Selection pressures on the DENV genome, analyzed per gene, at different stages of horizontal transmission.

<p>Ratios of the number of non-synonymous (NS) to synonymous (S) SNVs per gene are shown for <b>(A)</b> human- versus mosquito-derived (both abdomen and salivary gland) DENV populations, and <b>(B)</b> mosquito abdomen- versus salivary gland-derived DENV populations. Human-derived samples are a pool of DENV2 patient samples from this study and DENV1 and DENV3 patient samples from the EDEN study [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004052#pntd.0004052.ref019" target="_blank">19</a>]. Numbers of NS and S SNVs for each gene are indicated in tables below the graphs. *, p < 0.05; Fisher's exact test (M, p = 0.00439; E, p = 0.031; NS1, p = 0.002).</p

Frequencies of maintained SNVs compared to SNVs lost during horizontal transmission.

<p><b>(A)</b> Frequencies of DENV2 SNVs maintained from human to mosquito, versus those present only in the human. <b>(B)</b> Frequencies of DENV2 SNVs maintained from mosquito abdomen to mosquito salivary gland, versus those present only in the abdomen. <b>(C)</b> Frequencies of SNVs maintained in one mosquito per human-mosquito group, versus those maintained in more than 1 mosquito per group. Boxplots indicate medians and 25th and 75th percentiles; whiskers indicate minimum and maximum values. *, p < 0.05; ***, p < 0.0001; Mann-Whitney test.</p

Measures of intra-host DENV2 diversity in human and mosquito hosts.

<p><b>(A)</b> Number of SNVs; <b>(B)</b> Sum of SNV frequencies; <b>(C)</b> Average SNV frequency; <b>(D)</b> Standard error of the mean SNV frequency; all calculated on a per sample basis. Abd, abdomen; SG, salivary gland.</p

Loss and maintenance of SNVs during horizontal transmission.

<p><b>(A)</b> Percentage of SNVs maintained during transmission from human to mosquito and from mosquito abdomen to mosquito salivary gland. <b>(B)</b> Tracking of maintained SNVs. The number of instances of each scenario are shown; these include all occurrences of SNVs that were found to be maintained in more than one mosquito. <b>(C)</b> Percentage of SNVs maintained between members of a human-human transmission pair from the EDEN study.</p

Phasing SNVs into distinct variant viral genomes.

<p><b>(A)</b> Minimum numbers of distinct variant DENV genomes per sample, in human- mosquito abdomen-, and mosquito salivary gland-derived DENV2 populations. <b>(B)</b> Transmission network for patient-mosquito group 641. For each sample, consensus viral genomes are represented by circles outlined in bold (Hu, human; M1A, M2A, M3A, mosquito abdomens; M1SG, M2SG, M3SG, mosquito salivary glands), and variant genomes by circles radiating out of the consensus circle. Numbers within variant circles indicate the number of SNVs present in each variant genome. Pink connector lines represent maintenance of SNV across transmission stages, with numbers indicating the number of SNVs that were maintained.</p

Frequencies of maintained SNVs in the human, mosquito abdomen, and mosquito salivary gland.

<p>Red, non-synonymous SNVs; black, synonymous SNVs. SNV positions mentioned in the text are highlighted with arrows and drawn as dotted lines for ease of viewing.</p

SNVs maintained between EDEN transmission pairs.

<p>NS, non-synonymous; S, synonymous; aa, amino acid.</p><p>SNVs maintained between EDEN transmission pairs.</p

SNVs maintained from human to mosquito.

<p>NS, non-synonymous; S, synonymous; aa, amino acid.</p><p>SNVs maintained from human to mosquito.</p