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dc.contributor.author Bertrand, Yann
dc.contributor.author Töpel, Mats
dc.contributor.author Elväng, Annelie
dc.contributor.author Melik, Wessam
dc.contributor.author Johansson, Magnus
dc.date.accessioned 2012-11-07T18:02:16Z
dc.date.available 2012-11-07T18:02:16Z
dc.date.issued 2012-02-22
dc.identifier doi:10.5061/dryad.504636cd
dc.identifier.citation Bertrand Y, Töpel M, Elväng A, Melik W, Johansson M (2012) First dating of a recombination event in mammalian tick-borne flaviviruses. PLoS ONE, 7(2): e31981.
dc.identifier.uri http://hdl.handle.net/10255/dryad.37480
dc.description The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus TBEV. We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window period of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses
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dc.relation.isreferencedby doi:10.1371/journal.pone.0031981
dc.relation.isreferencedby PMID:22384119
dc.subject mammalian tick-borne flavivirus group
dc.subject Bayesian dating
dc.subject recombination
dc.subject Louping ill virus
dc.subject Tick-borne encephalitis virus
dc.subject network
dc.subject phylogeny
dc.title Data from: First dating of a recombination event in mammalian tick-borne flaviviruses
dc.type Article *
dwc.ScientificName Tick-borne encephalitis virus
dc.contributor.correspondingAuthor Bertrand, Yann
prism.publicationName PLoS ONE

Files in this package

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Title ALN1
Downloaded 52 times
Description Alignment that contains 41 complete nucleotide sequences of Tick-borne encephalitis virus and three out-groups selected among LGTV and OHFV, retrieved from Genbank in January 2011.
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Title ALN2
Downloaded 48 times
Description Alignment that contains 28 sequences from ALN1 of known collection dates (from 1937 to 2008), with the deletion of out-groups and strains with unusual sampling locations. Non coding flanking regions and gap columns were removed.
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Title ALN2_1
Downloaded 39 times
Description Alignment derived from ALN2.fas that corresponds to the putative recombinant region (204nt).
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Title ALN2_2
Downloaded 46 times
Description Alignment derived from ALN2.fas with the deletion of the putative recombinant region.
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Title ALN2_C
Downloaded 43 times
Description Alignment derived from ALN2.fas that corresponds to the C-gene region.
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Title ALN2_E
Downloaded 42 times
Description Alignment derived from ALN2.fas that corresponds to the E-gene region.
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Title ALN2_NS1
Downloaded 43 times
Description Alignment derived from ALN2.fas that corresponds to the NS1-gene region.
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Title ALN2_NS2A
Downloaded 46 times
Description Alignment derived from ALN2.fas that corresponds to the NS2A-gene region.
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Title ALN2_NS2B
Downloaded 44 times
Description Alignment derived from ALN2.fas that corresponds to the NS2B-gene region.
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Title ALN2_NS3
Downloaded 46 times
Description Alignment derived from ALN2.fas that corresponds to the NS3-gene region.
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Title ALN2_NS4A
Downloaded 42 times
Description Alignment derived from ALN2.fas that corresponds to the NS4A-gene region.
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Title ALN2_NS4B
Downloaded 48 times
Description Alignment derived from ALN2.fas that corresponds to the NS4B-gene region.
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Title ALN2_NS5
Downloaded 49 times
Description Alignment derived from ALN2.fas that corresponds to the NS5-gene region.
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Title ALN2_PrM
Downloaded 45 times
Description Alignment derived from ALN2.fas that corresponds to the PrM-gene region.
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Title ALN3
Downloaded 48 times
Description Alignment based on ALN2.fas with the deletion of the E gene and the region of NS3 identified as a possible recombinant fragment.
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Title E_161
Downloaded 45 times
Description Alignment compiled from the 161 longest E-sequences from Tick-borne encephalitis virus species available in Genbank (1033 to 1491 nt in length) endowed with sampling dates (from 1931 to 2008) retrieved in January 2011.
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Title Beast_inference1_C
Downloaded 40 times
Description Beast xml file used in Beast inference 1 for the C-gene.
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Title Beast_inference1_E
Downloaded 45 times
Description Beast xml file used in Beast inference 1 for the E-gene.
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Title Beast_inference1_NS1
Downloaded 42 times
Description Beast xml file used in Beast inference 1 for the NS1-gene.
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Title Beast_inference1_NS2A
Downloaded 41 times
Description Beast xml file used in Beast inference 1 for the NS2A-gene.
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Title Beast_inference1_NS2B
Downloaded 47 times
Description Beast xml file used in Beast inference 1 for the NS2B-gene.
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Title Beast_inference1_NS3
Downloaded 49 times
Description Beast xml file used in Beast inference 1 for the NS3-gene.
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Title Beast_inference1_NS4A
Downloaded 49 times
Description Beast xml file used in Beast inference 1 for the NS4A-gene.
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Title Beast_inference1_NS4B
Downloaded 46 times
Description Beast xml file used in Beast inference 1 for the NS4B-gene.
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Title Beast_inference1_NS5
Downloaded 49 times
Description Beast xml file used in Beast inference 1 for the NS5-gene.
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Title Beast_inference1_PrM
Downloaded 45 times
Description Beast xml file used in Beast inference 1 for the PrM-gene.
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Title Beast_inference2_ALN2_1
Downloaded 43 times
Description Beast xml file used in Beast inference 2 for the putative recombinant region of the genome.
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Title Beast_inference2_ALN2_2
Downloaded 50 times
Description Beast xml file used in Beast inference 2 for the putative non-recombinant region of the genome.
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Title Beast_inference3
Downloaded 46 times
Description Beast xml file used in Beast inference 3 based on the 28 full length ORFs with both E-gene and the recombinant fragment omitted.
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Title Beast_inference4_E_161
Downloaded 41 times
Description Beast xml file used in Beast inference 4 for analysing the 161 longest E-sequences.
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Title Figure3_a_BI
Downloaded 50 times
Description Tree file corresponding to result of the Bayesian inference reported in Figure 3a.
Download Figure3_a_BI.nex (4.562Kb)
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Title Figure3_a_ML
Downloaded 52 times
Description Tree file corresponding to result of the Maximum Likelihood inference reported in Figure 3a.
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Title Figure3_b_BI
Downloaded 53 times
Description Tree file corresponding to result of the Bayesian inference reported in Figure 3b.
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Title Figure3_b_ML
Downloaded 46 times
Description Tree file corresponding to result of the Maximum Likelihood inference reported in Figure 3b.
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Title Beast_inference4_E_161_tree
Downloaded 52 times
Description Tree file corresponding to result of the Beast inference 4 described in Figure 5.
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