Fig. 1: Identification and genetic characterization of Zika virus DVGs with high fitness.

Virus populations enriched in DVGs, passaged in Vero or C6/36 cells, were sequenced and deletions identified. a Computationally-determined neighborhoods enriched with deletions in Vero or C6/36 cells are shown in a 2-dimensional plane representation of the Zika virus genome, with start and end positions of the identified deletions denoted as dots on the plane. Poisson p values for each neighborhood are shown. b Dynamics of deletion enrichment within DVG neighborhoods identified in Vero and C6/36 cells. Enrichment z-scores indicate total enrichment significance of deletions within each neighborhood from all replicates per passage. c, d Hexbin plot of deletions identified following Yellow fever virus 17D (c) or West Nile virus high MOI passaging in SW-13 or C6/36 cells, respectively. Identified deletions with defined start and end positions within each hexagon (>10 nt in length, bin = 100) are shown. The color of each hexagon is relative to the sum of the reads per million of deletions in all passages and replicates. For YFV, passages number 1, 8, 14, and 19 (n = 12) were sequenced and shown. For WNV, data from all passages and replicates (n = 3) are shown. e Putative Zika virus DVG-A genomes identified in Vero or C6/36 cells that conserve the open reading frame aligned against the Zika virus polyprotein. Aligned regions are shown in pink and deleted regions in gray. Dashed lines denote limits of proteins or relevant protein domains. Source data are provided in the Supplementary Data 1 and 2 for Vero and C6/36 data, respectively, and in Supplementary Data 3 and 4 for Yellow fever virus and West Nile virus, respectively.