1
|
Niu M, Wang C, Chen Y, Zou Q, Xu L. Identification, characterization and expression analysis of circRNA encoded by SARS-CoV-1 and SARS-CoV-2. Brief Bioinform 2024; 25:bbad537. [PMID: 38279648 PMCID: PMC10818166 DOI: 10.1093/bib/bbad537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/12/2023] [Accepted: 12/22/2023] [Indexed: 01/28/2024] Open
Abstract
Virus-encoded circular RNA (circRNA) participates in the immune response to viral infection, affects the human immune system, and can be used as a target for precision therapy and tumor biomarker. The coronaviruses SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) that have emerged in recent years are highly contagious and have high mortality rates. In coronaviruses, little is known about the circRNA encoded by the SARS-CoV-1/2. Therefore, this study explores whether SARS-CoV-1/2 encodes circRNA and characteristics and functions of circRNA. Based on RNA-seq data of SARS-CoV-1 and SARS-CoV-2 infections, we used circRNA identification tools (circRNA_finder, find_circ and CIRI2) to identify circRNAs. The number of circRNAs encoded by SARS-CoV-1 and SARS-CoV-2 was identified as 151 and 470, respectively. It can be found that SARS-CoV-2 shows more prominent circRNA encoding ability than SARS-CoV-1. Expression analysis showed that only a few circRNAs encoded by SARS-CoV-1/2 showed high expression levels, and the positive strand produced more abundant circRNAs. Then, based on the identified SARS-CoV-1/2-encoded circRNAs, we performed circRNA identification and characterization using the previously developed CirRNAPL. Finally, target gene prediction and functional enrichment analysis were performed. It was found that viral circRNA is closely related to cancer and has a potential role in regulating host cell functions. This study studied the characteristics and functions of viral circRNA encoded by coronavirus SARS-CoV-1/2, providing a valuable resource for further research on the function and molecular mechanism of coronavirus circRNA.
Collapse
Affiliation(s)
- Mengting Niu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic University, Shenzhen 518055, China
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Chunyu Wang
- Faculty of Computing, Harbin Institute of Technology, Harbin, Heilongjiang 150000, China
| | - Yaojia Chen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.4 Block 2 North Jianshe Road, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, No.4 Block 2 North Jianshe Road, Chengdu 610054, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic University, Shenzhen 518055, China
| |
Collapse
|
2
|
Rouet R, Henry JY, Johansen MD, Sobti M, Balachandran H, Langley DB, Walker GJ, Lenthall H, Jackson J, Ubiparipovic S, Mazigi O, Schofield P, Burnett DL, Brown SHJ, Martinello M, Hudson B, Gilroy N, Post JJ, Kelleher A, Jäck HM, Goodnow CC, Turville SG, Rawlinson WD, Bull RA, Stewart AG, Hansbro PM, Christ D. Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients. Nat Commun 2023; 14:687. [PMID: 36755042 PMCID: PMC9907207 DOI: 10.1038/s41467-023-36295-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Abstract
Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.
Collapse
Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Meghna Sobti
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | - Harikrishnan Balachandran
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Gregory J Walker
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia.,Prince of Wales Hospital, Sydney, NSW, Australia
| | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stephanie Ubiparipovic
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Ohan Mazigi
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Simon H J Brown
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Marianne Martinello
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | | | | | | | - Anthony Kelleher
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen-Nürnberg, Germany
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia
| | - Stuart G Turville
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - William D Rawlinson
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rowena A Bull
- UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.,Kirby Institute, UNSW Sydney, Sydney, NSW, Australia
| | - Alastair G Stewart
- UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.,Victor Chang Cardiac Research Institute, Sydney, NSW, Australia
| | | | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia. .,UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
| |
Collapse
|
3
|
Khoo WH, Jackson K, Phetsouphanh C, Zaunders JJ, Alquicira-Hernandez J, Yazar S, Ruiz-Diaz S, Singh M, Dhenni R, Kyaw W, Tea F, Merheb V, Lee FX, Burrell R, Howard-Jones A, Koirala A, Zhou L, Yuksel A, Catchpoole DR, Lai CL, Vitagliano TL, Rouet R, Christ D, Tang B, West NP, George S, Gerrard J, Croucher PI, Kelleher AD, Goodnow CG, Sprent JD, Powell JE, Brilot F, Nanan R, Hsu PS, Deenick EK, Britton PN, Phan TG. Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild/asymptomatic COVID-19. Clin Immunol 2023; 246:109209. [PMID: 36539107 PMCID: PMC9758763 DOI: 10.1016/j.clim.2022.109209] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/28/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop less severe coronavirus disease 2019 (COVID-19) than adults. The mechanisms for the age-specific differences and the implications for infection-induced immunity are beginning to be uncovered. We show by longitudinal multimodal analysis that SARS-CoV-2 leaves a small footprint in the circulating T cell compartment in children with mild/asymptomatic COVID-19 compared to adult household contacts with the same disease severity who had more evidence of systemic T cell interferon activation, cytotoxicity and exhaustion. Children harbored diverse polyclonal SARS-CoV-2-specific naïve T cells whereas adults harbored clonally expanded SARS-CoV-2-specific memory T cells. A novel population of naïve interferon-activated T cells is expanded in acute COVID-19 and is recruited into the memory compartment during convalescence in adults but not children. This was associated with the development of robust CD4+ memory T cell responses in adults but not children. These data suggest that rapid clearance of SARS-CoV-2 in children may compromise their cellular immunity and ability to resist reinfection.
