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Manuelpillai B, Zendt M, Chang-Rabley E, Ricotta EE. Stuck in pandemic uncertainty: a review of the persistent effects of COVID-19 infection in immune-deficient people. Clin Microbiol Infect 2024; 30:1007-1011. [PMID: 38552795 PMCID: PMC11254561 DOI: 10.1016/j.cmi.2024.03.027] [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: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/23/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND People who are immune-deficient/disordered (IDP) are underrepresented in COVID-19 studies. Specifically, there is limited research on post-SARS-CoV-2 infection outcomes, including viral persistence and long-term sequelae in these populations. OBJECTIVES This review aimed to examine the published literature on the occurrence of persistent SARS-CoV-2 positivity, relapse, reinfections, variant coinfection, and post-acute sequelae of COVID-19 in IDP. Although the available literature largely centred on those with secondary immunodeficiencies, studies on people with inborn errors of immunity are also included. SOURCES PubMed was searched using medical subject headings terms to identify relevant articles from the last 4 years. Articles on primary and secondary immunodeficiencies were chosen, and a special emphasis was placed on including articles that studied people with inborn errors of immunity. The absence of extensive cohort studies including these individuals has limited most articles in this review to case reports, whereas the articles focusing on secondary immunodeficiencies include larger cohort, case-control, and cross-sectional studies. Articles focusing solely on HIV/AIDS were excluded. CONTENT Scientific literature suggests that IDP of any age are more likely to experience persistent SARS-CoV-2 infections. Although adult IDP exhibits a higher rate of post-acute sequelae of COVID-19, milder COVID-19 infections in children may reduce their risk of experiencing post-acute sequelae of COVID-19. Reinfections and coinfections may occur at a slightly higher rate in IDP than in the general population. IMPLICATIONS Although IDP experience increased viral persistence and inter-host evolution, it is unlikely that enough evidence can be generated at the population-level to support or refute the hypothesis that infections in IDP are significantly more likely to result in variants of concern than infections in the general population. Additional research on the relationship between viral persistence and the rate of long-term sequelae in IDP could inform the understanding of the immune response to SARS-CoV-2 in IDP and the general population.
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Affiliation(s)
- Bevin Manuelpillai
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mackenzie Zendt
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Chang-Rabley
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Ricotta
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Persistent SARS-CoV-2 infection: significance and implications. THE LANCET. INFECTIOUS DISEASES 2024; 24:e453-e462. [PMID: 38340735 DOI: 10.1016/s1473-3099(23)00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
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Affiliation(s)
- Heather M Machkovech
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Huygens S, GeurtsvanKessel C, Gharbharan A, Bogers S, Worp N, Boter M, Bax HI, Kampschreur LM, Hassing RJ, Fiets RB, Levenga H, Afonso PM, Koopmans M, Rijnders BJA, Oude Munnink BB. Clinical and Virological Outcome of Monoclonal Antibody Therapies Across SARS-CoV-2 Variants in 245 Immunocompromised Patients: A Multicenter Prospective Cohort Study. Clin Infect Dis 2024; 78:1514-1521. [PMID: 38445721 PMCID: PMC11175671 DOI: 10.1093/cid/ciae026] [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: 09/22/2023] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Immunocompromised patients (ICPs) have an increased risk for a severe and prolonged COVID-19. SARS-CoV-2 monoclonal antibodies (mAbs) were extensively used in these patients, but data from randomized trials that focus on ICPs are lacking. We evaluated the clinical and virological outcome of COVID-19 in ICPs treated with mAbs across SARS-CoV-2 variants. METHODS In this multicenter prospective cohort study, we enrolled B-cell- and/or T-cell-deficient patients treated with casirivimab/imdevimab, sotrovimab, or tixagevimab/cilgavimab. SARS-CoV-2 RNA was quantified and sequenced weekly, and time to viral clearance, viral genome mutations, hospitalization, and death rates were registered. RESULTS Two hundred and forty five patients infected with the Delta (50%) or Omicron BA.1, 2, or 5 (50%) variant were enrolled. Sixty-seven percent were vaccinated; 78 treated as outpatients, of whom 2 required hospital admission, but both survived. Of the 159 patients hospitalized at time of treatment, 43 (27%) required mechanical ventilation or died. The median time to viral clearance was 14 days (interquartile range, 7-22); however, it took >30 days in 15%. Resistance-associated spike mutations emerged in 9 patients in whom the median time to viral clearance was 63 days (95% confidence interval, 57-69; P < .001). Spike mutations were observed in 1 of 42 (2.4%) patients after treatment with 2 active mAbs, in 5 of 34 (14.7%) treated with actual monotherapy (sotrovimab), and 3 of 20 (12%) treated with functional monotherapy (ie, tixagevimab/cilgavimab against tixagevimab-resistant variant). CONCLUSIONS Despite treatment with mAbs, morbidity and mortality of COVID-19 in ICPs remained substantial. Combination antiviral therapy should be further explored and may be preferred in severely ICPs.
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Affiliation(s)
- Sammy Huygens
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Corine GeurtsvanKessel
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Arvind Gharbharan
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Susanne Bogers
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Hannelore I Bax
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Linda M Kampschreur
- Department of Internal Medicine, Medical Center Leeuwarden, Leeuwarden, The Netherlands
| | - Robert-Jan Hassing
- Department of Internal Medicine, Rijnstate Hospital, Arnhem, The Netherlands
| | - Roel B Fiets
- Department of Internal Medicine, Amphia Hospital, Breda, The Netherlands
| | - Henriette Levenga
- Department of Internal Medicine, Groene Hart Gouda, Gouda, The Netherlands
| | - Pedro Miranda Afonso
- Department of Biostatistics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Bart J A Rijnders
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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4
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Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Rep Med 2024; 5:101553. [PMID: 38723626 PMCID: PMC11148769 DOI: 10.1016/j.xcrm.2024.101553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/10/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | | | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Centre for Free Electron Laser Science, Hamburg, Germany
| | - Muneeswaran Selvaraj
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas G Ritter
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Lizzie Stafford
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and University of Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Yuan Lui
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Martin Fellermeyer
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Michael I Barton
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mikhail A Kutuzov
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Omer Dushek
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK; Sir William Dunn School of Pathology, Oxford, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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5
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Santos JD, Sobral D, Pinheiro M, Isidro J, Bogaardt C, Pinto M, Eusébio R, Santos A, Mamede R, Horton DL, Gomes JP, Borges V. INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance. Genome Med 2024; 16:61. [PMID: 38659008 PMCID: PMC11044337 DOI: 10.1186/s13073-024-01334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification. RESULTS The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis. CONCLUSIONS The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).
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Affiliation(s)
- João Dourado Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinheiro
- Institute of Biomedicine-iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Carlijn Bogaardt
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rodrigo Eusébio
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - André Santos
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rafael Mamede
- Faculdade de Medicina, Instituto de Microbiologia, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel L Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Surrey, UK
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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6
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Guilbaud R, Franco Yusti AM, Leducq V, Zafilaza K, Bridier-Nahmias A, Todesco E, Soulie C, Fauchois A, Le Hingrat Q, Kramer L, Goulenok T, Salpin M, Daugas E, Dorent R, Ottaviani S, Zalcman G, Ghosn J, Choquet S, Cacoub P, Amoura Z, Barroux B, Pourcher V, Spano JP, Louet M, Marcelin AG, Calvez V, Charpentier C, Descamps D, Marot S, Ferré VM, Coppée R. Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study. J Infect Dis 2024; 229:1041-1049. [PMID: 37956413 DOI: 10.1093/infdis/jiad499] [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: 07/19/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics. METHODS From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host. RESULTS Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts. CONCLUSIONS This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.
