High diversity and evidence for inter-species transmission in astroviruses surveyed from bats in Zibabwae
Longitudinal Survey of Astrovirus infection in different bat species in Zimbabwe: Evidence of high genetic Astrovirus diversity
Recommendation: posted 31 October 2023, validated 03 November 2023
James, T. (2023) High diversity and evidence for inter-species transmission in astroviruses surveyed from bats in Zibabwae. Peer Community In Infections, 100085. 10.24072/pci.infections.100085
Most infectious diseases of humans are zoonoses, and many of these come from particularly species diverse reservoir taxa, such as bats, birds, and rodents (1). Because of our changing landscape, there is increased exposure of humans to wildlife diseases reservoirs, yet we have little basic information about prevalence, hotspots, and transmission factors of most zoonotic pathogens. Viruses are particularly worrisome as a public health risk due to their fast mutation rates and well-known cross-species transmission abilities. There is a global push to better survey wildlife for viruses (2), but these studies are difficult, and the problem is vast. Astroviruses (AstVs) comprise a diverse family of ssRNA viruses known from mammals and birds. Astroviruses can cause gastroenteritis in humans and are more common in elderly and young children, but the relationship of human to non-human Astroviridae as well as transmission routes are unclear. AstVs have been detected at high prevalence in bats in multiple studies (3,4), but it is unclear what factors, such as co-infecting viruses and bat reproductive phenology, influence viral shedding and prevalence.
In this recommended study, Vimbiso et al. (5) study the prevalence and diversity of astroviruses in different insectivorous and frugivorous chiropteran species roosting in trees, caves and building basements across Zimbabwe, a region never investigated for astroviruses. Using both pooled population samples and individual samples from 11 different sites, the authors screened for astrovirus prevalence via RT-PCR and identified bat taxa using mitochondrial gene sequencing. An overall prevalence of 10-14% infection was recorded. No clear association of increased astrovirus and coronavirus coinfection was detected, and although astrovirus infection varied over the season, it did not do so in consistent ways across the two primary sampling sites, Magweto and Chirundu. A phylogeny generated by sequencing all of the astrovirus positive samples showed evidence that most of the viral lineages are transmitting within species but across Zibabwae such that most phylogenetic lineages grouped viruses from the same host species together. However, there was ample evidence for interspecies transmission between bats. Finally, a small percentage of the total astrovirus diversity from Zibabwae clustered with sequences from humans. The timing and direction of the transmission between humans and bats need further investigation.
This study provides important baseline data about viral diversity and does an excellent job of capturing the spatial, temporal, host species, and sequence level dynamics of the astroviruses. There are clear limitations on how this study can be interpreted due to different sampling regimes and, in particular, the fact that each of the two primary sites was only explored for temporal variation over a single calendar year. That said, the grand diversity of astroviruses demonstrated in insectivorous bats in Zibabwae shows that we are only seeing the very tip of the iceberg with respect to viral diversity with zoonotic potential. As suggested by the reviewers, more studies like this are needed to understand the basic ecology of viruses and to aid in predicting epidemics.
1. Mollentze N, Streicker DG. Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts. Proceedings of the National Academy of Sciences. 2020 Apr 28;117(17):9423-30. https://doi.org/10.1073/pnas.1919176117
2. Carroll D, Daszak P, Wolfe ND, Gao GF, Morel CM, Morzaria S, et al. The Global Virome Project. Science. 2018 Feb 23;359(6378):872-4. https://doi.org/10.1126/science.aap7463
3. Lee SY, Son KD, Yong-Sik K, Wang SJ, Kim YK, Jheong WH, et al. Genetic diversity and phylogenetic analysis of newly discovered bat astroviruses in Korea. Arch Virol. 2018;163(11):3065-72. https://doi.org/10.1007/s00705-018-3992-6
4. Seltmann A, Corman VM, Rasche A, Drosten C, Czirják GÁ, Bernard H, et al. Seasonal Fluctuations of Astrovirus, But Not Coronavirus Shedding in Bats Inhabiting Human-Modified Tropical Forests. EcoHealth. 2017 Jun 1;14(2):272-84. https://doi.org/10.1007/s10393-017-1245-x
5. Vimbiso C, Hélène DN, Malika A, Getrude M, Valérie P, Ngoni C, et al. Longitudinal Survey of Astrovirus infection in different bat species in Zimbabwe: Evidence of high genetic Astrovirus diversity. bioRxiv, 2023.04.14.536987, ver. 6 peer-reviewed and recommended by Peer Community In Infections. https://doi.org/10.1101/2023.04.14.536987
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
This work was supported by grants of the Agence Nationale de la Recherche (grant ANR-14-CE14-0029), the French Ministry of Europe and Foreign Affairs (Fond de Solidarité pour les Projets Inno-vants, les sociétés civiles, la francophonie et le développement humain—CAZCOM Project, FSPI N°2019/88) and the AFD (French Agency for development- Projet PACMAN, AFD CWZ 1019 01 V).
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/2023.04.14.536987
Version of the preprint: 5
Author's Reply, 31 Oct 2023
Decision by Tim James, posted 26 Oct 2023, validated 27 Oct 2023
I want to thank the authors for carefully revising their paper and fully addressing most of the comments of the reviewers.
Before the final recommendation of the article I would like the authors to make the following changes.
1. Figure 4 is nicely improved. However, Reviewer 2 suggested that you convert this figure to a phylogram with branch lengths. The new figure legend says "the scale bar(e) represented the number of substitutions per site." However, this is clearly not the case as there are no meaningful branch lengths in the figure. This needs to either be corrected by using a phylogeny with branch lengths (highly recommended as this shows exactly how close the actual sequences are to each other in terms of nucleotide substitutions), or to delete that part of the legend and say that this is a cladogram and no branch lengths are shown. If you run PhyML on the data you should be able to get this phylogram with branch lengths, and then the bootstrap values are just mapped on top of that phylogram.
2. Since you will revise, please consider changing line 318 to "nucleotide" instead of "nucleotidic acid".
3. Also, lines 305-308 are basically two identical statements, so delete one.
I should be able to finalize the recommendation quickly if you can take care of these issues.
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2023.04.14.536987
Version of the preprint: 4
Author's Reply, 09 Oct 2023
Decision by Tim James, posted 25 Aug 2023, validated 25 Aug 2023
Thank you for submitting your manuscript for Peer Review via PCI Infections. Your manuscript has been carefully commented on by two reviewers. You will see they have a number of suggestions which, if taken into consideration, should greatly improve your manuscript. I believe if you are able to address these concerns, I will be able to recommend it via PCI infections. If you choose to revise, please send a coverletter describing your responses to each of the criticisms. Below are the reviews and one reviewer also included a marked up manuscript.
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