Individual bat virome analysis reveals co-infection and spillover among bats and virus zoonotic potential

Abstract

Bats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within individual bats, and hence the frequency of virus co-infection and spillover among them. We characterize the mammal-associated viruses in 149 individual bats sampled from Yunnan province, China, using an unbiased meta-transcriptomics approach. This reveals a high frequency of virus co-infection (simultaneous infection of bat individuals by multiple viral species) and spillover among the animals studied, which may in turn facilitate virus recombination and reassortment. Of note, we identify five viral species that are likely to be pathogenic to humans or livestock, based on phylogenetic relatedness to known pathogens or in vitro receptor binding assays. This includes a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV and SARS-CoV-2. In vitro assays indicate that this recombinant virus can utilize the human ACE2 receptor such that it is likely to be of increased emergence risk. Our study highlights the common occurrence of co-infection and spillover of bat viruses and their implications for virus emergence.

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

“…Some viruses appear to be predominantly associated with particular mosquito species, although sporadic host switching events are frequent, such as the case of Mosquito narna-like virus SC1. This phenomenon of frequent host switching has also been observed in rabies viruses of bats 34 , and in recent metagenomics studies in mammals 6 and ticks 7 . The frequent spillover events, along with the frequent co-infection of viruses within individual mosquitos, are likely to contribute to increased genetic diversity among viruses circulating in mosquito communities.…”

“…In addition, we excluded those viruses at very low abundance (RPM < 1) and at low genome coverage (coverage < 300 base-pairs, i.e., the length of two reads), which were also likely to be false-positives. These thresholds have been validated in our previous publications deploying RT-PCR re-confirmation 6,48 .…”

“…Metagenomic studies of individual insects are necessary to reveal the epidemiology and ecology of viruses without a priori knowledge of which viruses may be present 5 . Individual animal virome data sets are also valuable for investigating both virus-virus and virus-host interactions 4,6 . Many metagenomics studies have pooled individual insects by species or sampling location [7][8][9][10] .…”

Host specificity and geographic dispersion shape virome diversity in Rhinolophus bats

“…Geographic distribution of viral populations is another key factor in shaping the genetic diversity and evolutionary plasticity of viral populations [10]. Geographic co-occurrence provides opportunities for genomic exchange among genetically distinct viral populations [11]. For example, the building blocks of SARS-CoV genome, including the highly variable S gene, ORF3 and ORF8, were found in different SARSr-CoV viruses from a single bat cave [12].…”

“…Particularly, individual level metatranscriptome provides co-infection signals and high-quality viral genomes [11]. The high resolution offered by deep metatranscriptomic sequencing facilitates systematic comparisons of evolutionary and ecological patterns across diverse viral groups.…”