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Zhao Z, Bashiri S, Ziora ZM, Toth I, Skwarczynski M. COVID-19 Variants and Vaccine Development. Viruses 2024; 16:757. [PMID: 38793638 PMCID: PMC11125726 DOI: 10.3390/v16050757] [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: 04/22/2024] [Revised: 05/08/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), the global pandemic caused by severe acute respiratory syndrome 2 virus (SARS-CoV-2) infection, has caused millions of infections and fatalities worldwide. Extensive SARS-CoV-2 research has been conducted to develop therapeutic drugs and prophylactic vaccines, and even though some drugs have been approved to treat SARS-CoV-2 infection, treatment efficacy remains limited. Therefore, preventive vaccination has been implemented on a global scale and represents the primary approach to combat the COVID-19 pandemic. Approved vaccines vary in composition, although vaccine design has been based on either the key viral structural (spike) protein or viral components carrying this protein. Therefore, mutations of the virus, particularly mutations in the S protein, severely compromise the effectiveness of current vaccines and the ability to control COVID-19 infection. This review begins by describing the SARS-CoV-2 viral composition, the mechanism of infection, the role of angiotensin-converting enzyme 2, the host defence responses against infection and the most common vaccine designs. Next, this review summarizes the common mutations of SARS-CoV-2 and how these mutations change viral properties, confer immune escape and influence vaccine efficacy. Finally, this review discusses global strategies that have been employed to mitigate the decreases in vaccine efficacy encountered against new variants.
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Affiliation(s)
- Ziyao Zhao
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Sahra Bashiri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia; (Z.Z.); (S.B.); (I.T.)
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2
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 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 Severe Acute Respiratory Syndrome Coronavirus 2 Variants in 245 Immunocompromised Patients: A Multicenter Prospective Cohort Study. Clin Infect Dis 2024:ciae026. [PMID: 38445721 DOI: 10.1093/cid/ciae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Boussen I, Salmona M, Sicre De Fontbrune F, Xhaard A, De Castro N, Delaugerre C, Chaix ML, Molina JM. Failure of bamlanivimab with selection of E484K mutation in an allogeneic stem cell transplant recipient with nosocomial SARS-CoV-2 infection. Antivir Ther 2024; 29:13596535221097495. [PMID: 38353416 DOI: 10.1177/13596535221097495] [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] [Indexed: 02/16/2024]
Abstract
We report the case of an allogeneic stem cell transplant recipient with nosocomial acquisition of SARS-CoV-2 infection who received antispike neutralizing monoclonal antibody bamlanivimab 2 days after diagnosis of SARS-CoV-2 infection but progressed to severe COVID-19 pneumonia and died with the selection of E484K/Q resistance mutations to bamlanivimab.
