Dengue virus genomic data from Florida

Summary: Full-length Dengue virus genome from 2013 outbreak in Martin County, Florida. Data here.

Overview

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

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

Origin of the dengue virus outbreak in Martin County, Florida, USA 2013.

GitHub Commits

Resources

GitHub Repo
By: Andersen Lab

Origin Of The Dengue Virus Outbreak In Martin County, Florida, USA 2013
Virology Reports March-June;1-2:2-8 (2014)

Collaborators

Scott Michael
Florida Gulf Coast University

Sharon Isern
Florida Gulf Coast University

Funding

NIH_CTSA
PEW