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      Assessment of antibody dynamics and neutralizing activity using serological assay after SARS-CoV-2 infection and vaccination

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          Abstract

          The COVID-19 antibody test was developed to investigate the humoral immune response to SARS-CoV-2 infection. In this study, we examined whether S antibody titers measured using the anti-SARS-CoV-2 IgG II Quant assay (S-IgG), a high-throughput test method, reflects the neutralizing capacity acquired after SARS-CoV-2 infection or vaccination. To assess the antibody dynamics and neutralizing potency, we utilized a total of 457 serum samples from 253 individuals: 325 samples from 128 COVID-19 patients including 136 samples from 29 severe/critical cases (Group S), 155 samples from 71 mild/moderate cases (Group M), and 132 samples from 132 health care workers (HCWs) who have received 2 doses of the BNT162b2 vaccinations. The authentic virus neutralization assay, the surrogate virus neutralizing antibody test (sVNT), and the Anti-N SARS-CoV-2 IgG assay (N-IgG) have been performed along with the S-IgG. The S-IgG correlated well with the neutralizing activity detected by the authentic virus neutralization assay (0.8904. of Spearman’s rho value, p < 0.0001) and sVNT (0.9206. of Spearman’s rho value, p < 0.0001). However, 4 samples (2.3%) of S-IgG and 8 samples (4.5%) of sVNT were inconsistent with negative results for neutralizing activity of the authentic virus neutralization assay. The kinetics of the SARS-CoV-2 neutralizing antibodies and anti-S IgG in severe cases were faster than the mild cases. All the HCWs elicited anti-S IgG titer after the second vaccination. However, the HCWs with history of COVID-19 or positive N-IgG elicited higher anti-S IgG titers than those who did not have it previously. Furthermore, it is difficult to predict the risk of breakthrough infection from anti-S IgG or sVNT antibody titers in HCWs after the second vaccination. Our data shows that the use of anti-S IgG titers as direct quantitative markers of neutralizing capacity is limited. Thus, antibody tests should be carefully interpreted when used as serological markers for diagnosis, treatment, and prophylaxis of COVID-19.

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          Virological assessment of hospitalized patients with COVID-2019

          Coronavirus disease 2019 (COVID-19) is an acute infection of the respiratory tract that emerged in late 20191,2. Initial outbreaks in China involved 13.8% of cases with severe courses, and 6.1% of cases with critical courses3. This severe presentation may result from the virus using a virus receptor that is expressed predominantly in the lung2,4; the same receptor tropism is thought to have determined the pathogenicity-but also aided in the control-of severe acute respiratory syndrome (SARS) in 20035. However, there are reports of cases of COVID-19 in which the patient shows mild upper respiratory tract symptoms, which suggests the potential for pre- or oligosymptomatic transmission6-8. There is an urgent need for information on virus replication, immunity and infectivity in specific sites of the body. Here we report a detailed virological analysis of nine cases of COVID-19 that provides proof of active virus replication in tissues of the upper respiratory tract. Pharyngeal virus shedding was very high during the first week of symptoms, with a peak at 7.11 × 108 RNA copies per throat swab on day 4. Infectious virus was readily isolated from samples derived from the throat or lung, but not from stool samples-in spite of high concentrations of virus RNA. Blood and urine samples never yielded virus. Active replication in the throat was confirmed by the presence of viral replicative RNA intermediates in the throat samples. We consistently detected sequence-distinct virus populations in throat and lung samples from one patient, proving independent replication. The shedding of viral RNA from sputum outlasted the end of symptoms. Seroconversion occurred after 7 days in 50% of patients (and by day 14 in all patients), but was not followed by a rapid decline in viral load. COVID-19 can present as a mild illness of the upper respiratory tract. The confirmation of active virus replication in the upper respiratory tract has implications for the containment of COVID-19.
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            Structural basis of receptor recognition by SARS-CoV-2

