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Pasev M, Trifonova A, Velichkov A, Terzieva V. Duration of antibody response to the receptor binding domain of SARS-CoV-2 in infected or vaccinated individuals - A one year retrospective cohort study. Int Immunopharmacol 2024; 133:112084. [PMID: 38621337 DOI: 10.1016/j.intimp.2024.112084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
The 2019 coronavirus (COVID-19) pandemic raised many scientific and medical questions. Of interest are the duration and effectiveness of the humoral immune response, especially since part of the pandemic occurred in the presence of anti-SARS-CoV-2 vaccines. We retrospectively studied 564 serum samples from 393 post-infected and vaccinated individuals to investigate the longevity and magnitude of the anti-spike IgG response. Our results showed that SARS-CoV-2 anti-spike IgG antibodies are retained for nine-twelve months, in both groups. In the vaccinated group we found higher IgG levels, but with a steeper decrease in titer over the study period. The recovered group's antibody levels correlated well with the national infection trendline for 2021. Both groups showed different, but distinct neutralizing capabilities towards RBD. The anti-Spike IgG response was sustained and efficient, independently of the triggering event, infection or vaccination, with the adaptive capacity against new viral variants being more valuable after infection.
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Affiliation(s)
- Martin Pasev
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria
| | - Angelina Trifonova
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria
| | - Andrey Velichkov
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov", Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Velislava Terzieva
- Department of Clinical Microbiology and Virology, University Hospital Lozenetz, Sofia University "Sv. Kliment Ohridski", Sofia, Bulgaria; Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction "Acad. Kiril Bratanov", Bulgarian Academy of Sciences, Sofia, Bulgaria.
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Yang CR, Chang SY, Gong YN, Huang CG, Tung TH, Liu W, Chan TC, Hung KS, Shang HS, Tsai JJ, Kao CL, Wu HL, Daisy Liu LY, Lin WY, Fan YC, King CC, Ku CC. The emergence and successful elimination of SARS-CoV-2 dominant strains with increasing epidemic potential in Taiwan's 2021 outbreak. Heliyon 2023; 9:e22436. [PMID: 38107297 PMCID: PMC10724543 DOI: 10.1016/j.heliyon.2023.e22436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Taiwan's experience with severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003 guided its development of strategies to defend against SARS-CoV-2 in 2020, which enabled the successful control of Coronavirus disease 2019 (COVID-19) cases from 2020 through March 2021. However, in late-April 2021, the imported Alpha variant began to cause COVID-19 outbreaks at an exceptional rate in Taiwan. In this study, we aimed to determine what epidemiological conditions enabled the SARS-CoV-2 Alpha variant strains to become dominant and decline later during a surge in the outbreak. In conjunction with contact-tracing investigations, we used our bioinformatics software, CoVConvert and IniCoV, to analyze whole-genome sequences of 101 Taiwan Alpha strains. Univariate and multivariable regression analyses revealed the epidemiological factors associated with viral dominance. Univariate analysis showed the dominant Alpha strains were preferentially selected in the surge's epicenter (p = 0.0024) through intensive human-to-human contact and maintained their dominance for 1.5 months until the Zero-COVID Policy was implemented. Multivariable regression found that the epidemic periods (p = 0.007) and epicenter (p = 0.001) were two significant factors associated with the dominant virus strains spread in the community. These dominant virus strains emerged at the outbreak's epicenter with frequent human-to-human contact and low vaccination coverage. The Level 3 Restrictions and Zero-COVID policy successfully controlled the outbreak in the community without city lockdowns. Our integrated method can identify the epidemiological conditions for emerging dominant virus with increasing epidemiological potential and support decision makers in rapidly containing outbreaks using public health measures that target fast-spreading virus strains.
