Host taxonomy and environment shapes insectivore viromes and viral spillover risks in Southwestern China

Abstract

Background: Zoonotic viruses originating from small mammals pose significant challenges to public health on a global scale. Insectivores, serving as natural reservoirs for a diverse array of zoonotic viruses, are known to carry a multitude of viral species. However, compared to the extensive research conducted on rodents (Rodentia) and bats (Chiroptera), the role of insectivores in harboring and transmitting unknown pathogens remains underexplored, which may lead to a severe underestimation of their contributions and impact to global public health.

Results: This study employed a meta-transcriptomic approach to profile the viromes of 214 individual insectivores, encompassing 13 species from the families Soricidae, Erinaceidae, and Talpidae, collected across 12 counties in Yunnan Province, a recognized zoonotic hotspot. Based on virus reads, the analysis identified 42 viral families associated with vertebrates, highlighting significant virome diversity and host-specific viral tropisms among shrews, hedgehogs, and moles, along with notable geographic and environmental specificity of the viruses. Shrews exhibited greater viral richness and abundance compared to hedgehogs and moles, with variations influenced predominantly by host taxonomy, altitude, and geographic location. A total of 114 RNA-dependent RNA polymerase sequences were obtained, leading to the identification of 68 viruses, including 57 novel species. Instances of host jumping were observed in 11 viruses, with potential pathogenic viruses related to Mojiang paramyxovirus and members of the Hantaviridae family. Cross-species transmission was predominantly observed in viruses carried by shrews, while moles may play a pivotal role in facilitating viral transmission among insectivores.

Conclusions: This study enhances the understanding of the high diversity of mammalian viruses among insectivores in a relatively confined region and underscores the associations between virome composition and related zoonotic risks, providing a foundation for proactive measures to prevent and control the spillover of emerging zoonotic pathogens and potential future outbreaks. Video Abstract.

Keywords: Emerging infectious diseases; Environment; Insectivore; Viral evolution; Virome.

Fig. 1

Sample locations, landscapes, and wild insectivore compositions. a Distribution of mammals sampled in different counties in Yunnan Province, with different pie charts representing various mammal species and their percentages in each county, and the diameter of each pie chart indicating the number of samples collected. Altitude of each location is illustrated from lowest (green) to highest (red). b Landscape illustration depicting the habitats and altitudes of the collected insectivores. c Heatmap showing the number of samples collected from three insectivore groups in each county. d Rarefaction curve illustrating the insectivore sample sizes across different habitats and altitudes

Fig. 2

Characterization of insectivore viromes. a Heatmap based on the relative abundance of different host species, with Euclidean distance calculated and clustering performed using the complete method; insectivore types are displayed in various colors at the top. b Heatmap based on the relative abundance of the 30 most abundant viral families in each pooled sample, with sample locations listed on the left and species on the right; viral family names are at the bottom, and boxes colored from green to red represent the normalized viral reads for each sample. Abbreviations of locations and host species can be seen in Table S2. c Prevalence of viral families in host species and locations, where the x-axis represents the number of counties and the y-axis represents the number of host species in which a certain virus was found; the size of the circle denotes the reads per million for each viral family

Fig. 3

Environmental and host factors affecting viral diversity and distribution. a Difference in viral richness among different insectivores, with “*” indicating P < 0.05, “**”’ indicating P < 0.01, and “ns” indicating not significant. b Difference in viral abundance among different insectivores. c Relationships between virome composition and host phylogeny of different insectivore species based on the RPM table. d Difference in viral composition of shrews across different habitats and locations based on the RPM table. e and f Differences in Shannon index of shrews at different locations. g Difference in Shannon index of S. murinus at different locations and altitudes

Fig. 4

Phylogenetic diversity of vertebrate- and invertebrate-associated viruses. Phylogenetic trees were estimated based on amino acid sequences of the RdRp protein for RNA viruses and the replicase protein for DNA viruses. Phylogenetic inference was performed using the maximum likelihood (ML) method with 1000 bootstrap replicates. Branch lengths are indicated by the scale bar. Viruses identified in this study are color-marked according to their hosts, with blue, red, and yellow representing shrews, moles, and hedgehogs, respectively. Novel viruses discovered in this study are labeled with black rectangles, while viruses of known species are labeled with black circles. Human pathogenic viruses are indicated with black figures, and spillover-risk viruses are marked with yellow polygons. See also Fig. S1. Abbreviations of locations and host species can be seen in Table S2

Fig. 5

Cross-species transmission of viruses. a Overview of transmission across different host orders of known viruses. Black circles represent host orders of various viruses discovered by other studies. Orange circles represent host orders discovered by our study. Red rings denote new hosts discovered in our study. b Overview of transmission across host species, genus, and family for new viruses. c Venn diagrams illustrating the number of viruses in and shared by shrews, hedgehogs, and moles. d Host-virus correlation network. Node colors represent insectivore species and virus species, with node border colors indicating viruses that transmit among insectivores