1
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Bergquist T, Wax M, Bennett TD, Moffitt RA, Gao J, Chen G, Telenti A, Maher MC, Bartha I, Walker L, Orwoll BE, Mishra M, Alamgir J, Cragin BL, Ferguson CH, Wong HH, Deslattes Mays A, Misquitta L, DeMarco KA, Sciarretta KL, Patel SA. A framework for future national pediatric pandemic respiratory disease severity triage: The HHS pediatric COVID-19 data challenge. J Clin Transl Sci 2023; 7:e175. [PMID: 37745933 PMCID: PMC10514686 DOI: 10.1017/cts.2023.549] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction With persistent incidence, incomplete vaccination rates, confounding respiratory illnesses, and few therapeutic interventions available, COVID-19 continues to be a burden on the pediatric population. During a surge, it is difficult for hospitals to direct limited healthcare resources effectively. While the overwhelming majority of pediatric infections are mild, there have been life-threatening exceptions that illuminated the need to proactively identify pediatric patients at risk of severe COVID-19 and other respiratory infectious diseases. However, a nationwide capability for developing validated computational tools to identify pediatric patients at risk using real-world data does not exist. Methods HHS ASPR BARDA sought, through the power of competition in a challenge, to create computational models to address two clinically important questions using the National COVID Cohort Collaborative: (1) Of pediatric patients who test positive for COVID-19 in an outpatient setting, who are at risk for hospitalization? (2) Of pediatric patients who test positive for COVID-19 and are hospitalized, who are at risk for needing mechanical ventilation or cardiovascular interventions? Results This challenge was the first, multi-agency, coordinated computational challenge carried out by the federal government as a response to a public health emergency. Fifty-five computational models were evaluated across both tasks and two winners and three honorable mentions were selected. Conclusion This challenge serves as a framework for how the government, research communities, and large data repositories can be brought together to source solutions when resources are strapped during a pandemic.
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Affiliation(s)
| | - Marie Wax
- United States Department of Health and Human Services, Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Washington, DC, USA
| | | | | | - Jifan Gao
- University of Wisconsin-Madison, Madison, WI, USA
| | - Guanhua Chen
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Lorne Walker
- Oregon Health & Science University, Portland, OR, USA
| | | | | | | | | | - Christopher H. Ferguson
- United States Department of Health and Human Services, Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Washington, DC, USA
| | - Hui-Hsing Wong
- United States Department of Health and Human Services, Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Washington, DC, USA
| | - Anne Deslattes Mays
- United States Department of Health and Human Services, National Institutes of Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Leonie Misquitta
- United States Department of Health and Human Services, National Institutes of Health, National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Kerry A. DeMarco
- United States Department of Health and Human Services, Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Washington, DC, USA
| | - Kimberly L. Sciarretta
- United States Department of Health and Human Services, Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Washington, DC, USA
| | - Sandeep A. Patel
- United States Department of Health and Human Services, Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Washington, DC, USA
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2
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Momont C, Dang HV, Zatta F, Hauser K, Wang C, di Iulio J, Minola A, Czudnochowski N, De Marco A, Branch K, Donermeyer D, Vyas S, Chen A, Ferri E, Guarino B, Powell AE, Spreafico R, Yim SS, Balce DR, Bartha I, Meury M, Croll TI, Belnap DM, Schmid MA, Schaiff WT, Miller JL, Cameroni E, Telenti A, Virgin HW, Rosen LE, Purcell LA, Lanzavecchia A, Snell G, Corti D, Pizzuto MS. Author Correction: A pan-influenza antibody inhibiting neuraminidase via receptor mimicry. Nature 2023:10.1038/s41586-023-06385-x. [PMID: 37407829 DOI: 10.1038/s41586-023-06385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Affiliation(s)
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Andrea Minola
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - David M Belnap
- School of Biological Sciences, Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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3
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Momont C, Dang HV, Zatta F, Hauser K, Wang C, di Iulio J, Minola A, Czudnochowski N, De Marco A, Branch K, Donermeyer D, Vyas S, Chen A, Ferri E, Guarino B, Powell AE, Spreafico R, Yim SS, Balce DR, Bartha I, Meury M, Croll TI, Belnap DM, Schmid MA, Schaiff WT, Miller JL, Cameroni E, Telenti A, Virgin HW, Rosen LE, Purcell LA, Lanzavecchia A, Snell G, Corti D, Pizzuto MS. A pan-influenza antibody inhibiting neuraminidase via receptor mimicry. Nature 2023:10.1038/s41586-023-06136-y. [PMID: 37258672 DOI: 10.1038/s41586-023-06136-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/26/2023] [Indexed: 06/02/2023]
Abstract
Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift1 and suboptimal immune responses2. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.
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Affiliation(s)
| | - Ha V Dang
- Vir Biotechnology, San Francisco, CA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Andrea Minola
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | - Alex Chen
- Vir Biotechnology, San Francisco, CA, USA
| | | | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Tristan I Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK
| | - David M Belnap
- School of Biological Sciences, Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | | | | | | | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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4
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Bartha I, Ramos T, Pineda F, Vega F, Belver MT, Blanco C. Selective Allergy to Wedge Sole (Dicologlossa cuneata) due to ß-Parvalbumin. J Investig Allergol Clin Immunol 2023; 33:68-70. [PMID: 35332874 DOI: 10.18176/jiaci.0809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- I Bartha
- Allergy Department, Hospital Universitario de La Princesa. Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - T Ramos
- Allergy Department, Hospital Universitario de La Princesa. Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - F Pineda
- Application Laboratory, Diater Laboratories, Madrid, Spain
| | - F Vega
- Allergy Department, Hospital Universitario de La Princesa. Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - M T Belver
- Allergy Department, Hospital Universitario de La Princesa. Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain
| | - C Blanco
- Allergy Department, Hospital Universitario de La Princesa. Instituto de Investigación Sanitaria Princesa (IP), Madrid, Spain.,RETIC ARADYAL RD16/0006/0015, Instituto de Salud Carlos III, Madrid, Spain
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5
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Marzi R, Bassi J, Silacci-Fregni C, Bartha I, Muoio F, Culap K, Sprugasci N, Lombardo G, Saliba C, Cameroni E, Cassotta A, Low JS, Walls AC, McCallum M, Tortorici MA, Bowen JE, Dellota EA, Dillen JR, Czudnochowski N, Pertusini L, Terrot T, Lepori V, Tarkowski M, Riva A, Biggiogero M, Franzetti-Pellanda A, Garzoni C, Ferrari P, Ceschi A, Giannini O, Havenar-Daughton C, Telenti A, Arvin A, Virgin HW, Sallusto F, Veesler D, Lanzavecchia A, Corti D, Piccoli L. Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape. iScience 2023; 26:105726. [PMID: 36507220 PMCID: PMC9721160 DOI: 10.1016/j.isci.2022.105726] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/21/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Memory B cells (MBCs) generate rapid antibody responses upon secondary encounter with a pathogen. Here, we investigated the kinetics, avidity, and cross-reactivity of serum antibodies and MBCs in 155 SARS-CoV-2 infected and vaccinated individuals over a 16-month time frame. SARS-CoV-2-specific MBCs and serum antibodies reached steady-state titers with comparable kinetics in infected and vaccinated individuals. Whereas MBCs of infected individuals targeted both prefusion and postfusion Spike (S), most vaccine-elicited MBCs were specific for prefusion S, consistent with the use of prefusion-stabilized S in mRNA vaccines. Furthermore, a large fraction of MBCs recognizing postfusion S cross-reacted with human betacoronaviruses. The avidity of MBC-derived and serum antibodies increased over time resulting in enhanced resilience to viral escape by SARS-CoV-2 variants, including Omicron BA.1 and BA.2 sublineages, albeit only partially for BA.4 and BA.5 sublineages. Overall, the maturation of high-affinity and broadly reactive MBCs provides the basis for effective recall responses to future SARS-CoV-2 variants.
