Zoonotic disease and virome diversity in bats

Abstract

The emergence of zoonotic viral diseases in humans commonly reflects exposure to mammalian wildlife. Bats (order Chiroptera) are arguably the most important mammalian reservoir for zoonotic viruses, with notable examples including Severe Acute Respiratory Syndrome coronaviruses 1 and 2, Middle East Respiratory Syndrome coronavirus, henipaviruses and lyssaviruses. Herein, we outline our current knowledge on the diversity of bat viromes, particularly through the lens of metagenomic next-generation sequencing and in the context of disease emergence. A key conclusion is that although bats harbour abundant virus diversity, the vast majority of bat viruses have not emerged to cause disease in new hosts such that bats are better regarded as critical but endangered components of global ecosystems.

Figure 1

Taxonomic distribution of publicly available gene sequences of bat viruses. Plots show virus sequences on NCBI/GenBank in which the order Chiroptera or individual bat species are listed as hosts. (a) Percentage of bat virus sequences that belong to RNA virus families and (b) RNA virus sequences by year of NCBI release. (c) Percentage of bat virus sequences that belong to DNA virus families and (D) DNA virus sequences by year of NCBI release.

Figure 2

Number of publicly available virus gene sequences for each family of bats. The heat map shows (a) the number of RNA viruses and (b) the number of DNA viruses separated by virus family, and the corresponding bat host family as given on NCBI. Virus sequences with an unspecified bat host (i.e. host listed as Chiroptera) are represented as ‘unclassified Chiroptera’.

Figure 3

Representative phylogenetic diversity of bat coronaviruses. An amino acid alignment of the RdRp of the Coronaviridae was used to infer a maximum likelihood phylogeny using IQ-TREE [81]. The phylogeny was estimated using viruses from the four coronavirus genera as marked by coloured lines to the right of the phylogeny. The tree was mid-point rooted and bootstrap values are represented by coloured circles. Bat viruses are shown in red font and fall into the Alphacoronavirus and Betacoronavirus genera. Animal silhouettes representing host species are displayed next to viruses that do not list a host species in the virus name.

Figure 4

Representative phylogenetic diversity of bat paramyxoviruses. An amino acid alignment of the L protein that contains the RdRp of the Paramyxoviridae was used to infer a maximum likelihood tree using IQ-TREE [81]. The tree was mid-point rooted and bootstrap values are represented by coloured circles. Bat viruses are shown in red font. Animal silhouettes representing animal host species are displayed next to viruses that do not provide a host species in the virus name. The avian paramyxovirus clade has been collapsed to enhance visualisation.