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      SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

      research-article
      1 , , 1 , , 1 , 2 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 3 , 3 , 4 , 3 , 1 , 5 , 5 , 5 , 6 , 1 , 3 , 7 , 1 , 1 , 8 , 8 , PITCH Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, 3 , 1 , 1 , 2 , 1 , 3 , 9 ,
      Nature Microbiology
      Nature Publishing Group UK
      Molecular biology, Immunology, Viral infection, Vaccines

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          Abstract

          Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.

          Abstract

          The Omicron variant evades vaccine-induced neutralization but also fails to form syncytia, shows reduced replication in human lung cells and preferentially uses a TMPRSS2-independent cell entry pathway, which may contribute to enhanced replication in cells of the upper airway. Altered fusion and cell entry characteristics are linked to distinct regions of the Omicron spike protein.

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          Most cited references90

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          • Abstract: found
          • Article: found
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          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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            SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

            Summary The recent emergence of the novel, pathogenic SARS-coronavirus 2 (SARS-CoV-2) in China and its rapid national and international spread pose a global health emergency. Cell entry of coronaviruses depends on binding of the viral spike (S) proteins to cellular receptors and on S protein priming by host cell proteases. Unravelling which cellular factors are used by SARS-CoV-2 for entry might provide insights into viral transmission and reveal therapeutic targets. Here, we demonstrate that SARS-CoV-2 uses the SARS-CoV receptor ACE2 for entry and the serine protease TMPRSS2 for S protein priming. A TMPRSS2 inhibitor approved for clinical use blocked entry and might constitute a treatment option. Finally, we show that the sera from convalescent SARS patients cross-neutralized SARS-2-S-driven entry. Our results reveal important commonalities between SARS-CoV-2 and SARS-CoV infection and identify a potential target for antiviral intervention.
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              Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

              Structure of the nCoV trimeric spike The World Health Organization has declared the outbreak of a novel coronavirus (2019-nCoV) to be a public health emergency of international concern. The virus binds to host cells through its trimeric spike glycoprotein, making this protein a key target for potential therapies and diagnostics. Wrapp et al. determined a 3.5-angstrom-resolution structure of the 2019-nCoV trimeric spike protein by cryo–electron microscopy. Using biophysical assays, the authors show that this protein binds at least 10 times more tightly than the corresponding spike protein of severe acute respiratory syndrome (SARS)–CoV to their common host cell receptor. They also tested three antibodies known to bind to the SARS-CoV spike protein but did not detect binding to the 2019-nCoV spike protein. These studies provide valuable information to guide the development of medical counter-measures for 2019-nCoV. Science, this issue p. 1260
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                Author and article information

