Transcriptome Analysis of Viruses

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 4958

Special Issue Editor

Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary
Interests: molecular virology; genomics; virome; long-read sequencing; transcriptomics; microbiome

Special Issue Information

Dear Colleagues,

The current COVID-19 pandemic underscores the importance of the RNA-level analysis of viruses. Understanding the molecular mechanisms of these small pathogens is essential for developing a defense strategy against them. Rapidly evolving sequencing technologies (including RNA sequencing) and bioinformatics have revolutionized the field of molecular virology in the past decade. Next- and third-generation sequencing approaches enable us to analyze thousands of transcripts simultaneously. Third-generation long-read sequencing (LRS) has opened new avenues for a comprehensive understanding of how genes are expressed and connected with each other. LRS approaches, such as the single-molecule real-time (SMRT) technique from Pacific Biosciences, the nanopore sequencing method from Oxford Nanopore Technologies, and LoopSeq synthetic long-read sequencing from Loop Genomics allows distinguishing between transcript length variants, including splice and length variants, embedded RNAs, polycistronic transcripts, and alternatively spliced transcript isoforms. Several recent studies, using LRS approaches, have shown that the RNA profiles of viruses are much more complex than previously assumed. 

This Special Issue, “Transcriptome Analysis of Viruses”, aims to provide in-depth knowledge and an overview of the current results, focuses, and future directions of current research projects.

Therefore, we invite the submission of original research articles, reviews, and short communications on hot topics in this field.

Dr. Dóra Tombácz
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • DNA viruses
  • RNA viruses
  • transcriptomics
  • genomics
  • sequencing
  • transcriptome profiling
  • noncoding RNAs
  • lncRNAs
  • miRNAs
  • RNA editing
  • single-cell RNA sequencing
  • SARS-CoV-2 transcriptome
  • coronavirus transcriptome
  • bioinformatics

Published Papers (2 papers)

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Research

6 pages, 3403 KiB  
Communication
Possible Role of Accessory Proteins in the Viral Replication for the 20I/501Y.V1 (B.1.1.7) SARS CoV-2 Variant
by Dimpal A. Nyayanit, Prasad Sarkale, Anita Shete-Aich, Abhinendra Kumar, Savita Patil, Triparna Majumdar, Shrikant Baradkar, Pranita Gawande, Sreelekshmy Mohandas and Pragya D Yadav
Pathogens 2021, 10(12), 1586; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10121586 - 07 Dec 2021
Cited by 1 | Viewed by 1950
Abstract
The emergence of new severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) has been a global concern. The B.1.1.7 variant of SARS CoV-2 is reported to cause higher transmission. The study investigates the replication cycle and transcriptional pattern of the B.1.1.7 to hypothesis the [...] Read more.
The emergence of new severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) has been a global concern. The B.1.1.7 variant of SARS CoV-2 is reported to cause higher transmission. The study investigates the replication cycle and transcriptional pattern of the B.1.1.7 to hypothesis the possible role of different genes in viral replication. It was observed that the B.1.1.7 variant required a longer maturation time. The transcriptional response demonstrated higher expression of ORF6 and ORF8 compared to nucleocapsid transcript till the eclipse period which might influence higher viral replication. The number of infectious viruses titer is higher in the B.1.1.7, despite a lesser copy number than B.1, indicating higher transmissibility. The experimental evidence published linked ORF6 and ORF8 to play important role in replication and we also observed their higher expression. This leads us to hypothesis the possible role of ORF6 and ORF8 in B.1.1.7 higher replication which causes higher transmission. Full article
(This article belongs to the Special Issue Transcriptome Analysis of Viruses)
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17 pages, 3975 KiB  
Article
Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay
by Dóra Tombácz, István Prazsák, Gábor Torma, Zsolt Csabai, Zsolt Balázs, Norbert Moldován, Béla Dénes, Michael Snyder and Zsolt Boldogkői
Pathogens 2021, 10(8), 919; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10080919 - 21 Jul 2021
Cited by 3 | Viewed by 2257
Abstract
Viral transcriptomes that are determined using first- and second-generation sequencing techniques are incomplete. Due to the short read length, these methods are inefficient or fail to distinguish between transcript isoforms, polycistronic RNAs, and transcriptional overlaps and readthroughs. Additionally, these approaches are insensitive for [...] Read more.
Viral transcriptomes that are determined using first- and second-generation sequencing techniques are incomplete. Due to the short read length, these methods are inefficient or fail to distinguish between transcript isoforms, polycistronic RNAs, and transcriptional overlaps and readthroughs. Additionally, these approaches are insensitive for the identification of splice and transcriptional start sites (TSSs) and, in most cases, transcriptional end sites (TESs), especially in transcript isoforms with varying transcript ends, and in multi-spliced transcripts. Long-read sequencing is able to read full-length nucleic acids and can therefore be used to assemble complete transcriptome atlases. Although vaccinia virus (VACV) does not produce spliced RNAs, its transcriptome has a high diversity of TSSs and TESs, and a high degree of polycistronism that leads to enormous complexity. We applied single-molecule, real-time, and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of VACV gene expression. Full article
(This article belongs to the Special Issue Transcriptome Analysis of Viruses)
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