VThunter: a database for single-cell screening of virus target cells in the animal kingdom

Abstract

Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…Finally, although not focused primarily on COVID-19, two databases include it among broader information that may well help predict the appearance and spread of future viral pandemics. VThunter ( 67 ) looks at expression of viral receptors at a single-cell level across 47 animal species enabling the users to ask which species a given virus might infect or, conversely, to which viruses a given animal might be susceptible. ZOVER ( 68 ) unites and upgrades two previous databases to curate information on zoonotic viruses carried by rodent, bat and insect vectors: information includes mapping of viral families to host species and geographical virus distributions.…”

SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases

“…The CellMarker database records cell markers for human tissues and mouse tissues ( 31 ). VThunter presents the cell expression pattern of 107 virus receptors from 47 animal species ( 32 ).…”

Screening of cell‐virus, cell‐cell, gene‐gene crosstalk among animal kingdom at single cell resolution

“…Transcriptome studies can identify the cellular receptor profiles for the virus of interest, which may be an effective way to narrow down the suspected host and tissue list. 11 Identifying the host and tissue tropism is the first step towards understanding viral infection and pathogenesis, thus laying the foundation for the prevention and control of putative outbreaks in animals or humans. scRNAseq data can be utilised to explore conserved or divergent cell‐cell and gene‐gene cross‐talks among multiple species, 12 , 13 , 14 , 15 resulting in various molecular circuits important in development and diseases.…”

“…Thus, the viral receptor distribution may reveal the potential replicating niches of the viruses. Transcriptome studies can identify the cellular receptor profiles for the virus of interest, which may be an effective way to narrow down the suspected host and tissue list 11 . Identifying the host and tissue tropism is the first step towards understanding viral infection and pathogenesis, thus laying the foundation for the prevention and control of putative outbreaks in animals or humans.…”