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CFIA Withholds Fraser Valley Sequence and Cleavage Site
Recombinomics Commentary
December 9, 2014 23:00

RT-PCR and partial sequencing of the H and N gene segments indicates a poly-basic cleavage site in H5 consistent with Highly Pathogenic Avian Influenza Virus and the virus being a H5N2 Avian Influenza Virus with an IVPI of 2.96-2.98.

Results of gene sequencing indicate alow path cleavage site (NVPQRETR/GLFGAIA). The sequence is 99% related to another H5 virus (H5N2) from California in 2007. Closest match in Genbank is A/American green-winged teal/California/HKWF609/2007(H5N2), accession number: CY033444

The above comments (in red) acknowledge H5 and N2 sequencing on isolates from the current H5N2 high path outbreak in Fraser Valley (see map).  The report also notes that the H5N2 was isolated and sequenced by the Canadian National Center for Foreign Animal Diseases on December 4, so the CFIA has known the lineage since last week.

In contrast to the above absence of the cleavage site sequence or the lineage, the 2009 OIE report gave the sequence of the cleavage site as well as the most closely related sequence at Genbank for the H5 and N2 genes (in blue), confirming that the H5N2 was low path and a North American lineage.

The withholding of this information in the December 9, 2014 update raises serious concerns that the cleavage site sequence, as well as the H5 sequence, is closely related to the Fujian clade 2.3.4 which has been reported in poultry and wild birds in China in 2014 (see map).

The withholding of the lineage is in violation of the IHR (International Health Regulations) which is of great concern because Asia H5 has never been reported previously in the Americas.  The outbreak in the turkey farm (which was the 2009 index farm) is 2 miles from the US border, and circulation in wild birds would put US farms at significant risk.

The withholding of the sequence and lineage information also raises concerns on the CFIA transparency regarding human cases.  Clade 2.3.4 H5 has caused human cases in China when paired with N1 and a case in Laos (in 2014) when paired with N6.

The two N serotypes in human seasonal flu are N1 and N2, so the human case of H5N6 raises concerns that H5N2 would also lead to human transmission of Fujian clade 2.3.4.

The virus isolation and sequencing dates of December 4 leaves no doubt that CFIA knows the lineage of H5N2 in Fraser Valley, and the withholding of this information is hazardous to the world’s health.

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