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Affiliation(s)
- Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jessica Bassi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Istvan Bartha
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Francesco Muoio
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Gloria Lombardo
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | | | - Laura Pertusini
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Maciej Tarkowski
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Milan, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, Milan, Italy
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco, Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Paolo Ferrari
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | | | - Ann Arvin
- Vir Biotechnology, San Francisco, CA, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
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6
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Marzi R, Bassi J, Silacci-Fregni C, Bartha I, Muoio F, Culap K, Sprugasci N, Lombardo G, Saliba C, Cameroni E, Cassotta A, Low JS, Walls AC, McCallum M, Tortorici MA, Bowen JE, Dellota EA, Dillen JR, Czudnochowski N, Pertusini L, Terrot T, Lepori V, Tarkowski M, Riva A, Biggiogero M, Pellanda AF, Garzoni C, Ferrari P, Ceschi A, Giannini O, Havenar-Daughton C, Telenti A, Arvin A, Virgin HW, Sallusto F, Veesler D, Lanzavecchia A, Corti D, Piccoli L. Maturation of SARS-CoV-2 Spike-specific memory B cells drives resilience to viral escape. bioRxiv 2022:2022.09.30.509852. [PMID: 36203553 PMCID: PMC9536037 DOI: 10.1101/2022.09.30.509852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Memory B cells (MBCs) generate rapid antibody responses upon secondary encounter with a pathogen. Here, we investigated the kinetics, avidity and cross-reactivity of serum antibodies and MBCs in 155 SARS-CoV-2 infected and vaccinated individuals over a 16-month timeframe. SARS-CoV-2-specific MBCs and serum antibodies reached steady-state titers with comparable kinetics in infected and vaccinated individuals. Whereas MBCs of infected individuals targeted both pre- and postfusion Spike (S), most vaccine-elicited MBCs were specific for prefusion S, consistent with the use of prefusion-stabilized S in mRNA vaccines. Furthermore, a large fraction of MBCs recognizing postfusion S cross-reacted with human betacoronaviruses. The avidity of MBC-derived and serum antibodies increased over time resulting in enhanced resilience to viral escape by SARS-CoV-2 variants, including Omicron BA.1 and BA.2 sub-lineages, albeit only partially for BA.4 and BA.5 sublineages. Overall, the maturation of high-affinity and broadly-reactive MBCs provides the basis for effective recall responses to future SARS-CoV-2 variants.
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Affiliation(s)
- Roberta Marzi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jessica Bassi
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Istvan Bartha
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Francesco Muoio
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Katja Culap
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Gloria Lombardo
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | - M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | | | - Josh R Dillen
- Vir Biotechnology, San Francisco, CA, United States of America
| | | | - Laura Pertusini
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Maciej Tarkowski
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, Milan, Italy
| | - Maira Biggiogero
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Paolo Ferrari
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, Australia
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Science of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | - Amalio Telenti
- Vir Biotechnology, San Francisco, CA, United States of America
| | - Ann Arvin
- Vir Biotechnology, San Francisco, CA, United States of America
| | - Herbert W Virgin
- Vir Biotechnology, San Francisco, CA, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, United States of America
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, United States of America
| | | | - Davide Corti
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
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7
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Maher MC, Bartha I, Weaver S, di Iulio J, Ferri E, Soriaga L, Lempp FA, Hie BL, Bryson B, Berger B, Robertson DL, Snell G, Corti D, Virgin HW, Kosakovsky Pond SL, Telenti A. Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Sci Transl Med 2022; 14:eabk3445. [PMID: 35014856 PMCID: PMC8939770 DOI: 10.1126/scitranslmed.abk3445] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/06/2022] [Indexed: 12/17/2022]
Abstract
SARS-CoV-2 evolution threatens vaccine- and natural infection-derived immunity as well as the efficacy of therapeutic antibodies. To improve public health preparedness, we sought to predict which existing amino acid mutations in SARS-CoV-2 might contribute to future variants of concern. We tested the predictive value of features comprising epidemiology, evolution, immunology, and neural network-based protein sequence modeling, and identified primary biological drivers of SARS-CoV-2 intra-pandemic evolution. We found evidence that ACE2-mediated transmissibility and resistance to population-level host immunity has waxed and waned as a primary driver of SARS-CoV-2 evolution over time. We retroactively identified with high accuracy (area under the receiver operator characteristic curve, AUROC=0.92-0.97) mutations that will spread, at up to four months in advance, across different phases of the pandemic. The behavior of the model was consistent with a plausible causal structure wherein epidemiological covariates combine the effects of diverse and shifting drivers of viral fitness. We applied our model to forecast mutations that will spread in the future and characterize how these mutations affect the binding of therapeutic antibodies. These findings demonstrate that it is possible to forecast the driver mutations that could appear in emerging SARS-CoV-2 variants of concern. We validate this result against Omicron, showing elevated predictive scores for its component mutations prior to emergence, and rapid score increase across daily forecasts during emergence. This modeling approach may be applied to any rapidly evolving pathogens with sufficiently dense genomic surveillance data, such as influenza, and unknown future pandemic viruses.
