Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing

Wen Wen; Wenru Su; Hao Tang; Wenqing Le; Xiaopeng Zhang; Yingfeng Zheng; XiuXing Liu; Lihui Xie; Jianmin Li; Jinguo Ye; Xiuliang Cui; Yushan Miao; Depeng Wang; Jiantao Dong; Chuan-Le Xiao; Wei Chen; Hongyang Wang

Previous SARS studies have identified binding and neutralizing antibodies elicited by SARS-CoV infection. Their therapeutic effect is unclear [30] , although robust antibody responses could be induced [31] . In COVID-19 infection, although several lines of evidence have consistently indicated a decline in lymphocyte counts, the distinct immune characteristics at single-cell resolution are unclear. Our scRNA-seq analysis showed that, compared with the HCs, ERS patients have a lower ratio of T and NK cells, and these patients' T cells express higher levels of inflammatory genes, such as JUN, FOS, JUNB, and KLF6. In addition, high-throughput TCR sequencing identified expanded T cell clones in ERS patients. In LRS patients, the immunophenotype was different. In particular, LRS patients would have an increase in T and NK cells, with a lower expression of inflammatory genes. We also performed a detailed analysis of B cells in patients and identified a higher population of plasma cells than that in the HCs. We found that BCR contained highly expanded clones, indicating their SARS-CoV-2 specificity. Importantly, we found several loci unique to COVID-19 infection. The strongest pairing frequencies, IGHV3-23-IGHJ4, indicated a monoclonal state associated with SARS-CoV-2 specificity. Notably, numerous studies have reported biased usage of VDJ genes related to virus-specific antibodies. For example, IGHV3-30 and IGKV3-11 have been involved in encoding primary antibodies to neutralize human cytomegalovirus [32, 33] . In addition, IGHV3-30 and IGHV3-21 have been utilized to isolate influenza virus antibodies and used for the production of virus vaccines [34, 35] . Moreover, a recent study demonstrated that antibodies combining the IGHV3-15/IGLV1-40 segments had superior neutralizing activities against the Zaire Ebola virus [36] .