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Recombination as an Evolutionary Force in Animal Viruses

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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 9953

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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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Dear Colleagues,

Recombination has long been recognized as an important driver of evolution in viruses, particularly in those with RNA genomes, by rapidly creating genetic diversity. 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 allow adaptation to new environments and hosts. Indeed, recombination has been frequently associated with the emergence of new viruses and outbreaks, the expansion of the host range and species jump, changes in virulence and pathogenesis, the alteration of tissue tropism, evasion from 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 emphasis on recombination mechanisms, evolutionary aspects of recombination, and recombination as a driver of virus emergence and species jump. Novel bioinformatic approaches for the detection and characterization of recombination events in animal viruses are also welcome.

Dr. Joana Abrantes
Guest Editor

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Keywords

evolution
animal viruses
recombination
natural selection

Related Special Issue

Recombination as An Evolutionary Force in Animal Viruses 2022 in Viruses (2 articles)

Published Papers (3 papers)

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Research

19 pages, 7021 KiB

Open AccessEditor’s ChoiceArticle

Modular Evolution of Coronavirus Genomes

by Yulia Vakulenko, Andrei Deviatkin, Jan Felix Drexler and Alexander Lukashev

Viruses 2021, 13(7), 1270; https://0-doi-org.brum.beds.ac.uk/10.3390/v13071270 - 29 Jun 2021

Cited by 18 | Viewed by 3952

Abstract

The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses. Full article

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

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13 pages, 2412 KiB

Open AccessArticle

A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft

by Anthony Khalifeh, Simona Kraberger, Daria Dziewulska, Arvind Varsani and Tomasz Stenzel

Viruses 2021, 13(6), 964; https://0-doi-org.brum.beds.ac.uk/10.3390/v13060964 - 22 May 2021

Cited by 6 | Viewed by 2470

Abstract

Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the aim to study the spread and recombination dynamics of PiCV in the birds. Genome sequences of PiCV were determined from seven pigeons (seven tested PiCV positive) before they were housed together in a loft (n = 58 sequences) and thereafter from the ten pigeons from blood and cloacal swabs (n = 120). These 178 PiCV genome sequences represent seven genotypes (98% pairwise identity genotype demarcation), and they share >88% genome-wide pairwise identity. Recombination analysis revealed 13 recombination events, and a recombination hotspot spanning the 3′ prime region, the replication-associated protein (rep) gene and the intergenic region. A cold spot in the capsid protein-coding region of the genome was also identified. The majority of the recombinant regions were identified in the rep coding region. This study provides insights into the evolutionary dynamics of PiCV in pigeons kept under closed rearing systems. Full article

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

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16 pages, 1267 KiB

Open AccessArticle

Analysis of Whole-Genome Sequences of Infectious laryngotracheitis Virus Isolates from Poultry Flocks in Canada: Evidence of Recombination

by Ana Perez Contreras, Frank van der Meer, Sylvia Checkley, Tomy Joseph, Robin King, Madhu Ravi, Delores Peters, Kevin Fonseca, Carl A. Gagnon, Chantale Provost, Davor Ojkic and Mohamed Faizal Abdul-Careem

Viruses 2020, 12(11), 1302; https://0-doi-org.brum.beds.ac.uk/10.3390/v12111302 - 12 Nov 2020

Cited by 9 | Viewed by 2719

Abstract

Infectious laryngotracheitis virus (ILTV) is a herpes virus that causes an acute respiratory disease of poultry known as infectious laryngotracheitis (ILT). Chicken embryo origin (CEO) and tissue culture origin (TCO) live attenuated vaccines are routinely used for the control of ILT. However, vaccine virus is known to revert to virulence, and it has been recently shown that ILT field viral strains can undergo recombination with vaccinal ILTV and such recombinant ILT viruses possess greater transmission and pathogenicity potential. Based on complete or partial genes of the ILTV genome, few studies genotyped ILTV strains circulating in Canada, and so far, information is scarce on whole-genome sequencing or the presence of recombination in Canadian ILTV isolates. The objective of this study was to genetically characterize the 14 ILTV isolates that originated from three provinces in Canada (Alberta, British Columbia and Quebec). To this end, a phylogenetic analysis of 50 ILTV complete genome sequences, including 14 sequences of Canadian origin, was carried out. Additional phylogenetic analysis of the unique long, unique short and inverted repeat regions of the ILTV genome was also performed. We observed that 71%, 21% and 7% of the ILTV isolates were categorized as CEO revertant, wild-type and TCO vaccine-related, respectively. The sequences were also analyzed for potential recombination events, which included evidence in the British Columbia ILTV isolate. This event involved two ILTV vaccine (CEO) strains as parental strains. Recombination analysis also identified that one ILTV isolate from Alberta as a potential parental strain for a United States origin ILTV isolate. The positions of the possible recombination breakpoints were identified. These results indicate that the ILTV wild-type strains can recombine with vaccinal strains complicating vaccine-mediated control of ILT. Further studies on the pathogenicity of these ILTV strains, including the recombinant ILTV isolate are currently ongoing. Full article

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

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