the 'smart cycler' and also told me that he had already had somebody get in touch with Dr Donaldson. Of course, we have investigated the potential use of this instrument; it is a PCR-based instrument, which means that it is based on a polymerase chain reaction, where the virus contains RNA, you multiply the RNA through this chain reaction and it becomes very readily detectable, so it is a means of detecting the virus. The world's experts in this application of foot and mouth are Dr Donaldson and his team at Pirbright; they did not develop this in-field machine, that was developed in the United States for the use of the military. Now it is commercially available, but it is an untested machine and there are very serious questions to be asked about the use of that machine in the field, in particular the problem of cross-contamination. (sic) Now I have to stress that, if you are under laboratory conditions, Chairman, and you carry out these tests, you do get very accurate results. In the field, it is considerably more difficult to achieve this type of accuracy, particularly if you are going, as you want to do, to analyse a large number of animals, from animal to animal. And that cross-contamination problem has not been answered. We would like to see very distinct field tests on this instrument; but my final conclusion, from talking to all the experts, including Fred Brown, is that, unfortunately, it will not be available to us for this epidemic.

(Dr Donaldson) I will give you the background. I have not got the correspondence with me, but I have copied it to OST and I am quite happy to make the correspondence available to anyone else who might want it. I have known Roger Breeze for many years, he was a former Director of the Plum Island Animal Health Laboratory in the United States, where Dr Fred Brown is also based at the moment. In March, Dr Roger Breeze contacted me and said that he, working with the US military, had this 'smart cycler' equipment available, and he and his team would like to come to the United Kingdom and to test the equipment under field conditions to validate it during an outbreak situation; he was optimistic that it would be very helpful. He did say, in his correspondence, that the machine had not been validated for work with foot and mouth disease. I approached Jim Scudamore, Chief Veterinary Officer, and asked if this could be facilitated. Jim Scudamore's response was that he was very interested in the equipment and he would be very willing to collaborate with the USDA, but he suggested that this should be done after the epidemic had declined because there would be logistic problems in taking such equipment into the field. I sent a reply back to Roger Breeze, saying that the Chief Veterinary Officer was not willing to accommodate him at this particular point in time but would be willing to do so at a future date. I said, meantime, I would be willing to accommodate a scientist from the USDA at the Laboratory in Pirbright to test his equipment under standardised conditions, alongside PCR equipment which we already had and which is up and running and functioning. The particular attraction of what the USDA have been offering is that their equipment is portable; it is a small device, operated by a battery, which can link to a lap-top computer, and that, in turn, can convey the output of the test result through the Internet. I should point out that the piece of equipment costs in the region of £22,000, and there was no indication of what would happen to the equipment once it had been taken onto an affected farm, in other words, how it will be decontaminated. So I expressed that view, that we would be willing to collaborate, sent that back to Roger Breeze. The next communication I had was on a Thursday, saying that he, Roger Breeze, and his team would be arriving the following weekend to test out the equipment. I said that would not be convenient, that we would have to arrange a time to accommodate him in the Laboratory when we could find space and to do it properly. He, in turn, offered to show the equipment to us over the Internet. It was pointed out to me by colleagues that one of my scientific staff was about to make a visit to Plum Island and it would be an opportunity for him to see the equipment, which we understood had been developed in collaboration with Plum Island. That scientist went to Plum Island, he was hosted by Dr Peter Mason, who is the foremost molecular biologist at Plum Island, he asked to see the equipment; the response he got from Dr Peter Mason was that he had heard about the equipment but he had not seen it nor had he been involved in any validation of it. Subsequent to that there have been the pressures from Dr Fred Brown, I believe, through different channels, to have the 'smart cycler' tested. Since that time, I believe, Jim Scudamore has offered the services of MAFF. We had a visit last weekend from a Mr Mike Tass, I believe, who offered to take some of our equipment, which is portable, into the field and to test it alongside anything else that might be forthcoming, from whatever source; because I should add that the 'smart cycler' and other offers from the United States are not the only ones we have had. The normal scientific approach when pieces of equipment like this are represented is that data is provided to show that they do operate, and when that data is available through the scientific press then one can start looking at that data in relation to well-established, gold standard methods. That is the normal scientific approach. I would add and emphasise that we have no data from the Americans about the performance of their equipment for foot and mouth disease - they may have used it for other agents, I am not sure; and, I would repeat again, I have no indication that their equipment has been validated. So, I think, there we are, we are still willing to accommodate the Americans. Mr Jim Scudamore has offered, I think, to accommodate them in the field, and, well, we are willing to help if we can.

