Division of Infection and Immunity, University College London, WC1E 6BT London, UK.
Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, E1 2AT London, UK.
Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2212577120. doi: 10.1073/pnas.2212577120. Epub 2023 Jan 24.
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.
SARS-CoV-2 的刺突蛋白需要经过蛋白水解处理才能进入病毒。刺突蛋白中的多碱性弗林蛋白酶裂解位点（FCS），以及通过主要关注的变异株（VOC）进化而来的优化 FCS，与增强的感染性和传播性有关。在这里，我们展示了干扰素诱导的限制因子鸟苷结合蛋白（GBP）2 和 5 干扰弗林介导的刺突蛋白裂解，并抑制了早期谱系分离株武汉-Hu-1 和 VIC 的感染性。相比之下，VOCs Alpha 和 Delta 通过 GBP2/5 逃避限制，我们将其映射到这些 VOC 中存在的刺突取代 D614G。尽管抑制了刺突蛋白裂解，但这些病毒仍然对质膜 IFITM1 敏感，但对内体 IFITM2 和 3 不敏感，这与它们依赖 TMPRSS2 的质膜进入偏好一致。引人注目的是，我们发现 Omicron 在 VOC 中是独一无二的，它对限制因子 GBP2/5 敏感，对 IFITM1、2 和 3 也敏感。使用嵌合刺突突变体，我们对 Omicron 的表型进行了映射，并表明 S1 结构域决定了 Omicron 对 GBP2/5 的敏感性，而 S2'结构域决定了其对内体 IFITM2/3 的敏感性和对 TMPRSS2 非依赖性进入的偏好。我们提出，SARS-CoV-2 对 D614G 取代的进化使其能够逃避 GBP 限制因子，但 Omicron 对刺突变化的选择性压力，介导抗体逃逸和改变嗜性，是以增加对靶向病毒进入的先天免疫限制因子的敏感性为代价的。
