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.