New research by the University of Sydney offers important insights into how and when new coronavirus variants arise in bats.
Bats are beneficial to our ecosystems and economy but, as habitat destruction and environmental stressors put them in closer proximity to humans, disease risks can emerge. The research, published in Nature Communications today, offers an approach to anticipating the emergence of coronaviruses. It found young bats are infected more frequently and could be a key source of viral spillover into other species. The study also reveals the dynamics of coronaviruses circulating in Australian bats, which pose no known risk to humans.
Endemic in bat populations, most coronaviruses never infect humans. When they do, as with the SARS, COVID-19 and MERS outbreaks, they typically spill over from bats via a bridging animal host.
"Coronaviruses tend not to be of major concern to bats," said Dr Alison Peel from the University's School of Veterinary Science , who led the study. "But they can behave differently if they spill over to new species."
In one of the most comprehensive single studies of its type, the researchers collected more than 2,500 faecal samples, via which bats shed coronaviruses, over three years. Samples were taken from black flying foxes and grey-headed flying foxes at five roost sites across Australia's eastern seaboard.
Dr Alison Peel holds a black flying fox in Queensland in preparation for sampling. Credit: Kathleen Flynn
Viral testing of the samples showed coronaviruses were most prevalent in young bats between March and July, when they were weaning and approaching maturity. This was consistent across the three-year study. Particularly notable was the high proportion of bats infected with multiple coronaviruses at once.
"We were surprised by that high rate of co-infection among juveniles and subadults," Dr Peel said. "Co-infection presents the opportunity for a single cell to become infected with multiple viruses, an important natural precursor to the generation of new strains."
The six coronaviruses detected in the study were nobecoviruses, a subclass which does not jump to humans. Three of these were new. They were useful to analyse because they pose minimal risk to people but are the evolutionary cousins of sarbecoviruses, so-called SARS-like viruses which are more prone to spill across to other species. Understanding the evolution of nobecoviruses offers parallel insights into the evolution of more dangerous coronaviruses.
"We safely tracked how and when coronaviruses circulated naturally in bat populations. Using genomics to track infections to individual animals," Dr John-Sebastian Eden , a study co-author from the Westmead Insitute for Medical Research and the University's Faculty of Medicine and Health .
"The results offer a model for scientists looking to understand coronavirus emergence and future risks in bat populations around the world. By focusing on co-infections in young bats during certain periods, researchers might better predict the natural evolution and emergence of riskier coronaviruses before they pose a risk to human health."
Dr Peel said more research is needed to understand why young bats are more susceptible to infection and co-infection.
"It could be the result of newly weaned animals whose immune systems are still developing or the stress faced by teenage bats looking for a mate for the first time," she said.
The changing environment could also be a factor.
"We know from previous research on other viruses that habitat loss caused by encroaching human populations and food shortages can create stress in bats that weakens immunity and makes them susceptible to infections. It will be important to find out if that's also the case for coronaviruses."
Dr Peel and Dr Eden's research began in 2020, as the COVID-19 pandemic took hold. It built on earlier research into the spread of Hendra virus, which also originates in bats.
"It's rare to see this scale and depth of data in virological research, even among human viruses," said Dr Peel. "The gathering of samples from both individual bats and beneath roosts, and the tracking of individual strains across multiple sites and years, provides a strong foundation for ongoing research into the role of environmental stress on coronavirus emergence."
Research
Alison J. Peel, et al., 'Synchronized seasonal excretion of multiple coronaviruses coincides with high rates of coinfection in immature bats'. (Nature Communications) DOI: 10.1038/s41467-025-61521-7
Funding
The project was supported by the US National Science Foundation, and the US Defence Advanced Research Projects Agency's PREEMPT program Cooperative Agreement. Dr Peel was supported by an Australian Research Council DECRA fellowship and a University of Sydney Horizons Fellowship.