Collapse
Affiliation(s)
- Weng Hua Khoo
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | | | | | - John J. Zaunders
- Centre for Applied Medical Research, St Vincent's Hospital, Sydney, Australia
| | - José Alquicira-Hernandez
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Seyhan Yazar
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | | | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Rama Dhenni
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Wunna Kyaw
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Fiona Tea
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children's Hospital at Westmead, Sydney, Australia
| | - Vera Merheb
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children's Hospital at Westmead, Sydney, Australia
| | - Fiona X.Z. Lee
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children's Hospital at Westmead, Sydney, Australia
| | - Rebecca Burrell
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | | | - Archana Koirala
- Kids Research, The Children's Hospital at Westmead, Sydney, Australia
| | - Li Zhou
- Kids Research, The Children's Hospital at Westmead, Sydney, Australia
| | - Aysen Yuksel
- Kids Research, The Children's Hospital at Westmead, Sydney, Australia
| | - Daniel R. Catchpoole
- Kids Research, The Children's Hospital at Westmead, Sydney, Australia,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, Australia
| | - Catherine L. Lai
- Kids Research, The Children's Hospital at Westmead, Sydney, Australia
| | | | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Sydney, Australia,Centre for Immunology and Allergy Research, The Westmead Institute for Medical Research, Sydney, Australia,Respiratory Tract Infection Research Node, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, Australia
| | - Nicholas P. West
- Systems Biology and Data Science, Menzies Health Institute QLD, Griffith University, Parklands, Australia
| | - Shane George
- Departments of Emergency Medicine and Children's Critical Care, Gold Coast University Hospital, Southport, QLD, Australia,School of Medicine and Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - John Gerrard
- Department of Infectious Diseases and Immunology, Gold Coast University Hospital, Southport, QLD, Australia
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | | | - Christopher G. Goodnow
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia,UNSW Cellular Genomics Futures Institute, UNSW Sydney, Sydney, Australia
| | - Jonathan D. Sprent
- Garvan Institute of Medical Research, Sydney, Australia,St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Joseph E. Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, Australia,UNSW Cellular Genomics Futures Institute, UNSW Sydney, Sydney, Australia
| | - Fabienne Brilot
- Brain Autoimmunity Group, Kids Neuroscience Centre, Kids Research at the Children's Hospital at Westmead, Sydney, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia,Brain and Mind Centre, The University of Sydney, Sydney, Australia
| | - Ralph Nanan
- Charles Perkins Centre Nepean, University of Sydney, Sydney, Australia
| | - Peter S. Hsu
- Kids Research, The Children's Hospital at Westmead, Sydney, Australia,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, Australia
| | - Elissa K. Deenick
- Garvan Institute of Medical Research, Sydney, Australia,Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Philip N. Britton
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia,The Children's Hospital at Westmead, Sydney Children's Hospitals Network, Sydney, Australia
| | - Tri Giang Phan
- Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia.
| |
Collapse
|
4
|
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged pathogenic human coronavirus that belongs to the sarbecovirus lineage of the genus Betacoronavirus. The ancestor strain has evolved into a number of variants of concern, with the Omicron variant of concern now having many distinct sublineages. The ongoing COVID-19 pandemic caused by SARS-CoV-2 has caused serious damage to public health and the global economy, and one strategy to combat COVID-19 has been the development of broadly neutralizing antibodies for prophylactic and therapeutic use. Many are in preclinical and clinical development, and a few have been approved for emergency use. Here we summarize neutralizing antibodies that target four key regions within the SARS-CoV-2 spike (S) protein, namely the N-terminal domain and the receptor-binding domain in the S1 subunit, and the stem helix region and the fusion peptide region in the S2 subunit. Understanding the characteristics of these broadly neutralizing antibodies will accelerate the development of new antibody therapeutics and provide guidance for the rational design of next-generation vaccines.
