1
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Stalman EW, Wieske L, Keijser JBD, van Dam KPJ, Kummer LYL, Wilbrink MF, van Kempen ZLE, Killestein J, Volkers AG, Tas SW, Boekel L, Wolbink GJ, van der Kooi AJ, Raaphorst J, Löwenberg M, Takkenberg RB, D'Haens GRAM, Spuls PI, Bekkenk MW, Musters AH, Post NF, Bosma AL, Hilhorst ML, Vegting Y, Bemelman FJ, Voskuyl AE, Broens B, Sanchez AP, van Els CACM, de Wit J, Rutgers A, de Leeuw K, Horváth B, Verschuuren JJGM, Ruiter AM, van Ouwerkerk L, van der Woude D, Allaart RCF, Teng YKO, van Paassen P, Busch MH, Brusse E, van Doorn PA, Baars AE, Hijnen D, Schreurs CRG, van der Pol WL, Goedee HS, Steenhuis M, Keijzer S, Cristianawati O, Brinke AT, Verstegen NJM, Zwinderman KAH, van Ham SM, Rispens T, Welkers MR, Jonges M, Eftimov F, Kuijpers TW. Clinical and humoral responses after SARS-CoV-2 breakthrough infections in patients with immunosuppressants. J Allergy Clin Immunol 2024:S0091-6749(24)00503-7. [PMID: 38763170 DOI: 10.1016/j.jaci.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024]
Abstract
BACKGROUND Despite impaired humoral responses in patients treated with immunosuppressants (ISPs), recent studies found similar severity of SARS-CoV-2 breakthrough infections compared to controls. One potential explanation is the rapid generation humoral responses upon infection, but evidence is lacking. OBJECTIVES To investigate longitudinal dynamics of the SARS-CoV-2 antibody repertoire after SARS-CoV-2 delta and omicron breakthrough infections in patients with immune-mediated inflammatory diseases (IMID) on ISPs and controls. METHODS As prospective sub-study of the national Target-to-B! (T2B!) consortium, we included IMID patients on ISPs and controls who reported SARS-CoV-2 breakthrough infections between July 1, 2021, and April 1, 2022. To get an impression of the dynamics of the antibody repertoire, three antibody titers of wild-type RBD, wild-type S, and omicron RBD were measured at four time points after SARS-CoV-2 breakthrough infections. RESULTS We included 302 IMID patients on ISPs and 178 controls. Antibody titers increased up to 28 days after breakthrough infections in both groups. However, in IMID patients on anti-CD20 therapy and sphingosine-1 phosphate receptor (S1P) modulators, antibody titers were considerably lower compared to controls. In the anti-TNF group, we observed slightly lower antibody titers in the early stages and a faster decline of antibodies after infection compared to controls. Breakthrough infections were mostly mild and hospitalization was required in less than 1% of the cases. CONCLUSIONS Most ISPs do not influence the dynamics of the SARS-CoV-2 antibody repertoire and exhibit a rapid recall response with cross-reactive antibody clones towards new viral variants. However, in patients treated with anti-CD20 therapy or S1P modulators, the dynamics were greatly impaired, and to a lesser extent in those anti-TNF. Nevertheless, only a few severe breakthrough cases were reported.
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Affiliation(s)
- Eileen W Stalman
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Luuk Wieske
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Clinical Neurophysiology, St Antonius Hospital, Nieuwegein, The Netherlands
| | - Jim B D Keijser
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Koos P J van Dam
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Laura Y L Kummer
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Maarten F Wilbrink
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Zoé L E van Kempen
- Department of Neurology, Amsterdam UMC, VU University medical center, Amsterdam, the Netherlands
| | - Joep Killestein
- Department of Neurology, Amsterdam UMC, VU University medical center, Amsterdam, the Netherlands
| | - Adriaan G Volkers
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Sander W Tas
- Amsterdam Rheumatology and immunology Center, Amsterdam UMC, Department of Rheumatology and Clinical Immunology, University of Amsterdam, Amsterdam, the Netherlands
| | - Laura Boekel
- Amsterdam Rheumatology and immunology Center, Amsterdam UMC, Department of Rheumatology and Clinical Immunology, University of Amsterdam, Amsterdam, the Netherlands
| | - Gerrit J Wolbink
- Amsterdam Rheumatology and immunology Center, Amsterdam UMC, Department of Rheumatology and Clinical Immunology, University of Amsterdam, Amsterdam, the Netherlands
| | - Anneke J van der Kooi
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Joost Raaphorst
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - R Bart Takkenberg
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Geert R A M D'Haens
- Department of Gastroenterology and Hepatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Phyllis I Spuls
- Department of Dermatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marcel W Bekkenk
- Department of Dermatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Annelie H Musters
- Department of Dermatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Nicoline F Post
- Department of Dermatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Angela L Bosma
- Department of Dermatology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marc L Hilhorst
- Department of Internal Medicine, Section of Nephrology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Yosta Vegting
- Department of Internal Medicine, Section of Nephrology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Frederique J Bemelman
- Department of Internal Medicine, Section of Nephrology, Amsterdam UMC, location Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Alexandre E Voskuyl
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and immunology Center, VU University medical center, Amsterdam, the Netherlands
| | - Bo Broens
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and immunology Center, VU University medical center, Amsterdam, the Netherlands
| | - Agner Parra Sanchez
- Amsterdam Rheumatology and immunology Center, Amsterdam UMC, Department of Rheumatology and Clinical Immunology, University of Amsterdam, Amsterdam, the Netherlands; Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and immunology Center, VU University medical center, Amsterdam, the Netherlands
| | - Cécile A C M van Els
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands; Faculty of Veterinary Medicine, Utrecht University Utrecht, The Netherlands
| | - Jelle de Wit
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Abraham Rutgers
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, Groningen, The Netherlands
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, Groningen, The Netherlands
| | - Barbara Horváth
- Department of Dermatology, Center for Blistering Diseases, University Medical Center Groningen, University Groningen, Groningen, The Netherlands
| | | | - Annabel M Ruiter
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lotte van Ouwerkerk
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Diane van der Woude
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Renée C F Allaart
- Department of Rheumatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Y K Onno Teng
- Centre of expertise for lupus-, vasculitis- and complement-mediated systemic diseases, Department of Internal Medicine - Nephrology section, Leiden University Medical Centre, Leiden, The Netherlands
| | - Pieter van Paassen
- Department of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Matthias H Busch
- Department of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Esther Brusse
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Pieter A van Doorn
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Adája E Baars
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Dirkjan Hijnen
- Department of Dermatology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Corine R G Schreurs
- Department of Dermatology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - W Ludo van der Pol
- Brain center UMC Utrecht, department of neurology and neurosurgery, Utrecht, the Netherlands
| | - H Stephan Goedee
- Brain center UMC Utrecht, department of neurology and neurosurgery, Utrecht, the Netherlands
| | - Maurice Steenhuis
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Sofie Keijzer
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Olvi Cristianawati
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Anja Ten Brinke
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Niels J M Verstegen
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Koos A H Zwinderman
- Clinical Research Unit, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - S Marieke van Ham
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, the Netherlands
| | - Theo Rispens
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands
| | - Matthijs R Welkers
- Medical Microbiology and Infection Prevention department, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marcel Jonges
- Medical Microbiology and Infection Prevention department, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Filip Eftimov
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Disease, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
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Vogels CBF, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MRA, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Herzog KS, Fauver JR, Morrison AM, Michael SF, Grubaugh ND. DengueSeq: a pan-serotype whole genome amplicon sequencing protocol for dengue virus. BMC Genomics 2024; 25:433. [PMID: 38693476 PMCID: PMC11062901 DOI: 10.1186/s12864-024-10350-x] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes. RESULTS We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 10-100 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. CONCLUSIONS DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.
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Affiliation(s)
- Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Emma Taylor-Salmon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Isabel M Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Dennis Dijk
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC Location AMC, Amsterdam, The Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Timothy Locksmith
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Yibo Dong
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Namratha Tarigopula
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Omer Tekin
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Sarah Schmedes
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Charles Panzera
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Ian Stryker
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Julieta Vergara
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Edgar Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Kaylee S Herzog
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joseph R Fauver
- Department of Epidemiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Andrea M Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, USA.
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3
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Schuele L, Boter M, Nieuwenhuijse DF, Götz H, Fanoy E, de Vries H, Vieyra B, Bavalia R, Hoornenborg E, Molenkamp R, Jonges M, van den Ouden A, Simões M, van den Lubben M, Koopmans M, Welkers MRA, Oude Munnink BB. Circulation, viral diversity and genomic rearrangement in mpox virus in the Netherlands during the 2022 outbreak and beyond. J Med Virol 2024; 96:e29397. [PMID: 38235923 DOI: 10.1002/jmv.29397] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Mpox is an emerging zoonotic disease which has now spread to over 113 countries as of August 2023, with over 89,500 confirmed human cases. The Netherlands had one of the highest incidence rates in Europe during the peak of the outbreak. In this study, we generated 158 near-complete mpox virus (MPXV) genomes (12.4% of nationwide cases) that were collected throughout the Netherlands from the start of the outbreak in May 2022 to August 2023 to track viral evolution and investigate outbreak dynamics. We detected 14 different viral lineages, suggesting multiple introductions followed by rapid initial spread within the country. The estimated evolutionary rate was relatively high compared to previously described in orthopoxvirus literature, with an estimated 11.58 mutations per year. Genomic rearrangement events occurred at a rate of 0.63% and featured a large deletion event. In addition, based on phylogenetics, we identified multiple potential transmission clusters which could be supported by direct source- and contact tracing data. This led to the identification of at least two main transmission locations at the beginning of the outbreak. We conclude that whole genome sequencing of MPXV is essential to enhance our understanding of outbreak dynamics and evolution of a relatively understudied and emerging zoonotic pathogen.
