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PCR Insert Contains Key H5 Sequence from Dead PEI Goose

Recombinomics Commentary

June 21, 2006

Using polymerase chain reaction or PCR testing, the scientists searched for tiny bits of genetic material from flu viruses. They spotted enough to declare that they had found an influenza A virus of the H5 subtype.

`They found a little piece that matched the H5, enough of a little piece to say it's H5. However, they can't tell if the virus is alive or not,'' Bosse says.

But there wasn't sufficient material to tell if it was highly pathogenic or a virus of low pathogenicity, or what the neuraminidase _ the N in a flu virus's name _ subtype was.

The above description of testing on Prince Edward Island raises questions about the insert generated in the PCR test as well as the sequence of the insert.  The tiny bits of genetic information described above are primers.  The primers bind to the genetic information of the virus, and then the polymerase reaction fills in the gap between the primers using the virus RNA as a template.  Thus, the insert contains the sequence of the virus and it can be used to identify the viral sequence between the primers.

This insert was specific for H5, so it almost certainly included the HA cleavage site.   The sequence of the HA cleavage site is diagnostic for high pathogenic avian influence (HPAI) or low pathogenic avian influenza (LPAI).  Moreover, the GERRRKKR sequence at the cleavage site would indicate that the H5 was from the H5N1 Qinghai strain.

The Canadian Food Inspection Agency has maintained that the H5 in the dead goose was an incidental finding and the goose died of unknown causes.  The key test of this hypothesis is the sequence of the HA cleavage site.  If it has multiple basic amino acids, it is HPAI like the Qinghai strain of H5N1.  If the multi-basic amino acids are missing, then it is LPAI bird flu, as suggested.

The isolation of H5 virus is unlikely because the samples at Winnipeg have degraded and are now PCR negative.  In view of the state of the material in Winnipeg, the sequence of the insert created on Prince Edward Island should be released.  This sequences would answer to key questions, is the H5 from HPAI and is it from the Qinghai strain of H5N1.

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