Collapse
|
5
|
Phetsouphanh C, Khoo WH, Jackson K, Klemm V, Howe A, Aggarwal A, Akerman A, Milogiannakis V, Stella AO, Rouet R, Schofield P, Faulks ML, Law H, Danwilai T, Starr M, Munier CML, Christ D, Singh M, Croucher PI, Brilot-Turville F, Turville S, Phan TG, Dore GJ, Darley D, Cunningham P, Matthews GV, Kelleher AD, Zaunders JJ. High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells. Front Immunol 2022; 13:1032911. [PMID: 36544780 PMCID: PMC9762180 DOI: 10.3389/fimmu.2022.1032911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Background Long-term immunity to SARS-CoV-2 infection, including neutralizing antibodies and T cell-mediated immunity, is required in a very large majority of the population in order to reduce ongoing disease burden. Methods We have investigated the association between memory CD4 and CD8 T cells and levels of neutralizing antibodies in convalescent COVID-19 subjects. Findings Higher titres of convalescent neutralizing antibodies were associated with significantly higher levels of RBD-specific CD4 T cells, including specific memory cells that proliferated vigorously in vitro. Conversely, up to half of convalescent individuals had low neutralizing antibody titres together with a lack of receptor binding domain (RBD)-specific memory CD4 T cells. These low antibody subjects had other, non-RBD, spike-specific CD4 T cells, but with more of an inhibitory Foxp3+ and CTLA-4+ cell phenotype, in contrast to the effector T-bet+, cytotoxic granzymes+ and perforin+ cells seen in RBD-specific memory CD4 T cells from high antibody subjects. Single cell transcriptomics of antigen-specific CD4+ T cells from high antibody subjects similarly revealed heterogenous RBD-specific CD4+ T cells that comprised central memory, transitional memory and Tregs, as well as cytotoxic clusters containing diverse TCR repertoires, in individuals with high antibody levels. However, vaccination of low antibody convalescent individuals led to a slight but significant improvement in RBD-specific memory CD4 T cells and increased neutralizing antibody titres. Interpretation Our results suggest that targeting CD4 T cell epitopes proximal to and within the RBD-region should be prioritized in booster vaccines.
Collapse
Affiliation(s)
| | - Weng Hua Khoo
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | | | - Vera Klemm
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Annett Howe
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Anupriya Aggarwal
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Anouschka Akerman
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | | | | | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Megan L. Faulks
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Hannah Law
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Thidarat Danwilai
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Mitchell Starr
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - C. Mee Ling Munier
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | | | - Fabienne Brilot-Turville
- Brain and Mind Centre, Children’s Hospital at Westmead, University of Sydney, Sydney, NSW, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
| | - Stuart Turville
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Tri Giang Phan
- Garvan Institute of Medical Research, Sydney, NSW, Australia,St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW) Sydney, Sydney, NSW, Australia
| | - Gregory J. Dore
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - David Darley
- Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Philip Cunningham
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Gail V. Matthews
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Infectious Diseases, St. Vincent's Hospital, Sydney, NSW, Australia
| | - Anthony D. Kelleher
- Kirby Institute, University of New South Wales (UNSW), Sydney, NSW, Australia,Department of Immunology, St Vincent's Hospital, Sydney, NSW, Australia
| | - John J. Zaunders
- NSW State Reference Laboratory for HIV, St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia,*Correspondence: John J. Zaunders,
| |
Collapse
|
6
|
Aggarwal A, Akerman A, Milogiannakis V, Silva MR, Walker G, Stella AO, Kindinger A, Angelovich T, Waring E, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Jean T, Foster CSP, Christ D, Hoppe AC, Munier ML, Darley D, Churchill M, Stark DJ, Matthews G, Rawlinson WD, Kelleher AD, Turville SG. SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern. EBioMedicine 2022; 84:104270. [PMID: 36130476 DOI: 10.1101/2021.12.14.21267772] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/09/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. The introduction of global vaccine programs has contributed to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, Omicron BA.1 emerged, with substantially altered genetic differences and clinical effects from other variants of concern. