Full Genome of batCoV/MinFul/2018/SriLanka, a Novel Alpha-Coronavirus Detected in Miniopterus fuliginosus, Sri Lanka

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.

Keywords: Miniopterus fuliginosus; Sri Lanka; bat alphacoronavirus; cave-dwelling; coronavirus; full genome; one health; sympatric colony.

Figure 1

Location of the newly designed batCoV real-time RT-PCR assay (green labels) on the ORF1b gene (yellow), producing an amplicon of 121 bp at nucleotide position 16,286–16,406.

Figure 2

Extract of the first 100 amino acids (aa) of a multiple sequence alignment of the membrane protein from different α-CoVs and β-CoVs, calculated with MAFFT algorithm and visualized in Geneious Prime software with a color code for each aa. The novel strain batCoV/MinFul/2018/SriLanka is marked in red. α-CoVs of the subgenus Minunacovirus are marked with an asterisk.

Figure 3

Phylogenetic tree based on a full genome nucleotide (nt) alignment of the novel strain batCoV/MinFul/2018/SriLanka (bold) with selected α-CoVs and β-CoVs and specification of the subgenera. The γ-CoV avian infectious bronchitis virus (NC_001451) was included as an outgroup for the calculation. The phylogenetic tree was calculated with Bayesian algorithm, and 500,000 generations were calculated with a subsampling frequency of 100 and a burn-in of 10%. Substitution model GTR was selected with a gamma-distributed rate variation.

Figure 4

Phylogenetic tree based on an ORF1b nt alignment of the novel batCoV/MinFul/2018/SriLanka (bold) and selected CoV strains from different subgenera. The γ-CoV avian infectious bronchitis virus (NC_001451) was included as an outgroup for the calculation. The phylogenetic tree was calculated with the Bayesian algorithm, and 1 million generations were calculated with a subsampling frequency of 100 and a burn-in of 10%. Substitution model GTR was selected with a gamma-distributed rate variation.

Figure 5

Heatmap based on an ORF1b aa alignment of the novel batCoV/MinFul/2018/SriLanka (red) and 39 selected CoV strains.