Genetic distance, positive selection and predicted T cell epitopes.

Subjects are shown in descending order of those with the highest mean genetic distance, with positive selection occurring at the population level (all sequences), shown in the bottom row of the table.1 Mean substitutions/site for all time points per subject. Numbers are shown for the 1–2 year time point for each individual, since this is the one time point represented in all individuals, with the exception of NP 4, for whom the 4.9 year time point was the only one available.2 Sites listed in bold type were picked up by more than one method (FUBAR plus SLAC or FEL); those in standard type were indicated by FUBAR alone.3 Sites indicated by MEME.4 The majority species for each time point was entered into an online T cell epitope prediction tool tailored to the HLA type of the individual. Only epitopes predicted by more than one method are shown, and in order of where they occur from N- to C-terminus of Vpu. Numbering indicates the amino acid start and end positions. Where more than one similar epitope was predicted, for example two epitopes overlapping the same region but of 9 and 10 amino acids, the one with the highest predicted binding affinity is shown. Peptides in bold type have a high predicted affinity (0–50 nM); those in regular type have medium predicted affinity (51–500 nM).NP = none predicted.受试者按平均遗传距离由高至低排序，群体水平（所有序列）的正向选择结果展示于表格末行。 1 每位受试者所有时间点的每位点平均替换数。因该时间点为所有受试者共有的唯一检测时点，故展示每位个体1~2年时间点的数值；唯有NP 4例外，其仅可获取4.9年时间点的数据。 2 粗体标注的位点由至少两种方法检测得到（FUBAR联合SLAC或FEL）；常规字体标注的位点仅由FUBAR单独检测得到。 3 标注位点由MEME方法检测得到。 4 将每个时间点的优势物种输入针对个体HLA类型定制的在线T细胞表位（T cell epitope）预测工具。仅展示由至少两种方法预测得到的表位，并按其在Vpu蛋白中从N端到C端的出现顺序排列。编号标注氨基酸的起始与终止位置。若预测得到多个相似表位（例如同一区域重叠的9肽与10肽表位），则展示预测结合亲和力最高的表位。粗体标注的肽段预测亲和力较高（0~50 nM）；常规字体标注的肽段预测亲和力中等（51~500 nM）。NP代表未预测到表位。