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Li S, Zhang Y, Tong P, Yang W. Diagnosis with Metagenomic Next-Generation Sequencing (mNGS) technology and real-time PCR for SARS-CoV-2 Omicron detection using various nasopharyngeal swabs in SARS-CoV-2 Omicron. PLoS One 2024; 19:e0305289. [PMID: 39106263 DOI: 10.1371/journal.pone.0305289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/27/2024] [Indexed: 08/09/2024] Open
Abstract
BACKGROUND The SARS-CoV-2 Omicron variant, with the main subtypes BA.5.2 and BF.7 in China, led to off-target effects on the S and N genes from December 1, 2022, to January 31, 2023. The kits used for studying and developing these agents were not adequately and independently evaluated. It is important to verify the performance of commercial Real-Time quantitative PCR (RT-qPCR) tests. OBJECTIVE We conducted a clinical evaluation of two Real Time SARS-CoV-2 Omicron assays to verify their performance using various detection reagents and clinical specimens. METHODS We performed clinical evaluations of two existing Chinese SARS-CoV-2 Omicron RT-qPCR kits 2019-nCoV nucleic acid diagnostic kits (Fosun Biotechnology, National instrument registration 20203400299, Shanghai, China) and COVID-19 nucleic acid detection kits (eDiagnosis Biomedicine, National instrument registration 20203400212, Wuhan, China) and using BSD (Bondson) (Guangzhou Bondson Biotechnology Co. Ltd, batch number 2022101), quality controls provided by the inspection center and a large number of clinically confirmed specimens. RESULTS The concordance rates for the Fosun and eDiagnosis kits were 95% and 100%, respectively. The detection limit for the Fosun and eDiagnosis kits was verified to be 300 copies/mL and 500 copies/mL. The Fosun assay exhibited the largest coefficient of variation (CV) for ORF1ab and N gene at the detection limit concentration (4.80%, 3.49%), whereas eDiagnosis showed a smaller CV (0.93%, 1.10%). In the reference product from the Hangzhou Clinical Laboratory Center test, it was found that Fosun had the lowest sensitivity of 93.47% and a specificity of 100%, while eDiagnosis exhibited 100% for both sensitivity and specificity. The lowest single target gene detection rate of Fosun reagents was 68.7% for the ORF1ab gene and 87.5% for the N gene, while eDiagnosis detection rate was 100%. Among the clinical group S specimens, the missed detection rate of the Fosun reagent was 10.9%, which was higher than the 3.9% of eDiagnosis. However, there was no significant difference in the clinical diagnostic efficiency of the two reagents. CONCLUSIONS The ORF1ab and N assays of SARS-CoV-2 Omicron on the eDiagnosis platform yielded higher values compared to those on the Fosun platform. Consequently, the eDiagnosis kit has also been used as standard detection reagents. Considering that the Fosun reagent has a relatively low detection limit and targets three single genes, it is more advantageous as a confirmatory reagent for the new museum.
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Affiliation(s)
- Sujuan Li
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yuanhang Zhang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Pengcheng Tong
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Wei Yang
- Department of Clinical Laboratory, Hangzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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Colson P, Delerce J, Pontarotti P, Devaux C, La Scola B, Fantini J, Raoult D. Resistance-associated mutations to the anti-SARS-CoV-2 agent nirmatrelvir: Selection not induction. J Med Virol 2024; 96:e29462. [PMID: 38363015 DOI: 10.1002/jmv.29462] [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: 11/20/2023] [Revised: 01/21/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Mutations associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance to antiprotease nirmatrelvir were reported. We aimed to detect them in SARS-CoV-2 genomes and quasispecies retrieved in our institute before drug availability in January 2022 and to analyze the impact of mutations on protease (3CLpro) structure. We sought for 38 3CLpro nirmatrelvir resistance mutations in a set of 62 673 SARS-CoV-2 genomes obtained in our institute from respiratory samples collected between 2020 and 2023 and for these mutations in SARS-CoV-2 quasispecies for 90 samples collected in 2020, using Python. SARS-CoV-2 protease with major mutation E166V was generated with Swiss Pdb Viewer and Molegro Molecular Viewer. We detected 22 (58%) of the resistance-associated mutations in 417 (0.67%) of the genomes analyzed; 325 (78%) of these genomes had been obtained from samples collected in 2020-2021. APOBEC signatures were found for 12/22 mutations. We also detected among viral quasispecies from 90 samples some minority reads harboring any of 15 nirmatrelvir resistance mutations, including E166V. Also, we predicted that E166V has a very limited effect on 3CLpro structure but may prevent drug attachment. Thus, we evidenced that mutations associated with nirmatrelvir resistance pre-existed in SARS-CoV-2 before drug availability. These findings further warrant SARS-CoV-2 genomic surveillance and SARS-CoV-2 quasispecies characterization.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | | | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, Marseille, France
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, Marseille, France
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3
