Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses challenges to the effectiveness of neutralizing antibodies. Rational design of antibody cocktails is a realizable approach addressing viral immune evasion. However, evaluating the breadth of antibody cocktails is essential for understanding the development potential. Here, based on a replication competent vesicular stomatitis virus model that incorporates the spike of SARS-CoV-2 (VSV-SARS-CoV-2), we evaluated the breadth of a number of antibody cocktails consisting of monoclonal antibodies and bispecific antibodies by long-term passaging the virus in the presence of the cocktails. Results from over two-month passaging of the virus showed that 9E12 + 10D4 + 2G1 and 7B9-9D11 + 2G1 from these cocktails were highly resistant to random mutation, and there was no breakthrough after 30 rounds of passaging. As a control, antibody REGN10933 was broken through in the third passage. Next generation sequencing was performed and several critical mutations related to viral evasion were identified. These mutations caused a decrease in neutralization efficiency, but the reduced replication rate and ACE2 susceptibility of the mutant virus suggested that they might not have the potential to become epidemic strains. The 9E12 + 10D4 + 2G1 and 7B9-9D11 + 2G1 cocktails that picked from the VSV-SARS-CoV-2 system efficiently neutralized all current variants of concern and variants of interest including the most recent variants Delta and Omicron, as well as SARS-CoV-1. Our results highlight the feasibility of using the VSV-SARS-CoV-2 system to develop SARS-CoV-2 antibody cocktails and provide a reference for the clinical selection of therapeutic strategies to address the mutational escape of SARS-CoV-2.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Finelli L, Gupta V, Petigara T, Yu K, Bauer KA, Puzniak LA. Mortality among US patients hospitalized with SARS-CoV-2 infection in 2020. JAMA Netw Open. 2021;4:e216556.
Erikstrup C, Hother CE, Pedersen OBV, Molbak K, Skov RL, Holm DK, et al. Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors. Clin Infect Dis. 2021;72:249–53.
Giovanetti M, Benedetti F, Campisi G, Ciccozzi A, Fabris S, Ceccarelli G, et al. Evolution patterns of SARS-CoV-2: Snapshot on its genome variants. Biochem Biophys Res Commun. 2021;538:88–91.
Smith EC, Blanc H, Surdel MC, Vignuzzi M, Denison MR. Coronaviruses lacking exoribonuclease activity are susceptible to lethal mutagenesis: evidence for proofreading and potential therapeutics. PLoS Pathog. 2013;9:e1003565.
Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, et al. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet. 2021;22:757–73.
Magazine N, Zhang T, Wu Y, McGee MC, Veggiani G, Huang W. Mutations and evolution of the SARS-CoV-2 Spike Protein. Viruses. 2022;14:640.
Barnes CO, Jette CA, Abernathy ME, Dam KA, Esswein SR, Gristick HB, et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature. 2020;588:682–7.
Liu ZM, VanBlargan LA, Bloyet LM, Rothlauf PW, Chen RE, Stumpf S, et al. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe. 2021;29:477–88.
Watanabe Y, Allen JD, Wrapp D, McLellan JS, Crispin M. Site-specific glycan analysis of the SARS-CoV-2 spike. Science. 2020;369:330–3.
Shang J, Ye G, Shi K, Wan YS, Luo CM, Aihara H, et al. Structural basis of receptor recognition by SARS-CoV-2. Nature. 2020;581:221–4.
Wang ZJ, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature. 2021;592:616–22.
Hoffmann M, Arora P, Gross R, Seidel A, Hornich BF, Hahn AS, et al. SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. Cell. 2021;184:2384–93.
Kreye J, Reincke SM, Kornau HC, Sanchez-Sendin E, Corman VM, Liu HJ, et al. A therapeutic non-self-reactive SARS-CoV-2 antibody protects from lung pathology in a COVID-19 Hamster model. Cell. 2020;183:1058–69.
Brouwer PJM, Caniels TG, van der Straten K, Snitselaar JL, Aldon Y, Bangaru S, et al. Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science. 2020;369:643–50.
Cai Y, Zhang J, Xiao T, Lavine CL, Rawson S, Peng H, et al. Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants. Science. 2021;373:642–8.
Yin W, Xu Y, Xu P, Cao X, Wu C, Gu C, et al. Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody. Science. 2022;375:1048–53.
Cui Z, Liu P, Wang N, Wang L, Fan K, Zhu Q, et al. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell. 2022;185:860–71.
Gobeil SM, Henderson R, Stalls V, Janowska K, Huang X, May A, et al. Structural diversity of the SARS-CoV-2 Omicron spike. Mol Cell. 2022;82:2050–68.
Ku Z, Xie X, Davidson E, Ye X, Su H, Menachery VD, et al. Molecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape. Nat Commun. 2021;12:469.
Baum A, Ajithdoss D, Copin R, Zhou A, Lanza K, Negron N, et al. REGN-COV2 antibodies prevent and treat SARS-CoV-2 infection in rhesus macaques and hamsters. Science. 2020;370:1110–5.
