Results for 27 SNPs previously reported to be associated with EBV infection, immune response or EBV-positive disease.

<p>Results for 27 SNPs previously reported to be associated with EBV infection, immune response or EBV-positive disease.</p

Manhattan plots of the association between EBV copy number and human genetic variants in LCLs.

<p><b>A</b>. Results of the stage 2 GWAS of relative EBV copy number in 899 LCLs, derived from 12 populations. In total, ∼1.6 M SNPs, polymorphic in every population studied, were analysed using FaST-LMM. Each point represents a SNP. There were no SNPs with genome-wide significant p-values after correction for multiple testing. <b>B</b>. QQ plot showing the distribution of observed test statistics plotted against the expected (null) distribution (red line). The SNPs which fall below the red line suggest that the GWAS may be losing power to detect SNPs associated with EBV copy number. <b>C</b>. The strongest signal is located within an intron of protein tyrosine phosphatase receptor delta (<i>PTPRD</i>), SNP rs10959089 (p = 1.17×10-6). Plot C made with LocusZoom <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108384#pone.0108384-Pruim1" target="_blank">[56]</a>.</p

Samples used in this study.

<p>*Population names from 1000 Genomes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108384#pone.0108384-Abecasis1" target="_blank">[48]</a> and HapMap <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108384#pone.0108384-XX1" target="_blank">[22]</a>.</p><p>Samples used in this study.</p

Distribution of relative EBV copy number in LCLs from 12 populations.

<p><b>A</b>. Relative EBV copy number in 915 LCLs from 12 populations, including 97 parent-offspring trios. Range 16.07–29.02, mean 23.36 (SD±2.03). The data are not normally distributed (Shapiro-Wilk: W = 0.977, p-value  = 2.086⁻¹¹). <b>B</b>. Box and whisker plots showing the range (dotted lines), interquartile range (coloured boxes) and mean relative EBV copy number (central vertical lines) for the 12 populations included in this analysis.</p

Association between EBV copy number and human gene expression in LCLs.

<p>Manhattan plot showing the correlation between expression levels of 21,800 individual gene transcripts from microarray data and EBV copy number.</p

MOESM2 of Disease progression despite protective HLA expression in an HIV-infected transmission pair

Additional file 2: Figure S2. Sites of HLA-associated footprints in the donor from an HIV transmission pair at 8 months post-diagnosis aligned to B and CRF01_AE clade consensus sequence. Epitopes restricted by the favourable alleles expressed by the donor, A*3201, B*1302 and B*1401, are shown

Full genomes time summary

Tab-delimited text file detailing year of isolation and lineage of 2,651 full-length influenza B virus genomes from this study (Fig 1 source data)

Maximum likelihood trees

Compressed file of bootstrapped ML phylogenies inferred using RAxML and used to characterise influenza B virus genotypes

Summary of genotypes

Tab-delimited text file detailing inferred genotypes for influenza B viruses, representing over 10,000 strains including 2,651 complete genomes

Input files for antigenic analysis

Compressed file comprising of: tab-delimited HI data file, BEAST XML file for generation of set of empirical trees and XML file for running BMDS models for B/Yamagata and B/Victoria