Author Archives: salmonfarmscience
We made reference to this in our blog post yesterday, but today we realize we have never published this with any context.
Here’s the full story. Earlier this year Dr. Fred Kibenge’s lab at the University of PEI lost its OIE reference status. The lab had been been accredited by the OIE (World Organization for Animal Health) as a reference lab for ISA virus.
Despite what anti-salmon farming activists claim, the reasons why this status was pulled are crystal clear.
“OIE Reference Laboratories have a responsibility to provide high quality disease diagnostic services as global references to all Member Countries of the OIE particularly in the case of doubts or controversies about animal sample analyses,” states a press release from the OIE in Paris last year.
The OIE is therefore keen to maintain the highest technical and operational standards of all Reference Laboratories.
After different Member Countries pointed out questionable diagnostic results emanating from an OIE Reference Laboratory for Infectious Salmon Anaemia located at Atlantic Veterinary College (AVC) in Canada, the OIE decided to conduct an audit of the Reference Laboratory with independent OIE experts from 31 July to 2 August 2012.
Conclusions of the audit were unfavourable and showed that a series of weaknesses in the system have a direct impact on the quality of diagnoses conducted by the OIE Reference Laboratory at AVC.
But wait, there’s more.
After the OIE delegates from all member countries met for their annual general meeting in May this year, they agreed unanimously to pull the reference status from Kibenge’s lab.
The conclusions showed there were many serious problems with the lab (referred to below as “OIE-RL” for “OIE Reference Lab”)and how it was run.
- No evidence for any meaningful Quality System in the OIE‐RL
- OIE‐RL falls well short of acceptable Quality Standards
- OIE‐RL uses theOIE template for validation of tests, but needs to involve other laboratories in the process
- Competent laboratory analyst but lack of comprehensive records of continuing professional training and development
- The OIE expert recognises the importance of laboratory organisation and work flow patterns to avoid contamination, but has not optimised the system. Incompatible pre‐ and post‐PCR procedures were undertaken in the same laboratory.
- The OIE expert is clearly knowledgeable about ISA, with many peer reviewed publications, but has a research focus, rather than that of a diagnostician
- Results of tests reported without contextual interpretation
- No detailed investigation of apparently anomalous results
- No evidence of multidisciplinary engagement for disease investigation
- There is a need for much wider involvement with proficiency test/ring test schemes, either as participant or organiser
- Lack of contact and networking with other laboratories working on ISA
- Lack of understanding of general philosophy of mutual international support within which OIE operates
The biggest concern raised in the audit was that the lab was ignoring discrepancies in test results and reporting them with little or no interpretation. As we saw in BC, this left the data wide open to abuse and misinterpretation by Alexandra Morton, especially because she did not publish and share the actual lab reports.
As well, the audit raised concerns that the lab was using in-house methods instead of methods described in the OIE Aquatic Manual, and was ignoring obvious opportunities for follow-up tests that would have provided essential information.
Final reports are provided with limited interpretation even when the results of different assays were conflicting.
In an example provided to the panel, seven wild caught cutthroat trout were tested by PCR. The results showed all samples to be negative by real‐time RT‐PCR, while all fish were positive by the conventional segment 8 RT‐PCR and also with an in‐house conventional segment 6 RT‐PCR. In the absence of a real‐time RT‐PCR result to support the conventional RT‐PCR results the panel considers these results to be highly dubious, and that the results should be reported as inconclusive pending further investigation. As a general principle, no further testing should be necessary if a primary screening test (in this case real‐time RT‐PCR) gives a negative result. The rationale for carrying out “confirmatory” testing (conventional RT‐PCR) on negative samples is not clear.
We would regard it as a duty of the OIE‐RL to seek an explanation for these discrepancies. We consider there could be several explanations, including cross‐contamination in the laboratory, but also that the assays were indeed detecting a new genetic variant of ISAV not picked up by the real‐time RT‐PCR used. An obvious part of such an investigation would be the use of alternative real‐time assays as described in the OIE Aquatic Manual, but the panel understands that Dr F. Kibenge used an alternative in‐house real‐time assay to confirm the presence of ISAV and that these results were not shared nor was an explanation provided for the apparent failure of an assay recommended in the OIE manual.
