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      Serological Markers of SARS-CoV-2 Reinfection

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      a , b , c , c , c , d , e , c , f , c , c , f , c , g , h , i , h , i , h , i , h , i , g , g , j , e , e , e , e , e , k , b , l , m , n , g , e , c , o , p , q , e , h , p , q , r , s , , c , n ,
      ,
      mBio
      American Society for Microbiology
      SARS-CoV-2, reinfection, antibodies, humoral immunity, diagnostics, biomarkers

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          ABSTRACT

          As public health guidelines throughout the world have relaxed in response to vaccination campaigns against SARS-CoV-2, it is likely that SARS-CoV-2 will remain endemic, fueled by the rise of more infectious SARS-CoV-2 variants. Moreover, in the setting of waning natural and vaccine immunity, reinfections have emerged across the globe, even among previously infected and vaccinated individuals. As such, the ability to detect reexposure to and reinfection by SARS-CoV-2 is a key component for global protection against this virus and, more importantly, against the potential emergence of vaccine escape mutations. Accordingly, there is a strong and continued need for the development and deployment of simple methods to detect emerging hot spots of reinfection to inform targeted pandemic response and containment, including targeted and specific deployment of vaccine booster campaigns. In this study, we identify simple, rapid immune biomarkers of reinfection in rhesus macaques, including IgG3 antibody levels against nucleocapsid and FcγR2A receptor binding activity of anti-RBD antibodies, that are recapitulated in human reinfection cases. As such, this cross-species analysis underscores the potential utility of simple antibody titers and function as price-effective and scalable markers of reinfection to provide increased resolution and resilience against new outbreaks.

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          A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

          The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. We present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and de-labelling virus lineages that become unobserved and hence are likely inactive. By focusing on active virus lineages and those spreading to new locations this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.
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            Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

            The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1-5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2-also termed the Delta variant-is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein.
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              Waning Immune Humoral Response to BNT162b2 Covid-19 Vaccine over 6 Months

              Background Despite high vaccine coverage and effectiveness, the incidence of symptomatic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been increasing in Israel. Whether the increasing incidence of infection is due to waning immunity after the receipt of two doses of the BNT162b2 vaccine is unclear. Methods We conducted a 6-month longitudinal prospective study involving vaccinated health care workers who were tested monthly for the presence of anti-spike IgG and neutralizing antibodies. Linear mixed models were used to assess the dynamics of antibody levels and to determine predictors of antibody levels at 6 months. Results The study included 4868 participants, with 3808 being included in the linear mixed-model analyses. The level of IgG antibodies decreased at a consistent rate, whereas the neutralizing antibody level decreased rapidly for the first 3 months with a relatively slow decrease thereafter. Although IgG antibody levels were highly correlated with neutralizing antibody titers (Spearman’s rank correlation between 0.68 and 0.75), the regression relationship between the IgG and neutralizing antibody levels depended on the time since receipt of the second vaccine dose. Six months after receipt of the second dose, neutralizing antibody titers were substantially lower among men than among women (ratio of means, 0.64; 95% confidence interval [CI], 0.55 to 0.75), lower among persons 65 years of age or older than among those 18 to less than 45 years of age (ratio of means, 0.58; 95% CI, 0.48 to 0.70), and lower among participants with immunosuppression than among those without immunosuppression (ratio of means, 0.30; 95% CI, 0.20 to 0.46). Conclusions Six months after receipt of the second dose of the BNT162b2 vaccine, humoral response was substantially decreased, especially among men, among persons 65 years of age or older, and among persons with immunosuppression.
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                Author and article information

