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      Predicted Epitope Abundance Supports Vaccine-Induced Cytotoxic Protection Against SARS-CoV-2 Variants of Concern

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          Abstract

          The effect of emerging SARS-CoV-2 variants on vaccine efficacy is of critical importance. In this study, the potential impact of mutations that facilitate escape from the cytotoxic cellular immune response in these new virus variants for the 551 most abundant HLA class I alleles was analyzed. Computational prediction showed that most of these alleles, that cover >90% of the population, contain enough epitopes without escape mutations in the principal SARS-CoV-2 variants. These data suggest that the cytotoxic cellular immune protection elicited by vaccination is not greatly affected by emerging SARS-CoV-2 variants.

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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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            GISAID: Global initiative on sharing all influenza data – from vision to reality

            Ten years ago, a correspondence [1,2], signed by more than 70 championed ‘A global initiative on sharing avian flu data’ (GISAID) [3], leading to the GISAID Initiative in 2008. What started out as an expression of intent to foster international sharing of all influenza virus data and to publish results collaboratively has emerged as an indispensable mechanism for sharing influenza genetic sequence and metadata that embraces the interests and concerns of the wider influenza community, public health and animal health scientists, along with governments around the world. Today GISAID is recognised as an effective and trusted mechanism for rapid sharing of both published and ‘unpublished’ influenza data [4]. Its concept for incentivising data sharing established an alternative to data sharing via conventional public-domain archives. In 2006, the reluctance of data sharing, in particular of avian H5N1 influenza viruses, created an emergency bringing into focus certain limitations and inequities, such that the World Health Organization (WHO)’s Global Influenza Surveillance Network (now the Global Influenza Surveillance and Response System (GISRS) [5]) was criticised on several fronts, including limited global access to H5N1 sequence data that were stored in a database hosted by the Los Alamos National Laboratories in the United States (US) [6,7]. This data repository, set up with financial support from the US Centers for Disease Control and Prevention (CDC) as a first attempt to share ‘sensitive’ data from affected countries, but was accessible only to those who were also providing H5N1 sequence data. This limited-access approach restricted wider sharing of data prior to publication, which was vital for broader understanding of the progress of the emergent public and animal health threat. The need for greater transparency in data sharing and for acknowledgement of those contributing samples from H5N1-infected patients and animals and related genetic sequence data was not satisfied by sharing data after formal publication via public-domain databases. Scientists charged with the day to day responsibilities of running WHO Collaborating Centres (CCs) for Influenza, National Influenza Centres and the World Organisation for Animal Health (OIE)/ Food and Agriculture Organization of the United Nations (FAO) [8] reference laboratories, were therefore eager to play a key role and provide scientific oversight in the creation and development of GISAID’s data sharing platform that soon became essential for our work. A unique collaboration ensued, involving, in addition to members of WHO’s GISRS and OIE/FAO reference laboratories, the wider influenza research community along with officials in governmental institutions and non-governmental organisations. Facilitated by a well-connected broadcast executive with background in licensing of intellectual property, an agreement was drawn up on the sharing of genetic data to meet emergency situations, without infringing intellectual property rights - the GISAID Database Access Agreement (DAA). The DAA governs each individual’s access to and their use of data in GISAID’s EpiFlu database [9]. It was this alliance between scientists and non-scientists, with a diversity of knowledge and experience, involved in drawing up an acceptable simple, yet enforceable, agreement which gained the trust and respect of the scientific community and public health and animal health authorities. The essential features of the DAA encourage sharing of data by securing the provider’s ownership of the data, requiring acknowledgement of those providing the samples and producing the data, while placing no restriction on the use of the data by registered users adhering to the DAA. It essentially defines a code of conduct between providers and users of data, cementing mutual respect for their respective complementary contributions, and upholding the collaborative ethos of WHO’s GISRS, initially established 65 years ago this year [5]. Launched in 2008, the EpiFlu database was of key importance in the response to the 2009 influenza A(H1N1) pandemic, allowing countries to readily follow the evolution of the new virus as it spread globally [10]. Acceptance of