Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences

Tolou, Hugues; Couissinier-Paris, Patricia; Durand, Jean Paul; Mercier, V.; Jj, De Pina; Micco, Philippe de; Billoir, Frédérique; Charrel, Rémi N.; Lamballerie, Xavier de

doi:10.1099/0022-1317-82-6-1283

Cited by 123 publications

(85 citation statements)

References 21 publications

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“…Sporadic recombinants have been detected for flaviviruses such as hepatitis C (38, 39), dengue virus (40,41), and West Nile virus (42). However, some of these reports, as in dengue, have been shown to be the product of sequencing error (43), and it is generally agreed that if recombination occurs, it is rare.…”

Section: Resultsmentioning

confidence: 99%

Topology of viral evolution

Chan

Carlsson

Rabadán

2013

Proc. Natl. Acad. Sci. U.S.A.

225

189

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The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate. n On the Origin of the Species in 1859, Darwin first proposed the phylogenetic tree as a structure to describe the evolution of phenotypic attributes. Since then, the advancement of modern sequencing has spurred development of a number of phylogenetic inference methods (1, 2). The tree structure effectively models vertical or clonal evolution, mediated by random mutations over multiple generations (Fig. 1A). Phylogenetic trees, however, cannot capture horizontal, or reticulate, events, which occur when distinct clades merge together to form a new hybrid lineage ( Fig. 1B and SI Appendix, Fig. S1). In nature, horizontal evolution can occur through species hybridization in eukaryotes, lateral gene transfer in bacteria, recombination and reassortment in viruses, viral integration in eukaryotes, and fusion of genomes of symbiotic species (e.g., mitochondria). These horizontal genetic exchanges create incompatibilities that mischaracterize the species tree (3). Doolittle (4) argued that molecular phylogeneticists have failed to identify the "true tree of life" because the history of living organisms cannot be understood as a tree. One may wonder what other mathematical structures beyond phylogeny can capture the richness of evolutionary processes.Current techniques that detect reticulate events can be divided into phylogenetic and nonphylogenetic methodologies. Phylogenetic methods detect incongruence in the tree structure of different segments (5-8). Nonphylogenetic methods probe for homoplasies (shared character traits independently arising in different lineages by convergent or parallel evolution) or similar inconsistencies in sequence alignment (9-...

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Section: Resultsmentioning

confidence: 99%

Topology of viral evolution

Chan

Carlsson

Rabadán

2013

Proc. Natl. Acad. Sci. U.S.A.

225

189

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“…However, the co-circulation of different DENV populations, including different genotypes, is a factor that increases the chances of the occurrence of mixed infections both in the mosquito vector and in the human host [45,46], which in turn could favor the occurrence of recombination, as observed in Brazil, where different DENV-1 lineages from genotype V have been co-circulating. Although it is not possible to determine whether recombination has occurred in the mosquito vector, the human host or in vitro (during virus replication in C6/36 cells), or when these events might have occurred among the Brazilian DENV-1 isolates, recombination events have already been described in natural populations, including intra and inter-genotypic recombinants, as described for DENV-1 and DENV-2 [19,45,[47][48][49]. Although it is likely that most recombinant events are deleterious and thus eliminated by purifying selection, some of them could result in an increase in the fitness of the virus.…”

Section: Discussionmentioning

confidence: 99%

“…Although it is likely that most recombinant events are deleterious and thus eliminated by purifying selection, some of them could result in an increase in the fitness of the virus. These events could have important implications for virus evolution, virulence, and diagnosis and for the development of vaccines and therapeutic drugs [45,47,49].…”

Section: Discussionmentioning

confidence: 99%

Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement

et al. 2012

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“…Tolou et al, 2001;Uzcategui et al, 2001;, hepaciviruses (GB virus C/hepatitis G virus) (Worobey & Holmes, 2001) and Japanese encephalitis or St Louis encephalitis virus (Twiddy & Holmes, 2003). There have been few reports on recombination between HCV strains of different genotypes (Kalinina et al, 2002;Yun et al, 1996) and it has been suggested that these events are rare in vivo and that the resultant recombinants are usually not viable (Simmonds et al, 1994;Smith & Simmonds, 1997).…”

Section: Introductionmentioning

confidence: 99%

Evidence of intratypic recombination in natural populations of hepatitis C virus

Colina

Casañe

Vásquez³

et al. 2004

Journal of General Virology

114

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Hepatitis C virus (HCV) has high genomic variability and, since its discovery, at least six different types and an increasing number of subtypes have been reported. Genotype 1 is the most prevalent genotype found in South America. In the present study, three different genomic regions (59UTR, core and NS5B) of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions. Phylogenetic analysis using 59UTR-core sequences found strain PE22 to be related to subtype 1b. However, the same analysis using the NS5B region found it to be related to subtype 1a. To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossover event had taken place in the NS5B protein. We discuss the consequences of this observation on HCV genotype classification, laboratory diagnosis and treatment of HCV infection.

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Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences

Cited by 123 publications

References 21 publications

Topology of viral evolution

Topology of viral evolution

Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement

Evidence of intratypic recombination in natural populations of hepatitis C virus

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