                Contributors
                Role: Invited Editor
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                25 January 2022
                Jan-Feb 2022
                25 January 2022
                : 13
                : 1
                : e02141-21
                Affiliations
                [a ] Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
                [b ] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
                [c ] Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
                [d ] PhD Program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
                [e ] Space Exploration Technologies Corp., Hawthorne, California, USA
                [f ] PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
                [g ] Department of Pediatrics, Vanderbilt University Medical Centergrid.412807.8, , Nashville, Tennessee, USA
                [h ] Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
                [i ] Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
                [j ] Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
                [k ] Institute of Virology, University Hospital, University of Bonn, and German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
                [l ] Harvard T.H. Chan School of Public Health, Cambridge, Massachusetts, USA
                [m ] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
                [n ] Massachusetts Consortium on Pathogen Readiness, Boston, Massachusetts, USA
                [o ] Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
                [p ] Brigham and Women’s Hospital, Department of Emergency Medicine, Boston, Massachusetts, USA
                [q ] Harvard Medical School, Harvard University, Cambridge, Massachusetts, USA
                [r ] Harvard Humanitarian Initiative, Boston, Massachusetts, USA
                [s ] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
                Duke Human Vaccine Institute
                Duke University Medical Center
                Author notes

                Sameed M. Siddiqui, Kathryn A. Bowman, Alex L. Zhu, Stephanie Fischinger, Samuel Beger, and Jenny S. Maron contributed equally. Author order was based on project leadership. Dan H. Barouch, Anil S. Menon, Eric J. Nilles, Douglas A. Lauffenburger, and Galit Alter also contributed equally.

                The authors declare a conflict of interest. G.A. is a founder of Seromyx Systems Inc., a company developing platform technology that describes the antibody immune response. G.A.'s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. N.H. receives grant funding from Sanofi S.A. and Quidel Corporation. P.S. is a co-founder of, shareholder in, and advisor to Sherlock Biosciences, Inc, as well as a Board member of and shareholder in Danaher Corporation. E.R.M., A.S.M., L.C., K.M., J.S., S.M., and S.S. are employees of Space Exploration Technologies Corp. All other authors have declared that no conflict of interest exists.

                Author information
                https://orcid.org/0000-0002-7131-3691
                https://orcid.org/0000-0002-0335-6390
                https://orcid.org/0000-0001-5127-4659
                https://orcid.org/0000-0002-7680-9215
                Article
                02141-21 mbio.02141-21
                10.1128/mbio.02141-21
                8787477
                35073738
                9ddbf972-7c81-4a5d-89a7-2cf59c022a22
                Copyright © 2022 Siddiqui et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 21 July 2021
                : 13 December 2021
                Page count
                supplementary-material: 10, Figures: 4, Tables: 0, Equations: 0, References: 46, Pages: 15, Words: 10726
                Funding
                Funded by: MassCPR;
                Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Funded by: HHS | Centers for Disease Control and Prevention (CDC), FundRef https://doi.org/10.13039/100000030;
                Award ID: U01GH002238
                Award Recipient :
                Funded by: HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID), FundRef https://doi.org/10.13039/100000060;
                Award Recipient :
                Funded by: HHS | National Institutes of Health (NIH), FundRef https://doi.org/10.13039/100000002;
                Award ID: U01CA260476
                Award ID: 3R37AI080289-11S1
                Award ID: 1R01AI146785-01A1
                Award ID: 75N93019C00052
                Award ID: 75N93019C00071
                Award ID: R01AI152158
                Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Funded by: HHS | U.S. Food and Drug Administration (FDA), FundRef https://doi.org/10.13039/100000038;
                Award ID: HHSF223201810172C
                Award Recipient :
                Funded by: National Aeronautics and Space Administration (NASA), FundRef https://doi.org/10.13039/100000104;
                Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Funded by: Ragon Institute of MGH, MIT and Harvard (Ragon Institute), FundRef https://doi.org/10.13039/100012802;
                Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Categories
                Research Article
                immunology, Immunology
                Custom metadata
                January/February 2022

                Life sciences
                sars-cov-2,reinfection,antibodies,humoral immunity,diagnostics,biomarkers
                Life sciences
                sars-cov-2, reinfection, antibodies, humoral immunity, diagnostics, biomarkers

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