Striking Antibody Evasion Manifested By The Omicron Variant Of SARS-CoV-2

Contact: Audrey Hu Whatsapp/hp: 0086 13880143964 Email: audrey.hu@wecistanche.com

Lihong Liu1,7, Sho Iketani1,2,7, Yicheng Guo1,7, Jasper F-W. Chan3,4,7, Maple Wang1,7, Liyuan Liu5,7, Yang Luo1,

Hin Chu3,4, Yiming Huang5, Manoj S. Nair1, Jian Yu1, Kenn K-H. Chik4, Terrence T-T. Yuen3, Chemin Yoon3, Kelvin K-W. To3,4,

Honglin Chen3,4, Michael T. Yin1,6, Magdalena E. Sobieszczyk1,6, Yaoxing Huang1, Harris H. Wang5, Zizhang Sheng1, Kwok-Yung Yuen3,4 & David D. Ho1,2,6 

1 Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.

2 Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.

3 State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, Hong Kong, China.

4 Centre for Virology, Vaccinology, and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, Hong Kong, China.

5 Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.

6 Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA.

7 These authors contributed equally: Lihong Liu, Sho Iketani, Yicheng Guo, Jasper F-W. Chan, Maple Wang, Liyuan Liu

The Omicron (B.1.1.529) variant of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) was only recently detected in southern Africa, but its subsequent spread has been extensive, both regionally and globally1. It is expected to become dominant in the coming weeks2, probably due to enhanced transmissibility. A striking feature of this variant is the large number of spike mutations3 that pose a threat to the efficacy of current COVID-19 (coronavirus disease 2019) vaccines and antibody therapies4. This concern is amplified by the findings from our study. We found B.1.1.529 to be markedly resistant to neutralization by serum not only from convalescent patients but also from individuals vaccinated with one of the four widely used COVID-19 vaccines. Even serum from persons vaccinated and boosted with mRNA-based vaccines exhibited substantially diminished neutralizing activity against B.1.1.529. By evaluating a panel of monoclonal antibodies to all known epitope clusters on the spike protein, we noted that the activity of 17 of the 19 antibodies tested was either abolished or impaired, including ones currently authorized or approved for use in patients. In addition, we also identified four new spike mutations (S371L, N440K, G446S, and Q493R) that confer greater antibody resistance to B.1.1.529. The Omicron variant presents a serious threat to many existing COVID-19 vaccines and therapies, compelling the development of new interventions that anticipate the evolutionary trajectory of SARS-CoV-2.

improve immunity cistanche supplement

The COVID-19 (coronavirus disease 2019) pandemic rages on, as the causative agent, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), continues to evolve. Many diverse viral variants have emerged (Fig. 1a), each characterized by mutations in the spike protein that raise concerns of both antibody evasion and enhanced transmission. The Beta (B.1.351) variant was found to be most refractory to antibody neutralization4 and thus compromised the efficacy of vaccines5–7 and therapeutic antibodies. The Alpha (B.1.1.7) variant became dominant globally in early 2021 due to an edge in transmission8 only to be replaced by the Delta (B.1.617.2) variant, which exhibited an even greater propensity to spread coupled with a moderate level of antibody resistance9. Then came the Omicron (B.1.1.529) variant, first detected in southern Africa in November 20213,10,11 (Fig. 1a). It has since spread rapidly in the region, as well as to over 60 countries, gaining traction even where the Delta variant is prevalent. The short doubling time (2-3 days) of Omicron cases suggests it could become dominant soon2. Moreover, its spike protein contains an alarming number of >30 mutations (Fig. 1b and Extended Data Fig. 1), including at least 15 in the receptor-binding domain (RBD), the principal target for neutralizing antibodies. These extensive spike mutations raise the specter that current vaccines and therapeutic antibodies would be greatly compromised. This concern is amplified by the findings we now report.