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Kampouri E, Hill JA, Dioverti V. COVID-19 after hematopoietic cell transplantation and chimeric antigen receptor (CAR)-T-cell therapy. Transpl Infect Dis 2023; 25 Suppl 1:e14144. [PMID: 37767643 DOI: 10.1111/tid.14144] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
More than 3 years have passed since Coronavirus disease 2019 (COVID-19) was declared a global pandemic, yet COVID-19 still severely impacts immunocompromised individuals including those treated with hematopoietic cell transplantation (HCT) and chimeric antigen receptor-T-cell therapies who remain at high risk for severe COVID-19 and mortality. Despite vaccination efforts, these patients have inadequate responses due to immunosuppression, which underscores the need for additional preventive approaches. The optimal timing, schedule of vaccination, and immunological correlates for protective immunity remain unknown. Antiviral therapies used early during disease can reduce mortality and severity due to COVID-19. The combination or sequential use of antivirals could be beneficial to control replication and prevent the development of treatment-related mutations in protracted COVID-19. Despite conflicting data, COVID-19 convalescent plasma remains an option in immunocompromised patients with mild-to-moderate disease to prevent progression. Protracted COVID-19 has been increasingly recognized among these patients and has been implicated in intra-host emergence of SARS-CoV-2 variants. Finally, novel SARS-CoV2-specific T-cells and natural killer cell-boosting (or -containing) products may be active against multiple variants and are promising therapies in immunocompromised patients.
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Affiliation(s)
- Eleftheria Kampouri
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Joshua A Hill
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Veronica Dioverti
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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4
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Talukder P, Saha A, Roy S, Ghosh G, Roy DD, Barua S. Drugs for COVID-19 Treatment: A New Challenge. Appl Biochem Biotechnol 2023; 195:3653-3670. [PMID: 36961509 PMCID: PMC10037400 DOI: 10.1007/s12010-023-04439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
COVID-19 infection is a new disease and our knowledge is limited; day in and day out more and more interesting yet diverse observations are reported by the different research groups from different corners of the world. So, there is an urgent requirement of the invention of some effective and efficient drugs that can carry out the end of the deadly viral infection. Throughout the world, there have been many efforts carried out in different labs to invent such a drug and also identifying any pre-existing drugs which can carry out the killing of the virus. In this review, an effort has been made to understand the potential drugs which can be used against the SARS-CoV-2 viral infection. Again, the strategies on the current and the future drug discovery mechanisms against the SARS-CoV-2 are also mentioned. The different drugs made and the drugs re-used and also the drugs which are in the making process in different research laboratories across the world are also mentioned. To combat this unexpected crisis, we still need some more efforts from the different scientific communities around the world for finding a cure against this viral infection and this is needed to be done for the prevention of more loss of human life.
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Affiliation(s)
- Pratik Talukder
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India.
| | - Arunima Saha
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Sohini Roy
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Gargi Ghosh
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Debshikha Dutta Roy
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
| | - Snejuti Barua
- Department of Biotechnology, University of Engineering and Management, Kolkata University Area, Plot, Street Number 03, Action Area III, B/5, Newtown, Kolkata, West Bengal, 700156, India
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5
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Dioverti V, Boghdadly ZE, Shahid Z, Waghmare A, Abidi MZ, Pergam S, Boeckh M, Dadwal S, Kamboj M, Seo S, Chemaly RF, Papanicolaou GA. Revised Guidelines for Coronavirus Disease 19 Management in Hematopoietic Cell Transplantation and Cellular Therapy Recipients (August 2022). Transplant Cell Ther 2022; 28:810-821. [PMID: 36103987 PMCID: PMC9464362 DOI: 10.1016/j.jtct.2022.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 01/17/2023]
Abstract
This document is intended as a guide for diagnosis and management of Coronavirus Disease 2019 (COVID-19), caused by the virus SARS-CoV-2, in adult and pediatric HCT and cellular therapy patients. This document was prepared using available data and with expert opinion provided by members of the (ASTCT) Infectious Diseases Special Interest Group (ID-SIG) and is an update of pervious publication. Since our original publication in 2020, the NIH and IDSA have published extensive guidelines for management of COVID-19 which are readily accessible ( NIH Guidelines , IDSA Guidelines ). This update focuses primarily on issues pertaining specifically to HCT/cellular therapy recipients. Information provided in this manuscript may change as new information becomes available.