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Affiliation(s)
- Inès Boussen
- Department of Infectious Diseases, Saint Louis and Lariboisière Hospitals, APHP, Paris, France
| | - Maud Salmona
- Virology Department, Saint Louis Hospital, Paris, France
- INSERM U976, INSIGHT team, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | | | - Aliénor Xhaard
- Hematology and Transplantation Department, Saint Louis Hospital, Paris, France
| | - Nathalie De Castro
- Department of Infectious Diseases, Saint Louis and Lariboisière Hospitals, APHP, Paris, France
| | - Constance Delaugerre
- Virology Department, Saint Louis Hospital, Paris, France
- INSERM U944, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | - Marie-Laure Chaix
- Virology Department, Saint Louis Hospital, Paris, France
- INSERM U944, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | - Jean-Michel Molina
- Department of Infectious Diseases, Saint Louis and Lariboisière Hospitals, APHP, Paris, France
- INSERM U944, Institut de Recherche Saint Louis, Université de Paris, Paris, France
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Focosi D, McConnell S, Sullivan DJ, Casadevall A. Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment. Drug Resist Updat 2023; 71:100991. [PMID: 37572569 DOI: 10.1016/j.drup.2023.100991] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/18/2023] [Accepted: 07/30/2023] [Indexed: 08/14/2023]
Abstract
The mutation rate of the Omicron sublineage has led to baseline resistance against all previously authorized anti-Spike monoclonal antibodies (mAbs). Nevertheless, in case more antiviral mAbs will be authorized in the future, it is relevant to understand how frequently treatment-emergent resistance has emerged so far, under different combinations and in different patient subgroups. We report the results of a systematic review of the medical literature for case reports and case series for treatment-emergent immune escape, which is defined as emergence of a resistance-driving mutation in at least 20% of sequences in a given host at a given timepoint. We identified 32 publications detailing 216 cases that included different variants of concern (VOC) and found that the incidence of treatment emergent-resistance ranged from 10% to 50%. Most of the treatment-emergent resistance events occurred in immunocompromised patients. Interestingly, resistance also emerged against cocktails of two mAbs, albeit at lower frequencies. The heterogenous therapeutic management of those cases doesn't allow inferences about the clinical outcome in patients with treatment-emergent resistance. Furthermore, we noted a temporal correlation between the introduction of mAb therapies and a subsequent increase in SARS-CoV-2 sequences across the globe carrying mutations conferring resistance to that mAb, raising concern as to whether these had originated in mAb-treated individuals. Our findings confirm that treatment-emergent immune escape to anti-Spike mAbs represents a frequent and concerning phenomenon and suggests that these are associated with mAb use in immunosuppressed hosts.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Italy.
| | - Scott McConnell
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David J Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [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: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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Devaux CA, Fantini J. Possible contribution of rare alleles of human ACE2 in the emergence of SARS-CoV-2 variants escaping the immune response. Front Immunol 2023; 14:1252367. [PMID: 37885880 PMCID: PMC10598458 DOI: 10.3389/fimmu.2023.1252367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
Since the start of the SARS-CoV-2 pandemic, the rapid replacement of one lineage by another has been observed. Indeed, SARS-CoV-2 is evolving through a quasispecies mechanism leading to post-infection mutation selection under positive evolutionary pressure (host-driven viral evolution). These mutations may reduce the effectiveness of the specific neutralizing immune response against the virus. We provide here evidence that apart from the selection of SARS-CoV-2 variants by the immune system, selection by the cellular receptor can just as well select variants which escape neutralization.
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Affiliation(s)
- Christian A. Devaux
- Institut National des Sciences Biologiques (INSB), Centre National de la Recherche Scientifique (CNRS), Marseille, France
- Microbes, Evolution, Phylogénie et Infections, Faculté de Pharmacie, Aix Marseille Université, Marseille, France
| | - Jacques Fantini
- Institut National de la Santé et de la Recherche Médicale (INSERM) U_1072, Faculté des Sciences, Aix-Marseille Université, Marseille, France
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Ku JH, Sy LS, Qian L, Ackerson BK, Luo Y, Tubert JE, Lee GS, Florea A, Bruxvoort KJ, Talarico CA, Qiu S, Tian Y, Tseng HF. Vaccine effectiveness of the mRNA-1273 3-dose primary series against COVID-19 in an immunocompromised population: A prospective observational cohort study. Vaccine 2023:S0264-410X(23)00498-X. [PMID: 37173268 PMCID: PMC10154542 DOI: 10.1016/j.vaccine.2023.04.075] [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: 01/19/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Data on the effectiveness of the 3-dose mRNA-1273 primary series are limited, particularly in comparison to 2 doses. Given suboptimal COVID-19 vaccine uptake among immunocompromised populations, it is important to monitor the effectiveness of fewer than the recommended doses in this population. METHODS We conducted a matched cohort study at Kaiser Permanente Southern California to evaluate the relative vaccine effectiveness (rVE) of the 3-dose series vs 2 doses of mRNA-1273 in preventing SARS-CoV-2 infection and severe COVID-19 outcomes among immunocompromised individuals. RESULTS We included 21,942 3-dose recipients who were 1:1 matched with randomly selected 2-dose recipients (third doses accrued 08/12/2021-12/31/2021, with follow-up through 01/31/2022). Adjusted rVE of 3 vs 2 doses of mRNA-1273 against SARS-CoV-2 infection, COVID-19 hospitalization, and COVID-19 hospital death were 55.0 % (95 % CI: 50.8-58.9 %), 83.0 % (75.4-88.3 %), and 87.1 % (30.6-97.6 %), respectively. CONCLUSION Three doses of mRNA-1273 were associated with a significantly higher rVE against SARS-CoV-2 infection and severe outcomes, compared to 2 doses. These findings were consistent across subgroups of demographic and clinical characteristics, and mostly consistent across subgroups of immunocompromising conditions. Our study highlights the importance of completing the 3-dose series for immunocompromised populations.