cistanche echinacoside: improve immunity

Serum neutralization of B.1.1.529

We first examined the neutralizing activity of serum collected in the Spring of 2020 from COVID-19 patients, who were presumably infected with the wild-type SARS-CoV-2 (9-120 days post-symptoms) (see Methods and Extended Data Table 1). Samples from 10 individuals were tested for neutralization against both D614G (WT) and B.1.1.529 pseudoviruses. While robust titers were observed against D614G, a significant drop (>32-fold) in ID50 (50% infectious dose) titers was observed against B.1.1.529, with only 2 samples showing titers above the limit of detection (LOD) (Fig. 1c and Extended Data Fig. 2a). We then assessed the neutralizing activity of sera from individuals who received one of the four widely used COVID-19 vaccines: BNT162b2 (Pfizer, 15-213 days post-vaccination), mRNA-1273 (Moderna, 6-177 days post-vaccination), Ad26.COV2.S ( Johnson & Johnson, 50-186 days post-vaccination), and ChAdOx1 nCoV-19 (AstraZeneca, 91-159 days post-vaccination) (see Methods and Extended Data Table 2). In all cases, a substantial loss in neutralizing potency was observed against B.1.1.529 (Fig. 1d and Extended Data Fig. 2b-f). For the two mRNA-based vaccines, BNT162b2 and mRNA-1273, a >21-fold and >8.6-fold decrease in ID50 was seen, respectively. We note that, for these two groups, we specifically chose samples with high titers such that the fold-change in titer could be better quantified, so the difference in the number of samples having titers above the LOD (6/13 for BNT162b2 versus 11/12 for mRNA-1273) may be favorably biased. Within the Ad26.COV2.S and ChAdOx1 nCOV- 19 groups, all samples were below the LOD against B.1.1.529, except for two Ad26.COV2.S samples from patients with a previous history of SARS-CoV-2 infection (Fig. 1d). Collectively, these results suggest that individuals who were previously infected or fully vaccinated remain at risk for B.1.1.529 infection.

Fig. 1 | ResistanceofB.1.1.529toneutralizationbysera. a,

Fig.2 ResistanceofB.1.1.529toneutralizationbymonoclonal antibodies. FootprintsofRBD-directed antibodies,withmutationswithinB.1.1.529 highlighted in cyan. Approved authorized antibodies are bolded. The receptor-binding motif(RBM) residues are highlighted in yellow.b, Footprints of NTD-directed antibodies,withmutationswithinB.1.1.529 highlighted in cyan. The NTD supersite residues are highlighted in light pink. c, Neutralization of D614G and B.1.1.529 pseudoviruses by RBD-directed and NTD-directed mAbs. d, Neutralization D614G and B.1.1.529+R346K pseudoviruses by RBD-directed and NTD-directed mAbs. Data represent one of two independent experiments.

Booster shots are now routinely administered in many countries 6 months after full vaccination. Therefore, we also examined the serum neutralizing activity of individuals who had received three homologous mRNA vaccinations (13 with BNT162b2 and 2 with mRNA-1273, 14-90 days post-vaccination). Every sample showed lower activity in neutralizing B.1.1.529, with a mean drop of 6.5-fold compared to WT (Fig. 1d). Although all samples had titers above the LOD, the substantial loss inactivity may still pose a risk for B.1.1.529 infection despite the booster vaccination.

We then confirmed the above findings by testing a subset of the BNT162b2 and mRNA-1273 vaccine serum samples using authentic SARS-CoV-2 isolates: wild type and B.1.1.529. Again, a substantial decrease in the neutralization of B.1.1.529 was observed, with mean drops of >6.0-fold and >4.1-fold for the fully vaccinated group and the boosted group, respectively (Fig. 1e).