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Affiliation(s)
| | - Istvan Bartha
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Steven Weaver
- Department of Biology Institute for Genomics and Evolutionary Medicine Temple University, Philadelphia, PA 19122
| | | | - Elena Ferri
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Leah Soriaga
- Vir Biotechnology, San Francisco, California 94158, USA
| | | | - Brian L. Hie
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Bryan Bryson
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bonnie Berger
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Computer Science and Artificial Intelligence Laboratory. Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow GS1 1QH, UK
| | - Gyorgy Snell
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Davide Corti
- Vir Biotechnology, San Francisco, California 94158, USA
| | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, California 94158, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sergei L. Kosakovsky Pond
- Department of Biology Institute for Genomics and Evolutionary Medicine Temple University, Philadelphia, PA 19122
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8
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Pinto D, Sauer MM, Czudnochowski N, Low JS, Tortorici MA, Housley MP, Noack J, Walls AC, Bowen JE, Guarino B, Rosen LE, di Iulio J, Jerak J, Kaiser H, Islam S, Jaconi S, Sprugasci N, Culap K, Abdelnabi R, Foo C, Coelmont L, Bartha I, Bianchi S, Silacci-Fregni C, Bassi J, Marzi R, Vetti E, Cassotta A, Ceschi A, Ferrari P, Cippà PE, Giannini O, Ceruti S, Garzoni C, Riva A, Benigni F, Cameroni E, Piccoli L, Pizzuto MS, Smithey M, Hong D, Telenti A, Lempp FA, Neyts J, Havenar-Daughton C, Lanzavecchia A, Sallusto F, Snell G, Virgin HW, Beltramello M, Corti D, Veesler D. Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science 2021; 373:1109-1116. [PMID: 34344823 PMCID: PMC9268357 DOI: 10.1126/science.abj3321] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/29/2021] [Indexed: 12/11/2022]
Abstract
The spillovers of betacoronaviruses in humans and the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlight the need for broad coronavirus countermeasures. We describe five monoclonal antibodies (mAbs) cross-reacting with the stem helix of multiple betacoronavirus spike glycoproteins isolated from COVID-19 convalescent individuals. Using structural and functional studies, we show that the mAb with the greatest breadth (S2P6) neutralizes pseudotyped viruses from three different subgenera through the inhibition of membrane fusion, and we delineate the molecular basis for its cross-reactivity. S2P6 reduces viral burden in hamsters challenged with SARS-CoV-2 through viral neutralization and Fc-mediated effector functions. Stem helix antibodies are rare, oftentimes of narrow specificity, and can acquire neutralization breadth through somatic mutations. These data provide a framework for structure-guided design of pan-betacoronavirus vaccines eliciting broad protection.
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Affiliation(s)
- Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Maximilian M. Sauer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barbara Guarino
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | | | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Lotte Coelmont
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Pietro E. Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Faculty of Medicine, University of Zurich, 8057 Zurich, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
| | - Samuele Ceruti
- Intensive Care Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Matteo S. Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - David Hong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | | | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, 3000 Leuven, Belgium
| | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Herbert W. Virgin
- Vir Biotechnology, San Francisco, CA 94158, USA
- UT Southwestern Medical Center, Dallas, TX 75390, USA
- Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, Di Iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Fregni CS, Abdelnabi R, Foo SYC, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Virgin HW, Whelan SPJ, Snell G, Bloom JD, Corti D, Veesler D, Pizzuto MS. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature 2021; 597:103-108. [PMID: 34280951 PMCID: PMC9341430 DOI: 10.1038/s41586-021-03817-4] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023]
Abstract
The recent emergence of SARS-CoV-2 variants of concern1-10 and the recurrent spillovers of coronaviruses11,12 into the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here we describe a human monoclonal antibody designated S2X259, which recognizes a highly conserved cryptic epitope of the receptor-binding domain and cross-reacts with spikes from all clades of sarbecovirus. S2X259 broadly neutralizes spike-mediated cell entry of SARS-CoV-2, including variants of concern (B.1.1.7, B.1.351, P.1, and B.1.427/B.1.429), as well as a wide spectrum of human and potentially zoonotic sarbecoviruses through inhibition of angiotensin-converting enzyme 2 (ACE2) binding to the receptor-binding domain. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. We show that prophylactic and therapeutic administration of S2X259 protects Syrian hamsters (Mesocricetus auratus) against challenge with the prototypic SARS-CoV-2 and the B.1.351 variant of concern, which suggests that this monoclonal antibody is a promising candidate for the prevention and treatment of emergent variants and zoonotic infections. Our data reveal a key antigenic site that is targeted by broadly neutralizing antibodies and will guide the design of vaccines that are effective against all sarbecoviruses.
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Affiliation(s)
- M Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Samantha K Zepeda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | - Michael A Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Leuven, Belgium
| | | | | | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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10
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Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, di iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, Bartha I, Housley MP, Lempp FA, Rosen LE, Dellota E, Kaiser H, Montiel-Ruiz M, Zhou J, Addetia A, Guarino B, Culap K, Sprugasci N, Saliba C, Vetti E, Giacchetto-Sasselli I, Silacci Fregni C, Abdelnabi R, Caroline Foo SY, Havenar-Daughton C, Schmid MA, Benigni F, Cameroni E, Neyts J, Telenti A, Snell G, Virgin HW, Whelan SP, Bloom JD, Corti D, Veesler D, Pizzuto MS. Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody. bioRxiv 2021:2021.04.07.438818. [PMID: 33851169 PMCID: PMC8043460 DOI: 10.1101/2021.04.07.438818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2X259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2X259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2X259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.
