Variant frequencies from targeted sequencing for Dam E.

Variant frequencies from targeted sequencing for Dam E.</p

Primers used for targeted sequencing and their corresponding start and stop positions in the ZIKV genome.

Primers used for targeted sequencing and their corresponding start and stop positions in the ZIKV genome.</p

Variant frequencies from targeted sequencing for Dam B.

Variant frequencies from targeted sequencing for Dam B.</p

Variant frequencies in whole genome vs. targeted sequencing evaluating ZIKV diversity in late stages of vertical transmission for matched placentas and fetal brains from Dam F.

Variant frequencies in whole genome vs. targeted sequencing evaluating ZIKV diversity in late stages of vertical transmission for matched placentas and fetal brains from Dam F.</p

Graphical representation of variable sites from targeted sequencing of early stages of vertical transmission.

Sequencing data summarized in Tables 1–3 is shown. All variable sites across all three dams are plotted, with each nucleotide represented by a different color. Ref indicates the reference nucleotide, and proportions of reference vs. alternate allele are represented in each bar graph. Plac = placenta, Fet = fetal body, nr = no reads. Matched tissues are separated by light gray lines, different samples are separated by dark gray lines.</p

Variant frequencies in inoculum and whole genome sequencing for combined placentas and fetuses from set 1 evaluating ZIKV diversity during early stages of vertical transmission.

Variant frequencies in inoculum and whole genome sequencing for combined placentas and fetuses from set 1 evaluating ZIKV diversity during early stages of vertical transmission.</p

Variant frequencies in whole genome vs. targeted sequencing evaluating ZIKV diversity in late stages of vertical transmission for matched placentas and fetal brains from Dam E.

Variant frequencies in whole genome vs. targeted sequencing evaluating ZIKV diversity in late stages of vertical transmission for matched placentas and fetal brains from Dam E.</p

Variant frequencies from targeted sequencing for Dam C.

Variant frequencies from targeted sequencing for Dam C.</p

Graphical representation of variable sites and dominant variants from targeted sequencing of late stages of vertical transmission and neuroinvasion.

A) Sequencing data summarized in Tables 1–3 is shown. All variable sites across all three dams are plotted. Ref indicates the reference nucleotide, and proportions of reference vs. alternate allele are represented in each bar graph. Plac = placenta, Fetus = representation of both fetal body and fetal brain variants as they were identical. Matched tissues are separated by light gray lines, different samples are separated by dark gray lines. B) Sequence logos for the dominant variants found across multiple fetuses in multiple dams for the four sites contained in the two dominant variant haplotypes are shown. The site position is listed at the top, and the frequency of the nucleotide is represented by the size of the base letter. Reference refers to the inoculum reference nucleotide. For the eight matched samples where the shared dominant sites were the same in both the fetal body and fetal brain, these ZIKV populations are summarized as a single “Fetus” logo. For the two samples that did not have matching fetal body and fetal brain populations, the ZIKV genomes are split into separate Fetal body (F. Body) and Fetal Brain (F. Brain) logos. The nucleotide frequency was not depicted if it was not part of the sample’s haplotype and was 100% reference.</p

Time course of ZIKV RNA levels in placentas, fetal bodies, and fetal heads during vertical transmission.

Pregnant AIR mice were inoculated at 7 days post-mating. A-D) At 7, 11, 13, and 14 dpi, mice were euthanized and tissues analyzed by RT-qPCR for ZIKV RNA in (A) placentas, (B) whole fetus or fetal bodies, and (C) fetal heads. D) ZIKV RNA levels in fetal bodies selected for sequencing and the matched head (not sequenced) is plotted with lines connecting tissue from the same fetus. Dashed lines denote mock-inoculated levels in the tissues. Each dam is represented by a different color, and each tissue by an individual symbol.</p