In recent years, there has been growing concern over the H5N1 influenza virus. It was first identified in birds three decades ago and has now gradually found its way to humans. H5N1 is a strain of the influenza virus harbouring type 5 haemagglutinin (H5) and type 1 neuraminidase (N1) surface proteins, which help in viral entry and spread, respectively.
Researchers led by Kesavardhana Sannula, Assistant Professor in the Department of Biochemistry, Indian Institute of Science (IISc) have now discovered that the currently circulating 2.3.4.4b clade of H5N1 has specific mutations in its genome that increase its human adaptive potential. Clade represents a group of organisms having a common ancestor.
"The 2.3.4.4b clade has infected many mammalian species and is adapting to [non-human] mammals, which is a concern for human adaptation," says Kesavardhana. "The clade is panzootic, causing unprecedented mortality in birds and mammals, along with several sporadic human infections."
When the influenza virus enters a new organism, it can develop genetic mutations. This helps the virus adapt to the new host. The researchers were trying to decode whether the 2.3.4.4b clade was evolving to produce crucial adaptations in its proteins that allow it to infect humans. They also wanted to decipher which host animals can potentially accelerate this adaptation, giving the virus a leg up in scaling the evolutionary ladder.
Kesavardhana's team took a computational approach and analysed 7,000 protein sequences of 2.3.4.4b H5N1 found in birds, 820 sequences from non-human mammals, and 35,000 human H1N1 and H3N2 sequences, in order to identify which amino acids are under selection pressure – rapidly changing. They used multiple sequence alignment (a tool to identify similar regions in multiple proteins), constructed phylogenetic trees (which represent how species have diverged from their common ancestor over time) and annotated specific variations in all the proteins of H5N1 infecting non-human mammals and humans.
The team found an increased number of mutations specifically in the viral polymerase complex (PA, PB2), nucleoproteins, and haemagglutinin (HA) proteins. Once they identified these mutations, the team classified them depending on whether the mutations can help the virus spread from non-human mammals to humans (adaptive) or simply survive in the non-human host (barrier). Finally, they developed a simple mathematical approach and estimated the human adaptive potential for the 2.3.4.4b clade.
The team was also able to pinpoint animals that would be likely to harbour virus strains with the highest human adaptive potential. Interestingly, viruses that can adapt to fox hosts seemed to have higher adaptive potential than cattle-adapted strains. "It is very surprising," Kesavardhana says.
Based on their findings, the researchers suggest that enhanced and proactive surveillance measures need to be implemented.
"This clade is acquiring the same key mutations that pandemic human influenza strains possess, which could be a growing risk," says Ranjana Nataraj, Project Associate at the Department of Biochemistry and the study's first author.
