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Media Myth On H5N2 Lineage In Fraser Valley
Recombinomics Commentary
December 10, 2014 12:15

It’s a more contagious and fatal form of the same virus that affected some 70,000 B.C. birds in 2009, a sign of the way these viruses can mutate, said Harpreet Kochhar, Canada’s chief veterinary officer.

VANCOUVER - The type of avian influenza responsible for an outbreak at poultry farms in southwestern British Columbia is H5N2, a source has confirmed — the same virus behind at least three other previous outbreaks at Canadian farms.
VANCOUVER - The virus at the centre of an avian influenza outbreak in British Columbia's Fraser Valley is the H5N2 strain, the Canadian Food Inspection Agency said Thursday — the same variety behind at least three previous outbreaks at Canadian farms.

The above comments from two of many media sources, create the illusion that the 2014 high path H5N2 is the same virus responsible for three prior low path outbreaks in Canada, but has evolved to a more virulent form.  However, the latest OIE update from Canada makes no such claim, and the failure to note that the lineage is North American or to release the H5 polybasic cleavage site strongly suggests the H5 is an Asian lineage which is likely Fujian clade 2.3.4, which is currently circulating in wild birds in Asia as multiple sero-types, including H5N2.

The first comment above (in red), by Canada’s chief veterinary officer uses the term “same virus” when in fact only the sero-type, H5N2 is the same.

Similarly, the two quotes in blue are from three versions of the same story.  The first version claimed that one of the three prior H5N2 outbreaks in Canada involved high path, which was corrected in the second version.  However, both stories (first blue quote) used the same opening term stating that the 2014 virus was “the same” as the prior H5N2 outbreaks, which again is only accurate for the serotype.  The second blue quote offers clarification that it is the “same variety” which is in reference to the H5N2 serotype, but also leaves the impression that the lineage matches the earlier outbreaks, which involved the North American lineage.

In the past Canada's OIE reports have cited the North American lineage, which is easily determined after a sequence is generated.  The short description of the strain or clade refers to the sequence of the H, which is easily compared to prior sequences, which can be broadly classified as North American or Asian.  The H sequence also contains the cleavage site, which has a single basic amino acid in front of the GLF in low path sequences, and cleavage by a host encoded protease is required for infection.  If multiple basic amino acids are present adjacent to the GLF sequence, multiple protease, which are expressed in a cell type manner, can cleave the H0 precursor, allowing for infection of multiple cell types.  This polybasic cleavage site is associated with highly pathogenic avian influenza (HPAI).

The 2004 there was a low path H7N3 outbreak in Fraser Valley, which was not immediately contained.  The H7 evolved into a high path form, which led to the culling of 17 million birds,

This type of change for H5 has also been noted elsewhere, but prior to the current outbreak, H5 has not been reported in Canada.  Moreover, the initial and subsequent OIE report did not cite any evidence for an initial low path infection.  Consequently, attention was focused on the lineage of the H5, since high path H5 has also not been reported in wild birds in North America.
In contrast to the H5 history in North America, high path H5 is common in wild birds (and poultry) in Asia,  H5 lineages from Asia are easily distinguished from North America, and the Fujian strain is currently circulating in many countries in eastern Asia and recently in three countries in Europe.  The serotype of these recent outbreaks in Europe is H5N8, but the same Fujian clade 2.3.4 H5 has been found in multiple serotypes in Asia, including H5N2.  The ressortants (H5N1, H5N2, H5N3, H5N5, H5N6, H5N8) in Asia also raise the possibilty that a Fujian clade 2.3.4 H5 could be associated with various gene segements from Asia and/or North America via reassortment (including N2).

Thus, the absence of low path in the 2014 H5N2 outbreak in Fraser Valley, as well as the absence of reported high path H5 in wild birds infected with a North American lineage, has created interest in the sequence of the cleavage site and the lineage of H5N2.

The December 9 OIE report noted that CFIA had obtained the sequence of the cleavage site, as well as additional data for H5 and N2, but the lineage was not cited and the cleavage site was not released.  The low path North American lineage has one basic amino acid adjacent to GLF (RETR), while the Fujian strain generally has RERRRKR or REKRRKR (the T is replaced by four consecutive basic amino acids), so publication of the cleavage site would strongly suggest an Fujian clade 2.3.4 if either polybasic  sequence was present.  Similarly, addition sequence data for H5 or N2 would easily determine if one or both gene segments were of Asian lineage.
The withholding of this information strongly suggests that the H5 has a polybasic cleavage site because it is of Asian origin, which has never been reported in birds in North America, and the withholding of this information is in violation of the UN’s IHR (International Heath Regulations), which require notification to WHO within 24 hours of lab results (which were known December 4).

The presence of Fujian clade 2.3.4 in wild birds is a serious health concern for Canada and American countries to the south, including the United States farms located within 10 kilometers of the fifth farm identified in Fraser Valley (see map). 

Thus, the CDC should obtain samples and publish the sequences, which are hazardous to the world’s health, and Canada should be cited for the IHR violation.

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