                Contributors
                brian.willett@glasgow.ac.uk
                joe.grove@glasgow.ac.uk
                emma.thomson@glasgow.ac.uk
                Journal
                Nat Microbiol
                Nat Microbiol
                Nature Microbiology
                Nature Publishing Group UK (London )
                2058-5276
                7 July 2022
                7 July 2022
                2022
                : 7
                : 8
                : 1161-1179
                Affiliations
                [1 ]GRID grid.8756.c, ISNI 0000 0001 2193 314X, MRC-University of Glasgow Centre for Virus Research, , University of Glasgow, ; Glasgow, UK
                [2 ]GRID grid.8756.c, ISNI 0000 0001 2193 314X, School of Mathematics & Statistics, , University of Glasgow, ; Glasgow, UK
                [3 ]GRID grid.413301.4, ISNI 0000 0001 0523 9342, NHS Greater Glasgow & Clyde, ; Glasgow, UK
                [4 ]GRID grid.5335.0, ISNI 0000000121885934, MRC Biostatistics Unit, , University of Cambridge, ; Cambridge, UK
                [5 ]GRID grid.508718.3, Public Health Scotland, ; Glasgow, UK
                [6 ]GRID grid.11914.3c, ISNI 0000 0001 0721 1626, School of Medicine, , University of St Andrews, ; St Andrews, UK
                [7 ]GRID grid.39489.3f, ISNI 0000 0001 0388 0742, NHS Lothian, ; Edinburgh, UK
                [8 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, University of Oxford, ; Oxford, UK
                [9 ]GRID grid.8991.9, ISNI 0000 0004 0425 469X, London School of Hygiene and Tropical Medicine, ; London, UK
                [10 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, , University of Oxford, ; Oxford, UK
                [11 ]GRID grid.8348.7, ISNI 0000 0001 2306 7492, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, ; Oxford, UK
                [12 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Oxford Centre For Global Health Research, Nuffield Department of Clinical Medicine, , University of Oxford, ; Oxford, UK
                [13 ]GRID grid.501272.3, ISNI 0000 0004 5936 4917, Mahidol-Oxford Tropical Medicine Research Unit, ; Bangkok, Thailand
                [14 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Translational Gastroenterology Unit, , University of Oxford, ; Oxford, UK
                [15 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, NIHR Oxford Biomedical Research Centre, , University of Oxford, ; Oxford, UK
                [16 ]GRID grid.11835.3e, ISNI 0000 0004 1936 9262, Department of Infection, Immunity and Cardiovascular Disease, , University of Sheffield, ; Sheffield, UK
                [17 ]GRID grid.31410.37, ISNI 0000 0000 9422 8284, Sheffield Teaching Hospitals NHS Foundation Trust, ; Sheffield, UK
                [18 ]GRID grid.10025.36, ISNI 0000 0004 1936 8470, NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, , University of Liverpool, ; Liverpool, UK
                [19 ]GRID grid.513149.b, Tropical and Infectious Disease Unit, , Liverpool University Hospitals NHS Foundation Trust, Liverpool Health Partners, ; Liverpool, UK
                [20 ]GRID grid.6572.6, ISNI 0000 0004 1936 7486, Institute of Cancer and Genomic Science, College of Medical and Dental Science, , University of Birmingham, ; Birmingham, UK
                [21 ]GRID grid.412563.7, ISNI 0000 0004 0376 6589, University Hospitals Birmingham NHS Foundation Trust, ; Birmingham, UK
                [22 ]GRID grid.1006.7, ISNI 0000 0001 0462 7212, Translational and Clinical Research Institute Immunity and Inflammation Theme, , Newcastle University, ; Newcastle, UK
                [23 ]GRID grid.420004.2, ISNI 0000 0004 0444 2244, Department of Infection and Tropical Medicine, , Newcastle upon Tyne Hospitals NHS Foundation Trust, ; Newcastle, UK
