While not a huge surprise – given the ever-growing diversity of H5 avian viruses in general and previous reports of multiple reassortants of H5N8 in Korea – this morning Japan’s National Agriculture and Food Research Organization (NARO) has announced that an analysis of the recent H5N8 outbreak in Miyazaki Prefecture shows it differs enough from previous Japanese outbreaks to be considered a different sub clade.
First some excerpts from the press release (machine translated), then I’ll return with a bit more.
- December 26, 2014
- Highly pathogenic avian influenza occurred in Miyazaki Prefecture in 2014 - analysis of genome sequences for verification of the origin of the virus -
Analysis of genomic sequences for the verification from the virus -
The whole genome sequence of the causative virus of highly pathogenic avian influenza that occurred in the poultry farm in Miyazaki Prefecture in December 2014 (HPAI) I was deciphered.
This occurs with the cases of wild birds in Chiba Prefecture of poultry farms and in November of Kumamoto Prefecture of this year in April, has been shown that there is no direct association.
January 2014 or later, Korean house Kinya has continued to prevalent in wild bird H5N8 subtype highly pathogenic avian influenza virus 1) (Highly Pathogenic Avian Influenza Virus: HPAIV), the poultry of Kumamoto Prefecture in April in Japan cause the occurrence of HPAI in place since November, feces of Chiba Prefecture of wild birds (ducks), and is separated from Kagoshima Prefecture of vine, etc.. In addition, has been reported the occurrence of HPAI is caused by viruses of the same subtype in November and later Europe and North America of poultry, etc..
The NARO National Institute of Animal Health, HPAI causative virus of that occurred in the poultry farm in Miyazaki Prefecture in December 16, 2014 is H5N8 subtype 2) as well as to identify that it is a HPAIV, of all of the genes of this virus The nucleotide sequence I was quickly determined.
And are separated by the South Korea and Europe on the Chiba strains and public gene information database that has been separated from the feces of ducks in Kumamoto stocks and November 2014 that has been separated from dead chickens the determined nucleotide sequence in April 2014 I made a comparative analysis of the H5N8 subtype HPAIV gene.
This time, isolated virus (Miyazaki Ltd.) is, Kumamoto stock, Chiba stock, and South Korea since January, is derived from a common ancestor with the H5N8 subtype HPAIV that have occurred in the European poultry since November It is now clear.
On the other hand, Miyazaki strain, from the difference of gene sequences, Kumamoto stocks and Chiba stock, and Europe generated stock has been clearly distinguished.
HPAI that occurred in this Miyazaki Prefecture, Kumamoto Prefecture of poultry farms in April this year, the cases of wild birds in Chiba Prefecture in November found that direct relationship does not. This will be different from the one that occurred in April 2014, after the fall, we have suggested that at least two types of H5N8 subtype HPAIV are newly entering the country.
From the fact that mutation of the amino acid sequence deduced to be involved in the infection to humans was observed, Miyazaki strains I are considered less likely to infect humans directly.
Until now, all of the Japanese H5N8 samples (and most Korean and European samples) have all fallen from the same branch of the H5 188.8.131.52 phylogenic tree (highlighted in yellow below), a clade that includes the H5N1 and H5N6 viruses as well.
It will be interesting to see exactly where this Miyazaki virus falls into the H5 phylogenic tree.
Influenza viruses are constantly throwing the genetic dice, and while most of these variants will be evolutionary failures and fade away quickly, sometimes a `biologically fit’ and competitive strain appears and thrives.
Influenza viruses normally evolve through a process called antigenic drift – a relatively slow process where minor amino acid substitutions accrue during (flawed) reproduction – but sometimes a new `hybrid’ virus will emerge from a process called antigenic shift, or reassortment.
Reassortment of two Avian Viruses Producing a Hybrid (Reassortant) Virus
Shift occurs when one virus swap out chunks of their genetic code with gene segments from another virus. Like viral tinker toys, these interchangeable parts allow for the creation of many different hybrids. While far less common than drift, shift can produce abrupt and sometimes dramatic changes to the virus (see NIAID Video: How Influenza Pandemics Occur).
When an avian influenza virus remains in its reservoir host (predominantly waterfowl) – to which it is already well adapted – it usually changes very slowly. When it enters a new host population – like commercial poultry – it can begin to evolve rapidly, producing numerous clades and subclades.
After a decade of pretty much only having to worry about H5N1 (2003-2013), over the past couple of years we’ve seen the sudden emergence and/or spread of multiple clades of HPAI avian H5N8, H5N6, H5N3, and H5N2 along side H7N9, H10N8 and a handful of `minor players’ like canine & equine H3N8, canine H3N2, and even H10N7 in marine mammals.
The concern is - while one can’t predict where any of these viruses will end up - the greater the diversity of novel viruses in circulation, the greater the chances of someday seeing one jump to, and adapt to, humans.
For more on this rapidly expanding array of novel flu viruses you may wish to revisit: