ISA in B.C.?

There is some explosive news unfolding at the moment.

According to a press release from SFU, “The highly contagious marine influenza virus, Infectious Salmon Anaemia (ISA) has for the first time been officially reported after being found in the Pacific on B.C.’s central coast.”

Wow! Really!? According to the press release, “The virus was found in two of 48 sockeye smolts collected as part of a long-term study, led by Routledge, on the collapse of Rivers Inlet sockeye populations. Dr. Fred Kibenge of the ISA reference laboratory at the Atlantic Veterinary College in P.E.I. made the diagnosis and notified the Canadian Food Inspection Agency (CFIA) of the positive results for the European strain of ISA virus.”

That’s a serious claim to make. Has it been confirmed by the Canadian Food Inspection Agency? Apparently not, we hear.

Yet there is a press conference, a media release and a story already in the Vancouver Sun about this proclaiming that the sky is falling.

This seems decidedly anti-scientific. Announcing you have been proven right before getting full confirmation sounds suspicious. Plus, the host of anti-salmon farming quotes and language in the SFU press release (e.g. the repeated use of the cattle-farming term “feedlot,” which has negative connotations, instead of the neutral “salmon farm”) are surprising for a university-sanctioned press release.

Aren’t universities supposed to be neutral? Aren’t they supposed to be bastions of excellence and prudence?

Even if the two smolts, after further investigation, do indeed show they have ISA and that the samples are from B.C., it’s concerning that the science has taken a back seat to emotion, rhetoric and an obvious anti-aquaculture agenda. Because if they are confirmed, no one will bother to look for any other explanation but aquaculture.

They are making the facts fit the hypothesis.

In fact, science is so far in the back seat here it’s in the trunk. The press release mentions no actual facts other than that two smolts contained the virus. That’s it. The rest is speculation and fear-mongering. We are not exaggerating. Read the press release for yourself and try and spot the scientific facts. There is only one, as we explain above, and even that has not been confirmed as a fact yet.

What is going on here?

We all know why Ms. Alexandra Morton would say this. This is familiar territory for her, and she has been trying to link farms with the decline of wild salmon for more than a decade. Fair enough; but the science has not backed up her doomsday predictions.

Rick Routledge, SFU professor, is a statistician working on a long-term study of Rivers Inlet. He and his team are looking at long-term trends to see if they can find an explanation for the salmon return declines in the region. Why is he involved in this? That’s an interesting question we would like to see answered.

Once we hear if the ISA test results are actually true or not.

Meanwhile, we are aghast that SFU would publish something so flawed as factual, without waiting for science to bear it out.

UPDATE 4:00 p.m. Oct. 17, 2011

Ms. Alexandra Morton was kind enough to publish the lab results on her blog. We have re-hosted them here. They show some interesting information which people reporting on this story need to know.

First and foremost, the samples are tiny. They are tissue samples from sockeye smolt hearts, likely slivers which are usually taken for testing from adult-size fish. To get an idea of how small that sample would be, take a look at this photo:

A sockeye smolt. Source: adfg.alaska.gov

Now with that in mind, let’s learn a little bit about how PCR tests work. PCR stands for Polymerase Chain Reaction, and is defined by Wikipedia as “a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.”

PCR tests can be very effective and are now commonly used in all sorts of medical laboratories as well as criminal forensics labs.

However, they have some pitfalls. PCR tests can be highly susceptible to contamination because of the way they work:

It is often said that the most critical source of PCR contamination is DNA from previous PCRs.  Again, a PCR produces many DNA copies of the target DNA sequences.  Due to shear number, these copies (called amplicons) are a hazard for future PCRs.  In terms of DNA typing, stray amplicons could contribute single or multiple alleles to a genetic profile.  This would manifest itself in the form of producing, for example, an extra dot on a DQA1 or PM typing strip or an extra band in an STR profile.  The fact that the contaminating dot or band is in fact extra may or may not reveal itself.  Thus, amplicons can lead to mistyping.

However, a more dangerous source of contamination is what is called genomic DNA.  This is DNA that hasn’t yet been amplified.  Genomic DNA doesn’t have the high concentration of the target DNA copies but is a hazard because genomic DNA could produce an entirely false DNA profile.  Full profile contaminants have been documented on multiple occasions and in multiple laboratories.  Partial profile contaminants are more common and sometimes constitute a poorly recognized risk in using partial profiles in evidentiary samples as evidence.  When contamination occurs there is rarely any way to confirm how it happened.

For example, suppose evidence item #1 has little to no DNA or has DNA degraded beyond the ability to function in a PCR.  Suppose further that item #2 is a defendants reference blood stain that would typically have a high concentration of undegraded genomic DNA from the defendant.  If item #2 comes in close proximity with item #1, or comes in contact with item #1, the genomic DNA from item #2 may contaminate item #1.  Subsequent DNA typing of contaminated item #1 will give the false impression that the defendant contributed DNA to item #1 during a crime.  Similarly, when there are multiple items of evidence with some having larger amounts of DNA and some much lower, cross-contamination is an important consideration.

This is not to say that all PCR-based results are due to cross-contamination.  However, the ease of cross-contamination and its potentially misleading effects may sometimes be under-appreciated, especially in the context of match probabilities reported to be extremely rare.

Did you catch that?

There’s nothing wrong with PCR testing. But if match probabilities show up which are extremely rare, use caution. You may have a contamination issue that needs to be investigated and verified.

So how does that apply to the latest news?

Given the concerns with PCR contamination, and given the extremely small sample sizes, we should be re-testing before announcing to the world that ISA is in B.C. don’t you think?

Unfortunately, according to the lab results, we can’t retest the results or do further investigation because the samples were so small they were all used up.

And this sort of information is what SFU uses to announce “Lethal Atlantic Virus found in Pacific Salmon?”

Once again, real science takes time. But we suppose the personalities behind this announcement couldn’t wait to get their names in the newspaper and couldn’t be bothered to wait for the science to catch up.

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2 thoughts on “ISA in B.C.?”

  1. How is it possible to “use up” the sample tested for ISA? The very basis of science is all hypotheses must be falsifiable. Is this not against standard practices to leave no sample leftover for re-testing?

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