Abstract
Vesicular stomatitis Indiana virus (VSIV) of genus Vesiculovirus, species Indiana Vesiculovirus (formerly as Vesicular stomatitis virus, VSV) causes a disease in livestock that is very similar to the foot and mouth disease, thereby an outbreak may lead to significant economic loss. Long-read sequencing (LRS) -based approaches already reveal a hidden complexity of the transcriptomes in several viruses. This technique has been utilized for the sequencing of the VSIV genome, but our study is the first for the application of this technique for the profiling of the VSIV transcriptome. Since LRS is able to sequence full-length RNA molecules, it thereby provides more accurate annotation of the transcriptomes than the traditional short-read sequencing methods. The objectives of this study were to assemble the complete transcriptome of using nanopore sequencing, to ascertain cell-type specificity and dynamics of viral gene expression, and to evaluate host gene expression changes induced by the viral infection. We carried out a time-course analysis of VSIV gene expression in human glioblastoma and primate fibroblast cell lines using a nanopore-based LRS approach and applied both amplified and direct cDNA sequencing (as well as cap-selection) for a fraction of samples. Our investigations revealed that, although the VSIV genome is simple, it generates a relatively complex transcriptomic architecture. In this study, we also demonstrated that VSIV transcripts vary in structure and exhibit differential gene expression patterns in the two examined cell types.
Highlights
Vesicular stomatitis Indiana virus (VSIV) is a negative single-stranded RNA virus belonging to the Rhabdoviridae family [1]
Our investigations revealed that the simple VSIV genome encodes a relatively complex transcriptomic architecture, which differs in the two investigated cell lines with regard of both the structure and the kinetics of transcripts
Several novel transcription start sites (TSSs) and associated transcripts of VSIV were identified using amplified and non-amplified cDNA nanopore sequencing and by a bioinformatic method that detected the entire length of reads that span from a TSS to the transcription end sites (TESs)
Summary
Vesicular stomatitis Indiana virus (VSIV) is a negative single-stranded RNA virus belonging to the Rhabdoviridae family [1]. The virus causes a zoonotic disease, and the infection spreads between mammalian hosts via insect bites or direct contact [2]. The virus causes only mild symptoms in humans [3,4], including fever, myalgia, headache, vomiting [5], enlarged lymph nodes and conjunctivitis, it causes vesicular disease in animals including horses, cattle and, especially, pigs [6], which are the natural host of the virus [7]. The fusion between the viral envelope and the endosomal membrane is facilitated by the activated G protein, which leads to the release of the viral helical nucleocapsid into the cytoplasm of the host cell
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