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Affiliation(s)
- M. Alejandra Tortorici
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institut Pasteur and CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | | | - Tyler N. Starr
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Roberta Marzi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Fabrizia Zatta
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Zhaoqian Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Samantha K. Zepeda
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Martina Beltramello
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | | | | | | | | | - Jiayi Zhou
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Amin Addetia
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Eneida Vetti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | | | - Rana Abdelnabi
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | - Shi-Yan Caroline Foo
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | - Michael A. Schmid
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Johan Neyts
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, Belgium
| | | | | | | | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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Piccoli L, Ferrari P, Piumatti G, Jovic S, Rodriguez BF, Mele F, Giacchetto-Sasselli I, Terrot T, Silacci-Fregni C, Cameroni E, Jaconi S, Sprugasci N, Bartha I, Corti D, Uguccioni M, Lanzavecchia A, Garzoni C, Giannini O, Bernasconi E, Elzi L, Albanese E, Sallusto F, Ceschi A. Risk assessment and seroprevalence of SARS-CoV-2 infection in healthcare workers of COVID-19 and non-COVID-19 hospitals in Southern Switzerland. Lancet Reg Health Eur 2021; 1:100013. [PMID: 34173621 PMCID: PMC7833818 DOI: 10.1016/j.lanepe.2020.100013] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hospital healthcare workers (HCW), in particular those involved in the clinical care of COVID-19 cases, are presumably exposed to a higher risk of acquiring the disease than the general population. METHODS Between April 16 and 30, 2020 we conducted a prospective, SARS-CoV-2 seroprevalence study in HCWs in Southern Switzerland. Participants were hospital personnel with varying COVID-19 exposure risk depending on job function and working site. They provided personal information (including age, sex, occupation, and medical history) and self-reported COVID-19 symptoms. Odds ratio (OR) of seropositivity to IgG antibodies was estimated by univariate and multivariate logistic regressions. FINDINGS Among 4726 participants, IgG antibodies to SARS-CoV-2 were detected in 9.6% of the HCWs. Seropositivity was higher among HCWs working on COVID-19 wards (14.1% (11.9-16.5)) compared to other hospital areas at medium (10.7% (7.6-14.6)) or low risk exposure (7.3% (6.4-8.3)). OR for high vs. medium wards risk exposure was 1.42 (0.91-2.22), P = 0.119, and 1.98 (1.55-2.53), P<0.001 for high vs. low wards risk exposure. The same was for true for doctors and nurses (10.1% (9.0-11.3)) compared to other employees at medium (7.1% (4.8-10.0)) or low risk exposure (6.6% (5.0-8.4)). OR for high vs. medium profession risk exposure was 1.37 (0.89-2.11), P = 0.149, and 1.75 (1.28-2.40), P = 0.001 for high vs. low profession risk exposure. Moreover, seropositivity was higher among HCWs who had household exposure to COVID-19 cases compared to those without (18.7% (15.3-22.5) vs. 7.7% (6.9-8.6), OR 2.80 (2.14-3.67), P<0.001). INTERPRETATION SARS-CoV-2 antibodies are detectable in up to 10% of HCWs from acute care hospitals in a region with high incidence of COVID-19 in the weeks preceding the study. HCWs with exposure to COVID-19 patients have only a slightly higher absolute risk of seropositivity compared to those without, suggesting that the use of PPE and other measures aiming at reducing nosocomial viral transmission are effective. Household contact with known COVID-19 cases represents the highest risk of seropositivity. FUNDING Henry Krenter Foundation, Ente Ospedaliero Cantonale and Vir Biotechnology.
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Affiliation(s)
- Luca Piccoli
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Paolo Ferrari
- Department of Internal Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, Australia
| | - Giovanni Piumatti
- Division of Primary Care, Population Epidemiology Unit, Geneva University Hospitals, Geneva, Switzerland
- nstitute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Bellinzona, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Blanca Fernandez Rodriguez
- Institute for Research in Biomedicine, Bellinzona, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Bellinzona, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Elisabetta Cameroni
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Istvan Bartha
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Davide Corti
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Bellinzona, Università della Svizzera italiana, Bellinzona, Switzerland
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele (Milan), Italy
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Bellinzona, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Olivier Giannini
- Department of Internal Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Enos Bernasconi
- Department of Internal Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Luigia Elzi
- Department of Internal Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Emiliano Albanese
- nstitute of Public Health, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Bellinzona, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
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Naret O, Chaturvedi N, Bartha I, Hammer C, Fellay J. Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes. Front Genet 2018; 9:266. [PMID: 30105048 PMCID: PMC6078058 DOI: 10.3389/fgene.2018.00266] [Citation(s) in RCA: 8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/02/2018] [Indexed: 11/23/2022] Open
Abstract
Studies of host genetic determinants of pathogen sequence variations can identify sites of genomic conflicts, by highlighting variants that are implicated in immune response on the host side and adaptive escape on the pathogen side. However, systematic genetic differences in host and pathogen populations can lead to inflated type I (false positive) and type II (false negative) error rates in genome-wide association analyses. Here, we demonstrate through a simulation that correcting for both host and pathogen stratification reduces spurious signals and increases power to detect real associations in a variety of tested scenarios. We confirm the validity of the simulations by showing comparable results in an analysis of paired human and HIV genomes.
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Affiliation(s)
- Olivier Naret
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nimisha Chaturvedi
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian Hammer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital, Lausanne, Switzerland
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13
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McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N, Del Amo J, Gill MJ, Gilmour J, Kellam P, Kelleher AD, Sönnerborg A, Wolinsky SM, Zangerle R, Post FA, Fisher M, Haas DW, Walker BD, Porter K, Goldstein DB, Sandhu MS, de Bakker PIW, Fellay J. Evaluating the Impact of Functional Genetic Variation on HIV-1 Control. J Infect Dis 2017; 216:1063-1069. [PMID: 28968755 PMCID: PMC5853944 DOI: 10.1093/infdis/jix470] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022] Open
Abstract
Background Previous genetic association studies of human immunodeficiency virus-1 (HIV-1) progression have focused on common human genetic variation ascertained through genome-wide genotyping. Methods We sought to systematically assess the full spectrum of functional variation in protein coding gene regions on HIV-1 progression through exome sequencing of 1327 individuals. Genetic variants were tested individually and in aggregate across genes and gene sets for an influence on HIV-1 viral load. Results Multiple single variants within the major histocompatibility complex (MHC) region were observed to be strongly associated with HIV-1 outcome, consistent with the known impact of classical HLA alleles. However, no single variant or gene located outside of the MHC region was significantly associated with HIV progression. Set-based association testing focusing on genes identified as being essential for HIV replication in genome-wide small interfering RNA (siRNA) and clustered regularly interspaced short palindromic repeats (CRISPR) studies did not reveal any novel associations. Conclusions These results suggest that exonic variants with large effect sizes are unlikely to have a major contribution to host control of HIV infection.
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Affiliation(s)
- Paul J McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Laboratory, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Sara L Pulit
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
| | - Deepti Gurdasani
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York
| | - Cristina Pomilla
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Namrata Gupta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Elizabeth H Young
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Julia Del Amo
- Centro Nacional de Epidemiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M John Gill
- Department of Medicine, University of Calgary, Canada
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, United Kingdom
| | - Paul Kellam
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Research Department of Infection, Division of Infection and Immunity, University College London, United Kingdom
| | - Anthony D Kelleher
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, Australia
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Steven M Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago
| | - Robert Zangerle
- Department of Dermatology and Venereology, Medical University Innsbruck, Austria
| | | | - Martin Fisher
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Boston
- Howard Hughes Medical Institute, Chevy Chase
| | | | | | - Manjinder S Sandhu
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, United Kingdom
| | - Paul I W de Bakker
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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14
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McLaren PJ, Shea PR, Bartha I, Fellay J. A39 Human exome sequencing to evaluate the impact of rare coding variation on HIV-1 control. Virus Evol 2017; 3:vew036.038. [PMID: 28845244 PMCID: PMC5565923 DOI: 10.1093/ve/vew036.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- P J McLaren
- National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - P R Shea
- Institute for Genomic Medicine Columbia University, New York, NY, USA
| | - I Bartha
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - J Fellay
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
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15
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Ansari MA, Pedergnana V, L C Ip C, Magri A, Von Delft A, Bonsall D, Chaturvedi N, Bartha I, Smith D, Nicholson G, McVean G, Trebes A, Piazza P, Fellay J, Cooke G, Foster GR, Hudson E, McLauchlan J, Simmonds P, Bowden R, Klenerman P, Barnes E, Spencer CCA. Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus. Nat Genet 2017; 49:666-673. [PMID: 28394351 PMCID: PMC5873514 DOI: 10.1038/ng.3835] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/10/2017] [Indexed: 12/11/2022]
Abstract
Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control.
