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Quest for Conserved RNAs in Viral Genomes
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Quest for Conserved RNAs in Viral Genomes

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 3927

Special Issue Editor

Dr. Michael T. Wolfinger

E-Mail Website
Guest Editor
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Vienna, Austria
Interests: RNA structure prediction; RNA folding dynamics; conserved RNAs; virus bioinformatics

Special Issue Information

Dear Colleagues,

Evolutionarily conserved RNAs and their mechanisms are actively investigated across all domains of life. Yet, our general knowledge of conserved, functional RNAs in viruses is restricted to a set of well-studied examples. Novel experimental techniques, together with the increased availability of cheap sequencing technologies, have leveraged the accessibility of viral (meta)genome data in the last couple of years. This has opened new perspectives for the comparative analysis of viral genomes, allowing us to better understand the evolutionary traits associated with functional RNAs, such as virus–host interaction, host range specificity, pathogenicity and immune escape, as well as virus origin.

In the Special Issue ‘The Quest for Conserved RNAs in Viral Genomes’, we would like to bring together both experimental and theoretical research related to the study of evolutionarily conserved (structured and unstructured) RNAs in viruses. Original articles and reviews are welcome, ranging from the analysis of individual species to comparative screens of large-scale datasets.

Dr. Michael T. Wolfinger
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes 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 2600 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

  • RNA structure
  • conserved RNA
  • non-coding RNA
  • comparative structure analysis
  • functional conservation
  • analysis of large-scale data sets related to RNA structure
  • structure probing
  • virus bioinformatics

Published Papers (1 paper)

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Research

17 pages, 1449 KiB  
Article
Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus
by Thomas Spicher, Markus Delitz, Adriano de Bernardi Schneider and Michael T. Wolfinger
Genes 2021, 12(2), 239; https://doi.org/10.3390/genes12020239 - 08 Feb 2021
Cited by 6 | Viewed by 3359
Abstract
Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks [...] Read more.
Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide. Full article
(This article belongs to the Special Issue Quest for Conserved RNAs in Viral Genomes)
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