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. 2019 Oct 24;11(11):979.
doi: 10.3390/v11110979.

Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Ping Liu  1 , Wu Chen  2 , Jin-Ping Chen  3
Affiliations

Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica)

Ping Liu et al. Viruses. .

Abstract

Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.

Keywords: Coronavirus; Manis javanica; Sendai virus; molecular epidemiology; virome.

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Conflict of interest statement

The authors declare that the research described herein was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The percentage of sequences related to the most abundant viral families among all virus reads, indicated in the same colors for each main viral category. Taxonomic classification of viruses is consistent across samples. Samples are characterized according to the number of sequences from each sample classified by taxonomic family. Virus families are indicated by the color code on the bottom.
Figure 2
Figure 2
Heatmap of contigs with the top 30 abundance of sequence reads in each sample. The pangolin samples are listed below the heatmap. Information of contigs and the virus families they belong to is provided in the right text column. The boxes colored from blue to red represent the abundance of virus reads aligned to each contig.
Figure 3
Figure 3
The phylogenetic tree of the Sendai virus from Malayan pangolin and other hosts. The analysis was inferred using the Maximum Likelihood method based on iqtree [24]. Branch bootstrap values are shown and were based on 1000 replicates. The black star indicates a contig of the Sendai virus from M. javanica in 2019.
Figure 4
Figure 4
The phylogenetic tree of each gene of the Sendai virus from Malayan pangolin and other hosts. The analysis was inferred using the Maximum Likelihood method based on iqtree [24]. Branch bootstrap values are shown and were based on 1000 replicates. The black star indicates a contig of the Sendai virus from M. javanica in 2019.
Figure 5
Figure 5
The phylogenetic tree of Conronavirus from Malayan pangolin and other hosts. The analysis was inferred using the Maximum Likelihood method based on iqtree [24]. Branch bootstrap values are shown and were based on 1000 replicates. The black star indicates a contig of the Sendai virus from M. javanica in 2019.
See this image and copyright information in PMC

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