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5, presently has an outgrowth advantage over BA.2 and other BA.2 sub-lineages. Here we study the neutralisation of Omicron BA.1, BA.2 and BA.5 and pre-Omicron variants using a range of vaccine and convalescent sera and therapeutic monoclonal antibodies using a live virus neutralisation assay. Using primary nasopharyngeal swabs, we also tested the relative fitness of BA.5 compared to pre-Omicron and Omicron viral lineages in their ability to use the ACE2-TMPRSS2 pathway. METHODS Using low passage clinical isolates of Clade A.2.2, Beta, Delta, BA.1, BA.2 and BA.5, we determined humoral neutralisation in vitro in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. We then determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a genetically engineered ACE2/TMPRSS2 cell line in the presence and absence of the TMPRSS2 inhibitor Nafamostat. FINDINGS Peak responses to 3 doses of BNT162b2 vaccine were associated with a 9-fold reduction in neutralisation for Omicron lineages BA.1, BA.2 and BA.5. Concentrated pooled human IgG from convalescent and vaccinated donors and BNT162b2 vaccination with BA.1 breakthrough infections were associated with greater breadth of neutralisation, although the potency was still reduced 7-fold across all Omicron lineages. Testing of clinical grade antibodies revealed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab for the BA.5. Whilst the infectivity of BA.1 and BA.2 was attenuated in ACE2/TMPRSS2 entry, BA.5 was observed to be equivalent to that of an early 2020 circulating clade and had greater sensitivity to the TMPRSS2 inhibitor Nafamostat. INTERPRETATION Observations support all Omicron variants to significantly escape neutralising antibodies across a range of vaccination and/or convalescent responses. Potency of therapeutic monoclonal antibodies is also reduced and differs across Omicron lineages. The key difference of BA.5 from other Omicron sub-variants is the reversion in tropism back to using the well-known ACE2-TMPRSS2 pathway, utilised efficiently by pre-Omicron lineages. Monitoring if these changes influence transmission and/or disease severity will be key for ongoing tracking and management of Omicron waves globally. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).
Collapse
Affiliation(s)
- Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Andrea Kindinger
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Thomas Angelovich
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Emily Waring
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | | | - Nathan Roth
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Anna Condylios
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Malinna Yeang
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Maureen Wong
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Mee Ling Munier
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - David Darley
- St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Melissa Churchill
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Australia
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Gail Matthews
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, New South Wales, Australia; St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
| |
Collapse
|
7
|
Willett BJ, Grove J, MacLean OA, Wilkie C, De Lorenzo G, Furnon W, Cantoni D, Scott S, Logan N, Ashraf S, Manali M, Szemiel A, Cowton V, Vink E, Harvey WT, Davis C, Asamaphan P, Smollett K, Tong L, Orton R, Hughes J, Holland P, Silva V, Pascall DJ, Puxty K, da Silva Filipe A, Yebra G, Shaaban S, Holden MTG, Pinto RM, Gunson R, Templeton K, Murcia PR, Patel AH, Klenerman P, Dunachie S, Haughney J, Robertson DL, Palmarini M, Ray S, Thomson EC. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat Microbiol 2022; 7:1161-1179. [PMID: 35798890 PMCID: PMC9352574 DOI: 10.1038/s41564-022-01143-7] [Citation(s) in RCA: 274] [Impact Index Per Article: 137.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
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.
Collapse
Affiliation(s)
- Brian J Willett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Craig Wilkie
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Diego Cantoni
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sam Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Nicola Logan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Shirin Ashraf
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Maria Manali
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Agnieszka Szemiel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Elen Vink
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Chris Davis
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Patawee Asamaphan
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - David J Pascall
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | | | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Matthew T G Holden
- Public Health Scotland, Glasgow, UK
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | - Pablo R Murcia
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | | | | | | | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Surajit Ray
- School of Mathematics & Statistics, University of Glasgow, Glasgow, UK
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
- NHS Greater Glasgow & Clyde, Glasgow, UK.
