Retrospective Genomic Characterization of a 2017 Dengue Virus Outbreak, Burkina Faso

This repo holds data used in the manuscript: Letizia AG, Pratt CB, Wiley MR, Fox AT, Mosore M, Agbodzi B, et al. Retrospective Genomic Characterization of a 2017 Dengue Virus Outbreak, Burkina Faso. Emerg Infect Dis. 2022;28(6):1198-1210. https://doi.org/10.3201/eid2806.212491

BEAST analysis

All whole genome sequences were downloaded from ViPR trimmed to the coding sequence for each dengue virus serotype, 10% randomly subsampled and all Africa-origin sequences retained. Sequences were aligned and xml files generated for use with BEAST

• DENV1_subset.fasta
• DENV2_subset.fasta
• DENV3_subset.fasta
• DENV1_subset.xml
• DENV2_subset.xml
• DENV3_subset.xml

E gene sequences

All sequences were downloaded from ViPR, aligned and trimmed to the E-gene.

• DENV1_Egene.fasta
• DENV2_Egene.fasta
• DENV3_Egene.fasta

Amino acid alignments

All sequences were downloaded from ViPR, aligned, trimmed to the prME region, and translated to amino acid.

• DENV1_prME_aa.fasta
• DENV2_prME_aa.fasta
• DENV3_prME_aa.fasta