Zika virus Genome sequencing and assembly

Our major goal was to sequence the stock of Zika virus that we used to infect rhesus macaques. We wanted to determine how many sites in the genome of the population of replicating Zika viruses had variation at a frequency of greater than 5%, relative to the Genbank sequence (KJ776791). Then, we sequenced the replicating population of Zika virus at day 4 post infection to determine if there was any selection for de novo sequence variants by this time point. We were unable to obtain reasonable sequence data from much later after infection because the virus loads were too low to obtain high quality sequences across the whole genome.