- London School of Hygiene and Tropical Medicine, London, UK.
| |
Collapse
|
8
|
Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: Implications for immune escape and transmission. Rev Med Virol 2022; 32:e2381. [PMID: 35856385 PMCID: PMC9349777 DOI: 10.1002/rmv.2381] [Citation(s) in RCA: 211] [Impact Index Per Article: 105.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022]
Abstract
The first dominant SARS‐CoV‐2 Omicron variant BA.1 harbours 35 mutations in its Spike protein from the original SARS‐CoV‐2 variant that emerged late 2019. Soon after its discovery, BA.1 rapidly emerged to become the dominant variant worldwide and has since evolved into several variants. Omicron is of major public health concern owing to its high infectivity and antibody evasion. This review article examines the theories that have been proposed on the evolution of Omicron including zoonotic spillage, infection in immunocompromised individuals and cryptic spread in the community without being diagnosed. Added to the complexity of Omicron's evolution are the multiple reports of recombination events occurring between co‐circulating variants of Omicron with Delta and other variants such as XE. Current literature suggests that the combination of the novel mutations in Omicron has resulted in the variant having higher infectivity than the original Wuhan‐Hu‐1 and Delta variant. However, severity is believed to be less owing to the reduced syncytia formation and lower multiplication in the human lung tissue. Perhaps most challenging is that several studies indicate that the efficacy of the available vaccines have been reduced against Omicron variant (8–127 times reduction) as compared to the Wuhan‐Hu‐1 variant. The administration of booster vaccine, however, compensates with the reduction and improves the efficacy by 12–35 fold. Concerningly though, the broadly neutralising monoclonal antibodies, including those approved by FDA for therapeutic use against previous SARS‐CoV‐2 variants, are mostly ineffective against Omicron with the exception of Sotrovimab and recent reports suggest that the Omicron BA.2 is also resistant to Sotrovimab. Currently two new Omicron variants BA.4 and BA.5 are emerging and are reported to be more transmissible and resistant to immunity generated by previous variants including Omicron BA.1 and most monoclonal antibodies. As new variants of SARS‐CoV‐2 will likely continue to emerge it is important that the evolution, and biological consequences of new mutations, in existing variants be well understood.
Collapse
Affiliation(s)
- Lok Bahadur Shrestha
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Charles Foster
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - William Rawlinson
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,Serology and Virology Division, Department of Microbiology, New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Nicodemus Tedla
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, New South Wales, Australia.,The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| |
Collapse
|
9
|
Langley DB, Schofield P, Jackson J, Herzog H, Christ D. Crystal structures of human neuropeptide Y (NPY) and peptide YY (PYY). Neuropeptides 2022; 92:102231. [PMID: 35180645 DOI: 10.1016/j.npep.2022.102231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 10/19/2022]
Abstract
Neuropeptide Y (NPY), peptide YY (PYY) and pancreatic polypeptide (PP) form the evolutionarily conserved pancreatic polypeptide family. While the fold is widely utilized in nature, crystal structures remain elusive, particularly for the human forms, with only the structure of a distant avian form of PP reported. Here we utilize a crystallization chaperone (antibody Fab fragment), specifically recognizing the amidated peptide termini, to solve the structures of human NPY and human PYY. Intriguingly, and despite limited sequence identity (~50%), the structure of human PYY closely resembles that of avian PP, highlighting the broad structural conservation of the fold throughout evolution. Specifically, the PYY structure is characterized by a C-terminal amidated α-helix, preceded by a backfolded poly-proline N-terminus, with the termini in close proximity to each other. In contrast, in the structure of human NPY the N-terminal component is disordered, while the helical component of the peptide is observed in a four-helix bundle type arrangement, consistent with a propensity for multimerization suggested by NMR studies.
Collapse
Affiliation(s)
- David B Langley
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Jenny Jackson
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia
| | - Herbert Herzog
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, New South Wales 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia.
| |
Collapse
|
10
|
Jeong BS, Cha JS, Hwang I, Kim U, Adolf-Bryfogle J, Coventry B, Cho HS, Kim KD, Oh BH. Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants. MAbs 2022; 14:2021601. [PMID: 35030983 PMCID: PMC8765073 DOI: 10.1080/19420862.2021.2021601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Coronavirus disease 2019, caused by SARS-CoV-2, remains an on-going pandemic, partly due to the emergence of variant viruses that can “break-through” the protection of the current vaccines and neutralizing antibodies (nAbs), highlighting the needs for broadly nAbs and next-generation vaccines. We report an antibody that exhibits breadth and potency in binding the receptor-binding domain (RBD) of the virus spike glycoprotein across SARS coronaviruses. Initially, a lead antibody was computationally discovered and crystallographically validated that binds to a highly conserved surface of the RBD of wild-type SARS-CoV-2. Subsequently, through experimental affinity enhancement and computational affinity maturation, it was further developed to bind the RBD of all concerning SARS-CoV-2 variants, SARS-CoV-1 and pangolin coronavirus with pico-molar binding affinities, consistently exhibited strong neutralization activity against wild-type SARS-CoV-2 and the Alpha and Delta variants. These results identify a vulnerable target site on coronaviruses for development of pan-sarbecovirus nAbs and vaccines.
