As modulation of Nef function over the natural history of infection is supported by some [64], [65] (though not all [66]) studies, and a minority of historic Nef clones were derived from persons with known or suspected early infection, we indirectly assessed infection stage as a potential confounder by including Nef sequences from 52 modern chronic and 34 early infection patients not included in previous analyses (sampled a median of 72 [IQR 48–92] days after infection) in our comparison group. Here, S100B is linked to infection.