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Affiliation(s)
- Leonard Schuele
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David F Nieuwenhuijse
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hannelore Götz
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Ewout Fanoy
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Dermatology, Amsterdam UMC, Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Bruno Vieyra
- Department of Public Health, (Infectious Disease Control and Center Sexual Health) Public Health Service Rotterdam-Rijnmond, Rotterdam, Netherlands
| | - Roisin Bavalia
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Elske Hoornenborg
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | | | - Margarida Simões
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Mariken van den Lubben
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Matthijs R A Welkers
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
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4
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Vogels CB, Hill V, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MR, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Morrison AM, Michael SF, Grubaugh ND. DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus. medRxiv 2023:2023.10.13.23296997. [PMID: 37873191 PMCID: PMC10592998 DOI: 10.1101/2023.10.13.23296997] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background The increasing burden of dengue virus on public health due to more explosive and frequent outbreaks highlights the need for improved surveillance and control. Genomic surveillance of dengue virus not only provides important insights into the emergence and spread of genetically diverse serotypes and genotypes, but it is also critical to monitor the effectiveness of newly implemented control strategies. Here, we present DengueSeq, an amplicon sequencing protocol, which enables whole-genome sequencing of all four dengue virus serotypes. Results We developed primer schemes for the four dengue virus serotypes, which can be combined into a pan-serotype approach. We validated both approaches using genetically diverse virus stocks and clinical specimens that contained a range of virus copies. High genome coverage (>95%) was achieved for all genotypes, except DENV2 (genotype VI) and DENV 4 (genotype IV) sylvatics, with similar performance of the serotype-specific and pan-serotype approaches. The limit of detection to reach 70% coverage was 101-102 RNA copies/μL for all four serotypes, which is similar to other commonly used primer schemes. DengueSeq facilitates the sequencing of samples without known serotypes, allows the detection of multiple serotypes in the same sample, and can be used with a variety of library prep kits and sequencing instruments. Conclusions DengueSeq was systematically evaluated with virus stocks and clinical specimens spanning the genetic diversity within each of the four dengue virus serotypes. The primer schemes can be plugged into existing amplicon sequencing workflows to facilitate the global need for expanded dengue virus genomic surveillance.
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Affiliation(s)
- Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Lauren M. Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Emma Taylor-Salmon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, NSW, Australia
| | - Dennis Dijk
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC location AMC, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC location AMC, Amsterdam, The Netherlands
| | - Matthijs R.A. Welkers
- Department of Medical Microbiology & Infection Prevention, Amsterdam UMC location AMC, Amsterdam, The Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Timothy Locksmith
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Yibo Dong
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Namratha Tarigopula
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Omer Tekin
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Sarah Schmedes
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, United States of America
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Charles Panzera
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Ian Stryker
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Julieta Vergara
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, United States of America
| | - Edgar Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, United States of America
| | - Andrea M. Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, United States of America
| | - Scott F. Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
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5
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Carbo EC, Mourik K, Boers SA, Munnink BO, Nieuwenhuijse D, Jonges M, Welkers MRA, Matamoros S, van Harinxma Thoe Slooten J, Kraakman MEM, Karelioti E, van der Meer D, Veldkamp KE, Kroes ACM, Sidorov I, de Vries JJC. A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2. Eur J Clin Microbiol Infect Dis 2023; 42:701-713. [PMID: 37017810 PMCID: PMC10075175 DOI: 10.1007/s10096-023-04590-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees Mourik
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefan A Boers
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastien Matamoros
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Joost van Harinxma Thoe Slooten
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Margriet E M Kraakman
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Karin Ellen Veldkamp
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Igor Sidorov
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C de Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
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6
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de Vries HJ, Götz HM, Bruisten S, van der Eijk AA, Prins M, Oude Munnink BB, Welkers MR, Jonges M, Molenkamp R, Westerhuis BM, Schuele L, Stam A, Boter M, Hoornenborg E, Mulders D, van den Lubben M, Koopmans M. Mpox outbreak among men who have sex with men in Amsterdam and Rotterdam, the Netherlands: no evidence for undetected transmission prior to May 2022, a retrospective study. Euro Surveill 2023; 28. [PMID: 37103788 DOI: 10.2807/1560-7917.es.2023.28.17.2200869] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
Since May 2022, over 21,000 mpox cases have been reported from 29 EU/EEA countries, predominantly among men who have sex with men (MSM). The Netherlands was the fourth most affected country in Europe, with more than 1,200 cases and a crude notification rate of 70.7 per million population. The first national case was reported on 10 May, yet potential prior transmission remains unknown. Insight into prolonged undetected transmission can help to understand the current outbreak dynamics and aid future public health interventions. We performed a retrospective study and phylogenetic analysis to elucidate whether undetected transmission of human mpox virus (hMPXV) occurred before the first reported cases in Amsterdam and Rotterdam. In 401 anorectal and ulcer samples from visitors to centres for sexual health in Amsterdam or Rotterdam dating back to 14 February 2022, we identified two new cases, the earliest from 6 May. This coincides with the first cases reported in the United Kingdom, Spain and Portugal. We found no evidence of widespread hMPXV transmission in Dutch sexual networks of MSM before May 2022. Likely, the mpox outbreak expanded across Europe within a short period in the spring of 2022 through an international highly intertwined network of sexually active MSM.
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Affiliation(s)
- Henry J de Vries
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, the Netherlands
- Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Department of Dermatology, Amsterdam UMC, location University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Hannelore M Götz
- Department of Public Health, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Public Health, Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Sylvia Bruisten
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | | | - Maria Prins
- Amsterdam UMC location University of Amsterdam, Department of Infectious Diseases, Meibergdreef 9, Amsterdam, the Netherlands
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Matthijs Ra Welkers
- Amsterdam UMC location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Marcel Jonges
- Amsterdam UMC location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, the Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Brenda M Westerhuis
- Amsterdam UMC location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Leonard Schuele
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Arjen Stam
- Amsterdam UMC location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Elske Hoornenborg
- Amsterdam Institute for Infection and Immunology, Infectious Diseases, Amsterdam, the Netherlands
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Daphne Mulders
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Mariken van den Lubben
- Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC University Medical Center, Rotterdam, the Netherlands
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7
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Affiliation(s)
- Marieke de Regt
- Department of Internal Medicine, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Rogier Ooijevaar
- Department of Internal Medicine, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, location AMC, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, location AMC, Amsterdam, The Netherlands
| | - Alex Wagemakers
- Department of Medical Microbiology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands.
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8
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Birnie E, Biemond JJ, Appelman B, de Bree GJ, Jonges M, Welkers MRA, Wiersinga WJ. Development of Resistance-Associated Mutations After Sotrovimab Administration in High-risk Individuals Infected With the SARS-CoV-2 Omicron Variant. JAMA 2022; 328:1104-1107. [PMID: 35913747 PMCID: PMC9344387 DOI: 10.1001/jama.2022.13854] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study investigates whether resistance-associated mutations develop after treatment with sotrovimab in high-risk patients infected with the SARS-CoV-2 Omicron variant.
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MESH Headings
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Neutralizing/adverse effects
- Antibodies, Neutralizing/pharmacology
- Antibodies, Neutralizing/therapeutic use
- COVID-19/genetics
- COVID-19/virology
- Drug Resistance, Viral/drug effects
- Drug Resistance, Viral/genetics
- Humans
- Mutation
- SARS-CoV-2/drug effects
- SARS-CoV-2/genetics
- COVID-19 Drug Treatment
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Affiliation(s)
- Emma Birnie
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jason J. Biemond
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Brent Appelman
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Godelieve J. de Bree
- Division of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Matthijs R. A. Welkers
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - W. Joost Wiersinga
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
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9
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Tutu van Furth AM, van der Kuip M, van Els AL, Fievez LCR, van Rijckevorsel GGC, van den Ouden A, Jonges M, Welkers MRA. Paediatric monkeypox patient with unknown source of infection, the Netherlands, June 2022. Euro Surveill 2022; 27:2200552. [PMID: 35866435 PMCID: PMC9306258 DOI: 10.2807/1560-7917.es.2022.27.29.2200552] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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] [Indexed: 12/29/2022] Open
Abstract
Since May 2022, an international monkeypox (MPX) outbreak has been ongoing in more than 50 countries. While most cases are men who have sex with men, transmission is not restricted to this population. In this report, we describe the case of a male child younger than 10 years with MPX in the Netherlands. Despite thorough source tracing, a likely source of infection has not been identified. No secondary cases were identified in close contacts.
