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. 2022 Oct 14;12(1):17239.
doi: 10.1038/s41598-022-22134-y.

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Affiliations

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

Xiaozhou He et al. Sci Rep. .

Abstract

Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Satellite map (left) and topographic map (right) of the rodent collection area on the eastern Tibetan Plateau of China. Shiqu county is highlighted yellow, and Sichuan province is marked in light gray, the geographic coordinate of collection site (E97°44′3E.67", N33°10′40.40") is marked on the topographic map. The map was generated by SuperMap (http://www.supermapol.com/).
Figure 2
Figure 2
Proportion of viral sequence reads with BLASTX hits to the specified virus families. (A) Proportion in each library. The y-axis is the percentage of viral reads distribute to each classification, or that were unclassified viruses. The sample ID is shown on the x-axis. The percentage of reads was determined based on the raw number of viral-related reads. (B) Proportion in total viral reads.
Figure 3
Figure 3
Venn diagram of viral families shared in the five tissues. The numbers represent viral families found in each tissue. A total of 48 viral taxa were analyzed and displayed, which included 46 viral families, one unclassified virus and one unclassified Bacteriophage.
Figure 4
Figure 4
Heatmap based on the distance matrix calculated by the Euclidean distance method according to the normalized number of reads belonging to each viral family in 20 pools. X axis shows sample names, and the Y axis the names of viral families. Red to blue, highest to lowest abundance of viral reads according to viral family. The hierarchical clustering is based on the Euclidean distance matrix calculated from the normalized read count. A total of 48 viral taxa were analyzed and displayed, which included 46 viral families, one unclassified virus and one unclassified Bacteriophage. The heatmap was generated by Hiplot (v0.2.0, https://hiplot.com.cn).
Figure 5
Figure 5
Phylogenetic relationships of hepatovirus variants based on analyses of the P1 protein (A) and 3CD protein (B). Branch lengths are drawn to a scale of aa substitutions per site. Numbers above individual branches indicate bootstrap support, only values > 80% are shown. Vole hepatovirus variants are marked by a black dot, sample ID were labeled in parentheses.
Figure 6
Figure 6
Phylogenetic analyses of hepacivirus variants based on the NS5B (A) and NS3 (B) protein. Branch lengths are drawn to a scale of aa substitutions per site. Numbers above individual branches indicate bootstrap support, only values > 80% are shown. Hepacivirus variants are marked by a black dot, sample ID were labeled in parentheses.
Figure 7
Figure 7
Phylogenetic relationships of vole rotavirus A based on the VP1 (RdRp) protein (A) and VP6 protein (B). Branch lengths are drawn to a scale of aa substitutions per site. Numbers above individual branches indicate bootstrap support, only values > 80% are shown. Novel rotavirus A variants are marked by a black dot, sample ID were labeled in parentheses.
Figure 8
Figure 8
Phylogenetic analyses of picobirnavirus genomes on the basis of the segment 2 (RdRp) aa sequence. Branch lengths are drawn to a scale of aa substitutions per site. Numbers above individual branches indicate the bootstrap support, only values > 80% are shown. The novel variants of picobirnavirus are marked with a black dot, sample ID were labeled in parentheses.

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