Characterization of individual bat viromes reveals the co-infection, spillover and emergence risk of potential zoonotic viruses

Viral diversity and abundance in bats are incompletely understood. Here, analyzing individual bat viromes, the authors observe a high frequency of co-infection and spillover among the animals and identify viruses with the potential to infect humans or livestock.
Characterization of individual bat viromes reveals the co-infection, spillover and emergence risk of potential zoonotic viruses

Bats are natural hosts for many zoonotic viruses, including pathogens that have significant public health impacts, such as SARS coronaviruses, Ebola viruses, Nipah viruses, and others. Although extensive research has been conducted at the population or community level, greatly expanding our knowledge of the viral diversity carried by bats and identifying a range of novel viruses with potential to infect humans, there is still a lack of studies investigating bat virome at the individual scale. Consequently, our understanding of viral diversity within individual animals, their driving factors, patterns of virus co-infection, and the frequency of cross-species virus transmission remains limited.

In the present study, we collected rectum samples from 149 bats in Yunnan province, China, between 2015 and 2019 for meta-transcriptomic analysis (Fig. 1). Our results revealed a high level of viral diversity  within bat individuals. A total of 55 bat-associated virus species were identified, of which 42 virus species were likely to be novel viral species. We found a high frequency of virus co-infection (Fig. 2) and cross-species transmission (Fig. 3) among bat individuals. Such high frequency of co-infection and cross-species tranmission can potentially increases the opportunities for viral recombination and reassortment, and thereby enriching the genetic diversity of viruses circulating in populations of wild animals. We also observed that the transmission of viruses between bat individuals is strongly constrained by both host phylogenetic distance and spatial distance. In other words, the further the genetic relationship between hosts and the less overlap in their territories, the less likely viral transmission is to occur (Fig. 3).

Our results further revealed virus species that are potentially pathogenic to humans or livestock, including a novel recombinant strain of Sarbecovirus (a subgenus of the genus Betacoronavirus, Coronaviridae). We evaluated the potential human infectivity of these viruses based on phylogenetic relatedness to known pathogens, and performed in vitro and in silico receptor-binding assays especially for the novel Sarbecovirus.

In conclusion, using an individual virome approach we revealed a high frequency of virus co-infection and inter-species transmission among bats. The discovery of a diverse array of bat-associated viruses, including those potentially pathogenic to humans and livestock, emphasizes the need for continued vigilance in monitoring bat populations as potential sources of emerging infectious diseases. The identification of a novel recombinant Sarbecovirus that can utilize the human ACE2 receptor raises concerns about the potential for future zoonotic spillover events. Further research into the diversity and abundance of viruses within bats is necessary to better understand the risks associated with zoonotic transmission and to inform the development of strategies for disease prevention and control.

Fig.1 | Overview of the samples analyzed in this study. a Locations in Yunnan province China where bat samples were taken.  b Phylogeny of bats, including those sampled as part of this study.
Fig. 2 | Comparison of mammal-associated virus diversity among different bat taxa. a Virus abundance and the number of virus species in individual bats. b Comparison of the number of viruses per individual host among six bat genera. c Comparison of the prevalence of 11 viral families among different host genera and species.
Fig. 3 | The virus-sharing network of bats. a The virus-sharing network reveals connectivity among viromes of different bat taxa.  The relationship between the number of shared viruses with phylogenetic (b) or geographic distance (c) between pairs of host individuals.

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