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Review 1: "Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses"

The reviewers found this preprint to be reliable but note that the authors overstate the zoonotic risk and immediate relevance of their results.

Published onApr 05, 2023
Review 1: "Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses"
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key-enterThis Pub is a Review of
Individual bat viromes reveal the co-infection, spillover and emergence risk of potential zoonotic viruses

ABSTRACTBats are reservoir hosts for many zoonotic viruses. Despite this, relatively little is known about the diversity and abundance of viruses within bats at the level of individual animals, and hence the frequency of virus co-infection and inter-species transmission. Using an unbiased meta-transcriptomics approach we characterised the mammalian associated viruses present in 149 individual bats sampled from Yunnan province, China. This revealed a high frequency of virus co-infection and species spillover among the animals studied, with 12 viruses shared among different bat species, which in turn facilitates virus recombination and reassortment. Of note, we identified five viral species that are likely to be pathogenic to humans or livestock, including a novel recombinant SARS-like coronavirus that is closely related to both SARS-CoV-2 and SARS-CoV, with only five amino acid differences between its receptor-binding domain sequence and that of the earliest sequences of SARS-CoV-2. Functional analysis predicts that this recombinant coronavirus can utilize the human ACE2 receptor such that it is likely to be of high zoonotic risk. Our study highlights the common occurrence of inter-species transmission and co-infection of bat viruses, as well as their implications for virus emergence.

RR:C19 Evidence Scale rating by reviewer:

  • Reliable. The main study claims are generally justified by its methods and data. The results and conclusions are likely to be similar to the hypothetical ideal study. There are some minor caveats or limitations, but they would/do not change the major claims of the study. The study provides sufficient strength of evidence on its own that its main claims should be considered actionable, with some room for future revision.



In the study entitled, “Individual bat viromes reveal the co-infection, spillover, and emergence risk of potential zoonotic viruses,” Wang et al. examined viral diversity among individual wild bats using meta-transcriptomic sequencing and quantified cross-species transmission using host phylogeny and geographic sampling. The study also attempted to evaluate the pathogenic potential of identified viruses using phylogenetic analysis and molecular dynamics simulations. The authors characterized the distribution and phylogeny of mammalian-associated viruses across individual bat species and discovered frequent co-infection by two or more viruses. Several viruses including SARS-related coronaviruses were identified, as well. Overall, this paper provides interesting evidence that is useful for understanding the potential for zoonotic spillover among this population.

Using meta-transcriptomic sequencing, the authors demonstrated instances of co-infection within individual bats and an inverse relationship between paired host distance and virome similarity, building on prior work in this area (1). Additional individual-level characteristics (such as roost size) could be relevant for additional analyses but fall outside the scope of this study. The authors reported a high prevalence of co-infection, particularly among Rhinolophus spp. Prior studies have implicated Rhinolophus spp. as important facilitators of inter-family switching of coronaviruses (2). In addition, the authors demonstrated an inverse relationship between phylogenetic and geographical distance and the shared number of viruses, also supporting prior work.

The most novel findings in this study are its identification and analysis of two SARS-related coronaviruses. One in particular named BtSY2 had similar key proteins to human coronaviruses, displayed evidence of recombination at one site, and further genetic similarity to other bat coronaviruses. From this evidence, the authors ultimately proposed that spillover may occur via viral co-infection in related bat species.

The authors did not discuss limitations of their study methodology in their discussion. Notably, their findings regarding BtSY2 do not readily suggest proximity of the virus to pathogenicity in humans. The authors conducted a computational functional analysis to predict the ability of BtSY2 to bind to the human ACE2 receptor involved in SARS-CoV-2 viral entry, but with no in vitro assays. This methodology is understandable given the scope of the study, and the authors acknowledge that these results “tentatively suggest that BtSY2 may be able to replicate rapidly with similar virulence as SARS-CoV.” However, the authors did not acknowledge that the whole genome similarity of BtSY1 and BtSY2 does not necessarily translate to human pathogenicity. By not adequately acknowledging the gulf between genetic similarity and actual functioning in vivo, the authors overstated the immediate relevance of their results. Future work should also consider the low incidence of co-infection in Aselliscus spp reported in this study and the potential impact this might have on overall spillover risk within bats, given that this species sits as an intermediary between the two identified subnets. While much of this study supports prior work, it nevertheless offers critically needed insights and additional evidence for the risks and partial mechanisms of zoonotic spillover from bats.

1. Anthony SJ, Epstein JH, Murray KA, et al. A Strategy To Estimate Unknown Viral Diversity in Mammals.mBio. 2013;4(5):e00598-13. doi:10.1128/mBio.00598-13

  1. Latinne A, Hu B, Olival KJ, Zhu G, Zhang L, Li H, et al. Origin and cross-species transmission of bat coronaviruses in China. Nat Commun. 2020 Aug 25;11(1):4235.

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