the GISAID sharing mechanism by providers and users of data, and the confidence of the influenza community, were further illustrated in 2013 by the unprecedented immediate release of the genetic sequences of Influenza A(H7N9) viruses from the first human cases, by Chinese scientists at the WHO Collaborating Centre for Influenza in Beijing [11,12]. Such events reaffirmed GISAID’s applicability to timely sharing of crucial influenza data. The subsequent use of the sequence data to generate, develop and test candidate vaccine viruses by synthetic biology within a few weeks also demonstrated how GISAID successfully bridged this important ‘technological’ gap [13,14]. The paper by Bao et al. from Jiangsu province of China published in this issue once again confirms the importance of the timely sharing of data on the evolution of the A(H7N9) viruses for global risk assessment. The authors analysed the recently isolated H7N9 viruses form the fifth wave in Jiangsu province, and the results showed no significant viral mutations in key functional loci even though the H7N9 viruses are under continuous dynamic reassortment and there is genetic heterogeneity. These findings should help to reduce concerns raised, even though the number of human infection with H7N9 virus increased sharply during the fifth wave in China. GISAID provides the data-sharing platform particularly used by GISRS, through which sequence data considered by the WHO CCs in selecting viruses recommended for inclusion in seasonal and pre-pandemic vaccines are shared openly and on which research scientists, public and animal health officials and the pharmaceutical industry depend. Such openness of the most up-to-date data assists in an understanding of and enhances the credibility of the WHO recommendations for the composition of these seasonal and potential-pandemic vaccines. Furthermore, in promoting the prompt sharing of data from potential pandemic zoonotic virus infections, as well as from seasonal influenza viruses, GISAID ensures a key tenet of the WHO Pandemic Influenza Preparedness (PIP) Framework [15], highlighting the critical role it plays in mounting an effective mitigating response. GISAID’s ability to facilitate efficient global collaborations, such as the Global Consortium for H5N8 and Related Influenza Viruses [16,17], is central to monitoring phylogeographic interrelationships among, for example, H5 subtype viruses in wild and domestic birds in relation to their incidence, cross-border spread and veterinary impact, and assessing risk to animal and human health [18]. Traditional public-domain archives such as GenBank, where sharing and use of data takes place anonymously, fulfil a need for an archive of largely published data; however, that conventional method of data exchange notably has not been successful in encouraging rapid sharing of important data in epidemic or (potential) pandemic situations, such as those caused by Middle East respiratory syndrome coronavirus (MERS-CoV) and Ebola viruses. While the GISAID EpiFlu database is hosted and its sustainability ensured through the commitment of the Federal Republic of Germany [19], the establishment of GISAID and development of the EpiFlu database was reliant to a large extent on philanthropy of one individual and voluntary contributions and generosity of many others, together with some initial financial provision by the US CDC and the German Max Planck Society. That GISAID has become accepted as a pragmatic means of meeting the needs of the influenza community in part reflects the particular characteristics of influenza and the continual need for year-round monitoring of the viruses circulating worldwide, essential for the biannual vaccine recommendations and assessment of the risk posed by frequent zoonotic infections by animal influenza viruses [20]. In the meantime, calls for an equivalent mechanism to promote the timely sharing of data in other urgent epidemic settings go largely unfulfilled [21,22]. A recent publication considered whether the ‘paradigm shift’ in data sharing by GISAID could be applied more generally to assist in preparedness for and response to other emergent infectious threats, such as those posed by Ebola virus [21] and Zika virus [23]. Such a trusted system could complement and take full advantage of the latest advances in rapid sequencing of specimens in the laboratory and in the field, for outbreak investigation [24]. Given the crucial importance of genetic data in improving our understanding of the progress of an emergent, potentially devastating epidemic, the effectiveness of GISAID in influenza pandemic preparedness is self-evident and provides important lessons for future pandemic threats. While the genetic makeup and the necessary associated data of the different viruses are distinct requiring separate databases/compartments for unambiguous analysis, the modi operandi for sharing genetic data are generic and the GISAID mechanism could be applied to other emerging pathogens. Indeed, the wider implementation of such a data sharing mechanism should be key in concerted efforts to contain spread of disease in animals and threats to human health, in realising the concept of One Health.
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              COVID-19 vaccine BNT162b1 elicits human antibody and TH1 T-cell responses