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Affiliation(s)
- M Azim Ansari
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Martin School, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Vincent Pedergnana
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Camilla L C Ip
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Annette Von Delft
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - David Bonsall
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | | | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Graham Cooke
- Wright-Fleming Institute, Imperial College London, London, UK
| | | | | | - Emma Hudson
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine and the NIHR Oxford BRC, University of Oxford, Oxford, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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16
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Asgari S, McLaren PJ, Peake J, Wong M, Wong R, Bartha I, Francis JR, Abarca K, Gelderman KA, Agyeman P, Aebi C, Berger C, Fellay J, Schlapbach LJ. Corrigendum: Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis. Front Immunol 2016; 7:447. [PMID: 27790221 PMCID: PMC5081341 DOI: 10.3389/fimmu.2016.00447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Samira Asgari
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul J McLaren
- National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jane Peake
- Lady Cilento Children's Hospital , Brisbane, QLD , Australia
| | - Melanie Wong
- Children's Hospital Westmead , Sydney, NSW , Australia
| | - Richard Wong
- Pathology Queensland Central Laboratory, Royal Brisbane and Women's Hospital , Brisbane, QLD , Australia
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua R Francis
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Royal Darwin Hospital, Darwin, NT, Australia
| | - Katia Abarca
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile , Santiago , Chile
| | | | - Philipp Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern , Bern , Switzerland
| | - Christoph Aebi
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern , Bern , Switzerland
| | | | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luregn J Schlapbach
- Lady Cilento Children's Hospital, Brisbane, QLD, Australia; Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Paediatric Critical Care Research Group (PCCRG), Mater Research, University of Queensland, Brisbane, QLD, Australia
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17
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Asgari S, McLaren PJ, Peake J, Wong M, Wong R, Bartha I, Francis JR, Abarca K, Gelderman KA, Agyeman P, Aebi C, Berger C, Fellay J, Schlapbach LJ. Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis. Front Immunol 2016; 7:357. [PMID: 27703454 PMCID: PMC5028722 DOI: 10.3389/fimmu.2016.00357] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/01/2016] [Indexed: 01/10/2023] Open
Abstract
One out of three pediatric sepsis deaths in high income countries occur in previously healthy children. Primary immunodeficiencies (PIDs) have been postulated to underlie fulminant sepsis, but this concept remains to be confirmed in clinical practice. Pseudomonas aeruginosa (P. aeruginosa) is a common bacterium mostly associated with health care-related infections in immunocompromised individuals. However, in rare cases, it can cause sepsis in previously healthy children. We used exome sequencing and bioinformatic analysis to systematically search for genetic factors underpinning severe P. aeruginosa infection in the pediatric population. We collected blood samples from 11 previously healthy children, with no family history of immunodeficiency, who presented with severe sepsis due to community-acquired P. aeruginosa bacteremia. Genomic DNA was extracted from blood or tissue samples obtained intravitam or postmortem. We obtained high-coverage exome sequencing data and searched for rare loss-of-function variants. After rigorous filtrations, 12 potentially causal variants were identified. Two out of eight (25%) fatal cases were found to carry novel pathogenic variants in PID genes, including BTK and DNMT3B. This study demonstrates that exome sequencing allows to identify rare, deleterious human genetic variants responsible for fulminant sepsis in apparently healthy children. Diagnosing PIDs in such patients is of high relevance to survivors and affected families. We propose that unusually severe and fatal sepsis cases in previously healthy children should be considered for exome/genome sequencing to search for underlying PIDs.
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Affiliation(s)
- Samira Asgari
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul J McLaren
- National HIV and Retrovirology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jane Peake
- Lady Cilento Children's Hospital , Brisbane, QLD , Australia
| | - Melanie Wong
- Children's Hospital Westmead , Sydney, NSW , Australia
| | - Richard Wong
- Pathology Queensland Central Laboratory, Royal Brisbane and Women's Hospital , Brisbane, QLD , Australia
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua R Francis
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia; Royal Darwin Hospital, Darwin, NT, Australia
| | - Katia Abarca
- Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile , Santiago , Chile
| | | | - Philipp Agyeman
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern , Bern , Switzerland
| | - Christoph Aebi
- Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern , Bern , Switzerland
| | | | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luregn J Schlapbach
- Lady Cilento Children's Hospital, Brisbane, QLD, Australia; Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Paediatric Critical Care Research Group (PCCRG), Mater Research, University of Queensland, Brisbane, QLD, Australia
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18
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Junier T, Rotger M, Biver E, Ledergerber B, Barceló C, Bartha I, Kovari H, Schmid P, Fux C, Bernasconi E, Brun Del Re C, Weber R, Fellay J, Tarr PE. Contribution of Genetic Background and Clinical Risk Factors to Low-Trauma Fractures in Human Immunodeficiency Virus (HIV)-Positive Persons: The Swiss HIV Cohort Study. Open Forum Infect Dis 2016; 3:ofw101. [PMID: 27419173 PMCID: PMC4943531 DOI: 10.1093/ofid/ofw101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 04/18/2016] [Accepted: 05/15/2016] [Indexed: 01/09/2023] Open
Abstract
Background. The impact of human genetic background on low-trauma fracture (LTF) risk has not been evaluated in the context of human immunodeficiency virus (HIV) and clinical LTF risk factors. Methods. In the general population, 6 common single-nucleotide polymorphisms (SNPs) associate with LTF through genome-wide association study. Using genome-wide SNP arrays and imputation, we genotyped these SNPs in HIV-positive, white Swiss HIV Cohort Study participants. We included 103 individuals with a first, physician-validated LTF and 206 controls matched on gender, whose duration of observation and whose antiretroviral therapy start dates were similar using incidence density sampling. Analyses of nongenetic LTF risk factors were based on 158 cases and 788 controls. Results. A genetic risk score built from the 6 LTF-associated SNPs did not associate with LTF risk, in both models including and not including parental hip fracture history. The contribution of clinical LTF risk factors was limited in our dataset. Conclusions. Genetic LTF markers with a modest effect size in the general population do not improve fracture prediction in persons with HIV, in whom clinical LTF risk factors are prevalent in both cases and controls.