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Affiliation(s)
- A Marceline Tutu van Furth
- Amsterdam UMC location Vrije Universiteit Amsterdam, Emma Children’s Hospital, Department of Paediatric Infectious Diseases and Immunology, Amsterdam, The Netherlands,Amsterdam Institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Martijn van der Kuip
- Amsterdam UMC location Vrije Universiteit Amsterdam, Emma Children’s Hospital, Department of Paediatric Infectious Diseases and Immunology, Amsterdam, The Netherlands,Amsterdam Institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Anne L van Els
- Amsterdam UMC location Vrije Universiteit Amsterdam, Emma Children’s Hospital, Department of Paediatric Infectious Diseases and Immunology, Amsterdam, The Netherlands,Amsterdam Institute for Infection and Immunity, Infectious diseases, Amsterdam, The Netherlands
| | - Lydia CR Fievez
- Public Health Service Amsterdam, Dept. of Infectious Diseases, Amsterdam, The Netherlands
| | - Gini GC van Rijckevorsel
- Public Health Service Amsterdam, Dept. of Infectious Diseases, Amsterdam, The Netherlands,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | - Marcel Jonges
- Amsterdam UMC location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands
| | - Matthijs RA Welkers
- Amsterdam UMC location AMC, University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Amsterdam, The Netherlands,Public Health Service Amsterdam, Public Health Laboratory, Amsterdam, The Netherlands
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10
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Kolodziej L, Hordijk S, Koopsen J, Maas J, Thung H, Spijkerman I, Jonges M, Bomers M, Sikkens J, de Jong M, Zonneveld R, Schinkel J. Risk of SARS-CoV-2 transmission upon return to work in RNA-positive healthcare workers. J Hosp Infect 2022; 124:72-78. [PMID: 35288252 PMCID: PMC8916832 DOI: 10.1016/j.jhin.2022.02.024] [Citation(s) in RCA: 4] [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: 11/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Healthcare workers (HCWs) are at risk for coronavirus disease 2019 (COVID-19), and for spreading severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) amongst colleagues and patients. AIM To study the presence of SARS-CoV-2 RNA and possible onward transmission by HCWs upon return to work after COVID-19, and association with disease severity and development of antibodies over time. METHODS Unvaccinated HCWs with positive SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) were recruited prospectively. Data on symptoms were collected via telephone questionnaires on days 2, 7, 14 and 21 after a positive test. Upon return to work, repeat SARS-CoV-2 RT-PCR was performed and serum was collected. Repeat serum samples were collected at weeks 4, 8, 12 and 16 to determine antibody dynamics over time. Phylogenetic analysis was conducted to investigate possible transmission events originating from HCWs with a positive repeat RT-PCR. FINDINGS Sixty-one (84.7%) participants with mild/moderate COVID-19 had a repeat SARS-CoV-2 RT-PCR performed upon return to work (median 13 days after symptom onset), of which 30 (49.1%) were positive with a median cycle threshold (Ct) value of 29.2 (IQR 26.9-29.9). All HCWs developed antibodies against SARS-CoV-2. No significant differences in symptomatology and presence of antibodies were found between repeat RT-PCR-positive and -negative HCWs. Eleven direct colleagues of six participants with a repeat RT-PCR Ct value <30 tested positive after the HCW returned to work. Phylogenetic and epidemiologic analysis did not indicate onward transmission through HCWs who were SARS-CoV-2 RNA positive upon return to work. CONCLUSIONS HCWs regularly return to work with substantial SARS-CoV-2 RNA loads. However, this study found no evidence for subsequent in-hospital transmission.
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Affiliation(s)
- L.M. Kolodziej
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands,Corresponding author. Address: Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands. Tel.: + 316 19809909. (L.M. Kolodziej)
| | - S. Hordijk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - J. Koopsen
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - J.J. Maas
- Department of Occupational Health, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - H.T. Thung
- Department of Occupational Health, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - I.J.B. Spijkerman
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - M. Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - M.K. Bomers
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Centres, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - J.J. Sikkens
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam University Medical Centres, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - M.D. de Jong
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - R. Zonneveld
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
| | - J. Schinkel
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, the Netherlands
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11
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Iglói Z, van Loo IHM, Demandt AMP, Franssen K, Jonges M, van Gelder M, Erkens-Hulshof S, van Alphen LB. Controlling a human parainfluenza virus-3 outbreak in a haematology ward in a tertiary hospital: the importance of screening strategy and molecular diagnostics in relation to clinical symptoms. J Hosp Infect 2022; 126:56-63. [PMID: 35483642 DOI: 10.1016/j.jhin.2022.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Human parainfluenza 3 (HPIV-3) outbreak at the haemato-oncology ward of the Maastricht University Medical Center in the summer of 2016. AIM To describe an effective strategy to control the largest reported HPIV-3 outbreak at an adult haematology-oncology ward in the Netherlands by implementing infection control measures and molecular epidemiology investigation. METHODS Clinical, patient and diagnostic data were both pro- and retrospectively collected. HPIV-3 real-time-PCR (HPIV-3 RT-PCR) was validated using oropharyngeal rinse samples. Screening of all new and admitted patients was implemented to identify asymptomatic infection or prolonged shedding of HPIV-3 allowing cohort isolation. FINDINGS The HPIV-3 outbreak occurred between 9 July and 28 September 2016 and affected 53 patients. HPIV-3 RT-PCR on oropharyngeal rinse samples demonstrated an up to tenfold higher sensitivity compared to pharyngeal swabs. Monitoring showed that at first positive PCR, 20 patients (38%) were asymptomatic (of which 11 remained asymptomatic) and the average duration of shedding was 14 days (range 1-58). Asymptomatic patients had lower viral load, shorter period of viral shedding (≤14 days) and were mostly immune competent oncology patients. The outbreak was under control 5 weeks after implementation of screening of asymptomatic patients. CONCLUSION Implementation of a sensitive screening method identified both symptomatic and asymptomatic patients which had lower viral load and allowed early cohort isolation. This is especially important in a ward that combines patients with varying immune status, since both immunocompromised and immune competent patients are likely to spread the HPIV-3 virus, either through prolonged shedding or through asymptomatic course of disease.
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Affiliation(s)
- Zsófia Iglói
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Inge H M van Loo
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Astrid M P Demandt
- Department of Internal Medicine, Division of Hematology, GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Karen Franssen
- Infection Control, Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, The Netherlands
| | - Michel van Gelder
- Department of Internal Medicine, Division of Hematology, GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sandra Erkens-Hulshof
- Infection Control, Department of Medical Microbiology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Faculty of Health, Medicine and Life Sciences, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ Maastricht, The Netherlands.
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12
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Koopsen J, van Ewijk CE, Bavalia R, Cornelissen A, Bruisten SM, de Gee F, Han AX, de Jong M, de Jong MD, Jonges M, Khawaja N, Koene FM, van der Lubben M, Mikulic I, Rebers SP, Russell CA, Schinkel J, Schreijer AJ, den Uil JA, Welkers MR, Leenstra T. Epidemiologic and Genomic Analysis of SARS-CoV-2 Delta Variant Superspreading Event in Nightclub, the Netherlands, June 2021. Emerg Infect Dis 2022; 28:1012-1016. [PMID: 35271792 PMCID: PMC9045423 DOI: 10.3201/eid2805.212019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report a severe acute respiratory syndrome coronavirus 2 superspreading event in the Netherlands after distancing rules were lifted in nightclubs, despite requiring a negative test or vaccination. This occurrence illustrates the potential for rapid dissemination of variants in largely unvaccinated populations under such conditions. We detected subsequent community transmission of this strain.
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13
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de 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M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, 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Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - 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 and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Molenkamp R, Fanoy E, Derickx L, de Groot T, Jonges M, Leenstra T, Nijhuis R, Pas S, Vahidnia A, von Wintersdorff C, Mulder B, Koopmans M. Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, the Netherlands, June to July 2021. ACTA ACUST UNITED AC 2021; 26. [PMID: 34622759 PMCID: PMC8511753 DOI: 10.2807/1560-7917.es.2021.26.40.2100921] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We evaluated routine testing with SARS-CoV-2 Delta variant-specific RT-PCR in regional hospital laboratories in addition to centralised national genomic surveillance in the Netherlands during June and July 2021. The increase of the Delta variant detected by RT-PCR correlated well with data from genomic surveillance and was available ca 2 weeks earlier. This rapid identification of the relative abundance and increase of SARS-CoV-2 variants of concern may have important benefits for implementation of local public health measures.