Sequencing followed by a phylogenetic analysis would most probably provide essential information, however Dr Kibenge considered this to be a research issue and had simply reported his findings, even though we were told that further investigation had been initiated.
In conclusion, the panel had concerns that Dr F. Kibenge may deviate from his standard procedures that follow recommendations in the Aquatic Manual, and use alternative non‐validated in‐house methodologies. There seemed to be a lack of appreciation of the obligations on a Reference Laboratory forthorough investigation of dubious orillogicalresults,together with the need for evaluation of the biological significance of results.
There you have it. No conspiracy, just bad science.
We kind of figured the “Stand up for Science” rally in Vancouver yesterday would end up like this.
While some legitimate scientists did get up and speak, most of the rally was about how Stephen Harper and pipelines are bad.
Fair enough. But there’s plenty of other venues for that. We get it, Fin Donnely and the federal NDP. You hate Harper and the Conservatives. But for a rally that was supposed to be about keeping politics out of science, it was pretty damned political.
Of course, our favourite pseudoscientist was there to spout her litany of lies about salmon farms. Here’s what she said, according to the Vancouver Observer.
In 2011 we had the Cohen inquiry into why our biggest population of wild salmon is declining and I read the records of a government scientist who said he saw the evidence of European viruses known to kill massive numbers of salmon, he saw evidence that those diseases that are in the farmed salmon that are in the ocean in British Columbia.
No. Wrong. This is NOT WHAT HAPPENED and the vet who wrote those records, Dr. Gary Marty, has repeatedly corrected this lie. He puts it bed quite effectively in this letter published last spring in the Association of Professional Biology’s official newsletter.
“Alexandra Morton’s article did not mention that every fish in my database was tested for ISAV using highly sensitive and specific RT-PCR tests, and that all results were negative–no virus,” Marty writes (see page 5).
However, Morton continues to ignore the science in favour of furthering her conspiracy theory opinion.
This changed my life. I responded. I have organized a national salmon sampling program.
Really? A national sampling program? Where is the data, Alex? For all we know, you’re taking donation money people think you’re spending on tests, and socking it away in your RRSP. We have no idea, because you publish none of your test results, you just expect everyone to take your word for it. That’s not science. That’s taking advantage of your cult of personality.
The laboratories and I published in Virology Journal, the top journal on viruses. We published that the virus had come to BC in approximately 2007 and it matched a virus in Norway. How did that happen? Viruses don’t fly.
Um. No. Again, no. That’s not what the study really says. What it really says, is that PRV in Canada is a very close (but not exact) match for PRV in Norway. The paper states:
It is not known how the virus could have been transmitted from Norway to Canada since there have never been any authorized direct imports of Atlantic salmon eggs from Norway since 1985; recent imports have been from Washington State-USA (2001) and Iceland (2004–2009) . There is no information about the PRV situation in Washington State or Iceland. Horizontal spread and/or introduction of virus through wild fish migration are not reasonable routes of transmission.
Morton continues with another lie.
The lab I’m using was stripped of its international authority, humiliated amongst his peers. Nobody will say why.
I’ll take “Bullshit” for $1,000, Alex. The OIE (World Organization for Animal Health) published its report online last year explaining why. They pulled the lab’s reference status because they had many concerns, not least of which was that “the cramped, untidy conditions of the laboratories, particularly the general laboratory [room 329(S)] where both sample preparation and post‐PCR analysis were performed in close proximity to each other… The panel believes that there is a serious risk that the integrity of the test samples will be compromised.”
…. I am taking up the role of regulator…. People ask me how I will get the government to accept the results of my research. I don’t have enough years left in my life to get them to accept the results. I need you to accept the results, to stand by my findings.
Perhaps, Alex, you could start by holding yourself to the same level of transparency you demand from everyone else. Publish your test results. All of them. Show your work
Because, to paraphrase, science without data is scientific malpractice.