Abstract
Coronaviruses (CoV) are divided into the genera α-CoVs, β-CoVs, γ-CoVs and δ-CoVs. Of these, α-CoVs and β-CoVs are solely capable of causing infections in humans, resulting in mild to severe respiratory symptoms. Bats have been identified as natural reservoir hosts for CoVs belonging to these two genera. Consequently, research on bat populations, CoV prevalence in bats and genetic characterization of bat CoVs is of special interest to investigate the potential transmission risks. We present the genome sequence of a novel α-CoV strain detected in rectal swab samples of Miniopterus fuliginosus bats from a colony in the Wavul Galge cave (Koslanda, Sri Lanka). The novel strain is highly similar to Miniopterus bat coronavirus 1, an α-CoV located in the subgenus of Minunacoviruses. Phylogenetic reconstruction revealed a high identity of the novel strain to other α-CoVs derived from Miniopterus bats, while human-pathogenic α-CoV strains like HCoV-229E and HCoV-NL63 were more distantly related. Comparison with selected bat-related and human-pathogenic strains of the β-CoV genus showed low identities of ~40%. Analyses of the different genes on nucleotide and amino acid level revealed that the non-structural ORF1a/1b are more conserved among α-CoVs and β-CoVs, while there are higher variations in the structural proteins known to be important for host specificity. The novel strain was named batCoV/MinFul/2018/SriLanka and had a prevalence of 50% (66/130) in rectal swab samples and 58% (61/104) in feces samples that were collected from Miniopterus bats in Wavul Galge cave. Based on the differences between strain batCoV/MinFul/2018/SriLanka and human-pathogenic α-CoVs and β-CoVs, we conclude that there is a rather low transmission risk to humans. Further studies in the Wavul Galge cave and at other locations in Sri Lanka will give more detailed information about the prevalence of this virus.
Highlights
Coronaviruses (CoVs) are the members of the family Coronavirinae within the orderNidovirales, and they can cause respiratory diseases in animals and humans [1]
While γ-CoVs and δ-CoVs are probably derived from bird CoVs, α-CoVs and β-CoVs can be found in a variety of bat species, which are being discussed as their potential natural reservoir [5]
We were able to obtain the full genome of an α-CoV strain named batCoV/MinFul/2018/SriLanka from Miniopterus fuliginosus bats from Sri Lanka
Summary
Coronaviruses (CoVs) are the members of the family Coronavirinae within the order Nidovirales, and they can cause respiratory diseases in animals and humans [1]. While the ORF1a/1b-coding sequences (CDS) are generally considered as highly conserved gene sections since they need to maintain protein functionality, the structural proteins are rather susceptible to substitutions on gene and protein levels These variations, especially in the spike protein, can lead to differences in their infectivity and host specificity. While γ-CoVs and δ-CoVs are probably derived from bird CoVs, α-CoVs and β-CoVs can be found in a variety of bat species, which are being discussed as their potential natural reservoir [5] These two genera are prevalent in a wide range of other mammals (wildlife and domestic animals) and humans. A thorough genomic characterization and understanding of the genotypical and phenotypical differences between α-CoVs and β-CoVs can help to provide understanding of the human-pathogenic potential of different CoVs
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