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Affiliation(s)
- Jennifer H Ku
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA.
| | - Lina S Sy
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Lei Qian
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Bradley K Ackerson
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Yi Luo
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Julia E Tubert
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Gina S Lee
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Ana Florea
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Katia J Bruxvoort
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA; Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35233, USA
| | | | - Sijia Qiu
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Yun Tian
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA
| | - Hung Fu Tseng
- Department of Research and Evaluation, Kaiser Permanente Southern California, 100 S. Los Robles Ave., Pasadena, CA 91101, USA; Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, 98 S. Los Robles Ave., Pasadena, CA 91101, USA
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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: 4] [Impact Index Per Article: 4.0] [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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Focosi D, McConnell S, Casadevall A. The Omicron variant of concern: Diversification and convergent evolution in spike protein, and escape from anti-Spike monoclonal antibodies. Drug Resist Updat 2022; 65:100882. [PMID: 36260961 PMCID: PMC9528072 DOI: 10.1016/j.drup.2022.100882] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 01/17/2023]
Abstract
WHO-defined SARS-CoV-2 variants of concern (VOC) drive therapeutics and vaccine development. The Omicron VOC is dominating the arena since November 2021, but the number of its sublineages is growing in complexity. Omicron represent a galaxy with a myriad of stars that suddenly rise and expand before collapsing into apparent extinction when a more fit sublineage appears. This has already happened with BA.1, BA.2, and BA.4/5 and is happening with BA.2.75. We review here the current PANGO phylogeny, focusing on sublineages with Spike mutations, and show how frequently xxxxxxxx convergent evolution has occurred in these sublineages. We finally summarize how Omicron evolution has progressively defeated the anti-Spike monoclonal antibodies authorized so far, leaving clinicians to again fall back on COVID19 convalescent plasma from vaccinated donors as the only antibody-based therapy available.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health and School of Medicine, Baltimore, MD, USA
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11
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Simons LM, Ozer EA, Gambut S, Dean TJ, Zhang L, Bhimalli P, Schneider JR, Mamede JI, Ison MG, Karmali R, Gordon LI, Lorenzo-Redondo R, Hultquist JF. De novo emergence of SARS-CoV-2 spike mutations in immunosuppressed patients. Transpl Infect Dis 2022; 24:e13914. [PMID: 35899968 PMCID: PMC9353292 DOI: 10.1111/tid.13914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/21/2022] [Accepted: 06/30/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND The continuing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with decreased susceptibility to neutralizing antibodies is of clinical importance. Several spike mutations associated with immune escape have evolved independently in association with different variants of concern (VOCs). How and when these mutations arise is still unclear. We hypothesized that such mutations might arise in the context of persistent viral replication in immunosuppressed hosts. METHODS Nasopharyngeal specimens were collected longitudinally from two immunosuppressed patients with persistent SARS-CoV-2 infection. Plasma was collected from these same patients late in disease course. SARS-CoV-2 whole genome sequencing was performed to assess the emergence and frequency of mutations over time. Select Spike mutations were assessed for their impact on viral entry and antibody neutralization in vitro. RESULTS Our sequencing results revealed the intrahost emergence of spike mutations that are associated with circulating VOCs in both immunosuppressed patients (del241-243 and E484Q in one patient, and E484K in the other). These mutations decreased antibody-mediated neutralization of pseudotyped virus particles in cell culture, but also decreased efficiency of spike-mediated cell entry. CONCLUSIONS These observations demonstrate the de novo emergence of SARS-CoV-2 spike mutations with enhanced immune evasion in immunosuppressed patients with persistent infection. These data suggest one potential mechanism for the evolution of VOCs and emphasize the importance of continued efforts to develop antiviral drugs for suppression of viral replication in hospitalized settings.
