NEW YORK – An international team led by investigators in Hong Kong has used genomic epidemiology to explore the origins and spread of H5N1 influenza A bird flu strains classified as "highly pathogenic avian influenza" (HPAI), which has become particularly widespread and deadly for global bird populations over the past two years.
"Since November 2021, this H5N1 virus has caused unprecedented outbreaks in diverse wild bird species across five continents and a significant rise in incidental infections in wild carnivores, mink farms, and marine mammals," senior and corresponding author Vijaykrishna Dhanasekaran, head of the pathogen lab at the University of Hong Kong's School of Public Health, and his colleagues wrote.
As they reported in Nature on Wednesday, the researchers brought together HPAI outbreak data from the United Nations Food and Agriculture Organization and the World Organization for Animal Health, focusing on isolates from a hemagglutinin (HA) subtype known as the 22.214.171.124b clade. The data spanned almost two decades since 2005, highlighting shifts and recombination events involving bird flu strains from distinct N1 and N8 neuraminidase (NA) subtypes.
"A better understanding of the ecological properties that enhance and sustain transmission in wild birds and the consequences of poultry vaccination with variable uptake will be crucial to mitigate future HPAI outbreaks, which pose unpredictable epizootic, zoonotic, and pandemic threats," the authors wrote, noting that more than 69 million domestic birds were culled due to the recent bird flu outbreak from January to June of 2022 alone.
Along with whole-genome sequencing data for more than 10,000 HPAI isolates found in the Global Initiative on Sharing All Influenza Data (GISAID) database, representing strains collected in Asia, Europe, Africa, and North America from 2005 to 2022, the available epidemiological, spatial, and phylogenetic data made it possible for the team to assess the genetic makeup of virus strains contributing to local outbreaks, resurgent events, or more widespread outbreaks over time.
In particular, the team found that clade 126.96.36.199b HPAI H5N1 viruses that were behind the rampant bird deaths reported since late 2021 arose in Europe through reassortment between H5N1 viruses in wild birds and less pathogenic wild and domestic bird flu strains, leading to an outbreak strain that has largely replaced H5N8 viruses from clade 188.8.131.52b.
"These results highlight a shift in the HPAI H5 epicenter beyond Asia and indicate that increasing persistence of HPAI H5 in wild birds is facilitating geographic and host range expansion, accelerating dispersion velocity and increasing reassortment potential," the authors reported.
Prior to that, the team explained, distinct outbreak strains turned up in different parts of the world, including an outbreak from 2016 to 2017 that involved HPAI H5 viruses endemic to Asia and an outbreak originating in Africa in 2020/2021 that involved an HA- and receptor binding site-mutated version of H5N8 from the 184.108.40.206b clade.
"As earlier outbreaks of H5N1 and H5N8 were caused by more stable genomic constellations, these recent changes reflect adaptation across the domestic bird-wild bird interface," the authors reported, noting that "[e]limination strategies in domestic birds therefore remain a high priority to limit future epizootics."
They added that genomic surveillance around the world is currently "limited and biased across time, geography, and host species," and suggested that "it is necessary to enhance global surveillance and improve multifaceted mitigation strategies for outbreak prevention and response."