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Affiliation(s)
- Romane Guilbaud
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Anna-Maria Franco Yusti
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Valentin Leducq
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Karen Zafilaza
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Bridier-Nahmias
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Eve Todesco
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Cathia Soulie
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Fauchois
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Quentin Le Hingrat
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Laura Kramer
- Service de Pharmacie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Tiphaine Goulenok
- Service de Médecine Interne, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Mathilde Salpin
- Service de Pneumologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Eric Daugas
- Service de Néphrologie, Université Paris Cité, Inserm U1149, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Richard Dorent
- Service de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sébastien Ottaviani
- Service de Rhumatologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Gérard Zalcman
- Service d'Oncologie Thoracique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
- Service de Maladies Infectieuses, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sylvain Choquet
- Service d'Hématologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Patrice Cacoub
- Service de Médecine Interne et Immunologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Zahir Amoura
- Service de Médecine Interne 2, Centre National de Référence des Histiocytoses, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Benoit Barroux
- Service d'Urologie et de Transplantation Rénale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valérie Pourcher
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service de Maladies Infectieuses et Tropicales, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service d'Oncologie Médicale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Martine Louet
- Service de Santé au Travail, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Vincent Calvez
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Charlotte Charpentier
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Diane Descamps
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Stéphane Marot
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valentine Marie Ferré
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Romain Coppée
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
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Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [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: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
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Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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8
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Harari S, Miller D, Fleishon S, Burstein D, Stern A. Using big sequencing data to identify chronic SARS-Coronavirus-2 infections. Nat Commun 2024; 15:648. [PMID: 38245511 PMCID: PMC10799923 DOI: 10.1038/s41467-024-44803-4] [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: 09/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants. One leading hypothesis suggests these variants may have emerged during chronic infections of immunocompromised individuals, but limited data from these cases hinders comprehensive analyses. Here, we harnessed millions of SARS-CoV-2 genomes to identify potential chronic infections and used language models (LM) to infer chronic-associated mutations. First, we mined the SARS-CoV-2 phylogeny and identified chronic-like clades with identical metadata (location, age, and sex) spanning over 21 days, suggesting a prolonged infection. We inferred 271 chronic-like clades, which exhibited characteristics similar to confirmed chronic infections. Chronic-associated mutations were often high-fitness immune-evasive mutations located in the spike receptor-binding domain (RBD), yet a minority were unique to chronic infections and absent in global settings. The probability of observing high-fitness RBD mutations was 10-20 times higher in chronic infections than in global transmission chains. The majority of RBD mutations in BA.1/BA.2 chronic-like clades bore predictive value, i.e., went on to display global success. Finally, we used our LM to infer hundreds of additional chronic-like clades in the absence of metadata. Our approach allows mining extensive sequencing data and providing insights into future evolutionary patterns of SARS-CoV-2.
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Affiliation(s)
- Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Shay Fleishon
- Israeli Health Intelligence Agency, Public Health Division, Ministry of Health, Jerusalem, Israel
| | - David Burstein
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.
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9
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Overbeck V, Taylor BP, Turcinovic J, Qiu X, Schaeffer B, Seitz S, Curry SR, Hanage WP, Connor JH, Kuppalli K. Successful treatment of SARS-CoV-2 in an immunocompromised patient with persistent infection for 245 days: A case report. Heliyon 2024; 10:e23699. [PMID: 38223743 PMCID: PMC10784163 DOI: 10.1016/j.heliyon.2023.e23699] [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] [Received: 08/15/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024] Open
Abstract
Background Immunocompromised patients receiving B-cell-depleting therapies are at increased risk of persistent SARS-CoV-2 infection, with many experiencing fatal outcomes. We report a successful outcome in a patient with rheumatoid arthritis (RA) on rituximab diagnosed with COVID-19 in July 2020 with persistent infection for over 245 days. Results The patient received numerous treatment courses for persistent COVID-19 infection, including remdesivir, baricitinib, immunoglobulin and high doses of corticosteroids followed by a prolonged taper due to persistent respiratory symptoms and cryptogenic organizing pneumonia. Her clinical course was complicated by Pseudomonas aeruginosa sinusitis with secondary bacteremia, and cytomegalovirus (CMV) viremia and pneumonitis. SARS-CoV-2 positive RNA samples were extracted from two nasopharyngeal swabs and sequenced using targeted amplicon Next-Generation Sequencing which were analyzed for virus evolution over time. Viral sequencing indicated lineage B.1.585.3 SARS-CoV-2 accumulated Spike protein mutations associated with immune evasion and resistance to therapeutics. Upon slowly decreasing the patient's steroids, she had resolution of her symptoms and had a negative nasopharyngeal SARS-CoV-2 PCR and serum CMV PCR in March 2021. Conclusion A patient with RA on B-cell depleting therapy developed persistent SARS-CoV-2 infection allowing for virus evolution and had numerous complications, including viral and bacterial co-infections with opportunistic pathogens. Despite intra-host evolution with a more immune evasive SARS-CoV-2 lineage, it was cleared after 245 days with reconstitution of the patient's immune system.
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Affiliation(s)
- Victoria Overbeck
- Departments of Epidemiology and Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Bradford P. Taylor
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Xueting Qiu
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Beau Schaeffer
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Scott Seitz
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Scott R. Curry
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - John H. Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Krutika Kuppalli
- Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
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10
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Seth-Smith H, Vesenbeckh S, Egli A, Ott S. SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing. BMJ Case Rep 2023; 16:e255255. [PMID: 38087481 PMCID: PMC10728978 DOI: 10.1136/bcr-2023-255255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
The evolution of SARS-CoV-2 within immunocompromised hosts who fail to clear the virus over many months has been proposed as a route to the development of Variants of Concern (VoCs). We present a case of an immunocompromised male patient with a prolonged SARS-CoV-2 infection. During hospitalisation, 7 weeks after first diagnosis, his condition worsened to require continuous ventilation support. Resolution of symptoms was observed after convalescent plasma therapy. Whole genome sequencing of the virus showed Pango lineage B.1.221. Between the first sample and the second from bronchoalveolar lavage fluid 7 weeks later, we identified eight mutations, including minor variants, which could be used to estimate the chronology of mutations. This suggests an elevated mutation rate, in-host accumulation of mutations and further evidence for sources of VoCs. Prolonged SARS-CoV-2 infections in immunocompromised hosts increase the likelihood of hospital stays and morbidity, and also pose an increased risk to global public health.
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Affiliation(s)
- Helena Seth-Smith
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Silvan Vesenbeckh
- Department of Pulmonology, University Hospital Zurich, Zurich, Switzerland
- Department of Pulmonology, Sankt Claraspital, Basel, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Sebastian Ott
- Department of Pulmonology, Sankt Claraspital, Basel, Switzerland
- Department of Pulmonology, Inselspital University Hospital Bern, Bern, Switzerland
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11
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Bi D, Luo X, Chen Z, Xie Z, Zang N, Mo L, Liu Z, Lin Y, Qin Y, Tang X, Lin L, Wang Y, Cao L, Zhao F, Zhou J, Wei S, Xi S, Ma Q, Lin J. Genomic epidemiology reveals early transmission of SARS-CoV-2 and mutational dynamics in Nanning, China. Heliyon 2023; 9:e23029. [PMID: 38125422 PMCID: PMC10731232 DOI: 10.1016/j.heliyon.2023.e23029] [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] [Received: 08/04/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are a fatal pathogen resulting in substantial morbidity and mortality, and posing a great threat to human health with epidemics and pandemics. METHODS Next-generation sequencing (NGS) was performed to investigate the SARS-CoV-2 genomic characterization. Phylogenetic analysis of SARS-CoV-2 genomes was used to probe the evolutionary. Homology protein structure modelling was done to explore potential effect of the mutations. RESULTS The eighty genome sequences of SARS-CoV-2 obtained from the thirty-nine patients with COVID-19. A novel variant with mutation H625R concomitant with S50L in spike glycoprotein had been identified. Phylogenetic analysis revealed that SARS-CoV-2 variants belong to several distinct lineages. Homology modelling indicated that variant with mutation H625R and S50L increases flexibility of S1 subunit. CONCLUSIONS SARS-CoV-2 genomes are constantly evolving by accumulation of point mutations. The amino acid H625R in combination with S50L may have a significant impact on the interaction between spike glycoprotein and ACE2.
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Affiliation(s)
- DeWu Bi
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - XiaoLu Luo
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - ZhenCheng Chen
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
| | - ZhouHua Xie
- Department of Respiratory Medicine, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - Ning Zang
- Guangxi Medical Research Center, Guangxi Medical University, Nanning, China
| | - LiDa Mo
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - ZeDuan Liu
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - YanRong Lin
- Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - YaQin Qin
- Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - XiKe Tang
- Department of Critical Care Medicine, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - Lü Lin
- Emergency Department, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - YuanLi Wang
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
| | - LiangLi Cao
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
| | - FeiJun Zhao
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, China
| | - JinAi Zhou
- Guangxi Medical Research Center, Guangxi Medical University, Nanning, China
| | - ShanQiu Wei
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - ShaoYong Xi
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - QiuYing Ma
- Department of Clinical Laboratory, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
| | - JianYan Lin
- Key Laboratory of Infectious Diseases, The Fourth People's Hospital of Nanning, Nanning, China
- Affiliated Infectious Disease Hospital of Nanning, Guangxi Medical University, Nanning, China
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12
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Kim D, Kim J, Kim M, Park H, Park S, Maharjan S, Baek K, Kang BM, Kim S, Park MS, Lee Y, Kwon HJ. Analysis of spike protein variants evolved in a novel in vivo long-term replication model for SARS-CoV-2. Front Cell Infect Microbiol 2023; 13:1280686. [PMID: 38029235 PMCID: PMC10655031 DOI: 10.3389/fcimb.2023.1280686] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The spectrum of SARS-CoV-2 mutations have increased over time, resulting in the emergence of several variants of concern. Persistent infection is assumed to be involved in the evolution of the variants. Calu-3 human lung cancer cells persistently grow without apoptosis and release low virus titers after infection. Methods We established a novel in vivo long-term replication model using xenografts of Calu-3 human lung cancer cells in immunodeficient mice. Virus replication in the tumor was monitored for 30 days and occurrence of mutations in the viral genome was determined by whole-genome deep sequencing. Viral isolates with mutations were selected after plaque forming assays and their properties were determined in cells and in K18-hACE2 mice. Results After infection with parental SARS-CoV-2, viruses were found in the tumor tissues for up to 30 days and acquired various mutations, predominantly in the spike (S) protein, some of which increased while others fluctuated for 30 days. Three viral isolates with different combination of mutations produced higher virus titers than the parental virus in Calu-3 cells without cytopathic effects. In K18-hACE2 mice, the variants were less lethal than the parental virus. Infection with each variant induced production of cross-reactive antibodies to the receptor binding domain of parental SARS-CoV-2 S protein and provided protective immunity against subsequent challenge with parental virus. Discussion These results suggest that most of the SARS-CoV-2 variants acquired mutations promoting host adaptation in the Calu-3 xenograft mice. This model can be used in the future to further study SARS-CoV-2 variants upon long-term replication in vivo.