                [24 ]GRID grid.439436.f, ISNI 0000 0004 0459 7289, Barking, Havering and Redbridge University Hospitals NHS Trust, ; Romford, UK
                [25 ]GRID grid.139534.9, ISNI 0000 0001 0372 5777, Barts Health NHS Trust, ; London, UK
                [26 ]GRID grid.412915.a, ISNI 0000 0000 9565 2378, Belfast Health and Social Care Trust, ; Belfast, UK
                [27 ]GRID grid.440486.a, ISNI 0000 0000 8958 011X, Betsi Cadwaladr University Health Board, ; Bangor, UK
                [28 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Big Data Institute, Nuffield Department of Medicine, , University of Oxford, ; Oxford, UK
                [29 ]GRID grid.440172.4, ISNI 0000 0004 0376 9309, Blackpool Teaching Hospitals NHS Foundation Trust, ; Blackpool, UK
                [30 ]GRID grid.17236.31, ISNI 0000 0001 0728 4630, Bournemouth University, ; Bournemouth, UK
                [31 ]GRID grid.5335.0, ISNI 0000000121885934, Cambridge Stem Cell Institute, , University of Cambridge, ; Cambridge, UK
                [32 ]GRID grid.24029.3d, ISNI 0000 0004 0383 8386, Cambridge University Hospitals NHS Foundation Trust, ; Cambridge, UK
                [33 ]GRID grid.273109.e, ISNI 0000 0001 0111 258X, Cardiff and Vale University Health Board, ; Cardiff, UK
                [34 ]GRID grid.5600.3, ISNI 0000 0001 0807 5670, Cardiff University, ; Cardiff, UK
                [35 ]GRID grid.420545.2, ISNI 0000 0004 0489 3985, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, , Guy’s and St Thomas’ NHS Foundation Trust, ; London, UK
                [36 ]GRID grid.4701.2, ISNI 0000 0001 0728 6636, Centre for Enzyme Innovation, , University of Portsmouth, ; Portsmouth, UK
                [37 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Centre for Genomic Pathogen Surveillance, , University of Oxford, ; Oxford, UK
                [38 ]GRID grid.240404.6, ISNI 0000 0001 0440 1889, Clinical Microbiology Department, Queens Medical Centre, , Nottingham University Hospitals NHS Trust, ; Nottingham, UK
                [39 ]GRID grid.269014.8, ISNI 0000 0001 0435 9078, Clinical Microbiology, , University Hospitals of Leicester NHS Trust, ; Leicester, UK
                [40 ]GRID grid.412907.9, County Durham and Darlington NHS Foundation Trust, ; Darlington, UK
                [41 ]GRID grid.4563.4, ISNI 0000 0004 1936 8868, Deep Seq, School of Life Sciences, Queens Medical Centre, , University of Nottingham, ; Nottingham, UK
                [42 ]GRID grid.24029.3d, ISNI 0000 0004 0383 8386, Department of Infectious Diseases and Microbiology, , Cambridge University Hospitals NHS Foundation Trust, ; Cambridge, UK
                [43 ]GRID grid.5335.0, ISNI 0000000121885934, Department of Medicine, , University of Cambridge, ; Cambridge, UK
                [44 ]GRID grid.415192.a, ISNI 0000 0004 0400 5589, Department of Microbiology, , Kettering General Hospital, ; Kettering, UK
                [45 ]Department of Microbiology, South West London Pathology, London, UK
                [46 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Department of Zoology, , University of Oxford, ; Oxford, UK
                [47 ]GRID grid.5335.0, ISNI 0000000121885934, Division of Virology, Department of Pathology, , University of Cambridge, ; Cambridge, UK
                [48 ]GRID grid.270474.2, ISNI 0000 0000 8610 0379, East Kent Hospitals University NHS Foundation Trust, ; Canterbury, UK
                [49 ]GRID grid.507581.e, ISNI 0000 0001 0033 9432, East Suffolk and North Essex NHS Foundation Trust, ; Colchester, UK
                [50 ]GRID grid.439656.b, ISNI 0000 0004 0466 4605, East Sussex Healthcare NHS Trust, ; St. Leonards-on-Sea, UK
                [51 ]GRID grid.476396.9, ISNI 0000 0004 0403 3782, Gateshead Health NHS Foundation Trust, ; Gateshead, UK