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Affiliation(s)
- Chin-Rur Yang
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
| | - Sui-Yuan Chang
- Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
- Dept. of Laboratory Medicine, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
- Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
| | - Chung-Guei Huang
- Dept. of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, 33302, Taiwan, ROC
- Dept. of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan, ROC
| | - Tsung-Hua Tung
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
- Dept. of Health, Taipei City Government, Taipei, Taiwan, ROC
| | - Wei Liu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Ta-Chien Chan
- Research Center for Humanities and Social Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Dept. of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 11490, Taiwan, ROC
| | - Jih-Jin Tsai
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan, ROC
- Tropical Medicine Center, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, 80756, Taiwan, ROC
| | - Chuan-Liang Kao
- Department (Dept.) of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Hui-Lin Wu
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, 10051, Taiwan, ROC
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan, ROC
| | - Li-Yu Daisy Liu
- Division of Biometry, Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan, ROC
| | - Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Yi-Chin Fan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, NTU 17 Xu-Zhou Road, Taipei, 10055, Taiwan, ROC
| | - Chia-Chi Ku
- Graduate Institute of Immunology, College of Medicine, National Taiwan University, 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, ROC
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Treeza M M, Augustine S, Mathew AA, Kanthlal S, Panonummal R. Targeting Viral ORF3a Protein: A New Approach to Mitigate COVID-19 Induced Immune Cell Apoptosis and Associated Respiratory Complications. Adv Pharm Bull 2023; 13:678-687. [PMID: 38022818 PMCID: PMC10676557 DOI: 10.34172/apb.2023.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/15/2022] [Accepted: 01/20/2023] [Indexed: 12/01/2023] Open
Abstract
Infection with SARS-CoV-2 is a growing concern to the global well-being of the public at present. Different amino acid mutations alter the biological and epidemiological characteristics, as well as immune resistance of SARS-CoV-2. The virus-induced pulmonary impairment and inflammatory cytokine storm are directly related to its clinical manifestations. But, the fundamental mechanisms of inflammatory responses are found to be the reason for the death of immune cells which render the host immune system failure. Apoptosis of immune cells is one of the most common forms of programmed cell death induced by the virus for its survival and virulence property. ORF3a, a SARS-CoV-2 accessory viral protein, induces apoptosis in host cells and suppress the defense mechanism. This suggests, inhibiting SARS-CoV-2 ORF3a protein is a good therapeutic strategy for the treatment in COVID-19 infection by promoting the host immune defense mechanism.
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Affiliation(s)
- Minu Treeza M
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Sanu Augustine
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | | | - S.K. Kanthlal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
| | - Rajitha Panonummal
- Amrita School of Pharmacy, Amrita Institute of Medical Sciences & Research Centre, Amrita Vishwa Vidyapeetham, Kochi-682041, India
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4
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Abstract
The coronavirus disease 19 (COVID-19) has been rampant since 2019, severely affecting global public health, and causing 5.75 million deaths worldwide. So far, many vaccines have been developed to prevent the infection of SARS-CoV-2 virus. However, the emergence of new variants may threat vaccine recipients as they might evade immunological surveillance that depends on the using of anti-SARS-CoV-2 antibody to neutralize the viral particles. Recent studies have found that recipients who received two doses of vaccination plus an additional booster shoot were able to quickly elevate neutralization response and immune response against wild-type SARS-CoV-2 virus and some initially appeared viral variants. In this review, we assessed the real-world effectiveness of different COVID-19 vaccines by population studies and neutralization assays and compared neutralization responses of booster vaccines in vitro. Finally, as the efficacy of COVID-19 vaccine is expected to decline over time, continued vaccination should be considered to achieve a long-term immune protection against coronavirus.