cistanche and cistanche extract benefit: improve immunity

Antibody neutralization of B.1.1.529

To understand the types of antibodies in serum that lost neutralizing activity against B.1.1.529, we assessed the neutralization profile of 19 well-characterized monoclonal antibodies (mAbs) to the spike protein, including 17 directed to RBD and 2 directed to the N-terminal domain (NTD). We included mAbs that have been authorized or approved for clinical use, either individually or in combination: REGN10987 (imdevimab)12, REGN10933 (casirivimab)12, COV2-2196 (tixagevimab)13, COV2-2130 (cilgavimab)13, LY-CoV555 (bamlanivimab)14, CB6 (etesevimab)15, Brii-196 (amubarvimab)16, Brii-198 (romlusevimab)16, and S309 (sotrovimab)17. We also included other mAbs of interest: 910-3018, ADG-219, DH104720, S2X25921, and our antibodies 1-20, 2-15, 2-7, 4-18, 5-7, and 10-4022–24. The footprints of mAbs with structures available were drawn in relation to the mutations found in B.1.1.529 RBD (Fig. 2a) and NTD (Fig. 2b). The risk to each of the 4 classes25 of RBD mAbs, as well as to the NTD mAbs, was immediately apparent. Indeed, neutralization studies on B.1.1.529 pseudovirus showed that 17 of the 19 mAbs tested lost neutralizing activity completely or partially (Fig. 2c and Extended Data Fig. 3). The potency of class 1 and class 2 RBD mAbs all dropped by >100-fold, as did the more potent mAbs in RBD class 3 (REGN10987, COV2-2130, and 2-7). The activities of S309 and Brii-198 were spared. All mAbs in RBD class 4 lost neutralization potency against B.1.1.529 by at least 10-fold, as did mAb directed to the antigenic supersite26 (4-18) or the alternate site23 (5-7) on NTD. Strikingly, all four combination mAb drugs in clinical use lost substantial activity against B.1.1.529, likely abolishing or impairing their efficacy in patients.

Approximately 10% of the B.1.1.529 viruses in GISAID1 (Global Initiative on Sharing All Influenza Data) also contain an additional RBD mutation, R346K, which is the defining mutation for the Mu (B.1.621) variant27. We, therefore, constructed another pseudovirus (B.1.1.529+R346K) containing this mutation for additional testing using the same panel of mAbs (Fig. 2d). The overall findings resembled those already shown in Fig. 2c, with the exception that the neutralizing activity of Brii 198 was abolished. In fact, nearly the entire panel of antibodies was essentially rendered inactive against this minor form of the Omicron variant. The fold changes in IC50 of the mAbs against B.1.1.529 and B.1.1.529+R346K relative to D614G are summarized in the first two rows of Fig. 3a. The remarkable loss of activity observed for all classes of mAbs against B.1.1.529 suggest that perhaps the same is occurring in the serum of convalescent patients and vaccinated individuals.

Mutations conferring antibody resistance

To understand the specific B.1.1.529 mutations that confer antibody resistance, we next tested individually the same panel of 19 mAbs against pseudoviruses for each of the 34 mutations (excluding D614G) found in B.1.1.529 or B.1.1.529+R346K. Our findings not only confirmed the role of known mutations at spike residues 142-145, 417, 484, and 501 in conferring resistance to NTD or RBD (class 1 or class 2) antibodies4 but also revealed several mutations that were previously not known to have functional importance to neutralization (Fig. 3a and Extended Data Fig. 4). Q493R, previously shown to affect the binding of CB6 and LY-CoV55528 as well as polyclonal sera29, mediated resistance to CB6 (class 1) as well as to LY-CoV555 and 2-15 (class 2), findings that could be explained by the abolishment of hydrogen bonds due to the long side chain of arginine and induced steric clashes with CDRH3 in these antibodies (Fig. 3b, left panels).

Both N440K and G446S mediated resistance to REGN10987 and 2-7 (class 3), observations that could also be explained by steric hindrance (Fig. 3b, middle panels). The most striking and perhaps unexpected finding was that S371L broadly affected neutralization by mAbs in all 4 RBD classes (Fig. 3a and Extended Data Fig. 4). While the precise mechanism of this resistance is unknown, in silico modeling suggested two possibilities (Fig. 3b, right panels). First, in the RBD-down state, mutating Ser to Leu results in an interference with the N343 glycan, thereby possibly altering its conformation and affecting class 3 antibodies that typically bind this region. Second, in the RBD-up state, S371L may alter the local conformation of the loop consisting of S371-S373-S375, thereby affecting the binding of class 4 antibodies that generally target a portion of this loop24. It is not clear how class 1 and class 2 RBD mAbs are affected by this mutation.