                [52 ]GRID grid.424537.3, ISNI 0000 0004 5902 9895, Great Ormond Street Hospital for Children NHS Foundation Trust, ; London, UK
                [53 ]GRID grid.83440.3b, ISNI 0000000121901201, Great Ormond Street Institute of Child Health (GOS ICH), , University College London (UCL), ; London, UK
                [54 ]Guy’s and St. Thomas’ Biomedical Research Centre, London, UK
                [55 ]GRID grid.420545.2, ISNI 0000 0004 0489 3985, Guy’s and St. Thomas’ NHS Foundation Trust, ; London, UK
                [56 ]GRID grid.439351.9, ISNI 0000 0004 0498 6997, Hampshire Hospitals NHS Foundation Trust, ; Basingstoke, UK
                [57 ]GRID grid.271308.f, ISNI 0000 0004 5909 016X, Health Services Laboratories, ; London, UK
                [58 ]GRID grid.413964.d, ISNI 0000 0004 0399 7344, Heartlands Hospital, Birmingham, ; Birmingham, UK
                [59 ]GRID grid.42629.3b, ISNI 0000000121965555, Hub for Biotechnology in the Built Environment, , Northumbria University, ; Newcastle upon Tyne, UK
                [60 ]GRID grid.9481.4, ISNI 0000 0004 0412 8669, Hull University Teaching Hospitals NHS Trust, ; Hull, UK
                [61 ]GRID grid.417895.6, ISNI 0000 0001 0693 2181, Imperial College Healthcare NHS Trust, ; London, UK
                [62 ]GRID grid.7445.2, ISNI 0000 0001 2113 8111, Imperial College London, ; London, UK
                [63 ]GRID grid.451349.e, Infection Care Group, St George’s University Hospitals NHS Foundation Trust, ; London, UK
                [64 ]GRID grid.264200.2, ISNI 0000 0000 8546 682X, Institute for Infection and Immunity, , St George’s University of London, ; London, UK
                [65 ]GRID grid.8756.c, ISNI 0000 0001 2193 314X, Institute of Biodiversity, Animal Health & Comparative Medicine, , University of Glasgow, ; Glasgow, UK
                [66 ]GRID grid.6572.6, ISNI 0000 0004 1936 7486, Institute of Microbiology and Infection, , University of Birmingham, ; Birmingham, UK
                [67 ]GRID grid.487226.d, ISNI 0000 0004 1793 1581, Isle of Wight NHS Trust, ; Newport, UK
                [68 ]GRID grid.429705.d, ISNI 0000 0004 0489 4320, King’s College Hospital NHS Foundation Trust, ; London, UK
                [69 ]GRID grid.13097.3c, ISNI 0000 0001 2322 6764, King’s College London, ; London, UK
                [70 ]Liverpool Clinical Laboratories, Liverpool, UK
                [71 ]GRID grid.439813.4, ISNI 0000 0000 8822 7920, Maidstone and Tunbridge Wells NHS Trust, ; Maidstone, UK
                [72 ]GRID grid.498924.a, ISNI 0000 0004 0430 9101, Manchester University NHS Foundation Trust, ; Manchester, UK
                [73 ]GRID grid.439664.a, ISNI 0000 0004 0368 863X, Microbiology Department, , Buckinghamshire Healthcare NHS Trust, ; Aylesbury, UK
                [74 ]GRID grid.439664.a, ISNI 0000 0004 0368 863X, Microbiology Department, , Buckinghamshire Healthcare NHS Trust, ; Aylesbury, UK
                [75 ]GRID grid.416187.d, ISNI 0000 0004 0400 8130, Microbiology, Royal Oldham Hospital, ; Oldham, UK
                [76 ]GRID grid.5335.0, ISNI 0000000121885934, MRC Biostatistics Unit, , University of Cambridge, ; Cambridge, UK
                [77 ]GRID grid.301713.7, ISNI 0000 0004 0393 3981, MRC-University of Glasgow Centre for Virus Research, ; Glasgow, UK
                [78 ]GRID grid.1006.7, ISNI 0000 0001 0462 7212, Newcastle University, ; Newcastle upon Tyne, UK
                [79 ]GRID grid.413301.4, ISNI 0000 0001 0523 9342, NHS Greater Glasgow and Clyde, ; Glasgow, UK
                [80 ]GRID grid.39489.3f, ISNI 0000 0001 0388 0742, NHS Lothian, ; Edinburgh, UK
                [81 ]GRID grid.240367.4, ISNI 0000 0004 0445 7876, Norfolk and Norwich University Hospitals NHS Foundation Trust, ; Norwich, UK
