Wednesday, January 24, 2018

Japan: Kagawa H5N6 Outbreak Genetically Distinct From Shimane Isolate


In early November several dead mute swans were discovered in Matsue, Shimane Prefecture which were quickly determined to have been infected by the H5N6 virus. 
A couple of weeks later, we learned from Tottori University: The Shimane HPAI H5N6 Was A New Reassortment - not a return of the HPAI H5N6 virus which had arrived from China the previous winter.
Instead this new virus was a reassortment of the H5N8 virus which ravaged Europe last winter and an (unidentified) European HxN6 virus - and was reportedly similar to another H5N6 reassortment briefly reported from Greece last March.

Reassortment Of H5N8 & European HXN6 - Tottori University

While last year's dominant HPAI H5 viruses (H5N8 & Asian H5N6) remained surprisingly absent this winter, over the next few weeks other countries in Asia (South Korea & Taiwan) - and by December in Europe-  (The Netherlands, Switzerland, Germany & most recently the UK) had reported outbreaks of this newly reassorted (European) H5N6 virus.
While not spreading anywhere near as aggressively as H5N8 did last year, this newly emerged HPAI H5N6 virus appears to have (at least temporarily) usurped last year's HPAI contenders in Eastern Europe and Northern & Western Europe. 
The Asian H5N6 virus and last year's aggressive H5N8 virus have not disappeared entirely, since H5N6 is still being reported in China, and H5N8 is reportedly rife in parts of the Middle East, and continues to be reported from Africa. 
Nothing stays static for very long in the world of influenza, and within weeks of arriving in South Korea we saw South Korea Reporting A`Second Strain' Of The Newly Reassorted H5N6 Virus.
Today we've a similar report from Japan's NARO (National Agriculture and Food Research Organization) which reports that the Poultry Outbreak Identified As HPAI H5N6 in Kagawa Prefecture earlier this month is `genetically distinct' from the H5N6 virus which was isolated from the dead mute swans in Shimane Prefecture not quite three months ago.
While both viruses are similar, and are a product of a reassortment between the H5N8 virus and a European HxN6 virus - without giving details - in the words of NARO, they indicate `at least two types of H5N6 subtype HPAIV invade domestically in this winter.'
First the (translated) Press release, then I'll return with a postscript. 

Press release (translated)
(Research Results) On the Origin of Causative Virus of Highly Pathogenic Avian Influenza Occurred in Kagawa Prefecture

- Highly pathogenic avian influenza virus across the continent -

Information release date: Wednesday, January 24, 2018

Agricultural Organization Animal Health Research Division conducted a whole genome analysis of causative virus of highly pathogenic avian influenza that occurred in Kagawa Prefecture in January this year and this virus is the H5N8 subtype highly pathogenic avian influenza infected in Europe last winter It is revealed that it is the virus and the gene reassortment virus of HxN6 subtype avian influenza virus. Vigilance is necessary so that the highly pathogenic avian influenza virus carried by wild birds will not invade into the poultry farm.


The causative virus (Kagawa stock) of highly pathogenic avian influenza (HPAI) 1) occurred in Kagawa prefecture on January 11, 2018 is highly pathogenic avian influenza virus of H5N6 subtype 2) avian influenza virus: HPAIV) 3). The virus showed high pathogenicity to kill chickens within 24 hours in an intravenous vaccination test prescribed by the International Organization for Animal Health (OIE) (OIE).

The whole genome sequence of the Kagawa strain was deciphered and compared with the known influenza A virus of 8 gene segments 4), 7 out of 8 gene segments showed H5N8 subtype HPA IV prevalent in Europe last year , And the NA gene was derived from the HxN6 subtype avian influenza virus (Hx means that the HA subtype is unknown) distributed in wild birds of the Eurasian continent.
It was genetically related to H5N6 subtype HPAIV isolated from Shimane Prefecture's Kobe butterfly in November 2017 but it is clearly distinguishable.
This indicates that at least two types of H5N6 subtype HPAIV invade domestically in this winter.
No tolerance to the antiviral agent neuraminidase inhibitor was found in the deduced amino acid sequence of this virus. Also, there are no known amino acid mutations that increase infectivity to mammals.
Agricultural Research Institute Animal health research department is going to investigate infectivity of this virus to poultry in the future and virus excretion etc in future.

