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      Why do RNA viruses recombine?

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          Key Points

          • RNA viruses are able to undergo two forms of recombination: RNA recombination, which (in principle) can occur in any type of RNA virus, and reassortment, which is restricted to those viruses with segmented genomes.

          • Rates of RNA recombination vary markedly among RNA viruses. Some viruses, particularly those with negative-sense single-stranded genomes, exhibit such low rates of recombination that they are effectively clonal. By contrast, some positive-sense single-stranded RNA viruses and some retroviruses such as HIV exhibit high rates of recombination that can exceed the rates of mutation when measured per nucleotide.

          • Although recombination is often argued to represent a form of sexual reproduction, there is little evidence that recombination in RNA viruses evolved as a way of creating advantageous genotypes or removing deleterious mutations. In particular, there is no association between recombination frequency and the burden of a deleterious mutation. Similarly, there is little evidence that recombination could have been selected as a form of genetic repair.

          • The strongest association for rates of recombination in RNA viruses is with genome structure. Hence, negative-sense single-stranded RNA viruses may recombine at low rates because of the restrictive association of genomic RNA in a ribonucleoprotein complex, as well as a lack of substrates for template switching, whereas some retroviruses recombine rapidly because their virions contain two genome copies and template switching between these copies is an inevitable part of the viral replication cycle.

          • We therefore hypothesize that recombination in RNA viruses is a mechanistic by-product of the processivity of the viral polymerase that is used in replication, and that it varies with genome structure.

          Abstract

          Recombination can be an important evolutionary force for RNA viruses, but the rate of recombination varies greatly between different RNA viruses. In this Analysis article, Simon-Loriere and Holmes describe the mechanisms of recombination for RNA viruses and the role of these mechanisms in viral evolution.

          Abstract

          Recombination occurs in many RNA viruses and can be of major evolutionary significance. However, rates of recombination vary dramatically among RNA viruses, which can range from clonal to highly recombinogenic. Here, we review the factors that might explain this variation in recombination frequency and show that there is little evidence that recombination is favoured by natural selection to create advantageous genotypes or purge deleterious mutations, as predicted if recombination functions as a form of sexual reproduction. Rather, recombination rates seemingly reflect larger-scale patterns of viral genome organization, such that recombination may be a mechanistic by-product of the evolutionary pressures acting on other aspects of virus biology.

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          Most cited references108

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          Deleterious mutations and the evolution of sexual reproduction.

          The origin and maintenance of sexual reproduction continues to be an important problem in evolutionary biology. If the deleterious mutation rate per genome per generation is greater than 1, then the greater efficiency of selection against these mutations in sexual populations may be responsible for the evolution of sex and related phenomena. In modern human populations detrimental mutations with small individual effects are probably accumulating faster than they are being eliminated by selection.
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            Influenza: lessons from past pandemics, warnings from current incidents.

            Recent outbreaks of highly pathogenic avian influenza A virus infections (H5 and H7 subtypes) in poultry and in humans (through direct contact with infected birds) have had important economic repercussions and have raised concerns that a new influenza pandemic will occur in the near future. The eradication of pathogenic avian influenza viruses seems to be the most effective way to prevent influenza pandemics, although this strategy has not proven successful so far. Here, we review the molecular factors that contribute to the emergence of pandemic strains.
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              Evolutionary aspects of recombination in RNA viruses.

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                Author and article information

                Contributors
                ech15@psu.edu
                Journal
                Nat Rev Microbiol
                Nat. Rev. Microbiol
                Nature Reviews. Microbiology
                Nature Publishing Group UK (London )
                1740-1526
                1740-1534
                4 July 2011
                2011
                : 9
                : 8
                : 617-626
                Affiliations
                [1 ]GRID grid.29857.31, ISNI 0000 0001 2097 4281, Department of Biology, , Center for Infectious Disease Dynamics, Mueller Laboratory, The Pennsylvania State University, ; University Park, 16802 Pennsylvania USA
                [2 ]GRID grid.453035.4, ISNI 0000 0004 0533 8254, Fogarty International Center, National Institutes of Health, ; Bethesda, 20892 Maryland USA
                Article
                BFnrmicro2614
                10.1038/nrmicro2614
                3324781
                21725337
                db3c214f-c87d-4565-81d3-84ed310bf04e
                © Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2011

                This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.

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                © Springer Nature Limited 2011

                virology,evolution,evolutionary biology,viral genetics,retrovirus

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