Evolution of SARS-CoV-2 to antibodies

To gain insight into the antibody resistance of B.1.1.529 relative to previous SARS-CoV-2 variants, we evaluated the neutralizing activity of the same panel of neutralizing mAbs against pseudoviruses for B.1.1.78, B.1.52630, B.1.42931, B.1.617.29, P.132, and B.1.35133. It is evident from these results (Fig. 4 and Extended Data Fig. 5) that previous variants developed resistance only to NTD antibodies and class 1 and class 2 RBD antibodies. Here B.1.1.529, with or without R346K, has made a big mutational leap by becoming not only nearly completely resistant to class 1 and class 2 RBD antibodies, but also substantial resistance to both class 3 and class 4 RBD antibodies. B.1.1.529 is now the most complete “escapee” from neutralization by currently available antibodies.

benefit of cistanche supplement: improve immunity

Discussion

The Omicron variant struck fear almost as soon as it was detected to be spreading in South Africa. That this new variant would transmit more readily has come true in the ensuing weeks2. The extensive mutations found in its spike protein raised concerns that the efficacy of current COVID-19 vaccines and antibody therapies might be compromised. Indeed, in this study, sera from convalescent patients (Fig. 1c) and vaccinees (Figs. 1d and 1e) showed markedly reduced neutralizing activity against B.1.1.529. Other studies have found similar losses34–38. These findings are in line with emerging clinical data on the Omicron variant demonstrating higher rates of reinfection11 and vaccine breakthroughs. In fact, recent reports showed that the efficacy of two doses of BNT162b2 vaccine has dropped from over 90% against the original SARS-CoV-2 strain to approximately 40% and 33% against B.1.1.529 in the United Kingdom39 and South Africa40, respectively. Even a third booster shot may not adequately protect against Omicron infection39,41, although the protection against a disease still makes it advisable to administer booster vaccinations. Vaccines that elicited lower neutralizing titers35,42 are expected to fare worse against B.1.1.529.

The nature of the loss in serum neutralizing activity against B.1.1.529 could be discerned from our findings on a panel of mAbs directed to the viral spike. The neutralizing activities of all four major classes of RBD mAbs and two distinct classes of NTD mAbs are either abolished or impaired (Figs. 2c and 2d). In addition to previously identified mutations that confer antibody resistance4, we have uncovered four new spike mutations with functional consequences. Q493R confers resistance to some class 1 and class 2 RBD mAbs; N440K and G446S confer resistance to some class 3 RBD mAbs, and S371L confers global resistance to many RBD mAbs via mechanisms that are not yet apparent. While performing these mAb studies, we also observed that nearly all the currently authorized or approved mAb drugs are rendered weak or inactive by B.1.1.529 (Figs. 2c and 3a). In fact, the Omicron variant that contains R346K almost flattens the antibody therapy landscape for COVID-19 (Fig. 2d and 3a).

The scientific community has chased after SARS-CoV-2 variants for a year. As more and more of them appeared, our interventions directed to the spike became increasingly ineffective. The Omicron variant has now put an exclamation mark on this point. It is not too far-fetched to think that this SARS-CoV-2 is now only a mutation or two away from being pan-resistant to current antibodies, either monoclonal or polyclonal. We must devise strategies that anticipate the evolutional direction of the virus and develop agents that target better conserved viral elements.

cistanche supplement: improve immunity

Reference

1. Shu, Y. & McCauley, J. GISAID: Global initiative on sharing all influenza data - from vision to reality.

2. Grabowski, F., Kochańczyk, M. & Lipniacki, T. Omicron strain spreads with the doubling time of 3.2—3.6 days in South Africa province of Gauteng that achieved herd immunity to Delta variant. medRxiv,

3. Scott, L. et al. Track Omicron’s spread with molecular data. Science, eabn4543,

4. Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130-135,

5. Abu-Raddad, L. J., Chemaitelly, H., Butt, A. A. &National Study Group for, C.-V. Effectiveness of the BNT162b2 Covid-19 Vaccine against the B.1.1.7 and B.1.351 Variants. N Engl J Med 385, 187-189, https://doi.org/10.1056/NEJMc2104974 (2021).

