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Akerman A, Milogiannakis V, Jean T, Esneau C, Silva MR, Ison T, Fichter C, Lopez JA, Chandra D, Naing Z, Caguicla J, Li D, Walker G, Amatayakul-Chantler S, Roth N, Manni S, Hauser T, Barnes T, Condylios A, Yeang M, Wong M, Foster CSP, Sato K, Lee S, Song Y, Mao L, Sigmund A, Phu A, Vande More AM, Hunt S, Douglas M, Caterson I, Britton W, Sandgren K, Bull R, Lloyd A, Triccas J, Tangye S, Bartlett NW, Darley D, Matthews G, Stark DJ, Petoumenos K, Rawlinson WD, Murrell B, Brilot F, Cunningham AL, Kelleher AD, Aggarwal A, Turville SG. Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level. EBioMedicine 2023; 90:104545. [PMID: 37002990 PMCID: PMC10060887 DOI: 10.1016/j.ebiom.2023.104545] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND The Omicron era of the COVID-19 pandemic commenced at the beginning of 2022 and whilst it started with primarily BA.1, it was latter dominated by BA.2 and the related sub-lineage BA.5. Following resolution of the global BA.5 wave, a diverse grouping of Omicron sub-lineages emerged derived from BA.2, BA.5 and recombinants thereof. Whilst emerging from distinct lineages, all shared similar changes in the Spike glycoprotein affording them an outgrowth advantage through evasion of neutralising antibodies. METHODS Over the course of 2022, we monitored the potency and breadth of antibody neutralization responses to many emerging variants in the Australian community at three levels: (i) we tracked over 420,000 U.S. plasma donors over time through various vaccine booster roll outs and Omicron waves using sequentially collected IgG pools; (ii) we mapped the antibody response in individuals using blood from stringently curated vaccine and convalescent cohorts. (iii) finally we determine the in vitro efficacy of clinically approved therapies Evusheld and Sotrovimab. FINDINGS In pooled IgG samples, we observed the maturation of neutralization breadth to Omicron variants over time through continuing vaccine and infection waves. Importantly, in many cases, we observed increased antibody breadth to variants that were yet to be in circulation. Determination of viral neutralization at the cohort level supported equivalent coverage across prior and emerging variants with isolates BQ.1.1, XBB.1, BR.2.1 and XBF the most evasive. Further, these emerging variants were resistant to Evusheld, whilst increasing neutralization resistance to Sotrovimab was restricted to BQ.1.1 and XBF. We conclude at this current point in time that dominant variants can evade antibodies at levels equivalent to their most evasive lineage counterparts but sustain an entry phenotype that continues to promote an additional outgrowth advantage. In Australia, BR.2.1 and XBF share this phenotype and, in contrast to global variants, are uniquely dominant in this region in the later months of 2022. INTERPRETATION Whilst the appearance of a diverse range of omicron lineages has led to primary or partial resistance to clinically approved monoclonal antibodies, the maturation of the antibody response across both cohorts and a large donor pools importantly observes increasing breadth in the antibody neutralisation responses over time with a trajectory that covers both current and known emerging variants. FUNDING This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (SGT, GM & WDR), Medical Research Future Fund Antiviral Development Call grant (WDR), the New South Wales Health COVID-19 Research Grants Round 2 (SGT & FB) and the NSW Vaccine Infection and Immunology Collaborative (VIIM) (ALC). Variant modeling was supported by funding from SciLifeLab's Pandemic Laboratory Preparedness program to B.M. (VC-2022-0028) and by the European Union's Horizon 2020 research and innovation programme under grant agreement no. 101003653 (CoroNAb) to B.M.
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Affiliation(s)
- Anouschka Akerman
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | | | - Tyra Jean
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Camille Esneau
- Hunter Medical Research Institute, University of Newcastle, Callaghan, Australia
| | - Mariana Ruiz Silva
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Timothy Ison
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Christina Fichter
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Joseph A Lopez
- Brain Autoimmunity Group, Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, School of Medical Sciences, New South Wales, Australia
| | - Deborah Chandra
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Zin Naing
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Joanna Caguicla
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Daiyang Li
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Gregory Walker
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | | | - Nathan Roth
- Department of Bioanalytical Sciences, Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Sandro Manni
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Hauser
- Plasma Product Development, Research & Development, CSL Behring AG, Bern, Switzerland
| | - Thomas Barnes
- 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
| | - Charles S P Foster
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Kenta Sato
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Sharon Lee
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Yang Song
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Lijun Mao
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Allison Sigmund
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | - Amy Phu
- Research & Education Network, Westmead Hospital, WSLHD, New South Wales, Australia
| | | | - Stephanie Hunt
- Royal Prince Alfred Hospital, SLHD, New South Wales, Australia
| | - Mark Douglas
- The Westmead Institute for Medical Research, Westmead, New South Wales, Australia; Centre for Infectious Diseases and Microbiology, Sydney Institute for Infectious Diseases, The University of Sydney at Westmead Hospital, Westmead, NSW, Australia
| | - Ian Caterson
- Royal Prince Alfred Hospital, SLHD, New South Wales, Australia
| | - Warwick Britton
- The Centenary Institute, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Kerrie Sandgren
- The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Rowena Bull
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Andrew Lloyd
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Jamie Triccas
- Sydney Institute for Infectious Diseases and the Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia
| | - Stuart Tangye
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Nathan W Bartlett
- Hunter Medical Research Institute, University of Newcastle, Callaghan, Australia
| | - David Darley
- 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
| | - Damien J Stark
- Molecular Diagnostic Medicine Laboratory, Sydpath, St Vincent's Hospital, Sydney, New South Wales, Australia
| | - Kathy Petoumenos
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - William D Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology, Randwick, Australia
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Fabienne Brilot
- Brain Autoimmunity Group, Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, School of Medical Sciences, New South Wales, Australia
| | - Anthony L Cunningham
- The Westmead Institute for Medical Research, Westmead, New South Wales, 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
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, New South Wales, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, New South Wales, Australia.
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