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Affiliation(s)
- Tianhong Li
- Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Kathy Qian Luo
- Faculty of Health Sciences, University of Macau, Macao SAR, China.,Ministry of Education-Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macao SAR, China
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5
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Cosar B, Karagulleoglu ZY, Unal S, Ince AT, Uncuoglu DB, Tuncer G, Kilinc BR, Ozkan YE, Ozkoc HC, Demir IN, Eker A, Karagoz F, Simsek SY, Yasar B, Pala M, Demir A, Atak IN, Mendi AH, Bengi VU, Cengiz Seval G, Gunes Altuntas E, Kilic P, Demir-Dora D. SARS-CoV-2 Mutations and their Viral Variants. Cytokine Growth Factor Rev 2022; 63:10-22. [PMID: 34580015 PMCID: PMC8252702 DOI: 10.1016/j.cytogfr.2021.06.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022]
Abstract
Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed. Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications. The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein. In this review, a literature survey in the scope of the increasing SARS-CoV-2 mutations and the viral variations is conducted. In the light of current knowledge, the various disguises of the mutant SARS-CoV-2 forms and their apparent differences from the original strain are examined as they could possibly aid in finding the most appropriate therapeutic approaches.
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Affiliation(s)
- Begum Cosar
- Başkent University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, Ankara, Turkey
| | - Zeynep Yagmur Karagulleoglu
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Sinan Unal
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | | | - Dilruba Beyza Uncuoglu
- Ankara University, Graduate School of Natural and Applied Sciences, Department of Biology, Ankara, Turkey
| | - Gizem Tuncer
- Hacettepe University, Graduate School of Science and Engineering, General Biology Program, Ankara, Turkey; HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey
| | - Bugrahan Regaip Kilinc
- Kastamonu University, School of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey; Kastamonu University, School of Engineering and Architecture, Department of Biomedical Engineering, Kastamonu, Turkey
| | - Yunus Emre Ozkan
- Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, Kocaeli, Turkey
| | - Hikmet Ceyda Ozkoc
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey
| | | | - Ali Eker
- Akdeniz University, Faculty of Medicine, Antalya, Turkey
| | | | | | - Bunyamin Yasar
- Alanya Alaaddin Keykubat University, Department of Molecular Medicine, Antalya, Turkey
| | - Mehmetcan Pala
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, Sivas, Turkey
| | - Aysegul Demir
- Üsküdar University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Irem Naz Atak
- Ankara University, Faculty of Science, Department of Biology, Ankara, Turkey
| | - Aysegul Hanife Mendi
- Gazi University, Faculty of Dentistry, Department of Basic Sciences, Division of Medical Microbiology, Ankara, Turkey
| | - Vahdi Umut Bengi
- Gülhane Training and Research Hospital, Faculty of Dentistry, Department of Periodontology, Ankara, Turkey
| | - Guldane Cengiz Seval
- Ankara University, School of Medicine Department of Hematology, Cebeci, Ankara, Turkey
| | | | - Pelin Kilic
- HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey; Ankara University, Stem Cell Institute, Ankara, Turkey.
| | - Devrim Demir-Dora
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Gene and Cell Therapy, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Medical Biotechnology, Antalya, Turkey.