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Affiliation(s)
| | - Ewout Fanoy
- Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
| | - Leonie Derickx
- Public Health Service Gelderland-Zuid, Nijmegen, the Netherlands
| | - Theun de Groot
- Department of Clinical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Tjalling Leenstra
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands
| | - Roel Nijhuis
- Laboratory for Medical Microbiology and Medical Immunology, Meander Medical Center, Amersfoort, the Netherlands
| | - Suzan Pas
- Microvida Laboratory for Medical Microbiology, Amphia Hospital, Breda, the Netherlands
| | - Ali Vahidnia
- Testing Agency, Ministry of Health, Welfare and Sport, Zeist, the Netherlands
| | - Christian von Wintersdorff
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Bert Mulder
- Department of Clinical Microbiology and Infectious Diseases, Canisius-Wilhelmina Hospital, Nijmegen, the Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
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15
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Koopsen J, Dekker M, Thung P, Jonges M, Vennema H, Leenstra T, Eggink D, Welkers MRA, Struijs PAA, Reusken C, van Mansfeld R, de Jong MD, Schinkel J, Spijkerman IJB. Rapid reinfection with SARS-CoV-2 variant-of-concern Alpha detected in a nurse during an outbreak at a non-covid inpatient ward: lessons learned. Antimicrob Resist Infect Control 2021; 10:137. [PMID: 34565476 PMCID: PMC8474951 DOI: 10.1186/s13756-021-01008-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/07/2021] [Indexed: 11/10/2022] Open
Abstract
We describe the lessons learned during a SARS-CoV-2 variant-of-concern Alpha outbreak investigation at a normal care unit in a university hospital in Amsterdam in December 2020. The outbreak consisted of nine nurses and two roomed-in patient family members. (attack rate 18%). One nurse tested positive with a phylogenetically distinct variant, after a documented infection 83 days prior. Three key points were taken from this investigation. First, it was controlled by adherence to existing guidelines, despite increased transmissibility of the variant. Second, viral sequencing can inform transmission cluster inference, but the epidemiological context is essential to draw appropriate conclusions. Third, reinfections with Alpha variants can occur rapidly after primary infection.
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Affiliation(s)
- Jelle Koopsen
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Mireille Dekker
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
| | - Philip Thung
- Department of Occupational Health and Safety, Amsterdam UMC, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Tjalling Leenstra
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Dirk Eggink
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter A A Struijs
- Department of Orthopedic Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Chantal Reusken
- Centre for Infectious Disease Control, WHO COVID-19 Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rosa van Mansfeld
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ingrid J B Spijkerman
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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16
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Sikkens JJ, Buis DTP, Peters EJG, Dekker M, Schinkel M, Reijnders TDY, Schuurman AR, de Brabander J, Lavell AHA, Maas JJ, Koopsen J, Han AX, Russell CA, Schinkel J, Jonges M, Matamoros S, Jurriaans S, van Mansfeld R, Wiersinga WJ, Smulders YM, de Jong MD, Bomers MK. Serologic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Infection Among Hospital Health Care Workers. JAMA Netw Open 2021; 4:e2118554. [PMID: 34319354 PMCID: PMC9437910 DOI: 10.1001/jamanetworkopen.2021.18554] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
IMPORTANCE It is unclear when, where, and by whom health care workers (HCWs) working in hospitals are infected with SARS-CoV-2. OBJECTIVE To determine how often and in what manner nosocomial SARS-CoV-2 infection occurs in HCW groups with varying exposure to patients with COVID-19. DESIGN, SETTING, AND PARTICIPANTS This cohort study comprised 4 weekly measurements of SARS-CoV-2-specific antibodies and collection of questionnaires from March 23 to June 25, 2020, combined with phylogenetic and epidemiologic transmission analyses at 2 university hospitals in the Netherlands. Included individuals were HCWs working in patient care for those with COVID-19, HCWs working in patient care for those without COVID-19, and HCWs not working in patient care. Data were analyzed from August through December 2020. EXPOSURES Varying work-related exposure to patients infected with SARS-CoV-2. MAIN OUTCOMES AND MEASURES The cumulative incidence of and time to SARS-CoV-2 infection, defined as the presence of SARS-CoV-2-specific antibodies in blood samples, were measured. RESULTS Among 801 HCWs, there were 439 HCWs working in patient care for those with COVID-19, 164 HCWs working in patient care for those without COVID-19, and 198 HCWs not working in patient care. There were 580 (72.4%) women, and the median (interquartile range) age was 36 (29-50) years. The incidence of SARS-CoV-2 was increased among HCWs working in patient care for those with COVID-19 (54 HCWs [13.2%; 95% CI, 9.9%-16.4%]) compared with HCWs working in patient care for those without COVID-19 (11 HCWs [6.7%; 95% CI, 2.8%-10.5%]; hazard ratio [HR], 2.25; 95% CI, 1.17-4.30) and HCWs not working in patient care (7 HCWs [3.6%; 95% CI, 0.9%-6.1%]; HR, 3.92; 95% CI, 1.79-8.62). Among HCWs caring for patients with COVID-19, SARS-CoV-2 cumulative incidence was increased among HCWs working on COVID-19 wards (32 of 134 HCWs [25.7%; 95% CI, 17.6%-33.1%]) compared with HCWs working on intensive care units (13 of 186 HCWs [7.1%; 95% CI, 3.3%-10.7%]; HR, 3.64; 95% CI, 1.91-6.94), and HCWs working in emergency departments (7 of 102 HCWs [8.0%; 95% CI, 2.5%-13.1%]; HR, 3.29; 95% CI, 1.52-7.14). Epidemiologic data combined with phylogenetic analyses on COVID-19 wards identified 3 potential HCW-to-HCW transmission clusters. No patient-to-HCW transmission clusters could be identified in transmission analyses. CONCLUSIONS AND RELEVANCE This study found that HCWs working on COVID-19 wards were at increased risk for nosocomial SARS-CoV-2 infection with an important role for HCW-to-HCW transmission. These findings suggest that infection among HCWs deserves more consideration in infection prevention practice.
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Affiliation(s)
- Jonne J. Sikkens
- Department of Internal Medicine, Amsterdam
Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije
Universiteit Amsterdam, Amsterdam, the Netherlands
| | - David T. P. Buis
- Department of Internal Medicine, Amsterdam
Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije
Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Edgar J. G. Peters
- Section Infectious Diseases, Department of
Internal Medicine, Amsterdam Infection and Immunity Institute, Amsterdam University
Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Mireille Dekker
- Department of Medical Microbiology and Infection
Prevention, Amsterdam Infection and Immunity Institute, Amsterdam University Medical
Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Michiel Schinkel
- Center for Experimental Molecular Medicine,
Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers,
University of Amsterdam, Amsterdam, the Netherlands
| | - Tom D. Y. Reijnders
- Center for Experimental Molecular Medicine,
Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers,
University of Amsterdam, Amsterdam, the Netherlands
| | - Alex. R. Schuurman
- Center for Experimental Molecular Medicine,
Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers,
University of Amsterdam, Amsterdam, the Netherlands
| | - Justin de Brabander
- Center for Experimental Molecular Medicine,
Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers,
University of Amsterdam, Amsterdam, the Netherlands
| | - A. H. Ayesha Lavell
- Department of Internal Medicine, Amsterdam
Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije
Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jaap J. Maas
- Department of Occupational Health and Safety,
Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the
Netherlands
| | - Jelle Koopsen
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Alvin X. Han
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Colin A. Russell
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Sébastien Matamoros
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Suzanne Jurriaans
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Rosa van Mansfeld
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - W. Joost Wiersinga
- Division of Infectious Diseases, Department of
Internal Medicine, Amsterdam Infection and Immunity Institute, Amsterdam University
Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Yvo M. Smulders
- Department of Internal Medicine, Amsterdam
Infection and Immunity Institute, Amsterdam University Medical Centers, Vrije
Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Menno D. de Jong
- Department of Medical Microbiology and Infection
Prevention, Amsterdam University Medical Centers, University of Amsterdam,
Amsterdam, the Netherlands
| | - Marije K. Bomers
- Section Infectious Diseases, Department of
Internal Medicine, Amsterdam Infection and Immunity Institute, Amsterdam University
Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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17
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van Rossen TM, van Prehn J, Koek A, Jonges M, van Houdt R, van Mansfeld R, Kuijper EJ, Vandenbroucke-Grauls CMJE, Budding AE. Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples. Antimicrob Resist Infect Control 2021; 10:23. [PMID: 33514422 PMCID: PMC7845108 DOI: 10.1186/s13756-020-00881-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/06/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Background Clostridioides difficile is the most common cause of nosocomial diarrhea. Ribotyping of cultured strains by a PCR-based test is used to study potential transmission between patients. We aimed to develop a rapid test that can be applied directly on fecal samples for simultaneous detection and ribotyping of C. difficile, as well as detection of toxin genes. Methods We developed a highly specific and sensitive primer set for simultaneous detection and ribotyping of C. difficile directly on total fecal DNA. Toxin genes were detected with primers adapted from Persson et al. (Clin Microbiol Infect 14(11):1057–1064). Our study set comprised 130 fecal samples: 65 samples with positive qPCR for C. difficile toxin A/B genes and 65 C. difficile qPCR negative samples. PCR products were analyzed by capillary gel electrophoresis. Results Ribosomal DNA fragment peak profiles and toxin genes were detected in all 65 C. difficile positive fecal samples and in none of the 65 C. difficile negative samples. The 65 samples were assigned to 27 ribotypes by the Dutch reference laboratory. Our peak profiles corresponded to these ribotypes, except for two samples. During a C. difficile outbreak, patients were correctly allocated to the outbreak-cluster based on the results of direct fecal ribotyping, before C. difficile isolates were cultured and conventionally typed. Conclusion C. difficile ribotyping directly on fecal DNA is feasible, with sensitivity and specificity comparable to that of diagnostic toxin gene qPCR and with ribotype assignment similar to that obtained by conventional typing on DNA from cultured isolates. This supports simultaneous diagnosis and typing to recognize an outbreak.