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Affiliation(s)
- Thomas Junier
- Swiss Institute of Bioinformatics, Ecole Polytechnique Fédérale de Lausanne
| | - Margalida Rotger
- Institute of Microbiology , University Hospital Center, University of Lausanne
| | - Emmanuel Biver
- Department of Bone Diseases , Geneva University Hospitals and Faculty of Medicine
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology , University Hospital Zurich, University of Zurich
| | - Catalina Barceló
- Institute of Microbiology , University Hospital Center, University of Lausanne
| | - Istvan Bartha
- Swiss Institute of Bioinformatics, Ecole Polytechnique Fédérale de Lausanne
| | - Helen Kovari
- Division of Infectious Diseases and Hospital Epidemiology , University Hospital Zurich, University of Zurich
| | - Patrick Schmid
- Division of Infectious Diseases , Kantonsspital St. Gallen
| | - Christoph Fux
- Division of Infectious Diseases , Kantonsspital Aarau, University of Basel
| | - Enos Bernasconi
- Division of Infectious Diseases , Ospedale Regionale , Lugano
| | - Claudia Brun Del Re
- Department of Infectious Diseases , Bern University Hospital, University of Bern
| | - Rainer Weber
- Division of Infectious Diseases and Hospital Epidemiology , University Hospital Zurich, University of Zurich
| | - Jacques Fellay
- Swiss Institute of Bioinformatics, Ecole Polytechnique Fédérale de Lausanne,; Division of Infectious Diseases, University Hospital, Lausanne
| | - Philip E Tarr
- Infectious Diseases Service, Kantonsspital Baselland , University of Basel , Bruderholz , Switzerland
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19
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An P, Penugonda S, Thorball CW, Bartha I, Goedert JJ, Donfield S, Buchbinder S, Binns-Roemer E, Kirk GD, Zhang W, Fellay J, Yu XF, Winkler CA. Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia. PLoS Genet 2016; 12:e1005921. [PMID: 26942578 PMCID: PMC4778847 DOI: 10.1371/journal.pgen.1005921] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Human APOBEC3 cytidine deaminases are intrinsic resistance factors to HIV-1. However, HIV-1 encodes a viral infectivity factor (Vif) that degrades APOBEC3 proteins. In vitro APOBEC3F (A3F) anti-HIV-1 activity is weaker than A3G but is partially resistant to Vif degradation unlike A3G. It is unknown whether A3F protein affects HIV-1 disease in vivo. To assess the effect of A3F gene on host susceptibility to HIV- acquisition and disease progression, we performed a genetic association study in six well-characterized HIV-1 natural cohorts. A common six-Single Nucleotide Polymorphism (SNP) haplotype of A3F tagged by a codon-changing variant (p. I231V, with allele (V) frequency of 48% in European Americans) was associated with significantly lower set-point viral load and slower rate of progression to AIDS (Relative Hazards (RH) = 0.71, 95% CI: 0.56, 0.91) and delayed development of pneumocystis pneumonia (PCP) (RH = 0.53, 95% CI: 0.37-0.76). A validation study in the International Collaboration for the Genomics of HIV (ICGH) showed a consistent association with lower set-point viral load. An in vitro assay revealed that the A3F I231V variant may influence Vif mediated A3F degradation. Our results provide genetic epidemiological evidence that A3F modulates HIV-1/AIDS disease progression.
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Affiliation(s)
- Ping An
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail: (PA); (CAW)
| | - Sudhir Penugonda
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Christian W. Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Istvan Bartha
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sharyne Donfield
- Rho, Inc., Chapel Hill, North Carolina, United States of America
| | - Susan Buchbinder
- San Francisco Department of Public Health, San Francisco, California, United States of America
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Gregory D. Kirk
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xiao-Fang Yu
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Cheryl A. Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
- * E-mail: (PA); (CAW)
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20
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Perkins MR, Bartha I, Timmer JK, Liebner JC, Wolinsky D, Wollinsky D, Günthard HF, Hauser C, Bernasconi E, Hoffmann M, Calmy A, Battegay M, Telenti A, Douek DC, Fellay J. The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals. J Infect Dis 2015; 212:578-84. [PMID: 25701868 DOI: 10.1093/infdis/jiv089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 11/17/2014] [Accepted: 02/09/2015] [Indexed: 11/13/2022] Open
Abstract
Systemic immune activation, a major determinant of human immunodeficiency virus (HIV) disease progression, is the result of a complex interplay between viral replication, dysregulation of the immune system, and microbial translocation due to gut mucosal damage. Although human genetic variants influencing HIV load have been identified, it is unknown how much the host genetic background contributes to interindividual differences in other determinants of HIV pathogenesis such as gut damage and microbial translocation. Using samples and data from 717 untreated participants in the Swiss HIV Cohort Study and a genome-wide association study design, we searched for human genetic determinants of plasma levels of intestinal fatty acid-binding protein (I-FABP/FABP2), a marker of gut damage, and of soluble CD14 (sCD14), a marker of lipopolysaccharide bioactivity and microbial translocation. We also assessed the correlations between HIV load, sCD14, and I-FABP. Although we found no genome-wide significant determinant of the tested plasma markers, we observed strong associations between sCD14 and both HIV load and I-FABP, shedding new light on the relationships between processes that drive progression of untreated HIV infection.
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Affiliation(s)
- Molly R Perkins
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Istvan Bartha
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne Swiss Institute of Bioinformatics, Lausanne Institute of Microbiology, University Hospital and University of Lausanne
| | - J Katherina Timmer
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Julia C Liebner
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - David Wolinsky
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - David Wollinsky
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich
| | - Christoph Hauser
- University Clinic of Infectious Diseases, University Hospital Bern and University of Bern
| | | | - Matthias Hoffmann
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen
| | - Alexandra Calmy
- HIV Unit, Department of Internal Medicine, Geneva University Hospital
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, Departments of Clinical and Biomedical Research, University Hospital Basel, University of Basel, Switzerland
| | - Amalio Telenti
- Institute of Microbiology, University Hospital and University of Lausanne
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne Swiss Institute of Bioinformatics, Lausanne
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21
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Bartha I, Danya T, Nemeth A. Surgical strategy in massive colorectal bleeding. Acta Chir Iugosl 2004; 51:91-2. [PMID: 15771297 DOI: 10.2298/aci0402091b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Several pathologic disorders can become a source of severe gastrointestinal bleeding. The most frequently observed entities responsible for massive colorectal bleeding are diverticulae, intestinal angiodysplasias, inflammatory bowel diseases and cancers. In order to choose the bes--surgical method to stop the hemorrhage and cure the disease; it is mandatory to properly identify the origin and location of the bleeding. It is a common experience that the usually advised diagnostic methods often yield disappointing results in urgent cases. The presented case shows that selective angiography can lead to the fastest diagnosis in angiodysplasia and with surgery a definitive result can be obtained.
