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

Abstract

At the end of 2021 a new SARS-CoV-2 variant, Omicron, emerged and quickly spread across the world. It has been demonstrated that Omicrons high number of Spike mutations lead to partial immune evasion from even polyclonal antibody responses, allowing frequent re-infection and vaccine breakthroughs. However, it seems unlikely these antigenic differences alone explain its rapid growth; here we show Omicron replicates rapidly in human primary airway cultures, more so even than the previously dominant variant of concern, Delta. Omicron Spike continues to use human ACE2 as its primary receptor, to which it binds more strongly than other variants. Omicron Spike mediates enhanced entry into cells expressing several different animal ACE2s, including various domestic avian species, horseshoe bats and mice suggesting it has an increased propensity for reverse zoonosis and is more likely than previous variants to establish an animal reservoir of SARS-CoV-2. Unlike other SARS-CoV-2 variants, however, Omicron Spike has a diminished ability to induce syncytia formation. Furthermore, Omicron is capable of efficiently entering cells in a TMPRSS2-independent manner, via the endosomal route. We posit this enables Omicron to infect a greater number of cells in the respiratory epithelium, allowing it to be more infectious at lower exposure doses, and resulting in enhanced intrinsic transmissibility.

SARS-CoV-2 variants’-Alpha, Delta, and Omicron D614G and P681R/H mutations impact virus entry, fusion, and infectivity

“…5a). These ndings suggests Omicron spike preferentially enter through ACE2-mediated endocytosis and this is in support with recent studies which showed Omicron preferentially enters cells by endocytic pathway 29,51 . In contrast, highly virulent variants like Delta could use both a) endocytic pathway and activation of S1/S2 protein mediated by Cathepsin B/L proteases and b) cell surface entry by activation of S1/S2 using serine protease TMPRSS2.…”

“…Peacock. P.T et, al and group have recently shown 29 , Omicron viruses usage TMPRSS2 independent entry pathway. In our study, we found both the variants and mutants pseudoviruses entry to host cell is markedly reduced when treated with Cathepsin L inhibitor like E64d (Fig.…”

“…Currently circulating Omicron variant contains ~33 mutations in spike protein and also harbors the D614G and P681H mutations as similar to Alpha variant. The new Omicron variant was found to be enhanced transmissibility but with milder symptoms 18 . Baric RS et.al have showed D614G mutation allows highly t virus which can e ciently replicate in nasal airway thus could result in high transmission and more stable than the ancestral Wuhan-1 strain and the single mutation is associated with high infectivity as compared to ancestral virus 19 .…”

“…The other key mutations present in the Delta or Omicron variants might have effect in the spike conformation. Peacock P. Thomas et.al have recently shown introduction of Q498R in Alpha variant, which is also present in Omicron, increases binding to soluble hACE2 29 .…”

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

“…This unusual pattern of mutations results in significant immune escape in vitro and in an enhanced reinfection potential in vivo ( Cele et al, 2021 ; Garcia-Beltran et al, 2021 ; Schmidt et al, 2021 ; Willett et al, 2022 ). Moreover, omicron displays an altered cellular tropism and cell entry mechanism, which depends on the acquisition of an enhanced ability to rely on the TMPRSS2-independent endosomal route ( Peacock et al, 2022 ; Willett et al, 2022 ). It is presently unclear whether and to which extent the XLI insertion provides a contribution to the unique biological properties of this variant.…”