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Affiliation(s)
- Tessel M van Rossen
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands.
| | - Joffrey van Prehn
- Center for Infectious Diseases, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Alex Koek
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Robin van Houdt
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Rosa van Mansfeld
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Ed J Kuijper
- Center for Infectious Diseases, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
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18
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López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, Sayiner A, Madsen TV, Auvinen E, Kufner V, Huber M, Rodriguez C, Jonges M, Hönemann M, Susi P, Sousa H, Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol 2020; 134:104691. [PMID: 33278791 DOI: 10.1016/j.jcv.2020.104691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
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Affiliation(s)
- F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, United Kingdom.
| | - Sander Van Boheemen
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Ondrej Cinek
- Department of Paediatrics and Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic.
| | - Arzu Sayiner
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Virology. Izmir, Turkey.
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | - Eeva Auvinen
- Department of Virology, Helsinki University Hospital Laboratory and University of Helsinki, Helsinki, Finland.
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christophe Rodriguez
- Microbiology Department and NGS Platform, University Hospital Henri Mondor (APHP), Créteil, France.
| | - Marcel Jonges
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Finland.
| | - Hugo Sousa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.
| | - Paul E Klapper
- Faculty of Biology, Medicine, and Health, Division of Infection, Immunity, and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.
| | - Alba Pérez-Cataluňa
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Lia van der Hoek
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Rob Schuurman
- Department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Els Keyaerts
- Laboratorium Klinische en Epidemiologische Virologie (Rega Instituut), Leuven, Belgium.
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | | | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Javier Buesa
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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19
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Mollers M, Jonges M, Pas SD, van der Eijk AA, Dirksen K, Jansen C, Gelinck LBS, Leyten EMS, Thurkow I, Groeneveld PHP, van Gageldonk-Lafeber AB, Koopmans MP, Timen A. Follow-up of Contacts of Middle East Respiratory Syndrome Coronavirus-Infected Returning Travelers, the Netherlands, 2014. Emerg Infect Dis 2016; 21:1667-9. [PMID: 26291986 PMCID: PMC4550153 DOI: 10.3201/eid2109.150560] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Notification of 2 imported cases of infection with Middle East respiratory syndrome coronavirus in the Netherlands triggered comprehensive monitoring of contacts. Observed low rates of virus transmission and the psychological effect of contact monitoring indicate that thoughtful assessment of close contacts is prudent and must be guided by clinical and epidemiologic risk factors.
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20
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Jonges M, van Leuken J, Wouters I, Koch G, Meijer A, Koopmans M. Wind-Mediated Spread of Low-Pathogenic Avian Influenza Virus into the Environment during Outbreaks at Commercial Poultry Farms. PLoS One 2015; 10:e0125401. [PMID: 25946115 PMCID: PMC4422664 DOI: 10.1371/journal.pone.0125401] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/23/2015] [Indexed: 02/06/2023] Open
Abstract
Avian influenza virus-infected poultry can release a large amount of virus-contaminated droppings that serve as sources of infection for susceptible birds. Much research so far has focused on virus spread within flocks. However, as fecal material or manure is a major constituent of airborne poultry dust, virus-contaminated particulate matter from infected flocks may be dispersed into the environment. We collected samples of suspended particulate matter, or the inhalable dust fraction, inside, upwind and downwind of buildings holding poultry infected with low-pathogenic avian influenza virus, and tested them for the presence of endotoxins and influenza virus to characterize the potential impact of airborne influenza virus transmission during outbreaks at commercial poultry farms. Influenza viruses were detected by RT-PCR in filter-rinse fluids collected up to 60 meters downwind from the barns, but virus isolation did not yield any isolates. Viral loads in the air samples were low and beyond the limit of RT-PCR quantification except for one in-barn measurement showing a virus concentration of 8.48 x 10(4) genome copies/m(3). Air samples taken outside poultry barns had endotoxin concentrations of ~50 EU/m(3) that declined with increasing distance from the barn. Atmospheric dispersion modeling of particulate matter, using location-specific meteorological data for the sampling days, demonstrated a positive correlation between endotoxin measurements and modeled particulate matter concentrations, with an R(2) varying from 0.59 to 0.88. Our data suggest that areas at high risk for human or animal exposure to airborne influenza viruses can be modeled during an outbreak to allow directed interventions following targeted surveillance.
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Affiliation(s)
- Marcel Jonges
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Jeroen van Leuken
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Institute for Risk Assessment Sciences, Faculty of Veterinary Sciences, Utrecht University, Utrecht, The Netherlands
| | - Inge Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Sciences, Utrecht University, Utrecht, The Netherlands
| | - Guus Koch
- Central Veterinary Institute, Wageningen University & Research Center, Lelystad, The Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marion Koopmans
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
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21
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Welkers MRA, Jonges M, Jeeninga RE, Koopmans MPG, de Jong MD. Improved detection of artifactual viral minority variants in high-throughput sequencing data. Front Microbiol 2015; 5:804. [PMID: 25657642 PMCID: PMC4302989 DOI: 10.3389/fmicb.2014.00804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/29/2014] [Indexed: 02/05/2023] Open
Abstract
High-throughput sequencing (HTS) of viral samples provides important information on the presence of viral minority variants. However, detection and accurate quantification is limited by the capacity to distinguish biological from artificial variation. In this study, errors related to the Illumina HiSeq2000 library generation and HTS process were investigated by determining minority variant frequencies in an influenza A/WSN/1933(H1N1) virus reverse-genetics plasmid pool. Errors related to amplification and sequencing were determined using the same plasmid pool, by generation of infectious virus using reverse genetics followed by in duplo reverse-transcriptase PCR (RT-PCR) amplification and HTS in the same sequence run. Results showed that after “best practice” quality control (QC), within the plasmid pool, one minority variant with a frequency >0.5% was identified, while 84 and 139 were identified in the RT-PCR amplified samples, indicating RT-PCR amplification artificially increased variation. Detailed analysis showed that artifactual minority variants could be identified by two major technical characteristics: their predominant presence in a single read orientation and uneven distribution of mismatches over the length of the reads. We demonstrate that by addition of two QC steps 95% of the artifactual minority variants could be identified. When our analysis approach was applied to three clinical samples 68% of the initially identified minority variants were identified as artifacts. Our study clearly demonstrated that, without additional QC steps, overestimation of viral minority variants is very likely to occur, mainly as a consequence of the required RT-PCR amplification step. The improved ability to detect and correct for artifactual minority variants, increases data resolution and could aid both past and future studies incorporating HTS. The source code has been made available through Sourceforge (https://sourceforge.net/projects/mva-ngs).
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Affiliation(s)
- Matthijs R A Welkers
- Department of Medical Microbiology, Academic Medical Centre Amsterdam, Netherlands
| | - Marcel Jonges
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment Bilthoven, Netherlands ; Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rienk E Jeeninga
- Department of Medical Microbiology, Academic Medical Centre Amsterdam, Netherlands
| | - Marion P G Koopmans
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment Bilthoven, Netherlands ; Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre Amsterdam, Netherlands
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22
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Reusken CB, Farag EA, Jonges M, Godeke GJ, El-Sayed AM, Pas SD, Raj VS, Mohran KA, Moussa HA, Ghobashy H, Alhajri F, Ibrahim AK, Bosch BJ, Pasha SK, Al-Romaihi HE, Al-Thani M, Al-Marri SA, AlHajri MM, Haagmans BL, Koopmans MP. Middle East respiratory syndrome coronavirus (MERS-CoV) RNA and neutralising antibodies in milk collected according to local customs from dromedary camels, Qatar, April 2014. ACTA ACUST UNITED AC 2014; 19. [PMID: 24957745 DOI: 10.2807/1560-7917.es2014.19.23.20829] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Antibodies to Middle East respiratory syndrome coronavirus (MERS-CoV) were detected in serum and milk collected according to local customs from 33 camels in Qatar, April 2014. At one location, evidence for active virus shedding in nasal secretions and/or faeces was observed for 7/12 camels; viral RNA was detected in milk of five of these seven camels. The presence of MERS-CoV RNA in milk of camels actively shedding the virus warrants measures to prevent putative food-borne transmission of MERS-CoV.
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Affiliation(s)
- C B Reusken
- Erasmus Medical Center, Rotterdam, the Netherlands
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23
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Kraaij-Dirkzwager M, Timen A, Dirksen K, Gelinck L, Leyten E, Groeneveld P, Jansen C, Jonges M, Raj S, Thurkow I, van Gageldonk-Lafeber R, van der Eijk A, Koopmans M. Middle East respiratory syndrome coronavirus (MERS-CoV) infections in two returning travellers in the Netherlands, May 2014. ACTA ACUST UNITED AC 2014; 19. [PMID: 24906375 DOI: 10.2807/1560-7917.es2014.19.21.20817] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two patients, returning to the Netherlands from pilgrimage in Medina and Mecca, Kingdom of Saudi Arabia, were diagnosed with Middle East respiratory syndrome coronavirus (MERS-CoV) infection in May 2014. The source and mode of transmission have not yet been determined. Hospital-acquired infection and community-acquired infection are both possible.
