Summary
Full-length Dengue virus genome from 2013 outbreak in Martin County, Florida.
Methods
Serum was obtained from a single patient during the 2013 Dengue virus serotype 1 outbreak in Martin County in Florida. Patient serum (250uL) was inoculated into a T-25 flask of C6/36 cells, incubated @ RT for 20 days, blind passaged, and incubated for another 31 days. After this first passage, the sample was split into two and one sample (DV1_Vero) was subject to one additional passage in Vero cells, and the other sample (DV1_c6/36) was subject to one additional passage in C6/36 cells.
Sequencing
RNA was extracted and metagenomic sequencing was performed on the Illumina MiSeq after rRNA depletion following the protocol in Matranga et al. (Genome Biol 2014).
Samples
DV1_vero One passage in C6/36 cells, one additional passage in Vero cells DV1_c6/36 One passage in C6/36 cells, one additional passage in C6/36 cells
Both consensus sequences were identical - this was confirmed by additional sequencing of biological replicates (separate RNA extractions)
Alignment
ORF-complete DENV-1 genomes were downloaded from ViPR and an alignment together with the Martin County DENV-1 sequence was created using MAFFT.
Tree
A tree was created based on the MAFFT multiple sequence alignment using RAxML.
References
Origin of the dengue virus outbreak in Martin County, Florida, USA 2013.
Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!
Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
data@andersen-lab.com