Recombinomics | Elegant Evolution

Home Founder What's New In The News Consulting

H1N1 Consulting

Paradigm Shift

Viral Evolution

Intervention Monitoring

Vaccine Screening

Vaccine Development

Expression Profiling

Drug Discovery

Custom Therapies


AudioNov20 Dec12 Dec18 Dec22 RSS Feed twitterNews Now                         


Three Fujian H5N8 Sub-Clades Co-Circulate In Japan
Recombinomics Commentary
December 27, 2014 11:00

National Institute of Animal Health in Tsukuba, Japan has released a full set of H5N8 sequences, A/chicken/Miyazaki/7/2014, from a tracheal swab from a dead chicken in Miyazaki (collected December 16).  The sequences follow the recent release of another full set of H5N8 sequences, A/crane/Kagoshima/KU1/2014, from a tracheal swab of a sick white naped crane (collected November 23 by researchers at Kagoshima University).  Both groups are commended for the rapid release of these important sequences.
Prior November H5N8 sequences from healthy birds in Japan (
A/duck/Chiba/26-372-48/2014 and A/duck/Chiba/26-372-61/2014) were Fujian clade, which had evolved from the early 2014 outbreak in South Korea, and were very closely related to November / December sequences from multiple sites in multiple countries in Europe (Germany, Netherlands, England, and Italy) including A/turkey/Germany-MV/R2472/2014, A/Ch/Netherlands/14015526, A/duck/England/36254/14, and A/turkey/Italy/14VIR7898-10/2014, suggesting migration from summer sites in Russia and/or Mongolia, which is supported by a December 25 OIE report of the detection of H5N8 in a healthy Eurasian wigeon shot in September in northeastern Russia (see map) and tested in December.  Sequences from that case have not been released, but are similar to the cases in Europe and Japan.
The two sets of recent sequences from Japan are also Fujian clade, which evolved from the sequences from South Korea, but are distinct from the earlier sequences from Japan and Europe, as well as each other.  All 8 gene segments fall into the same lineages as each of the above sequences, but have independently evolved  and represent unique introductions leading to co-circulation of three distinct sub-clades in Japan.
The relationship of these three subclades to the recently reported H5N2 and H5N8 outbreaks in Canada and the United States is unclear.  The H5N8 reported from four dead pet falcons in Lyndon, Washington, who had been fed a wigeon caught near Wiser Lake, as well as the H5N8 at a small holding in Winston, Oregon, were cited as having greater than 99% identity with the South Korea sequences, for both H5 and N8 suggesting the sequences matched the initial sequences from Japan and Europe.  However, the recent sequences leaves open the possibility that the US sequences match the more recent distinct sub-clades represented by the sets described above.
This possibility is higher for the H5N2 sequence from a northern pintail at Wiser Lake (see map), which had an H5 that was only 98% identical to H5 from South Korea.  These US sequences were generated by the FDA, which usually deposits sequences at Genbank, which doesn’t have the more recent H5N8 sequences detailed above, which are at GISAID, so it is unclear if the South Korean sequences are the closest match in the public databases.
Similarly, the CFIA in Canada has noted that the H5N2 sequences in British Columbia have 5 H5N8 gene segments, including Fujian H5, as well as 3 North American gene segments, including N2, but the percent identity has not been cited and the recent announcement on completion of sequences from multiple farms did not cite the 5 to 3 ratio, leaving open the possibility of multiple constellations associated with a Fujian H5 and a North American N2.
The added complexity introduced by the three distinct sub-clades in Japan, as well as the announcement of H5N8 in northeast Russia in September, highlights the need for the rapid release of sequences from Canada, United States, and Russia.

Media Link

Recombinomics Presentations

Recombinomics Publications

Recombinomics Paper at Nature Precedings

Home | Founder | What's New | In The News | Contact Us

© 2014 Recombinomics.  All rights reserved.