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Affiliation(s)
- M Kraaij-Dirkzwager
- National Institute for Public Health and the Environment (RIVM) National Coordination Centre for Communicable Disease Control, Bilthoven, the Netherlands
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24
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Jonges M, Welkers MRA, Jeeninga RE, Meijer A, Schneeberger P, Fouchier RAM, de Jong MD, Koopmans M. Emergence of the virulence-associated PB2 E627K substitution in a fatal human case of highly pathogenic avian influenza virus A(H7N7) infection as determined by Illumina ultra-deep sequencing. J Virol 2014; 88:1694-702. [PMID: 24257603 PMCID: PMC3911586 DOI: 10.1128/jvi.02044-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/12/2013] [Indexed: 11/20/2022] Open
Abstract
Avian influenza viruses are capable of crossing the species barrier and infecting humans. Although evidence of human-to-human transmission of avian influenza viruses to date is limited, evolution of variants toward more-efficient human-to-human transmission could result in a new influenza virus pandemic. In both the avian influenza A(H5N1) and the recently emerging avian influenza A(H7N9) viruses, the polymerase basic 2 protein (PB2) E627K mutation appears to be of key importance for human adaptation. During a large influenza A(H7N7) virus outbreak in the Netherlands in 2003, the A(H7N7) virus isolated from a fatal human case contained the PB2 E627K mutation as well as a hemagglutinin (HA) K416R mutation. In this study, we aimed to investigate whether these mutations occurred in the avian or the human host by Illumina Ultra-Deep sequencing of three previously uninvestigated clinical samples obtained from the fatal case. In addition, we investigated three chicken samples, two of which were obtained from the source farm. Results showed that the PB2 E627K mutation was not present in any of the chicken samples tested. Surprisingly, the avian samples were characterized by the presence of influenza virus defective RNA segments, suggestive for the synthesis of defective interfering viruses during infection in poultry. In the human samples, the PB2 E627K mutation was identified with increasing frequency during infection. Our results strongly suggest that human adaptation marker PB2 E627K has emerged during virus infection of a single human host, emphasizing the importance of reducing human exposure to avian influenza viruses to reduce the likelihood of viral adaptation to humans.
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Affiliation(s)
- Marcel Jonges
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Rienk E. Jeeninga
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Adam Meijer
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Peter Schneeberger
- Department of Medical Microbiology and Infection Control, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
| | | | - Menno D. de Jong
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Marion Koopmans
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
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25
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Haagmans BL, Al Dhahiry SHS, Reusken CBEM, Raj VS, Galiano M, Myers R, Godeke GJ, Jonges M, Farag E, Diab A, Ghobashy H, Alhajri F, Al-Thani M, Al-Marri SA, Al Romaihi HE, Al Khal A, Bermingham A, Osterhaus ADME, AlHajri MM, Koopmans MPG. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2014. [PMID: 24355866 DOI: 10.1016/s1473-30991370690-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
BACKGROUND Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe lower respiratory tract infection in people. Previous studies suggested dromedary camels were a reservoir for this virus. We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. METHODS We took nose swabs, rectal swabs, and blood samples from all camels on the Qatari farm. We tested swabs with RT-PCR, with amplification targeting the E gene (upE), nucleocapsid (N) gene, and open reading frame (ORF) 1a. PCR positive samples were tested by different MERS-CoV specific PCRs and obtained sequences were used for phylogentic analysis together with sequences from the linked human cases and other human cases. We tested serum samples from the camels for IgG immunofluorescence assay, protein microarray, and virus neutralisation assay. FINDINGS We obtained samples from 14 camels on Oct 17, 2013. We detected MERS-CoV in nose swabs from three camels by three independent RT-PCRs and sequencing. The nucleotide sequence of an ORF1a fragment (940 nucleotides) and a 4·2 kb concatenated fragment were very similar to the MERS-CoV from two human cases on the same farm and a MERS-CoV isolate from Hafr-Al-Batin. Eight additional camel nose swabs were positive on one or more RT-PCRs, but could not be confirmed by sequencing. All camels had MERS-CoV spike-binding antibodies that correlated well with the presence of neutralising antibodies to MERS-CoV. INTERPRETATION Our study provides virological confirmation of MERS-CoV in camels and suggests a recent outbreak affecting both human beings and camels. We cannot conclude whether the people on the farm were infected by the camels or vice versa, or if a third source was responsible. FUNDING European Union projects EMPERIE (contract number 223498), ANTIGONE (contract number 278976), and the VIRGO consortium.
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Affiliation(s)
- Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Said H S Al Dhahiry
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Chantal B E M Reusken
- Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Monica Galiano
- Virus Reference Department, Public Health England, London, UK
| | - Richard Myers
- Virus Reference Department, Public Health England, London, UK
| | - Gert-Jan Godeke
- Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Marcel Jonges
- Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands; Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands.
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26
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Haagmans BL, Al Dhahiry SHS, Reusken CBEM, Raj VS, Galiano M, Myers R, Godeke GJ, Jonges M, Farag E, Diab A, Ghobashy H, Alhajri F, Al-Thani M, Al-Marri SA, Al Romaihi HE, Al Khal A, Bermingham A, Osterhaus ADME, AlHajri MM, Koopmans MPG. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 2013; 14:140-5. [PMID: 24355866 PMCID: PMC7106553 DOI: 10.1016/s1473-3099(13)70690-x] [Citation(s) in RCA: 447] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe lower respiratory tract infection in people. Previous studies suggested dromedary camels were a reservoir for this virus. We tested for the presence of MERS-CoV in dromedary camels from a farm in Qatar linked to two human cases of the infection in October, 2013. METHODS We took nose swabs, rectal swabs, and blood samples from all camels on the Qatari farm. We tested swabs with RT-PCR, with amplification targeting the E gene (upE), nucleocapsid (N) gene, and open reading frame (ORF) 1a. PCR positive samples were tested by different MERS-CoV specific PCRs and obtained sequences were used for phylogentic analysis together with sequences from the linked human cases and other human cases. We tested serum samples from the camels for IgG immunofluorescence assay, protein microarray, and virus neutralisation assay. FINDINGS We obtained samples from 14 camels on Oct 17, 2013. We detected MERS-CoV in nose swabs from three camels by three independent RT-PCRs and sequencing. The nucleotide sequence of an ORF1a fragment (940 nucleotides) and a 4·2 kb concatenated fragment were very similar to the MERS-CoV from two human cases on the same farm and a MERS-CoV isolate from Hafr-Al-Batin. Eight additional camel nose swabs were positive on one or more RT-PCRs, but could not be confirmed by sequencing. All camels had MERS-CoV spike-binding antibodies that correlated well with the presence of neutralising antibodies to MERS-CoV. INTERPRETATION Our study provides virological confirmation of MERS-CoV in camels and suggests a recent outbreak affecting both human beings and camels. We cannot conclude whether the people on the farm were infected by the camels or vice versa, or if a third source was responsible. FUNDING European Union projects EMPERIE (contract number 223498), ANTIGONE (contract number 278976), and the VIRGO consortium.
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Affiliation(s)
- Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Said H S Al Dhahiry
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Chantal B E M Reusken
- Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Monica Galiano
- Virus Reference Department, Public Health England, London, UK
| | - Richard Myers
- Virus Reference Department, Public Health England, London, UK
| | - Gert-Jan Godeke
- Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Marcel Jonges
- Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands; Centre for Infectious Disease Research, Diagnostics and Screening, Division of Virology, National Institute for Public Health and the Environment, Bilthoven, Netherlands.
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27
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Jonges M, Meijer A, Fouchier RA, Koch G, Li J, Pan JC, Chen H, Shu YL, Koopmans MP. Guiding outbreak management by the use of influenza A(H7Nx) virus sequence analysis. Euro Surveill 2013; 18:20460. [PMID: 23611030] [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: 06/02/2023] Open
Abstract
The recently identified human infections with avian influenza A(H7N9) viruses in China raise important questions regarding possible source and risk to humans. Sequence comparison with an influenza A(H7N7) outbreak in the Netherlands in 2003 and an A(H7N1) epidemic in Italy in 1999–2000 suggests that widespread circulation of A(H7N9) viruses must have occurred in China. The emergence of human adaptation marker PB2 E627K in human A(H7N9) cases parallels that of the fatal A(H7N7) human case in the Netherlands.
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Affiliation(s)
- M Jonges
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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28
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Jonges M, Meijer A, Fouchier RA, Koch G, Li J, Pan JC, Chen H, Shu YL, Koopmans MP. Guiding outbreak management by the use of influenza A(H7Nx) virus sequence analysis. Euro Surveill 2013. [DOI: 10.2807/ese.18.16.20460-en] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- M Jonges
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A Meijer
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - R A Fouchier
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - G Koch
- Central Veterinary Institute, Wageningen University and Research Center, Lelystad, the Netherlands
| | - J Li
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - J C Pan
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - H Chen
- National Avian Influenza Reference Laboratory, Harbin Veterinary Research Institute, Harbin, China
| | - Y L Shu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - M P Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Department of Virology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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29
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Ypma RJF, Jonges M, Bataille A, Stegeman A, Koch G, van Boven M, Koopmans M, van Ballegooijen WM, Wallinga J. Genetic data provide evidence for wind-mediated transmission of highly pathogenic avian influenza. J Infect Dis 2012; 207:730-5. [PMID: 23230058 DOI: 10.1093/infdis/jis757] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Outbreaks of highly pathogenic avian influenza in poultry can cause severe economic damage and represent a public health threat. Development of efficient containment measures requires an understanding of how these influenza viruses are transmitted between farms. However, the actual mechanisms of interfarm transmission are largely unknown. Dispersal of infectious material by wind has been suggested, but never demonstrated, as a possible cause of transmission between farms. Here we provide statistical evidence that the direction of spread of avian influenza A(H7N7) is correlated with the direction of wind at date of infection. Using detailed genetic and epidemiological data, we found the direction of spread by reconstructing the transmission tree for a large outbreak in the Netherlands in 2003. We conservatively estimate the contribution of a possible wind-mediated mechanism to the total amount of spread during this outbreak to be around 18%.
