Friday, November 4, 2011

Testing for ISA: Dr. Marty Responds

Dr. Gary Marty responded to my email below in a very detailed and technical response. I appreciate Dr. Marty's time in responding to my queries. I hope Dr. Marty will forgive me for doubting the efficacy and, for lack of better phrase, scientific sincerity in the testing regime for ISA in farmed salmon in recent years.

That is, I have no doubt that salmon farmers are very concerned for their own stocks and any outbreaks of ISA, for which I'm sure they test religiously. What I do not believe is that if any salmon farm tested positive for ISA that the public would have been alerted, or any testing done to see the effects on wild fish.

As the DFO Minister admitted in response to a 2005 petition to the Auditor General (by David Suzuki Fdn, the Georgia Strait Alliance et al) regarding the federal failure to test for diseases in salmon farms:

"The aquaculture industry is one of the fastest growing food production activities in the world. In Canada, aquaculture is a relatively new industry that has expanded rapidly over the last two decades. The Government of Canada recognizes the significant benefits to society associated with aquaculture and has made sustainable aquaculture development a key federal priority."
Which has unfortunately, in practice, meant that we're chasing the money and damn the consequences. Salmon farming is a $653 million dollar industry in Canada annually, and this buys some significant lobbying assistance.

The onus is very much on those employed by government—whether bureaucrats or scientists— to blow the whistle when they know they are being used in bad faith to stall or delay precautionary action that would prevent a catastrophe.

Dear Tyee,

By law, the UPEI finding that 3 Pacific salmon samples were positive by PCR for ISAV is under investigation by CFIA. It is unethical for any medical professional to comment on their investigation while it is ongoing. However, I can provide some general information about how medical professionals scrutinize PCR test results.

Imagine that the Animal Health Centre tested some sticklebacks for infectious pancreatic necrosis virus (IPNV) using the same PCR test that we used on samples from 4,726 farm salmon over the past 8 years; imagine that 3 of 60 tests came back positive. All tests on the farm salmon were negative, so we have a high degree of confidence that our farms are free of IPNV and they are not the source of IPNV.

The next question is whether the results in the stickleback are true positives or false positives. PCR tests detect only a very small segment of the entire virus genome; they do not detect the entire genome. We need to be sure that the small piece of DNA/RNA detected by the PCR test really is the virus as opposed to some other material that also contains the same small piece of DNA/RNA; this is especially important when dealing with a new species (e.g., stickleback) in which the PCR test has not been validated. Also, PCR tests are highly sensitive, and contamination might occur from a source other than the original sample.

Immediately, our veterinary virologist would question the results because IPNV is not known to be in BC, and sticklebacks are not known to be susceptible to IPNV. False positive results are relatively common, and we have several options for validating our findings. At a minimum, our virologist would probably do the following:

1) determine the size of the amplified PCR product (is it the size that it is supposed to be?);
2) sequence the nucleic acid in the PCR product (does the sequence match IPNV?).

Until these basic things have been confirmed, we would not report a positive test result.

We would also try to culture the virus on cell lines known to support the growth of IPNV. We do this because PCR tests can detect DNA/RNA sequences that are not complete viruses. Virus culture can take several weeks.

A separate question is whether the fish have the disease, Infectious Pancreatic Necrosis. Fish can often harbour a virus with no signs of disease. I would want to know if the stickleback had "classic lesions" of IPN. If histopathology was not included as part of our diagnostic process, we would be unable to conclude whether a PCR test result was associated with the disease IPN.

These are some of the standard procedures that we use in our laboratory to avoid reporting false test results.


Gary Marty

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