Integrated single-cell analysis revealed immune dynamics during Ad5-nCoV immunization

Hao Tang,Wen Wen,Yingfeng Zheng,Lihua Hou,Haijia Chen,Zhaomin Li,Hongyang Wang,Xiuliang Cui,Chuanle Xiao,Jiayong Zhong,Qiqi Cao,Xiangyang Chi,Shuzhen Chen,Fang Li,Shipo Wu,Wenru Su

doi:10.1038/s41421-021-00300-2

Abstract

Coronavirus disease 2019 (COVID-19), driven by SARS-CoV-2, is a severe infectious disease that has become a global health threat. Vaccines are among the most effective public health tools for combating COVID-19. Immune status is critical for evaluating the safety and response to the vaccine, however, the evolution of the immune response during immunization remains poorly understood. Single-cell RNA sequencing (scRNA-seq) represents a powerful tool for dissecting multicellular behavior and discovering therapeutic antibodies. Herein, by performing scRNA/V(D)J-seq on peripheral blood mononuclear cells from four COVID-19 vaccine trial participants longitudinally during immunization, we revealed enhanced cellular immunity with concerted and cell type-specific IFN responses as well as boosted humoral immunity with SARS-CoV-2-specific antibodies. Based on the CDR3 sequence and germline enrichment, we were able to identify several potential binding antibodies. We synthesized, expressed and tested 21 clones from the identified lineages. Among them, one monoclonal antibody (P3V6-1) exhibited relatively high affinity with the extracellular domain of Spike protein, which might be a promising therapeutic reagent for COVID-19. Overall, our findings provide insights for assessing vaccine through the novel scRNA/V(D)J-seq approach, which might facilitate the development of more potent, durable and safe prophylactic vaccines.

Highlights

The coronavirus disease 2019 (COVID‐19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), affects 191 countries and territories
We identified five monoclonal antibodies, and the most potent mAb, P3V6-1, exhibited a medium effective concentration (EC50) of 0.02598 μg/mL against the extracellular domain (ECD) of the S protein (S-ECD)
Cells are annotated based on differential expression analysis on orthogonally discovered clusters. c Heatmap revealing the scaled expression of differentially expressed genes (DEGs) for B cells, natural killer (NK) and T cells, and myeloid cells. d ScRNA-seq visualization with t-distributed stochastic neighbor embedding (t-SNE) analysis of peripheral blood mononuclear cells (PBMCs) (n = 92,456) from all participants and timepoints sampled, and t-SNE annotated by timepoints and colored by individuals. e Proportions of major cell types from each participant at different timepoints assayed in this study. f Proportions of different cell types in the total PBMCs from participants at different timepoints by scRNA-seq

Summary

Introduction

The coronavirus disease 2019 (COVID‐19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), affects 191 countries and territories. Complications may include pneumonia and acute respiratory distress syndrome. The impact on global health and the scale of socioeconomic damage is driving intense vaccine development, accelerated by multiple novel technology platforms. Genotypic and protein structural analysis of potent neutralizing antibodies from convalescent donors has shed some light on vaccine design[2,3,4,5]. Spike glycoprotein (S protein) is responsible for the initial binding of host cells through angiotensin-converting enzyme 2 (ACE2). Because of the binding and protruding nature of S protein and its receptor-binding domain (RBD), most investigators are pursuing S protein or the RBD as vaccine targets

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Conclusion