The Asian HPAI H5N1 virus (clade 0) - which first appeared in Guangdong Province in the mid 1990s - has since evolved into dozens of clades and scores of genotypes - most of which have disappeared, supplanted by the generation of more `fit' viruses.
Whether through antigenic drift or reassortment with other circulating viruses (see graphic below), the H5N1 virus is constantly evolving. And this includes the creation of new subtypes, like H5N2, H5N6, and H5N8.
As a result, the H5N1 viruses that circulate in Egypt differ considerably from the ones found in Indonesia, or China, or Bangladesh. The most recent WHO report finds clade 18.104.22.168 viruses circulating in Egypt, clade 22.214.171.124c viruses in China, West Africa, and Southeast Asia, and clade 126.96.36.199a viruses in Bangladesh, Bhutan and India.
Within each of these clades (based on the HA gene), there can be multiple subtypes (HA paired with a different NA gene i.e. H5N2, H5N6, H5N8), and even dozens of genotypes (based on the makeup of each subtype's internal genes).
Differences in virulence and transmissibility exist between these clades, subclades, and genotypes which may help explain the difference in impacts we've seen over time, and around the world (see Differences In Virulence Between Closely Related H5N1 Strains).
Last March, in Sci Reports: Continual Antigenic Diversification Of HPAI H5N1 In China & Around the World, we looked at H5N1's evolution from 2004 to 2013 (prior to the emergence of H5N8 & H5N6).
Today we've a very long, detailed report in Emerging Microbes & Infections that describes the emergence of a new genotype of H5N1 clade 188.8.131.52a in ducks in Bangladesh in 2015. This new genotype contained five internal genes from LPAI Eurasian-lineage avian influenza A viruses, likely introduced by migratory birds.
Within a few months of its first detection, this new genotype had replaced the previously circulating H5N1 viruses in that region. I've only included a few excerpts from a much longer article. Follow the link to read it in its entirety.
Citation: Emerging Microbes & Infections (2017) 6, e72; doi:10.1038/emi.2017.60
Published online 9 August 2017
Role of domestic ducks in the emergence of a new genotype of highly pathogenic H5N1 avian influenza A viruses in Bangladesh
Subrata Barman1, Atanaska Marinova-Petkova1,*, M Kamrul Hasan2, Sharmin Akhtar2, Rabeh El-Shesheny1,3, Jasmine CM Turner1, John Franks1, David Walker1, Jon Seiler1, Kimberly Friedman1, Lisa Kercher1, Trushar Jeevan1, Daniel Darnell1, Ghazi Kayali4,5, Lisa Jones-Engel6, Pamela McKenzie1, Scott Krauss1, Richard J Webby1, Robert G Webster1 and Mohammed M Feeroz2
Correspondence: MM Feeroz, E-mail: email@example.com; RG Webster, E-mail: firstname.lastname@example.org
Highly pathogenic avian influenza H5N1 viruses were first isolated in Bangladesh in February 2007. Subsequently, clades 2.2.2, 184.108.40.206 and 220.127.116.11a were identified in Bangladesh, and our previous surveillance data revealed that by the end of 2014, the circulating viruses exclusively comprised clade 18.104.22.168a.
We recently determined the status of circulating avian influenza viruses in Bangladesh by conducting surveillance of live poultry markets and waterfowl in wetland areas from February 2015 through February 2016. Until April 2015, clade 22.214.171.124a persisted without any change in genotype.
However, in June 2015, we identified a new genotype of H5N1 viruses, clade 126.96.36.199a, which quickly became predominant. These newly emerged H5N1 viruses contained the hemagglutinin, neuraminidase and matrix genes of circulating 188.8.131.52a Bangladeshi H5N1 viruses and five other genes of low pathogenic Eurasian-lineage avian influenza A viruses.
Some of these internal genes were closely related to those of low pathogenic viruses isolated from ducks in free-range farms and wild birds in a wetland region of northeastern Bangladesh, where commercially raised domestic ducks have frequent contact with migratory birds.
These findings indicate that migratory birds of the Central Asian flyway and domestic ducks in the free-range farms in Tanguar haor-like wetlands played an important role in the emergence of this novel genotype of highly pathogenic H5N1 viruses.(SNIP)
Although HPAI H5N1 and LPAI H9N2 viruses cocirculate and coinfect birds in the LPMs in Bangladesh, they rarely produce reassortants. The reassortants that have been detected failed to become established and disappeared. In contrast, the LPAI viruses isolated from migratory waterfowl and domestic duck farms in the Tanguar haor do reassort with circulating HPAI H5N1 viruses. This has generated a new genotype of HPAI H5N1 viruses that are now dominant and represent the current threat to domestic poultry and humans in this region.
To date, there have been no reports of these newly emerged H5N1 viruses in humans. Continued surveillance of the LPMs and wetland areas in Bangladesh is necessary for pandemic preparedness and to mitigate overall public health concerns.(Continue . . . . . )
Aside from the important discovery of a new reassortant H5N1 virus that is now entrenched in Bangladesh, this is a reminder that the H5N1 threat - while recently overshadowed by H7N9 - hasn't gone away.
It is also further evidence of the impact of migratory birds on the evolution of HPAI avian flu viruses.A role that goes far beyond simply spreading HPAI viruses around the globe, but also includes delivering interchangeable genetic `building blocks' to areas where HPAI viruses are currently entrenched, aiding and abetting the creation of new genotypes.