Jan 1-6 2003 ~ "we did attempt to validate Fred Brown's test and it didn't pass the validation"

(warmwell note. There were many mistakes in the .pdf documents quoted below - probably as a result of scanning rather than poor typing. We have attempted to correct them where the sense was not clear. The emphasis is ours.)

The statement made by Roger Breeze of USDA to the Royal Society Enquiry


Roger Breeze []
22 April 2002 2354
Foot and Mouth Enquiry: For Dr. Geoffrey Findlay

Dr. Fred Brown has drawn my attention to statements provided to the Royal Society's Committee of Enquiry after a meeting with Dr. Chris Bostock, Dr. Alex Donaldson, Dr. Soren Alexandersen and Dr. P. Mellor.
Under "IDiagnostics Paragraph 8" is the statement that "The Laboratory had also tested the Cepheid Smart Cycler. Originally, Dr. Roger Breeze, USDA, had been invited to Pirbright to compare the performance of the Smart Cycler with a lab-based RT-PCR system, but this invitation had not been taken up. Subsequently, in the summer, an employee of the company associated with the device came over to set up the equipment and reagents. Using those reagents, the test had very poor sensitivity, but Pirbright had investigated other reagents and the use of those developed for its own RT-PCR test had resulted in comparable sensitivity to the latter. "

The Agricultural Research Service (ARS) of USDA has been developing real time PCR reagents to detect the List A diseases of the OIE. By February 2001 we had developed and tested in the laboratory a remarkable assay that detected all 7 serotypes of FMD virus and differentiated FMD virus from other vesicular diseases of livestock and from other RNA viruses. This assay was performed on either the Cepheid Smart Cycler or the Idaho Technology RAPID machine: both these machines can be monitored from a distance over the internet.

This RT-PCR test is more sensitive than cell culture. During February and March 2001, we found that this test detected the presence of FMD virus in experimentally infected cattle, sheep and swine before clinical signs of disease were detectable: in other words, this was a preclinical test. The test takes about 60 minutes and sample preparation can be minimal - if vesicular fluid is sampled, for example.

In early March 2001, I telephoned Dr. Donaldson to inform him of the USDA RT-PCR test and offered to make the equipment and reagents available. Now the design and purpose of the two instruments we have chosen and the format of the reagents are specifically suited to performance of diagnostic tests on the farm or close to the site of the problem. There are cheaper instruments that will do the same job at a fixed site in the laboratory but these are not robust enough to use on the farm. Given the extensive validation studies in vitro and in vivo that had already taken place at Plum Island, our expectations were that after a short familiarization period (1 to 2 days) for UK colleagues at Pirbright we would be able to take the devices and tests into the field during the 2 0 0 1 FMD outbreak in cooperation with UK authorities from Pirbright or MAFF.

Such studies would have provided the US and UK with valuable data under field conditions: we would have used these data to support USDA licensure and OIE test approval.

Unfortunately, yet understandably, Pirbright staff were too busy coping with the demands of epidemic control to explore new technology during the spring and summer of 2001 . As a result, my offer to provide the latest diagnostic technology was not taken up.

Fortunately, we were able to take the devices and test system into the field in Uruguay in November 2001, where they performed splendidly on farm in a remote area.

ARS is conducting this FMD research in partnership with Tetracore Inc., a reagents company that has a license to commercialize the technology.

Cepheid and Idaho Technology have no involvement in FMD diagnostic research design or performance - they are solely instrument suppliers.

I have been puzzled by the Pirbright statements that Cepheid provided FMD reagents because Cepheid has no involvement in PCR primer design for Tetracore/ARS and the details of the ARS primers have not been disclosed to Cepheid. I do not know the details of the reagents Cepheid provided to Pirbright but I can assure you that these were not the reagents proprietary to ARS/Tetracore that are used in the US test.

The details of the ARS FMD test will be published June 1, 2002 in the Journal of the American Veterinary Medical Association: I am trying to have a galley proof sent to your enquiry under publication embargo until June 1 so that your committee has the scientific data in hand as soon as possible.

Finally, I should clarify some misleading statements about the ARS FMD test. Test reagents are pre-packaged such that contamination is not a problem. Sample preparation is minimized. We envision these devices being taken onto the farm by federal diagnosticians for the index case and then kept close at hand beyond the farm quarantine boundary thereafter.

I must re-emphasize that the ARS test is intended to be used as an on-farm test (although it can be a central laboratory test) because time and timeliness are the critical issues in stamping out an epidemic.

