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Special Issue Editor

Dr. Joana Abrantes

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Guest Editor

1. Research Centre in Biodiversity and Genetic Resources (CIBIO), Research Network in Biodiversity and Evolutionary Biology (InBIO), University of Porto, Porto, Portugal
2. Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
Interests: RNA viruses; rabbit hemorrhagic disease virus; virus evolution; virus recombination; species jump; immunogenetics
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Special Issue Information

Dear Colleagues,

Recombination has long been recognized as an important driver of evolution in viruses through the rapid creation of genetic diversity, particularly in those with RNA genomes. Such diversity is achieved through a non-reciprocal combination of genomic segments from at least two viruses that co-infect the same host cell. The new genomic architecture of the resulting recombinant virus can positively contribute to viral fitness and can successfully adapt to new environments and hosts. Indeed, recombination is frequently associated with the emergence of new viruses and outbreaks, expansion of the host range and species jump, changes in virulence and pathogenesis, alterations of tissue tropism, and the evasion of host immunity and antiviral resistance.

This Special Issue of Viruses aims to gather a series of articles—original research and reviews—on recombination in RNA and DNA animal viruses, with an emphasis on recombination mechanisms, the evolutionary aspects of recombination, and recombination as a driver of virus emergence and species jump. Novel bioinformatic approaches to the detection and characterization of recombination events in animal viruses are also welcome.

Dr. Joana Abrantes
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. Viruses 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.

Related Special Issue

Published Papers (2 papers)

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Research

17 pages, 4147 KiB

Open AccessArticle

Patterns and Temporal Dynamics of Natural Recombination in Noroviruses

by Yulia A. Vakulenko, Artem V. Orlov and Alexander N. Lukashev

Viruses 2023, 15(2), 372; https://doi.org/10.3390/v15020372 - 28 Jan 2023

Cited by 4 | Viewed by 1943

Abstract

Noroviruses infect a wide range of mammals and are the major cause of gastroenteritis in humans. Recombination at the junction of ORF1 encoding nonstructural proteins and ORF2 encoding major capsid protein VP1 is a well-known feature of noroviruses. Using all available complete norovirus sequences, we systematically analyzed patterns of natural recombination in the genus Norovirus both throughout the genome and across the genogroups. Recombination events between nonstructural (ORF1) and structural genomic regions (ORF2 and ORF3) were found in all analyzed genogroups of noroviruses, although recombination was most prominent between members of GII, the most common genogroup that infects humans. The half-life times of recombinant forms (clades without evidence of recombination) of human GI and GII noroviruses were 10.4 and 8.4–11.3 years, respectively. There was evidence of many recent recombination events, and most noroviruses that differed by more than 18% of nucleotide sequence were recombinant relative to each other. However, there were no distinct recombination events between viruses that differed by over 42% in ORF2/3, consistent with the absence of systematic recombination between different genogroups. The few inter-genogroup recombination events most likely occurred between ancient viruses before they diverged into contemporary genogroups. The recombination events within ORF1 or between ORF2/3 were generally rare. Thus, noroviruses routinely exchange full structural and nonstructural blocks of the genome, providing a modular evolution. Full article

(This article belongs to the Special Issue Recombination as An Evolutionary Force in Animal Viruses 2022)

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15 pages, 2697 KiB

Open AccessArticle

A Naturally Occurring Microhomology-Mediated Deletion of Three Genes in African Swine Fever Virus Isolated from Two Sardinian Wild Boars

by Mariangela Stefania Fiori, Luca Ferretti, Antonello Di Nardo, Lele Zhao, Susanna Zinellu, Pier Paolo Angioi, Matteo Floris, Anna Maria Sechi, Stefano Denti, Stefano Cappai, Giulia Franzoni, Annalisa Oggiano and Silvia Dei Giudici

Viruses 2022, 14(11), 2524; https://doi.org/10.3390/v14112524 - 14 Nov 2022

Cited by 1 | Viewed by 1467

Abstract

African swine fever virus (ASFV) is the etiological agent of a lethal disease of domestic pigs and wild boars. ASF threatens the pig industry worldwide due to the lack of a licensed vaccine or treatment. The disease has been endemic for more than 40 years in Sardinia (Italy), but an intense campaign pushed it close to eradication; virus circulation was last detected in wild boars in 2019. In this study, we present a genomic analysis of two ASFV strains isolated in Sardinia from two wild boars during the 2019 hunting season. Both isolates presented a deletion of 4342 base pairs near the 5′ end of the genome, encompassing the genes MGF 360-6L, X69R, and MGF 300-1L. The phylogenetic evidence suggests that the deletion recently originated within the Sardinia ecosystem and that it is most likely the result of a non-allelic homologous recombination driven by a microhomology present in most Sardinian ASFV genomes. These results represent a striking example of a genomic feature promoting the rapid evolution of structural variations and plasticity in the ASFV genome. They also raise interesting questions about the functions of the deleted genes and the potential link between the evolutionary timing of the deletion appearance and the eradication campaign. Full article

(This article belongs to the Special Issue Recombination as An Evolutionary Force in Animal Viruses 2022)

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