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Affiliation(s)
- I Bartha
- 1st Department of Surgery, University of Debrecen, Hungary
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22
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Berczi C, Bocsi J, Bartha I, Math J, Balazs G. Prognostic value of DNA ploidy status in patients with rectal cancer. Anticancer Res 2002; 22:3737-41. [PMID: 12552986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
BACKGROUND A retrospective study was performed to measure the prognostic value of DNA ploidy status and proliferative index (PI) for survival in patients with rectal cancer. PATIENTS AND METHODS Fifty-two patients underwent curative surgery for rectal carcinoma. Ten tumors were in Stage I, 25 cancers were in Stage II, and 17 of them were in Stage III. Using flow cytometry the nuclear DNA content of the tumor cells was measured. RESULTS There were 25 DNA diploid and 27 DNA aneuploid carcinomas. Aneuploid DNA content did not show higher occurrence in advanced tumors. The mean survival was 59 months in the case of DNA diploid carcinoma, while it was 47 months in the case of DNA aneuploid cancer. The mean PI of the DNA diploid cancers was 8%. The PI of DNA aneuploid tumors was 22%. High PI (PI > 10%) was observed in 32 carcinomas while low PI (PI < 10%) occurred in 20 cases. Patients with aneuploid DNA content and high PI had significantly worse survival compared to patients with diploid DNA content while low PI. Locoregional and distant metastases occurred more frequently in patients with aneuploid tumor. By univariate analysis, tumor size, lymph node involvement, DNA ploidy status and PI all correlated with prognosis. However, multivariate analysis showed that TNM stage and PI were the only significant prognostic factors for survival. CONCLUSION The survival and disease-free survival of patients with diploid DNA content was better compared to aneuploid cases. The results suggest that DNA ploidy status is important in determining the biological behaviour of rectal carcinomas, although the multivariate analysis did not prove its significant influence. The PI were independent negative prognostic factors for survival.
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Affiliation(s)
- Cs Berczi
- 1st Department of Surgery, University of Debrecen, Késmark str. 7/C., 4029, Debrecen, Hungary.
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23
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Szucs-Farkas Z, Toth J, Szollosi Z, Peter M, Bartha I. Pseudoaneurysm and ilio-caval fistula caused by malignant fibrous histiocytoma of the aorta--CT diagnosis and angiographic confirmation. Eur Radiol 2002; 12:450-3. [PMID: 11870448 DOI: 10.1007/s003300100909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2000] [Revised: 03/05/2001] [Accepted: 03/12/2001] [Indexed: 10/28/2022]
Abstract
We report a case of a malignant fibrous histiocytoma (MFH) of the aortic bifurcation, which manifested as a pseudoaneurysm with the formation of an ilio-caval fistula, a complication about which, to our knowledge, nothing has been published previously. Spiral CT, catheter arteriography and venography were complementary in the diagnostic procedure.
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Affiliation(s)
- Zsolt Szucs-Farkas
- Department of Radiology, University of Debrecen, Medical and Health Science Center, Nagyerdei krt. 98, P.O. Box 4, 4012 Debrecen, Hungary.
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24
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Damjanovich L, Kósa C, Bartha I. [The importance of recognizing hereditary non-polyposis colonic carcinoma]. Magy Seb 2001; 54:88-90. [PMID: 11339097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The clinical diagnosis of hereditary nonpolyposis colon carcinoma (HNPCC) can be made in more than 5% of all colorectal cancer cases, depending on the stringency of criteria used. The disease is inherited in an autosomal dominant fashion but penetrance is lower than 100%. The diagnosis must be verified by the demonstration of germline mutations of DNA "mismatch repair" genes. Although yet an exception in our national health practice, these tests are routinely applied in some centers abroad. The recognition of the syndrome is important since these patients can enter a surveillance program and may be cured. The most important pertaining information is summarized through the demonstration of our own case.
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Affiliation(s)
- L Damjanovich
- Debreceni Egyetem Orvos- és Egészségtudományi Centrum I. sz. Sebészeti Klinika, 4012 Debrecen, Pf. 27
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25
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Bartha I, Damjanovich L, Kósa C, Nèmeth A. [New technique for surgical treatment of enterovaginal fistula]. Magy Seb 2001; 54:86-7. [PMID: 11339096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Enterovaginal fistulas most frequently occur following abdominal tumors, inflammatory bowel disease and radiation therapy. There is a tendency for spontaneous closure, although a surgical intervention is necessary in more than 50% of the cases. Mortality is between 15-25%. The quality of life is significantly worsened by an enterovaginal fistula of a patient already suffering from a malignant disease. To relieve the patient from her distressing situation a mucous fistula was constructed by exclusion of the small bowel loop participating in the formation of the fistula track. Bowel continuity was restored by anastomosis. The patient's quality of life improved significantly. This operation was performed in three cases without complications. We recommend this procedure as an alternative technique to improve our patients' quality of life.
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Affiliation(s)
- I Bartha
- Debreceni Egyetem Orvos- és Egészségtudományi Centrum I. sz. Sebészeti Klinika, 4012 Debrecen, Pf. 27.
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26
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Lapis KY, Bocsi J, Tóvári J, Bartha I, Timár J, Rásó E. Antiinvasive effects of Tiazofurin on liver-metastatic human colon carcinoma xenografts. Anticancer Res 1996; 16:3323-31. [PMID: 9042307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The effect of Tiazofurin (TR)-a C nucleoside with significant antineoplastic activity-have been studied on the liver metastasis formation of human colorectal carcinoma xenografts. TR treatment (especially at a dose of 300 mg/kg bwt) produced significant inhibition of metastasis formation in the liver and induced a significant and dose dependent decrease in the serum CEA level. There was not clear connection between the alteration of the weight of the primary tumor bearing spleen and the anti-metastatic activity of TR. In tumor cells derived from tumors obtained from TR treated animals a considerable decrease was observed in the expression of MMP2 metalloproteinase. Furthermore, TR induced a significant dose dependent inhibition of the microinvasiveness of colon carcinoma cells on EHS matrix. Based on the data presented here and published elsewhere, the authors suggest that in the remarkable liver metastasis inhibitory effects of TR modulation and the nonproliferative events of the multistep metastatic cascade plays an important role.
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Affiliation(s)
- K Y Lapis
- First Institute of Pathology and Experimental Cancer Research, Semmelweis University of Medicine, Budapest, Hungary.