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6
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Cassaniti I, Bergami F, Percivalle E, Gabanti E, Sammartino JC, Ferrari A, Adzasehoun KMG, Zavaglio F, Zelini P, Comolli G, Sarasini A, Piralla A, Ricciardi A, Zuccaro V, Maggi F, Novazzi F, Simonelli L, Varani L, Lilleri D, Baldanti F. Humoral and cell-mediated response against SARS-CoV-2 variants elicited by mRNA vaccine BNT162b2 in healthcare workers: a longitudinal observational study. Clin Microbiol Infect 2022; 28:301.e1-301.e8. [PMID: 34582981 PMCID: PMC8464022 DOI: 10.1016/j.cmi.2021.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To assess the humoral and cell-mediated response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) elicited by the mRNA BNT162b2 vaccine in SARS-CoV-2-experienced and -naive subjects against a reference strain and SARS-CoV-2 variants. METHODS The humoral response (including neutralizing antibodies) and T-cell-mediated response elicited by BNT162b2 vaccine in 145 healthcare workers (both naive and positive for previous SARS-CoV-2 infection) were evaluated. In a subset of subjects, the effect of SARS-CoV-2 variants on antibody level and cell-mediated response was also investigated. RESULTS Overall, 125/127 naive subjects (98.4%) developed both neutralizing antibodies and specific T cells after the second dose of vaccine. Moreover, the antibody and T-cell responses were effective against viral variants since SARS-CoV-2 NT Abs were still detectable in 55/68 (80.9%) and 25/29 (86.2%) naive subjects when sera were challenged against β and δ variants, respectively. T-cell response was less affected, with no significant difference in the frequency of responders (p 0.369). Of note, two doses of vaccine were able to elicit sustained neutralizing antibody activity against all the SARS-CoV-2 variants tested in SARS-CoV-2-experienced subjects. CONCLUSIONS BNT162b2 vaccine elicited a sustained humoral and cell-mediated response in immunocompetent subjects after two-dose administration of the vaccine, and the response seemed to be less affected by SARS-CoV-2 variants, the only exceptions being the β and δ variants. Increased immunogenicity, also against SARS-CoV-2 variant strains, was observed in SARS-CoV-2-experienced subjects. These results suggest that triple exposure to SARS-CoV-2 antigens might be proposed as valuable strategy for vaccination campaigns.
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Affiliation(s)
- Irene Cassaniti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical Surgical Diagnostic and Paediatric Sciences, Università degli Studi di Pavia, Italy
| | - Federica Bergami
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Gabanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Josè Camilla Sammartino
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alessandro Ferrari
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Kodjo Messan Guy Adzasehoun
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Zavaglio
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Paola Zelini
- Obstetrics and Gynaecology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giuditta Comolli
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Laboratory of Biochemistry-Biotechnology and Advanced Diagnostics, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonella Sarasini
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Valentina Zuccaro
- Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Fabrizio Maggi
- Laboratory of Microbiology, ASST Sette Laghi, Varese, Italy; Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Federica Novazzi
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Luca Simonelli
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Daniele Lilleri
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical Surgical Diagnostic and Paediatric Sciences, Università degli Studi di Pavia, Italy
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7
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von Stillfried S, Freeborn B, Windeck S, Boor P, Böcker J, Schmidt J, Tholen P, Röhrig R, Majeed R, Wienströer J, Bremer J, Weis J, Knüchel R, Breitbach A, Bülow RD, Cacchi C, Wucherpfennig S, Märkl B, Claus R, Dhillon C, Schaller T, Sipos E, Spring O, Braun G, Römmele C, Kling E, Kröncke T, Wittmann M, Hirschbühl K, Heppner FL, Meinhardt J, Radbruch H, Streit S, Horst D, Elezkurtaj S, Quaas A, Göbel H, Friemann J, Hansen T, Titze U, Lorenzen J, Reuter T, Woloszyn J, Baretton G, Hilsenbeck J, Meinhardt M, Pablik J, Sommer L, Holotiuk O, Meinel M, Esposito I, Crudele G, Seidl M, Mahlke N, Hartmann A, Haller F, Eichhorn P, Lange F, Amann KU, Coras R, Ingenwerth M, Rawitzer J, Schmid KW, Theegarten D, Gradhand E, Smith K, Wild P, Birngruber CG, Schilling O, Werner M, Acker T, Gattenlöhner S, Franz J, Metz I, Stadelmann C, Stork L, Thomas C, Zechel S, Ströbel P, Fathke C, Harder A, Wickenhauser C, Glatzel M, Matschke