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Affiliation(s)
- Dongbum Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jinsoo Kim
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Minyoung Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Heedo Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sangkyu Park
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Sony Maharjan
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Kyeongbin Baek
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Bo Min Kang
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Suyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Younghee Lee
- Department of Biochemistry, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Hyung-Joo Kwon
- Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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13
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Moreno A, Manning K, Azeem MI, Nooka AK, Ellis M, Manalo RJ, Switchenko JM, Wali B, Kaufman JL, Hofmeister CC, Joseph NS, Lonial S, Dhodapkar KM, Dhodapkar MV, Suthar MS. Divergence of variant binding/neutralizing antibodies following SARS-CoV-2 booster vaccines in myeloma: Impact of hybrid immunity. RESEARCH SQUARE 2023:rs.3.rs-3293339. [PMID: 37790523 PMCID: PMC10543400 DOI: 10.21203/rs.3.rs-3293339/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
We characterized virus-neutralization and spike-binding antibody profiles in myeloma patients following monovalent or bivalent-SARS-CoV-2 booster vaccination. Vaccination improves the breadth of binding antibodies but not neutralization activity against current variants. Hybrid immunity and immune imprinting impact vaccine-elicited immunity.
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Affiliation(s)
- Alberto Moreno
- Emory Vaccine Center, Emory University, Atlanta, GA
- Emory National Primate Research Center, Atlanta, GA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Kelly Manning
- Emory Vaccine Center, Emory University, Atlanta, GA
- Emory National Primate Research Center, Atlanta, GA
| | - Maryam I. Azeem
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA
| | - Ajay K. Nooka
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Madison Ellis
- Emory Vaccine Center, Emory University, Atlanta, GA
- Emory National Primate Research Center, Atlanta, GA
| | - Renee Julia Manalo
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
| | | | - Bushra Wali
- Emory Vaccine Center, Emory University, Atlanta, GA
- Emory National Primate Research Center, Atlanta, GA
| | - Jonathan L. Kaufman
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Craig C. Hofmeister
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Nisha S. Joseph
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Sagar Lonial
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Kavita M. Dhodapkar
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Madhav V. Dhodapkar
- Department of Hematology/Medical Oncology, Emory University, Atlanta, GA
- Winship Cancer Institute, Atlanta, GA
| | - Mehul S. Suthar
- Emory Vaccine Center, Emory University, Atlanta, GA
- Emory National Primate Research Center, Atlanta, GA
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
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14
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Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.22.23294416. [PMID: 37662226 PMCID: PMC10473782 DOI: 10.1101/2023.08.22.23294416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Background Prolonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear. Methods Adults aged ≥18 years were enrolled at 5 hospitals and followed from 4/11/2022 - 2/1/2023. Eligible patients were SARS-CoV-2-positive in the previous 14 days and had a moderate or severely immunocompromising condition or treatment. Nasal specimens were tested by rRT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. Results We enrolled 150 patients with: B cell malignancy or anti-B cell therapy (n=18), solid organ or hematopoietic stem cell transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B cell malignancy (n=23), and autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) were rRT-PCR-positive and 12 (8%) were culture-positive ≥21 days after initial SARS-CoV-2 detection or illness onset. Patients with B cell dysfunction had longer duration of rRT-PCR-positivity compared to those with autoimmune/autoinflammatory conditions (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations were identified in 5 individuals who were rRT-PCR-positive >56 days; 61% were in the receptor-binding domain (RBD). Mutations shared by multiple individuals were rare (<5%) in global circulation. Conclusions In this cohort, prolonged replication-competent Omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting >56 days accumulated spike mutations, which were distinct from those seen globally.
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Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, Michigan
| | - Jennie H Kwon
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H Keipp Talbot
- Departments of Medicine and Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Wesley H Self
- Vanderbilt Institute for Clinical and Translational Research and Department of Emergency Medicine and, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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15
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Moreno A, Manning K, Azeem MI, Nooka AK, Ellis M, Manalo RJ, Switchenko JM, Wali B, Kaufman JL, Hofmeister CC, Joseph NS, Lonial S, Dhodapkar KM, Dhodapkar MV, Suthar MS. Divergence of variant binding/neutralizing antibodies following SARS-CoV-2 booster vaccines in myeloma: Impact of hybrid immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553767. [PMID: 37662390 PMCID: PMC10473610 DOI: 10.1101/2023.08.17.553767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We characterized virus-neutralization and spike-binding antibody profiles in myeloma patients following monovalent or bivalent-SARS-CoV-2 booster vaccination. Vaccination improves the breadth of binding antibodies but not neutralization activity against current variants. Hybrid immunity and immune imprinting impact vaccine-elicited immunity.
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16
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Bunce M, Geoghegan JL, Winter D, de Ligt J, Wiles S. Exploring the depth and breadth of the genomics toolbox during the COVID-19 pandemic: insights from Aotearoa New Zealand. BMC Med 2023; 21:213. [PMID: 37316857 DOI: 10.1186/s12916-023-02909-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/13/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Genomic technologies have become routine in the surveillance and monitoring of the coronavirus disease 2019 (COVID-19) pandemic, as evidenced by the millions of SARS-CoV-2 sequences uploaded to international databases. Yet the ways in which these technologies have been applied to manage the pandemic are varied. MAIN TEXT Aotearoa New Zealand was one of a small number of countries to adopt an elimination strategy for COVID-19, establishing a managed isolation and quarantine system for all international arrivals. To aid our response, we rapidly set up and scaled our use of genomic technologies to help identify community cases of COVID-19, to understand how they had arisen, and to determine the appropriate action to maintain elimination. Once New Zealand pivoted from elimination to suppression in late 2021, our genomic response changed to focusing on identifying new variants arriving at the border, tracking their incidence around the country, and examining any links between specific variants and increased disease severity. Wastewater detection, quantitation and variant detection were also phased into the response. Here, we explore New Zealand's genomic journey through the pandemic and provide a high-level overview of the lessons learned and potential future capabilities to better prepare for future pandemics. CONCLUSIONS Our commentary is aimed at health professionals and decision-makers who might not be familiar with genetic technologies, how they can be used, and why this is an area with great potential to assist in disease detection and tracking now and in the future.
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Affiliation(s)
- Michael Bunce
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
- Department of Conservation, Wellington, 6011, New Zealand
| | - Jemma L Geoghegan
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - David Winter
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Kenepuru, Porirua, 5022, New Zealand.
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.
- Te Pūnaha Matatini, Auckland, New Zealand.
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17
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Morita R, Kubota-Koketsu R, Lu X, Sasaki T, Nakayama EE, Liu YC, Okuzaki D, Motooka D, Wing JB, Fujikawa Y, Ichida Y, Amo K, Goto T, Hara J, Shirano M, Yamasaki S, Shioda T. COVID-19 relapse associated with SARS-CoV-2 evasion from CD4 + T-cell recognition in an agammaglobulinemia patient. iScience 2023; 26:106685. [PMID: 37124420 PMCID: PMC10116114 DOI: 10.1016/j.isci.2023.106685] [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: 06/30/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023] Open
Abstract
A 25-year-old patient with a primary immunodeficiency lacking immunoglobulin production experienced a relapse after a 239-day period of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Viral genetic sequencing demonstrated that SARS-CoV-2 had evolved during the infection period, with at least five mutations associated with host cellular immune recognition. Among them, the T32I mutation in ORF3a was found to evade recognition by CD4+ T cells. The virus found after relapse showed an increased proliferative capacity in vitro. SARS-CoV-2 may have evolved to evade recognition by CD4+ T cells and increased in its proliferative capacity during the persistent infection, likely leading to relapse. These mutations may further affect viral clearance in hosts with similar types of human leukocyte antigens. The early elimination of SARS-CoV-2 in immunocompromised patients is therefore important not only to improve the condition of patients but also to prevent the emergence of mutants that threaten public health.
