On May 21^st, 2021, Xiaoliang Xie’s group from Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG) in Peking University, collaborating with labs from Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, and Beijing Youan Hospital, Capital Medical University jointly published their research results on Cell Research, entitled Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. They studied the humoral immune response to circulating SARS-CoV-2 variants, such as B.1.351, of the plasma and neutralizing antibodies (Nabs) elicited by CoronaVac (inactivated vaccine), ZF2001 (RBD-subunit vaccine), and natural infection by using high-throughput single-cell sequencing, cryo-electron microscopy, virus neutralization experiments, and other approaches.

　　The research group used high-throughput single-cell V(D)J sequencing to sequence and express 831 anti-spike protein antibodies from memory B cells in the peripheral blood of CoronaVac vaccinees, ZF2001 vaccinees, as well as COVID-19 convalescents, and 86 potent SARS-CoV-2 NAbs were selected to test their neutralization ability against circulating mutants, including B.1.351. Pseudovirus neutralization test experiments showed that near half anti-RBD NAbs showed major neutralization reductions against the K417N/E484K/N501Y mutation combination, with E484K being the dominant cause. High-resolution cryo-EM structures revealed that the 242–244 deletion (242–244Δ) would abolish most neutralization activity of anti-NTD NAbs by interrupting the conformation of NTD antigenic supersite, indicating a much less diversity of anti-NTD NAbs than anti-RBD NAbs.

　　Responses of anti-RBD and anti-NTD SARS-CoV-2 NAbs to B.1.351.

　　To further confirm the diversity of anti-RBD antibodies, the research team analyzed the neutralizing ability of 18 VH3-53/VH3-66 genotype antibodies against the South African strain. VH3-53/VH3-66 antibodies are co-occurring antibodies in different infected individuals, and the epitopes and structures of these antibodies on RBD are highly identical. VH3-53/VH3-66 recurrent antibodies respond differently to RBD variants, and K417N compromises the majority of neutralizing activity through reduced polar contacts with complementarity determining regions according to structural analysis.

　　Similar to the results of the neutralizing antibody, the plasma of both convalescents and CoronaVac vaccinee showed a trend of decreasing neutralizing activity against B.1.351. The results of the pseudovirus and authentic virus neutralization experiments showed that B.1.351 would cause a major reduction in neutralization by convalescent plasma and CoronaVac vaccinee plasma through E484K and 242–244Δ, with the effects being additive. However, ZF2001 vaccinees exhibit a two-time higher tolerance to B.1.351 variants in both pseudovirus and authentic virus assays than CoronaVac vaccinees and convalescents. ZF2001 did not induce anti-NTD antibodies; thus, IgG binding is only affected by B.1.351 RBD mutants but not NTD mutants. Thus, this property causes ZF2001 to be only compromised by RBD mutations, with the 242–244Δ showing no effects.

　　Neutralization of B.1.351 by convalescent, CoronaVac, and ZF2001 vaccinee plasma.

　　This study also found the fact that an extended three-dose (day 0/30/140) leads to better neutralizing activity and tolerance to B.1.351 than the standard three-dose administration group (day 0/30/60). This phenomenon is likely due to additional antibody maturations acquired through continuous hypermutations before the third-dose boost. These results suggest that once variant strains spread on a large scale and in a rapid way, especially those mutants that carry mutations disrupting the NTD supersite, a third booster shot of vaccines utilizing RBD as the antigen should be ideal for providing adequate protection.

　　Dr. Yunlong Cao, Ph.D. candidates Ayijiang Yisimayi, Yali Bai, Weijin Huang, Xiaofeng Li, Zhiying Zhang, and Tianjiao Yuan are the co-first authors of this paper. Professor Xiaoliang Xie, Dr. Yunlong Cao, Prof. Junyu Xiao from Peking University, Professor Yingmei Feng from Beijing You'an Hospital, Prof. Youchun Wang from National Institutes for Food and Drug Control, and Prof. Chengfeng Qin from the Academy of Military Medical Sciences are the co-corresponding authors of this paper. This project is financially supported by the Beijing Advanced Innovation Center for Genomics in Peking University and the Ministry of Science and Technology of China.