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Affiliation(s)
- Veronica Dioverti
- Assistant Professor of Medicine, Johns Hopkins University, Baltimore, Maryland.
| | - Zeinab El Boghdadly
- Assistant Professor of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Zainab Shahid
- Attending physician, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alpana Waghmare
- Associate Professor of Pediatrics, University of Washington, Seattle, Washington; Fred Hutchinson Cancer Center, Seattle, Washington
| | - Maheen Z Abidi
- Assistant Professor of Medicine, University of Colorado, Denver, Colorado
| | - Steven Pergam
- Professor, Fred Hutchinson Cancer Research Center, Associate Professor, University of Washington, Seattle, Washington
| | - Michael Boeckh
- Fred Hutchinson Cancer Center, Seattle, Washington; Professor of Medicine, University of Washington, Seattle, Washington
| | | | - Mini Kamboj
- Associate Professor of Medicine, Weill Cornell Medical College, New York, New York; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan Seo
- Memorial Sloan Kettering Cancer Center, New York, New York; Professor of Clinical Medicine, Weill Cornell Medical College, New York, New York
| | - Roy F Chemaly
- Professor of Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Genovefa A Papanicolaou
- Memorial Sloan Kettering Cancer Center, New York, New York; Professor of Medicine, Weill Cornell Medical College, New York, New York
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6
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Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, Lavrard P, Bader W, Lagier JC, Fournier PE, La Scola B, Raoult D. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Sci Rep 2022; 12:18721. [PMID: 36333340 PMCID: PMC9636146 DOI: 10.1038/s41598-022-22060-z] [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: 07/12/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p < 0.001). In the detailed analysis, we found a greater difference between persistent and non-persistent patients with non-severe COVID 19, and between the two groups infected with clade 20A. Furthermore, we found minority N501Y and P681H mutation clouds in all patients, with no significant differences found both groups. The question of the SARS-CoV-2 viral variants' genesis remains to be further investigated, with the need to prevent new viral propagations and their consequences, and quasi-species analysis could be an important key to watch out.
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Affiliation(s)
- Pierre Dudouet
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Anthony Levasseur
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Mamadou Beye
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jeremy Delerce
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Emilie Burel
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Lavrard
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Wahiba Bader
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Bernard La Scola
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- grid.483853.10000 0004 0519 5986IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France ,grid.5399.60000 0001 2176 4817Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour Le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, Aix-Marseille Univ., 27 Boulevard Jean Moulin, 13005 Marseille, France
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COVID-19 Update: The Golden Time Window for Pharmacological Treatments and Low Dose Radiation Therapy. RADIATION 2022. [DOI: 10.3390/radiation2030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
At the beginning of the COVID-19 emergence, many scientists believed that, thanks to the proofreading enzyme of SARS-CoV-2, the virus would not have many mutations. Our team introduced the concept of radiation at extremely low doses in an attempt to establish selected pressure-free treatment approaches for COVID-19. The capacity of low-dose radiation to modulate excessive inflammatory responses, optimize the immune system, prevent the occurrence of dangerous cytokine storm, regulate lymphocyte counts, and control bacterial co-infections as well as different modalities were proposed as a treatment program for patients with severe COVID-19-associated pneumonia. There is now substantial evidence which indicates that it would be unwise not to further investigate low-dose radiation therapy (LDRT) as an effective remedy against COVID-19-associated pneumonia.
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Rivalta B, Amodio D, Giancotta C, Santilli V, Pacillo L, Zangari P, Cotugno N, Manno EC, Finocchi A, Bernardi S, Colagrossi L, Gentile L, Russo C, Perno CF, Rossi P, Cancrini C, Palma P. Case Report: Successful Treatment With Monoclonal Antibodies in One APDS Patient With Prolonged SARS-CoV-2 Infection Not Responsive to Previous Lines of Treatment. Front Immunol 2022; 13:891274. [PMID: 35799775 PMCID: PMC9253383 DOI: 10.3389/fimmu.2022.891274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/18/2022] [Indexed: 11/15/2022] Open
Abstract
We described the case of a patient affected by activated PI3K-kinase delta syndrome (APDS) and a long-lasting and pauci-symptomatic SARS-CoV-2 infection, treated with multiple therapeutic agents including remdesivir and SARS-CoV-2-neutralizing monoclonal antibodies. We detected the clearance of the virus 105 days from the first positive swab and 7 days after monoclonal antibody administration. At genotyping, the SARS-CoV-2 virus resulted as wild type on all samples tested. This case shows the monoclonal antibodies’ good tolerability and efficacy in reducing viral shedding in long-lasting infections refractory to other treatments.
