Mike Coston is the Owner/Editor of Avian Flu Diary

Just over 5 months ago we first learned of a new reassortant avian flu subtype called H5N6 which had infected local poultry – and killed a 49 year old man – in Nanchong City (see Sichuan China: 1st Known Human Infection With H5N6 Avian Flu). Although Low Pathogenic H5N6 had been identified previously in wild birds  in Taiwan, Germany, Sweden and the United States this new strain was classified as highly pathogenic.

And like the H5N8 virus which emerged last January in South Korea, this new virus appeared to be a reassortant of the H5N1 avian flu virus.

Flu Viruses are made up of 8 gene segments, and when two flu viruses infect the same cell in a host simultaneously, they can sometimes swap genetic material and create a new hybrid  or reassortant virus. This is how novel subtypes arise and how some pandemic viruses have been created in the past.


Most reassortant viruses are evolutionary failures, but every once in awhile a more `fit’ virus emerges.

After making an initial appearance in south central China last spring, the reassorted H5N6 virus laid low over the summer, but over the past 30 days has made appearances both in Vietnam and in China.

Public domain image/Ben Rudiak-Gould
Public domain image/Ben Rudiak-Gould

With outbreaks showing up over the past 30 days spread across more than 2000 miles of eastern Asia, concerns that we could see more outbreaks this fall and winter (along with the expected return of H7N9 and H5N1) run pretty high.  And of course, all of these viruses continue to reassort and evolve into new clades and occasionally new subtypes.

Last year, in  EID Journal: Predicting Hotspots for Influenza Virus Reassortment, we looked at research that ranked eastern China as one of the globe’s top breeding grounds for new flu strains.

And indeed, over the past two years we’ve seen the emergence of no less than four new subtypes (H7N9, H10N8, H5N8, H5N6) from this region that pose significant risks to poultry or human health.

While the assumption has been that this new H5N6 virus was a reassortant of the existing H5N1 virus, we’ve a whole-genome sequence analysis published this week that provides new insight into this subtype’s parentage.  The virus is apparently 7 parts avian H5N1, and 1 part avianH6N6, as described below:

Phylogenetic analyses showed that the NA gene belonged to the same clade with H6N6 viruses currently circulating in China, such as A/duck/Guangxi/Gxd-7/2011 t (up to 98% nucleotide identity with the reference strains), whereas the other seven genes were found to be more similar to those of eastern Asian H5N1 AIV strains (95 to 99% nucleotide identity)..

The complete analysis is available as an open-access report in Genome Announcements at the link below.

Whole-Genome Sequence of a Reassortant H5N6 Avian Influenza Virus Isolated from a Live Poultry Market in China, 2013

Xian QiLunbiao CuiHuiyan YuYiyue GeFengyang Tang


An avian influenza virus, A/environment/Zhenjiang/C13/2013(H5N6), was isolated from a live poultry market in eastern China. Phylogenetic analysis showed that the isolate was a novel reassortant virus with a neuraminidase (NA) gene from H6N6 viruses and the other seven genes from H5N1 viruses, which may pose a potential threat to human and animal health.

(Continue . . . )

Influenza reassortments happen all the time and mostly outside the view of scientists. Most will end up as viral flashes in the pan, unable to compete with more biologically fit flu viruses, and will quickly disappear into the evolutionary dustbin.

But with so many new subtypes now in circulation – and ample opportunities to reassort in birds, pigs, humans and other mammals – the potential exists for the offspring of one of these viral trysts to hit the reassortment jackpot, and emerge as the next pandemic virus.

See the Original post HERE