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Affiliation(s)
- Lacy M. Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Stephanie Gambut
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Taylor J. Dean
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Li Zhang
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Pavan Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - João I. Mamede
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA
| | - Michael G. Ison
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Surgery, Division of Organ Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Reem Karmali
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Chicago, IL, USA
| | - Leo I. Gordon
- Department of Medicine, Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
| | - Judd F. Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, USA
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12
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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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13
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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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14
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Focosi D, Maggi F, McConnell S, Casadevall A. Spike mutations in SARS-CoV-2 AY sublineages of the Delta variant of concern: implications for the future of the pandemic. Future Microbiol 2022; 17:219-221. [PMID: 35164530 PMCID: PMC8846359 DOI: 10.2217/fmb-2021-0286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Daniele Focosi
- 1North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy,Author for correspondence:
| | - Fabrizio Maggi
- 2Department of Medicine & Surgery, University of Insubria, Varese, Italy,3Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy
| | - Scott McConnell
- 4Department of Medicine, Johns Hopkins School of Public Health & School of Medicine, Baltimore, MD 21287, USA
| | - Arturo Casadevall
- 4Department of Medicine, Johns Hopkins School of Public Health & School of Medicine, Baltimore, MD 21287, USA
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15
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front Immunol 2022; 13:801522. [PMID: 35222380 PMCID: PMC8863680 DOI: 10.3389/fimmu.2022.801522] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants' immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants' partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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16
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Convalescent plasma improves overall survival in patients with B-cell lymphoid malignancy and COVID-19: a longitudinal cohort and propensity score analysis. Leukemia 2022; 36:1025-1034. [PMID: 35105946 PMCID: PMC8805670 DOI: 10.1038/s41375-022-01511-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/01/2022] [Accepted: 01/17/2022] [Indexed: 12/26/2022]
Abstract
Patients with hematological malignancy and COVID-19 display a high mortality rate. In such patients, immunosuppression due to underlying disease and previous specific treatments impair humoral response, limiting viral clearance. Thus, COVID-19 convalescent plasma (CCP) therapy appears as a promising approach through the transfer of neutralizing antibodies specific to SARS-CoV-2. We report the effect of CCP in a cohort of 112 patients with hematological malignancy and COVID-19 and a propensity score analysis on subgroups of patients with B-cell lymphoid disease treated (n = 81) or not (n = 120) with CCP between May 1, 2020 and April 1, 2021. The overall survival of the whole cohort was 65% (95% CI = 56-74.9) and 77.5% (95% CI = 68.5-87.7) for patients with B-cell neoplasm. Prior anti-CD20 monoclonal antibody therapy was associated with better overall survival, whereas age, high blood pressure, and COVID-19 severity were associated with a poor outcome. After an inverse probability of treatment weighting approach, we observed in anti-CD20-exposed patients with B-cell lymphoid disease a decreased mortality of 63% (95% CI = 31-80) in the CCP-treated group compared to the CCP-untreated subgroup, confirmed in the other sensitivity analyses. Convalescent plasma may be beneficial in COVID-19 patients with B-cell neoplasm who are unable to mount a humoral immune response.