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Affiliation(s)
- Beatrice Rivalta
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Donato Amodio
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Carmela Giancotta
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Veronica Santilli
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Lucia Pacillo
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Paola Zangari
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Nicola Cotugno
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Emma Concetta Manno
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Andrea Finocchi
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Stefania Bernardi
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Luna Colagrossi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Leonarda Gentile
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Cristina Russo
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Multimodal Medicine Research Area, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Paolo Rossi
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Caterina Cancrini
- Research Unit of Primary Immunodeficiencies, Immune and Infectious Diseases Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Paolo Palma
- Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
- Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics (DPUO), Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- *Correspondence: Paolo Palma,
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9
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Burel E, Colson P, Lagier JC, Levasseur A, Bedotto M, Lavrard-Meyer P, Fournier PE, La Scola B, Raoult D. Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient. Viruses 2022; 14:1266. [PMID: 35746737 PMCID: PMC9227898 DOI: 10.3390/v14061266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but only a single patient's sample was analyzed, and the virus was not isolated. Here, we report the gradual emergence of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and the recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. An analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient's follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying the genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the appearance of new viruses.
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Affiliation(s)
- Emilie Burel
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Marielle Bedotto
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
| | - Philippe Lavrard-Meyer
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (E.B.); (P.C.); (J.-C.L.); (A.L.); (M.B.); (P.L.-M.); (P.-E.F.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche Pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
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10
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Wassenaar TM, Wanchai V, Buzard G, Ussery DW. The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2. FEMS Microbiol Rev 2022; 46:fuac003. [PMID: 35076068 PMCID: PMC9075578 DOI: 10.1093/femsre/fuac003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 11/22/2022] Open
Abstract
The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020, there was a global wave of one variant that went largely unnoticed, possibly because its members were divided over several sublineages (B.1.177 and sublineages B.1.177.XX). We collectively call this Janus, and it was eventually replaced by the Alpha (B.1.1.7) variant of concern (VoC), next replaced by Delta (B.1.617.2), which itself might soon be replaced by a fourth pandemic wave consisting of Omicron (B.1.1.529). We observe that splitting up and redefining variant lineages over time, as was the case with Janus and is now happening with Alpha, Delta and Omicron, is not helpful to describe the epidemic waves spreading globally. Only ∼5% of the 30 000 nucleotides of the SARS-CoV-2 genome are found to be variable. We conclude that a fourth wave of the pandemic with the Omicron variant might not be that different from other VoCs, and that we may already have the tools in hand to effectively deal with this new VoC.
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Affiliation(s)
- Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576 Zotzenheim, Germany
| | - Visanu Wanchai
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 772205, USA
| | | | - David W Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 772205, USA
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11
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Giraud-Gatineau A, Kaba L, Boschi C, Devaux C, Casalta JP, Gautret P, Chaudet H, Colson P, Raoult D. Control of common viral epidemics but not of SARS-CoV-2 through the application of hygiene and distancing measures. J Clin Virol 2022; 150-151:105163. [PMID: 35472752 PMCID: PMC9013017 DOI: 10.1016/j.jcv.2022.105163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 03/12/2022] [Accepted: 04/13/2022] [Indexed: 12/21/2022]
Abstract
Background We systematically survey respiratory and gastrointestinal infections of viral origin in samples sent to our university hospital institute in Marseille, southern France. Here, we evaluated whether the measures implemented to fight COVID-19 had an effect on the dynamics of viral respiratory or gastrointestinal infections. Methods We analysed PCR performed and positive for the diagnoses of viral respiratory and gastrointestinal infections over five years (January 2017-February 2021). Data were collected from our epidemiological surveillance system (MIDaS). Dates and contents of French measures against SARS-CoV-2 were collected from: https://www.gouvernement.fr/info-coronavirus/les-actions-du-gouvernement. Results Over the 2017-2021 period, 990,364 analyses were carried out for respiratory infections not including SARS-CoV-2, 510,671 for SARS-CoV-2 and 27,719 for gastrointestinal infections. During winter 2020–2021, when the most restrictive lockdown measures were in place in France, a marked decrease of infections with influenza viruses (one case versus 1,839-1,850 cases during 2017-2020 cold seasons) and with the RSV (56 cases versus 988-1,196 cases during 2017-2020 cold seasons) was observed, demonstrating the relative effectiveness of these measures on their occurrence. SARS-CoV-2 incidence seemed far less affected. Rhinoviruses, parainfluenza 3 virus, and the coronavirus NL63 remained at comparable levels. Also, the norovirus winter season positivity rates decreased continuously and significantly over time from 9.3% in 2017–2018 to 2.0% in 2020–2021. Conclusion The measures taken to control COVID-19 were effective against lower respiratory tract infections viruses and gastroenteritis agents, but not on the agents of the common winter cold and SARS-CoV-2. This suggests that more specific measures to prevent COVID-19 and upper respiratory tract infections need to be discovered to limit the spread of this epidemic.