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Affiliation(s)
- Ryo Morita
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tadahiro Sasaki
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - James Badger Wing
- Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Yasunori Fujikawa
- Department of Medical Laboratory, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Yuji Ichida
- Department of Pharmacy, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Kiyoko Amo
- Department of Pediatric Emergency Medicine, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Tetsushi Goto
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Michinori Shirano
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
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18
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Riddell AC, Cutino-Moguel T. The origins of new SARS-COV-2 variants in immunocompromised individuals. Curr Opin HIV AIDS 2023; 18:148-156. [PMID: 36977190 DOI: 10.1097/coh.0000000000000794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
PURPOSE OF REVIEW To explore the origins of new severe acute respiratory coronavirus 2 (SARS-CoV-2) variants in immunocompromised individuals and whether the emergence of novel mutations in these individuals is responsible for the development of variants of concern (VOC). RECENT FINDINGS Next generation sequencing of samples from chronically infected immunocompromised patients has enabled identification of VOC- defining mutations in individuals prior to the emergence of these variants worldwide. Whether these individuals are the source of variant generation is uncertain. Vaccine effectiveness in immunocompromised individuals and with respect to VOCs is also discussed. SUMMARY Current evidence on chronic SARS-CoV-2 infection in immunocompromised populations is reviewed including the relevance of this to the generation of novel variants. Continued viral replication in the absence of an effective immune response at an individual level or high levels of viral infection at the population level are likely to have contributed to the appearance of the main VOC.
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Affiliation(s)
- Anna C Riddell
- Department of Virology, Division of Infection, Barts Health NHS Trust, London, UK
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19
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Ambadapoodi RS, Arnold FW, Chariker JH, Glynn A, Lauer W, Marimuthu S, Rouchka EC, Smith ML, Wolf LA. Persistent SARS-CoV-2 Infection in a Multiple Sclerosis Patient on Ocrelizumab: A Case Report. RESEARCH SQUARE 2023:rs.3.rs-2768759. [PMID: 37066424 PMCID: PMC10104259 DOI: 10.21203/rs.3.rs-2768759/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
A 44-year-old female patient with multiple sclerosis (MS) treated with ocrelizumab was hospitalized with SARS-CoV-2 pneumonia three times over the course of five months, eventually expiring. Viral sequencing of samples from her first and last admissions suggests a single persistent SARS-CoV-2 infection. We hypothesize that her immunocompromised state, due to MS treatment with an immunosuppressive monoclonal antibody, prevented her from achieving viral clearance.
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Affiliation(s)
| | - Forest W. Arnold
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
| | - Julia H. Chariker
- Neuroscience Training Department, University of Louisville, Louisville, KY
| | - Alex Glynn
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
| | - William Lauer
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY
| | - Subathra Marimuthu
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
| | - Eric C. Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY
| | - Leslie A. Wolf
- Division of Infectious Diseases, School of Medicine, University of Louisville, Louisville, KY
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20
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Qiu S, Chen Z, Zhu A, Zeng Q, Liu H, Liu X, Ye F, Jin Y, Wu J, Yang C, Wang Q, Chen F, Chen L, Tian S, Du X, Hu Q, Cheng J, Chen C, Li F, Sun J, Wang Y, Zhao J, Zhao J, Song H. Successful clearance of persistent SARS-CoV-2 asymptomatic infection following a single dose of Ad5-nCoV vaccine. Signal Transduct Target Ther 2023; 8:123. [PMID: 36922500 PMCID: PMC10015148 DOI: 10.1038/s41392-023-01345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/29/2022] [Accepted: 02/09/2023] [Indexed: 03/17/2023] Open
Abstract
Persistent asymptomatic (PA) SARS-CoV-2 infections have been identified. The immune responses in these patients are unclear, and the development of effective treatments for these patients is needed. Here, we report a cohort of 23 PA cases carrying viral RNA for up to 191 days. PA cases displayed low levels of inflammatory and interferon response, weak antibody response, diminished circulating follicular helper T cells (cTfh), and inadequate specific CD4+ and CD8+ T-cell responses during infection, which is distinct from symptomatic infections and resembling impaired immune activation. Administration of a single dose of Ad5-nCoV vaccine to 10 of these PA cases elicited rapid and robust antibody responses as well as coordinated B-cell and cTfh responses, resulting in successful viral clearance. Vaccine-induced antibodies were able to neutralize various variants of concern and persisted for over 6 months, indicating long-term protection. Therefore, our study provides an insight into the immune status of PA infections and highlights vaccination as a potential treatment for prolonged SARS-CoV-2 infections.
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Affiliation(s)
- Shaofu Qiu
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China
| | - Zhao Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Airu Zhu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Qiuhui Zeng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Hongbo Liu
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China
| | - Xiaoqing Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Feng Ye
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Yingkang Jin
- Pediatric Pulmonary Department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Center for Disease Control and Prevention, 510399, Guangzhou, Guangdong, China
| | - Chaojie Yang
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China
| | - Qi Wang
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China
| | - Fangli Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Lan Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Sai Tian
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China
| | - Xinying Du
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China
| | - Qingtao Hu
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Jinling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Canjie Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Fang Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China
| | - Jingxian Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China. .,Guangzhou Laboratory, Bio-island, 510320, Guangzhou, Guangdong, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, 510182, Guangzhou, Guangdong, China. .,Guangzhou Laboratory, Bio-island, 510320, Guangzhou, Guangdong, China. .,Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, 510060, Guangzhou, Guangdong, China. .,Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, 518112, Shenzhen, Guangdong, China.
| | - Hongbin Song
- The Chinese PLA Center for Disease Control and Prevention, 100071, Beijing, China.
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21
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. Cell Rep Med 2023; 4:100943. [PMID: 36791724 PMCID: PMC9906997 DOI: 10.1016/j.xcrm.2023.100943] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, CT, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott C Roberts
- Infectious Disease, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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22
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Andrés C, González-Sánchez A, Jiménez M, Márquez-Algaba E, Piñana M, Fernández-Naval C, Esperalba J, Saubi N, Quer J, Rando-Segura A, Miarons M, Codina MG, Ruiz-Camps I, Pumarola T, Abrisqueta P, Antón A. Emergence of Delta and Omicron variants carrying resistance-associated mutations in immunocompromised patients undergoing sotrovimab treatment with long-term viral excretion. Clin Microbiol Infect 2023; 29:240-246. [PMID: 36067943 DOI: 10.1016/j.cmi.2022.08.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To monitor the early emergence of genetic mutations related to reduced susceptibility to monoclonal anti-body (mAb)-based treatment in immunocompromised patients with long-term viral excretion using whole-genome sequencing at a tertiary university hospital in Barcelona, Spain. METHODS Serial severe acute respiratory syndrome coronavirus 2-positive samples (mid-December 2021-mid-March 2022) from eight immunosuppressed, fully vaccinated patients (for solid-organ transplantation or haematologic malignancies) with long-term viral excretion despite undergoing mAb therapy (sotrovimab) for coronavirus disease 2019 were selected. Whole-genome sequencing was performed following the ARTIC, version 4.1, protocol on the MiSeq platform. Mutations in the coding sequence of the spike protein with a frequency of ≥5% were studied. RESULTS A total of 37 samples from the studied cases were analysed. All the cases, except one, were confirmed to have the Omicron variant BA.1; one had Delta (AY.100). Thirty-four different mutations were detected within the receptor-binding domain of the spike protein in 62.5% of patients, eight of which were not lineage related and located in the sotrovimab target epitope (P337L, E340D, E340R, E340K, E340V, E340Q, R346T and K356T). Except for P337L, all changes showed a significant increase in frequency or fixation after the administration of sotrovimab. Some of them have been associated with either reduced susceptibility to mAb therapy, such as those at position 340, or the acquisition of a new glycosylation site (346 and 356 positions). CONCLUSIONS This study highlights the importance of monitoring for early in vivo selection of mutations associated with reduced susceptibility to mAb therapy, especially in immunocompromised patients receiving anti-viral drugs, whose immune response is not able to control viral replication, resulting in long-term viral shedding, and those receiving selective evolution pressure. Virologic surveillance of genetically resistant viruses to available anti-viral therapies is considered a priority for both patients and the community.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Moraima Jiménez
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Ester Márquez-Algaba
- Department of Infectious Diseases. Vall d'Hebron University Hospital, Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Candela Fernández-Naval
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Juliana Esperalba
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut of Research, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Av. Monforte de Lemos, Madrid, Spain; Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, Bellaterra, Spain
| | - Ariadna Rando-Segura
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Marta Miarons
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Maria Gema Codina
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Isabel Ruiz-Camps
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Infectious Diseases. Vall d'Hebron University Hospital, Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain.
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
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23
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Abstract
The COVID-19 pandemic has been accompanied by SARS-CoV-2 evolution and emergence of viral variants that have far exceeded initial expectations. Five major variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) have emerged, each having both unique and overlapping amino acid substitutions that have affected transmissibility, disease severity, and susceptibility to natural or vaccine-induced immune responses and monoclonal antibodies. Several of the more recent variants appear to have evolved properties of immune evasion, particularly in cases of prolonged infection. Tracking of existing variants and surveillance for new variants are critical for an effective pandemic response.