6. Madhi, S. A. et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. N Engl J Med 384, 1885-1898,(2021).

7. Sadoff, J. et al. Safety, and Efficacy of Single-Dose Ad26.COV2.S Vaccine against Covid-19. N Engl J Med 384, 2187-2201.

8. Davies, N. G. et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 372.

9. Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114-119.

10. Hadfield, J. et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 34, 4121-4123.

11. Pulliam, J. R. C. et al. Increased risk of SARS-CoV-2 reinfection associated with the emergence of the Omicron variant in South Africa. medRxiv.

12. Hansen, J. et al. Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science 369, 1010-1014.

13. Zost, S. J. et al. Potently neutralizing and protective human antibodies against SARS-CoV-2. Nature 584, 443-449.

14. Jones, B. E. et al. The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates. Sci Transl Med 13.

15. Shi, R. et al. A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature 584, 120-124.

16. Ju, B. et al. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature 584, 115-119.

17. Pinto, D. et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature 583, 290-295.

18. Banach, B. B. et al. Paired heavy- and light-chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses. Cell Rep 37, 109771.

19. Rappazzo, C. G. et al. Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody. Science 371, 823-829.

20. Li, D. et al. In vitro and in vivo functions of SARS-CoV-2 infection-enhancing and neutralizing antibodies. Cell 184, 4203-4219 e4232.

21. Tortorici, M. A. et al. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature 597, 103-108, https://doi.org/10.1038/s41586-021-03817-4 (2021).

22. Liu, L. et al. Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature 584, 450-456, https://doi.org/10.1038/s41586-020-2571-7 (2020).

23. Cerutti, G. et al. Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Cell Rep 37.

24. Liu, L. et al. Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses.

25. Barnes, C. O. et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies.

26. Cerutti, G. et al. Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe 29, 819-833 e817.

27. Uriu, K. et al. Neutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum. N Engl J Med.

28. Starr, T. N., Greaney, A. J., Dingens, A. S. & Bloom, J. D. Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Cell Rep Med 2, 100255.

29. Amanat, F. et al. SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2. Cell 184, 3936-3948 e3910.

30. Annavajhala, M. K. et al. Emergence, and expansion of SARS-CoV-2 B.1.526 after identification in New York. Nature 597, 703-708.

31. Zhang, W. et al. Emergence of a Novel SARS-CoV-2 Variant in Southern California. JAMA 325, 1324-1326.

32. Faria, N. R. et al. Genomics and epidemiology of P.1 SARS-CoV-2 lineage in Manaus, Brazil.

33. Legally, H. et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 592, 438-443.

34. Schmidt, F. et al. Plasma neutralization properties of the SARS-CoV-2 Omicron variant. medRxiv (2021).

35. Garcia-Beltran, W. F. et al. mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant.

36. Cameroni, E. et al. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicronantigenic shift. bioRxiv (2021).

37. Doria-Rose, N. A. et al. Booster of mRNA-1273 Vaccine Reduces SARS-CoV-2 Omicron Escape from Neutralizing Antibodies. medRxiv (2021).

38. Planas, D. et al. Considerable escape of SARS-CoV-2 variant Omicron to antibody neutralization. bioRxiv (2021).

39. Andrews, N. et al. Effectiveness of COVID-19 vaccines against the Omicron (B.1.1.529) variant of concern. medRxiv.

40. Wroughton, L. in The Washington Post (2021).

41. Kuhlmann, C. et al. Breakthrough Infections with SARS-CoV-2 Omicron Variant Despite Booster Dose of mRNA Vaccine. SSRN.

42. Cromer, D. et al. Neutralising antibody titers as predictors of protection against SARS-CoV-2 variants and the impact of boosting: a meta-analysis. Lancet Microbe.