At present monitoring of bio-risks is largely reactive.
Laboratory testing of samples is used really to confirm the opinion of an experienced person in the field who has seen what he/she thinks is Myrtle Rust or kauri dieback. From taking a sample and sending it to a laboratory to getting back a result will take 10 days at least and maybe as long as four weeks.
Once the lab has received the sample it may need to be cultured so that enough material can be generated to test. Pathogens under laboratory conditions often grow slowly or not at all. During this waiting time the problem will only get worse. As a management tool this is useless.
We can look at this specifically in the context of the mycoplasma bovis outbreak in July 2017. Recently workers at the MPI laboratories wrote to their employers to point out that even by working seven days per week, they could come nowhere near keeping up with the requested number of tests. They are receiving 7000 requests per week and can cope with about 2000. Without more trained people the system is close to collapse.
In the case of M. bovis the cost is a major problem. Each test costs $50. However, the margin of error on the test may be as high as 20 per cent.
This means to get a definite positive or negative the test may need to be repeated 10 times per animal. In other words, $500 per animal. This means a herd of 1000 cows may cost half a million dollars to fully test.
If the test is positive you lose your herd and the $500,000. If it is negative you are $500,000 out of pocket anyway.
The fact that these tests need expensive specialist equipment and highly trained technicians means that citizen science is locked out. The ideal would be that a farmer or some other non-science specialist could do a few days training and then administer a test on site and get a result in a few hours at most.
The other ideal in DNA diagnostics would be to be proactive. This means detecting the pathogens before the disease takes hold and putting a management strategy in place before damage occurs. What this means is not simply walking the fields and looking for the yellow pustules of Myrtle Rust. When they appear, it is too late. The disease has taken hold.
Proactive testing would mean taking swabs from leaves and hard surfaces in the area and testing for the presence of the spores before the disease actually shows. Unfortunately, at the moment the time and expense of processing the many samples needed makes it impractical.
Other diseases such as kauri dieback present other problems. The pathogen may be present on a tree, but the tree does not get the disease while another succumbs. This probably means environmental factors are important but again due to the cost and time involved in testing sufficient data has not yet been gathered to make a judgement. If the environmental factor proves to be more important than the actual presence of the pathogen the cure is likely to be cheaper and less potentially toxic to the environment.
So what Winkworth's work is heading towards is a test that can be done by anyone with minimal training, is cheap (because testing one plant or one animal does not tell you what is happening in the rest of the orchard or the herd) and allows a management decision to be made rapidly in the field.
Traditionally, DNA diagnostics have been carried out using a heavy machine that costs $20,000 and needs expensive chemicals to run.
The main function of this machine is to accurately change the temperature of the samples. This has the result of "amplifying" the tiny amounts of DNA until enough is present to test.
Winkworth has been working on a technique called "isothermal amplification". This runs at a constant temperature making the technology cheaper, lighter and more robust.
The result is a plastic box with a cover which is less than half the size of an ice cream container and easily portable (he passed it around the audience). Under the lid are eight holes which take test tubes containing the sample material and on the end is a connector for a 12V supply (so could be plugged into car or tractor). The device is controlled by Bluetooth from a smartphone.
Once the test is complete the smartphone sends the data to an online database for analysis and a result comes back in minutes.
He also explained the title of his talk "Test in a teacup".
He is talking about a test that could be carried out using a cup of water kept at the right temperature.
Better still, he enthused, would be a test that runs at human body temperature. The test tube could be simply kept in the armpit of the tester for a specific time.
He had mentioned testing for diseases like Ebola in Africa where the first sign of an outbreak is when people start dying. If everybody in a village could be tested using a simple, cheap test before symptoms appear, and at-risk people isolated, many lives could be saved.
