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Special Issue "Recombination in 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 April 2011)

Special Issue Editor

Guest Editor
Dr. Matteo Negroni

CNRS-UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France
Website | E-Mail
Fax: +33 (0)388602218

Special Issue Information

Dear Colleagues,

Viruses are in a perpetual arm race with their hosts. Camouflage is a common strategy viruses use to escape to the immune system (either innate or adaptive) of their hosts. This generally translates in a propensity to develop replication strategies that are, at different extents, prone to the insertion of mutations in their genome. Accumulation of mutations is nevertheless limited by the need to maintain viability and its own genetic identity. Keeping the subtle equilibrium between these two contrasting forces is vital for viruses, it often influences their pathogenic potential, and can be at the origin of outbreaks of infection of relevance for public health.

Recombination is an important source of genetic variability in viruses, particularly for viruses possessing an RNA genome. The remarkable power of recombination resides in its ability, in a single infectious cycle, to generate new combinations of mutations. This is important at two regards: one is that recombination does not generate new mutations but reshuffles pre-existing ones, whose compatibility with viral survival has already been established. This is expected to increase the probability of having a viable recombinant progeny. On the other hand, the fact that, in general, several mutations are simultaneously introduced through the recombination process, is expected to favour the opposite outcome: that a high proportion of recombinant products will not be viable. Finally, recombination in concert with natural selection, can be responsible of combining advantageous mutations, as well as removing deleterious ones, by far the most abundant type of mutations found in nature.

For many viruses the generation of recombinant variants has been associated to important moments in the processes of adaptation, gain of pathogenic potential or increased spreading. Here we intend to present several of these cases and to provide an overlook of the implications of recombination for viral evolution from the theoretical standpoint. A life style involving increasing travelling with the result of an extensive intermingling of viruses, the making a reality of intervention strategies (as transgenic crops and gene therapy) often based on the use of viral vectors, all are issues for which an improved understanding of the role of recombination in viral evolution becomes increasingly urgent.

Dr. Matteo Negroni
Guest Editor

Keywords

  • recombination
  • viruses
  • evolution
  • genetic variability
  • natural selection

Published Papers (6 papers)

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Research

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Open AccessArticle Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus
Viruses 2011, 3(9), 1777-1799; doi:10.3390/v3091777
Received: 8 August 2011 / Revised: 24 August 2011 / Accepted: 5 September 2011 / Published: 23 September 2011
Cited by 19 | PDF Full-text (1175 KB) | Supplementary Files
Abstract
Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and
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Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus. Full article
(This article belongs to the Special Issue Recombination in Viruses)

