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. 2021 Oct;12(10):751-755.
doi: 10.1007/s13238-020-00807-6. Epub 2020 Nov 25.

Single cell RNA and immune repertoire profiling of COVID-19 patients reveal novel neutralizing antibody

Fang Li #  1 , Meng Luo #  2 , Wenyang Zhou #  2 , Jinliang Li #  3 , Xiyun Jin  2 , Zhaochun Xu  2 , Liran Juan  2 , Zheng Zhang  3 , Yuou Li  3 , Renqiang Liu  1 , Yiqun Li  2 , Chang Xu  2 , Kexin Ma  2 , Huimin Cao  2 , Jingwei Wang  3 , Pingping Wang  4 , Zhigao Bu  5 , Qinghua Jiang  6   7
Affiliations

Single cell RNA and immune repertoire profiling of COVID-19 patients reveal novel neutralizing antibody

Fang Li et al. Protein Cell. 2021 Oct.
No abstract available

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Figures

Figure 1
Figure 1
Identification of clonally expanded BCR groups and neutralizing antibodies. (A) Overview of experimental design. PBMC samples from recovered COVID-19 patients at discharge were collected and simultaneously performed single cell RNA-seq with 5′VDJ capture and deep B cell repertoire sequencing. (B) UMAP map of B cells from twelve COVID-19 patients and eight healthy controls, which formed a gradient of transcriptional states from naïve B cells to an activated memory B cells then to plasma cells. (C) Barplot showing the percentages for different B cell subgroups identified from single cell analysis, including naïve B cell (C10), resting memory B cells (C16), activated B cells (C24) and plasma cells (C27). Error bar labels one standard deviation of the data. Statistical significance was estimated using two-sided Wilcoxon rank sum test. ns, P > 0.05. (D) BCR diversity compared between patients and a control cohort of 235 deep BCR-seq samples. The diversity was measured using D50, which is proven robust to sequencing library size. P value was estimated using two-sided Wilcoxon test. (E) Pie chart showing the percentage of the 9 different Ig heavy chain isotypes of COVID-19 patients and healthy controls. Numbers in the parentheses are the averaged percentage of the corresponding Ig isotype across all the individuals, calculated using deep BCR-seq data. (F). UMAP plot shows the 347 potential antigen-specific BCRs are enriched in activated B cells (C24) and plasma cells (C27). (G) Lineage tree of selected BCRs heavy chain groups, with aligned DNA sequences as reference on the right. Different nucleotides are labeled with different colors, with translational frame marked beneath each plot. Each node represents a BCR clone, with color indicating the Ig isotype. The size of node reflects the frequency (in read counts) of the clone. (H) Competition binding to the COVID-19 virus RBD between antibody GD1-68 and GD1-69 and ACE2. X-axis represented the concentration of these two antibodies and Y-axis stood for percentage of uninterrupted RBD/ACE2 interaction. IC50, half-maximum inhibitory concentration. (I) The neutralization potency of GD1-69 was determined by pseudovirus-based neutralization assay. The mixtures of SARS-CoV-2 pseudovirus and serially diluted antibodies were added to HEK293T cells stably overexpressing human ACE2 (293T-ACE2 cells). IC50 values were calculated by fitting the cytopathic effect from serially diluted antibody to a sigmoidal dose-response curve. (J) The neutralization activity of the antibody GD1-69 was performed using a plaque reduction neutralization test assay. Serial dilutions of GD1-69 were incubated with SARS-CoV-2, and then added to pre-plated Vero E6 cell monolayers. The cells were incubated for 48 h with agarose overlay. Neutralizing titers (IC50 values) were calculated as the maximum antibody dilution yielding a 50% reduction in the number of plaques relative to that for control IgG protein
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