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Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; , ,
| | - Ghady Haidar
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; , ,
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA; , ,
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24
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Viral Population Heterogeneity and Fluctuating Mutational Pattern during a Persistent SARS-CoV-2 Infection in an Immunocompromised Patient. Viruses 2023; 15:v15020291. [PMID: 36851504 PMCID: PMC9962589 DOI: 10.3390/v15020291] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023] Open
Abstract
Literature offers plenty of cases of immunocompromised patients, who develop chronic and severe SARS-CoV-2 infections. The aim of this study is to provide further insight into SARS-CoV-2 evolutionary dynamic taking into exam a subject suffering from follicular lymphoma, who developed a persistent infection for over 7 months. Eight nasopharyngeal swabs were obtained, and were analyses by qRT-PCR for diagnostic purposes. All of them were considered eligible (Ct < 30) for NGS sequencing. Sequence analysis showed that all sequences matched the B.1.617.2 AY.122 lineage, but they differed by few mutations identifying three genetically similar subpopulations, which evolved during the course of infection, demonstrating that prolonged replication is paralleled with intra-host virus evolution. These evidences support the hypothesis that SARS-CoV-2 adaptive capacities are able to shape a heterogeneous viral population in the context of immunocompromised patients. Spill-over of viral variants with enhanced transmissibility or immune escape capacities from these subjects is plausible.
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25
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Immunocompromised Patients with Protracted COVID-19: a Review of “Long Persisters”. CURRENT TRANSPLANTATION REPORTS 2022; 9:209-218. [DOI: 10.1007/s40472-022-00385-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Purpose of Review
Certain immunocompromised individuals are at risk for protracted COVID-19, in which SARS-CoV-2 leads to a chronic viral infection. However, the pathogenesis, diagnosis, and management of this phenomenon remain ill-defined.
Recent Findings
Herein, we review key aspects of protracted SARS-CoV-2 infection in immunocompromised individuals, or the so-called long persisters, and describe the clinical presentation, risk factors, diagnosis, and treatment modalities of this condition, as well as intra-host viral evolution. Based on the available data, we also propose a framework of criteria with which to approach this syndrome.
Summary
Protracted COVID-19 is an uncharacterized syndrome affecting patients with B-cell depletion; our proposed diagnostic approach and definitions will inform much needed future research.
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26
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Kumata R, Sasaki A. Antigenic escape is accelerated by the presence of immunocompromised hosts. Proc Biol Sci 2022; 289:20221437. [PMID: 36350217 PMCID: PMC9653221 DOI: 10.1098/rspb.2022.1437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/17/2022] [Indexed: 04/01/2024] Open
Abstract
The repeated emergence of SARS-CoV-2 escape mutants from host immunity has obstructed the containment of the current pandemic and poses a serious threat to humanity. Prolonged infection in immunocompromised patients has received increasing attention as a driver of immune escape, and accumulating evidence suggests that viral genomic diversity and emergence of immune-escape mutants are promoted in immunocompromised patients. However, because immunocompromised patients comprise a small proportion of the host population, whether they have a significant impact on antigenic evolution at the population level is unknown. We consider an evolutionary epidemiological model that combines antigenic evolution and epidemiological dynamics. Applying this model to a heterogeneous host population, we study the impact of immunocompromised hosts on the evolutionary dynamics of pathogen antigenic escape from host immunity. We derived analytical formulae of the speed of antigenic evolution in heterogeneous host populations and found that even a small number of immunocompromised hosts in the population significantly accelerates antigenic evolution. Our results demonstrate that immunocompromised hosts play a key role in viral adaptation at the population level and emphasize the importance of critical care and surveillance of immunocompromised hosts.
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Affiliation(s)
- Ryuichi Kumata
- Department of Evolutionary Studies of Biosystems, The Graduate University of Advanced Studies, SOKENDAI, Hayama, Kanagawa 2400139, Japan
| | - Akira Sasaki
- Department of Evolutionary Studies of Biosystems, The Graduate University of Advanced Studies, SOKENDAI, Hayama, Kanagawa 2400139, Japan
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27
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Halfmann PJ, Minor NR, Haddock III LA, Maddox R, Moreno GK, Braun KM, Baker DA, Riemersa KK, Prasad A, Alman KJ, Lambert MC, Florek K, Bateman A, Westergaard R, Safdar N, Andes DR, Kawaoka Y, Fida M, Yao JD, Friedrich TC, O’Connor DH. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual. Virus Evol 2022; 9:veac104. [PMID: 37692895 PMCID: PMC10491860 DOI: 10.1093/ve/veac104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 09/12/2023] Open
Abstract
Prolonged infections in immunocompromised individuals may be a source for novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population.
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Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Nicholas R Minor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Luis A Haddock III
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Robert Maddox
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kasen K Riemersa
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Ankur Prasad
- Division of Allergy, Pulmonary and Critical Care Medicine, School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705-2281, USA
| | - Kirsten J Alman
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Matthew C Lambert
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Allen Bateman
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Ryan Westergaard
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Nasia Safdar
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - David R Andes
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Madiha Fida
- Division of Infectious Diseases, Mayo Clinic, 200 First St. SW, Rochester, Rochester, Minnesota 55905, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
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28
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Hettle D, Hutchings S, Muir P, Moran E. Persistent SARS-CoV-2 infection in immunocompromised patients facilitates rapid viral evolution: Retrospective cohort study and literature review. CLINICAL INFECTION IN PRACTICE 2022; 16:100210. [PMID: 36405361 PMCID: PMC9666269 DOI: 10.1016/j.clinpr.2022.100210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 10/03/2022] [Accepted: 11/03/2022] [Indexed: 11/17/2022] Open
Abstract
Background Most patients with SARS-CoV-2 are non-infectious within 2 weeks, though viral RNA may remain detectable for weeks. However there are reports of persistent SARS-CoV-2 infection, with viable virus and ongoing infectivity months after initial detection. Beyond individuals, viral evolution during persistent infections may be accelerated, driving emergence of mutations associated with viral variants of concern. These patients often do not meet inclusion criteria for clinical trials, meaning clinical and virologic characteristics, and optimal management strategies are poorly evidence-based. Methods We analysed cases of SARS-CoV-2 infection from a regional testing laboratory in South-West England between March 2020 and December 2021, with at least two SARS-CoV-2 positive samples separated by ≥ 56 days were identified. Excluding those with confirmed or likely re-infection, we identified patients with persistent infection, characterised by an ongoing clinical syndrome consistent with COVID-19 alongside monophyletic viral lineage of SARS-CoV-2. We examined clinical and virologic characteristics, treatment, and outcome. We further performed a literature review investigating cases of persistent SARS-CoV-2 infection, reviewing patient characteristics and treatment. Results We identified six patients with persistent SARS-CoV-2 infection. All were hypogammaglobulinaemic and had underlying haematological malignancy, with four having received B-cell depleting therapy. Evidence of viral evolution, including accrual of mutations associated with variants of concern, was demonstrated in five cases. Four patients ultimately cleared SARS-CoV-2. In two patients, clearance followed treatment with casirivimab/imdevimab. Both survived beyond thirty days following viral clearance, having experienced infections of 305- and 269-days duration respectively, after failed attempts at clearance with alternative therapies. We found 60 cases of confirmed persistent infection in the literature, with a further 31 probable cases. Of those, 80% of patients treated with monoclonal antibodies cleared SARS-CoV-2, and none died. Conclusion Haematological malignancy and patients receiving B-cell depleting therapies represent key groups at risk of persistent SARS-CoV-2 infection. Throughout persistent infection, SARS-CoV-2 can evolve rapidly, giving rise to significant mutations, including those implicated in variants of concern. Monoclonal antibodies appear to be a promising therapeutic option, potentially in combination with antivirals, crucial for individuals, and for public health.
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Affiliation(s)
- David Hettle
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
| | - Stephanie Hutchings
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
- United Kingdom Health Security Agency (UKHSA) South-West Regional Laboratory, Southmead Hospital, Bristol BS10 5NB, United Kingdom
| | - Peter Muir
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
- United Kingdom Health Security Agency (UKHSA) South-West Regional Laboratory, Southmead Hospital, Bristol BS10 5NB, United Kingdom
| | - Ed Moran
- Department of Infection Sciences, Southmead Hospital, Bristol BS10 5NB, United Kingdom
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29
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DeWolf S, Laracy JC, Perales MA, Kamboj M, van den Brink MRM, Vardhana S. SARS-CoV-2 in immunocompromised individuals. Immunity 2022; 55:1779-1798. [PMID: 36182669 PMCID: PMC9468314 DOI: 10.1016/j.immuni.2022.09.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/24/2022] [Accepted: 09/08/2022] [Indexed: 12/15/2022]
Abstract
Immunocompromised individuals and particularly those with hematologic malignancies are at increased risk for SARS-CoV-2-associated morbidity and mortality due to immunologic deficits that limit prevention, treatment, and clearance of the virus. Understanding the natural history of viral infections in people with impaired immunity due to underlying conditions, immunosuppressive therapy, or a combination thereof has emerged as a critical area of investigation during the COVID-19 pandemic. Studies focused on these individuals have provided key insights into aspects of innate and adaptive immunity underlying both the antiviral immune response and excess inflammation in the setting of COVID-19. This review presents what is known about distinct states of immunologic vulnerability to SARS-CoV-2 and how this information can be harnessed to improve prevention and treatment strategies for immunologically high-risk populations.
