SARS-CoV2 manipulates multiple NK ligands and inhibits NK activation, but this can be overcome by ADNKA, which is strongly activated by non-Spike targeting antibodies

SARS-CoV2 is recognised the antagonise the interferon response, and functioning interferon responses are critical in determining the severity of disease. However, whether the virus antagonises cellular immunity has not been determined. We used quantitative plasma membrane proteomics in lung epithelial cells to investigate viral manipulation of cell surface ligands, revealing that SARS-CoV2 does not affect HLA-I levels, but downregulates B7-H6, MICA, ULBP2, and Nectin1. Downregulation of these activating NK ligands correlated with a reduction in NK activation in response to infected cells. However, this activation could be overcome through antibody dependent NK activation (ADNKA). Surprisingly, monoclonal anti-spike antibodies were relatively poor activators of ADNKA, however expression of additional viral proteins, including ORF3a and Nucleocapsid, also led to NK activation following addition of antibodies. Furthermore, depletion of Spike antibodies revealed that while the neutralising response was dominated by anti-spike antibodies, these played a minor role in ADNKA against infected cells. Finally, we showed that anti-spike antibodies do mediate ADNKA following vaccination, but that by relying solely on spike to prime ADNKA, this response is considerably weaker than the responses seen following natural infection, and are not boosted by a second vaccine dose. Thus, the addition of extra viral proteins such as nucleocapsid to vaccines may recruit additional effector functions more strongly, reducing the impact of spike mutations on vaccine escape.

已有研究证实，严重急性呼吸综合征冠状病毒2型（SARS-CoV2）可拮抗干扰素应答，而功能性干扰素应答是决定疾病严重程度的关键因素。然而，该病毒是否会拮抗细胞免疫尚未明确。本研究采用肺上皮细胞的定量质膜蛋白质组学技术，探究病毒对细胞表面配体的调控作用，结果显示新冠病毒不会影响人类白细胞抗原I型（HLA-I）的表达水平，但可下调B7-H6、MICA、ULBP2及Nectin1的表达。上述活化性自然杀伤细胞（NK）配体的下调，与感染细胞诱导的NK细胞活化水平降低相关。不过，该抑制效应可通过抗体依赖性NK细胞活化（ADNKA）予以逆转。令人意外的是，单克隆抗刺突蛋白（spike）抗体介导ADNKA的活化能力相对较弱；而当额外表达包括开放读码框3a（ORF3a）与核衣壳蛋白（Nucleocapsid）等病毒蛋白后，加入抗体即可触发NK细胞活化。此外，刺突抗体的耗竭实验显示，尽管中和应答以抗刺突蛋白抗体为主，但这类抗体在针对感染细胞的ADNKA中仅发挥次要作用。最后，本研究证实，接种疫苗后产生的抗刺突蛋白抗体确实可介导ADNKA，但仅依赖刺突蛋白诱导ADNKA时，该应答强度远低于自然感染后产生的应答，且无法通过第二剂疫苗加强该应答。因此，在疫苗中加入核衣壳蛋白等额外病毒蛋白，可更有效地募集更多效应功能，从而降低刺突蛋白突变对疫苗逃逸的影响。