Additional file 1 of HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity

Additional file 1. In vitro Nef functional measurements and E values of patient-derived Nef clones. Excel file showing in vitro Nef functional measurements (SERINC5 down-regulation, CD4 down-regulation, HLA-I down-regulation and alteration of TCR signalling) for Nef clones derived from individuals in early subtype C infection. Nef functions are expressed relative to SF2 Nef (where SF2 Nef function = 1). E values, which are a proxy for overall Nef function in vivo, have been predicted by computational modelling for each of these patient-derived Nef clones (17) and are shown alongside the in vitro Nef functional measurements. dE0 values were derived from the Nef fitness landscape Ising model (only the consensus amino acid present at each residue was modelled explicitly) for each Nef clone, while dE90 values were derived from the Nef fitness landscape Potts model (each amino acid present at each residue was modelled explicitly). Clinical measurements, including viral load set point (log10 copies/ml), rate of CD4+ T cell decline (cells/mm3 per month), baseline viral load (log10 copies/ml), baseline CD4+ T cell count (cells/mm3) and follow-up time (the number of days from first CD4+ T cell count to last CD4+ T cell count available) are also shown.

附件1。患者来源Nef克隆的体外Nef功能测定及E值。本Excel文件记录了早期C亚型感染个体来源的Nef克隆的体外Nef功能测定结果（包括SERINC5下调、CD4下调、人类白细胞抗原I型（HLA-I）下调以及T细胞受体（TCR）信号通路改变）。Nef功能以SF2 Nef为参照进行定量（SF2 Nef功能值设为1）。E值作为体内整体Nef功能的替代指标，已通过计算建模对上述所有患者来源的Nef克隆进行了预测（文献17），并与体外Nef功能测定结果一并列出。dE₀值来源于针对每个Nef克隆的Nef适合度景观伊辛模型（Ising模型）（仅对每个位点的共识氨基酸进行显式建模），而dE₉₀值则来源于Nef适合度景观波特模型（Potts模型）（对每个位点存在的所有氨基酸均进行显式建模）。本文件同时列出了各项临床检测指标，包括病毒载量设定点（log₁₀拷贝/毫升）、CD4+ T细胞下降速率（cells/mm³/月）、基线病毒载量（log₁₀拷贝/毫升）、基线CD4+ T细胞计数（cells/mm³）以及随访时长（从首次CD4+ T细胞计数到末次可获取CD4+ T细胞计数的天数）。