Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China

Abstract

The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens. This study aimed to characterize the virome, analyze the phylogenetic evolution, and determine the diversity of rodent-borne viruses in Hainan Province, China. We collected 682 anal and throat samples from rodents, combined them into 28 pools according to their species and location, and processed them for next-generation sequencing and bioinformatics analysis. The diverse viral contigs closely related to mammals were assigned to 22 viral families. Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus, coronavirus, astrovirus, pestivirus, parvovirus, and papillomavirus. We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling, and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species, and their rodent hosts have not been previously reported to carry these viruses. These results expand our knowledge of viral classification and host range and suggest that there are highly diverse, undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas.

Keywords: Novel viruses; Phylogenetic analysis; Rodents; Virome; Wildlife.

Fig. 1

Sample collection in Hainan Province and metagenomics of rodents according to species and locations. The maps of Haikou City, Baisha County, Dongfang City, Lingao County, Tunchang County, Lingshui County, Ledong County, Chengmai County, and Sanya City in Hainan Province show the locations of the samples. Rodent numbers and species are also shown on the map in different shapes, colors, and sizes.

Fig. 2

Rodent-related virome profile in the metagenomics sequencing data from the 28 pools. Expression is reported in log2 (TPM), where TPM refers to transcripts per million. Based on high-throughput annotation of viral family information, the phylogenetic tree at the top of the graph is constructed, and the virus species labeled at the bottom correspond to the viral families. A phylogenetic tree on the left side of the graph was built based on virus hosts.

Fig. 3

Phylogenetic tree of arenaviruses (AreVs). Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (LG ​+ ​G ​+ ​I) based on amino-acid sequences of partial L protein (RdRp) of AreVs. AreVs identified in this study are marked in red. Each novel viral host and sample site are marked by pentagrams and dots of different colors. The inner and outer rings, represent the representative viral species and genus of the Arenaviridae, respectively.

Fig. 4

Phylogenetic tree of coronaviruses (CoVs). A The phylogenetic tree is based on the amino acid sequences of complete RdRp. B The phylogenetic tree is based on the amino acid sequences of complete spike (S) of CoVs. Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (WAG ​+ ​G). The branch that included the novel coronavirus identified in the present study is marked in red. Each novel viral host and sample site are marked by pentagrams and dots of different colors. The inner and outer blocks, respectively, represent the representative viral species and genus of the Coronaviridae.

Fig. 5

Phylogenetic tree of pestiviruses (PestVs). Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (rtREV ​+ ​G) based on the amino acid sequences of the complete RdRp (NS5) of PestVs. All pestVs identified in this study are marked with red blocks. Each novel viral host and sample site are marked by pentagrams and dots of different colors. The outer ring markes the representative viral species of Flaviviridae.

Fig. 6

Phylogenetic tree of astroviruses (AstroVs). A The phylogenetic tree is based on the amino acid sequences of complete RdRp. B The phylogenetic tree is based on the amino acid sequences of complete CP genes. Phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (mtREV ​+ ​G ​+ ​I). All astroVs identified in this study are marked with red blocks. Each novel viral host and sample site are marked by pentagrams and dots of different colors. The inner and outer blocks, respectively, represent the representative viral species and genus of the Astroviridae.

Fig. 7

Phylogenetic tree of parvoviruses (ParVs) and papillomaviruses (PVs). A The phylogenetic trees were constructed by the maximum likelihood method using the best-fit models (rtREV ​+ ​G ​+ ​I) based on the amino acid sequences of complete NS of ParVs. B The phylogenetic trees are based on the amino acid sequences of E1-E2-L2-L1 of PVs and constructed by the maximum likelihood method using the best-fit models (LG ​+ ​G). All ParVs and PVs identified in this study are marked with red blocks. Each novel viral host and sample site are marked by pentagrams and dots of different colors. The inner and outer blocks, respectively, represent the representative viral genus and subfamily of the Parvoviridae and Papillomaviridae.

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