Influenza virus provides first evidence of bats’ potential as an intermediate host

Zoonotic diseases occur when harmful germs in an animal spread to people. Many examples of these exist throughout history, including the original SARS-CoV-1 outbreak in East Asia in 2002. In that outbreak, bats were the source of the zoonotic disease. Since then, researchers have found many more viruses within bat populations, though bat influenza viruses appear to have a distinct evolutionary history from influenza viruses circulating in birds or humans. 

In a multinational collaboration, St. Jude scientists recently found that at least one influenza strain isolated from bats resembles a more recent crossover event, with characteristics of both mammalian and avian viruses. The findings, published recently in Nature Communications, suggest bats may be an intermediate influenza host, posing a zoonotic infection risk to humans.

“We showed bats are a real source of viruses that do have zoonotic threat to humans,” said senior co-corresponding author Richard Webby, PhD, St. Jude Department of Host-Microbe Interactions. “We’ve seen that time and time again, and though we didn’t think bats were a big player in the circle of flu infections across species, these findings suggest maybe they are.”

Influenza viruses use two proteins to enter and exit cells: hemagglutinin (H) and neuraminidase (N), respectively. There are 18 H subtypes and 11 N subtypes, with specific combinations associated with a primary host, such as H1N1, which primarily infects mammals. Most bat flu viruses are H17N10 or H18N11, evolutionarily distinct from those in other mammals or birds. 

The study found an influenza virus taken from an Egyptian bat (Rousettus aegyptiacus) in 2017 appeared to have avian flu traits. Prior research with the new Egyptian virus showed it was H9N2, suggesting a novel crossover event between birds and bats. 

“This virus looked like a more recent transmission of a virus typically found in chickens,” Webby said. “It was an unusual finding in that it wasn’t one of these typical bat flu viruses. It was an avian flu virus that jumped back into bats, and then it clearly had been in bats for a bit of time because it had picked up a number of mutations.”

Those mutations motivated further investigation to determine if the virus posed any threat to other mammals, such as humans.

A new intermediate host for zoonotic influenza virus

Influenza virus did not originally evolve to infect mammals. Instead, influenza virus’ natural reservoir is waterfowl. Most avian-adapted viruses have attachment proteins that bind to molecules specific to bird cells, as opposed to their analogs in humans. To reach humans, avian influenza must first enter an intermediate host with both avian and mammalian molecules for the attachment protein to bind; then, the virus can recombine into novel H and N combinations with mutations that enable binding to molecules from both hosts. 

Swine contain both these features, making them standard intermediate hosts for flu viruses between birds and humans. Findings from the study showed the bat-derived virus contained features of both mammalian and avian-adapted viruses despite only having one of the features typically thought required to drive this evolution (the mammalian molecules that bind the attachment protein).

“We found bats are another potential intermediate host where a virus from the source of most Influenza A virus, birds, can occur,” Webby said. “Upon avian virus replication, bats can at least make the virus lean towards being more mammalian-like.”

Many biological characteristics of the virus appeared mammalian-like. It showed greater resistance to acidic conditions and an ability to replicate in human lung cells and mouse lungs. In addition, the virus could not infect mallard duck cells, a significant reservoir for H9N2 viruses. It also replicated in a better model for human respiratory disease, ferrets, and could transfer using both direct contact and airborne transmission between ferrets.

“The ferret-to-ferret transmission is probably the most concerning element we found,” Webby said. “It is a property usually associated with mammalian-adapted and, particularly, human-adapted viruses. For the few H9N2 viruses previously identified that could infect mammals, they required direct contact.”

No clear threat to humans yet

While some of the findings are concerning, the virus also had some more avian-like traits, indicating that it is not ready for a jump to humans. The viral replication in the human lung was more similar to an avian virus, only replicating well in a rare and difficult-to-access cell population. 

“The upper respiratory tract in humans doesn’t harbor many of the receptors that avian viruses like, but the lower respiratory tract does,” Webby said. “In terms of replication in these tissues, the virus does seem more avian-like, which is good because it means they are less likely to infect humans well.”

The study is a first step in assessing the novel influenza strain. Without knowing how widespread the strain is in bats, any potential crossover remains difficult to predict. With the number of mammalian adaptations, the new bat virus represents a higher risk than a normal H9N2 virus in birds. However, further exploration will enable scientists to better understand what kind of threat, if any, it may pose. 

The virus’s very existence, however, indicates a more general principle — we do not currently know every potential species from which a zoonotic influenza virus may emerge.

“Between this virus and the ongoing H5 pandemic virus [bird flu], influenza is showing us that there may be a much wider array of hosts than we thought,” Webby said. “I think we’re now starting to realize that the spectrum of flu hosts is wider and does include bats, and these flu viruses have some mammalian properties. But they’re clearly not all the way there yet.”