Wednesday, January 31, 2018

EID Journal: Novel HPAI A(H5N6) Virus in the Netherlands, December 2017


By now most are aware that the HPAI H5N6 virus which arrived last November in Japan and South Korea - and turned up in the Netherlands in December - is not the Asian H5N6 virus which has caused at least 18 human infections and a number of deaths in China, but rather a descendant of the HPAI H5N8 virus which sparked last year's record epizootic in Europe.
In late November a report from Japan's Tottori University: Shimane HPAI H5N6 A New Reassortment identified samples collected two weeks earlier in Shimane Prefecture as being similar to a novel reassortment reported in Greece towards the end of last year's European epizootic. 

Essentially a reassortment between HPAI H5N8 and an (as yet) unidentified LPAI HxN6 virus from Europe (see chart below).

Over the next couple of weeks additional H5N6 viruses were discovered in South Korea and Taiwan - all described as being `similar' to the sample recovered in Greece the previous March - although genetically distinct variants were reported (see South Korea Reports `Second Strain' Of Newly Reassorted H5N6 Virus).
On December 9th, in Netherlands Bird Flu Identified As Reassorted H5N6, the Wageningen Bioveterinary Research Institute, described recently recovered H5N6 viruses from a Biddinghuizen poultry farm also as being similar to the H5N6 viruses recently detected in Japan and South Korea.
We say `similar' because influenza viruses are constantly changing and evolving through antigenic drift (replication errors) and antigenic shift (reassortment) and so exact matches are rare. There can be dozens of genotypes, and many more minor variants, among viruses of the same subtype. 
Today we have a new analysis of the Netherlands H5N6 virus published this week in the CDC's EID Journal which shows that while similar to the newly reported H5N6 virus in Asia and its predecessor isolated in Greece, it is a genetically distinct reassortment.
A link to, and a few selected excerpts from, yesterday's EID study. But most will want to follow the link to read the report in its entirety. 

Figure 2. Schematic representation of the HPAI H5N6 reassortant virus detected in the Netherlands. Two variants of HPAI H5N8 were detected in 2016; they have different PA gene segments, called PA I and PA II. The novel virus evolved from H5N8 viruses having a PA II gene segment, but obtained both novel NA and PB2 gene segments. The H5N6 viruses detected in Greece, Japan, and Taiwan ha evolved from H5N8 viruses that have a PA I gene segment and have a N6 segment similar to the virus detected in the Netherlands. HPAI, highly pathogenic avian influenza; PB, polymerase basic; PA, polymerase; HA, hemagglutinin; NP, nucleoprotein; NA, neuraminidase; MP, matrix protein; NS, nonstructural protein.

Novel Highly Pathogenic Avian Influenza A(H5N6) Virus in the Netherlands, December 2017

Nancy Beerens Comments to Author , Guus Koch, Rene Heutink, Frank Harders, D.P. Edwin Vries, Cynthia Ho, Alex Bossers, and Armin Elbers


A novel highly pathogenic avian influenza A(H5N6) virus affecting wild birds and commercial poultry was detected in the Netherlands in December 2017. Phylogenetic analysis demonstrated that the virus is a reassortant of H5N8 clade viruses and not related to the Asian H5N6 viruses that caused human infections.


Since 2013, HPAI H5N6 viruses have emerged in poultry and caused sporadic infections in humans in Asia, raising global concerns regarding their potential as human pandemic threats. H5N6 viruses constitute >34 distinct genotypes, of which 4 were detected in humans (9). 

To genetically characterize the novel H5N6 subtype influenza virus detected in the Netherlands, we sequenced the full genome of the viruses found at the duck farm, and in the 2 mute swans and the tufted duck (GISAID [] accession nos. EPI ISL 287907, EPI ISL 288409, EPI ISL 288410, and EPI ISL 288412), as described previously (4).
Database searches (GISAID and GenBank) showed that these viruses are highly similar to the HPAI H5N8 clade viruses, which were detected previously in wild birds at the Russia–Mongolia border in May 2016 (10), for the gene segments polymerase basic 1 (PB1), polymerase acidic (PA), HA, nucleoprotein (NP), matrix protein (MP), and nonstructural protein (NS) (Table). The polymerase basic 2 (PB2) and NA segments shared sequence similarity with Eurasian low pathogenicity avian influenza (LPAI) viruses.
Moreover, the N6 gene of the H5N6 viruses found in the Netherlands showed high homology to those detected in Greece in February and in Japan and Taiwan in November–December 2017.

Of note, the N6 segment of the virus in the Netherlands is closely related to, but distinct from, that of the H5N6 viruses detected in Greece, Japan, and Taiwan in 2017. Furthermore, the virus in the Netherlands has PB2 and PA segments that are distinct from those found in the viruses from Greece, Japan, and Taiwan (Figure 2). These results indicate that H5N6 virus in the Netherlands is a reassortant of HPAI H5N8 subtype that obtained novel PB2 and NA segments.

Finally, we analyzed the genome of the novel H5N6 virus for potential zoonotic signatures associated with increased human risk (Technical Appendix[PDF - 2.73 MB - 12 pages] Table 2). We found that the virus has a typical avian receptor specificity and identified no sequence signatures associated with increased airborne transmission.
In the MP and NS genes, we identified mutations that were associated with increased virulence, but similar mutations have been found in other H5 clade viruses. Our analysis demonstrated that the virus may have reduced sensitivity to treatment with the antiviral drug oseltamivir.


A novel reassortant HPAI H5N6 virus affected wild birds and commercial poultry in the Netherlands in December 2017. Phylogenetic analysis demonstrated that the virus is related to the HPAI H5N8 clade viruses but contains novel PB2 and NA segments derived from Eurasian LPAI viruses.
The N6 gene segment is related to that of HPAI H5N6 viruses found in Greece, Japan, and Taiwan, for which a common ancestor was estimated around November 2015. In addition, the H5N6 virus in the Netherlands differs from that in Greece by the PA and PB2 gene segments. This suggests that the H5N6 virus in the Netherlands did not result from continued circulation of the virus in Greece (or Europe) that was detected in February 2017 but likely represents a separate introduction related to wild bird migration in fall 2017.
The reassortment events may have occurred on breeding grounds in Siberia, where large numbers of wild birds congregate, and the virus may have spread by long-distance flights of infected migratory birds (6).

Phylogenetic analysis demonstrated that the virus is not related to the zoonotic Asian H5N6 strains that cause infections in humans. Furthermore, genetic analysis identified no sequence features related to increased human risk. There are no indications that mammals (such as humans) can be infected by the novel reassortant HPAI H5N6 viruses detected in the Netherlands, Greece, Japan, and Taiwan. We recommend further studies in mammals (ferrets or mice) to provide experimental data on the virulence for mammals.

Dr. Beerens is a senior scientist and head of the National Reference Laboratory for Avian Influenza and Newcastle Disease in the Netherlands. Her research interests focus on molecular virology, genetics, and virus evolution.
 For more on the growing diversity of these recently emerged HPAI H5N6 viruses you may wish to revisit:

Japan: Kagawa H5N6 Outbreak Genetically Distinct From Shimane Isolate
South Korea: Pathogenicity Testing Of Gochang Reassorted H5N6 Virus
OIE: Taiwan H5N6 Identified As Similar To New Reassortant Reported In Japan

No comments: