Standing HA phenotypic breadth shapes H5N1 cross-host potential

Area of Science:

• Virology
• Evolutionary Biology
• Genomics

Background:

• Linking viral genetic variation to functional traits is crucial for understanding virus emergence and cross-host transmission.
• Highly pathogenic avian influenza A virus (H5N1) clade 2.3.4.4b has shown extensive circulation and adaptation in North America.
• The hemagglutinin (HA) protein is a key determinant of influenza virus host tropism and receptor binding.

Purpose of the Study:

• To investigate the evolution of predicted hemagglutinin (HA) phenotypic traits in North American H5N1 clade 2.3.4.4b viruses.
• To understand how viral populations adapt and diversify during circulation in different hosts, specifically avian and bovine.
• To develop a framework for identifying H5N1 variants with cross-host potential for enhanced surveillance.

Main Methods:

• Reconstruction of predicted HA phenotypic traits across approximately 13,000 H5N1 clade 2.3.4.4b virus genomes.
• Analysis of viral population diversity and selective pressures in avian and cattle hosts.
• Bioinformatic prediction of protein properties from viral sequence data.

Main Results:

• Widespread avian influenza circulation in North America led to broad HA phenotypic diversity, subsequently refined by selective sweeps in avian hosts.
• Following introduction into dairy cattle, H5N1 viruses exhibited renewed HA diversification, including increased ability to bind to α2,6-linked sialosides.
• This diversification occurred despite high conservation within the HA receptor-binding domain, indicating adaptation from existing viral population breadth.

Conclusions:

• Cattle-associated H5N1 HA phenotypes can emerge from standing variation within circulating viral populations and continue to diversify.
• Viral adaptation in new hosts like cattle may not follow a simple, stepwise path of canonical receptor-binding substitutions.
• The developed framework offers a scalable strategy for prioritizing H5N1 variants with cross-host-relevant features for targeted surveillance and research.