Collapse
Affiliation(s)
- Bo-Seong Jeong
- Department of Biological Sciences, Kaist Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jeong Seok Cha
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Insu Hwang
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Uijin Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jared Adolf-Bryfogle
- Institute for Protein Innovation, Boston, MA, USA.,Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian Coventry
- Molecular Engineering & Sciences Institute & Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Kyun-Do Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Byung-Ha Oh
- Department of Biological Sciences, Kaist Institute for the Biocentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| |
Collapse
|
11
|
Laroche A, Orsini Delgado ML, Chalopin B, Cuniasse P, Dubois S, Sierocki R, Gallais F, Debroas S, Bellanger L, Simon S, Maillère B, Nozach H. Deep mutational engineering of broadly-neutralizing nanobodies accommodating SARS-CoV-1 and 2 antigenic drift. MAbs 2022; 14:2076775. [PMID: 35593235 PMCID: PMC9132424 DOI: 10.1080/19420862.2022.2076775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here, we report the molecular engineering of nanobodies that bind with picomolar affinity to both SARS-CoV-1 and SARS-CoV-2 receptor-binding domains (RBD) and are highly neutralizing. We applied deep mutational engineering to VHH72, a nanobody initially specific for SARS-CoV-1 RBD with little cross-reactivity to SARS-CoV-2 antigen. We first identified all the individual VHH substitutions that increase binding to SARS-CoV-2 RBD and then screened highly focused combinatorial libraries to isolate engineered nanobodies with improved properties. The corresponding VHH-Fc molecules show high affinities for SARS-CoV-2 antigens from various emerging variants and SARS-CoV-1, block the interaction between ACE2 and RBD, and neutralize the virus with high efficiency. Its rare specificity across sarbecovirus relies on its peculiar epitope outside the immunodominant regions. The engineered nanobodies share a common motif of three amino acids, which contribute to the broad specificity of recognition. Our results show that deep mutational engineering is a very powerful method, especially to rapidly adapt existing antibodies to new variants of pathogens.
Collapse
Affiliation(s)
- Adrien Laroche
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Maria Lucia Orsini Delgado
- CEA, INRAE, Medicines and Healthcare Technologies Department, SPI, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Cuniasse
- CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Steven Dubois
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphaël Sierocki
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France.,Deeptope SAS, Massy, France
| | - Fabrice Gallais
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze, France
| | - Stéphanie Debroas
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze, France
| | - Laurent Bellanger
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris Saclay, Bagnols-sur-Cèze, France
| | - Stéphanie Simon
- CEA, INRAE, Medicines and Healthcare Technologies Department, SPI, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, Gif-sur-Yvette, France
| |
Collapse
|
12
|
Burnett DL, Jackson KJL, Langley DB, Aggrawal A, Stella AO, Johansen MD, Balachandran H, Lenthall H, Rouet R, Walker G, Saunders BM, Singh M, Li H, Henry JY, Jackson J, Stewart AG, Witthauer F, Spence MA, Hansbro NG, Jackson C, Schofield P, Milthorpe C, Martinello M, Schulz SR, Roth E, Kelleher A, Emery S, Britton WJ, Rawlinson WD, Karl R, Schäfer S, Winkler TH, Brink R, Bull RA, Hansbro PM, Jäck HM, Turville S, Christ D, Goodnow CC. Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability. Immunity 2021; 54:2908-2921.e6. [PMID: 34788600 PMCID: PMC8554075 DOI: 10.1016/j.immuni.2021.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022]
Abstract
Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies.
