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Table 4 The association between Nef functions and dE90 values

From: HIV-1 subtype C Nef-mediated SERINC5 down-regulation significantly contributes to overall Nef activity

Nef functiona

Univariable analysis

Multivariable analysis

Coeff.

SE

p value

Coeff.

SE

p value

CD4 down-regulation

 − 3.64

1.53

0.02

 − 0.24

2.23

0.92

HLA-I down-regulation

 − 2.10

1.59

0.19

0.19

1.91

0.92

Alteration of TCR signalling

0.99

1.70

0.56

1.26

1.46

0.39

SERINC5 down-regulation

 − 4.91

1.60

0.003

 − 5.32

1.73

0.003

  1. dE90 values were derived from the Nef fitness landscape Potts model (each amino acid present at each residue was modelled explicitly) for each Nef clone and serve as a proxy for in vivo Nef fitness [17]
  2. Coeff., coefficient; SE, standard error
  3. aNef functions were standardised (by subtracting the mean and dividing by the standard deviation) so that coefficients were comparable