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Affiliation(s)
- Audrey Giraud-Gatineau
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), camp de Sainte Marthe, BP 40026, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Lancei Kaba
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France; Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Jean-Paul Casalta
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France;; French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), camp de Sainte Marthe, BP 40026, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.
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12
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Acharjee A, Stephen Kingsly J, Kamat M, Kurlawala V, Chakraborty A, Vyas P, Vaishnav R, Srivastava S. Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet? Expert Rev Proteomics 2022; 19:197-212. [PMID: 35655386 DOI: 10.1080/14789450.2022.2085564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The challenges posed by emergent strains of SARS-CoV-2 need to be tackled by contemporary scientific approaches, with proteomics playing a significant role. AREAS COVERED In this review, we provide a brief synthesis of the impact of proteomics technologies in elucidating disease pathogenesis and classifiers for the prognosis of COVID-19 and propose proteomics methodologies that could play a crucial role in understanding emerging variants and their altered disease pathology. From aiding the design of novel drug candidates to facilitating the identification of T cell vaccine targets, we have discussed the impact of proteomics methods in COVID-19 research. Techniques varied as mass spectrometry, single-cell proteomics, multiplexed ELISA arrays, high-density proteome arrays, surface plasmon resonance, immunopeptidomics, and in silico docking studies that have helped augment the fight against existing diseases were useful in preparing us to tackle SARS-CoV-2 variants. We also propose an action plan for a pipeline to combat emerging pandemics using proteomics technology by adopting uniform standard operating procedures and unified data analysis paradigms. EXPERT OPINION The knowledge about the use of diverse proteomics approaches for COVID-19 investigation will provide a framework for future basic research, better infectious disease prevention strategies, improved diagnostics, and targeted therapeutics.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Madhura Kamat
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | - Vishakha Kurlawala
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | | | - Priyanka Vyas
- Department of Biotechnology and Botany, Mahila PG Mahavidyalaya, J. N. V University, Jodhpur, India
| | - Radhika Vaishnav
- Department of Life Sciences, Ivy Tech Community College, Indianapolis, Indiana, USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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13
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Focosi D, Maggi F, McConnell S, Casadevall A. Very low levels of remdesivir resistance in SARS-COV-2 genomes after 18 months of massive usage during the COVID19 pandemic: A GISAID exploratory analysis. Antiviral Res 2022; 198:105247. [PMID: 35033572 PMCID: PMC8755559 DOI: 10.1016/j.antiviral.2022.105247] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Pisa, Italy.
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy; Laboratory of Microbiology, ASST Sette Laghi, Varese, 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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14
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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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15
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Sensitivity of two SARS-CoV-2 variants with spike protein mutations to neutralising antibodies. Virus Genes 2021; 57:502-509. [PMID: 34608598 PMCID: PMC8489549 DOI: 10.1007/s11262-021-01871-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 infections elicit a humoral immune response capable of neutralising the virus. However, multiple variants have emerged with mutations in the spike protein amongst others, the key target of neutralising antibodies. We evaluated the neutralising efficacy of 89 serum samples from patients, infected with SARS-CoV-2 in the beginning of 2020, against two virus variants isolated from acutely infected patients and harbouring spike protein mutations. One isolate was assigned to lineage B.1.351 (MUC-IMB-B.1.351) whilst the other (MUC-484) was isolated from an immunocompromised patient, sharing some but not all mutations with B.1.351 and representing a transitional variant. Both variants showed a significant reduction in neutralisation sensitivity compared to wild-type SARS-CoV-2 with MUC-IMB-B.1.351 being almost completely resistant to neutralisation. The observed reduction in neutralising activity of wild-type-specific antibodies against both variants suggests that individual mutations in the spike protein are sufficient to confer a potent escape from the humoral immune response. In addition, the effect of escape mutations seems to accumulate, so that more heavily mutated variants show a greater loss of sensitivity to neutralisation up to complete insensitivity as observed for MUC-IMB-B.1.351. From a clinical point of view, this might affect the efficacy of (monoclonal) antibody treatment of patients with prolonged infections as well as patients infected with variants other than the donor. At the same, this could also negatively influence the efficacy of current vaccines (as they are based on wild-type spike protein) emphasising the need to thoroughly surveil the emergence and distribution of variants and adapt vaccines and therapeutics accordingly.
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