            Summary A novel SARS-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans 1,2 . A key to tackling this epidemic is to understand the virus’s receptor recognition mechanism, which regulates its infectivity, pathogenesis and host range. SARS-CoV-2 and SARS-CoV recognize the same receptor - human ACE2 (hACE2) 3,4 . Here we determined the crystal structure of SARS-CoV-2 receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex of hACE2. Compared with SARS-CoV RBD, a hACE2-binding ridge in SARS-CoV-2 RBD takes a more compact conformation; moreover, several residue changes in SARS-CoV-2 RBD stabilize two virus-binding hotspots at the RBD/hACE2 interface. These structural features of SARS-CoV-2 RBD enhance its hACE2-binding affinity. Additionally, we showed that RaTG13, a bat coronavirus closely related to SARS-CoV-2, also uses hACE2 as its receptor. The differences among SARS-CoV-2, SARS-CoV and RaTG13 in hACE2 recognition shed light on potential animal-to-human transmission of SARS-CoV-2. This study provides guidance for intervention strategies targeting receptor recognition by SARS-CoV-2.
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              SARS-CoV-2 variants, spike mutations and immune escape

              Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of ‘variants of concern’, that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. There is emerging evidence of reduced neutralization of some SARS-CoV-2 variants by postvaccination serum; however, a greater understanding of correlates of protection is required to evaluate how this may impact vaccine effectiveness. Nonetheless, manufacturers are preparing platforms for a possible update of vaccine sequences, and it is crucial that surveillance of genetic and antigenic changes in the global virus population is done alongside experiments to elucidate the phenotypic impacts of mutations. In this Review, we summarize the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets. The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been characterized by the emergence of mutations and so-called variants of concern that impact virus characteristics, including transmissibility and antigenicity. In this Review, members of the COVID-19 Genomics UK (COG-UK) Consortium and colleagues summarize mutations of the SARS-CoV-2 spike protein, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets.
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                Author and article information

                Contributors
                Role: Writing – original draft
                Role: Writing – review & editing
                Role: Investigation
                Role: Data curation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Investigation
                Role: Funding acquisition
                Role: Investigation
                Role: Methodology
                Role: Methodology
                Role: Resources
                Role: Investigation
                Role: Supervision
                Role: Resources
                Role: Methodology
                Role: Conceptualization
                Role: Conceptualization
                Role: Conceptualization
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                19 September 2023
                2023
                19 September 2023
                : 18
                : 9
                : e0291670
                Affiliations
                [1 ] Department of Clinical Laboratory, Juntendo University Hospital, Tokyo, Japan
                [2 ] Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [3 ] Medical Technology Innovation Center, Juntendo University, Tokyo, Japan
                [4 ] Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [5 ] Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
                [6 ] Department of Emergency Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
                [7 ] Department of Cardiovascular Biology and Medicine, Juntendo University Faculty of Medicine, Tokyo, Japan
                [8 ] Department of Coloproctological Surgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [9 ] Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
                [10 ] Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
                Waseda University: Waseda Daigaku, JAPAN
                Author notes

                Competing Interests: The reagent used in this study were partially provided by abbott, but the study was performed by scientifically proper methods without any bias. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

                Author information
                https://orcid.org/0000-0003-1149-5048
                https://orcid.org/0000-0002-3820-9542
                https://orcid.org/0000-0003-1646-9930
                https://orcid.org/0000-0002-3734-0346
                Article
                PONE-D-22-35551
                10.1371/journal.pone.0291670
                10508622
                37725623
                91ed95ba-2e4b-4bd2-a107-996db83e2aa9
                © 2023 Takahashi et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 29 December 2022
                : 1 September 2023
                Page count
                Figures: 4, Tables: 0, Pages: 11
                Funding
                Funded by: JP20fk0108472
                Award ID: JP20fk0108472
                Award Recipient :
                Funded by: 22K15675
                Award ID: 22K15675
                Award Recipient :
                This research was partially supported by Japan Agency for Medical Research and Development under Grant Number JP20fk0108472 to TN and by Japan Society for the Promotion of Science Grants-in Aid for Scientific Research under Grant Number 22K15675 to ST. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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