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17
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Sabin AP, Richmond CS, Kenny PA. Emergence and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient. Diagn Microbiol Infect Dis 2022; 103:115656. [PMID: 35231807 PMCID: PMC8810429 DOI: 10.1016/j.diagmicrobio.2022.115656] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 02/08/2023]
Abstract
The implementation of monoclonal antibody therapeutics during the COVID-19 pandemic altered the selective pressures encountered by SARS-CoV-2, raising the possibility of selection for resistant variants. Within-host viral evolution was reported in treated immunocompromised individuals but whether this signifies a real risk of onward transmission is unclear. We used a regional SARS-CoV-2 sequencing program to monitor lineages with clinically relevant variants in identified patients, which facilitated analysis of parameters potentially relevant to new variant emergence. Here we describe a newly acquired spike E484K mutation detected within the B.1.311 lineage. Multiple individuals in 2 households of the same extended family were infected. The timing and patterns of spread were consistent with de novo emergence of this E484K variant in the bamlanivimab-treated index patient. Our study suggests that the selective pressures introduced by the widespread administration of these antibodies may warrant increased genomic surveillance to identify and mitigate spread of therapy-induced variants.
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18
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Bao H, Guo Y, Chang MH, McSweeney T, Golia AM, Cowman K, Bartash R, Anosike BI, Nori P. Expanding the scope and visibility of ambulatory stewardship programs with novel coronavirus disease 2019 (COVID-19) therapeutics. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e73. [PMID: 36483336 PMCID: PMC9726567 DOI: 10.1017/ash.2022.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 05/07/2023]
Abstract
Antimicrobial stewardship programs (ASPs) can be expanded to the outpatient setting to serve as a first line of defense against coronavirus disease 19 (COVID-19) hospitalizations and to reduce the burden on emergency departments and acute-care hospitals. Given the numerous emergency use authorizations of monoclonal antibodies and oral antivirals, ASPs possess the expertise and leadership to direct ambulatory COVID-19 initiatives and transform it into a predominantly outpatient illness. In this review, we summarize the critical role and benefits of an ASP-championed ambulatory COVID-19 therapeutics program.
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Affiliation(s)
- Hongkai Bao
- Department of Pharmacy, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
- Author for correspondence: Hongkai Bao, Department of Pharmacy, Montefiore Health System, Wakefield Division, 600 E 233rd Street G-55, Bronx, NY10466. E-mail:
| | - Yi Guo
- Department of Pharmacy, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Mei H. Chang
- Department of Pharmacy, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Terrence McSweeney
- Department of Pharmacy, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Austin M. Golia
- Department of Pharmacy, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Kelsie Cowman
- Network Performance Group, Montefiore Health System, Bronx, New York
- Division of Infectious Diseases, Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Rachel Bartash
- Division of Infectious Diseases, Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Brenda I. Anosike
- Division of Infectious Diseases, Children’s Hospital at Montefiore, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
| | - Priya Nori
- Division of Infectious Diseases, Department of Medicine, Montefiore Health System, Albert Einstein College of Medicine, Bronx, New York
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19
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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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20
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Bronstein Y, Adler A, Katash H, Halutz O, Herishanu Y, Levytskyi K. Evolution of spike mutations following antibody treatment in two immunocompromised patients with persistent COVID-19 infection. J Med Virol 2021; 94:1241-1245. [PMID: 34755363 PMCID: PMC8661643 DOI: 10.1002/jmv.27445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/07/2021] [Indexed: 01/02/2023]
Abstract
Immunocompromised patients have an increased risk of persistent COVID‐19 disease. We report here the clinical course of two patients with hematologic malignancies hospitalized due to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection. In both patients, viral evolution including new spike gene mutations that occurred following treatment with anti‐SARS‐CoV‐2 antibodies preparations, including convalescent plasma and bamlanivimab. These cases demonstrate the possibility of antibody‐resistant SARS‐CoV‐2 infections evolution in immunocompromised patients. Patients with hematologic malignancies are at risk of persistent SARS‐CoV‐2 infection. Using anti‐SRAS‐CoV‐2 antibody preparations in immunocompromised patients may lead to the evolution of antibody‐resistant SRAS‐CoV‐2 infections. Antibody‐resistant SRAS‐CoV‐2 infections might have severe epidemiological implications.
