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Virus Evolution and Mutagenesis
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Virus Evolution and Mutagenesis

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

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 13102

Special Issue Editors

Prof. Dr. Louis M. Mansky

E-Mail Website
Guest Editor
Institute for Molecular Virology, Division of Basic Sciences, University of Minnesota, Minneapolis, MN, USA
Interests: human retroviruses; virus assembly; reverse transcription; retroviral diversity and evolution; antiretroviral
Special Issues, Collections and Topics in MDPI journals
Prof. Esteban Domingo Solans

E-Mail Website
Guest Editor
CSIC-UAM - Centro de Biología Molecular Severo Ochoa (CBM), Madrid, Spain
Interests: RNA virus quasispecies; quasispecies dynamics; lethal mutagenesis

Special Issue Information

Dear Colleagues,

Experimental evolution has immensely benefited from the study of viral evolution. Viruses have relatively rapid replication rates, which allows for the quantitative study of mutational processes and their impact on evolutionary rates, natural selection and population diversity. In particular, RNA viruses are known to exhibit high mutation rates and generate virus quasispecies, which harbor populations of closely-related genomes (i.e., mutant swarms or clouds) that lends to direct experimentation of fitness selection, adaptation, and virus evolution in connection with viral pathogenesis. The parallels between viral quasispecies and that of tumor cell heterogeneity and dynamics have also led to deeper insights into both areas of investigation.

This Special Issue on "Virus Evolution and Mutagenesis" seeks author contributions on topics that include replication fidelity, virus mutagenesis, mutation rates, population complexity, insights from deep sequencing, error thresholds, lethal mutagenesis, mutation-selection balance, recombination, fitness landscapes, mutational robustness, virus complementation/interference, and tumor cell heterogeneity and dynamics.

Prof. Esteban Domingo Solans
Prof. Louis M. Mansky
Guest Editors

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

  • mutation rate
  • quasispecies
  • population dynamics
  • deep sequencing
  • lethal mutagenesis
  • tumor cell heterogeneity

Published Papers (4 papers)

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Research

17 pages, 2999 KiB  
Article
Divergent Mutational Landscapes of Consensus and Minority Genotypes of West Nile Virus Demonstrate Host and Gene-Specific Evolutionary Pressures
by Haley S. Caldwell, Erica Lasek-Nesselquist, Paisley Follano, Laura D. Kramer and Alexander T. Ciota
Genes 2020, 11(11), 1299; https://doi.org/10.3390/genes11111299 - 30 Oct 2020
Cited by 6 | Viewed by 2412
Abstract
Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the [...] Read more.
Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the capacity for swarm plasticity is likely to be particularly important for arthropod-borne viruses (arboviruses) that cycle between taxonomically divergent hosts. Despite this, characterization of the relationship between the selective pressures and genetic signatures of the mutant swarm and consensus sequences is lacking. To clarify this, we analyzed previously generated whole genome, deep-sequencing data from 548 West Nile virus samples isolated from avian tissues or mosquitoes in New York State from 1999–2018. Both consensus level (interhost) and minority level (intrahost) nucleotide and amino acid sequences were analyzed, and diversity at each position was calculated across the genome in order to assess the relationship between minority and consensus sequences for individual genes and hosts. Our results indicate that consensus sequences are an inept representation of the overall genetic diversity. Unique host and gene-specific signatures and selective pressures were identified. These data demonstrate that an accurate and comprehensive understanding of arbovirus evolution and adaptation within and between hosts requires consideration of minority genotypes. Full article
(This article belongs to the Special Issue Virus Evolution and Mutagenesis)
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13 pages, 770 KiB  
Article
Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P–GI.1d Strains
by Joana Abrantes, Ana M. Lopes, Evelyne Lemaitre, Harri Ahola, Fereshteh Banihashem, Clément Droillard, Stéphane Marchandeau, Pedro J. Esteves, Aleksija Neimanis and Ghislaine Le Gall-Reculé
Genes 2020, 11(8), 910; https://doi.org/10.3390/genes11080910 - 09 Aug 2020
Cited by 11 | Viewed by 2510
Abstract
Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of [...] Read more.
Recombination is one of the major sources of genetic variation in viruses. RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P–GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P–GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P–GI.2, we hypothesize that GI.3P–GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences. Full article
(This article belongs to the Special Issue Virus Evolution and Mutagenesis)
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15 pages, 1238 KiB  
Article
Coding-Gene Coevolution Analysis of Rotavirus Proteins: A Bioinformatics and Statistical Approach
by Nabil Abid, Giovanni Chillemi and Marco Salemi
Genes 2020, 11(1), 28; https://doi.org/10.3390/genes11010028 - 24 Dec 2019
Cited by 2 | Viewed by 3567
Abstract
Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral [...] Read more.
Rotavirus remains a major cause of diarrhea in infants and young children worldwide. The permanent emergence of new genotypes puts the potential effectiveness of vaccines under serious question. The distribution of unusual genotypes subject to viral fitness is influenced by interactions among viral proteins. The present work aimed at analyzing the genetic constellation and the coevolution of rotavirus coding genes for the available rotavirus genotypes. Seventy-two full genome sequences of different genetic constellations were analyzed using a genetic algorithm. The results revealed an extensive genome-wide covariance network among the 12 viral proteins. Altogether, the emergence of new genotypes represents a challenge to the outcome and success of vaccination and the coevolutionary analysis of rotavirus proteins may boost efforts to better understand the interaction networks of proteins during viral replication/transcription. Full article
(This article belongs to the Special Issue Virus Evolution and Mutagenesis)
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16 pages, 1705 KiB  
Article
RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination
by Hyejeong Kim, Victor D. Ellis III, Andrew Woodman, Yan Zhao, Jamie J. Arnold and Craig E. Cameron
Genes 2019, 10(12), 968; https://doi.org/10.3390/genes10120968 - 25 Nov 2019
Cited by 8 | Viewed by 3548
Abstract
Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type [...] Read more.
Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type enzyme. In the context of the KH virus, RdRp-coding sequence evolves, selecting for the following substitutions: I331F (IF, motif-C) and P356S (PS, motif-D). We have evaluated IF-KH, PS-KH, and IF-PS-KH viruses and enzymes. The speed and fidelity of each double mutant are equivalent. Each exhibits a unique recombination phenotype, with IF-KH being competent for copy-choice recombination and PS-KH being competent for forced-copy-choice recombination. Although the IF-PS-KH RdRp exhibits biochemical properties within twofold of wild type, the virus is impaired substantially for recombination in cells. We conclude that there are biochemical properties of the RdRp in addition to speed and fidelity that determine the mechanism and efficiency of recombination. The interwoven nature of speed, fidelity, the undefined property suggested here, and recombination makes it impossible to attribute a single property of the RdRp to fitness. However, the derivatives described here may permit elucidation of the importance of recombination on the fitness of the viral population in a background of constant polymerase speed and fidelity. Full article
(This article belongs to the Special Issue Virus Evolution and Mutagenesis)
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