A new clade 2.3.4.4b H5N1 highly pathogenic avian influenza genotype detected in Europe in 2021

Despite their widespread distribution, only a single genotype variant of clade 2.3.4.4b H5N1 influenza viruses has been found so far in Europe. Here, we report the detection of a new highly pathogenic avian influenza H5N1 genotype in geese and ducks from a backyard farm in the Czech Republic. Phylogenetic analysis revealed that the Czech H5N1 virus retained the A/Eurasian_Wigeon/Netherlands/1/2020-like backbone with an altered PB2 segment obtained from co-circulating low-pathogenic avian influenza viruses.

Automated summary

A new highly pathogenic avian influenza H5N1 genotype was detected in geese and ducks from a backyard farm in the Czech Republic. The Czech H5N1 virus retained the A/Eurasian_Wigeon/Netherlands/1/2020-like backbone but had an altered PB2 segment obtained from co-circulating low-pathogenic avian influenza viruses.