J, Krasemann S, Dietz E, Edler C, Fitzek A, Fröb D, Heinemann A, Heinrich F, Klein A, Kniep I, Lohner L, Möbius D, Ondruschka B, Püschel K, Schädler J, Schröder AS, Sperhake JP, Aepfelbacher M, Fischer N, Lütgehetmann M, Pfefferle S, Jonigk D, Werlein C, Domke LM, Hartmann L, Klein I, Schirmacher P, Schwab C, Röcken C, Langer D, Roth W, Strobl S, Rudelius M, Delbridge C, Kasajima A, Kuhn PH, Slotta-Huspenina J, Weichert W, Weirich G, Stock K, Barth P, Schnepper A, Wardelmann E, Evert K, Evert M, Büttner A, Manhart J, Nigbur S, Bösmüller H, Fend F, Granai M, Klingel K, Warm V, Steinestel K, Umathum VG, Rosenwald A, Vogt N, Kurz F. [Update on collaborative autopsy-based research in German pathology, neuropathology, and forensic medicine]. Pathologie (Heidelb) 2022; 43:101-105. [PMID: 36114379 PMCID: PMC9483541 DOI: 10.1007/s00292-022-01117-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/30/2022] [Indexed: 01/02/2023]
Abstract
BACKGROUND Autopsies are a valuable tool for understanding disease, including COVID-19. MATERIALS AND METHODS The German Registry of COVID-19 Autopsies (DeRegCOVID), established in April 2020, serves as the electronic backbone of the National Autopsy Network (NATON), launched in early 2022 following DEFEAT PANDEMIcs. RESULTS The NATON consortium's interconnected, collaborative autopsy research is enabled by an unprecedented collaboration of 138 individuals at more than 35 German university and non-university autopsy centers through which pathology, neuropathology, and forensic medicine autopsy data including data on biomaterials are collected in DeRegCOVID and tissue-based research and methods development are conducted. More than 145 publications have now emerged from participating autopsy centers, highlighting various basic science and clinical aspects of COVID-19, such as thromboembolic events, organ tropism, SARS-CoV‑2 detection methods, and infectivity of SARS-CoV-2 at autopsy. CONCLUSIONS Participating centers have demonstrated the high value of autopsy and autopsy-derived data and biomaterials to modern medicine. The planned long-term continuation and further development of the registry and network, as well as the open and participatory design, will allow the involvement of all interested partners.
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Affiliation(s)
- Saskia von Stillfried
- Institut für Pathologie, Universitätsklinik RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Deutschland
| | - Benita Freeborn
- Institut für Pathologie, Universitätsklinik RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Deutschland
| | - Svenja Windeck
- Institut für Pathologie, Universitätsklinik RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Deutschland
| | - Peter Boor
- Institut für Pathologie, Universitätsklinik RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Deutschland ,Medizinische Klinik II (Nephrologie und Immunologie), Universitätsklinik RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Deutschland ,Elektronenmikroskopische Einrichtung, Universitätsklinik RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Deutschland
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8
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Lai A, Bergna A, Menzo S, Zehender G, Caucci S, Ghisetti V, Rizzo F, Maggi F, Cerutti F, Giurato G, Weisz A, Turchi C, Bruzzone B, Ceccherini Silberstein F, Clementi N, Callegaro A, Sagradi F, Francisci D, Venanzi Rullo E, Vicenti I, Clementi M, Galli M; collaborative group SCIRE SARS-CoV-2 Italian Research Enterprise. Circulating SARS-CoV-2 variants in Italy, October 2020-March 2021. Virol J 2021; 18:168. [PMID: 34391446 DOI: 10.1186/s12985-021-01638-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impacting the effectiveness of current vaccines. We report the data obtained in several Italian regions involved in the SARS-CoV-2 variant monitoring from the beginning of the epidemic and spanning the period from October 2020 to March 2021.
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9
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Abstract
Epstein-Barr virus (EBV) infects most people worldwide and persists for life due to complicated interplay between lytic infection and multiple types of latent infections. While usually asymptomatic, EBV is a causative agent in several types of cancer and has a strong association with multiple sclerosis. Exactly how EBV promotes these diseases and why they are rare consequences of infection are incompletely understood. Here I will discuss current ideas on disease induction by EBV, including the importance of lytic protein expression in the context of latent infection as well as the possible importance of specific EBV variants in disease induction.
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Affiliation(s)
- Lori Frappier
- Department of Molecular Genetics, University of Toronto, 661 University Ave, Suite 1600, Toronto, ON, M5G 1M1, Canada.
