Novel coronavirus identified in Swedish bank voles

By Shanet Susan AlexReviewed by Aimee MolineuxMar 1 2022

In a recent study posted to the bioRxiv* preprint server, researchers discovered a new coronavirus (CoV), named Grimso virus, in Swedish bank voles (Myodes glareolus) using samples collected between 2015 and 2017.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Myodes glareolus, or bank vole, is a commonly found rodent species in Europe. Moreover, they are well-known hosts for numerous zoonotic pathogens like Francisella tularensis and Puumala orthohantavirus. Various BetaCoV and AlphaCoV from Myodes glareolus in the United Kingdom (UK), Poland, France, and Germany have been identified during previous investigations. Hence, the Myodes glareolus species is probably a potent reservoir for the CoVs.

About the study

In the current research, the scientists conducted a virome investigation of Swedish bank voles collected in Grimsö, Sweden. The team reported two genome sequences, Grimso215 and Grimso2306, of a novel BetaCoV named the Grimso virus, described their evolutionary association with other rodent CoVs, and also their prevalence over three years.

Samples procured from Myodes glareolus between 2015 and 2017 were screened for CoVs employing an in-house polymerase chain reaction (PCR) test and a published pan-CoV reverse transcriptase-PCR (RT-PCR) test. The partial spike (S) gene sequences were obtained from the samples by Sanger sequencing. The partial S gene sequences were then subjected to pairwise genetic investigations. The partial Grimso virus S gene sequences were further analyzed using Bayesian phylogeny. The genetic analyses were conducted to determine the evolutionary relationship of the Grimso virus with other CoVs found in rodents.

Findings

The results show that of the samples collected from 266 Myodes glareolus, nine were positive for a novel CoV according to the in-house PCR test. Of the nine Grimso virus-positive samples, the partial S gene sequences were collected from seven samples.

The RNA sequencing of Grimso2306 and Grimso215 samples revealed a near-complete CoV sequence and a full-length CoV sequence, respectively. The Grimso virus genome encodes for membrane protein (M), nucleocapsid protein (N), envelop protein (E), S protein, and hemagglutinin esterase (HE). The Grimso215 and Grimso2305 strains were related to a known rodent BetaCoV diversity, and established a unique lineage within the subgenus Embecovirus, according to phylogenetic studies based on the N, S, and ORF1b gene sequences.

The pairwise sequence identity of the Grimso215 strain with other rodent CoVs varied from 44−67% and 55−79% at the amino acid and nucleotide levels, respectively, confirming Grimso virus was unique and divergent from the previously characterized rodent CoVs. The Grimso2306 and Grimso215 genomes had 95.6% sequence similarity at the nucleotide level in 1,338 sites. In addition, the Grimso virus was hypothesized to be frequently found in bank voles based on the recurrent detection in three years and an overall prevalence of 3.4%.

Phylogenetic investigations indicate the Myodes glareolus harbor around three virus species from BetaCoV and AlphaCoV genera. In particular, four viruses extracted from the bank voles in Poland, the UK, and Germany were closely associated with Lucheng Rn rat CoV (LRNV) in the AlphaCoV genera. Further, the phylogenetic analyses also identified two different Embecoviruses linked with bank voles.

Conclusions

The study findings demonstrated a novel and highly diverse Embecovirus, named the Grimso virus, in Swedish Myodes glareolus.  The pairwise genetic examinations conducted in the study revealed that the partial Grimso2306 and Grimso215 sequences shared 94-100% and 98-100% sequence identity at the amino acid and nucleotide levels, respectively. Interestingly, the Grimso virus sequences exhibited less than 50% and less than 60% sequence similarity with other rodent BetaCoV at the amino acid and nucleotide levels, respectively.

Further, the Grimso virus sequences form a unique monophyletic group that clusters with other rodent-borne Embecoviruses with robust statistical support.

Collectively, the findings indicate that various distinct Grimso-like viruses co-circulate in the bank vole species, albeit additional studies are required for an in-depth understanding of their transmission ecology. In addition, the study revealed that closely similar CoVs are widely spread across Europe and solely associated with Myodes glareolus and other vole species, suggesting bank voles are probably natural hosts for the Grimso virus. This inference further indicates a long-standing host-virus relationship.

The present findings highlight the significance of long-term surveillance of CoVs in wild rodents to obtain an in-depth understanding of the ecology of CoVs in reservoir populations. Nonetheless, the Grimso virus' potential impact on animal and human health remains unknown.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources