Scientific Updates

Nature | Yunlong Cao's Team Reveals Mechanism of Reshaping SARS-CoV-2 Immune Imprinting

  The continuous emergence of SARS-CoV-2 variants with immune evasion capabilities underscores the need for updating the components of COVID-19 vaccines. However, the immune imprinting caused by vaccination with the ancestral strain can weaken the antibody response to infections with these variants or to the updated variant vaccines. Therefore, exploring vaccination strategies that can mitigate or reshape the immune imprinting from the ancestral strain is extremely important.

  On November 22, 2023, the research group led by YunlongCao at the Biomedical Pioneering Innovation Center (BIOPIC) of Peking University/Changping Laboratorypublished a research article online in Nature titled "Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting". This paper offers new insights into the dynamics of SARS-CoV-2 immune imprinting. Employing high-throughput single-cell V(D)J sequencing and deep mutational scanning (DMS) technologies, the study revealed that double exposures to the Omicron variant (either through infection or vaccination), following vaccination with the ancestral strain, led to a high proportion of Omicron-specific neutralizing antibodies. This ameliorated the immune imprinting observed after a single exposure to Omicron post-ancestral strain vaccination, a situation in which a large proportion of antibodies target cross-binding, non-neutralizing epitopes.Furthermore, these Omicron-specific antibodies mostly targeted new receptor-binding domain (RBD) epitopes. Although they did not neutralize the ancestral strain, they exhibited remarkable broad-spectrum neutralizing capabilities against the Omicron variant lineage. The study also utilized DMS data to predict the evolutionary hotspots of the future XBB lineage. This research not only provides a deep understanding of the immune imprinting phenomenon at the level of monoclonal antibody epitopes but also offers important theoretical guidance for the updating and usage strategies of global COVID-19 vaccines.  

  In this paper, researchers utilized mice immunized by SARS-CoV-2 variants and a cohort of individuals infected with the Omicron variant to study the immune imprinting induced by the vaccinesagainstthe ancestral strain, with a particular focus on people who experienced reinfection with the Omicron variant.The study found that following vaccination with the ancestralstrain, a single exposure to anOmicron variant strain (either through vaccination or infection) resulted in a strong immune imprinting effect, with the intensity of the imprinting increasing as the antigenic distance between the Omicronstrain and the ancestral strain increased. However, the immune imprinting of the original strain was significantly attenuatedin both people who were infected twice and mice that were vaccinated twice with two Omicron strains. In terms of antigen-specific B cells, the proportion of Omicron-specific memory B cells in the population infected twice far exceeded that in the population exposed only once, and the antibodies encoded by these memory B cells exhibited a higher level of somatic hypermutation and antigen affinity compared to those from a single infection. Additionally, these Omicron-specific antibodies exhibitedsignificantly stronger neutralizing activity against the Omicron lineage compared to antibodies that cross-bind with the ancestral strain.

  To further explain the improved immune imprinting following a secondOmicroninfection, the study utilized previously developed high-throughput DMS technology, to identify the escaping mutations and binding sites of the antibodies on RBD. Compared to a single post-vaccination Omicroninfection, the proportion of antibodies targeting non-neutralizing epitopes in individuals infected twice was significantly reduced, indicating a substantial alleviation of immune imprinting (Figure 1). The research also discovered that these Omicron-specific antibodies targeted some novel RBD epitopes and exhibited remarkableneutralizing activity against the latest Omicron subvariants, such as XBB.1.5, thus explaining the improved immune imprinting and robust serum neutralization response after a second exposureto Omicron variant strains.


  Figure 1. Epitope groups of BA.5 RBD-targeting monoclonal antibodies isolated from individuals who had either a single post-vaccination infection or two infections (Left). Antibody epitope distribution among individuals with different infection histories. Epitope groups of non-neutralizing or weakly neutralizing monoclonal antibodies (E2.2, E3, and F1) are marked with dashed lines (Right).

  Additionally, this study utilized DMS data of a large amount of antibodies to predict the evolutionary hotspots on the RBD of XBB.1.5. Experiments confirmed that combined mutations at these sites could enhance the immune evasion capability of XBB.1.5, while maintaining a high affinity for the ACE2 receptor. Several of these predicted mutations have already appeared frequently in the real world.

  The article suggests abandoning the ancestral strain component in the current updates to the COVID-19 vaccine antigens, because the ancestral strain component may continuously activate cross-reactive and non-neutralizing antibodies due to immune imprinting.This recommendation has already been adopted by the WHO and the U.S. FDA. Moreover, according to the findings of the paper, individuals who have not yet been infected with the Omicron variant should receive two doses of the updated booster vaccine, and those who have already been infected with a variant strain should be vaccinated with a boostercontaining the latest variant, to elicit a robust broad-spectrum neutralizing antibody response.

  Yunlong Cao of Peking University and Changping Laboratory is the corresponding author of this article; AyijiangYisimayi, Weiliang Song, Jing Wang, Fanchong Jian of Peking University, Yuanling Yu of Changping Laboratory, and Xiaosu Chen of Nankai University are the co-first authors. This work was strongly supported by Youchun Wang, XiaoliangSunneyXie, RonghuaJin of Changping Laboratory, and Zhongyang Shen of Tianjin First Central Hospital.

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  For more details about Yunlong Cao's lab, visit: The team is currently seeking postdoctoral researchers specializing in immunology, virology, and vaccinology. They offer competitive compensation and encourage you to join the team! Contact information can be found on lab website.