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Corona Viruses and Bats Have Been Evolving Together for Millions of Years

Different groups of bats have their own unique strains of corona virus. Bats do a lot of good for the world--they pollinate plants, they eat disease-carrying insects, and they help disperse seeds that help with the regeneration of tropical forest trees. Bats and a range of other mammal groups are also natural carriers of corona viruses. To better understand this very diverse family of viruses, which includes the specific corona virus behind COVID-19, scientists compared the different kinds of corona viruses living in 36 bat species from the western Indian Ocean and nearby areas of Africa. They found that different groups of bats at the genus, and in some cases family, level had their own unique strains of corona virus, revealing that bats and corona viruses have been evolving together for millions of years. "We found that there's a deep evolutionary history between bats and corona viruses," says Steve Goodman, PhD, MacArthur Field Biologist at Chicago's Field Museum and an author of a paper just published in Scientific Reports detailing the discovery. "Developing a better understanding of how corona viruses evolved can help us build public health programs in the future." The study was led by Université de La Réunion scientists Léa Joffrin, PhD, and Camille Lebarbenchon, PhD, who conducted the genetic analyses in the laboratory of "Processus Infectieux en Milieu Insulaire Tropical (PIMIT)" on Réunion Island, focusing on emerging infectious diseases on islands in the western Indian Ocean. The open-access Scientific Reports article was published online on April 23, 2020, and is titled “Bat Coronavirus Phylogeography in the Western Indian Ocean.” Many people use "corona virus" as a synonym for "COVID-19," the kind of corona virus causing the current pandemic. However, there are a vast number of different types of corona viruses, potentially as many as there are different bat species, and most of them are not known to be transferred to humans and pose no known threat. The corona viruses carried by the bats studied in this paper are different from the one behind COVID-19, but by learning about corona viruses in bats in general, the researchers believe we can better understand the virus affecting us today.

STUDY SEEKS TO PROVIDE SUPPORT FOR BETTER UNDERSTANDING OF VIRUS TRANSFER TO HUMANS

All animals have viruses that live inside them, and bats, as well as a range of other mammal groups, happen to be natural carriers of corona viruses. These corona viruses don't appear to be harmful to the bats, but there's potential for them to be dangerous to other animals if the viruses have opportunities to jump between species. This study examines the genetic relationships between different strains of corona viruses and the animals they live in, which sets the stage for a better understanding of the transfer of viruses from animals to humans.

SAMPLING BATS FOR CORONA VIRUSES

Dr. Goodman, who has been based on Madagascar for several decades, and his colleagues took swab samples and, in some cases, blood samples, from more than a thousand bats representing 36 species found on islands in the western Indian Ocean and coastal areas of the African nation of Mozambique. Eight percent of the bats they sampled were carrying a coronavirus.

"This is a very rough estimate of the proportion of infected bats. There is increasing evidence for seasonal variation in the circulation of these viruses in bats, suggesting that this number may significantly vary according to the time of the year," says Camille Lebarbenchon, PhD, a disease ecologist at the Université de La Réunion.

GENETIC ANALYSES OF CORONA VIRUSES FOUND IN SAMPLED BATS

The researchers ran genetic analyses of the corona viruses present in these bats. By comparing the corona viruses isolated and sequenced in the context of this study with ones from other animals including dolphins, alpacas, and humans, the scientists were able to build a giant corona virus family tree. This family tree shows how the different kinds of corona virus are related to each other.

"We found that, for the most part, each of the different genera of families of bats for which corona virus sequences were available had their own strains," says Dr. Goodman.

"Moreover, based on the evolutionary history of the different bat groups, it is clear that there is a deep co-existence between bats (at the level of genus and family) and their associated corona viruses."
For example, fruit bats of the family Pteropodidae from different continents and islands formed a cluster in their tree and were genetically different from the coronavirus strains of other groups of bats found in the same geographical zones.

INTER-SPECIES SPREAD OF CORONA STRAINS AMONG BATS IS VERY RARE

The team found that, in rare cases, bats of different families, genera, and species that live in the same caves and have closely spaced day roost sites shared the same strain of corona virus. But in this study, the transmission between species is the exception, not the rule.

"It is quite reassuring that the transmission of corona virus in the region between two bat species seems to be very rare, given the high diversity of bat corona viruses. Next, we need to understand environmental, biological, and molecular factors leading to these rare shifts" says Léa Joffrin, PhD, a disease ecologist who worked on bat corona virus during her PhD at the Université de La Réunion.

UNDERSTANDING EVOLUTION OF DIFFERENT CORONA STRAINS COULD BE KEY TO PREVENTING FUTURE CORONA OUTBREAKS

Learning how different strains of corona virus evolved could be key for preventing future corona virus outbreaks.

"Before you can actually figure out programs for public health and try to deal with the possible shift of certain diseases to humans, or from humans to animals, you have to know what's out there. This is kind of the blueprint," says Dr. Goodman.

SEROLOGY TARGETING DIFFERENT CORONA STRAINS

Co-author Patrick Mavingui, PhD, a microbial ecologist and Head of the PIMIT Laboratory adds, "The development of serological methods targeting corona virus strains circulating in the Indian Ocean will help show whether there have already been discrete passages in human populations, and their interaction with the hosts will allow a better understanding of the emergence risk."

IMPORTANCE OF MUSEUM COLLECTIONS

The study also highlights the importance of museum collections, says Dr. Goodman. The researchers used, in part, bat specimens housed in the Field Museum, to confirm the identities of the animals employed in this study. These voucher specimens helped them confidently say which bats from which geographical regions, hosted the different strains of corona viruses.

HELP ALSO FROM GENETIC DATABASES

The research also drew from genetic databases like GenBank. "This information is important for public health, and the point of departure is closely linked to museum specimens," says Dr. Goodman. "We're able to use museum material to study the evolution of a group of viruses and its potential applications across wildlife in the world."

BATS VERY IMPORTANT FOR ECOSYSTEM FUNCTIONING

Dr. Goodman also notes that, despite the fact that bats carry corona viruses, we shouldn't respond by harming or culling of bats in the name of public health.

"There's abundant evidence that bats are important for ecosystem functioning, whether it be for the pollination of flowers, dispersal of fruits, or the consumption of insects, particularly insects that are responsible for transmission of different diseases to humans," he says.

"The good they do for us outweighs any potential negatives."

STUDY COLLABORATORS

This study was contributed to by researchers from the PIMIT laboratory (Université de La Réunion/INSERM/CNRS/IRD), Association Vahatra, the Field Museum, Eduardo Mondlane University, University of Kwa-Zulu Natal, the National Parks and Conservation Service of Mauritius, the Seychelles Ministry of Health, and Instituto Nacional de Saúde.

[Press release] [Scientific Reports article]