              An effective vaccine is needed to halt the spread of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic. Recently, we reported safety, tolerability and antibody response data from an ongoing placebo-controlled, observer-blinded phase I/II coronavirus disease 2019 (COVID-19) vaccine trial with BNT162b1, a lipid nanoparticle-formulated nucleoside-modified mRNA that encodes the receptor binding domain (RBD) of the SARS-CoV-2 spike protein1. Here we present antibody and T cell responses after vaccination with BNT162b1 from a second, non-randomized open-label phase I/II trial in healthy adults, 18-55 years of age. Two doses of 1-50 μg of BNT162b1 elicited robust CD4+ and CD8+ T cell responses and strong antibody responses, with RBD-binding IgG concentrations clearly above those seen in serum from a cohort of individuals who had recovered from COVID-19. Geometric mean titres of SARS-CoV-2 serum-neutralizing antibodies on day 43 were 0.7-fold (1-μg dose) to 3.5-fold (50-μg dose) those of the recovered individuals. Immune sera broadly neutralized pseudoviruses with diverse SARS-CoV-2 spike variants. Most participants had T helper type 1 (TH1)-skewed T cell immune responses with RBD-specific CD8+ and CD4+ T cell expansion. Interferon-γ was produced by a large fraction of RBD-specific CD8+ and CD4+ T cells. The robust RBD-specific antibody, T cell and favourable cytokine responses induced by the BNT162b1 mRNA vaccine suggest that it has the potential to protect against COVID-19 through multiple beneficial mechanisms.
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                Author and article information

                Contributors
                URI : https://loop.frontiersin.org/people/293543
                URI : https://loop.frontiersin.org/people/708415
                URI : https://loop.frontiersin.org/people/741518
                URI : https://loop.frontiersin.org/people/754801
                Journal
                Front Immunol
                Front Immunol
                Front. Immunol.
                Frontiers in Immunology
                Frontiers Media S.A.
                1664-3224
                25 November 2021
                2021
                25 November 2021
                : 12
                : 732693
                Affiliations
                [1] 1 Intrahospital Infection Laboratory, National Center of Microbiology, Instituto de Salud Carlos III , Majadahonda, Spain
                [2] 2 Acquired Immune Deficiency Syndrome (AIDS) Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III , Majadahonda, Spain
                [3] 3 Presentation and Immune Regulation Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III , Majadahonda, Spain
                Author notes

                Edited by: Jochen Mattner, University of Erlangen Nuremberg, Germany

                Reviewed by: Varun Jaiswal, Gachon University, South Korea; Nadia A. Atai, Massachusetts General Hospital and Harvard Medical School, United States

                *Correspondence: Antonio J. Martín-Galiano, mgaliano@ 123456isciii.es ; Daniel López, dlopez@ 123456isciii.es

                This article was submitted to Vaccines and Molecular Therapeutics, a section of the journal Frontiers in Immunology

                Article
                10.3389/fimmu.2021.732693
                8656262
                2d6c366d-80fc-4d07-aff3-341f4c1fc8cb
                Copyright © 2021 Martín-Galiano, Díez-Fuertes, McConnell and López

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 29 June 2021
                : 08 November 2021
                Page count
                Figures: 4, Tables: 1, Equations: 0, References: 27, Pages: 7, Words: 3808
                Funding
                Funded by: Ministerio de Ciencia e Innovación , doi 10.13039/501100004837;
                Award ID: MPY 388/18 , MPY 509/19 , MPY 222-20
                Categories
                Immunology
                Original Research

                Immunology
                sars-cov-2,escape mutant,hla,vaccine,t cell epitope,epidemic
                Immunology
                sars-cov-2, escape mutant, hla, vaccine, t cell epitope, epidemic

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