Review

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Open AccessReview Recombination in Hepatitis C Virus
Viruses 2011, 3(10), 2006-2024; doi:10.3390/v3102006
Received: 20 September 2011 / Accepted: 13 October 2011 / Published: 24 October 2011
Cited by 31 | PDF Full-text (291 KB)
Abstract
Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high
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Hepatitis C virus (HCV) is a Flavivirus with a positive-sense, single-stranded RNA genome of about 9,600 nucleotides. It is a major cause of liver disease, infecting almost 200 million people all over the world. Similarly to most RNA viruses, HCV displays very high levels of genetic diversity which have been used to differentiate six major genotypes and about 80 subtypes. Although the different genotypes and subtypes share basic biological and pathogenic features they differ in clinical outcomes, response to treatment and epidemiology. The first HCV recombinant strain, in which different genome segments derived from parentals of different genotypes, was described in St. Petersburg (Russia) in 2002. Since then, there have been only a few more than a dozen reports including descriptions of HCV recombinants at all levels: between genotypes, between subtypes of the same genotype and even between strains of the same subtype. Here, we review the literature considering the reasons underlying the difficulties for unequivocally establishing recombination in this virus along with the analytical methods necessary to do it. Finally, we analyze the potential consequences, especially in clinical practice, of HCV recombination in light of the coming new therapeutic approaches against this virus. Full article
(This article belongs to the Special Issue Recombination in Viruses)
Open AccessReview Recombination in Eukaryotic Single Stranded DNA Viruses
Viruses 2011, 3(9), 1699-1738; doi:10.3390/v3091699
Received: 8 June 2011 / Revised: 18 August 2011 / Accepted: 5 September 2011 / Published: 13 September 2011
Cited by 62 | PDF Full-text (3832 KB)
Abstract
Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides
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Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution. Full article
(This article belongs to the Special Issue Recombination in Viruses)
Open AccessReview Mechanisms and Factors that Influence High Frequency Retroviral Recombination
Viruses 2011, 3(9), 1650-1680; doi:10.3390/v3091650
Received: 21 June 2011 / Revised: 18 August 2011 / Accepted: 25 August 2011 / Published: 9 September 2011
Cited by 29 | PDF Full-text (4166 KB)
Abstract
With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between
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With constantly changing environmental selection pressures, retroviruses rely upon recombination to reassort polymorphisms in their genomes and increase genetic diversity, which improves the chances for the survival of their population. Recombination occurs during DNA synthesis, whereby reverse transcriptase undergoes template switching events between the two copackaged RNAs, resulting in a viral recombinant with portions of the genetic information from each parental RNA. This review summarizes our current understanding of the factors and mechanisms influencing retroviral recombination, fidelity of the recombination process, and evaluates the subsequent viral diversity and fitness of the progeny recombinant. Specifically, the high mutation rates and high recombination frequencies of HIV-1 will be analyzed for their roles in influencing HIV-1 global diversity, as well as HIV-1 diagnosis, drug treatment, and vaccine development. Full article
(This article belongs to the Special Issue Recombination in Viruses)
Open AccessReview Recombination between Poliovirus and Coxsackie A Viruses of Species C: A Model of Viral Genetic Plasticity and Emergence
Viruses 2011, 3(8), 1460-1484; doi:10.3390/v3081460
Received: 2 June 2011 / Revised: 3 August 2011 / Accepted: 3 August 2011 / Published: 17 August 2011
Cited by 48 | PDF Full-text (2734 KB)
Abstract
Genetic recombination in RNA viruses was discovered many years ago for poliovirus (PV), an enterovirus of the Picornaviridae family, and studied using PV or other picornaviruses as models. Recently, recombination was shown to be a general phenomenon between different types of enteroviruses of
[...] Read more.
Genetic recombination in RNA viruses was discovered many years ago for poliovirus (PV), an enterovirus of the Picornaviridae family, and studied using PV or other picornaviruses as models. Recently, recombination was shown to be a general phenomenon between different types of enteroviruses of the same species. In particular, the interest for this mechanism of genetic plasticity was renewed with the emergence of pathogenic recombinant circulating vaccine-derived polioviruses (cVDPVs), which were implicated in poliomyelitis outbreaks in several regions of the world with insufficient vaccination coverage. Most of these cVDPVs had mosaic genomes constituted of mutated poliovaccine capsid sequences and part or all of the non-structural sequences from other human enteroviruses of species C (HEV-C), in particular coxsackie A viruses. A study in Madagascar showed that recombinant cVDPVs had been co-circulating in a small population of children with many different HEV-C types. This viral ecosystem showed a surprising and extensive biodiversity associated to several types and recombinant genotypes, indicating that intertypic genetic recombination was not only a mechanism of evolution for HEV-C, but an usual mode of genetic plasticity shaping viral diversity. Results suggested that recombination may be, in conjunction with mutations, implicated in the phenotypic diversity of enterovirus strains and in the emergence of new pathogenic strains. Nevertheless, little is known about the rules and mechanisms which govern genetic exchanges between HEV-C types, as well as about the importance of intertypic recombination in generating phenotypic variation. This review summarizes our current knowledge of the mechanisms of evolution of PV, in particular recombination events leading to the emergence of recombinant cVDPVs. Full article
(This article belongs to the Special Issue Recombination in Viruses)
Open AccessReview Homologous Recombination in Negative Sense RNA Viruses
Viruses 2011, 3(8), 1358-1373; doi:10.3390/v3081358
Received: 3 June 2011 / Revised: 12 July 2011 / Accepted: 22 July 2011 / Published: 4 August 2011
Cited by 31 | PDF Full-text (135 KB)
Abstract
Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally
[...] Read more.
Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur. Full article
(This article belongs to the Special Issue Recombination in Viruses)

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