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Sequencing Study Uncovers MERS-Related Coronavirus in Swiss Bats

NEW YORK – A team from the University of Zurich and the Bat Foundation Switzerland used a metagenomic sequencing-based screening strategy to identify dozens of DNA and RNA viruses in stationary and migratory bat species in Switzerland, including a coronavirus related to the MERS-CoV behind Middle East respiratory syndrome.

For a paper published in PLOS One on Wednesday, the researchers did DNA sequencing and RNA sequencing on fecal, stool, or organ tissue samples from some 7,000 bats spanning 18 species found at sites in Switzerland over several years. By comparing sequences in these samples to those from available databases, they tracked down representatives from more than three dozen viral families — a set that contained viruses in 16 viral families linked to infections in other vertebrate species.

In particular, the team noted, metagenomic sequencing on stool samples collected at one of the Vespertilio murinus bat colonies considered led to a nearly complete genome sequence for a coronavirus that was most closely related to MERS-CoV. Even so, it remains to be seen whether this virus can jump to other species, as well as the possible consequences of such infection.

"It will be interesting to study the zoonotic potential of this bat betacoronavirus and to monitor the colony in which it was detected over time as this would allow [us] to assess the accumulation of mutations in the COV genome in a natural reservoir host," co-senior and co-corresponding author Jakub Kubacki, a researcher at the University of Zurich's Institute of Virology, and his colleagues wrote.

Using pooled metagenomic DNA sequencing and RNA-seq, the researchers searched for recognizable viral sequences in fresh fecal or organ tissue samples collected from healthy living, diseased, or deceased bats at colonies across Switzerland from 2015 to 2020. The bats considered came from 14 species native to Switzerland and four migratory species.

With these sequences, the team got a look at the viruses found in Swiss bats, in general, as well as the virome features that differed between bats from different sites, species, sample types, and so on. While the majority of the vertebrate-related viral sequences came from the Circoviridae family, for example, the bats tested also carried viruses from Genomoviridae, Coronaviridae, and Adenoviridae families, along with viral families previously reported in insect, plant, or fungal hosts.

In an email, Kubacki called next-generation sequencing, or NGS, "ideal to study the so-called virome, the entirety of viruses present in a specific environment" and noted that the University of Zurich "is the first Swiss veterinary diagnostic laboratory to offer NGS for diagnostic purposes, particularly for unknown cause of diseases, herd screening, and monitoring or discovering new viruses in environmental samples."

"Metagenomic analysis of ground stool samples of bat colonies represents an ideal noninvasive high-throughput method to monitor the complexity of the viral genome diversity," he and his co-authors reasoned. "It allows also to detect viruses with zoonotic potential and to assess the potential risk for their transmission to other species including humans."

The team's analyses highlighted sequences corresponding to 39 viral families, including coronaviruses, adenoviruses, hepeviruses, rotaviruses, and parvoviruses. The collection included sequences that lined up with 16 viral families previously found in other vertebrate hosts, hinting at the zoonotic potential of the bat-borne viruses.

"Human interaction with wildlife is one of the major contributors to zoonotic spillover and this impact should be reassessed," the authors wrote, noting that the "first assessment of the virome of Swiss bats forms a platform for future in-depth studies to investigate changes in virus prevalence, virus biology, virus-host interaction, and virus emergence."