Omission of non-poly(A) viral transcripts from the tissue level atlas of the healthy human virome

Signe Altmäe,Nerea M Molina,Alberto Sola-Leyva

doi:10.1186/s12915-020-00907-z

Abstract

A recent paper in BMC Biology entitled “A tissue level atlas of the healthy human virome” by Kumata et al. describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project. Using a workflow that maps the GTEx sequences to the human genome, then screens unmapped sequences to detect viral transcripts, the authors present a quantitative analysis of the presence of different viruses in the non-diseased tissues of over 500 individuals and assess the impact of these viruses on host gene expression. Here we draw attention to an issue not acknowledged in this study. Namely, by relying solely on GTEx datasets, which are enriched for transcripts with poly(A) tails, the analysis will have missed non-poly(A) viral transcripts, rendering this tissue level atlas of the virome incomplete.A commentary on Kumata et al. (BMC Biol 18:55, 2020).

Highlights

A recent paper in BMC Biology entitled “A tissue level atlas of the healthy human virome” by Kumata et al describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project
Kumata et al conclude that mainly DNA viruses shape the healthy human virome as most of the detected viruses in their study were DNA viruses, they acknowledge the possibility that the detection sensitivity of RNA viruses could have been lower [10]
Especially RNA viruses lack poly(A) tail [5, 6], which could be one solid explanation why RNA viruses were under-detected and DNA viruses predominated in the study by Kumata et al Before other researchers are motivated to apply their meta-transcriptomic study approach [10] to other datasets with the aim of revealing the impact of viral infections on human health, we would like to highlight that the choice of sequencing protocol is crucial in obtaining and interpreting the study findings

Summary

Introduction

A recent paper in BMC Biology entitled “A tissue level atlas of the healthy human virome” by Kumata et al describes a meta-transcriptomic analysis of RNA-sequencing datasets from the Genotype-Tissue Expression (GTEx) Project. * Correspondence: signealtmae@ugr.es; 1Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain 2Instituto de Investigación Biosanitaria ibs.GRANADA, 18014 Granada, Spain Full list of author information is available at the end of the article evolution, especially in positive-strand RNA viruses as for instance are dengue virus, West Nile virus, Japanese encephalitis virus, yellow fever virus, Zika virus, bovine viral diarrhea virus, and hepatitis C virus in the Flaviviridae family [4–6].

Results

Conclusion