Eosinophils protect against SARS-CoV-2 following a vaccine breakthrough infection

Waning immunity and the emergence of immune evasive SARS-CoV-2 variants jeopardize vaccine efficacy and contribute to breakthrough infections. The immune response that promotes vaccine-induced protection against SARS-CoV-2 breakthrough infection remains poorly understood. To model breakthrough infections, we vaccinated mice with a low dose vaccine formulation containing MF59-like adjuvant with prefusion-stabilized SARS-CoV-2 spike protein and challenged with immune evasive B.1.351 variant. Here, we show that eosinophils are required for protection against SARS-CoV-2 during a vaccine breakthrough infection. We found that vaccine breakthrough infection leads to a 2-log reduction in lung viral burden with restricted replication within the large airways as compared to naïve infected mice. Despite reduced antiviral gene expression, infected vaccinated mice show increased immune cell infiltration, characterized by monocytes, interstitial macrophages, and eosinophils, but with reduced activation markers into the lung parenchyma as compared to infected naïve mice. Single cell RNA-seq revealed that viral RNA was highly associated with eosinophils that corresponded to an IFN-γ biased phenotype and expression of antiviral genes including Cystatin B, an inhibitor of cysteine protease involved in SARS-CoV-2 entry via the endosome. Monocytes from infected vaccinated, but not naïve, mice showed high expression for eosinophil chemoattractant Ccl24 (eotaxin-2). Antibody-mediated depletion of eosinophils prior to infection of vaccinated mice resulted in increased virus replication and viral antigen staining deep in the lungs as compared to isotype control infected vaccinated mice. These results demonstrate the importance of eosinophils in vaccine-mediated protection and highlight the need for durable antibody responses that protect against lung infection and inflammation. Two mice in each group were either unvaccinated and mock infected, unvaccinated and infected, or vaccinated and infected using the AddaVax protein subunit vaccine and B.1.351 strain of the SARC-CoV-2 virus

免疫力衰减与免疫逃逸型严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变异株的出现，不仅会削弱疫苗保护效力，还会引发突破性感染。目前学界对于介导疫苗诱导的抗SARS-CoV-2突破性感染免疫保护的具体免疫应答机制，仍知之甚少。为构建突破性感染的动物模型，我们使用含有MF59样佐剂（MF59-like adjuvant）与预融合稳定化SARS-CoV-2刺突蛋白的低剂量疫苗制剂免疫小鼠，随后以免疫逃逸型B.1.351变异株对小鼠进行攻毒。本研究证实，在疫苗突破性感染过程中，嗜酸性粒细胞是介导抗SARS-CoV-2免疫保护的关键细胞。我们发现，与未免疫感染小鼠相比，疫苗突破性感染可使肺部病毒载量降低2个对数级，且病毒复制局限于大气道内。尽管抗病毒基因表达水平有所下降，但与未免疫感染小鼠相比，免疫后感染小鼠的肺部免疫细胞浸润程度更高，浸润细胞以单核细胞、间质巨噬细胞与嗜酸性粒细胞为主，但肺实质内的细胞激活标志物水平更低。单细胞RNA测序（single cell RNA-seq）结果显示，病毒RNA与嗜酸性粒细胞高度相关，这类嗜酸性粒细胞呈现干扰素-γ（IFN-γ）偏表型，并表达包括胱抑素B（Cystatin B）在内的抗病毒基因；胱抑素B是一种半胱氨酸蛋白酶抑制剂，可通过内体途径参与SARS-CoV-2的入侵过程。免疫后感染小鼠的单核细胞可高表达嗜酸性粒细胞趋化因子Ccl24（Ccl24，又名嗜酸性粒细胞趋化因子-2 eotaxin-2），而未免疫小鼠的单核细胞无此特征。与同型对照处理的免疫后感染小鼠相比，在免疫小鼠攻毒前通过抗体介导耗竭嗜酸性粒细胞，会导致肺部深处的病毒复制与病毒抗原染色信号增强。上述结果证实了嗜酸性粒细胞在疫苗介导的免疫保护中的重要作用，并提示需要诱导持久的抗体应答，以抵御肺部感染与炎症损伤。本研究每组纳入2只小鼠，分别为未免疫且模拟感染个体、未免疫且攻毒个体，以及经AddaVax蛋白亚单位疫苗（AddaVax protein subunit vaccine）免疫后以SARS-CoV-2 B.1.351毒株攻毒的个体。