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Affiliation(s)
- Rolf J F Ypma
- Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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Jonges M, Rahamat-Langendoen J, Meijer A, Niesters HG, Koopmans M. Sequence-based identification and characterization of nosocomial influenza A(H1N1)pdm09 virus infections. J Hosp Infect 2012; 82:187-93. [PMID: 23013789 DOI: 10.1016/j.jhin.2012.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 03/30/2012] [Accepted: 08/08/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Highly transmissible viruses such as influenza are a potential source of nosocomial infections and thereby cause increased patient morbidity and mortality. AIM To assess whether influenza virus sequence data can be used to link nosocomial influenza transmission between individuals. METHODS Dutch A(H1N1)pdm09-positive specimens from one hospital (N = 107) were compared with samples from community cases (N = 685). Gene fragments of haemagglutinin, neuraminidase and PB2 were sequenced and subsequently clustered to detect patients infected with identical influenza viruses. The probability of detecting a second patient was calculated for each hospital cluster against the background diversity observed in hospital and community strains. All clusters were further analysed for possible links between patients. FINDINGS Seventeen A(H1N1)pdm09 hospital clusters were detected of which eight had a low probability of occurrence compared with background diversity (P < 0.01). Epidemiological analysis confirmed a total of eight nosocomial infections in four of these eight clusters, and a mother-child combination in a fifth cluster. The nine clusters with a high probability of occurrence involved community cases of influenza without a known epidemiological link. CONCLUSION If a background sequence dataset is available, the detection of hospital sequence clusters that differ from dominant community strains can be used to select clusters requiring further investigation by hospital hygienists before a nosocomial influenza outbreak is epidemiologically suspected.
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Affiliation(s)
- M Jonges
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands.
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Van Borm S, Jonges M, Lambrecht B, Koch G, Houdart P, van den Berg T. Molecular epidemiological analysis of the transboundary transmission of 2003 highly pathogenic avian influenza H7N7 outbreaks between the Netherlands and Belgium. Transbound Emerg Dis 2012; 61:86-90. [PMID: 22994451 DOI: 10.1111/tbed.12009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Indexed: 11/27/2022]
Abstract
The 2003 outbreak of Highly pathogenic avian influenza (HPAI) A(H7N7) in the Netherlands, Belgium and Germany resulted in significant genetic diversification that proved informative for tracing transmission events. Building on previous investigations on the Dutch outbreak, we focused on the potential transnational transmissions between the Netherlands and Belgium. Although no clear epidemiological links could be identified from the tracing data, the transmission network based on concatenated HA-NA-PB2 sequences supports at least three independent introductions from the Netherlands to Belgium and suggests one possible introduction form Belgium back to the Netherlands. Two introductions in the Belgian province of Limburg occurred from nearby farms in the Dutch province of Limburg. One introduction resulted in three secondary infected farms, while a second introduction did not cause secondary infections. The third introduction into Belgium occurred in the north of the Antwerp province, very close to the national border, and originated from the North of the Dutch province Brabant (long distance transmission, >65 km). The virus spread to two additional Belgian farms, one of which may be the source of a secondarily infected farm in the Netherlands. One infected turkey farm in the province of Antwerp (Westmalle) was geographically close to the latter introduction, but genetically clustered with the first introduction event in the Limburg province. Epidemiological tracing data could neither confirm nor exclude whether this outbreak was a result from long distance contacts within Belgium or whether this farm presented a fourth independent transboundary introduction. These multiple transnational transmissions of HPAI in spite of reinforced biosecurity measures and trade restrictions illustrate the importance of international cooperation, legislation and standardization of tools to combat transboundary diseases.
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Affiliation(s)
- S Van Borm
- Department of Virology, Veterinary and Agrochemical Research Center, Ukkel, Belgium
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Meijer A, Jonges M, van Beek P, Swaan CM, Osterhaus AD, Daniels RS, Hurt AC, Koopmans MP. Oseltamivir-resistant influenza A(H1N1)pdm09 virus in Dutch travellers returning from Spain, August 2012. Euro Surveill 2012. [DOI: 10.2807/ese.17.36.20266-en] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two Dutch travellers were infected with oseltamivir-resistant influenza A(H1N1)pdm09 viruses with an H275Y neuraminidase substitution in early August 2012. Both cases were probably infected during separate holidays at the Catalonian coast (Spain). No epidemiological connection between the two cases was found, and neither of them was treated with oseltamivir before specimen collection. Genetic analysis of the neuraminidase gene revealed the presence of previously described permissive mutations that may increase the likelihood of such strains emerging and spreading widely.
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Affiliation(s)
- A Meijer
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - M Jonges
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - P van Beek
- Preparedness and Response Unit, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - C M Swaan
- Preparedness and Response Unit, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - A D Osterhaus
- Viroscience laboratory, Erasmus Medical Centre, Rotterdam, the Netherlands
- National Influenza Centre, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - R S Daniels
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Medical Research Council (MRC) National Institute for Medical Research, London, United Kingdom
| | - A C Hurt
- World Health Organization Collaborating Centre for Reference and Research on Influenza, North Melbourne, Victoria, Australia
| | - M P Koopmans
- Viroscience laboratory, Erasmus Medical Centre, Rotterdam, the Netherlands
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Meijer A, Jonges M, van Beek P, Swaan CM, Osterhaus AD, Daniels RS, Hurt AC, Koopmans MP. Oseltamivir-resistant influenza A(H1N1)pdm09 virus in Dutch travellers returning from Spain, August 2012. Euro Surveill 2012; 17:20266. [PMID: 22971326] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Two Dutch travellers were infected with oseltamivir-resistant influenza A(H1N1)pdm09 viruses with an H275Y neuraminidase substitution in early August 2012. Both cases were probably infected during separate holidays at the Catalonian coast (Spain). No epidemiological connection between the two cases was found, and neither of them was treated with oseltamivir before specimen collection. Genetic analysis of the neuraminidase gene revealed the presence of previously described permissive mutations that may increase the likelihood of such strains emerging and spreading widely.
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Affiliation(s)
- A Meijer
- Laboratory for Infectious Diseases and Screening, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Dijkstra F, Jonges M, van Beek R, Donker GA, Schellevis FG, Koopmans M, van der Sande MAB, Osterhaus ADME, Boucher CAB, Rimmelzwaan GF, Meijer A. Influenza A(H1N1) Oseltamivir Resistant Viruses in the Netherlands During the Winter 2007/2008. Open Virol J 2012; 5:154-62. [PMID: 22253652 PMCID: PMC3249654 DOI: 10.2174/1874357901105010154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 08/30/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Antiviral susceptibility surveillance in the Netherlands was intensified after the first reports about the emergence of influenza A(H1N1) oseltamivir resistant viruses in Norway in January, 2008. METHODS Within the existing influenza surveillance an additional questionnaire study was performed to retrospectively assess possible risk factors and establish clinical outcome of all patients with influenza virus A(H1N1) positive specimens. To discriminate resistant and sensitive viruses, fifty percent inhibitory concentrations for the neuramidase inhibitors oseltamivir and zanamivir were determined in a neuraminidase inhibition assay. Mutations previously associated with resistance to neuramidase inhibitors and M2 blockers (amantadine and rimantadine) were searched for by nucleotide sequencing of neuraminidase and M2 genes respectively. RESULTS Among 171 patients infected with A(H1N1) viruses an overall prevalence of oseltamivir resistance of 27% (95% CI: 20-34%) was found. None of influenza A(H1N1) oseltamivir resistant viruses tested was resistant against amantadine or zanamivir. Patient characteristics, underlying conditions, influenza vaccination, symptoms, complications, and exposure to oseltamivir and other antivirals did not differ significantly between patients infected with resistant and sensitive A(H1N1) viruses. CONCLUSION In 2007/2008 a large proportion of influenza A(H1N1) viruses resistant to oseltamivir was detected. There were no clinical differences between patients infected with resistant and sensitive A(H1N1) viruses. Continuous monitoring of the antiviral drug sensitivity profile of influenza viruses is justified, preferably using the existing sentinel surveillance, however, complemented with data from the more severe end of the clinical spectrum. In order to act timely on emergencies of public health importance we suggest setting up a surveillance system that can guarantee rapid access to the latter.