Much reference continues to be made to the relative sensitivities of cell culture and RT-PCR and to the need for spurious comparisons with lab-based PCR instruments

In our assay, RT-PCR is more sensitive than cell culture. When it is possible to do cell culture on the farm - or use fragile lab-based PCR devices in vehicles - we can have a direct head to head challenge of technologies, but until then, the ARS RT-PCR for FMD is the new standard for on-site diagnosis of FMD. We are pursuing the appropriate licensing of this test by US regulatory authorities and approval by OIE.

extract of letter from Roger Breeze, sent as further evidence to Royal Society Enquiry
This letter was sent also to the Lessons Learned Inquiry and given by hand to Lord Whitty

link: "....Our real time PCR assay for foot and mouth disease (W) has been validated in the laboratory: it has proven to be a pre-clinical test for infection in cattle, swine and sheep, it detects all 7 serotypes of FMD virus and differentiates this infection from other viral diseases that cause similar clinical signs.

The test is more sensitive than viral culture and will detect as few as 10 virus particles.

The research paper with these results will appear soon in the Journal of the American Veterinary Medical Association.

We have now begun to use this PCR test for field research and recently conducted a study in Uruguay, looking for carrier animals in a herd that had recovered from a FMD infection. This research is in progress and will be published in due course. It is not a “validation” of the test so much as it is a demonstration that FMD detection can take place in remote places in a country without a national FMD diagnostic capacity.

Such a study could not have been conducted on site using cell culture. I will be sure to send a copy of the paper to Tony Garland.

Some eight months after we had disclosed the existence of our x;h/lD test to Dr. Donaldson, we read in the Veterinary Record that the Pirbright Laboratory had subsequently established a relationship with Cepheid and conducted some experiments with FpvfB reagents supplied by that company (data published by Alex Donaldson and others in the Veterinary Record, 2001).

I have no idea what those reagents were because the paper does not describe them. But I can be sure that these reagents were not those developed by USDA-ARS and Tetracore because Cepheid does not have this proprietary information.

I hope there has been no confusion in Britain between the Cepheid mystery test and the real time PCR test developed at Plum Island.

I did consider writing to the Veterinary Record at the time to clarify this but decided this was not worthwhile since Donaldson's letter was largely anecdotal and Cepheid clearly had no capability in FMD detection, so it was hard to believe anyone would take his comments seriously: it seemed better to wait for our paper to be published with the supporting data. Correspondence columns are not the ideal place to set out new principles for control of the world's most dangerous animal diseases. When the.Plum Island paper is published the current state of the art in FlMD virus detection will be clear.

Periodically, there are major shifts in technology and history shows that many people have problems adjusting to these - the Luddites are the classical example.

The last FMD outbreak in the U.S. was in 1929 and at that time diagnosis was on-farm and somewhat leisurely. Veterinarians travelled to the farm by train and car and communicated by telegraph with Was.hington DC. There were 1x0 Jab tests available and diagnosis was achieved the farm by inoculating a cow, pig and horse with materials h m suspected cases. The choice was between FAID and vesicular stomatitis infection and differential diagnosis depend upon which combination of animals got sick. When FMD hit Mexico in 1946, there was no laboratory in the Americas where a diagnosis could be made: samples from infected animals were sent by sea to Pirbright. By the time the results were telegraphed back weeks later, the infection was all over Mexico and a 6 year struggle had begun.

When the Plum Island laboratory was opened in 1956, it was the first FMD diagnostic capability in this hemisphere and it seemed miraculous to American farmers that a vet could travel by train and car to a farm, collect samples from a cow suspected of having FMD, take those samples to an airport, and put them on a plane to New York, where someone would carry them by road and sea to a lab from which an answer could be obtained in a few days and communicated by telephone.

I'm sure there must have been some old timers who thought that clinical diagnosis on farm was adequate and new technology was unnecessary, just as there are some now who think new ideas will not replace the old.

We in are the only scientists in the U.S. who can do research with FMD virus and we take this responsibility very seriously. For several years we have been studying major animal disease epidemics overseas to see what lessons we can learn to protect the US. Notable examples are FMD in Taiwan, Japan and South Korea, classical swine fever in the Netherlands and Rift valley fever in Saudi Arabia/Yemen. It is very clear that whatever the value of existing control strategies, including diagnosis by ccU culture in specialised laboratories, these are not effective in preventing catastrophic disease losses, even in small countries.

We do not accept that a national catastrophe every generation is the necessary price of having livestock populations susceptible to FMD or classical swine fever. We are not prepared to continue with traditional approaches that do not work. We do believe that we can develop new technologies to prevent and control FMD in the U.S. First, some facts: the distance ji-from New York to San Francisco is the same as that from London to Baghdad. U.S. livestock susceptible to FMD number about 200 million. U.S. agriculture is remarkably mobile and decades of freedom from FMD and other serious diseases have accustomed us to being able to transport animals and products nationwide in hours. The U.S. is unique in what it stands to lose from a FMD epidemic and in the scope of the response that will be necessary to control an outbreak.

