Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections data. Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections data

Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection . Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naïve B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance. Overall design: SARS-CoV-2 antigen specific (PE+) memory B cells were sorted by fluoresence activated cell sorting (FACS) and analyzed using scRNA-seq

疫苗诱导免疫或可影响新冠病毒（SARS-CoV-2）变异株漂移表位的后续新生应答，但由于难以招募首次暴露于新冠病毒即为原发性感染的未接种疫苗对照组人群，该效应难以被量化。通过地方、州级及国家级新冠病毒检测项目，我们成功招募了两类康复人群队列：一类为原发性感染康复者，另一类为疫苗接种后感染德尔塔（Delta）或奥密克戎BA.1变异株的康复者。无论感染的变异株类型如何，相较于未接种疫苗即发生感染者，疫苗接种后感染者的刺突蛋白（Spike）特异性抗体应答及中和抗体应答水平均更高。以变异株特异性记忆B细胞作为新生应答的标志物进行分析后，我们发现德尔塔与奥密克戎BA.1感染会导致免疫优势格局发生显著改变：部分漂移表位仅能引发极微弱的应答，即便在原发性感染中亦是如此。既往疫苗诱导免疫对这类新生应答仅存在轻微的负向影响，但该影响与交叉反应性记忆B细胞并无关联，这一结果不支持幼稚B细胞受到竞争性抑制的假说。我们的研究结论为：针对漂移表位的新生B细胞应答被削弱，主要源于免疫优势层级的改变——该改变甚至在原发性感染中即可显现；而预存免疫仅发挥了较为温和的作用，其机制可能与抗原清除加速有关。

实验整体设计：通过荧光激活细胞分选（Fluorescence Activated Cell Sorting, FACS）分选出新冠病毒抗原特异性（PE+）记忆B细胞，并采用单细胞RNA测序（scRNA-seq）对其进行分析。