There are
SO MANY issues with the DFO/CFIA "approved" PCR and cell culture testing - any
SINGLE ONE of the many points below should be used as a rationale for
*NOT* relying upon this testing regime to identify and assess impacts to wild stocks using their methodology:
1/ CFIA has repeated stated that their focus/
raison d'être is to
"protect trade" (including trade in aquaculture products through the Sanitary and Phytosanitary Agreement of the WTO (
https://www.wto.org/english/tratop_e/sps_e/spsagr_e.htm) rather than the public's resources - along with "
winning the PR war". Several important components (i.e. Acts, regulations and testing protocols) are often ignored in the discussion over appropriateness of the testing methodology. One of many includes compartmentalization (
http://www.inspection.gc.ca/animals/aquatic-animals/diseases/finfish/eng/1450409829304/1450409830112) - where if you grow fish products from a zone with a reportable disease (
http://www.inspection.gc.ca/animals...es/reportable/eng/1322940971192/1322941111904) - you can't ship live or fresh products or eggs to a "declared free" zone (ftp://ftp.fao.org/docrep/fao/005/y1238e/y1238e08.pdf). The zones and the "declaration status" are at:
http://www.inspection.gc.ca/animals/aquatic-animals/diseases/finfish/eng/1450409829304/1450409830112
Simply put - Canada's fish farm industry could loose certain markets under the application of Article 1.4.6 of the OIE Aquatic Animal Health Code (
http://www.oie.int/index.php?id=171&L=0&htmfile=chapitre_aqua_ani_surveillance.htm) if ISAv was declared to exist by CFIA. And you are not getting that market back if you are excluded to markets due to disease issues - because the wild stocks have it. Mum's the word.
2/ If the government admits that ISAv and/or PRv with HMSI - or any new, novel disease was released into the wild stocks with noticeable population-level impacts - you can be sure that the Justice Lawyers - along with the fish farm lawyers - have briefed certain government officials that a class action law suit will soon be forthcoming. That's why they want to keep attempting to deny the link between HMSI and PRv, IMHO. Let that narly sleeping dog lie is the intent. They then use the excuse of the Privacy Act to deny any attempts to use the FOI act to get answers on fish farm disease. Protecting "trade", again.
3/ The industry and the government co-operated in tracking an IHN outbreaks (St-Hilaire et al., 2002; Saksida, 2006) and then developing an agent-based model to track those disease particles through the Broughton's (Garver et al., 2013). They could have done that with PRV or ISAv, as well - but they haven't. They could also use these results to update their siting criteria - but they haven't. Know why? IHN is a "native" disease (Endemic). No risk in admitting it is here - and dealing with it. It would be difficult to track IHN as an impact from the industry to wild stocks. Although the industry could elevate the levels of IHN shed and available to infect non-infected wild stocks - in this case, they did not release a novel new virus onto wild stocks - unlike ISAv and PRV which are from the fish farming industry. Law suit if you admit they let ISAv and HMSI happen. Nothing to see here folks - move along.
4/ The actual PCR testing methodology has numerous known "holes" in that method - that I believe were planned. Let me explain. The letters PCR stand for "
Polymerase chain reaction" - the "chain" part being a method of amplification - the "polymerase" part being a very specific key/enzyme.
So - it starts with already identifying a specific DNA/RNA clip from the virsus - and as we know - viruses mutate. So that means that you can only test for what you know - and that
evolving viruses may be undetected using this method. In particular, HPR0 ISAv can't be cell-cultured - can be endemic in areas where ISA outbreaks have occurred and given the right conditions – it can mutate to the virulent ISAV-HPRΔ form
Secondly - the numbers of thermal cycles (amplification) that it takes for CFIA/DFO to admit they generated a "positive" verses a "false positive" is
arbitrary and is based on what CFIA/DFO would see as virus levels in cultured (caged) fish. Caged fish are the couch potatoes of the sea - and could withstand much higher viral loads since they generally don't need to run away from predators. Using the same cycle cut-off as a determination for a "positive" for wild fish is inappropriate and scientifically unsupported. It's just more hocus-pocus - nothing to see here folks - move along.
Third - The fact that there was a "false positive" doesn't mean that there wasn't those viral bits in the tissues to begin with. There isn't a ISAv fairy that I know going around innoculating these tests. However, the lesser titre levels from the wild samples might not be quite enough to trigger a reaction in the cell culture. It sure doesn't mean that there was no ISAv - or that the sample was ISAv-free.
Fourth - many viruses are quite fragile (esp. ISAv). You need to use an appropriate preservative that allows the virus to stay "alive" (as much as any virus is alive) and reproduce in the PCR testing. Freezing denatures DNA and many viruses. If they manage to get a "false positive" when using frozen tissue - that would mean that there was more virus in the tissues before freezing - and that is of concern when declaring a "false positive". There should be a correction applied - but is not done by CFIA/DFO. Instead they complain that the sample was degraded - and use that complaint to summarily dismiss the results. Enter the communications departments and PR firms.
Fifth - The "confirmation" of the PCR test usually uses cell culture. Different strains of virus will be more or less successful in differing cells from different species, and different organs, and at different temperatures. It is difficult to get a positive - and as the above point mentioned - the virus needs to be "preserved" appropriately so that it can reproduce in cell culture.
Sixth - You have to sample the right number (function of prevalence) and at the right time, since when testing for the infectious agent (e.g. PCR) - the virus may only be in the individual host tested for a few days. From the Miller study (Di Cicco et al. (2017):
- Alternately, in sampling programs that may capture only a small number of fish on a farm, whether in response to a mortality event or as in the Audit program, as a random sampling event at non-peak stages of disease, it may be difficult to diagnose HSMI with a high degree of confidence
- to date, lack of access to representative samples throughout the life cycle limits the conclusions possible for the natural history of the complex relationship between PRV and HSMI in wild fish populations.
Seventh - Why did they go with PCR/cell culture anways? There are other alternatives - lateral flow immunochromatographic assays (even one for ISAv: Adams and Thompson 2010) and Miller's genomics work. Maybe those methods work way too damn well.
I think I'll stop there - and reiterate that during an outbreak - before recently-affected wild fish die and/or get eaten - that would be the time to assess what that infection means - assess the virulence and mortality/morbidity - but guess what?
The government is scared of that happening and refuses to release fish health information.