Also, our agricultural industries are arranged quite differently from other countries.

In California, 2000 cow dairies are not unusual and these are clustered such that there are hundreds of thousands of dairy cows within a small radius. Farmers milk their animals continuously, 24 hours a day: a succession of milk tankers is filled and sent to the processing plant, there is no milk storage capacity on farm m . If there were a suspected FMD case and a 3 kilometer quarantine standstill area was imposed, there would be an immediate and major crisis over what to do with dens of thousands of gallons of milk - no place to store it on farm, no way to get it to the processing plant, no way to spill it on the ground or pour it down the drains because of environmental pollution. It took only two hours to take samples to Plum Island to get a diagnosis, this would still be two days of chaos on farms in the quarantine zone. We believe answers need to be found in minutes or hours.

.... time is the critical element in FMD control. We do not pretend that we can always hope to prevent a FMD outbreak in the U.S., but what we want to be able to do is to ensure that the outbreak follows the curve shown in line “C”, rather than line “A”. Integral to following line C is that infected herds are quickly identified and slaughtered to prevent the infection spreading to others. We could not hope to do this in the U.S. by taking samples to Plum Island - it would simply take too long and cause too many other problems, as in California.

One would like to believe that in an epidemic all the infected herds are detected by cell culture, perhaps via two passages in the most sensitive tissue culture systems, as Tony Garland points out.

The reality is very different - there is usually no laboratory data at all when the decision is made to slaughter and this decision is dictated more by geography than virus detection by any method. Many people have asked me recently if there are any cattle or sheep naturally resistant to FMD - but how would we know this when any resistant animals& would be killed along with all the rest because they were in the wrong place at the wrong time - the wrong place being within 3 kilometers of an outbreak

I do not believe U.S. farmers would accept that their life's work - bloodlines developed over generations in many cases - should be wiped out without clear evidence of infection.

Nor do thy have to.

I must now digress a little about the PCR test. PCR is well established in the laboratory. The portable devices we are using offer all the power of the lab but at the site of of the problem.

There is no issue of cross contamination or distinguishing live from dead FMD virus: there is no FMD virus, live or dead on farms in the U.S.

If the PCR test finds virus on a farm it can only be that there is a serious animal health problem in progress. Much has also been made of the so-called comparison between results from the portable real time PCR device and those from culture. There is no comparison. When it is possible to do cell culture in a portable format on the farm we can arrange a head to head test, but until then, the portable real time PCR test is the only way to identify FMD virus definitively on site. Our test system is NOT intended for laboratory use - there are cheaper devices that do much the same thing. It is designed for rapid results at the site of the problem.

This raises the key question: what would one do differently to control FMD if detection could be provided in minutes on site rather than after days of waiting?

If there is nothing one would do differently, then real time PCR has no value. We believe very strongly that there are many new opportunities after immediate detection and these can be achieved through a command and control program like "LEADERS" that will allow all available resources to be deployed in a science-driven manner in the first hours and days after infection is detected. I won't get into this subject here, it is too lengthy, but it is central to our strategy of nipping infection in the bud and following line C above. It does occur to me that the current debate in Britain has the wrong focus - on whether specific technologies ars valid rather than on what disease outcomes are desired - and it is from desired outcomes that new technologies will flow. For example, we desire that an epidemic follow Iine C above - which requires rapid detection and slaughter of infected herds and flock. With this as a desired outcome, local rapid detection capacity is essential so that in the first few hours after finding FMD on a farm we could sample every herd in the vicinity for FMD - not just those in a set radius - and deal with those that were infected within 24 hours. This might be done without going on the farm if milk heading to the processing plant were sampled. There is no right or wrong answer about the value of rapid PCR versus cell culture - it depends on what type of epidemic you are prepared to live with. If line A is adequate, new technologies are not needed. We are currently proceeding with the research that will lead to regulatory approval of this new generation of tests, first by USDA and then by OIE. This will not be a quick process. Current U.S. policies for control of FMD arc largely the same as those in U.K. Our job in research is to provide new tools that OIE regulatory agencies can add to their arsenal if they choose. Lack of current validation is not the issue. As I said above, the first thing is to decide what kind of outbreak you can live with - and if you want line C, new technologies will be needed If there should be an outbreak before these are validated, there will be two choices - use them without validation or follow line A or B.