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SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

ABSTRACT: On 24^th November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and those infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of the large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses and uses mutations that confer tight binding to ACE2 to unleash evolution driven by immune escape. This leads to a large number of mutations in the ACE2 binding site and rebalances receptor affinity to that of earlier pandemic viruses.

SUBMITTER: Dejnirattisai W

PROVIDER: S-EPMC8723827 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature

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SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

Dejnirattisai Wanwisa W Huo Jiandong J Zhou Daming D Zahradník Jiří J Supasa Piyada P Liu Chang C Duyvesteyn Helen M E HME Ginn Helen M HM Mentzer Alexander J AJ Tuekprakhon Aekkachai A Nutalai Rungtiwa R Wang Beibei B Dijokaite Aiste A Khan Suman S Avinoam Ori O Bahar Mohammad M Skelly Donal D Adele Sandra S Johnson Sile Ann SA Amini Ali A Ritter Thomas G TG Mason Chris C Dold Christina C Pan Daniel D Assadi Sara S Bellass Adam A Omo-Dare Nicola N Koeckerling David D Flaxman Amy A Jenkin Daniel D Aley Parvinder K PK Voysey Merryn M Costa Clemens Sue Ann SA Naveca Felipe Gomes FG Nascimento Valdinete V Nascimento Fernanda F Fernandes da Costa Cristiano C Resende Paola Cristina PC Pauvolid-Correa Alex A Siqueira Marilda M MM Baillie Vicky V Serafin Natali N Kwatra Gaurav G Da Silva Kelly K Madhi Shabir A SA Nunes Marta C MC Malik Tariq T Openshaw Peter J M PJM Baillie J Kenneth JK Semple Malcolm G MG Townsend Alain R AR Huang Kuan-Ying A KA Tan Tiong Kit TK Carroll Miles W MW Klenerman Paul P Barnes Eleanor E Dunachie Susanna J SJ Constantinides Bede B Webster Hermione H Crook Derrick D Pollard Andrew J AJ Lambe Teresa T Paterson Neil G NG Williams Mark A MA Hall David R DR Fry Elizabeth E EE Mongkolsapaya Juthathip J Ren Jingshan J Schreiber Gideon G Stuart David I DI Screaton Gavin R GR

Cell 20220104 3

On 24<sup>th</sup> November 2021, the sequence of a new SARS-CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titers of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic Alpha, Beta, Gamma, or Delta are substantially reduced, or the sera failed to neutralize. Titers against Omicron are boosted by third vaccine doses and are high in both vaccinated individuals and t ...[more]

PMID: 35081335

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Project description:BackgroundThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variants have risen to dominance, which contains far more mutations in the spike protein in comparison to previously reported variants, compromising the efficacy of most existing vaccines or therapeutic monoclonal antibodies. Nanobody screened from high-throughput naïve libraries is a potential candidate for developing preventive and therapeutic antibodies.MethodsFour nanobodies specific to the SARS-CoV-2 wild-type receptor-binding domain (RBD) were screened from a naïve phage display library. Their affinity and neutralizing activity were evaluated by surface plasmon resonance assays, surrogate virus neutralization tests, and pseudovirus neutralization assays. Preliminary identification of the binding epitopes of nanobodies by peptide-based ELISA and competition assay. Then four multivalent nanobodies were engineered by attaching the monovalent nanobodies to an antibody-binding nanoplatform constructed based on the lumazine synthase protein cage nanoparticles isolated from the Aquifex aeolicus (AaLS). Finally, the differences in potency between the monovalent and multivalent nanobodies were compared using the same methods.ResultsThree of the four specific nanobodies could maintain substantial inhibitory activity against the Omicron (B.1.1.529), of them, B-B2 had the best neutralizing activity against the Omicron (B.1.1.529) pseudovirus (IC50 = 1.658 μg/mL). The antiviral ability of multivalent nanobody LS-B-B2 was improved in the Omicron (B.1.1.529) pseudovirus assays (IC50 = 0.653 μg/mL). The results of peptide-based ELISA indicated that LS-B-B2 might react with the linear epitopes in the SARS-CoV-2 RBD conserved regions, which would clarify the mechanisms for the maintenance of potent neutralization of Omicron (B.1.1.529) preliminary.ConclusionOur study indicated that the AaLS could be used as an antibody-binding nanoplatform to present nanobodies on its surface and improve the potency of nanobodies. The multivalent nanobody LS-B-B2 may serve as a potential agent for the neutralization of SARS-CoV-2 variants.

Dataset Information

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

Publications

SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses.

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