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10
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Raturi M, Kusum A, Kala M, Mittal G, Sharma A, Bansal N. Locally harvested Covid-19 convalescent plasma could probably help combat the geographically determined SARS-CoV-2 viral variants. Transfus Clin Biol 2021; 28:300-302. [PMID: 33971318 PMCID: PMC8103771 DOI: 10.1016/j.tracli.2021.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/21/2021] [Accepted: 05/04/2021] [Indexed: 01/28/2023]
Abstract
The only effective way to provide individuals with herd immunity against the novel coronavirus [SARS-CoV-2] is to administer an effective vaccine that will help check the current pandemic status. In India, the central drugs standard control organization (CDSCO) has granted the emergency-use authorization [EUA] to three vaccines namely, Covishield (live vaccine, Oxford AstraZeneca, United Kingdom being manufactured by the Serum Institute of India), Covaxin (inactivated vaccine, Bharat Biotech, India) and Sputnik V (live vaccine, Gamaleya, Russia). However, there is a rising need for the efficacy of the vaccines to be proven against the "SARS-CoV-2 viral variants." Also, human plasma is polyclonal in nature with an inherent propensity to identify multiple epitopes of either an antigen or pathogen. With this context in mind, the researchers hypothesize that using COVID-19 convalescent plasma [CCP] harvested from the locally recovered individuals [i.e. potential CCP donors] may be particularly beneficial in combating not only the founder SARS-CoV-2 virus but also the geographically determined SARS-CoV-2 variants among the regionally affected COVID-19 patients.
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Affiliation(s)
- Manish Raturi
- Department of Immunohematology and Blood Transfusion, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, Jolly Grant, 248016 Dehradun, Uttarakhand, India.
| | - Anuradha Kusum
- Department of Pathology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, Jolly Grant, 248016 Dehradun, Uttarakhand, India
| | - Mansi Kala
- Department of Pathology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, Jolly Grant, 248016 Dehradun, Uttarakhand, India
| | - Garima Mittal
- Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, Jolly Grant, 248016 Dehradun, Uttarakhand, India
| | - Anita Sharma
- Department of Biochemistry, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, Jolly Grant, 248016 Dehradun, Uttarakhand, India
| | - Naveen Bansal
- Department of Transfusion Medicine, VCSG Government Institute of Medical Science and Research, Srinagar, Uttarakhand, India
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11
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Pfefferle S, Günther T, Kobbe R, Czech-Sioli M, Nörz D, Santer R, Oh J, Kluge S, Oestereich L, Peldschus K, Indenbirken D, Huang J, Grundhoff A, Aepfelbacher M, Knobloch JK, Lütgehetmann M, Fischer N. SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany. Clin Microbiol Infect 2021; 27:130.e5-130.e8. [PMID: 33007476 PMCID: PMC7524521 DOI: 10.1016/j.cmi.2020.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Investigation whether in depth characterization of virus variant patterns can be used for epidemiological analysis of the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection clusters in Hamburg, Germany. METHODS Metagenomic RNA-sequencing and amplicon-sequencing and subsequent variant calling in 25 respiratory samples from SARS-CoV-2 infected patients involved in the earliest infection clusters in Hamburg. RESULTS Amplikon sequencing and cluster analyses of these SARS-CoV-2 sequences allowed the identification of the first infection cluster and five non-related infection clusters occurring at the beginning of the viral entry of SARS-CoV-2 in the Hamburg metropolitan region. Viral genomics together with epidemiological analyses revealed that the index patient acquired the infection in northern Italy and transmitted it to two out of 134 contacts. Single nucleotide polymorphisms clearly distinguished the virus variants of the index and other clusters and allowed us to track in which sequences worldwide these mutations were first described. Minor variant analyses identified the transmission of intra-host variants in the index cluster and household clusters. CONCLUSIONS SARS-CoV-2 variant tracing allows the identification of infection clusters and the follow up of infection chains occurring in the population. Furthermore, the follow up of minor viral variants in infection clusters can provide further resolution on transmission events indistinguishable at a consensus sequence level.
