Japan's NARO: Genomic Sequencing Analysis Of This Fall's HPAI H5N8 Virus

 

#15,681

While we await further information on the COVID variants detected in the UK (B.1.1.7) and South Africa (501Y.V2), we've a report from Japan's NARO (National Agriculture and Food Research Organization) on the origins of this year's record setting avian influenza epizootic. 

While it never completely went away, for the past three years the world has seen a decided downturn in HPAI H5 outbreaks in wild birds and in poultry, credited in large part to China's massive H5+H7 poultry vaccination campaign of 2017. 

By the early fall of 2020, however, we began to see increased HPAI H5N8 activity in both Europe, and in East Asia, leading to the loss of tens of millions of birds (see Japan, South Korea & Europe Report More HPAI H5 Outbreaks) over the past 3 months.

We've also seen a pair of H5N6 human infections, and one H5N1 human case, in the past 3 months. Over the weekend, we've seen several reports of wild migratory bird die offs in India, suggestive of avian influenza (see FluTrackers Thread).

In order to determine the lineage, source and potential threat of these ever-changing viruses, whole genomic sequencing is undertaken.  Last fall, in Pre-Print: Novel Incursion of a HPAI H5N8 Virus in the Netherlands, October 2020. we saw this year's fresh introduction of HPAI H5N8 in Northern Europe described as `genetically distinct' from recently circulating strains.

In contrast, we have report from Japan's NARO that describes the HPAI H5N8 viruses that arrived last November as showing `. . . a similarity with the H5N8 subtype HPAIV which was prevalent in Europe last winter.'

First the English language report, then I'll return with a postscript.

H5N8 subtype traveling over the Eurasian continent to Japan

Updated:January 4, 2021 (Monday)

-Highly pathogenic avian influenza virus-

The National Institute of Animal Health, NARO (NIAH) had conducted a whole-genome sequence analysis of the virus that caused the Highly Pathogenic Avian Influenza Virus (HPAIV) outbreak on 5 and 8 November in Kagawa prefecture, Japan. Investigation suggests the HPAIV from the outbreak in Europe last winter was brought into Japan by migratory birds flying over the Eurasian continent this year. Poultry farmers need to be extra cautious not to let the wild birds bring the HPAIV to poultry barns.

Overview

On 4 and 7 November 2020, an increasing number of dead chickens were reported in two poultry barns in Kagawa Prefecture, Japan. After analysis, influenza A viruses were detected from the dead chickens (Kagawa 1 and Kagawa 2 strains), and NIAH concluded both strains as subtype H5N8. Following the criteria adopted by the World Organization for Animal Health (OIE), the virus was determined as HPAIV.

NIAH decoded the whole-genome sequence of Kagawa 1 and Kagawa 2 strains and the eight gene segments were compared with those from already known influenza A viruses. As a result, all of the gene segments showed a similarity with the H5N8 subtype HPAIV which was prevalent in Europe last winter.

In addition, Kagawa 1 and 2 strains showed high homology with the H5N8 subtype HPAIV which had been isolated from the feces of wild birds in Hokkaido in October 2020 in all eight gene segments. These facts indicate that the recent outbreaks in western Japan were caused by the virus brought into the country by migratory birds.

The deduced amino acid sequence of the virus showed no trace of resistant mutation to neuraminidase or viral RNA polymerase inhibitors. There was also no sign of amino acid mutation to increase the infectivity of the virus to mammals.

NIAH continues to investigate the infectivity of this virus to poultry and the virus excretion.

          (Continue . . . .)

Although rather short on details, this report suggests that the current Asian epizootic is based on a different lineage of HPAI H5N8 than the outbreaks we've seen in Europe this fall. 

Both HPAI viruses were undoubtedly carried in by migratory birds, probably from their summer roosting spots in Siberia. But Siberia is a very large place, and supports numerous roosting areas and feeds several migratory flyways that funnel birds both east and west each winter.

Making it not that unusual that we'd see genetic differences within the same HPAI subtype as turn up in different parts of the world. 

A study, published in 2016 (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1), suggests that waterfowl pick up new HPAI viruses in the spring (likely from poultry or terrestrial birds) on their way to their summer breeding spots - where they spread and potentially evolve - and then redistribute them on their southbound journey the following fall.

This pattern is repeated year after year, and supports the mixing and matching of viruses, that help drive avian influenza's evolution through both reassortment (antigenic shift) and antigenic drift.  Even when we've seen several years of decreased avian flu activity - such as we had since the summer 2017 - HPAI viruses can always reinvent themselves.   

All of which keeps HPAI viruses on our radar, for both their epizootic and zoonotic potential.