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Affiliation(s)
- Yotam Bronstein
- Department of Internal Medicine D, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Adler
- Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haytham Katash
- Department of Internal Medicine B, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ora Halutz
- Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yair Herishanu
- Department of Hematology, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katia Levytskyi
- Clinical Microbiology Laboratory, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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21
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Early Administration of Bamlanivimab in Combination with Etesevimab Increases the Benefits of COVID-19 Treatment: Real-World Experience from the Liguria Region. J Clin Med 2021; 10:jcm10204682. [PMID: 34682805 PMCID: PMC8538905 DOI: 10.3390/jcm10204682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/22/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Monoclonal antibodies, such as bamlanivimab and etesevimab combination (BEC), have been proposed for patients with mild or moderate coronavirus disease 2019 (COVID-19). However, few studies have assessed the factors associated with the early administration of BEC or the impact of early BEC treatment on the clinical evolution of the patients. We conducted a retrospective cohort study of all adults with COVID-19 who received BEC at three institutions in the Liguria region. The primary endpoint was to investigate the clinical variables associated with early BEC infusion. Secondary endpoints were 30-day overall mortality and the composite endpoint of requirement of hospital admission or need for supplemental oxygen during the 30-day follow-up period. A total of 127 patients (median age 70 years; 56.7% males) received BEC. Of those, 93 (73.2%) received BEC within 5 days from symptoms onset (early BEC). Patients with a higher Charlson comorbidity index were more likely to receive early treatment (odds ratio (OR) 1.60, 95% confidence interval (CI) 1.04–2.45; p = 0.03) in contrast to those reporting fever at presentation (OR 0.26, 0.08–0.82; p = 0.02). Early BEC was associated with lower likelihood of hospital admission or need for supplemental oxygen (OR 0.19, 0.06–0.65; p = 0.008). Five patients who received early BEC died during the follow-up period, but only one of them due to COVID-19-related causes. Early bamlanivimab and etesevimab combination was more frequently administered to patients with a high Charlson comorbidity index. Despite this, early BEC was associated with a lower rate of hospital admission or need for any supplementary oxygen compared to late administration. These results suggest that efforts should focus on encouraging early BEC use in patients with mild–moderate COVID-19 at risk for complications.
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22
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Angarone M, Kumar RN, Stosor V. Organ transplant patients, COVID-19, and neutralizing monoclonal antibodies: The glass is half full. Transpl Infect Dis 2021; 23:e13724. [PMID: 34534401 PMCID: PMC8646454 DOI: 10.1111/tid.13724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/11/2023]
Affiliation(s)
- Michael Angarone
- Division of Infectious DiseasesNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Rebecca N. Kumar
- Division of Infectious Diseases and Tropical MedicineGeorgetown University Medical CenterWashington, D.C.USA
| | - Valentina Stosor
- Division of Infectious DiseasesNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
- Division of Organ TransplantationNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
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23
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Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2. Viruses 2021; 13:v13081642. [PMID: 34452507 PMCID: PMC8402761 DOI: 10.3390/v13081642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
An Emergency Use Authorization was issued in the United States and in Europe for a monoclonal antibody monotherapy to prevent severe COVID-19 in high-risk patients. This study aimed to assess the risk of emergence of mutations following treatment with a single monoclonal antibody. Bamlanivimab was administered at a single dose of 700 mg in a one-hour IV injection in a referral center for the management of COVID-19 in France. Patients were closely monitored clinically and virologically with nasopharyngeal RT-PCR and viral whole genome sequencing. Six patients were treated for a nosocomial SARS-CoV-2 infection, all males, with a median age of 65 years and multiple comorbidities. All patients were infected with a B.1.1.7 variant, which was the most frequent variant in France at the time, and no patients had E484 mutations at baseline. Bamlanivimab was infused in the six patients within 4 days of the COVID-19 diagnosis. Four patients had a favorable outcome, one died of complications unrelated to COVID-19 or bamlanivimab, and one kidney transplant patient treated with belatacept died from severe COVID-19 more than 40 days after bamlanivimab administration. Virologically, four patients cleared nasopharyngeal viral shedding within one month after infusion, while two presented prolonged viral excretion for more than 40 days. The emergence of E484K mutants was observed in five out of six patients, and the last patient presented a Q496R mutation potentially associated with resistance. CONCLUSIONS: These results show a high risk of emergence of resistance mutants in COVID-19 patients treated with monoclonal antibody monotherapy.
