Link between Primate Lentiviral Coreceptor Usage and Nef Function

• CXCR4-tropic SIVsmm strains lose the TCR-CD3 downmodulation activity of Nef
• Residues I123 and L146 in the Nef core region are critical for TCR-CD3 interaction
• Viral tropism for CXCR4+ T cells promotes changes in Nef allowing T cell activation
• Downmodulation of TCR-CD3 is advantageous during acute SIVsmm infection

SummarySimian immunodeficiency virus (SIVsmm) infection of sooty mangabeys (Cercocebus atys) is characterized by stable CD4+ T cell counts despite high plasma levels of CCR5-tropic viruses. However, in rare instances, SIVsmm acquires CXCR4 coreceptor tropism and causes severe CD4+ T cell depletion, albeit without clinical signs of immunodeficiency. Here, we show that CXCR4-tropic SIVsmm strains lost their ability to downmodulate TCR-CD3 by evolving unusual Nef mutations that initially reduced (I132V) and subsequently disrupted (I123L and L146F) interaction with the CD3 ζ chain. This coevolution of Env and Nef function suggests that CD3 downmodulation is advantageous for viral replication in activated CCR5+ memory T cells, but not in resting naive CXCR4+ T cells that have not yet undergone TCR-CD3-mediated stimulation. This may explain why HIV-1, which generally lacks the CD3 downmodulation function, commonly switches to CXCR4 usage, whereas this is extremely rare for SIV strains that have retained this Nef activity.

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