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Fujian H5N8 Diversity In Kagoshima Japan & North America
Recombinomics Commentary
December 31, 2014 23:00

Recently released H5N8 sequences from Japan (A/crane/Kagoshima/KU1/2014 and A/chicken/Miyazaki/7/2014) were distinct from the H5N8 sequences in Chiba, Japan (A/duck/Chiba/26-372-48/2014 and A/duck/Chiba/26-372-61/2014), as well as sequences in Europe (Germany, Netherlands, England, and Italy) and the recently released sequences from Russia (A/wigeon/Sakha/1/2014).  The crane and chicken sequences were distinct from each other, but were most closely related to a sub-clade created by recent sequences from Korea and Japan isolated in early 2014 (A/chicken/kumamoto/1-7/2014, A/Baikal teal/Korea/H41/2014, A/bean goose/Korea/H53/2014, A/Baikal teal/Korea/H66/2014, A/Baikal teal/Korea/H68/2014 A/breeder duck/Korea/H128/2014, A/broiler duck/Korea/H145/2014, A/broiler duck/Korea/H48/2014, A/broiler duck/Korea/H49/2014, A/bean goose/Korea/H40/2014).

Today Kagoshima University released sequences from H5N8 in water from a crane roost in Kagoshima (A/environment/Kagoshima/KU-ngr-H/2014) which was most closely related the sub-clade in Europe, Russia, and Chiba.  The above crane sample was collected on November 23, while the water was collected on December 1.  Thus, although both samples were collected from a similar location and only 8 days apart, they represented two distinct sub-clades.
This type of diversity is also present in the three sequences in the United States.  The H5 in the H5N2 in Washington and the H5N8 in Oregon are most closely related to A/bean goose/Korea/H40/2014, indicating they are distinct from the sublade in Europe, Russia and two locations in Japan (Chiba and Kagoshima), and may be closer to A/crane/Kagoshima/KU1/2014 or A/chicken/Miyazaki/7/2014, but the Oregon H5N8 sequence has an identity of 99.3% while the Washington H5N2 sequence identity is only 98% when compared to the same A/bean goose/Korea/H40/2014 sequence, indicating the two H5’s in the US are distinct from each other assuming the sequences used by the USDA are representative of the full sequence.  Similarly, the H5N8 in Washington is also distinct because it is most closely related to A/coot/Korea/H81/2014, which is distinct from the two US sequences as well as Europe/Russia/Chiba, which are most closely related to A/broiler duck/Korea/Baun2/2014.
Thus, although the USDA has not yet released any sequences, the most closely related Korea sequences indicate all three H5s in the US are distinct from each other, as well as the Europe/Russia/Chiba sub-clade, and the relationship of the H5N2 in the US to the H5N2 in British Columbia is unclear because CFIA has not released any sequences or cited the most closely related public sequences.
Agencies in Europe, Japan, and Russia have promptly released sequences a few days after OIE filings, but the lag in release by the CFIA and USDA is glaring, as is the diversity in these sequences with each other, as well as published sequences. 

These sequences should be released immediately.

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