                [82 ]GRID grid.436599.4, ISNI 0000 0000 9416 9237, Norfolk County Council, ; Norwich, UK
                [83 ]GRID grid.507531.5, ISNI 0000 0004 0484 7081, North Cumbria Integrated Care NHS Foundation Trust, ; Carlisle, UK
                [84 ]GRID grid.439355.d, ISNI 0000 0000 8813 6797, North Middlesex University Hospital NHS Trust, ; London, UK
                [85 ]GRID grid.487275.b, North Tees and Hartlepool NHS Foundation Trust, ; Stockton on Tees, UK
                [86 ]GRID grid.451090.9, ISNI 0000 0001 0642 1330, Northumbria Healthcare NHS Foundation Trust, ; Newcastle upon Tyne, UK
                [87 ]GRID grid.42629.3b, ISNI 0000000121965555, Northumbria University, ; Newcastle upon Tyne, UK
                [88 ]Path Links, Northern Lincolnshire and Goole NHS Foundation Trust, Grimsby, UK
                [89 ]GRID grid.418709.3, ISNI 0000 0004 0456 1761, Portsmouth Hospitals University NHS Trust, ; Portsmouth, UK
                [90 ]GRID grid.454053.3, ISNI 0000 0004 0494 5490, Public Health Agency, Northern Ireland, ; Belfast, UK
                [91 ]GRID grid.271308.f, ISNI 0000 0004 5909 016X, Public Health England, ; London, UK
                [92 ]GRID grid.271308.f, ISNI 0000 0004 5909 016X, Public Health England, Cambridge, ; Cambridge, UK
                [93 ]GRID grid.271308.f, ISNI 0000 0004 5909 016X, Public Health England, Colindale, ; London, UK
                [94 ]GRID grid.508718.3, Public Health Scotland, ; Edinburgh, UK
                [95 ]GRID grid.439475.8, ISNI 0000 0004 6360 002X, Public Health Wales, ; Cardiff, UK
                [96 ]GRID grid.40368.39, ISNI 0000 0000 9347 0159, Quadram Institute Bioscience, ; Norwich, UK
                [97 ]GRID grid.415490.d, ISNI 0000 0001 2177 007X, Queen Elizabeth Hospital, Birmingham, ; Birmingham, UK
                [98 ]GRID grid.4777.3, ISNI 0000 0004 0374 7521, Queen’s University Belfast, ; Belfast, UK
                [99 ]Royal Brompton and Harefield Hospitals, London, UK
                [100 ]GRID grid.419309.6, ISNI 0000 0004 0495 6261, Royal Devon and Exeter NHS Foundation Trust, ; Exeter, UK
                [101 ]GRID grid.437485.9, ISNI 0000 0001 0439 3380, Royal Free London NHS Foundation Trust, ; London, UK
                [102 ]GRID grid.4701.2, ISNI 0000 0001 0728 6636, School of Biological Sciences, , University of Portsmouth, ; Portsmouth, UK
                [103 ]GRID grid.4701.2, ISNI 0000 0001 0728 6636, School of Pharmacy & Biomedical Sciences, , University of Portsmouth, ; Portsmouth, UK
                [104 ]GRID grid.31410.37, ISNI 0000 0000 9422 8284, Sheffield Teaching Hospitals NHS Foundation Trust, ; Sheffield, UK
                [105 ]GRID grid.440194.c, ISNI 0000 0004 4647 6776, South Tees Hospitals NHS Foundation Trust, ; Middlesbrough, UK
                [106 ]Southwest Pathology Services, Taunton, UK
                [107 ]GRID grid.4827.9, ISNI 0000 0001 0658 8800, Swansea University, ; Swansea, UK
                [108 ]GRID grid.420004.2, ISNI 0000 0004 0444 2244, The Newcastle upon Tyne Hospitals NHS Foundation Trust, ; Newcastle upon Tyne, UK
                [109 ]GRID grid.470208.9, ISNI 0000 0004 0415 9545, The Queen Elizabeth Hospital King’s Lynn NHS Foundation Trust, ; King’s Lynn, UK
                [110 ]GRID grid.5072.0, ISNI 0000 0001 0304 893X, The Royal Marsden NHS Foundation Trust, ; London, UK
                [111 ]GRID grid.439674.b, ISNI 0000 0000 9830 7596, The Royal Wolverhampton NHS Trust, ; Wolverhampton, UK
                [112 ]GRID grid.6572.6, ISNI 0000 0004 1936 7486, Turnkey Laboratory, , University of Birmingham, ; Birmingham, UK
                [113 ]GRID grid.83440.3b, ISNI 0000000121901201, University College London Division of Infection and Immunity, ; London, UK
