Evidence for homologous recombination in Chikungunya Virus

Casal, Pablo E.; Chouhy, Diego; Bolatti, Elisa Maria; Pérez, Germán; Stella, Emma J.; Giri, Adriana A.

doi:10.1016/j.ympev.2015.01.016

Cited by 18 publications

(20 citation statements)

References 35 publications

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“…Recombination has played an important role as a mechanism of diversification and evolution for RNA viruses, resulting in new species, genera, or even new families, including the chimeric ancestors of the present-day alphavirus clade 1 , 25 , 26 . Genomic recombination has also been observed previously within the alphavirus genera 27 – 29 , as phylogenetic analyses have indicated that Sindbis and Eastern equine encephalitis viruses gave rise to the Western equine encephalitis virus complex 25 . More recently, intra-species recombination, potentially involved in the cross-species transmission process, was identified for CHIKV based on nucleotide identify and phylogenetic tree incongruence analyses 27 .…”

Section: Introductionsupporting

confidence: 64%

“…Genomic recombination has also been observed previously within the alphavirus genera 27 – 29 , as phylogenetic analyses have indicated that Sindbis and Eastern equine encephalitis viruses gave rise to the Western equine encephalitis virus complex 25 . More recently, intra-species recombination, potentially involved in the cross-species transmission process, was identified for CHIKV based on nucleotide identify and phylogenetic tree incongruence analyses 27 . However, the extent of intra-species recombination for MAYV has not been investigated, nor the role of recombination in evolution and its relationship with MAYV spread among human populations.…”

Section: Introductionsupporting

confidence: 64%

“…Recombination in RNA viruses can be of major evolutionary significance. Recombination processes allows viruses to acquire key adaptive mutations in a single step that might enhance fitness, host tropism, or virulence 29 , such as the potential cross-species transmission effects of the recently identified CHIKV recombinant strain 27 . The ability and opportunity of MAYV to recombine are likely to provide a broader and more rapid search through the viral fitness landscape, thereby facilitating host adaptation 29 .…”

Section: Discussionmentioning

confidence: 99%

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Emergence of recombinant Mayaro virus strains from the Amazon basin

Mavian

Rife

Dollar

et al. 2017

Sci Rep

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Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents a barrier to prevention of further spread. We present a thorough spatiotemporal evolutionary study of MAYV full-genome sequences collected over the last sixty years within South America and Haiti, revealing recent recombination events and adaptation to a broad host and vector range, including Aedes mosquito species. We employed a Bayesian phylogeography approach to characterize the emergence of recombinants in Brazil and Haiti and report evidence in favor of the putative role of human mobility in facilitating recombination among MAYV strains from geographically distinct regions. Spatiotemporal characteristics of recombination events and the emergence of this previously neglected virus in Haiti, a known hub for pathogen spread to the Americas, warrants close monitoring of MAYV infection in the immediate future.

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Section: Introductionsupporting

confidence: 64%

Section: Introductionsupporting

confidence: 64%

Section: Discussionmentioning

confidence: 99%

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Emergence of recombinant Mayaro virus strains from the Amazon basin

Mavian

Rife

Dollar

et al. 2017

Sci Rep

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“…Mutation occurs during replication by mis-introduction of nucleotides by error-prone RNA-dependent RNA polymerases that lack proof-reading capacity. Recombination occurs when co-circulating lineages co-infect a host and mixed segments are incorporated into the descendent viruses [25].…”

Section: Conserved Rna Structure As Evolutionary Traitmentioning

confidence: 99%

Updated Phylogeny of Chikungunya Virus Reveals Lineage-Specific RNA Architecture

Schneider¹,

Ochsenreiter²,

Hostager³

et al. 2019

Preprint

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Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents, Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3'UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3'UTR architecture among different CHIKV lineages.

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“…Apart from DI, viral RNA genome may in some cases be rearranged. For the positive strand RNA virus, that rearrangement is very frequent, mainly because, during viral replication, RNA genome is naked in the cytoplasm and the RNA polymerase may jump from one replicative genome to another one [ 6 , 7 ]. In contrast, for negative strand RNA virus, recombination event has never been described, with a single exception for Respiratory Syncytial Virus for which a co-infection with two replication-competent viruses, knock-out for NS1/NS2 and G genes, resulted in the generation of a virus with a rearranged genome [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Efficient Co-Replication of Defective Novirhabdovirus

Rouxel

Mérour

Biacchesi

et al. 2016

Viruses

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We have generated defective Viral Hemorrhagic Septicemia Viruses (VHSV) which express either the green fluorescent protein (GFP) or a far-red fluorescent protein (mKate) by replacing the genes encoding the nucleoprotein N or the polymerase-associated P protein. To recover viable defective viruses, rVHSV-ΔN-Red and rVHSV-ΔP-Green, fish cells were co-transfected with both deleted cDNA VHSV genomes, together with plasmids expressing N, P and L of the RNA-dependent RNA polymerase. After one passage of the transfected cell supernatant, red and green cell foci were observed. Viral titer reached 107 PFU/mL after three passages. Infected cells were always red and green with the very rare event of single red or green cell foci appearing. To clarify our understanding of how such defective viruses could be so efficiently propagated, we investigated whether (i) a recombination event between both defective genomes had occurred, (ii) whether both genomes were co-encapsidated in a single viral particle, and (iii) whether both defective viruses were always replicated together through a complementation phenomenon or even as conglomerate. To address these hypotheses, genome and viral particles have been fully characterized and, thus, allowing us to conclude that rVHSV-ΔN-Red and rVHSV-ΔP-Green are independent viral particles which could propagate only by simultaneously infecting the same cells.

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Evidence for homologous recombination in Chikungunya Virus

Cited by 18 publications

References 35 publications

Emergence of recombinant Mayaro virus strains from the Amazon basin

Emergence of recombinant Mayaro virus strains from the Amazon basin

Updated Phylogeny of Chikungunya Virus Reveals Lineage-Specific RNA Architecture

Efficient Co-Replication of Defective Novirhabdovirus

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