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24
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Truffot A, Andréani J, Le Maréchal M, Caporossi A, Epaulard O, Germi R, Poignard P, Larrat S. SARS-CoV-2 Variants in Immunocompromised Patient Given Antibody Monotherapy. Emerg Infect Dis 2021; 27:2725-2728. [PMID: 34352197 PMCID: PMC8462331 DOI: 10.3201/eid2710.211509] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A 72-year-old immunocompromised man infected with severe acute respiratory syndrome coronavirus 2 received bamlanivimab monotherapy. Viral evolution was monitored in nasopharyngeal and blood samples by melting curve analysis of single-nucleotide polymorphisms and whole-genome sequencing. Rapid emergence of spike receptor binding domain mutations was found, associated with a compartmentalization of viral populations.
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25
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Pommeret F, Colomba J, Bigenwald C, Laparra A, Bockel S, Bayle A, Michot JM, Hueso T, Albiges L, Tiberghien P, Marot S, Jary A, Lacombe K, Barlesi F, Griscelli F, Colomba E. Bamlivimab + etesevimab therapy induces SARS-COV-2 immune escape mutations and secondary clinical deterioration in Covid-19 patients with B cell malignancies. Ann Oncol 2021; 32:1445-1447. [PMID: 34352377 PMCID: PMC8326208 DOI: 10.1016/j.annonc.2021.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- F Pommeret
- Department of Medical Oncology, Gustave Roussy, Villejuif, France.
| | - J Colomba
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - C Bigenwald
- Department of Hematology, Gustave Roussy, Villejuif, France
| | - A Laparra
- Department of Therapeutic Innovation and Early Trials, Gustave Roussy, Villejuif, France
| | - S Bockel
- Department of Radiotherapy, Gustave Roussy, Villejuif, France
| | - A Bayle
- Department of Therapeutic Innovation and Early Trials, Gustave Roussy, Villejuif, France
| | - J-M Michot
- Department of Therapeutic Innovation and Early Trials, Gustave Roussy, Villejuif, France
| | - T Hueso
- Department of Hematology, Gustave Roussy, Villejuif, France
| | - L Albiges
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - P Tiberghien
- Etablissement Français du Sang, La Plaine St-Denis, Saint-Denis, France; UMR RIGHT 1098 Inserm, Etablissement Français du Sang, Université de Franche-Comté, Besançon, France
| | - S Marot
- Virologie, Pitié-Salpêtrière, AP-HP, Sorbonne Université, Paris, France
| | - A Jary
- Virologie, Pitié-Salpêtrière, AP-HP, Sorbonne Université, Paris, France
| | - K Lacombe
- Inserm IPLESP, Sorbonne Université, Hôpital St Antoine, AP-HP, Paris, France
| | - F Barlesi
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Aix-Marseille University, CRCM, INSERM, CNRS, Marseille, France
| | | | - E Colomba
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
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26
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Chakraborty C, Bhattacharya M, Sharma AR. Present variants of concern and variants of interest of severe acute respiratory syndrome coronavirus 2: Their significant mutations in S‐glycoprotein, infectivity, re‐infectivity, immune escape and vaccines activity. Rev Med Virol 2021. [PMCID: PMC8420283 DOI: 10.1002/rmv.2270] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Newly arising variants of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are now a threat to global public health and are creating COVID‐19 surges in different countries. At the same time, there is limited knowledge about these emerging variants. Even if research data are available, it is varyingly scattered. In this review, we have discussed the appearance of significant alarming SARS‐CoV‐2 variants in