Figure 1. Unrooted phylogenetic trees for UL73 and UL74 based on amino acid sequences derived from 243 genome ... Figure 1. Unrooted phylogenetic trees.

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Figure 1. Unrooted phylogenetic trees for UL73 and UL74 based on amino acid sequences derived from 243 genome ... Figure 1. Unrooted phylogenetic trees for UL73 and UL74 based on amino acid sequences derived from 243 genome sequences, and a summary of genotypic linkages and frequencies. The site coverage cutoff value was 95%, leaving 134 sites in the UL73 tree (log likelihood, –1117.87) and 435 sites in the UL74 tree (log likelihood, –4153.86). Branch point robustness was inferred from 100 bootstrap replicates, and values of <70% are denoted by filled circles. Genotype branches are collapsed, and the numbers of substitutions per site, are shown by the scale. The UL73 sequence of strain HAN and the UL74 sequence of strain BE/23/2010 did not fall into the genotypes. The linkages between UL73 and UL74 genotypes are listed, followed by the frequencies of UL73 genotypes in the 243 genome sequences plus 383 single-gene sequences (243plus; 626 in total; Table 2), and the frequencies of the deduced linkages in the samples (milk; 26 in total; Table 3). The frequency of each genotype in the milk set was not significantly different (above P = .05) from that in the 243 plus 383 single gene set, as determined by random subsampling analysis (10 000 samplings of 26 genotypes from the set of 626). *Although no examples of this linkage were present in the datasets at levels in excess of the thresholds, at least one patient (258) was infected at subthreshold levels by a relevant strain (Supplementary Table 1). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. J Infect Dis, Volume 220, Issue 5, 03 May 2019, Pages 792–801, https://doi.org/10.1093/infdis/jiz209 The content of this slide may be subject to copyright: please see the slide notes for details.

Figure 2. UL73 and UL74 genotypes in milk samples collected from the left (L) and right (R) breasts of 4 human ... Figure 2. UL73 and UL74 genotypes in milk samples collected from the left (L) and right (R) breasts of 4 human immunodeficiency virus–infected donors at 16 weeks postpartum (Table 1). The inner and outer rings show the results obtained using short and long motifs, respectively. Short motif 3′ was used for UL74 (Table 2). The color key for genotypes is shown at the foot. Reads that did not meet the inclusion criteria for genotyping are shown as “other.” Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) 2019. Published by Oxford University Press for the Infectious Diseases Society of America.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. J Infect Dis, Volume 220, Issue 5, 03 May 2019, Pages 792–801, https://doi.org/10.1093/infdis/jiz209 The content of this slide may be subject to copyright: please see the slide notes for details.