key: cord-0915026-ahxamndu
authors: Ai, Jingwen; Wang, Xun; He, Xinyi; Zhao, Xiaoyu; Zhang, Yi; Jiang, Yuchao; Li, Minghui; Cui, Yuchen; Chen, Yanjia; Qiao, Rui; Li, Lin; Yang, Lulu; Li, Yi; Hu, Zixin; Zhang, Wenhong; Wang, Pengfei
title: Antibody Evasion of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages
date: 2022-05-08
journal: Cell Host Microbe
DOI: 10.1016/j.chom.2022.05.001
sha: 60df1b71fec3bd8637166b6f11405a434bc0f7ac
doc_id: 915026
cord_uid: ahxamndu

The SARS-CoV-2 Omicron variant has evolved into four sub-lineages, BA.1, BA.1.1, BA.2 and BA.3, with BA.2 becoming dominant worldwide. We and others have reported antibody evasion of BA.1 and BA.2, but side-by-side comparisons of Omicron sub-lineages to vaccine-elicited or monoclonal antibody (mAb)-mediated neutralization are necessary. Using VSV-based pseudovirus, we report that sera from individuals vaccinated by two doses of an inactivated whole-virion vaccine shows weak to no neutralization activity, while homologous or heterologous boosters markedly improve neutralization titers against all Omicron sub-lineages. We also present neutralization profiles against a 20-mAb panel, including 10 authorized or approved, against the Omicron sub-lineages, along with mAb mapping against single or combinatorial spike mutations. Most mAbs lost neutralizing activity, while some demonstrate distinct neutralization patterns among Omicron sub-lineages, reflecting antigenic differences. Collectively, our results suggest the Omicron sub-lineages threaten the neutralization efficacy of current vaccines and antibody therapeutics, highlighting the importance of vaccine boosters.

Although the selective advantage of BA.2 could be partially explained by its higher 59 transmissibility than BA.1 (Lyngse et al., 2022) , their relative immune evasion property 60 could also be counted. We (Ai et al., 2021; Wang et al., 2022) and others (Cameroni et 61 al., 2022; Cao et al., 2022; Carreño et al., 2022; Cele et al., 2022; Garcia-Beltran et al., 62 2022; Liu et al., 2022; Planas et al., 2022; VanBlargan et al., 2022) have reported that 63 BA.1 demonstrated considerable escape from neutralization by monoclonal antibodies 64 (mAbs) and sera from vaccinated individuals. BA.2 has also been reported to severely 65 dampen antibody neutralization (Bowen et al., 2022; Iketani et al., 2022) . However, 66 evaluation and comparison of susceptibility of all the major Omicron sub-lineages to 67 vaccine-elicited or mAb-mediated neutralization are urgently needed. In this study, 68 therefore, we constructed the Omicron sub-lineage pseudoviruses (PsVs) and compared 69 side-by-side their neutralization sensitivity to vaccinee sera as well as a panel of mAbs. 70 The first question we asked for the Omicron sub-lineages is their extent of immune (Table S1 ). Similar as we reported before (Wang et al., 2022) , although all the 75 sera showed neutralization activity against wild-type (WT) virus, the activity was 76 relatively weak with geometric mean neutralizing titers (GMTs) about 55, and when it 77 turned to BA.1, only 2/10 vaccinees showed marginal neutralization. When we tested 78 these sera on the three other sub-lineages, most of them showed no detectable activity 79 except a few had very weak neutralization against BA.2 and BA.3 (Figures 1D and 80 S1A). These results indicate that two-dose inactivated vaccine is inadequate to provide 81 full protection against these newly emerging Omicron variants. 82 Our previous study showed that a booster shot, either homologous or heterologous, can 83 reduce Omicron BA.1 escape from neutralizing antibodies (Wang et al., 2022) . To see 84 if this is the case for the other Omicron sub-lineages, we then collected and tested 20 85 samples from healthy adults who had a third boosting vaccination shot with the same 86 BBIBP-CorV vaccine (homologous booster group, Table S1 ). As shown in Figures 1E   87 and S1B, the sera had a neutralizing GMT against WT of 225 with 5-to 6-fold reduction 88 J o u r n a l P r e -p r o o f against BA.1, BA.1.1, BA.2 and BA.3, but at least 15/20 samples exhibiting detectable 89 neutralizing activity against all four sub-lineages. We also collected 18 sera from 90 individuals that received two doses of BBIBP-CorV followed by a protein subunit 91 vaccine (ZF2001) 4-8 months later (heterologous booster group, The emergence of the SARS-CoV-2 Delta variant led to an increasing number of 100 breakthrough infection cases, to gain insight into their chance of re-infection by 101 Omicron, we recruited 10 participants who were immunized with two-dose inactivated 102 vaccines before infected by Delta variant (Table S1 ). Serum samples were obtained 103 from them after 3-4 months of breakthrough infection and evaluated on WT and the 104 four Omicron sub-lineage PsVs ( Figures 1G and S1D ). We found that breakthrough 105 infection by Delta boosted the neutralizing antibody titers significantly to very high 106 levels against WT virus (GMT = 1,740). However, the neutralization titers for Omicron 107 sub-lineages were significantly reduced, more than 100-fold in comparison to WT. The 108 reduction level was much higher than that of the homologous and heterologous vaccine 109 booster groups, which may be associated with the antigenic difference between Delta 110 and Omicron variants.