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Affiliation(s)
- Susanne Pfefferle
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Robin Kobbe
- I. Medical Clinic and Polyclinic, Section Infectious Diseases, University Medical Centre Eppendorf, Hamburg, Germany
| | - Manja Czech-Sioli
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Dominic Nörz
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - René Santer
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Jun Oh
- Department of Pediatrics, University Medical Center Eppendorf, Hamburg, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute, Leibniz Institute for Tropical Medicine, Hamburg, Germany
| | - Kersten Peldschus
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Johannes K Knobloch
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Marc Lütgehetmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.
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12
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de Sousa E, Ligeiro D, Lérias JR, Zhang C, Agrati C, Osman M, El-Kafrawy SA, Azhar EI, Ippolito G, Wang FS, Zumla A, Maeurer M. Mortality in COVID-19 disease patients: Correlating the association of major histocompatibility complex (MHC) with severe acute respiratory syndrome 2 (SARS-CoV-2) variants. Int J Infect Dis 2020; 98:454-459. [PMID: 32693089 PMCID: PMC7368421 DOI: 10.1016/j.ijid.2020.07.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic factors such as the HLA type of patients may play a role in regard to disease severity and clinical outcome of patients with COVID-19. Taking the data deposited in the GISAID database, we made predictions using the IEDB analysis resource (TepiTool) to gauge how variants in the SARS-CoV-2 genome may change peptide binding to the most frequent MHC-class I and -II alleles in Africa, Asia and Europe. We caracterized how a single mutation in the wildtype sequence of of SARS-CoV-2 could influence the peptide binding of SARS-CoV-2 variants to MHC class II, but not to MHC class I alleles. Assuming the ORF8 (L84S) mutation is biologically significant, selective pressure from MHC class II alleles may select for viral varients and subsequently shape the quality and quantity of cellular immune responses aginast SARS-CoV-2. MHC 4-digit typing along with viral sequence analysis should be considered in studies examining clinical outcomes in patients with COVID-19.
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Affiliation(s)
- Eric de Sousa
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal.
| | - Dário Ligeiro
- Lisbon Centre for Blood and Transplantation (Instituto Português do Sangue e Transplantação, IPST, Lisbon, Portugal.
| | - Joana R Lérias
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal.
| | - Chao Zhang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China.
| | - Chiara Agrati
- National Institute for Infectious Diseases, Lazzaro Spallanzani, Rome, Italy.
| | - Mohamed Osman
- York Biomedical Research Institute, University of York, United Kingdom and Emerging and Re-Emerging Diseases, University of Khartoum, Sudan.
| | - Sherif A El-Kafrawy
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam I Azhar
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases, Lazzaro Spallanzani, Rome, Italy.
| | - Fu-Sheng Wang
- Treatment and Research Center for Infectious Diseases, The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China.
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK.
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal; I Medical Clinical, University of Mainz, Germany.
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13
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Ho CKY, Welkers MRA, Thomas XV, Sullivan JC, Kieffer TL, Reesink HW, Rebers SPH, de Jong MD, Schinkel J, Molenkamp R. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants. J Virol Methods 2015; 219:28-37. [PMID: 25818622 DOI: 10.1016/j.jviromet.2015.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/09/2023]
Abstract
We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing.
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Affiliation(s)
- Cynthia K Y Ho
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Matthijs R A Welkers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Xiomara V Thomas
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - James C Sullivan
- Department of Infectious Diseases, Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, USA.
| | - Tara L Kieffer
- Department of Infectious Diseases, Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139, USA.
| | - Henk W Reesink
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam 1104 AZ, The Netherlands.
| | - Sjoerd P H Rebers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Janke Schinkel
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
| | - Richard Molenkamp
- Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.
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