In recent years, HPAI in poultry has occurred in poultry by invasion of H5N1 subtype in 2010 - 11, H5N8 subtype in 2014 - 15, and H5N6 subtype in 2016 - 17 in Japan. These HPAIVs are called Eurasian type H5 subtype HPAIV because they have a common HA gene as H5 subtype HPAIV prevalent among poultry mainly in Asia since 2004. In 2014 - 15 and 2016 - 17, occurrence by Eurasian type H5 subtype HPAIV occurred frequently on the world scale, migratory birds are thought to be involved in the transportation of virus on the world scale.
H5N6 subtype HPAIV was detected in Shimane Prefecture in November 2017, and HPAIV of the same subtype has been detected in poultry and wild birds since November in Korea. These viruses were reported to be virus reassortment of the HxN6 subtype avian influenza virus 5) virus, which is distributed between the H5N8 subtype HPA IV prevalent in Europe in the winter of last year and wild birds living in the Eurasian continent It is.
Contents · Significance
  1. Kagawa Prefecture farm type A influenza virus that has been separated from the (Kagawakabu) that it is H5N6 subtype HPAIV has been confirmed.
  2. Eight all of the gene segments of Kagawakabu has showed the H5N6 subtype HPAIV (great black-backed gull, Ltd.) and the high homology that is separated from the great black-backed gull in the Netherlands in December 2017 (over 99%). Among one gene segments (NA genes), as well shows the great black-backed gull strain highly homologous (over 99%), NA gene and closely related avian influenza viruses circulating among birds that inhabit the Eurasian continent it was found is. From this, it is believed that this virus is a reassortment virus of last year's winter in the HxN6 subtypes circulating among the birds that inhabit the H5N8 subtype HPAIV and the Eurasian continent, which was popular in Europe bird flu virus you.
  3. We have last year also from the Mute Swan in Shimane Prefecture in November, H5N6 subtype HPAIV (Mute Swan Co., Ltd.) are separated, the homology of the gene of Kagawa stocks and great black-backed gull strains, than Kagawa shares and Mute Swan Co., Ltd. (97-99%) from the high it, this in the winter can be genetically distinction to domestic two types of H5N6 subtype HPAIV is believed to have invaded. The 2016 from the difference of gene homology - 2017 HPAI of the resulting virus that occurred in the winter hiding in the country, was denied revived the possibility.
  4. From the above, 2016 - 17 H5N8 subtype HPAIV that was popular in Europe in the year is taken to Siberia is a nesting areas during the breeding season of migratory birds, where causing a HxN6 subtype avian influenza virus and genetic reassortment, H5N6 subtype it will be considered to have been transported to the Netherlands and Japan to wintering of migratory birds as a type HPAIV ( Figure ).
Credit Japan's NARO

Each summer birds which overwinter in Asia, Europe, Africa, and North America head to the high latitudes to nest and feed on the abundant bloom of insects that come during the thaw. 
For many of these birds, Siberia is the destination of choice, and so birds from many regions spend the summer together, swapping both HPAI and LPAI viruses and occasionally producing new subtypes.
While most of these new subtypes are either harmless LPAI viruses, or are evolutionary failures, in recent years we've seen several efficient new HPAI viruses emerge, thrive, and then spread during the fall and winter via migratory birds (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1).
As more and more biologically `fit' and genetically distinct viruses are generated, and manage to return to this geographic `mixing vessel', the likelihood of seeing even more new subtypes emerge grows greater each year. 
Because, as we've seen over the past few years . . .  what happens in Siberia has a habit of not staying in Siberia.

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