the entire world. The study also discusses the properties of the substantial variant of concern (VOC) variants such as B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.427 (Epsilon) and B.1.429 (Epsilon). At the same time, the characteristic properties of some significant variant of interest (VOI) variants like B.1.525 (Eta), B.1.526 (Iota) (sublineage B.1.526.1), B.1.617 (sublineages B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3), P.2 (Zeta), P.3 (Theta), B.1.616 and B.1.427 have also been discussed. Here, we have explained some essential mutations for the VOC and VOI variants such as K417T/N, L452R, E484K, N501Y, D614G and P681R. Consecutively, we also highlighted the crucial clinical characteristics of the variants, such as transmissibility, infectivity, re‐infectivity, immune escape, vaccine activity and vaccine escape. Our comprehensive review will provide updated information on the newly appearing variants of SARS‐CoV‐2 and help the researchers to formulate strategies to curtail the COVID‐19 pandemic.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology School of Life Science and Biotechnology Adamas University Kolkata West Bengal India
| | | | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery Hallym University‐Chuncheon Sacred Heart Hospital Chuncheon‐si Gangwon‐do South Korea
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27
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Lee HK, Knabl L, Knabl L, Wieser M, Mur A, Zabernigg A, Schumacher J, Kaiser N, Furth PA, Hennighausen L. Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.27.21257952. [PMID: 34100027 PMCID: PMC8183026 DOI: 10.1101/2021.05.27.21257952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. B.1.1.7 (VOC-202012/01) has become the predominant variant in many countries and a new lineage (VOC-202102/02) harboring the E484K escape mutation in the B.1.1.7 background emerged in February 2021 1 . This variant is of concern due to reduced neutralizing activity by vaccine-elicited antibodies 2,3 . However, it is not known whether this single amino acid change leads to an altered immune response. Here, we investigate differences in the immune transcriptome in hospitalized patients infected with either B.1.1.7 (n=28) or B.1.1.7+E484K (n=12). RNA-seq conducted on PBMCs isolated within five days after the onset of COVID symptoms demonstrated elevated activation of specific immune pathways, including JAK-STAT signaling, in B.1.1.7+E484K patients as compared to B.1.1.7. Longitudinal transcriptome studies demonstrated a delayed dampening of interferon-activated pathways in B.1.1.7+E484K patients. Prior vaccination with BNT162b vaccine (n=8 one dose; n=1 two doses) reduced the transcriptome inflammatory response to B.1.1.7+E484K infection relative to unvaccinated patients. Lastly, the immune transcriptome of patients infected with additional variants (B.1.258, B.1.1.163 and B.1.7.7) displayed a reduced activation compared to patients infected with B.1.1.7. Acquisition of the E484K substitution in the B.1.1.7 background elicits an altered immune response, which could impact disease progression.
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Affiliation(s)
- Hye Kyung Lee
- National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | | | | | - Anna Mur
- Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria
| | - August Zabernigg
- Division of Internal Medicine, Krankenhaus Kufstein, Kufstein, Austria
| | - Jana Schumacher
- Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria
| | - Norbert Kaiser
- Division of Internal Medicine, Krankenhaus St. Johann, St. Johann, Austria
| | - Priscilla A. Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
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