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      Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination

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      Nature
      Nature Publishing Group UK
      Viral infection, SARS-CoV-2

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          Abstract

          SARS-CoV-2 Delta and Omicron are globally relevant variants of concern. Although individuals infected with Delta are at risk of developing severe lung disease, infection with Omicron often causes milder symptoms, especially in vaccinated individuals 1, 2 . The question arises of whether widespread Omicron infections could lead to future cross-variant protection, accelerating the end of the pandemic. Here we show that without vaccination, infection with Omicron induces a limited humoral immune response in mice and humans. Sera from mice overexpressing the human ACE2 receptor and infected with Omicron neutralize only Omicron, but not other variants of concern, whereas broader cross-variant neutralization was observed after WA1 and Delta infections. Unlike WA1 and Delta, Omicron replicates to low levels in the lungs and brains of infected animals, leading to mild disease with reduced expression of pro-inflammatory cytokines and diminished activation of lung-resident T cells. Sera from individuals who were unvaccinated and infected with Omicron show the same limited neutralization of only Omicron itself. By contrast, Omicron breakthrough infections induce overall higher neutralization titres against all variants of concern. Our results demonstrate that Omicron infection enhances pre-existing immunity elicited by vaccines but, on its own, may not confer broad protection against non-Omicron variants in unvaccinated individuals.

          Abstract

          Infection with Omicron after vaccination produces cross-neutralizing antibodies to other variants of concern, whereas this induces a limited response to non-Omicron variants in unvaccinated individuals.

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          SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls

          Memory T cells induced by previous pathogens can shape susceptibility to, and the clinical severity of, subsequent infections1. Little is known about the presence in humans of pre-existing memory T cells that have the potential to recognize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we studied T cell responses against the structural (nucleocapsid (N) protein) and non-structural (NSP7 and NSP13 of ORF1) regions of SARS-CoV-2 in individuals convalescing from coronavirus disease 2019 (COVID-19) (n = 36). In all of these individuals, we found CD4 and CD8 T cells that recognized multiple regions of the N protein. Next, we showed that patients (n = 23) who recovered from SARS (the disease associated with SARS-CoV infection) possess long-lasting memory T cells that are reactive to the N protein of SARS-CoV 17 years after the outbreak of SARS in 2003; these T cells displayed robust cross-reactivity to the N protein of SARS-CoV-2. We also detected SARS-CoV-2-specific T cells in individuals with no history of SARS, COVID-19 or contact with individuals who had SARS and/or COVID-19 (n = 37). SARS-CoV-2-specific T cells in uninfected donors exhibited a different pattern of immunodominance, and frequently targeted NSP7 and NSP13 as well as the N protein. Epitope characterization of NSP7-specific T cells showed the recognition of protein fragments that are conserved among animal betacoronaviruses but have low homology to 'common cold' human-associated coronaviruses. Thus, infection with betacoronaviruses induces multi-specific and long-lasting T cell immunity against the structural N protein. Understanding how pre-existing N- and ORF1-specific T cells that are present in the general population affect the susceptibility to and pathogenesis of SARS-CoV-2 infection is important for the management of the current COVID-19 pandemic.
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            Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies

            The SARS-CoV-2 B.1.1.529 (Omicron) variant contains 15 mutations of the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies requires immediate investigation. Here we use high-throughput yeast display screening 1,2 to determine the profiles of RBD escaping mutations for 247 human anti-RBD neutralizing antibodies and show that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A–F)—a grouping that is highly concordant with knowledge-based structural classifications 3–5 . Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups. Specifically, neutralizing antibodies in groups A–D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and Q493R. Antibodies in group E (for example, S309) 6 and group F (for example, CR3022) 7 , which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes. In total, over 85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was greatly undermined by Omicron, whereas VIR-7831 and DXP-604 still functioned at a reduced efficacy. Together, our data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus conserved region will remain most effective. Our results inform the development of antibody-based drugs and vaccines against Omicron and future variants.
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              Considerable escape of SARS-CoV-2 Omicron to antibody neutralization