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Affiliation(s)
- Susan DeWolf
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin C Laracy
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Mini Kamboj
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Santosha Vardhana
- Weill Cornell Medical College, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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30
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Keyel AC, Russell A, Plitnick J, Rowlands JV, Lamson DM, Rosenberg E, St George K. SARS-CoV-2 Vaccine Breakthrough by Omicron and Delta Variants, New York, USA. Emerg Infect Dis 2022; 28:1990-1998. [PMID: 36048774 PMCID: PMC9514330 DOI: 10.3201/eid2810.221058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recently emerged SARS-CoV-2 variants have greater potential than earlier variants to cause vaccine breakthrough infections. During emergence of the Delta and Omicron variants, a matched case-control analysis used a viral genomic sequence dataset linked with demographic and vaccination information from New York, USA, to examine associations between virus lineage and patient vaccination status, patient age, vaccine type, and time since vaccination. Case-patients were persons infected with the emerging virus lineage, and controls were persons infected with any other virus lineage. Infections in fully vaccinated and boosted persons were significantly associated with the Omicron lineage. Odds of infection with Omicron relative to Delta generally decreased with increasing patient age. A similar pattern was observed with vaccination status during Delta emergence but was not significant. Vaccines offered less protection against Omicron, thereby increasing the number of potential hosts for emerging variants.
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31
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Khatamzas E, Antwerpen MH, Rehn A, Graf A, Hellmuth JC, Hollaus A, Mohr AW, Gaitzsch E, Weiglein T, Georgi E, Scherer C, Stecher SS, Gruetzner S, Blum H, Krebs S, Reischer A, Leutbecher A, Subklewe M, Dick A, Zange S, Girl P, Müller K, Weigert O, Hopfner KP, Stemmler HJ, von Bergwelt-Baildon M, Keppler OT, Wölfel R, Muenchhoff M, Moosmann A. Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection. Nat Commun 2022; 13:5586. [PMID: 36151076 PMCID: PMC9508331 DOI: 10.1038/s41467-022-32772-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Antibodies against the spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can drive adaptive evolution in immunocompromised patients with chronic infection. Here we longitudinally analyze SARS-CoV-2 sequences in a B cell-depleted, lymphoma patient with chronic, ultimately fatal infection, and identify three mutations in the spike protein that dampen convalescent plasma-mediated neutralization of SARS-CoV-2. Additionally, four mutations emerge in non-spike regions encoding three CD8 T cell epitopes, including one nucleoprotein epitope affected by two mutations. Recognition of each mutant peptide by CD8 T cells from convalescent donors is reduced compared to its ancestral peptide, with additive effects resulting from double mutations. Querying public SARS-CoV-2 sequences shows that these mutations have independently emerged as homoplasies in circulating lineages. Our data thus suggest that potential impacts of CD8 T cells on SARS-CoV-2 mutations, at least in those with humoral immunodeficiency, warrant further investigation to inform on vaccine design. SARS-CoV-2 mutations associated with the escape from antibody-mediated neutralization have been widely reported. Here, in a patient with defective antibody responses, the authors find a potential association between SARS-CoV-2 mutations and CD8 T alterations to implicate possible contributions of CD8 T cells in evasion of SARS-CoV-2 from host immunity.
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Affiliation(s)
- Elham Khatamzas
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany. .,Division of Infectious Diseases and Tropical Medicine, Center for Infectious Diseases, Heidelberg Hospital, Heidelberg, Germany. .,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.
| | - Markus H Antwerpen
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexandra Rehn
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Johannes Christian Hellmuth
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Alexandra Hollaus
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Anne-Wiebe Mohr
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Erik Gaitzsch
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Tobias Weiglein
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Enrico Georgi
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,Department of Medicine I, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stephanie-Susanne Stecher
- Department of Medicine II, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stefanie Gruetzner
- Institute for Transfusion Medicine and Haemostasis, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Anna Reischer
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Alexandra Leutbecher
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Andrea Dick
- Laboratory for Immunogenetics, University of Munich, LMU, Munich, Germany
| | - Sabine Zange
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Philipp Girl
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Katharina Müller
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans-Joachim Stemmler
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Michael von Bergwelt-Baildon
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Oliver T Keppler
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Roman Wölfel
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Maximilian Muenchhoff
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Andreas Moosmann
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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32
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Heyer A, Günther T, Robitaille A, Lütgehetmann M, Addo MM, Jarczak D, Kluge S, Aepfelbacher M, Schulze Zur Wiesch J, Fischer N, Grundhoff A. Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection. Cell Rep Med 2022; 3:100735. [PMID: 36075217 PMCID: PMC9378267 DOI: 10.1016/j.xcrm.2022.100735] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/19/2022] [Accepted: 08/12/2022] [Indexed: 04/09/2023]
Abstract
We here investigate the impact of antiviral treatments such as remdesivir on intra-host genomic diversity and emergence of SARS-CoV2 variants in patients with a prolonged course of infection. Sequencing and variant analysis performed in 112 longitudinal respiratory samples from 14 SARS-CoV2-infected patients with severe disease progression show that major frequency variants do not generally arise during prolonged infection. However, remdesivir treatment can increase intra-host genomic diversity and result in the emergence of novel major variant species harboring fixed mutations. This is particularly evident in a patient with B cell depletion who rapidly developed mutations in the RNA-dependent RNA polymerase gene following remdesivir treatment. Remdesivir treatment-associated emergence of novel variants is of great interest in light of current treatment guidelines for hospitalized patients suffering from severe SARS-CoV2 disease, as well as the potential use of remdesivir to preventively treat non-hospitalized patients at high risk for severe disease progression.
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Affiliation(s)
- Andreas Heyer
- I. Department of Medicine, Gastroenterology and Hepatology, Sections of Infectious Diseases and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marylyn M Addo
- I. Department of Medicine, Gastroenterology and Hepatology, Sections of Infectious Diseases and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany; Institute of Infection Research and Vaccine Development (IIRVD), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Jarczak
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Schulze Zur Wiesch
- I. Department of Medicine, Gastroenterology and Hepatology, Sections of Infectious Diseases and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research (DZIF), Hamburg-Borstel-Lübeck-Riems, Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Gachoud D, Pillonel T, Tsilimidos G, Battolla D, Dumas D, Opota O, Fontana S, Vollenweider P, Manuel O, Greub G, Bertelli C, Rufer N. Antibody response and intra-host viral evolution after plasma therapy in COVID-19 patients pre-exposed or not to B-cell-depleting agents. Br J Haematol 2022; 199:549-559. [PMID: 36101920 PMCID: PMC9539045 DOI: 10.1111/bjh.18450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/19/2022] [Accepted: 08/28/2022] [Indexed: 12/16/2022]
Abstract
Administration of plasma therapy may contribute to viral control and survival of COVID-19 patients receiving B-cell-depleting agents that impair humoral immunity. However, little is known on the impact of anti-CD20 pre-exposition on the kinetics of SARS-CoV-2-specific antibodies. Here, we evaluated the relationship between anti-spike immunoglobulin G (IgG) kinetics and the clinical status or intra-host viral evolution after plasma therapy in 36 eligible hospitalized COVID-19 patients, pre-exposed or not to B-cell-depleting treatments. The majority of anti-CD20 pre-exposed patients (14/17) showed progressive declines of anti-spike IgG titres following plasma therapy, contrasting with the 4/19 patients who had not received B-cell-depleting agents (p = 0.0006). Patients with antibody decay also depicted prolonged clinical symptoms according to the World Health Organization (WHO) severity classification (p = 0.0267) and SARS-CoV-2 viral loads (p = 0.0032) before complete virus clearance. Moreover, they had higher mutation rates than patients able to mount an endogenous humoral response (p = 0.015), including three patients with one to four spike mutations, potentially associated with immune escape. No relevant differences were observed between patients treated with plasma from convalescent and/or mRNA-vaccinated donors. Our study emphasizes the need for an individualized clinical care and follow-up in the management of COVID-19 patients with B-cell lymphopenia.
