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Kemp SA, Collier DA, Datir R, Ferreira I, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Briggs J, van GM, Smith K, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth C, McCoy LE, Gupta RK. Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. medRxiv 2020:2020.12.05.20241927. [PMID: 33398302 PMCID: PMC7781345 DOI: 10.1101/2020.12.05.20241927] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against ΔH69/ΔV70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.
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Affiliation(s)
- S A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - D A Collier
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - R Datir
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Iatm Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - S Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - A Jahun
- Department of Pathology, University of Cambridge, Cambridge
| | - M Hosmillo
- Department of Pathology, University of Cambridge, Cambridge
| | - C Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - P Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - N Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | - K Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - E Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jag Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gils Mj van
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kgc Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - J R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - C Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - R Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - L Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - G Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - D D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - R A Goldstein
- Division of Infection and Immunity, University College London, London, UK
| | - A Smielewska
- Department of Pathology, University of Cambridge, Cambridge
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - J P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Addenbrookes' Hospital, Cambridge, UK
| | - T Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - I G Goodfellow
- Department of Pathology, University of Cambridge, Cambridge
| | - E Gkrania-Klotsas
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Cjr Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - L E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - R K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
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