Taking into account of all the serum samples, we also carried out a comparison between -24, 4-18, 4-19 (Cerutti et al., 2021b; Liu et al., 2020) and 5-7 (Cerutti et al., 134 2021a; Liu et al., 2020) . Overall, all four Omicron sub-lineages had severe impact on 135 most of the antibodies but they also showed important differences in neutralization 136 patterns. Among the authorized or approved mAbs, seven were either totally inactive 137 or severely impaired in neutralizing all four sub-lineages. S309, the only approved 138 antibody found to retain its neutralizing activity against the original form of Omicron 139 in our previous study (Wang et al., 2022) , lost more neutralizing activity against BA. appears to be another key mutation responsible for the loss in potency of many RBD 166 antibodies, and again, when it was tested in combination with G496S and Q498R, 167 apparent synergistic effect was seen for some mAbs (Table S2) 

The SARS-CoV-2 Omicron variant immediately raised alarms after its identification 180 and the scenario seems to getting worse with the emerging Omicron sub-lineages, like 181 BA.2, which has been reported to be inherently substantially more transmissible than 

We previously reported the markedly reduced neutralizing activity against BA.1 of 188 convalescent or BBIBP-CorV vaccination sera (Ai et al., 2021; Wang et al., 2022) .

Here, we showed all polyclonal sera also had a substantial loss in neutralizing activity 190 against the other Omicron sub-lineages, with drops comparable to or even greater than We also investigated the immune evasion capacity of Omicron sub-lineages with mAbs. 371, 823-829. 430 Saitou, N., and Nei, M. (1987) . The neighbor-joining method: a new method for reconstructing 431 phylogenetic trees. Mol Biol Evol 4, 406-425. 432 Shi, R., Shan, C., Duan, X., Chen, Z., Liu, P., Song, J., Song, T., Bi, X., Han, C., Wu, L., et al. (2020) sub-lineages to BBIBP-CorV vaccine-elicited neutralization, finding substantial evasion against two-dose, but not boosted, vaccinee sera. Single and combinatorial mutational analysis maps key residues along Omicron Spike that help facilitate evasion against monoclonal antibody-mediated neutralization.

Omicron variant showed lower neutralizing sensitivity than other SARS-CoV-2 variants to immune 361 sera elicited by vaccines after boost

Omicron BA.1 and BA.2 neutralizing activity elicited by a 364 comprehensive panel of human vaccines

Broadly neutralizing antibodies overcome SARS-CoV

Omicron antigenic shift

Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies

Single-dose mRNA vaccine effectiveness against SARS-373

CoV-2 in healthcare workers extending 16 weeks post-vaccination: a test-negative design from 374

Activity of convalescent and vaccine serum against 377 SARS-CoV-2 Omicron

Omicron extensively but incompletely escapes Pfizer 380