Ma H, Guo Y, Tang H, Tseng CK, Wang L, Zong H, et al. Broad ultra-potent neutralization of SARS-CoV-2 variants by monoclonal antibodies specific to the tip of RBD. Cell Discov. 2022;8:16.
Chen M, Zhang XE. Construction and applications of SARS-CoV-2 pseudoviruses: a mini review. Int J Biol Sci. 2021;17:1574–80.
Case JB, Rothlauf PW, Chen RE, Kafai NM, Fox JM, Smith BK, et al. Replication-competent vesicular stomatitis virus vaccine vector protects against SARS-CoV-2-mediated pathogenesis in mice. Cell Host Microbe. 2020;28:465–74.
Han L, Chen JS, Ding K, Zong HF, Xie YQ, Jiang H, et al. Efficient generation of bispecific IgG antibodies by split intein mediated protein trans-splicing system. Sci Rep.-Uk. 2017;7:8360.
Zong H, Han L, Chen J, Pan Z, Wang L, Sun R, et al. Kinetics study of the natural split Npu DnaE intein in the generation of bispecific IgG antibodies. Appl Microbiol Biotechnol. 2022;106:161–71.
Tang HE, Ke Y, Wang L, Wu MY, Sun T, Zhu JW. Recombinant decoy exhibits broad protection against omicron and resistance potential to future variants. Pharmaceuticals (Basel). 2022;15:1002.
Dieterle ME, Haslwanter D, Bortz RH, Wirchnianski AS, Lasso G, Vergnolle O, et al. A replication-competent vesicular stomatitis virus for studies of SARS-CoV-2 spike-mediated cell entry and its inhibition. Cell Host Microbe. 2020;28:486–96.
Lau SY, Wang P, Mok BWY, Zhang ANJX, Chu H, Lee ACY, et al. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction. Emerg Microbes Infec. 2020;9:837–42.
Gobeil SM, Henderson R, Stalls V, Janowska K, Huang X, May A, et al. Structural diversity of the SARS-CoV-2 Omicron spike. Mol Cell. 2022;82:2050–68.
Araf Y, Akter F, Tang YD, Fatemi R, Parvez MSA, Zheng C, et al. Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines. J Med Virol. 2022;94:1825–32.
Collier DA, De Marco A, Ferreira I, Meng B, Datir RP, Walls AC, et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature. 2021;593:136–41.
Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 vaccine against the B.1.351 Variant. N Engl J Med. 2021;384:1885–98.
Alter G, Yu J, Liu J, Chandrashekar A, Borducchi EN, Tostanoski LH, et al. Immunogenicity of Ad26.COV2.S vaccine against SARS-CoV-2 variants in humans. Nature. 2021;596:268–72.
Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, et al. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature. 2021;596:276–80.
Case JB, Rothlauf PW, Chen RE, Liu Z, Zhao H, Kim AS, et al. Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2. Cell Host Microbe. 2020;28:475–85.
Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020;9:e61312.
Timm C, Gupta A, Yin J. Robust kinetics of an RNA virus: Transcription rates are set by genome levels. Biotechnol Bioeng. 2015;112:1655–62.
Lagunas-Rangel FA, Chavez-Valencia V. What do we know about the antibody responses to SARS-CoV-2? Immunobiology. 2021;226:152054.
Acknowledgements
We would like to acknowledge following organizations and individuals for their assistances in the preparation of the manuscript: Professor Tao Sun of SJTU for providing technical and material supports in generating the VSV-SARS-CoV-2 system. This work was funded by the National Natural Science Foundation of China (81773621, 82073751 to JWZ); the National Science and Technology Major Project “Key New Drug Creation and Manufacturing Program” of China (No.2019ZX09732001-019 to JWZ); the Key R&D Supporting Program (Special support for developing medicine for infectious diseases) from the Administration of Chinese and Singapore Tianjin Eco-city to Jecho Biopharmaceuticals Ltd. Co.; Zhejiang University special COVID-19 grant 2020XGZX099 and Shanghai Jiao Tong University “Crossing Medical and Engineering” grant 20×190020003 to JWZ.
Author information
Authors and Affiliations
Contributions
LH, YQX and JWZ conceived the study and designed the experiments. HM, HFZ, JJL, YLY, YK, YJL, HNT and LW conducted the experiments. HM and JWZ wrote and revised the manuscript. SSW, YSY, MYW, YLB, BHZ, HYY, HJ and TS provided technical assistance. TS All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Ma, H., Zong, Hf., Liu, Jj. et al. Long-term passaging of pseudo-typed SARS-CoV-2 reveals the breadth of monoclonal and bispecific antibody cocktails. Acta Pharmacol Sin 44, 1455–1463 (2023). https://doi.org/10.1038/s41401-022-01043-w
Received:
Accepted:
Published:
Version of record:
Issue date:
DOI: https://doi.org/10.1038/s41401-022-01043-w
