SARS-CoV-2 evolution influences GBP and IFITM sensitivity

Abstract

SARS-CoV-2 spike requires proteolytic processing for viral entry. A polybasic furin-cleavage site (FCS) in spike, and evolution toward an optimized FCS by dominant variants of concern (VOCs), are linked to enhanced infectivity and transmission. Here we show interferon-inducible restriction factors Guanylate-binding proteins (GBP) 2 and 5 interfere with furin-mediated spike cleavage and inhibit the infectivity of early-lineage isolates Wuhan-Hu-1 and VIC. By contrast, VOCs Alpha and Delta escape restriction by GBP2/5 that we map to the spike substitution D614G present in these VOCs. Despite inhibition of spike cleavage, these viruses remained sensitive to plasma membrane IFITM1, but not endosomal IFITM2 and 3, consistent with a preference for TMPRSS2-dependent plasma membrane entry. Strikingly, we find that Omicron is unique among VOCs, being sensitive to restriction factors GBP2/5, and also IFITM1, 2, and 3. Using chimeric spike mutants, we map the Omicron phenotype and show that the S1 domain determines Omicron’s sensitivity to GBP2/5, whereas the S2’ domain determines its sensitivity to endosomal IFITM2/3 and preferential use of TMPRSS2-independent entry. We propose that evolution of SARS-CoV-2 for the D614G substitution has allowed for escape from GBP restriction factors, but the selective pressures on Omicron for spike changes that mediate antibody escape, and altered tropism, have come at the expense of increased sensitivity to innate immune restriction factors that target virus entry.

Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants

“…1d-f). Our approach is particularly relevant for comparing Omicron subvariants because spike mutations have been shown to alter tropism, increasing cathepsin-dependent endosomal entry and reducing dependence on cell surface TMPRSS2 17,18,20,21 , irrespective of virion spike cleavage efficiency (Extended Data Fig. 1c).…”

Restriction of Viral Glycoprotein Maturation by Cellular Protease Inhibitors

“…In contrast, virions pseudotyped with VSV G, which does not require a furin-mediated activation step, are not restricted [ 20 ]. More recently, GBP2 and GBP5 have also been shown to reduce SARS-CoV-2 infectivity by inhibiting the proteolytic processing of Spike [ 48 ]. However, as described in more detail below, some SARS-CoV-2 isolates were resistant to GBP-mediated restriction [ 48 ].…”

“…More recently, GBP2 and GBP5 have also been shown to reduce SARS-CoV-2 infectivity by inhibiting the proteolytic processing of Spike [ 48 ]. However, as described in more detail below, some SARS-CoV-2 isolates were resistant to GBP-mediated restriction [ 48 ].…”

“…Furthermore, the D614G mutation in Spike was suggested to result in the emergence of an additional elastase cleavage site upstream of the furin cleavage motif [ 59 ]. One interesting observation in this regard is that the D614G change allows the alpha and delta variants to escape GBP2/5-mediated restriction [ 48 ]. However, the exact role of neutrophil elastase in SARS-CoV-2 Spike maturation and a possible compensation of other Spike-priming proteases such as furin by neutrophil elastase remain to be determined.…”

London calling: The 5th UK Cellular Microbiology Network Meeting

“…Lucy Thorne (from Greg Towers' lab at University College London and new group leader at Imperial College London) described the convergent evolution of SARS‐CoV‐2 variants of concern to enhance innate immune suppression (Thorne et al., 2022). Ann‐Kathrin Reuschl (from Clare Jolly's lab at University College London) presented work on enhanced innate immune evasion by SARS‐CoV‐2 Omicron subvariants (Mesner et al., 2023).…”