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Affiliation(s)
- David Gachoud
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland,Medical Education Unit, School of Medicine, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Trestan Pillonel
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Gerasimos Tsilimidos
- Division of Hematology, Department of OncologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Dunia Battolla
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Dominique Dumas
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Onya Opota
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Stefano Fontana
- Interregional Blood Transfusion SRCBernSwitzerland,Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Peter Vollenweider
- Department of Internal MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Oriol Manuel
- Infectious Diseases Service and Transplantation Center, Department of MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Gilbert Greub
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland,Infectious Diseases Service and Transplantation Center, Department of MedicineLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Claire Bertelli
- Institute of MicrobiologyLausanne University Hospital and University of LausanneLausanneSwitzerland
| | - Nathalie Rufer
- Interregional Blood Transfusion SRCEpalingesSwitzerland,Department of OncologyLausanne University Hospital and University of LausanneEpalingesSwitzerland
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Averyanov AV, Danilevskaya OV. Diffuse Lung Disease in Convalescents of COVID-19. HERALD OF THE RUSSIAN ACADEMY OF SCIENCES 2022; 92:412-417. [PMID: 36091843 PMCID: PMC9447983 DOI: 10.1134/s1019331622040037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/11/2022] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
The most common causes of diffuse interstitial lung damage following COVID-19, often either imitate it but have a different nature or remain due to prolonged persistence of SARS-CoV-2 in the lower respiratory tract. A diagnostic algorithm is proposed to make mostly a correct diagnosis, the key element of which is study of the bronchoalveolar lavage fluid.
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Affiliation(s)
- A. V. Averyanov
- Pulmonology Research Institute, Federal Medical‒Biological Agency, Moscow, Russia
| | - O. V. Danilevskaya
- Pulmonology Research Institute, Federal Medical‒Biological Agency, Moscow, Russia
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35
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Laracy JC, Kamboj M, Vardhana SA. Long and persistent COVID-19 in patients with hematologic malignancies: from bench to bedside. Curr Opin Infect Dis 2022; 35:271-279. [PMID: 35849516 PMCID: PMC9922441 DOI: 10.1097/qco.0000000000000841] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE OF REVIEW Cancer patients, especially those with hematologic malignancies, are at increased risk for coronavirus disease 2019 (COVID-19)-related complications and mortality. We describe the incidence, clinical characteristics, risk factors, and outcomes of persistent COVID-19 infection in patients with hematologic malignancies. RECENT FINDINGS The syndrome of persistent COVID-19 in patients with hematologic malignancies manifests as a chronic protracted illness marked by waxing and waning or progressive respiratory symptoms and prolonged viral shedding. Immunosuppressed patients with lymphoid malignancies may serve as partially immune reservoirs for the generation of immune-evasive viral escape mutants. SUMMARY Persistent COVID-19 infection is a unique concern in patients with hematologic malignancies. While vaccination against severe acute respiratory syndrome coronavirus 2 has reduced the overall burden of COVID-19 in patients with hematologic cancers, whether vaccination or other novel treatments for COVID-19 prevent or alleviate this syndrome remains to be determined.
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Affiliation(s)
- Justin C. Laracy
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infection Control, Division of Quality and Safety, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infection Control, Division of Quality and Safety, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Santosha A. Vardhana
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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36
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Brandolini M, Dirani G, Taddei F, Zannoli S, Denicolò A, Arfilli V, Battisti A, Manera M, Mancini A, Grumiro L, Marino MM, Gatti G, Fantini M, Semprini S, Sambri V. Mutational induction in SARS-CoV-2 major lineages by experimental exposure to neutralising sera. Sci Rep 2022; 12:12479. [PMID: 35864211 PMCID: PMC9302871 DOI: 10.1038/s41598-022-16533-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
The ongoing evolution of SARS-CoV-2 and the emergence of new viral variants bearing specific escape mutations responsible for immune evasion from antibody neutralisation has required a more accurate characterisation of the immune response as one of the evolutive forces behind viral adaptation to a largely immunised human population. In this work, culturing in the presence of neutralising sera vigorously promoted mutagenesis leading to the acquisition of known escape mutations on the spike as well as new presumptive escape mutations on structural proteins whose role as target of the neutralizing antibody response might have been thus far widely neglected. From this perspective, this study, in addition to tracing the past evolution of the species back to interactions with neutralising antibody immune response, also offers a glimpse into future evolutive scenarios.
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Affiliation(s)
- Martina Brandolini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Silvia Zannoli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Agnese Denicolò
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Valentina Arfilli
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Arianna Battisti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Martina Manera
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Andrea Mancini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Laura Grumiro
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Maria Michela Marino
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Michela Fantini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Simona Semprini
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Greater Romagna Area Hub Laboratory, 47522, Cesena, Italy.
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES)-Alma Mater Studiorum, University of Bologna, 40138, Bologna, Italy.
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38
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
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39
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Markarian NM, Galli G, Patel D, Hemmings M, Nagpal P, Berghuis AM, Abrahamyan L, Vidal SM. Identifying Markers of Emerging SARS-CoV-2 Variants in Patients With Secondary Immunodeficiency. Front Microbiol 2022; 13:933983. [PMID: 35847101 PMCID: PMC9283111 DOI: 10.3389/fmicb.2022.933983] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Since the end of 2019, the world has been challenged by the coronavirus disease 2019 (COVID-19) pandemic. With COVID-19 cases rising globally, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, resulting in the emergence of variants of interest (VOI) and of concern (VOC). Of the hundreds of millions infected, immunodeficient patients are one of the vulnerable cohorts that are most susceptible to this virus. These individuals include those with preexisting health conditions and/or those undergoing immunosuppressive treatment (secondary immunodeficiency). In these cases, several researchers have reported chronic infections in the presence of anti-COVID-19 treatments that may potentially lead to the evolution of the virus within the host. Such variations occurred in a variety of viral proteins, including key structural ones involved in pathogenesis such as spike proteins. Tracking and comparing such mutations with those arisen in the general population may provide information about functional sites within the SARS-CoV-2 genome. In this study, we reviewed the current literature regarding the specific features of SARS-CoV-2 evolution in immunocompromised patients and identified recurrent de novo amino acid changes in virus isolates of these patients that can potentially play an important role in SARS-CoV-2 pathogenesis and evolution.
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Affiliation(s)
- Nathan M. Markarian
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Gaël Galli
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- CNRS, ImmunoConcEpT, UMR 5164, Université de Bordeaux, Bordeaux, France
- CHU de Bordeaux, FHU ACRONIM, Centre National de Référence des Maladies Auto-Immunes et Systémiques Rares Est/Sud-Ouest, Bordeaux, France
| | - Dhanesh Patel
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
| | - Mark Hemmings
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Priya Nagpal
- Department of Pharmacology, McGill University, Montréal, QC, Canada
| | | | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center and Research Group on Infectious Diseases in Production Animals, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- McGill University Research Centre on Complex Traits, Montréal, QC, Canada
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Wilkinson SAJ, Richter A, Casey A, Osman H, Mirza JD, Stockton J, Quick J, Ratcliffe L, Sparks N, Cumley N, Poplawski R, Nicholls SN, Kele B, Harris K, Peacock TP, Loman NJ. Recurrent SARS-CoV-2 mutations in immunodeficient patients. Virus Evol 2022; 8:veac050. [PMID: 35996593 PMCID: PMC9384748 DOI: 10.1093/ve/veac050] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/11/2022] [Accepted: 08/08/2022] [Indexed: 01/19/2023] Open
Abstract
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation. There is an apparent selective pressure for mutations that aid cell-cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.
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Affiliation(s)
- S A J Wilkinson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Alex Richter
- Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Anna Casey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Husam Osman
- Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Jeremy D Mirza
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joanne Stockton
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Josh Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Liz Ratcliffe
- Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Natalie Sparks
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Nicola Cumley
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Radoslaw Poplawski
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Samuel N Nicholls
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Beatrix Kele
- Virology Department, Royal London Hospital, Barts Health NHS Trust, London, EC1A 7BE, UK
| | - Kathryn Harris
- Virology Department, Royal London Hospital, Barts Health NHS Trust, London, EC1A 7BE, UK
- Department of Infectious Disease, Imperial College London, London, Westminster W2 1PG, UK
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41
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Harari S, Tahor M, Rutsinsky N, Meijer S, Miller D, Henig O, Halutz O, Levytskyi K, Ben-Ami R, Adler A, Paran Y, Stern A. Drivers of adaptive evolution during chronic SARS-CoV-2 infections. Nat Med 2022; 28:1501-1508. [PMID: 35725921 PMCID: PMC9307477 DOI: 10.1038/s41591-022-01882-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence. Analysis of mutations that arise in chronic SARS-CoV-2 infections shows both overlap and differences with mutations present in pandemic viral variants of concern, highlighting their distinct drivers of evolution.
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Affiliation(s)
- Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel
| | - Maayan Tahor
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Natalie Rutsinsky
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Suzy Meijer
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Miller
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel
| | - Oryan Henig
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ora Halutz
- Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Katia Levytskyi
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronen Ben-Ami
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Adler
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Paran
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel. .,Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel.
