Analysis of Zike virus variants after passage in animal models

Genomic sequence data generally is limited to the dominant, “consensus”, sequence, however, because RNA viruses exist within a host as genetically diverse “mutant spectra” viral phenotype is affected by both consensus and variant (“subconsensus”) genotypes. Variants can also persist at low levels within a host and serve as a reservoir of emergent genotypes, or alternatively may represent remnants of an ancestral genotype. To identify if any of the epidemic associated mutations represent “hot spots” of diversity in the genome, deep Illumina sequencing was performed on two different Zika virus (ZIKV ) strains after passage in vivo. A 2015 strain of ZIKV from Brazil (strain ZIKV/H.sapiens-tc/BRA/2015/Brazil_SPH2015, KU321639.1) was analyzed prior to and after passage in a pregnant macaque. Additionally, deep sequence data were obtained for a 2015 strain, PRVABC59 (accession # KU501215), from Puerto Rico before and after passage in mice.