a new study led by researchers from Uppsala University-Sweden along with scientists from the University of Oxford-UK, University of Sydney-Australia and the International Livestock Research Institute-Kenya has discovered a new strain of fast evolving betacoronaviruses that can be a threat to humans should it acquire the relevant mutations to jump to humans or participates in a recombinant event with the hundreds of SARS-CoV-2 coronavirus variants currently circulating around the world.
The new betacoronavirus currently being temporarily called the Grimso virus as it has been found in a type of rodents found not only in Sweden but also other parts of Europe known as bank voles (Myodes glareolus).
The study findings were published in the peer reviewed journal: Viruses.
Rodents are the primordial hosts of CoVs, and rodent CoVs constitute at least two subgenera, Luchacovirus and Embecovirus from genera Alphacoronavirus and Betacoronavirus, respectively [14,15]. In this study, we have discovered a highly divergent betacoronavirus (Grimso virus) in the Swedish bank voles.
The Grimso virus is highly divergent and genetically distinct from earlier described rodent CoVs based on the RNA-sequencing results, which also explains that we failed to detect any CoVs by using a published pan-coronavirus RT-PCR. By using the specific primers targeted to the spike gene, we have discovered nine samples which were positive in the PCR screening, with a continuous positivity for three years, which are 2/48 in 2015, 1/61 in 2016, and 6/157 in 2017.
We recovered two genome sequences from two strains of Grismo virus. The genomes of strains Grimso215 and Grimso2306 shared 95.6% sequence identity at the nucleotide level, with 1338 site differences.
This divergence is notably higher than the expected differences based on a typical substitution rate for coronaviruses of 0.001 substitutions per site per year [16,17], which under Poisson distribution predicts an accumulation of 61–121 substitutions over three years.
This observation suggests that either multiple strains of Grimso-like viruses are co-circulating in bank voles in Grimsö or that these viruses are transmitted regularly to bank voles from other species. One could also contemplate that the observed divergence could be associated with the temporal fluctuations in bank vole population density, leaving room for an increased viral transmission in a cyclic peak preceded by population turnover, similarly as previously described for Puumla Hantavirus dynamics in bank voles .
Nevertheless, with a prevalence of around 3.4% (9/266), we hypothesize that Swedish bank voles are competent hosts for the Grimso virus.
The wild animals provide pools of divergent virus species for interspecies transmission. The studies on the discovery of animal CoVs have been especially important since the emergence of human coronaviruses. The hidden diversity of CoVs has been explored in at least 37 rodent species distributed in Asia and Europe [3,4,15,19,20,21].
These studies point out that rodent CoVs have undergone frequent recombination and cross-species transmission events [15,20]. Previous studies found distinct CoVs in bank voles based on the partial sequences of the RdRp gene in the UK, Poland, Germany, and France [3,4].
Our phylogenetic analyses based on complete sequences of ORF1b, S, and N genes, as well as a partial RdRp gene, all suggested that bank voles carry one more divergent CoV, Grimso virus. Together, these observations suggest a relatively broad geographic distribution of CoVs in bank voles in Europe, which is indicative of possible long-term host–virus association.
Furthermore, as coronaviruses closely related to the Grimso virus have been detected in bank voles elsewhere in Europe, it further supports that this divergent coronavirus infects and circulates in Swedish bank voles.
To understand the zoonotic risks of Grismo virus, we analyzed the protein domain of the spike protein and hemagglutinin esterase. Due to the high divergence and the lack of isolated live virus, we could not yet identify the host receptor usage for this novel rodent CoV. However, we cannot neglect the zoonotic potential of Grimso virus to livestock or humans.
Together with mapping and continuous monitoring of the Grimso virus, further studies will aim to isolate the virus and assess the pathogenic profile.