Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source
1 Joint Research Unit ‘Genómica y Salud’ CSISP (FISABIO), Instituto Cavanilles/Universidad de Valencia, c/ Catedrático José Beltrán, 2 46980-Paterna, Valencia, Spain
2 Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Valencia, Spain
3 Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
4 Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
BMC Biology 2013, 11:76 doi:10.1186/1741-7007-11-76Published: 19 July 2013
Additional file 1:
Phylip-formatted file with the E1-E2 sequences used in the phylogenetic reconstruction and analyses of the outbreak.
Format: TXT Size: 1.7MB Download file
Additional file 2:
Nexus file corresponding to the maximum likelihood tree shown in Figure 3. Each sequence has been colored according to the coloring scheme used in that figure. The file can be opened and visualized with FigTree (available from http://tree.bio.ed.ac.uk/software/figtree webcite).
Format: TXT Size: 306KB Download file
Additional file 3:
Newick file used to test the alternative hypothesis for each patient suspected to be part of the outbreak. This tree was manually edited to replace the sequence labeled ‘test’ by the clade conformed by all the sequences derived from each patient and its likelihood was compared with that of the original tree (without the ‘test’ sequence).
Format: TXT Size: 39KB Download file
Additional file 4:
BEAST (‘Bayesian Evolutionary Analysis by Sampling Trees’) file used for deriving the date of infection of patients included in the outbreak. This file corresponds to patient 10,067 and the sequenced used was picked at random from the cloned E1-E2 sequences available for this patient. The same procedure, using one random E1-E2 sequence, was applied to the remaining patients in the outbreak.
Format: TXT Size: 55KB Download file
Additional file 5: Figure S1:
Comparison between estimates of infection dates obtained by the Bayesian method with a relaxed molecular clock implemented in BEAST (‘Bayesian Evolutionary Analysis by Sampling Trees’) and those obtained independently by the prosecution when more than one possible infection date was considered likely by the prosecution. Bayesian estimates are provided as medians and 95% highest posterior density (HPD) intervals. Prosecution estimates are shown as red (most likely date of infection as indicated during the trial) or dark-blue dots (alternative dates).
Format: PDF Size: 35KB Download file
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