Collapse
Affiliation(s)
- Deborah L Burnett
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia.
| | | | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | | | | | - Matt D Johansen
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | | | - Helen Lenthall
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Gregory Walker
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Bernadette M Saunders
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Hui Li
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Jake Y Henry
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alastair G Stewart
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia
| | - Franka Witthauer
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Nicole G Hansbro
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Claire Milthorpe
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | | | - Sebastian R Schulz
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Edith Roth
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | | | - Sean Emery
- Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - William D Rawlinson
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, SEALS Randwick, Sydney, NSW 2031, Australia
| | - Rudolfo Karl
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Simon Schäfer
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Thomas H Winkler
- Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Robert Brink
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Rowena A Bull
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Philip M Hansbro
- Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia
| | - Hans-Martin Jäck
- Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stuart Turville
- UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| |
Collapse
|
13
|
Miller NL, Clark T, Raman R, Sasisekharan R. An Antigenic Space Framework for Understanding Antibody Escape of SARS-CoV-2 Variants. Viruses 2021; 13:2009. [PMID: 34696440 PMCID: PMC8537311 DOI: 10.3390/v13102009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
The evolution of mutations in SARS-CoV-2 at antigenic sites that impact neutralizing antibody responses in humans poses a risk to immunity developed through vaccination and natural infection. The highly successful RNA-based vaccines have enabled rapid vaccine updates that incorporate mutations from current variants of concern (VOCs). It is therefore important to anticipate future antigenic mutations as the virus navigates the heterogeneous global landscape of host immunity. Toward this goal, we survey epitope-paratope interfaces of anti-SARS-CoV-2 antibodies to map an antigenic space that captures the role of each spike protein residue within the polyclonal antibody response directed against the ACE2-receptor binding domain (RBD) or the N-terminal domain (NTD). In particular, the antigenic space map builds on recently published epitope definitions by annotating epitope overlap and orthogonality at the residue level. We employ the antigenic space map as a framework to understand how mutations on nine major variants contribute to each variant's evasion of neutralizing antibodies. Further, we identify constellations of mutations that span the orthogonal epitope regions of the RBD and NTD on the variants with the greatest antibody escape. Finally, we apply the antigenic space map to predict which regions of antigenic space-should they mutate-may be most likely to complementarily augment antibody evasion for the most evasive and transmissible VOCs.
Collapse
Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (T.C.); (R.R.)
| |
Collapse
|
14
|
Kombe Kombe AJ, Zahid A, Mohammed A, Shi R, Jin T. Potent Molecular Feature-based Neutralizing Monoclonal Antibodies as Promising Therapeutics Against SARS-CoV-2 Infection. Front Mol Biosci 2021; 8:670815. [PMID: 34136533 PMCID: PMC8201996 DOI: 10.3389/fmolb.2021.670815] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022] Open
Abstract
The 2019-2020 winter was marked by the emergence of a new coronavirus (SARS-CoV-2) related disease (COVID-19), which started in Wuhan, China. Its high human-to-human transmission ability led to a worldwide spread within few weeks and has caused substantial human loss. Mechanical antiviral control approach, drug repositioning, and use of COVID-19 convalescent plasmas (CPs) were the first line strategies utilized to mitigate the viral spread, yet insufficient. The urgent need to contain this deadly pandemic has led searchers and pharmaceutical companies to develop vaccines. However, not all vaccines manufactured are safe. Besides, an alternative and effective treatment option for such an infectious disease would include pure anti-viral neutralizing monoclonal antibodies (NmAbs), which can block the virus at specific molecular targets from entering cells by inhibiting virus-cell structural complex formation, with more safety and efficiency than the CP. Indeed, there is a lot of molecular evidence about the protector effect and the use of molecular feature-based NmAbs as promising therapeutics to contain COVID-19. Thus, from the scientific publication database screening, we here retrieved antibody-related papers and summarized the repertory of characterized NmAbs against SARS-CoV-2, their molecular neutralization mechanisms, and their immunotherapeutic pros and cons. About 500 anti-SARS-CoV-2 NmAbs, characterized through competitive binding assays and neutralization efficacy, were reported at the writing time (January 2021). All NmAbs bind respectively to SARS-CoV-2 S and exhibit high molecular neutralizing effects against wild-type and/or pseudotyped virus. Overall, we defined six NmAb groups blocking SARS-CoV-2 through different molecular neutralization mechanisms, from which five potential neutralization sites on SARS-CoV-2 S protein are described. Therefore, more efforts are needed to develop NmAbs-based cocktails to mitigate COVID-19.
Collapse
Affiliation(s)
- Arnaud John Kombe Kombe
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ayesha Zahid
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ahmed Mohammed
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ronghua Shi
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
| |
Collapse
|