SIVsmm nef alleles derived from SMs with high or low CD4+ T cell counts do not show significant lineage-specific differences in Nef function. (A-D) Modulation of cellular receptors by primary nef alleles derived from different lineages of SIVsmm. Each symbol represents n-fold down-modulation of the indicated receptor molecule by one of the 22 NL4-3 recombinants expressing primary bulk SIVsmm nef alleles analyzed. Similar results were obtained in two independent experiments. L1 and L2 nef alleles were combined since they did not form two distinct clusters (Fig. 1). (E) Enhancement of virion infectivity by SIVsmm nef alleles. P4-CCR5 indicator cells were infected with HIV-1 NL4-3 IRES-eGFP constructs containing the indicated SIVsmm nef genes or a defective nef allele. Infections were performed in triplicate with two different virus stocks containing 1 ng p24 antigen. Each symbol represents the average value of the 6 measurements compared to the infectivity of the virus expressing the SIVmac239 Nef (100%). (F) Levels of NFAT-dependent luciferase reporter activity in Jurkat T cell cultures infected with HIV-1 variants expressing nef alleles from SIVsmm-infected SMs compared to the nef defective control. The luciferase reporter activities represent the average (± SD) of triple infections. Similar results were obtained in two independent experiments. For clarity animal FYb was excluded from the analysis in the right panel.