Fig 1.
Clinical time course and sample collection.
(A) Time line depicting the clinical presentation, duration of symptoms and timing of sample collection. Stars indicate days when blood samples were collected with the red star depicting the day of presentation. (B) Photograph of the left arm demonstrating the erythematous macular rash. (C) Approximate maximum likelihood phylogenetic tree of near full length ZIKV variant combined with 435 publicly available ZIKV sequences from NCBI viral genomes resource [20]. GenBank accession number are available (S1 Table). Tips are colored according to the sample sequence location. A set of 435 near full length sequence (9,038 bp) from the North America (in red), Central/South America (in blue), Europe (in green), Asia (in purple) and Oceania (in orange) were combined with the sample ZIKV SD001 (in black) and the phylogeny (midpoint rooted) was obtained using FastTree [32]. Scale bar (substitution/site) is indicated in the center. The tree topology shows the sample SD001 intermingled with sequences originating from Central/South America. A closeup of ZIKV SD001 and its nearest neighbors with GenBank accession numbers and country of origin are shown.
Table 1.
Viral diagnostic test results.
Fig 2.
Systemic immune response to ZIKV infection.
(A) Serum IP-10, MCP-1 and IL1RA levels before, during and after acute ZIKV infection. Cytokines were measured in duplicate with average shown at each time point. (B) Hierarchical clustering of the top induced genes (compared to convalescent samples) in PBMCs during acute ZIKV or acute DENV (GSE43777) infections at the indicated days post-onset of symptoms. (C) Heat map of select ISGs and cytokine genes relative expression to convalescent or baseline respectively of SD001 and rhesus macaque (GSE90868) during acute ZIKV infection [33].
Fig 3.
Cell-type specific and temporally regulated transcriptional response to ZIKV infection.
(A) Venn diagram of the number of induced genes (at least 2-fold) determined by RNA-seq of PBMCs alone compared to analysis of PBMCs and individual cell populations. (B) Number of induced genes (at least 2-fold) at d3, d6, or d17 relative to d48 POS in specified cell populations. Corresponding (C) functional and (D) promoter motif enrichments associated with induced genes at each time point. (E) Hierarchical clustering of top induced genes in each cell type at each time point relative to d48 POS. (F) Relative Log2 transformed FPKM RNA-seq counts for AIM2 in monocyte populations at indicated time points compared to d48 POS. (G) Relative Log2 transformed FPKM RNA-seq counts for AIM2 in denoted cell populations at d3 compared to d48 POS.
Fig 4.
Cell-type specific ATAC-seq and gene regulation.
(A) De novo motif enrichment at regions of open chromatin as defined by ATAC-seq in classical monocytes compared to NK cells at d6 POS. (B) Comparative motif enrichment of ATAC-seq peaks upregulated (Fold change > 3 and P-value < 0.001) at d6 compared to d17 POS in classical monocytes (blue) or NK cells (red). (C-E) UCSC browser visualization of RNA-seq (first panel) and ATAC-seq (second panel) near (C) IFIT2 and IFIT3, (D) APOBEC3A and (E) MKI67 gene loci in classical monocytes (blue) and NK cells (red). Potential transcription factor binding motifs associated with ATAC-seq peaks are denoted. Dashed box in IFIT3 denotes area shown in S4 Fig.
Fig 5.
Temporal development of neutralizing Ab responses during acute ZIKV infection.
(A-D) Neutralizing Ab titers against ZIKV strains (A) SD001 (B) FSS13025 and DENV strains (C) DENV1 West Pacific 74 and (D) DENV4 TVP-360 at indicated time points. Pre-infection and maximum NT50 titers are denoted for each virus.
Fig 6.
T cell immune phenotypes during acute ZIKV infection.
(A) Flow cytometry analysis of CD4+ and CD8+ T cell T effector memory (TEM), T effector memory RA (TEMRA), T naïve (TN) and T central memory (TCM) populations on d6 POS. (B) Relative percentages of T cell subsets on d6 POS during ZIKV infection and in 3 DENV-naïve and 2 DENV-immune control individuals. (C) Flow cytometry analysis of live CD3+ cells in one representative DENV-naïve and 2 DENV-immune controls and during acute ZIKV infection d6 and d240 POS. The percentage of live CD3+ cells that are CD4+CD8dim in each group is shown (D) Relative percentages of CD4+CD8dim among live CD3+ cells. (E) Flow cytometry analysis of the expression of CD45RA, the cytotoxicity marker CD226, and chemokine receptors CCR6, CCR4 and CXCR3 in indicated T cell populations. (F) Percent of live CD3+CD4+CD8dim T cells that are CD45RA+CD226+ and negative for CCR6, CCR4 and CXCR3 chemokine receptors.