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Affiliation(s)
- Frederika Dijkstra
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Meijer A, Jonges M, Abbink F, Ang W, van Beek J, Beersma M, Bloembergen P, Boucher C, Claas E, Donker G, van Gageldonk-Lafeber R, Isken L, de Jong A, Kroes A, Leenders S, van der Lubben M, Mascini E, Niesters B, Oosterheert JJ, Osterhaus A, Riesmeijer R, Riezebos-Brilman A, Schutten M, Sebens F, Stelma F, Swaan C, Timen A, van 't Veen A, van der Vries E, te Wierik M, Koopmans M. Oseltamivir-resistant pandemic A(H1N1) 2009 influenza viruses detected through enhanced surveillance in the Netherlands, 2009-2010. Antiviral Res 2011; 92:81-9. [PMID: 21767571 DOI: 10.1016/j.antiviral.2011.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 05/17/2011] [Accepted: 07/04/2011] [Indexed: 11/24/2022]
Abstract
Enhanced surveillance of infections due to the pandemic A(H1N1) influenza virus, which included monitoring for antiviral resistance, was carried out in the Netherlands from late April 2009 through late May 2010. More than 1100 instances of infection with the pandemic A(H1N1) influenza virus from 2009 and 2010 [A(H1N1) 2009] distributed across this period were analyzed. Of these, 19 cases of oseltamivir-resistant virus harboring the H275Y mutation in the neuraminidase (NA) were detected. The mean 50% inhibitory concentration (IC50) levels for oseltamivir- and zanamivir-susceptible A(H1N1) 2009 viruses were 1.4-fold and 2-fold, respectively, lower than for the seasonal A(H1N1) influenza viruses from 2007/2008; for oseltamivir-resistant A(H1N1) 2009 virus the IC50 was 2.9-fold lower. Eighteen of the 19 patients with oseltamivir-resistant virus showed prolonged shedding of the virus and developed resistance while on oseltamivir therapy. Sixteen of these 18 patients had an immunodeficiency, of whom 11 had a hematologic disorder. The two other patients had another underlying disease. Six of the patients who had an underlying disease died; of these, five had received cytostatic or immunosuppressive therapy. No indications for onward transmission of resistant viruses were found. This study showed that the main association for the emergence of cases of oseltamivir-resistant A(H1N1) 2009 virus was receiving antiviral therapy and having drug-induced immunosuppression or an hematologic disorder. Except for a single case of a resistant virus not linked to oseltamivir therapy, the absence of detection of resistant variants in community specimens and in specimens from contacts of cases with resistant virus suggested that the spread of resistant A(H1N1) 2009 virus was limited. Containment may have been the cumulative result of impaired NA function, successful isolation of the patients, and prophylactic measures to limit exposure.
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Affiliation(s)
- Adam Meijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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van der Vries E, Jonges M, Herfst S, Maaskant J, Van der Linden A, Guldemeester J, Aron GI, Bestebroer TM, Koopmans M, Meijer A, Fouchier RAM, Osterhaus ADME, Boucher CA, Schutten M. Evaluation of a rapid molecular algorithm for detection of pandemic influenza A (H1N1) 2009 virus and screening for a key oseltamivir resistance (H275Y) substitution in neuraminidase. J Clin Virol 2009; 47:34-7. [PMID: 19857993 PMCID: PMC7185517 DOI: 10.1016/j.jcv.2009.09.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [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: 08/03/2009] [Revised: 09/22/2009] [Accepted: 09/25/2009] [Indexed: 10/31/2022]
Abstract
BACKGROUND Rapid and specific molecular tests for identification of the recently identified pandemic influenza A/H1N1 2009 virus as well as rapid molecular tests to identify antiviral resistant strains are urgently needed. OBJECTIVES We have evaluated the performance of two novel reverse transcriptase polymerase chain reactions (RT-PCRs) targeting specifically hemagglutinin and neuraminidase of pandemic influenza A/H1N1 virus in combination with a conserved matrix PCR. In addition, we investigated the performance of a novel discrimination RT-PCR for detection of the H275Y resistance mutation in the neuraminidase gene. STUDY DESIGN Clinical performance of both subtype specific RT-PCR assays was evaluated through analysis of 684 throat swaps collected from individuals meeting the WHO case definition for the novel pandemic influenza virus. Analytical performance was analyzed through testing of 10-fold serial dilutions of RNA derived from the first Dutch sequenced and cultured confirmed case of novel pandemic influenza infection. Specificity and discriminative capacities of the H275Y discrimination assay were performed by testing wild type and recombinant H275Y pandemic influenza. RESULTS 121 throat swaps collected from April 2009 to July 2009 were positive by at least two out of three RT-PCRs, and negative for the seasonal H3/H1 subtype specific RT-PCR assays. 117 of these were tested positive for all three (Ct-values from 15.1 to 36.8). No oseltamivir resistance was detected. CONCLUSIONS We present a sensitive and specific approach for detection of pandemic influenza A/H1N1 2009 and a rapid RT-PCR assay detecting a primary oseltamivir resistance mutation which can be incorporated easily into clinical virology algorithms.
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Affiliation(s)
- E van der Vries
- Erasmus MC, Department of Virology, 's Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
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Gooskens J, Jonges M, Claas E, Meijer A, Kroes A. Prolonged Influenza Virus Infection during Lymphocytopenia and Frequent Detection of Drug‐Resistant Viruses. J Infect Dis 2009; 199:1435-41. [DOI: 10.1086/598684] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Gooskens J, Jonges M, Claas ECJ, Meijer A, van den Broek PJ, Kroes AM. Morbidity and mortality associated with nosocomial transmission of oseltamivir-resistant influenza A(H1N1) virus. JAMA 2009; 301:1042-6. [PMID: 19255111 DOI: 10.1001/jama.2009.297] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CONTEXT The sudden emergence and rapid spread of oseltamivir-resistant influenza A(H1N1) viruses with neuraminidase (NA) gene H274Y amino acid substitution is the hallmark of global seasonal influenza since January 2008. Viruses carrying this mutation are widely presumed to exhibit attenuated pathogenicity, compromised transmission, and reduced lethality. OBJECTIVE To investigate nosocomial viral transmission in a cluster of patients with influenza A(H1N1) virus infection. DESIGN, SETTING, AND PATIENTS Descriptive outbreak investigation of 2 hematopoietic stem cell transplant recipients and an elderly patient who developed hospital-acquired influenza A virus infection following exposure to an index patient with community-acquired H274Y-mutated influenza A(H1N1) virus infection in a medical ward at a Dutch university hospital in February 2008. The investigation included a review of the medical records, influenza virus polymerase chain reaction and culture, phenotypic oseltamivir and zanamivir susceptibility determination, and hemagglutinin chain 1 (HA(1)) gene and NA gene sequence analysis. MAIN OUTCOME MEASURE Phylogenetic relationship of patient cluster influenza A(H1N1) viruses and other 2007-2008 seasonal influenza A(H1N1) viruses. RESULTS Viral HA(1) and NA gene sequence analysis from the 4 patients revealed indistinguishable nucleotide sequences and phylogenetic clustering of H274Y-mutated, oseltamivir-resistant influenza A(H1N1) virus, confirming nosocomial transmission. Influenza virus pneumonia (3 patients) and attributable mortality (2 patients) during active infection was observed in patients with lymphocytopenia at onset. CONCLUSION Seasonal oseltamivir-resistant influenza A(H1N1) viruses with NA gene H274Y mutation are transmitted and retain significant pathogenicity and lethality in high-risk patients.
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MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Amino Acid Substitution
- Antiviral Agents/pharmacology
- Cross Infection/epidemiology
- Disease Transmission, Infectious
- Drug Resistance, Viral
- Enzyme Inhibitors/pharmacology
- Female
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/drug effects
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza, Human/epidemiology
- Influenza, Human/mortality
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Middle Aged
- Molecular Sequence Data
- Morbidity
- Neuraminidase/antagonists & inhibitors
- Neuraminidase/genetics
- Oseltamivir/pharmacology
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Affiliation(s)
- Jairo Gooskens
- Department of Medical Microbiology, E4-65, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands.
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Berkhoff EGM, Geelhoed-Mieras MM, Jonges M, Smith DJ, Fouchier RAM, Osterhaus ADME, Rimmelzwaan GF. An amino acid substitution in the influenza A virus hemagglutinin associated with escape from recognition by human virus-specific CD4+ T-cells. Virus Res 2007; 126:282-7. [PMID: 17420064 DOI: 10.1016/j.virusres.2007.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [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: 12/21/2006] [Revised: 02/22/2007] [Accepted: 02/23/2007] [Indexed: 11/28/2022]
Abstract
Influenza virus-specific CD4+ T-helper cells were cloned that recognized a virus strain isolated in 1981, but that failed to recognize more recent strains. The HLA-DR*1601-restricted epitope recognized was located in the hemagglutinin (HA(99-113)) and the naturally occurring A-->V substitution at position 106 was responsible for abrogating the recognition by HA(99-113)-specific CD4+ T-cells. This amino acid substitution was found in influenza A/H3N2 viruses that circulated between 1999 and 2005 and did not affect recognition by virus-specific antibodies. It was speculated that influenza viruses could evade recognition by virus-specific CD4+ T-cells, at least temporarily.
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Affiliation(s)
- Eufemia G M Berkhoff
- Department of Virology and Postgraduate School Molecular Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
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