                [114 ]GRID grid.439749.4, ISNI 0000 0004 0612 2754, University College London Hospital Advanced Pathogen Diagnostics Unit, ; London, UK
                [115 ]GRID grid.52996.31, ISNI 0000 0000 8937 2257, University College London Hospitals NHS Foundation Trust, ; London, UK
                [116 ]GRID grid.430506.4, ISNI 0000 0004 0465 4079, University Hospital Southampton NHS Foundation Trust, ; Southampton, UK
                [117 ]University Hospitals Dorset NHS Foundation Trust, Poole, UK
                [118 ]GRID grid.511096.a, University Hospitals Sussex NHS Foundation Trust, ; Worthing, UK
                [119 ]GRID grid.6572.6, ISNI 0000 0004 1936 7486, University of Birmingham, ; Birmingham, UK
                [120 ]GRID grid.12477.37, ISNI 0000000121073784, University of Brighton, ; Brighton, UK
                [121 ]GRID grid.5335.0, ISNI 0000000121885934, University of Cambridge, ; Cambridge, UK
                [122 ]GRID grid.8273.e, ISNI 0000 0001 1092 7967, University of East Anglia, ; Norwich, UK
                [123 ]GRID grid.4305.2, ISNI 0000 0004 1936 7988, University of Edinburgh, ; Edinburgh, UK
                [124 ]GRID grid.8391.3, ISNI 0000 0004 1936 8024, University of Exeter, ; Exeter, UK
                [125 ]GRID grid.10025.36, ISNI 0000 0004 1936 8470, University of Liverpool, ; Liverpool, UK
                [126 ]GRID grid.11835.3e, ISNI 0000 0004 1936 9262, University of Sheffield, ; Sheffield, UK
                [127 ]GRID grid.5491.9, ISNI 0000 0004 1936 9297, University of Southampton, ; Nottingham, UK
                [128 ]GRID grid.4563.4, ISNI 0000 0004 1936 8868, Virology, School of Life Sciences, Queens Medical Centre, , University of Nottingham, ; Nottingham, UK
                [129 ]GRID grid.416955.a, ISNI 0000 0004 0400 4949, Watford General Hospital, ; Watford, UK
                [130 ]GRID grid.4991.5, ISNI 0000 0004 1936 8948, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, , University of Oxford, ; Oxford, UK
                [131 ]GRID grid.10306.34, ISNI 0000 0004 0606 5382, Wellcome Sanger Institute, ; Hinxton, UK
                [132 ]GRID grid.413301.4, ISNI 0000 0001 0523 9342, West of Scotland Specialist Virology Centre, , NHS Greater Glasgow and Clyde, ; Glasgow, UK
                [133 ]GRID grid.507529.c, ISNI 0000 0000 8610 0651, Whittington Health NHS Trust, ; London, UK
                Author information
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                http://orcid.org/0000-0001-5390-7579
                http://orcid.org/0000-0003-0805-0195
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                http://orcid.org/0000-0002-5588-4232
                http://orcid.org/0000-0001-7080-8038
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                http://orcid.org/0000-0002-9442-2903
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                Article
                1143
                10.1038/s41564-022-01143-7
                9352574
                35798890
                86889db4-e0a4-4386-968f-f132ab05e8e0
                © The Author(s) 2022

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                History
                : 13 January 2022
                : 3 May 2022
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                Funded by: Health Data Research UK (HDR UK) 2021.0155)
                Funded by: FundRef https://doi.org/10.13039/501100000690, Research Councils UK (RCUK);
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                © The Author(s), under exclusive licence to Springer Nature Limited 2022

                molecular biology,immunology,viral infection,vaccines
                molecular biology, immunology, viral infection, vaccines

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