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. 2023 Aug 8;13(1):12859.
doi: 10.1038/s41598-023-39534-3.

Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka

Affiliations

Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka

Therese Muzeniek et al. Sci Rep. .

Abstract

Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Schematic illustration of the general NGS workflow (wet lab) with subsequent bioinformatic analysis of obtained data (dry lab). Created with BioRender.com.
Figure 2
Figure 2
Normalized comparison of viral hits from different sample types in MEGAN after diamond BLASTx. Sample types are depicted in the following order: oral swabs (OS), feces (F) and urine swabs (US). The intensity of green color represents the quantity of reads assigned to the respective viral family or order.
Figure 3
Figure 3
Phylogenetic tree based on the mNGS sequences obtained from the virome of F sample pools (highlighted in blue) and a selection of other astrovirus species. Turkey astrovirus (NC_002470) was used as outgroup. Phylogenetic reconstruction was calculated with the Bayesian MCMC algorithm: 500,000 generations were calculated with a subsampling frequency of 100 and a burn-in of 10%. The substitution model GTR was selected with a gamma-distributed rate variation. Visualized as molecular clock with uniform branch lengths.
Figure 4
Figure 4
Phylogenetic tree based on a 224-nt contig on the conserved ORF1B CDS of CoV obtained from the virome of US sample pools (highlighted in blue) and a selection of α-CoVs and β-CoVs as specified. For use as outgroup, the γ-CoV avian infectious bronchitis virus (NC_001451) was included in the calculation. Phylogenetic reconstruction was calculated with the Bayesian MCMC algorithm: 1,000,000 generations were calculated with a subsampling frequency of 100 and a burn-in of 10%. The substitution model GTR was selected with a gamma-distributed rate variation. Visualized as molecular clock with uniform branch lengths.
Figure 5
Figure 5
Phylogenetic tree based on the mNGS sequences obtained from the virome of US sample pools (highlighted in blue) and a selection of PMVs. Sendai virus (NC_001552) was selected as outgroup for the calculation. Phylogenetic reconstruction was calculated with the Bayesian MCMC algorithm: 1,000,000 generations were calculated with a subsampling frequency of 100 and a burn-in of 10%. The substitution model GTR was selected with a gamma-distributed rate variation. Visualized as molecular clock with uniform branch lengths.
Figure 6
Figure 6
Phylogenetic tree based on the mNGS sequences obtained from the virome of F sample pools (highlighted in blue) and a selection of picornaviruses. Human parechovirus 1 (NC_038319) was selected as outgroup for the calculation. Phylogenetic reconstruction was calculated with the Bayesian MCMC algorithm: 1,000,000 generations were calculated with a subsampling frequency of 100 and a burn-in of 10%. The substitution model GTR was selected with a gamma-distributed rate variation. Visualized as molecular clock with uniform branch lengths.

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