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27
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Tímár J, Diczházi C, Bartha I, Pogány G, Paku S, Rásó E, Tóvári J, Ladányi A, Lapis K, Kopper L. Modulation of heparan-sulphate/chondroitin-sulphate ratio by glycosaminoglycan biosynthesis inhibitors affects liver metastatic potential of tumor cells. Int J Cancer 1995; 62:755-61. [PMID: 7558426 DOI: 10.1002/ijc.2910620618] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Previous data have indicated that the proteoglycan (PG) pattern is different on tumor cells with different liver metastatic potential. We selected "conventional" glycosaminoglycan (GAG) biosynthesis inhibitors, beta-D-xyloside (BX), 2-deoxy-D-glucose (2-DG), ethane-l-hydroxy-l,l-diphosphonate (ETDP) and the newly discovered 5-hexyl-2-deoxyuridine (HUdR), to modulate PGs on highly metastatic/liver-specific 3LL-HH murine carcinoma and HT168 human melanoma cells and to influence their liver colonization potential. These compounds all induced remarkable changes in GAG biosynthesis, but to varying degrees: glucosamine labelling was affected mainly by 2-DG, and HUdR and sulphation by BX and HUdR. Furthermore, the ratio of heparan sulphate/chondroitin sulphate (HS/CS) of PGs was increased by ETDP and decreased after treatment by HUdR. In addition to changes in PG metabolism, tumor-cell proliferation and adhesion to fibronectin were affected; BX and 2-DG stimulated cell proliferation and adhesion, while HUdR inhibited both proliferation and adhesion. Most interestingly, HUdR, the most effective inhibitor of HS/HSPG, depressed the formation of liver colonies, while ETDP, the most effective inhibitor of CS/CSPG, stimulated the appearance of liver colonies. These observations indicated that, at least in these experimental systems, tumor cells with a high HS/CS ratio are more likely to form liver metastases; consequently, anti-HS agents could also be anti-metastatic.
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Affiliation(s)
- J Tímár
- First Institute of Pathology and Experimental Cancer Research, Semmelweis University of Medicine, Budapest, Hungary
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28
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Bartha I, Hajdu J, Bokor L, Kanyári Z, Damjanovich L. [Quality of life of post-colostomy patients]. Orv Hetil 1995; 136:1995-8. [PMID: 7566930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The psychosomatic care of patients after surgical treatment must comprise the analysis of quality of life with colostomy. Five different parameters were assessed of 100 colostomy patients. Sixty-one percent of our patients had skin irritation problems. Twenty-eight patients applied regular irrigation. Seventy-two percent of these had daily motions, 20% had bidaily, the remaining 8% had irregular bowel movements. Seventeen percent of the nonirrigating patients observed very irritating fecal discharge around the stoma. Embarrassing noises concomittant with bowel movements were observed by 42% and 45% struggled with bad odors. Irrigating patients had hardly any of these problems. For 65% of the patients the idea of having a colostoma meant the greatest psychological burden before the operation. The stress situation culminated in the immediate postoperative period in 10%. Forty percent of those asked were seriously worried about the reaction of their social environment. In 65% a significant decrease of social relations could be observed. Sixteen percent reported an increased social activity after colostomy had been performed. Sixty percent admitted considering the option of suicide at least once. Thirty-five percent revealed to have any kind of sexual problems after colostomy. Eight of our 100 colostomy patients experienced serious adverse reactions from their family members. In eighty percent of the cases family members showed great sympathy although they acted naively. The quality of life of colostomy patients may be best taken care of by qualified stomatherapists, out-patient proctology departments and the ileo-colostomy movement (ILCO).
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Affiliation(s)
- I Bartha
- Debreceni Orvostudományi Egyetem I. sz. Sebészeti Klinika
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29
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Bartha I, Bodrogi T, Sápy P. [Multiple primary cancer of the colon and rectum]. Orv Hetil 1989; 130:2077-80. [PMID: 2677907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Data of 33 patients operated on during 13 years because of primary multiple cancer of the colon are presented. The frequency of multiple occurrence was 4.1%. Synchronous tumors were observed in 1.8% (15 patients) and metachronous was (following 410 operations) 4.4% (18 patients). The attention is drawn to the relationship between polyps occurring simultaneously with colonic cancers and the following--metachronous tumors. Careful examinations must cover the period following the acute colon operation, as eliminating the cause of the emergency operation other--synchronous tumors or polyps may remain hidden. The significance of prevention and follow-up examinations in the treatment of metachronous tumors in stressed. It was stated that the malignancy and operability indices of the second tumor detected in this way did not differ significantly from the primary tumors. Preference was given to subtotal colectomy as operative principle in the treatment of metachronous cancers of the colon.
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30
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Haczku A, Lukács K, Bartha I, Mórocz I, Thomas B. [Essential hypertension caused by a virilizing adrenal tumor]. Orv Hetil 1989; 130:515-7. [PMID: 2726234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Authors report here an interesting case of a woman who has been treated for essential hypertension for 12 years. Beside the hypertension, an extreme virilization appeared. A large adenoma, originated from the left adrenal gland have been explored behind the clinical picture. After surgical removal of the adenoma, adrenocortical hormones decreased to the normal levels. Systemic blood pressure decreased considerably the virilisation showed gradual involution. The correct treatment of the patient was a decade late, resulting in the development of encephalopathic syndromes.
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33
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Bartha I, Bodrogi T, Németh A, Balázs G. [Experience with emergency colorectal surgery]. Orv Hetil 1986; 127:1949-50, 1955-6. [PMID: 3489916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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34
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Bartha I, Mórocz I, Németh A, Bodrogi T. [Endometriosis externa in the sigmoid and anus]. Orv Hetil 1986; 127:81-2, 85. [PMID: 3945488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Farkas M, Markos J, Szepesváry P, Bartha I, Szalontai G, Simon Z. A computer-aided system for organic functional group determinations. Anal Chim Acta 1981. [DOI: 10.1016/s0003-2670(00)00082-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Csáky G, Balázs G, Bartha I, Palágyi-Deák I. [Treatment of diffuse euthyroid juvenile goiter]. Orv Hetil 1979; 120:2545-7. [PMID: 530661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Balázs G, Csáky G, Lukács G, Bartha I. [Simultaneous occurrence of hyperthyreosis and thyroid carcinoma]. Chirurg 1978; 49:699-703. [PMID: 720162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The authors report on the morphological and clinical features of occult thyroid carcinomas confirmed by detailed histological examinations following the surgical treatment of hyperthyreotic goiters recurrent after prolonged thyreostatic treatment, as well as on the follow-up data of the patients. Joint occurrence of hyperthyroidism and thyroid tumors was observed in five patients, two of whom showed progressive endocrine ophthalmopathy. In the surgical preparations of three patients, chronic lymphocytic thyroiditis was also diagnosed. On the grounds of postoperative care, the authors draw conclusions of practical clinical significance. They take a stand on the questions of surgical and adjuvant treatment favored by them in the case of the joint occurrence of the two diseases.
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38
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Vigh G, Bartha I. [Burning of the genitalia of a woman because of jealousy. Repeated crime of a severe bodily injury committed with extraordinary cruelty]. Dtsch Z Gesamte Gerichtl Med 1969; 66:13-8. [PMID: 5351338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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