              The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa1-3. It has since spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of around 32 mutations in spike-located mostly in the N-terminal domain and the receptor-binding domain-that may enhance viral fitness and enable antibody evasion. Here we isolated an infectious Omicron virus in Belgium from a traveller returning from Egypt. We examined its sensitivity to nine monoclonal antibodies that have been clinically approved or are in development4, and to antibodies present in 115 serum samples from COVID-19 vaccine recipients or individuals who have recovered from COVID-19. Omicron was completely or partially resistant to neutralization by all monoclonal antibodies tested. Sera from recipients of the Pfizer or AstraZeneca vaccine, sampled five months after complete vaccination, barely inhibited Omicron. Sera from COVID-19-convalescent patients collected 6 or 12 months after symptoms displayed low or no neutralizing activity against Omicron. Administration of a booster Pfizer dose as well as vaccination of previously infected individuals generated an anti-Omicron neutralizing response, with titres 6-fold to 23-fold lower against Omicron compared with those against Delta. Thus, Omicron escapes most therapeutic monoclonal antibodies and, to a large extent, vaccine-elicited antibodies. However, Omicron is neutralized by antibodies generated by a booster vaccine dose.
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                Author and article information

                Contributors
                nadia.roan@gladstone.ucsf.edu
                charles.chiu@ucsf.edu
                doudna@berkeley.edu
                melanie.ott@gladstone.ucsf.edu
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                18 May 2022
                18 May 2022
                2022
                : 607
                : 7918
                : 351-355
                Affiliations
                [1 ]GRID grid.249878.8, ISNI 0000 0004 0572 7110, Gladstone Institutes, ; San Francisco, CA USA
                [2 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Biomedical Sciences Graduate Program, , University of California, San Francisco, ; San Francisco, CA USA
                [3 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Medicine, , University of California, San Francisco, ; San Francisco, CA USA
                [4 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Quantitative Biosciences Institute COVID-19 Research Group, , University of California, San Francisco, ; San Francisco, CA USA
                [5 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, UCSF-Abbott Viral Diagnostics and Discovery Center, ; San Francisco, CA USA
                [6 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Innovative Genomics Institute, , University of California, Berkeley, ; Berkeley, CA USA
                [7 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Laboratory Medicine, , University of California, San Francisco, ; San Francisco, CA USA
                [8 ]Michael Hulton Center for HIV Cure Research at Gladstone, San Francisco, CA USA
                [9 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Microbiology and Immunology, , University of California, San Francisco, ; San Francisco, CA USA
                [10 ]Curative Inc., San Dimas, CA USA
                [11 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Urology, , University of California, San Francisco, ; San Francisco, CA USA
                [12 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Medicine, Cardiovascular Research Institute, , University of California, San Francisco, ; San Francisco, CA USA
                [13 ]GRID grid.266102.1, ISNI 0000 0001 2297 6811, Department of Anesthesia, Cardiovascular Research Institute, , University of California, San Francisco, ; San Francisco, CA USA
                [14 ]GRID grid.236815.b, ISNI 0000 0004 0442 6631, California Department of Public Health, ; Richmond, CA USA
                [15 ]GRID grid.499295.a, ISNI 0000 0004 9234 0175, Chan Zuckerberg Biohub, ; San Francisco, CA USA
                [16 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Molecular and Cell Biology, , University of California, Berkeley, ; Berkeley, CA USA
                [17 ]GRID grid.184769.5, ISNI 0000 0001 2231 4551, Molecular Biophysics and Integrated Bioimaging Division, , Lawrence Berkeley National Laboratory, ; Berkeley, CA USA
                [18 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Howard Hughes Medical Institute, , University of California, Berkeley, ; Berkeley, CA USA
                [19 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Chemistry, , University of California, Berkeley, ; Berkeley, CA USA
                [20 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, California Institute for Quantitative Biosciences, , University of California, Berkeley, ; Berkeley, CA USA
                [21 ]GRID grid.19006.3e, ISNI 0000 0000 9632 6718, Department of Medicine, , University of California, Los Angeles, ; Los Angeles, CA USA
                Author information
                http://orcid.org/0000-0002-5766-9253
                http://orcid.org/0000-0001-9222-8130
                http://orcid.org/0000-0002-8930-745X
                http://orcid.org/0000-0002-6374-7211
                http://orcid.org/0000-0003-3039-8155
                http://orcid.org/0000-0001-5503-9349
                http://orcid.org/0000-0003-2915-2094
                http://orcid.org/0000-0001-9161-999X
                http://orcid.org/0000-0002-5697-1274
                Article
                4865
                10.1038/s41586-022-04865-0
                9279157
                35584773
                dbf5e14a-8904-4677-9afa-ad21640ede6b
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 January 2022
                : 12 May 2022
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                © The Author(s), under exclusive licence to Springer Nature Limited 2022

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                viral infection,sars-cov-2
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                viral infection, sars-cov-2

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