SARS-CoV-2 Spike evolution influences GBP and IFITM sensitivity

Abstract

SARS-CoV-2 spike requires proteolytic processing for viral entry. The presence of a polybasic furin-cleavage site (FCS) in spike, and evolution towards an optimised FCS by dominant variants of concern (VOCs), are linked to enhanced infectivity and transmission. Guanylate binding proteins (GBP) are interferon-inducible restriction factors that target furin-mediated processing of viral envelope proteins and limit infectivity. Here we investigated whether GBPs restrict SARS-CoV-2 infection, and whether VOCs have evolved spikes that escape restriction. We show that GBP2 and 5 interfere with cleavage of the spike proteins of Wuhan-Hu-1, Alpha, Delta and Omicron, consistent with furin inhibition by GBPs. However, while GBP2/5 restrict Wuhan-Hu-1 infectivity, Alpha and Delta escape restriction. GBP exposure in producer cells influences viral entry route into target cells, with a shift towards endosomal entry. We therefore investigated whether GBP-targeting of spike alters sensitivity to endosomal restriction factors, IFITMs. We find IFITM1, but not IFITM 2 or 3, inhibit infection of naturally-permissive epithelial cells by early-lineage SARS-CoV-2, as well as Alpha and Delta, however GBPs did not sensitise to IFITM restriction. Strikingly, we find Omicron is unique amongst VOCs, being sensitive to restriction by GBP2/5, and also IFITM1, 2 and 3. We conclude evolution of Alpha and Delta spikes have conferred resistance to GBP restriction, but this is not solely due to acquisition of an enhanced FCS. Notably, Omicron, which has evolved under different selective pressures, has selected for changes in spike that not only mediate antibody escape, and shift in cell tropism and entry, but also impact the sensitivity of Omicron to innate immunity, potentially contributing to altered pathogenesis.

The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein

“…Interestingly, analysis of the extent of S1/S2 cleavage of spike in PV revealed that Omicron (BA.1, BA.2 and BA.4) spikes were efficiently cleaved with almost no full length spike detectable in concentrated PV (Figure 4E). This is contrary to several previous reports 19,23 , but in line with a recent report from Mesner et al 40 . This also correlates with single amino acids changes adjacent to the FCS in Omicron -specifically N679K and P681H -that on their own enhance cleavage 41 (Extended data figure 5C,D).…”

COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history

“…It is also important to emphasise that given the observational nature of our study, the sequential spread of Omicron BA.1 and BA.2 in the United Kingdom, and the rapid expansion of third-dose vaccination in December 2021, it was not possible to determine whether differences we observed between Delta and the BA.1 and BA.2 VOCs were attributable to intrinsic differences between these variants, or waning of immune protection afforded by vaccination. The reported shift in COVID-19 symptoms between Delta and Omicron sub-variants may be driven by intrinsic differences in the biology of the virus itself, leading to modified host responses; mutations in the Spike protein of SARS-CoV-2 VOCs may directly impact on symptom profiles through changes in viral tropism (2, 3, 32, 33), However, detailed data on differences in the host response to different VOC in vaccinated, non-hospitalised adults are currently lacking, but are likely to involve an interplay between localised mucosal innate and early T-cell interferon-mediated systemic responses (2, 34, 35). Further studies to determine the mechanisms by which different and emerging VOCs affect the host response are urgently required, and will be a necessary counterpart to clinical studies in the assessment of future VOCs.…”

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

“…Endosomal cathepsins or cell surface TMPRSS2, are required to cleave spike at the S1-S2 boundary prior to ACE2 mediated entry 19,20 . A consequence of Omicron spike adaptation is the ability to use cathepsin dependent endosomal entry routes, with reduced dependence on TMPRSS2 13,21–23 . To examine Omicron evolution of cell entry in the most recent Omicron BA.5 isolate, we examined infectivity of viruses on Calu-3, where entry is largely TMPRSS2-dependent and Camostat sensitive (Fig.4a) and HeLa over-expressing ACE2, where entry is largely cathepsin-dependent and E64d sensitive (Fig.…”