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Sonnleitner ST, Prelog M, Sonnleitner S, Hinterbichler E, Halbfurter H, Kopecky DBC, Almanzar G, Koblmüller S, Sturmbauer C, Feist L, Horres R, Posch W, Walder G. Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host. Nat Commun 2022; 13:2560. [PMID: 35538074 PMCID: PMC9090742 DOI: 10.1038/s41467-022-30163-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19. Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.
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Affiliation(s)
- Sissy Therese Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria. .,Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stefanie Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Eva Hinterbichler
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Hannah Halbfurter
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Dominik B C Kopecky
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Giovanni Almanzar
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Ralf Horres
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gernot Walder
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
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The Ukrainian refugee crisis and the COVID-19 pandemic in Europe – Correspondence. Int J Surg 2022; 102:106671. [PMID: 35569760 PMCID: PMC9120829 DOI: 10.1016/j.ijsu.2022.106671] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/10/2022] [Indexed: 12/20/2022]
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Bansal N, Raturi M, Bansal Y. SARS-CoV-2 variants in immunocompromised COVID-19 patients: The underlying causes and the way forward. Transfus Clin Biol 2022; 29:161-163. [PMID: 34973463 PMCID: PMC8714679 DOI: 10.1016/j.tracli.2021.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/26/2021] [Indexed: 01/25/2023]
Affiliation(s)
- N. Bansal
- Department of Transfusion Medicine, VCSG Government Institute of Medical Science and Research, Srinagar, Uttarakhand, India,Corresponding author
| | - M. Raturi
- Department of Immunohematology and Blood Transfusion, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India
| | - Y. Bansal
- Department of Microbiology, VCSG Government Institute of Medical Science and Research, Srinagar, Uttarakhand, India
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Montejano R, Marcelo C, Falces-Romero I, Del Valle LG, De Soto T, Garcia-Rodríguez J, Arribas JR. Efficacy of sotrovimab for persistent coronavirus disease-2019 in a severely immunocompromised person living with HIV. AIDS 2022; 36:751-753. [PMID: 35323160 DOI: 10.1097/qad.0000000000003179] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | | | | | | | - Teresa De Soto
- Haematology Department, Hospital La Paz, IdiPAZ, Madrid, Spain
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Rahimi F, Darvishi M, Bezmin Abadi AT. Highly contagious but less severe COVID-19 caused by new SARS-CoV-2 sublineages may abate the pandemic. Int J Surg 2022; 99:106584. [PMID: 35219842 PMCID: PMC8872701 DOI: 10.1016/j.ijsu.2022.106584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Farid Rahimi
- Research School of Biology, The Australian National University, Ngunnawal and Ngambri Country, Canberra, Australia Infectious Diseases and Tropical Medicinal Research Center, AJA University of Medical Sciences, Tehran, Iran Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Saunders N, Planas D, Bolland WH, Rodriguez C, Fourati S, Buchrieser J, Planchais C, Prot M, Staropoli I, Guivel-Benhassine F, Porrot F, Veyer D, Péré H, Robillard N, Saliba M, Baidaliuk A, Seve A, Hocqueloux L, Prazuck T, Rey FA, Mouquet H, Simon-Lorière E, Bruel T, Pawlotsky JM, Schwartz O. Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2. EBioMedicine 2022; 77:103934. [PMID: 35290827 PMCID: PMC8917961 DOI: 10.1016/j.ebiom.2022.103934] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SARS-CoV-2 lineages are continuously evolving. As of December 2021, the AY.4.2 Delta sub-lineage represented 20 % of sequenced strains in the UK and had been detected in dozens of countries. It has since then been supplanted by Omicron. The AY.4.2 spike displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. METHODS We compared the Delta and the AY.4.2 spikes, by assessing their binding to antibodies and ACE2 and their fusogenicity. We studied the sensitivity of an authentic AY.4.2 viral isolate to neutralizing antibodies. FINDINGS The AY.4.2 spike exhibited similar binding to all the antibodies and sera tested, and similar fusogenicity and binding to ACE2 than the ancestral Delta spike. The AY.4.2 virus was slightly less sensitive than Delta to neutralization by a panel of monoclonal antibodies; noticeably, the anti-RBD Imdevimab showed incomplete neutralization. Sensitivity of AY.4.2 to sera from vaccinated individuals was reduced by 1.3 to 3-fold, when compared to Delta. INTERPRETATION Our results suggest that mutations in the NTD remotely impair the efficacy of anti-RBD antibodies. The spread of AY.4.2 was not due to major changes in spike fusogenicity or ACE2 binding, but more likely to a partially reduced neutralization sensitivity. FUNDING The work was funded by Institut Pasteur, Fondation pour la Recherche Médicale, Urgence COVID-19 Fundraising Campaign of Institut Pasteur, ANRS, the Vaccine Research Institute, Labex IBEID, ANR/FRM Flash Covid PROTEO-SARS-CoV-2 and IDISCOVR.
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Affiliation(s)
- Nell Saunders
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Delphine Planas
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Creteil, France
| | - William H Bolland
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France; Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France; Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Slim Fourati
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France; Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Julian Buchrieser
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Matthieu Prot
- G5 Evolutionary genomics of RNA viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Isabelle Staropoli
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France
| | | | - Françoise Porrot
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France
| | - David Veyer
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France; INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | - Hélène Péré
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France; INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | - Nicolas Robillard
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France
| | - Madelina Saliba
- Hôpital Européen Georges Pompidou, Laboratoire de Virologie, Service de Microbiologie, Paris, France
| | - Artem Baidaliuk
- G5 Evolutionary genomics of RNA viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Aymeric Seve
- CHR d'Orléans, service de maladies infectieuses, Orléans, France
| | | | - Thierry Prazuck
- CHR d'Orléans, service de maladies infectieuses, Orléans, France
| | - Felix A Rey
- Structural Virology Unit Institut Pasteur, Université de Paris, CNRS UMR3569, 75015 Paris, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Etienne Simon-Lorière
- G5 Evolutionary genomics of RNA viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Creteil, France
| | - Jean-Michel Pawlotsky
- Department of Virology, Hôpital Henri Mondor (AP-HP), Université Paris-Est, Créteil, France; Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Creteil, France.
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Affiliation(s)
- Anna Wald
- Department of Medicine, Epidemiology, and Laboratory Medicine & Pathology, University of Washington, Seattle
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Focosi D, Maggi F, Franchini M, McConnell S, Casadevall A. Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Int J Mol Sci 2021; 23:29. [PMID: 35008446 PMCID: PMC8744556 DOI: 10.3390/ijms23010029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/31/2022] Open
Abstract
The accelerated SARS-CoV-2 evolution under selective pressure by massive deployment of neutralizing antibody-based therapeutics is a concern with potentially severe implications for public health. We review here reports of documented immune escape after treatment with monoclonal antibodies and COVID-19-convalescent plasma (CCP). While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), a few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of the spike protein (e.g., ΔHV69-70, ΔLGVY141-144 and ΔAL243-244). The continuous genomic monitoring of non-responders is needed to better understand immune escape frequencies and the fitness of emerging variants.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy;
- Laboratory of Microbiology, Azienda Socio Sanitaria Territoriale Sette Laghi, 21100 Varese, Italy
| | - Massimo Franchini
- Division of Transfusion Medicine, Carlo Poma Hospital, 46100 Mantua, Italy;
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health, Baltimore, MD 21218, USA; (S.M.); (A.C.)
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health, Baltimore, MD 21218, USA; (S.M.); (A.C.)
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
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Torbati E, Krause KL, Ussher JE. The Immune Response to SARS-CoV-2 and Variants of Concern. Viruses 2021; 13:1911. [PMID: 34696342 PMCID: PMC8537260 DOI: 10.3390/v13101911] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/07/2023] Open
Abstract
At the end of 2019 a newly emerged betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the cause of an outbreak of severe pneumonia, subsequently termed COVID-19, in a number of patients in Wuhan, China. Subsequently, SARS-CoV-2 rapidly spread globally, resulting in a pandemic that has to date infected over 200 million individuals and resulted in more than 4.3 million deaths. While SARS-CoV-2 results in severe disease in 13.8%, with increasing frequency of severe disease with age, over 80% of infections are asymptomatic or mild. The immune response is an important determinant of outcome following SARS-CoV-2 infection. While B cell and T cell responses are associated with control of infection and protection against subsequent challenge with SARS-CoV-2, failure to control viral replication and the resulting hyperinflammation are associated with severe COVID-19. Towards the end of 2020, several variants of concern emerged that demonstrate increased transmissibility and/or evasion of immune responses from prior SARS-CoV-2 infection. This article reviews what is known about the humoral and cellular immune responses to SARS-CoV-2 and how mutation and structural/functional changes in the emerging variants of concern impact upon the immune protection from prior infection or vaccination.
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Affiliation(s)
- Elham Torbati
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
| | - Kurt L. Krause
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand;
- Vaccine Alliance Aotearoa New Zealand, Malaghan Institute of Medical Research, Wellington 6242, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1142, New Zealand
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