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.
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).
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)
ORF-complete DENV-1 genomes were downloaded from ViPR and an alignment together with the Martin County DENV-1 sequence was created using MAFFT.
A tree was created based on the MAFFT multiple sequence alignment using RAxML.